Project description:BackgroundExisting reporting guidelines pay insufficient attention to the detail and comprehensiveness reporting of surgical technique. The Surgical techniqUe rePorting chEcklist and standaRds (SUPER) aims to address this gap by defining reporting standards for surgical technique. The SUPER guideline intends to apply to articles that encompass surgical technique in any study design, surgical discipline, and stage of surgical innovation.MethodsFollowing the EQUATOR (Enhancing the QUAlity and Transparency Of health Research) Network approach, 16 surgeons, journal editors, and methodologists reviewed existing reporting guidelines relating to surgical technique, reviewed papers from 15 top journals, and brainstormed to draft initial items for the SUPER. The initial items were revised through a three-round Delphi survey from 21 multidisciplinary Delphi panel experts from 13 countries and regions. The final SUPER items were formed after an online consensus meeting to resolve disagreements and a three-round wording refinement by all 16 SUPER working group members and five SUPER consultants.ResultsThe SUPER reporting guideline includes 22 items that are considered essential for good and informative surgical technique reporting. The items are divided into six sections: background, rationale, and objectives (items 1 to 5); preoperative preparations and requirements (items 6 to 9); surgical technique details (items 10 to 15); postoperative considerations and tasks (items 16 to 19); summary and prospect (items 20 and 21); and other information (item 22).ConclusionsThe SUPER reporting guideline has the potential to guide detailed, comprehensive, and transparent surgical technique reporting for surgeons. It may also assist journal editors, peer reviewers, systematic reviewers, and guideline developers in the evaluation of surgical technique papers and help practitioners to better understand and reproduce surgical technique.Trial registrationhttps://www.equator-network.org/library/reporting-guidelines-under-development/reporting-guidelines-under-development-for-other-study-designs/#SUPER.
Project description:In this prospective observational study, non-invasive critical care echocardiography (CCE) was used to obtain quantitative hemodynamic parameters in 107 intensive care unit (ICU) patients; the parameters were then visualized in a novel web graph approach to increase the understanding and impact of CCE abnormalities, as an alternative to thermodilution techniques. Visualizing the CCE hemodynamic data in six-dimensional web graph plots was feasible in almost all ICU patients. In 23.1% of patients, significant tricuspid regurgitation prevented correlation between thermodilution techniques and echocardiographic hemodynamics. Two parameters of longitudinal right ventricular function (TAPSE and S') did not correlate in ICU patients. Clinical surrogate parameters of hemodynamic compromise did not correlate with measured hemodynamics. 26.2% of the patients with mean arterial pressures above 60 mmHg had cardiac indices (CI) below 2.5 L min-1·m-2. A CI below 2.2 L·min-1·m-2 was associated with a significant ICU survival disadvantage. CCE was feasible in addition or as an alternative to thermodilution techniques for the hemodynamic evaluation of ICU patients. Six-dimensional web graph plots visualized the hemodynamic states and were especially useful in conditions in which thermodilution methods were not reliable. Hemodynamic CCE identified patients with previously unknown low CI, which correlated with a higher ICU mortality.
Project description:The importance of fluorescence light microscopy for understanding cellular and sub-cellular structures and functions is undeniable. However, the resolution is limited by light diffraction (~200-250 nm laterally, ~500-700 nm axially). Meanwhile, super-resolution microscopy, such as structured illumination microscopy (SIM), is being applied more and more to overcome this restriction. Instead, super-resolution by stimulated emission depletion (STED) microscopy achieving a resolution of ~50 nm laterally and ~130 nm axially has not yet frequently been applied in plant cell research due to the required specific sample preparation and stable dye staining. Single-molecule localization microscopy (SMLM) including photoactivated localization microscopy (PALM) has not yet been widely used, although this nanoscopic technique allows even the detection of single molecules. In this study, we compared protein imaging within metaphase chromosomes of barley via conventional wide-field and confocal microscopy, and the sub-diffraction methods SIM, STED, and SMLM. The chromosomes were labeled by DAPI (4',6-diamidino-2-phenylindol), a DNA-specific dye, and with antibodies against topoisomerase IIα (Topo II), a protein important for correct chromatin condensation. Compared to the diffraction-limited methods, the combination of the three different super-resolution imaging techniques delivered tremendous additional insights into the plant chromosome architecture through the achieved increased resolution.
Project description:A key step in pharmacogenomic studies is the development of accurate prediction models for drug response based on individuals' genomic information. Recent interest has centered on semiparametric models based on kernel machine regression, which can flexibly model the complex relationships between gene expression and drug response. However, performance suffers if irrelevant covariates are unknowingly included when training the model. We propose a new semiparametric regression procedure, based on a novel penalized garrotized kernel machine (PGKM), which can better adapt to the presence of irrelevant covariates while still allowing for a complex nonlinear model and gene-gene interactions. We study the performance of our approach in simulations and in a pharmacogenomic study of the renal carcinoma drug temsirolimus. Our method predicts plasma concentration of temsirolimus as well as standard kernel machine regression when no irrelevant covariates are included in training, but has much higher prediction accuracy when the truly important covariates are not known in advance. Supplemental materials, including R code used in this manuscript, are available online.
