bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Note on the Concordance Invariant Epsilon
Authors: Wang Shida 
Published: June 2021

Abstract
We compare the smooth concordance invariants Upsilon, phi and epsilon. Previous work gave examples of knots with one of the Upsilon and phi invariants zero but the epsilon invariant nonzero. We build an infinite family of linearly independent knots with both the Upsilon and phi invariants zero but the epsilon invariant nonzero. This provides examples of knots with arbitrarily large concordance genus but vanishing bounds from the Upsilon and phi invariants.
Novel Integrative Modeling of Molecules and Morphology across Evolutionary Timescales
Authors: Ogilvie Huw A , Mendes Fábio K , Vaughan Timothy G , Matzke Nicholas J , Stadler Tanja , Welch David , Drummond Alexei J 
Published: June 2021

AbstractEvolutionary models account for either population- or species-level processes but usually not both. We introduce a new model, the FBD-MSC, which makes it possible for the first time to integrate both the genealogical and fossilization phenomena, by means of the multispecies coalescent (MSC) and the fossilized birth–death (FBD) processes. Using this model, we reconstruct the phylogeny representing all extant and many fossil Caninae, recovering both the relative and absolute time of speciation events. We quantify known inaccuracy issues with divergence time estimates using the popular strategy of concatenating molecular alignments and show that the FBD-MSC solves them. Our new integrative method and empirical results advance the paradigm and practice of probabilistic total evidence analyses in evolutionary biology.[Caninae; fossilized birth–death; molecular clock; multispecies coalescent; phylogenetics; species trees.]
Fast and Accurate Estimation of Species-Specific Diversification Rates Using Data Augmentation
Authors: Maliet Odile , Morlon Hélène 
Published: June 2021

Abstract
Diversification rates vary across species as a response to various factors, including environmental conditions and species-specific features. Phylogenetic models that allow accounting for and quantifying this heterogeneity in diversification rates have proven particularly useful for understanding clades diversification. Recently, we introduced the cladogenetic diversification rate shift model, which allows inferring multiple rate changes of small magnitude across lineages. Here, we present a new inference technique for this model that considerably reduces computation time through the use of data augmentation and provide an implementation of this method in Julia. In addition to drastically reducing computation time, this new inference approach provides a posterior distribution of the augmented data, that is the tree with extinct and unsampled lineages as well as associated diversification rates. In particular, this allows extracting the distribution through time of both the mean rate and the number of lineages. We assess the statistical performances of our approach using simulations and illustrate its application on the entire bird radiation.[Birth–death model; data augmentation; diversification; macroevolution.]
Ultrasound-based evaluation of the prevalence of abdominal cystic echinococcosis in the Turkestan region of Kazakhstan
Authors: Mustapayeva Aigerim , Luca D'Alessandro Gian , Doszhanova Gaukhar , Colpani Agnese , Sadybekov Nurbol , Baimakhanov Zhasulan , Assanov Ernar , Salybekov Samat , Kaniyev Shokan , Serikuly Erbol , Tagabayeva Lyazzat , Budke Christine M , Vola Ambra , Mariconti Mara , De Silvestri Annalisa , Yalisheva Sofyia , Sadykova Ainur , Zholdybay Zhamilya , Katarbayev Adil , Zhakenova Zhanar , Brunetti Enrico , Juszkiewicz Konrad , Duisenova Amangul , Manciulli Tommaso 
Published: June 2021

Abstract

Background
Human cystic echinococcosis (CE) is a zoonotic disease caused by Echinococcus granulosus sensu lato. CE is known to be endemic in some parts of Central Asia. We present findings from an ultrasound-based survey to estimate the prevalence of CE in the Turkestan oblast of Kazakhstan.

Methods
In October 2019, six villages were chosen based on records from a national surveillance dataset. Inhabitants aged 5–90 y were invited to undergo a free abdominal ultrasound to screen for CE cysts. All identified cysts were staged according to the WHO-endorsed classification for CE cysts.

