bluuebunny/crossref_metadata_2025_split huggingface dataset:
Scientific intuition inspired by machine learning-generated hypotheses
Authors: Friederich Pascal , Krenn Mario , Tamblyn Isaac , Aspuru-Guzik Alán 
Published: January 2021

Abstract
Machine learning with application to questions in the physical sciences has become a widely used tool, successfully applied to classification, regression and optimization tasks in many areas. Research focus mostly lies in improving the accuracy of the machine learning models in numerical predictions, while scientific understanding is still almost exclusively generated by human researchers analysing numerical results and drawing conclusions. In this work, we shift the focus on the insights and the knowledge obtained by the machine learning models themselves. In particular, we study how it can be extracted and used to inspire human scientists to increase their intuitions and understanding of natural systems. We apply gradient boosting in decision trees to extract human-interpretable insights from big data sets from chemistry and physics. In chemistry, we not only rediscover widely know rules of thumb but also find new interesting motifs that tell us how to control solubility and energy levels of organic molecules. At the same time, in quantum physics, we gain new understanding on experiments for quantum entanglement. The ability to go beyond numerics and to enter the realm of scientific insight and hypothesis generation opens the door to use machine learning to accelerate the discovery of conceptual understanding in some of the most challenging domains of science.
New horizons: managing antithrombotic dilemmas in patients with cerebral amyloid angiopathy
Authors: Kelly James 
Published: January 2021

Abstract
Cerebral amyloid angiopathy (CAA) most commonly presents with lobar intracerebral haemorrhage, though also with transient focal neurological episodes, cognitive impairment, as an incidental finding and rarely acutely or subacutely in patients developing an immune response to amyloid. Convexity subarachnoid haemorrhage, cortical superficial siderosis and lobar cerebral microbleeds are the other signature imaging features. The main implications of a diagnosis are the risk of intracerebral haemorrhage and frequent co-existence of antithrombotic indications. The risk of intracerebral haemorrhage varies by phenotype, being highest in patients with transient focal neurological episodes and lowest in patients with isolated microbleeds.
There is only one relevant randomised controlled trial to CAA patients with antithrombotic indications: RESTART showed that in patients presenting with intracerebral haemorrhage while taking antiplatelets, restarting treatment appeared to reduce recurrent intracerebral haemorrhage and improve outcomes. Observational and indirect data are reviewed relevant to other scenarios where there are antithrombotic indications. In patients with a microbleed-only phenotype, the risk of ischaemic stroke exceeds the risk of intracerebral haemorrhage at all cerebral microbleed burdens. In patients with atrial fibrillation (AF), left atrial appendage occlusion, where device closure excludes the left atrial appendage from the circulation, can be considered where the risk of anticoagulation seems prohibitive. Ongoing trials are testing the role of direct oral anticoagulant (DOACs) and left atrial appendage occlusion in patients with intracerebral haemorrhage/AF but in the interim, treatment decisions will need to be individualised and remain difficult.
Dissection Technique for Abdominoplasty With Scarpa Fascia Preservation: Comparative Study on Avulsion Technique Versus Diathermocoagulation
Authors: Torres-Silva Catarina , Pisco Andreia , Valença-Filipe Rita , Rebelo Marco , Peres Helena , Vásconez Luis , Costa-Ferreira António 
Published: January 2021

Abstract

Background
Many strategies have been developed to lower the high complication rate associated with a full abdominoplasty. The dissection technique may have a role to achieve this goal.

Objectives
The present study compared 2 different dissection techniques to perform a full abdominoplasty with Scarpa fascia preservation: avulsion technique and electrodissection.

Methods
A retrospective observational cohort study was performed in 2 health institutions from January 2005 to January 2019. A total of 251 patients were involved: 122 patients submitted to abdominoplasty employing the avulsion technique (Group A) and 129 with diathermocoagulation (coagulation mode) (Group B). The latter was further divided into group B1 (57 patients with device settings according to surgeon’s preferences) and B2 (72 patients with a specific regulation aiming at minimal tissue damage). Several variables were analyzed: population characteristics, time of hospital stay, time to drain removal, total and daily drain output, emergency department visits, readmission, reoperation, and local and systemic complications.

