bluuebunny/crossref_metadata_2025_split huggingface dataset:
Treatment of Panfacial Fractures and Three-Dimensional Outcome Analysis: The Occlusion First Approach
Authors: Choi Jong Woo , Kim Min Ji 
Published: April 2019

Abstract
Successful management of panfacial fractures requires an understanding of the component fracture patterns and the ability to relate them anatomically to the stable elements of the skull. However, there is no widespread agreement on the ideal approach to treatment of panfacial fractures and several techniques have been proposed. Here, the authors suggest the “occlusion first” approach, a technique that involves larger segment reduction as the initial step to provide an appropriate occlusal plane.
This retrospective study included data from patients undergoing open reduction and internal fixation of panfacial fractures between March 2005 and November 2017 by the occlusion first technique. The degree of reduction in the mid and lower face was evaluated using 3D CT. The causes of injury, combined fracture, and multidisciplinary consultation during postoperative management were reviewed.
The study population comprised 61 patients (47 male, 14 female) with a mean age of 47.6 years (range, 9–76 years). Analysis of 3D CT scans obtained from 42 patients showed no significant difference in hemifacial volume in the postoperative period (left hemifacial volume: 206.48 ± 68.35 cm3, right: 205.17 ± 66.27 cm3, P = 0.436).
The occlusion first approach, with initial reduction of larger segments, enables effective reconstruction of the multiple segments involved in panfacial fractures. The authors have demonstrated that this technique successfully restores the entire face, improves surgical reduction, acts as an orientation aid during surgery, and provides a template for the smaller segments. Therefore, this approach can facilitate the accurate and efficient reduction and fixation of panfacial fractures.
Tumor Long-interspersed Nucleotide Element-1 Methylation Level and Immune Response to Esophageal Cancer
Authors: Kosumi Keisuke , Baba Yoshifumi , Okadome Kazuo , Yagi Taisuke , Kiyozumi Yuki , Yoshida Naoya , Watanabe Masayuki , Baba Hideo 
Published: April 2019

Objective:
To examine the relationship between tumor long-interspersed nucleotide element-1 (LINE-1) methylation level and immune response to esophageal cancer.

Background:
Evidence points to a correlation between the abundance of immune cells and a favorable prognosis in esophageal cancer patients. Accumulating evidence indicates a critical role of tumor LINE-1 hypomethylation in the aggressive behavior of esophageal cancer, which in turn leads to an unfavorable prognosis.

Methods:
Utilizing a nonbiased database of 292 resected esophageal cancers, we measured tumor LINE-1 methylation level by pyrosequencing assay, and examined the relationship between LINE-1 methylation and the density of T cells (CD8 and FOXP3) and the lymphocytic reaction patterns (follicle lymphocytic reaction, peritumoral lymphocytic reaction, stromal lymphocytic reaction, and tumor-infiltrating lymphocytes) in esophageal carcinoma tissue.

Results:
LINE-1 hypomethylation was associated with male gender and advanced stage cancer (P = 0.03 and P = 0.048, respectively). Tumor LINE-1 methylation level was significantly positively associated with peritumoral lymphocytic reaction (P = 0.004), but not with others. Compared with LINE-1 hypermethylation group, LINE-1 hypomethylation group showed much lower level of peritumoral lymphocytic reaction (univariable odds ratio 0.32, 95% confidence interval 0.16–0.64, P = 0.002). In multivariable model to control for potential confounders including disease stage, the similar finding was observed (multivariable odds ratio 0.31, 95% confidence interval 0.14–0.66, P = 0.004).

Conclusions:
Tumor LINE-1 hypomethylation level is associated with a diminished peritumoral lymphocytic reaction, providing impetus for further investigations on potential interactive roles of tumor LINE-1 hypomethylation and host immunity in esophageal cancer development.
Procedure-specific Training for Robot-assisted Distal Pancreatectomy
Authors: Klompmaker Sjors , van der Vliet Walderik J. , Thoolen Stijn J. , Ore Ana Sofia , Verkoulen Koen , Solis-Velasco Monica , Canacari Elena G. , Kruskal Jonathan B. , Khwaja Khalid O. , Tseng Jennifer F. , Callery Mark P. , Kent Tara S. , Moser A. James 
Published: April 2019

Objective:
To train practicing surgeons in robot-assisted distal pancreatectomy (RADP) and assess the impact on 5 domains of healthcare quality.

Background:
RADP may reduce the treatment burden compared with open distal pancreatectomy (ODP), but studies on institutional training and implementation programs are scarce.

