bluuebunny/crossref_metadata_2025_split huggingface dataset:
An Algorithmic Approach to Managing Parotid Duct Injury Following Buccal Fat Pad Removal
Authors: Weissler Jason M , Mohamed Omar , Gryskiewicz Joseph M , Chopra Karan 
Published: April 2022

Abstract

The principles of achieving an aesthetically pleasing and harmonious facial appearance are influenced by our evolving understanding of the three-dimensional topography of the face coupled with novel approaches to midface volumization and contouring. In parallel with the evolving landscape of facial aesthetic surgery, an increasing number of publications have emerged focusing on the role of intraoral buccal fat pad removal (BFPR) for the purposes of aesthetic midface contouring. The authors sought to emphasize an underreported and potentially preventable and untoward complication involving iatrogenic parotid duct injury following BFPR. The purpose of this publication is 3-fold: (1) to review the relevant anatomy and literature on intraoral BFPR, (2) to present a case example of this complication, and (3) to discuss treatment options as part of a proposed management algorithm. The authors detail the surgical indications for performing BFPR and review the relevant anatomic considerations. Complication prevention strategies are outlined, and details regarding avoidance of parotid duct injury are reviewed. The diagnostic criteria and clinical presentation of parotid duct injuries following BFPR are comprehensively outlined. The authors present a clinically actionable algorithm for managing a suspected or diagnosed parotid duct injury following BFPR. A clinical case example is discussed to highlight this complication, the diagnostic criteria, and the systematic and algorithmic approach to management. Intraoral BFPR is an incredibly valuable and powerful procedure that can improve facial contour in patients with buccal lipodystrophy or buccal fat pad pseudoherniation. The authors propose a proper diagnostic approach and treatment algorithm to manage this untoward complication.

Level of Evidence: 5
Benchmarking of long-read sequencing, assemblers and polishers for yeast genome
Authors: Zhang Xue , Liu Chen-Guang , Yang Shi-Hui , Wang Xia , Bai Feng-Wu , Wang Zhuo 
Published: April 2022

Abstract

Background
The long reads of the third-generation sequencing significantly benefit the quality of the de novo genome assembly. However, its relatively high single-base error rate has been criticized. Currently, sequencing accuracy and throughput continue to improve, and many advanced tools are constantly emerging. PacBio HiFi sequencing and Oxford Nanopore Technologies (ONT) PromethION are two up-to-date platforms with low error rates and ultralong high-throughput reads. Therefore, it is urgently needed to select the appropriate sequencing platforms, depths and genome assembly tools for high-quality genomes in the era of explosive data production.

Methods
We performed 455 (7 assemblers with 4 polishing pipelines or without polishing on 13 subsets with different depths) and 88 (4 assemblers with or without polishing on 11 subsets with different depths) de novo assemblies of Yeast S288C on high-coverage ONT and HiFi datasets, respectively. The assembly quality was evaluated by Quality Assessment Tool (QUAST), Benchmarking Universal Single-Copy Orthologs (BUSCO) and the newly proposed Comprehensive_score (C_score). In addition, we applied four preferable pipelines to assemble the genome of nonreference yeast strains.

Results
The assembler plays an essential role in genome construction, especially for low-depth datasets. For ONT datasets, Flye is superior to other tools through C_score evaluation. Polishing by Pilon and Medaka improve accuracy and continuity of the preassemblies, respectively, and their combination pipeline worked well in most quality metrics. For HiFi datasets, Flye and NextDenovo performed better than other tools, and polishing is also necessary. Enough data depth is required for high-quality genome construction by ONT (&gt;80X) and HiFi (&gt;20X) datasets.
circRIP: an accurate tool for identifying circRNA–RBP interactions
Authors: Dong Xin , Chen Ke , Chen Wenbo , Wang Jun , Chang Liuping , Deng Jin , Wei Lei , Han Leng , Huang Chunhua , He Chunjiang 
Published: April 2022