Results
The general characteristics of both groups did not statistically significantly differ except for previous abdominal surgery. The diathermocoagulation group had a significantly lower length of hospital stay and time to drain removal. Moreover, these advantages were maximized when electrocautery was conducted with a specific low-voltage setting as significant differences were found. The other outcomes were identical.

Conclusions
Limiting the extension of electrodissection with the avulsion technique did not present any advantage. Utilizing diathermocoagulation (coagulation mode) during a full abdominoplasty with Scarpa fascia preservation, especially when it is aimed at minimal tissue damage, reduces patients’ time with drains.

Level of Evidence: 3
The Function-Preserving Frontalis Orbicularis Oculi Muscle Flap for the Correction of Severe Blepharoptosis With Poor Levator Function
Authors: Huang Shu-Hung , Lee Chia-Chen , Lai Hsin-Ti , Takahashi Hidenobu , Wang Yu-Chi , Lai Chung-Sheng 
Published: January 2021

Abstract

Background
Severe blepharoptosis with poor levator function (LF) has traditionally been managed with exogenous frontalis suspension but complications such as lagophthalmos, infection, and rejection are often reported.

Objectives
The aim of this study was to design a function-preserving frontalis orbicularis oculi muscle (FOOM) flap to correct severe blepharoptosis with poor LF. The long-term surgical outcome of the technique was assessed.

Methods
This retrospective study included only adult patients with severe blepharoptosis and poor LF, all of whom had their surgery performed by the senior surgeon over a 6-year period. Clinical assessment of LF, palpebral fissure height (PFH), marginal reflex distance 1 (MRD1), duration of follow-up, and postoperative complications were recorded.

Results
A total of 34 patients and 59 eyelids were recorded during a mean follow-up period of 17.7 months. Postoperative evaluation yielded mean [standard deviation] improvements of PFH gain of 5.62 [1.61] mm (P &lt; 0.001), and MRD1 and PFH increases of 4.03 [0.82] mm (P &lt; 0.001) and 8.94 [0.81] mm (P &lt; 0.001), respectively. All patients demonstrated normalization of orbicularis function: no lagophthalmos was observed at the 8-month postoperative follow-up. Recurrence of ptosis was recorded in 4 eyelids (6.78%). Revisions were performed in 2 eyelids (3.39%). No infection or granuloma was noted.

Conclusions
The function-preserving FOOM flap is a useful vector for frontalis suspension. Not only does it effectively address lagophthalmos as well as other complications, but it provides aesthetically pleasing outcomes in patients with severe blepharoptosis and poor LF.

Level of Evidence: 4
Labial Fat Grafting After Penile Inversion Vaginoplasty
Authors: Patel Viren , Morrison Shane D , Gujural Dev , Satterwhite Thomas 
Published: January 2021

Abstract

Background
Penile inversion vaginoplasty (PIV) has become the most commonly performed genital surgery for transfeminine patients. However, patients undergoing this procedure may still require revisions to achieve a satisfactory result.

Objectives
The authors report on the utilization of autologous fat grafting to the labia majora to improve results after PIV and complications that may predict the need for grafting.

Methods
A retrospective chart review was conducted of a single surgeon’s patients who underwent PIV between July 2014 and December 2019. Demographic information, operative information, and postoperative outcomes were abstracted from the health records. Wilcoxon rank sum tests and chi-squared test were employed for continuous variables and categorical, respectively.

Results
A total of 182 transfeminine and gender-diverse patients underwent PIV, with 6 patients (3.3%) eventually undergoing labial fat grafting. The most common indication for labial fat grafting was flattened labia majora (83%). All fat grafting procedures were performed concurrently with other revisions of the vaginoplasty. There were no demographic or medical history differences detected between the fat grafting and non-fat grafting groups. Patients who underwent labial fat grafting were more likely to suffer from introital stenosis (33% vs 6%, P = 0.007) and prolonged granulation tissue greater than 6 weeks after initial vaginoplasty (83% vs 32%; P = 0.01).

Conclusions
Labial fat grafting is a safe and effective method to address defects in the labia majora after PIV. Prolonged granulation tissue and introital stenosis may predict the need for labial fat grafting, possibly due to increased scarring and contracture at the surgical site.