Methods:
A retrospective, single-center, cohort study evaluating surgical performance during a procedure-specific training program for RADP (January 2006 to September 2017). Baseline and unadjusted outcomes were compared “before training” (ODP only; <June 2012) and “after training” (RADP and ODP; >June 2012). Exclusion criteria were neoadjuvant therapy, vascular- and unrelated organ resection. Run charts evaluated index length of stay (LOS) and 90-day comprehensive complication index. Cumulative sum charts of operating time (OT) assessed institutional learning. Adjusted outcomes after RADP versus ODP were compared using a secondary propensity-score-matched (1:1) analysis to determine clinical efficacy.

Results:
After screening, 237 patients were included in the before-training (133 ODP) and after-training (24 ODP, 80 RADP) groups. After initiation of training, mean perioperative blood loss decreased (−255 mL, P<0.001), OT increased (+65 min, P < 0.001), and median LOS decreased (−1 day, P < 0.001). All other outcomes remained similar (P>0.05). Over time, there were nonrandom (P < 0.05) downward shifts in LOS, while comprehensive complication index was unaffected. We observed 3 learning curve phases in OT: accumulation (<31 cases), optimization (case 31–65), and a steady-state (>65 cases). Propensity-score-matching confirmed reductions in index and 90-day LOS and blood loss with similar morbidity between RADP and ODP.

Conclusion:
Supervised procedure-specific training enabled successful implementation of RADP by practicing surgeons with immediate improvements in length of stay, without adverse effects on safety.
Surgery Improves Survival After Neoadjuvant Therapy for Borderline and Locally Advanced Pancreatic Cancer
Authors: Rangelova Elena , Wefer Agnes , Persson Saga , Valente Roberto , Tanaka Kimitaka , Orsini Nicola , Segersvärd Ralf , Arnelo Urban , Del Chiaro Marco 
Published: April 2019

Objective:
Neoadjuvant therapy (NAT) has become part of the multimodality treatment for borderline resectable pancreatic cancer (BRPC) and locally advanced pancreatic cancer (LAPC).

Summary Background Data:
It is currently uncertain which are the preferable NAT regimens, who benefits from surgery, and whether more aggressive surgical strategy is motivated.

Methods:
A retrospective cohort analysis was performed for all patients with BRPC/LAPC discussed and planned for NAT at multidisciplinary conference at Karolinska University Hospital from 2010 to 2017.

Results:
Of 233 patients eligible, 168 (72%) received NAT and were reevaluated for possibility of resection. A total of 156 (67%) patients (mean 64 yrs, 53% male) had pancreatic adenocarcinoma, comprising the study group for survival analysis. LAPC was diagnosed in 132 patients (85%), BRPC in 22 (14%), and resectable tumor in 2 (1.3%). Fifty patients (40.3%) received full-dose NAT. Only 54 (34.6%) had FOLFIRINOX. The overall survival among resected patients was similar for BRPC and LAPC (median survival 15.0 vs 14.5 mo, P = 0.4; and 31.9 vs 21.8 mo, P = 0.7, respectively). Resected patients had better survival than nonresected, irrespective of the type or whether full-dose NAT was given (median survival 22.4 vs 12.7 mo; 1-, 3-, and 5-yr survival: 86.4%, 38.9%, 26.9% vs 52.2%, 1.5%, 0%, respectively (P < 0001). For all preoperative values of Ca 19-9, surgical resection had positive impact on survival.

Conclusions:
All patients with BRPC/LAPC who do not progress during NAT should be considered for surgical resection, irrespective of the type or dose of NAT given. Higher levels of Ca 19-9 should not be considered an absolute contraindication for resection.
Does Rectocele on Defecography Equate to Rectocele on Physical Examination in Patients With Defecatory Symptoms?
Authors: Wallace Shannon L. , Torosis Michele , Rogo-Gupta Lisa 
Published: April 2019

Objectives
Our primary objective was to determine the association between rectocele size on defecography and physical examination in symptomatic patients. Our secondary objective was to describe the associations between both defecography and physical examination findings with defecatory symptoms and progression to surgical repair of rectocele.

Methods
We performed a retrospective review of all patients referred to a female pelvic medicine and reconstructive surgery clinic with a diagnosis of rectocele based on defecography and/or physical examination at a single institution from 2003 to 2017. Patients who did not have defecatory symptoms, did not undergo defecography imaging, or did not have a physical examination in a female pelvic medicine and reconstructive surgery clinic within 12 months of defecography imaging were excluded.