Abstract
Circular ribonucleic acids (RNAs) (circRNAs) are formed by covalently linking the downstream splice donor and the upstream splice acceptor. One of the most important functions of circRNAs is mainly exerted through binding RNA-binding proteins (RBPs). However, there is no efficient algorithm for identifying genome-wide circRNA–RBP interactions. Here, we developed a unique algorithm, circRIP, for identifying circRNA–RBP interactions from RNA immunoprecipitation sequencing (RIP-Seq) data. A simulation test demonstrated the sensitivity and specificity of circRIP. By applying circRIP, we identified 95 IGF2BP3-binding circRNAs based on the IGF2BP3 RIP-Seq dataset. We further identified 2823 and 1333 circRNAs binding to &gt;100 RBPs in K562 and HepG2 cell lines, respectively, based on enhanced cross-linking immunoprecipitation (eCLIP) data, demonstrating the significance to survey the potential interactions between circRNAs and RBPs. In this study, we provide an accurate and sensitive tool, circRIP (https://github.com/bioinfolabwhu/circRIP), to systematically identify RBP and circRNA interactions from RIP-Seq and eCLIP data, which can significantly benefit the research community for the functional exploration of circRNAs.
TRamWAy: mapping physical properties of individual biomolecule random motion in large-scale single-particle tracking experiments
Authors: Laurent François , Verdier Hippolyte , Duval Maxime , Serov Alexander , Vestergaard Christian L , Masson Jean-Baptiste 
Published: April 2022

AbstractMotivationSingle-molecule localization microscopy allows studying the dynamics of biomolecules in cells and resolving the biophysical properties of the molecules and their environment underlying cellular function. With the continuously growing amount of data produced by individual experiments, the computational cost of quantifying these properties is increasingly becoming the bottleneck of single-molecule analysis. Mining these data requires an integrated and efficient analysis toolbox.ResultsWe introduce TRamWAy, a modular Python library that features: (i) a conservative tracking procedure for localization data, (ii) a range of sampling techniques for meshing the spatio-temporal support of the data, (iii) computationally efficient solvers for inverse models, with the option of plugging in user-defined functions and (iv) a collection of analysis tools and a simple web-based interface.Availability and implementationTRamWAy is a Python library and can be installed with pip and conda. The source code is available at https://github.com/DecBayComp/TRamWAy.
SpatialExperiment: infrastructure for spatially-resolved transcriptomics data in R using Bioconductor
Authors: Righelli Dario , Weber Lukas M , Crowell Helena L , Pardo Brenda , Collado-Torres Leonardo , Ghazanfar Shila , Lun Aaron T L , Hicks Stephanie C , Risso Davide 
Published: April 2022

AbstractSummarySpatialExperiment is a new data infrastructure for storing and accessing spatially-resolved transcriptomics data, implemented within the R/Bioconductor framework, which provides advantages of modularity, interoperability, standardized operations and comprehensive documentation. Here, we demonstrate the structure and user interface with examples from the 10x Genomics Visium and seqFISH platforms, and provide access to example datasets and visualization tools in the STexampleData, TENxVisiumData and ggspavis packages.Availability and implementationThe SpatialExperiment, STexampleData, TENxVisiumData and ggspavis packages are available from Bioconductor. The package versions described in this manuscript are available in Bioconductor version 3.15 onwards.Supplementary informationSupplementary data are available at Bioinformatics online.
GEInfo: an R package for gene–environment interaction analysis incorporating prior information
Authors: Wang Xiaoyan , Liu Hongduo , Ma Shuangge 
Published: April 2022

AbstractSummaryGene–environment (G–E) interactions have important implications for many complex diseases. With higher dimensionality and weaker signals, G–E interaction analysis is more challenged than the analysis of main G (and E) effects. The accumulation of published literature makes it possible to borrow strength from prior information and improve analysis. In a recent study, a ‘quasi-likelihood + penalization’ approach was developed to effectively incorporate prior information. Here, we first extend it to linear, logistic and Poisson regressions. Such models are much more popular in practice. More importantly, we develop the R package GEInfo, which realizes this approach in a user-friendly manner. To facilitate direct comparison and routine data analysis, the package also includes functions for alternative methods and visualization.Availability and implementationThe package is available at https://CRAN.R-project.org/package=GEInfo.Supplementary informationSupplementary materials are available at Bioinformatics online.
Organ preservation in rectal cancer: review of contemporary management
Authors: Fleming Christina , Vendrely Véronique , Rullier Eric , Denost Quentin 
Published: April 2022

Abstract

Background
Organ preservation as a successful management for rectal cancer is an evolving field. Refinement of neoadjuvant therapies and extended interval to response assessment has improved tumour downstaging and cCR rates.