Level of Evidence: 4
Power-Assisted Liposculpture in Male Patients: A Spectrum of Definitions
Authors: Saad Ahmad , Altamirano-Arcos Carlos Alberto , Nahas Combina Luciano , Saad Mariam 
Published: January 2021

Abstract

Background
Liposculpture procedures have gained popularity over the last 2 decades with the evolution of surgeons’ skills and technological advancement. According to the 2018 The Aesthetic Society report, liposuction is the second-most popular aesthetic procedure in the United States.

Objectives
The authors aimed to demonstrate that a spectrum of liposculpture definitions can be achieved utilizing power-assisted liposuction (PAL). Also, the authors sought to describe the satisfaction and complication rates in mild-, moderate-, and high-definition groups utilizing the PAL technology.

Methods
The authors designed a single-center retrospective study, including male patients who underwent PAL liposculpture of the chest, abdomen, back, and arms. Inclusion criteria were male patients &gt;18 years of age and body mass index &lt;30 kg/m2. Measured outcomes included extent of definition, complication rates, and levels of satisfaction.

Results
Fifty male patients were included in this study between January 2018 and November 2019. The average age was 37.34 years (range = 25-56 years). The average body mass index was 26.4 kg/m2 (range = 24-30 years). A total of 54.3% of patients opted for high definition (HD), 36.4% for moderate definition, and 9.2% for mild definition. There were no major complications. The HD subgroup registered the highest incidence of minor complications (21%). Patient satisfaction levels were high in all 3 subgroups, with the highest scores in the HD subgroup (9.3/10).

Conclusions
A spectrum of definitions can be safely achieved utilizing the PAL technology, with high patient satisfaction in mild-, moderate-, and high-definition liposculpture subgroups and low complication rates.

Level of Evidence: 4
Semi–Let-Down and Semi–Push-Down Preservation Techniques: Maintaining the Intactness of the Distal Region
Authors: Öztürk Güncel 
Published: January 2021

AbstractBackgroundThe nose is an important part of the face and plays a significant role in interpersonal communication and self-esteem. Dorsal preservation techniques, such as the push-down and let-down techniques, are employed for dorsal hump reductions.ObjectivesIn this study, several approaches were defined in which the let-down and push-down techniques were applied depending on the patients’ needs.MethodsThe records of 64 patients were assessed retrospectively. The patients who underwent either the push-down or let-down technique for hump reduction and who were eligible for these new approaches were included. In this research, the distal part of the septum remained intact after both the push-down and let-down techniques. Patients were assessed before and 1 year after surgery employing the Rhinoplasty Outcome Evaluation (ROE).ResultsThe follow-up period ranged from 16 to 25 months (median of 19.2 months). The median ROE score before surgery was 61.6 (minimum: 58; maximum: 64) and increased to 92.2 (minimum: 82; maximum: 96) points 12 months after surgery. This increase in the ROE score was statistically significant (P &lt; 0.001). The excellent satisfaction rate was 93.75% according to the ROE scale.ConclusionsThese approaches for the let-down and push-down techniques will lead to better results and present different choices to surgeons. The present study is also the first to the author’s knowledge to demonstrate leaving behind an intact area of the distal septum in the push-down and let-down techniques.Level of Evidence: 4
Machine learning approaches for predicting biomolecule–disease associations
Authors: Ding Yulian , Lei Xiujuan , Liao Bo , Wu Fang-Xiang 
Published: January 2021

AbstractBiomolecules, such as microRNAs, circRNAs, lncRNAs and genes, are functionally interdependent in human cells, and all play critical roles in diverse fundamental and vital biological processes. The dysregulations of such biomolecules can cause diseases. Identifying the associations between biomolecules and diseases can uncover the mechanisms of complex diseases, which is conducive to their diagnosis, treatment, prognosis and prevention. Due to the time consumption and cost of biologically experimental methods, many computational association prediction methods have been proposed in the past few years. In this study, we provide a comprehensive review of machine learning-based approaches for predicting disease–biomolecule associations with multi-view data sources. Firstly, we introduce some databases and general strategies for integrating multi-view data sources in the prediction models. Then we discuss several feature representation methods for machine learning-based prediction models. Thirdly, we comprehensively review machine learning-based prediction approaches in three categories: basic machine learning methods, matrix completion-based methods and deep learning-based methods, while discussing their advantages and disadvantages. Finally, we provide some perspectives for further improving biomolecule–disease prediction methods.
TIPP2: metagenomic taxonomic profiling using phylogenetic markers
Authors: Shah Nidhi , Molloy Erin K , Pop Mihai , Warnow Tandy 
Published: January 2021