Results
Of 200 patients, 181 (90.5%) had a rectocele diagnosed on defecography and 170 (85%) had a rectocele diagnosed on physical examination. Pearson and Spearman tests of correlation both showed a positive relationship between the rectocele size on defecography and rectocele stage on physical examination; however, one was not reliable to predict the results of the other (Pearson correlation = 0.25; Spearman ρ = 0.29). The strongest predictor of surgery was rectocele stage on physical examination (P < 0.001). Size of rectocele on defecography was not a strong independent predictor for surgery (P = 0.01), although its significance improved with the addition of splinting (P = 0.004).

Conclusions
Our results suggest that rectocele on defecography does not necessarily equate to rectocele on physical examination in patients with defecatory symptoms. Rectocele on physical examination was more predictive for surgery than rectocele on defecography.
The Utility of ECMO After Liver Transplantation: Experience at a High-volume Transplant Center and Review of the Literature
Authors: Braun Hillary J. , Pulcrano Marisa E. , Weber Daniel J. , Padilla Benjamin E. , Ascher Nancy L. 
Published: April 2019

Background.
Extracorporeal membrane oxygenation (ECMO) artificially supports respiratory and cardiac function when conventional techniques fail. ECMO has been described as a treatment modality for acute pulmonary and cardiac failure following orthotopic liver transplantation (OLT). Here, we present a series of adult OLT recipients placed on ECMO after transplantation for both respiratory and cardiac indications and review the literature on the role of ECMO in the setting of OLT.

Methods.
For the patient series, we cross-referenced all patients who underwent OLT at our institution between 2007 and 2018 with the ECMO database of our institution and described these cases. For the literature review, we identified cases and series that described the use of ECMO after liver transplantation in adult recipients.

Results.
A total of 1792 patients underwent OLT. Eight patients were placed on ECMO (0.4%), 5 men and 3 women aged 28 to 68 years (4 venovenous and 4 venoarterial). Three of (38%) 8 patients survived to discharge and are alive today. In the literature, we identified 3 series and 12 case reports of ECMO following OLT, with the majority of the literature derived from the Asian OLT experience.

Conclusions.
ECMO following liver transplantation should be considered as a viable rescue strategy in patients with severe cardiopulmonary failure. ECMO is particularly effective if the cause of cardiopulmonary failure is recognized promptly and is thought to be transient. This is the largest series in the United States and demonstrates a 38% survival rate, which is comparable to other reports in the literature from Asia.
Modeling Bottom-Up and Top-Down Attention with a Neurodynamic Model of V1
Authors: Berga David , Otazu Xavier 
Published: April 2019

ABSTRACTPrevious studies suggested that lateral interactions of V1 cells are responsible, among other visual effects, of bottom-up visual attention (alternatively named visual salience or saliency). Our objective is to mimic these connections with a neurodynamic network of firing-rate neurons in order to predict visual attention. Early visual subcortical processes (i.e. retinal and thalamic) are functionally simulated. An implementation of the cortical magnification function is included to define the retinotopical projections towards V1, processing neuronal activity for each distinct view during scene observation. Novel computational definitions of top-down inhibition (in terms of inhibition of return and selection mechanisms), are also proposed to predict attention in Free-Viewing and Visual Search tasks. Results show that our model outpeforms other biologically-inpired models of saliency prediction while predicting visual saccade sequences with the same model. We also show how temporal and spatial characteristics of inhibition of return can improve prediction of saccades, as well as how distinct search strategies (in terms of feature-selective or category-specific inhibition) can predict attention at distinct image contexts.
Bayesian variable selection with a pleiotropic loss function in Mendelian randomization
Authors: Gkatzionis Apostolos , Burgess Stephen , Conti David V , Newcombe Paul J 
Published: April 2019

AbstractMendelian randomization is the use of genetic variants as instruments to assess the existence of a causal relationship between a risk factor and an outcome. A Mendelian randomization analysis requires a set of genetic variants that are strongly associated with the risk factor and only associated with the outcome through their effect on the risk factor. We describe a novel variable selection algorithm for Mendelian randomization that can identify sets of genetic variants which are suitable in both these respects. Our algorithm is applicable in the context of two-sample summary-data Mendelian randomization and employs a recently proposed theoretical extension of the traditional Bayesian statistics framework, including a loss function to penalize genetic variants that exhibit pleiotropic effects. The algorithm offers robust inference through the use of model averaging, as we illustrate by running it on a range of simulation scenarios and comparing it against established pleiotropy-robust Mendelian randomization methods. In a real data application, we study the effect of systolic and diastolic blood pressure on the risk of suffering from coronary heart disease. Based on a recent large-scale GWAS for blood pressure, we use 395 genetic variants for systolic and 391 variants for diastolic blood pressure. Both traits are shown to have significant risk-increasing effects on coronary heart disease risk.
Ancestry-specific polygenic scores and SNP heritability of 25(OH)D in African- and European-ancestry populations
Authors: Hatchell Kathryn E. , Lu Qionshi , Hebbring Scott J. , Michos Erin D. , Wood Alexis C. , Engelman Corinne D. 
Published: April 2019