Results
A total of 2252 individuals underwent ultrasound screening. Twenty-two (0.98%) individuals had CE, with a combined total of 33 cysts: 25 (75.7%) inactive (14 CE4, 11 CE5) and 8 (24.3%) active/transitional (2 CE1, 1 CE2, 3 CE3a, 2 CE3b). One patient had a postsurgical cavity. Sixty-eight patients (3.0%) reported CE prior to surgical treatment. In 25 (36.8%) previously diagnosed patients, albendazole prophylaxis was not used.

Conclusions
CE is endemic in the study region, with ongoing transmission. The number of surgically treated CE patients suggests an underestimation of the disease burden by the current surveillance system. Further studies on local CE epidemiology and the implementation of expert treatment recommendations are needed.
Phylogenetic assessment and systematic revision of the acoel family Isodiametridae
Authors: Atherton Sarah , Jondelius Ulf 
Published: June 2021

AbstractIsodiametridae is a large family of Acoela with 22 nominal genera and nearly 100 species. Unfortunately, systematics of Isodiametridae, as it stands, is highly problematic. Genera frequently have been proposed without reference to an explicit phylogenetic hypothesis, such that the current classification system holds little or no predictive power. Many taxa do not fit with the family diagnosis, and it is increasingly difficult to determine in which taxon a new species should be described. Herein, we reconstruct the phylogenetic relationships of Acoela with a focus on Isodiametridae using both previously published and new ribosomal and mitochondrial sequence data. Our dataset comprises sequences from 45 species representing 16 of the 22 isodiametrid genera. Our results recovered a well-supported Isodiametridae, but provided further evidence that the family and several genera within require revision. We have updated the classification system of Isodiametridae to be consistent with its phylogeny, including the transference of Otocelis to Otocelididae, Postaphanostoma and Faerlea to Mecynostomidae and Alluna to Actinoposthiidae. Six other genera are placed in synonymy. We review the morphological taxonomy and provide an identification key of the genera in the revised family.
Workplace-Based Entrustment Scales for the Core EPAs: A Multisite Comparison of Validity Evidence for Two Proposed Instruments Using Structured Vignettes and Trained Raters
Authors: Ryan Michael S. , Khan Asra R. , Park Yoon Soo , Chastain Cody , Phillipi Carrie , Santen Sally A. , Barron Beth A. , Obeso Vivian , Yingling Sandra L. ,   for the Core Entrustable Professional Activities for Entering Residency Pilot Program
Published: June 2021

Purpose
In undergraduate medical education (UME), competency-based medical education has been operationalized through the 13 Core Entrustable Professional Activities for Entering Residency (Core EPAs). Direct observation in the workplace using rigorous, valid, reliable measures is required to inform summative decisions about graduates’ readiness for residency. The purpose of this study is to investigate the validity evidence of 2 proposed workplace-based entrustment scales.

Method
The authors of this multisite, randomized, experimental study used structured vignettes and experienced raters to examine validity evidence of the Ottawa scale and the UME supervisory tool (Chen scale) in 2019. The authors used a series of 8 cases (6 developed de novo) depicting learners at preentrustable (less-developed) and entrustable (more-developed) skill levels across 5 Core EPAs. Participants from Core EPA pilot institutions rated learner performance using either the Ottawa or Chen scale. The authors used descriptive statistics and analysis of variance to examine data trends and compare ratings, conducted interrater reliability and generalizability studies to evaluate consistency among participants, and performed a content analysis of narrative comments.

Results
Fifty clinician-educators from 10 institutions participated, yielding 579 discrete EPA assessments. Both Ottawa and Chen scales differentiated between less- and more-developed skill levels (P < .001). The interclass correlation was good to excellent for all EPAs using Ottawa (range, 0.68–0.91) and fair to excellent using Chen (range, 0.54–0.83). Generalizability analysis revealed substantial variance in ratings attributable to the learner–EPA interaction (59.6% for Ottawa; 48.9% for Chen) suggesting variability for ratings was appropriately associated with performance on individual EPAs.