Abstract

Motivation
Metagenomics has revolutionized microbiome research by enabling researchers to characterize the composition of complex microbial communities. Taxonomic profiling is one of the critical steps in metagenomic analyses. Marker genes, which are single-copy and universally found across Bacteria and Archaea, can provide accurate estimates of taxon abundances in the sample.

Results
We present TIPP2, a marker gene-based abundance profiling method, which combines phylogenetic placement with statistical techniques to control classification precision and recall. TIPP2 includes an updated set of reference packages and several algorithmic improvements over the original TIPP method. We find that TIPP2 provides comparable or better estimates of abundance than other profiling methods (including Bracken, mOTUsv2 and MetaPhlAn2), and strictly dominates other methods when there are under-represented (novel) genomes present in the dataset.

Availability and implementation
The code for our method is freely available in open-source form at https://github.com/smirarab/sepp/blob/tipp2/README.TIPP.md. The code and procedure to create new reference packages for TIPP2 are available at https://github.com/shahnidhi/TIPP_reference_package.

Supplementary information
Supplementary data are available at Bioinformatics online.
Quantifying the link between craniodental morphology and diet in the Soricidae using geometric morphometrics
Authors: Tse Yuen Ting , Calede Jonathan J M 
Published: January 2021

AbstractDietary adaptations have often been associated with heightened taxonomic diversity. Yet, one of the most species-rich mammalian families, the Soricidae, is often considered to be ecologically and morphologically relatively homogenous. Here, we use geometric morphometrics to capture skull and dentary morphology in a broad sample of shrew species and test the hypothesis that morphological variation among shrew species reflects adaptations to food hardness. Our analyses demonstrate that morphology is associated with dietary ecology. Species that consume hard food items are larger and have specific morphological adaptions including an anteroposteriorly expanded parietal, an anteroposteriorly short and dorsoventrally tall rostrum, a mediolaterally wide palate, buccolingually wide cheek teeth, a large coronoid process and a dorsoventrally short jaw joint. The masseter muscle does not appear to play an important role in the strong bite force of shrews and the dentary is a better indicator of ecology than the skull. Our phylogenetic flexible discriminant function analysis suggests that the evolutionary history of shrews has shaped their morphology, canalizing dietary adaptations and enabling functional equivalence whereby different morphologies achieve similar dietary performances. Our work makes possible future studies of niche partitioning among sympatric species as well as the investigation of the diet of extinct soricids.
Assessment of Comorbid Depression and Anxiety in Inflammatory Bowel Disease Using Adaptive Testing Technology
Authors: Karpin Jordan E , Rodriguez Tina G , Traboulsi Cindy , Rai Victoria , Gibbons Robert D , Rubin David T 
Published: January 2021

AbstractBackgroundDepression and anxiety are comorbidities of inflammatory bowel disease (IBD), and it is now recommended to screen IBD patients for these conditions. We screened patients using a novel computerized adaptive testing technology and compared the screening results to measures of disease activity.MethodsConsecutive patients at our tertiary IBD clinic were asked to complete the validated CAT-MH survey (Adaptive Testing Technologies, Chicago, IL); we then reviewed disease and patient characteristics. Clinical remission status was determined based on clinical, laboratory, endoscopy, and imaging results. Statistical methods included Fisher exact test and Pearson chi-square tests to assess association. Univariable and multivariable analyses were performed.ResultsWe included 134 patients, of which 34 (25.3%) screened positive for depression and 18 (13.4%) screened positive for anxiety. We identified 19 (55.9%) and 10 (55.5%) patients who were previously undiagnosed for depression and anxiety, respectively. Patients in clinical remission were less likely to screen positive for depression (odds ratio 0.19; 95% confidence interval 0.07–0.50) and for anxiety (odds ratio 0.30; 95% confidence interval 0.10–0.91). Compared to patients with negative C-reactive protein values, patients with positive C-reactive protein were more likely to also screen positive for depression (P = 0.025) and anxiety (P = 0.15).ConclusionsWe demonstrate the utility of a novel testing technology for screening patients with IBD for depression and anxiety. We found a large number of patients with previously undiagnosed anxiety or depression and a significant positive association between clinically active IBD and these mental health conditions. This work supports and informs recommendations for mental health screening in the IBD population.
Endothelial cell metabolic memory causes cardiovascular dysfunction in diabetes
Authors: Yao Yufeng , Song Qixue , Hu Changqing , Da Xingwen , Yu Yubing , He Zuhan , Xu Chengqi , Chen Qiuyun , Wang Qing K 
Published: January 2021