Project description:A super-secondary structure (SSS) is a spatially unique ensemble of secondary structural elements that determine the three-dimensional shape of a protein and its function, rendering SSSs attractive as folding cores. Understanding known types of SSSs is important for developing a deeper understanding of the mechanisms of protein folding. Here, we propose a universal PSSNet machine-learning method for SSS recognition and segmentation. For various types of SSS segmentation, this method uses key characteristics of SSS geometry, including the lengths of secondary structural elements and the distances between them, torsion angles, spatial positions of Cα atoms, and primary sequences. Using four types of SSSs (βαβ-unit, α-hairpin, β-hairpin, αα-corner), we showed that extensive SSS sets could be reliably selected from the Protein Data Bank and AlphaFold 2.0 database of protein structures.
Project description:Accurate prediction of where and when typhoons (or named hurricanes which form over the North Atlantic Ocean) will make landfall is critical to protecting human lives and properties. Although the traditional method of typhoon track prediction based on the steering flow theory has been proven to be an effective way in most situations, it slipped up in some cases. Our analysis of the long-term Chinese typhoon records reveals that typhoons, especially super typhoons (those with maximum sustained surface winds of greater than 51?ms(-1)), have a trend to make landfalls toward warmer land in China over the past 50?years (1960-2009). Numerical sensitivity experiments using an advanced atmospheric model further confirm this finding. Our finding suggests an alternative approach to predict the landfall tracks of the most devastating typhoons in the southeastern China.
Project description:BackgroundA wide variety of surgical techniques are used to perform vasectomy. The purpose of this systematic review was to assess if any surgical techniques to isolate or occlude the vas are associated with better outcomes in terms of occlusive and contraceptive effectiveness, and complications.MethodsWe searched MEDLINE (1966-June 2003), EMBASE (1980-June 2003), reference lists of retrieved articles, urology textbooks, and our own files looking for studies comparing two or more vasectomy surgical techniques and reporting on effectiveness and complications. From 2,058 titles or abstracts, two independent reviewers identified 224 as potentially relevant. Full reports of 219 articles were retrieved and final selection was made by the same two independent reviewers using the same criteria as for the initial selection. Discrepancies were resolved by involving a third reviewer. Data were extracted and methodological quality of selected studies was assessed by two independent reviewers. Studies were divided in broad categories (isolation, occlusion, and combined isolation and occlusion techniques) and sub-categories of specific surgical techniques performed. Qualitative analyses and syntheses were done.ResultsOf 31 comparative studies (37 articles), only four were randomized clinical trials, most studies were observational and retrospective. Overall methodological quality was low. From nine studies on vas isolation, there is good evidence that the no-scalpel vasectomy approach decreases the risk of surgical complications, namely hematoma/bleeding and infection, compared with incisional techniques. Five comparative studies including one high quality randomized clinical trial provided good evidence that fascial interposition (FI) increases the occlusive effectiveness of ligation and excision. Results of 11 comparative studies suggest that FI with cautery of the vas lumen provides the highest level of occlusive effectiveness, even when leaving the testicular end open. Otherwise, firm evidence to support any occlusion technique in terms of increased effectiveness or decreased risk of complications is lacking.ConclusionsCurrent evidence supports no-scalpel vasectomy as the safest surgical approach to isolate the vas when performing vasectomy. Adding FI increases effectiveness beyond ligation and excision alone. Occlusive effectiveness appears to be further improved by combining FI with cautery. Methodologically sound prospective controlled studies should be conducted to evaluate specific occlusion techniques further.
Project description:Computational tools used for genomic analyses are becoming more accurate but also increasingly sophisticated and complex. This introduces a new problem in that these pieces of software have a large number of tunable parameters that often have a large influence on the results that are reported. We quantify the impact of parameter choice on transcript assembly and take some first steps toward generating a truly automated genomic analysis pipeline by developing a method for automatically choosing input-specific parameter values for reference-based transcript assembly using the Scallop tool. By choosing parameter values for each input, the area under the receiver operator characteristic curve (AUC) when comparing assembled transcripts to a reference transcriptome is increased by an average of 28.9% over using only the default parameter choices on 1595 RNA-Seq samples in the Sequence Read Archive. This approach is general, and when applied to StringTie, it increases the AUC by an average of 13.1% on a set of 65 RNA-Seq experiments from ENCODE. Parameter advisors for both Scallop and StringTie are available on Github.