Methods
This was a narrative review of the current evidence for all aspects of organ preservation in rectal cancer management, together with a review of the future direction of this field.

Results
Patients can be selected for organ preservation opportunistically, based on an unexpectedly good tumour response, or selectively, based on baseline tumour characteristics that predict organ preservation as a viable treatment strategy. Escalation in oncological therapy and increasing the time interval from completion of neaodjuvant therapy to tumour assessment may further increase tumour downstaging and complete response rates. The addition of local excision to oncological therapy can further improve organ preservation rates. Cancer outcomes in organ preservation are comparable to those of total mesorectal excision, with low regrowth rates reported in patients who achieve a complete response to neoadjuvant therapy. Successful organ preservation aims to achieve non-inferior oncological outcomes together with improved functionality and survivorship. Future research should establish consensus of follow-up protocols, and define criteria for oncological and functional success to facilitate patient-centred decision-making.

Conclusion
Modern neoadjuvant therapy for rectal cancer and increasing the interval to tumour response increases the number of patients who can be managed successfully with organ preservation in rectal cancer, both as an opportunistic event and as a planned treatment strategy.
Tailoring diagnosis and treatment in symptomatic gallstone disease
Authors: Latenstein Carmen S S , de Reuver Philip R 
Published: April 2022

Abstract

Background
There is a lack of consensus in selecting patients who do or do not benefit from surgery when patients present with abdominal pain and gallbladder stones are present. This review aimed to give an overview of results from recent trials and available literature to improve treatment decisions in patients with uncomplicated cholecystolithiasis.

Methods
First, an overview of different symptom criteria for laparoscopic cholecystectomy in patients with uncomplicated cholecystolithiasis is given, based on national and international guidelines. Second, treatment outcomes (absence of biliary colic, pain-free state, biliary and surgical complications) are summarized, with data from three clinical trials. Finally, personal advice for treatment decisions in patients with uncomplicated cholecystolithiasis is provided, based on recent trials, the available literature, and expert opinion.

Results
This review describes different guidelines and criteria sets for uncomplicated cholecystolithiasis, provides an overview of outcomes after cholecystectomy, and advises on treatment decisions in patients with abdominal pain and gallbladder stones. After cholecystectomy, biliary colic is resolved in 95 per cent of patients. However, non-specific abdominal pain persists in 40 per cent. Irritable bowel syndrome and functional dyspepsia significantly increase the risk of persistent pain. Age, previous abdominal surgery, baseline pain score on a visual analogue scale, pain characteristics, nausea, and heartburn are part of the SUCCESS criteria, and are associated with clinically relevant pain reduction after gallbladder removal.

Conclusion
The surgical community can now give more personalized advice on surgery to improve care for patients with abdominal pain and uncomplicated cholecystolithiasis.
The regulatory role of eosinophils in viral, bacterial, and fungal infections
Authors: Gaur Pratibha , Zaffran Ilan , George Tresa , Rahimli Alekberli Fidan , Ben-Zimra Micha , Levi-Schaffer Francesca 
Published: April 2022

AbstractEosinophils are innate immune cells typically associated with allergic and parasitic diseases. However, in recent years, eosinophils have also been ascribed a role in keeping homeostasis and in fighting several infectious diseases. Indeed, these cells circulate as mature cells in the blood and can be quickly recruited to the infected tissue. Moreover, eosinophils have all the necessary cellular equipment such as pattern recognition receptors (PRRs), pro-inflammatory cytokines, anti-bacterial proteins, and DNA traps to fight pathogens and promote an efficient immune response. This review summarizes some of the updated information on the role of eosinophils’ direct and indirect mediated interactions with pathogens.
The Impact of the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Pandemic on Substance Use in the United States
Authors: Ross Jennifer A , Malone Patrice K , Levy Sharon 
Published: April 2022