AbstractAims The aim of this study was to identify the molecular mechanism for hyperglycaemia-induced metabolic memory in endothelial cells (ECs), and to show its critical importance to development of cardiovascular dysfunction in diabetes.Methods and results Hyperglycaemia induces increased nuclear factor-κB (NF-κB) signalling, up-regulation of miR-27a-3p, down-regulation of nuclear factor erythroid-2 related factor 2 (NRF2) expression, increased transforming growth factor-β (TGF-β) signalling, down-regulation of miR-29, and induction of endothelial-to-mesenchymal transition (EndMT), all of which are memorized by ECs and not erased when switched to a low glucose condition, thereby causing perivascular fibrosis and cardiac dysfunction. Similar metabolic memory effects are found for production of nitric oxide (NO), generation of reactive oxygen species (ROS), and the mitochondrial oxygen consumption rate in two different types of ECs. The observed metabolic memory effects in ECs are blocked by NRF2 activator tert-butylhydroquinone and a miR-27a-3p inhibitor. In vivo, the NRF2 activator and miR-27a-3p inhibitor block cardiac perivascular fibrosis and restore cardiovascular function by decreasing NF-κB signalling, down-regulating miR-27a-3p, up-regulating NRF2 expression, reducing TGF-β signalling, and inhibiting EndMT during insulin treatment of diabetes in streptozotocin-induced diabetic mice, whereas insulin alone does not improve cardiac function.Conclusions Our data indicate that disruption of hyperglycaemia-induced EC metabolic memory is required for restoring cardiac function during treatment of diabetes, and identify a novel molecular signalling pathway of NF-κB/miR-27a-3p/NRF2/ROS/TGF-β/EndMT involved in metabolic memory.
Course of Disease in Patients with Microscopic Colitis: A European Prospective Incident Cohort Study
Authors: Verhaegh Bas P M , Münch Andreas , Guagnozzi Danila , Wildt Signe , Cebula Wojciech , Diac Andreea R , Fernández-Bañares Fernando , Al-Khalaf Magid A R , Pedersen Natalia , Kupcinskas Juozas , Bohr Johan , Macaigne Gilles , Lucendo Alfredo J , Lyutakov Ivan , Tontini Gian-Eugenio , Pigò Flavia , Russo Evangelos , Hjortswang Henrik , Miehlke Stephan , Munck Lars K 
Published: January 2021

Abstract

Background and Aims
The disease course of microscopic colitis [MC] is considered chronic but benign. However, this assumption is based on mainly retrospective studies, reporting on incomplete follow-up of selective cohorts. Systematic, prospective and unbiased data to inform patients and healthcare professionals on the expected course of the disease and real-life response to therapy are warranted.

Methods
A prospective, pan-European, multi-centre, web-based registry was established. Incident cases of MC were included. Data on patient characteristics, symptoms, treatment and quality of life were systematically registered at baseline and during real-time follow-up. Four disease course phenotypes were discriminated and described.

Results
Among 381 cases with complete 1-year follow-up, 49% had a chronic active or relapsing disease course, 40% achieved sustained remission after treatment and 11% had a quiescent course. In general, symptoms and quality of life improved after 3 months of follow-up. A relapsing or chronic active disease course was associated with significantly more symptoms and impaired quality of life after 1 year.

Conclusions
A minority of MC patients follow a quiescent disease course with spontaneous clinical improvement, whereas the majority suffer a chronic active or relapsing disease course during the first year after diagnosis, with persisting symptoms accompanied by a significantly impaired quality of life.