Conclusions
In a structured setting, both the Ottawa and Chen scales distinguished between preentrustable and entrustable learners; however, the Ottawa scale demonstrated more desirable characteristics. These findings represent a critical step forward in developing valid, reliable instruments to measure learner progression toward entrustment for the Core EPAs.
Does Quantitative Sensory Testing Improve Prediction of Chronic Pain Trajectories? A Longitudinal Study of Youth With Functional Abdominal Pain Participating in a Randomized Controlled Trial of Cognitive Behavioral Treatment
Authors: Morris Matthew C. , Bruehl Stephen , Stone Amanda L. , Garber Judy , Smith Craig , Palermo Tonya M. , Walker Lynn S. 
Published: June 2021

Objectives:Youth with functional abdominal pain (FAP) experience significant pain-related distress and functional impairment. Although quantitative sensory testing protocols have identified alterations in pain modulatory systems that distinguish youth with FAP from healthy controls, the extent to which evoked pain responses predict subsequent trajectories of pain symptoms and disability over and above established psychosocial risk factors is unclear.Methods:The present study included 183 adolescents with FAP who were enrolled in a randomized controlled trial comparing an 8-week, internet-delivered program of cognitive behavior therapy (n=90) or pain education (n=93). Participants completed a quantitative sensory testing protocol before the intervention and were followed for 12-month posttreatment.Results:Whereas adolescents with FAP who exhibited stronger baseline conditioned pain modulation (CPM) reported decreases in pain-related interference over follow-up (b=−0.858, SE=0.396,P=0.032), those with weaker CPM exhibited high, relatively stable levels of pain-related interference over time (b=−0.642, SE=0.400,P=0.110). CPM status predicted changes in pain-related interference after controlling for the effects of treatment condition and psychosocial risk factors. Static measures of pain sensitivity (ie, pain threshold, pain tolerance) and temporal summation of second pain were not associated with changes in measures of abdominal pain, gastrointestinal symptom severity, or pain-related interference over follow-up.Discussion:The present findings contribute to a growing literature on the predictive utility of quantitative sensory testing indices and suggest that CPM may complement existing psychosocial risk measures in determining individualized pain-related risk profiles.
Use of External Tissue Expanders to Assist in Reverse Sural Flap Donor Site Closure
Authors: Cox Cameron , Gaschen Paul D. , Foley David , MacKay Brendan 
Published: June 2021

Background:
Complex lower extremity injuries can cause large soft tissue defects that require reconstruction. In the distal third of the lower leg, the reverse sural artery fasciocutaneous flap is a viable coverage option due to its versatility, vascular supply, and ability to cover larger defects than other local pedicled flaps. Although advances in techniques have improved reliability of reverse sural flaps, complications such as donor site morbidity remain a challenge for surgeons. Donor wounds may be difficult to close, and delayed closure can increase the risk for infection and other postoperative complications. In these cases, donor site skin grafting can cause additional morbidity and/or mobility restrictions.

Methods:
In this case series, 16 patients underwent reconstruction with large reverse sural artery fasciocutaneous flaps and a continuous external tissue expander to assist in donor site closure.

Results:
One patient was lost to follow-up. All donor sites healed without complication with an average time to healing of 9.2 weeks (n = 15, range: 3–18). At the most recent follow-up, all flaps survived without complication.

Conclusions:
Given our success in 100% of patients, we purport that this system of enhanced closure may be a valuable adjunctive therapy in closing reverse sural artery fasciocutaneous flaps. We believe that this method may be useful in closing other difficult donor wounds.
ACUTE IDIOPATHIC MACULOPATHY
Authors: Pajtler Rosar Ana , Casalino Giuseppe , Cozzi Mariano , Pellegrini Marco , Bottoni Ferdinando , Dell'Arti Laura , Lavric Alenka , Umek Lan , Globocnik Petrovic Mojca , Pavesio Carlos , Vidovič Valentinčič Nataša , Staurenghi Giovanni 
Published: June 2021

Purpose:
To describe the clinical course and the multimodal imaging of acute idiopathic maculopathy.

Methods:
Medical records and multimodal imaging including color fundus photography, optical coherence tomography, and fundus autofluorescence were retrospectively reviewed. Recognition of the fundus autofluorescence patterns and their relationship with the disease duration, best-corrected visual acuity, and optical coherence tomography features represented the main outcome measures.