Abstract
The SARS-CoV-2 pandemic has been associated with dramatic increases in substance use, as marked by increased alcohol, nicotine, and cannabis sales. Lethal opioid overdoses also increased dramatically, especially during the initial phases of the epidemic when lockdowns and social isolation combined with increasing fentanyl contamination of the illicit drug supply resulted in more overdoses and fewer opportunities for rescue. Substance use, and especially inhalational drug use, increases the likelihood of both transmission and severe infection. Youth are especially vulnerable to substance use and have increased risk of long-term problems. These outcomes highlight the need for greater access to substance use treatment. Virtual treatment, which emerged as a promising format during the pandemic, may reduce access barriers. This article reviews trends in substance use during the pandemic, explores root causes of increased use and overdose, and examines the potential to increase treatment through virtual care, especially during future periods of disruption.
39: TREATMENT OF ANASTOMOTIC LEAKAGE AFTER ESOPHAGECTOMY (TENTACLE—ESOPHAGUS) STUDY: EFFICACY OF DIFFERENT INITIAL TREATMENT STRATEGIES FOR ANASTOMOTIC LEAKAGE
Authors: Ubels S , Verstegen M , Bouwense S , Hannink G , Siersema P , Klarenbeek B , Van Workum F , Rosman C 
Published: April 2022

Abstract

Background and aim
Anastomotic leakage (AL) is a common and severe complication after esophagectomy. It is largely unknown which primary treatments are most effective for which type of leak. We aimed to investigate the effectiveness of different primary treatments of AL after esophagectomy.

Methods
The TENTACLE—Esophagus study is an international retrospective cohort study, in which 1509 patients with AL after esophagectomy between 2011 and 2019 were included. Detailed data were collected regarding case mix, resection (e.g. minimally invasive resection), leakage characteristics (e.g. organ failure, leak circumference, intrathoracic contamination) and leakage treatment (e.g. hours from diagnosis to treatment, primary and secondary treatment modalities such as endoscopic, radiologic and surgical treatment). An elaborate data quality validation and data accuracy assessment were performed. Primary outcome was 90-day mortality and secondary outcomes included length of stay and leak healing time. Regression analysis will be used to analyze the effectiveness of primary treatments after correction for patient-, surgery-, and leakage characteristics, and leakage severity. Different clinically relevant leakage groups have been defined. Efficacy of different treatment strategies adjusted for leakage severity will be analyzed in these clinical groups. The full study protocol is accessible at www.tentaclestudy.com.

Results
Detailed data of 1509 patients with AL was collected from 71 centers in 20 countries. Data accuracy was 96.5%. Preliminary results showed that the overall 90-day mortality was 11.7%. The analysis of TENTACLE—Esophagus data is currently being performed and efficacy of different leakage treatment strategies is being assessed. The efficacy of initial leakage treatment strategies will be ready to be presented at the ESDE meeting.

Conclusion
This is the largest study on effectiveness of AL treatments. The final results on efficacy of primary leak treatments, which will be available for presentation at the ESDE meeting, could provide an evidence-based basis that can be used by clinicians to determine the preferred primary treatment strategy in patients with a given type of anastomotic leakage after esophagectomy.
56: EXTERNAL VALIDATION OF PET-BASED RADIOMIC MODELS TO IDENTIFY PATIENTS WITH RESIDUAL ESOPHAGEAL CANCER AFTER NEOADJUVANT CHEMORADIOTHERAPY
Authors: Valkema M , Beukinga J , Chatterjee A , Woodruff H , Lambin P , Bennink R , Schreurs W , Roef M , Valkema R , Lagarde S , Wijnhoven B , Plukker J , Van Lanschot J 
Published: April 2022

Abstract

Background and aim
High-throughput quantitative imaging (‘radiomics’) has been proposed to predict tumor response in various types of cancer. Internally validated radiomic models based on post-treatment PET features plus cT-stage have been developed (Beukinga et al. 2018) to detect residual tumor after neoadjuvant chemoradiotherapy for esophageal cancer. The aim of the present study was to externally validate the published models.

Methods
The external validation cohort comprised esophageal cancer patients who underwent chemoradiotherapy according to the CROSS regimen followed by immediate resection in four Dutch institutes between 2013–2019. Outcome was tumor regression grade (TRG) 1 (0% residual vital tumor) versus TRG-2-3-4 (≥ 1% tumor). Preoperative FDG-PET/CT was performed 6–12 weeks after nCRT. Gross tumor volumes on CT were transposed to post-treatment PET scans and were manually adapted in consensus by two investigators. Radiomic features were extracted using the open-source software ‘Pyradiomics’, with settings similar to the published models. Discrimination and calibration were assessed for the 6 internally validated models with optimism-corrected AUCs&gt;0.77.

Results
Some 189 patients were included in the external validation cohort. Baseline characteristics and outcome (TRG-1: 40/189 patients (21%); TRG2–3-4: 149/189 patients (79%)) were comparable to the derivation sample. Since features were dependent on different scanner manufacturers (data not shown), the cohort was reduced with only scans from Siemens scanners (n = 130), similar to the derivation sample. The model including cT-stage and the grey-level-co-occurrence-matrix feature ‘Joint Energy’ had highest AUC of 0.71 (95% CI 0.60–0.81), and a calibration slope and intercept of −0.19 and 2.83 respectively. At a probability threshold of 0.5, sensitivity was 81%, specificity 31% and balanced accuracy 56%.

Conclusion
The predictive performance of the previously developed radiomic models could not be replicated in the present multicenter external validation cohort. The decreased overall performance indicates overfitting of the models to the derivation sample. Possible causes are unintentional dependency of radiomic features on scanner types, scanning protocols, tumor delineation methods and timing of post-treatment FDG-PET/CT. We aim at improving the generalizability of the models, to enable future application in clinical decision-making for individual patients.
88: BRAIN METASTASIS INCIDENCE IN GASTRO-ESOPHAGEAL CANCER: A META-ANALYSIS
Authors: Sleiman M , Abbassi Z , Jung M , Toso C , Chevallay M , Mönig S 
Published: April 2022

Abstract

Background and aim
Upper gastrointestinal cancers (UGC) are a leading cause of cancer related deaths. Brain metastases (BM) from gastric and esophageal cancer are rare and associated with a poor survival time. In order to establish the most accurate incidence and characteristics of BM in UGC, we decide to review all studies and series published in the last years.

Methods
We searched the keywords ‘Gastric cancer OR Oesophageal Cancer + Cerebral Metastasis’ in Pubmed, EMBASE, Cochrane Library. Inclusion criteria were all studies treating with BM from UGC cancer. When inclusion criteria were met, we extracted the following endpoints for each study: author, year of publication, country of population, tumor localization, tumor histology, number of BM, synchronous or metachronous BM, other localization of metastases, surgical treatment of the primary tumor, different modality of BM treatment (surgery, steatosic radiosurgery, whole brain radiation, gamma knife surgery), survival and follow-up.

Results
In the final analysis, we included 52 studies. The number of patients with oesophageal tumor were described in 30 studies with 41636 patients from which 1234 patients (2.9%) had BM. 526 patients (63%) had an adenocarcinoma, 287 (34%) had a SCC and 17 (3%) other histology. BM was unique in 288 patients (50%) and multiples in 282 patients (50%). Combined radiotherapy and surgery was performed in 129 patients (17.9%). Surgical metastasectomy was performed in 172 patients (24.25%). Stereotaxic radiotherapy was delivered in 60 patients (8.5%). Whole brain radiotherapy was performed in 265 patients (35.9%), gamma knife surgery in 43 patients (5.9%), chemotherapy in 10 patients (1.6%) and no treatment in 43 patients (5.9%). Median survival was reported from 3 to 24 months. We identified 12 articles which matched criteria for gastric cancer with a total of 73.781 primary gastric tumors where 645 presented BM (0.87%). We could identify 159 patients with single BM (42.3%) compared to 217 patients with multiple BM (57.7%). We identified 434 adenocarcinoma which represent 81.1% of BM. Median survival was from 1.3 to 27 months with a median survival of 4.2 months.

Conclusion
BM from UGC are rare but with a low survival. Multimodal treatment is the most described treatment strategy.