Results:
Seventeen eyes of 16 patients (7 women; mean age 29.9 years) with a mean follow-up of 23.9 months were included. The mean best-corrected visual acuity at presentation was 0.63 ± 0.54 logarithm of the minimum angle of resolution (Snellen equivalent, 20/85). All but one patient had the best-corrected visual acuity recovery to 20/20. Four sequential patterns of fundus autofluorescence corresponding to 4 proposed stages of disease were observed. Patterns 1 (central hypoautofluorescence with surrounding hyperautofluorescence) and 2 (stippled hyperautofluorescence and hypoautofluorescence) were found at presentation. Patterns 3 (central hyperautofluorescence surrounded by hypoautofluorescence) and 4 (hypoautofluorescence) were observed during the disease course and/or at the last follow-up visit. Duration of the disease was significantly different between patterns at baseline and last visit. Pattern 1 significantly related to the presence of subretinal detachment (Fisher's exact test; P =0.003) on optical coherence tomography in comparison with Pattern 2. Pattern 4 showed unique homogeneously decreased autofluorescence with corresponding attenuation of retinal pigment epithelium and restored outer retinal layers on optical coherence tomography.

Conclusion:
A sequential disease staging based on multimodal imaging for acute idiopathic maculopathy is proposed. The recognition of the observed imaging patterns may help clinicians in the correct diagnosis and patient counseling.
Pleurodesis After Bronchial Occlusion for Inoperable Secondary Spontaneous Pneumothorax
Authors: Kida Hirotaka , Muraoka Hiromi , Morikawa Kei , Inoue Takeo , Mineshita Masamichi 
Published: June 2021

Background:
In many cases of secondary spontaneous pneumothorax (SSP), surgery is not feasible. Furthermore, in cases with a collapsed lung or numerous air leaks, pleurodesis is ineffective, and treatment options are severely limited. For these cases, bronchial occlusion might be the only effective treatment, despite the low success rate. If, however, bronchial occlusion can expand the lung and reduce air leakage, it can positively amplify later effects on pleurodesis, resulting in a powerful treatment. We reviewed the clinical data of patients who underwent bronchial occlusion with endobronchial Watanabe spigot (BO-EWS) and pleurodesis to investigate the usefulness of bronchial occlusion therapy in inoperable SSP patients.

Materials and Methods:
This single-center, retrospective study reviewed 36 cases of inoperable SSP patients who underwent pleurodesis after BO-EWS from April 2007 to October 2018. Twenty cases were allocated to the air leak analysis group, and 16 cases were included in the pneumothorax volume analysis group. The Robert David Cerfolio classification and the Collins method were used to evaluate air leak and pneumothorax volume, respectively.

Results:
Pneumothorax volumes decreased significantly after BO-EWS from 29.1%±17.3% to 12.1%±8.8%, while the air leak score decreased from 2.9±1.4 to 1.2±1.0. The success rate for chest tube removals in cases that underwent pleurodesis after BO-EWS was 85.0% (17/20).

Conclusions:
This study demonstrated the synergistic effectiveness of BO-EWS and the usefulness of pleurodesis treatment in inoperable SSP patients with lung collapse or numerous air leaks. We believe that this treatment will benefit patients with inoperable SSP which, until now, has had few treatment options.
Laparoscopic spleen-preserving distal pancreatectomy for epidermoid cyst in an intrapancreatic accessory spleen
Authors: Zheng Xiang , Zhou Bo , Sun Jing-Qing , Jin Ming , Yan Sheng 
Published: June 2021

Abstract

Rationale:
Pancreatic tail cystic lesions are increasingly encountered in clinical practice, however, it is difficult to make a correct diagnosis preoperatively because there are many types of pancreatic neoplastic and non-neoplastic cysts. Epidermoid cyst in an intrapancreatic accessory spleen (ECIPAS) is a rare non-neoplastic cyst locating in the pancreatic tail, and it is commonly misdiagnosed as another cystic neoplasm.

Patient concerns:
A 51-year-old man was admitted for investigation of abdominal pain. The physical examination and laboratory tests found no abnormalities, except for an elevation of carbohydrate antigen (CA)19-9. Imaging revealed a cystic lesion within the pancreatic tail, and the solid component surrounding the cyst was enhanced similarly to those of the splenic tissue.

Diagnosis:
ECIPAS was diagnosed based on the pathology after surgery. The mass was composed of a cyst and brown solid spleen-like tissue. The microscopic analysis demonstrated that the solid component was accessory splenic tissue, and the cyst wall was lined with a thin stratified squamous epithelium.

Interventions:
Laparoscopic spleen-preserving distal pancreatectomy was performed.

Outcomes:
The patient was discharged on day 5 postoperatively after an uneventful recovery. CA19-9 returned to normal after surgery. During a 2-years follow-up, there was no evidence of tumor recurrence.

Lessons:
Although rare ECIPAS should be considered in the differential diagnosis of pancreatic tail cystic lesions, and the typical imaging features might facilitate the preoperative diagnosis. Laparoscopic distal pancreatectomy is a safe and effective approach for treating ECIPAS.
Effects and safety of acne vulgaris with external application of herbal medicines
Authors: Zhou Jin , Li Xiaoxiao , Chen Haimin , Qi Zirong , Shao Shujun , Tang Yinshan , Jiang Chenglong 
Published: June 2021

Abstract

Background
Acne vulgaris (AV) is a common dermatologic disease. The morbidity is increasing annually. External application of herbal medicines (EAHM) has been pervasively used in the therapy of AV. EAHM , as the traditional Chinese therapy, is widely applied in clinical trials for AV. The aim of this review is to systematically evaluate the efficacy and safety of EAHM in the therapy for AV.

Methods
We will conduct an electronic search of 13 databases from their inception to May, 2020, including PubMed, EMBASE, MEDLINE, Web of Science, Cochrane Library, SpringerLink, WHO International Clinical Trials Registry Platform, Wanfang China database, China National Knowledge Infrastructure, Chinese Biomedical Literature Database, Chinese Scientific Journal Database, as well as China's Conference Papers Database and China Dissertation database. Other valid search strategies will also be retrieved to complete this review. All randomized controlled trials in which EAHM was used for the treatment of AV will be adopted. Two researchers will select eligible studies respectively according to a predefined protocol. Methodological quality will be assessed with Cochrane risk of bias by means of RevMan V.5.3.5 software.

Results
This systematic view will present a high-quality synthesis based on current evidence of EAHM intervention for AV patients.

Conclusion
The summary of our systematic view will provide evidence to judge whether EAHM is an effective and safe intervention for AV patients.
A nomogram incorporated lifestyle indicators for predicting nonalcoholic fatty liver disease
Authors: Peng Kaili , Wang Shuofan , Gao Linjiao , You Huaqiang 
Published: June 2021

Abstract
Non-alcoholic fatty liver disease (NAFLD) is the most common chronic liver disease, and its pathogenesis is complicated and triggered by unbalanced diet, sedentary lifestyle, and genetic background. The aim of this study was to construct and validate a nomogram incorporated lifestyle habits for predicting NAFLD incidence.
The overall cohort was divided into training set and test set as using computer-generated random numbers. We constructed the nomogram by multivariate logistic regression analysis in the training set. Thereafter, we validated this model by concordance index, the area under the receiver operating characteristic curve (ROC), net reclassification index, and a calibration curve in the test set. Additionally, we also evaluated the clinical usefulness of the nomogram by decision curve analysis.
There were no statistically significant differences about characteristics between training cohort (n = 748) and test cohort (n = 320). Eleven features (age, sex, body mass index, drinking tea, physical exercise, energy, monounsaturated fatty acids, polyunsaturated fatty acids, hypertension, hyperlipidemia, diabetes) were incorporated to construct the nomogram, concordance index, the area under the ROC curve, net reclassification index were 0.801, 0.801, and 0.084, respectively, indicating the nomogram have good discrimination of predicting NAFLD incidence. Also, the calibration curve showed good consistency between nomogram prediction and actual probability. Moreover, the decision curve showed that when the threshold probability of an individual is within a range from approximately 0.5 to 0.8, this model provided more net benefit to predict NAFLD incidence risk than the current strategies.
This nomogram can be regarded as a user-friendly tool for assessing the risk of NAFLD incidence, and thus help to facilitate management of NAFLD including lifestyle and medical interventions.