AbstractContextVitamin D inadequacy, assessed by 25-hydroxyvitamin D [25(OH)D], affects around 50% of adults in the United States and is associated with numerous adverse health outcomes. Blood 25(OH)D concentrations are influenced by genetic factors that may determine how much vitamin D intake is required to reach optimal 25(OH)D. Despite large genome-wide association studies (GWASs), only a small portion of the genetic factors contributing to differences in 25(OH)D levels has been discovered.ObjectiveTherefore, knowledge of a fuller set of genetic factors could be useful for risk prediction of 25(OH)D inadequacy, personalized vitamin D supplementation, and prevention of morbidity and mortality from deficient 25(OH)D.DesignUsing PRSice and weights from published African- and European-ancestry GWAS summary statistics, ancestry-specific polygenic scores (PGSs) were created to capture a more complete set of genetic factors.Patients or Other ParticipantsParticipants (European ancestry n=9,569, African ancestry n=2,761) came from three cohort studies.Main Outcome Measure(s)Blood concentrations of 25(OH)D.ResultsThe PGS for African ancestry was derived using all input SNPs (a p-value cut-off of 1.0) and had an R2of 0.3%; for European ancestry, the optimal PGS used a p-value cut-off of 3.5×10−4in the target/tuning dataset and had an R2of 1.0% in the validation cohort. Those with highest genetic risk had 25(OH)D that was 2.8-3.0 ng/ml lower than those with lowest genetic risk (p=0.0463 to 3.2×10−13), requiring an additional 467 to 500 IU of vitamin D intake to maintain equivalent 25(OH)D.ConclusionsPGSs are a powerful predictive tool that could be leveraged for personalized vitamin D supplementation to prevent the negative downstream effects of 25(OH)D inadequacy.
In silico evidence of unique behaviors of methionine in an in-register parallel beta-sheet amyloid, suggestive of its possible contribution to strain diversity of amyloids
Authors: Otaki Hiroki , Taguchi Yuzuru , Nishida Noriyuki 
Published: April 2019

AbstractMechanism of strain diversity of prions is a long-standing conundrum, because prions consist solely of abnormal isoform of prion protein (PrPSc) devoid of genetic material. Pathogenic properties of prions are determined by conformations of the constituent PrPScaccording to the protein-only hypothesis, and alterations to even a single residue can drastically change the properties when the residue is located at a critical position for the structure of PrPSc. Interestingly, methionine (Met) is often recognized as the polymorphic or species-specific residues responsible for species/strain barriers of prions, implying its unique influences on the structures of PrPSc. However, how it is unique is difficult to demonstrate due to lack of the detailed structures of PrPSc. Here we analyzed influences of Met substitutions on structures of an in-register parallel β-sheet amyloid of α-synuclein (αSyn) by molecular dynamics (MD) simulation, to extrapolate the results to PrPSc. The MD simulation revealed that Met uniquely stabilized a U-shaped β-arch of the Greek-key αSyn amyloid, whereas other hydrophobic amino acids tended to destabilize it. The stabilizing effect of Met was attributable to the long side chain without Cβ branching. Our findings exemplify specifically how and in what structure of an in-register parallel β-sheet amyloid Met can uniquely behave, and are suggestive of its influences on structures of PrPScand strain diversity of prions. We also discuss about relations between α-helix propensity and local structures of in-register parallel amyloids.
Peax Interactive Visual Pattern Search in Sequential Data Using Unsupervised Deep Representation Learning
Authors: Lekschas Fritz , Peterson Brant , Haehn Daniel , Ma Eric , Gehlenborg Nils , Pfister Hanspeter 
Published: April 2019

AbstractWe present Peax, a novel feature-based technique for interactive visual pattern search in sequential data, like time series or data mapped to a genome sequence. Visually searching for patterns by similarity is often challenging because of the large search space, the visual complexity of patterns, and the user’s perception of similarity. For example, in genomics, researchers try to link patterns in multivariate sequential data to cellular or pathogenic processes, but a lack of ground truth and high variance makes automatic pattern detection unreliable. We have developed a convolutional autoencoder for unsupervised representation learning of regions in sequential data that can capture more visual details of complex patterns compared to existing similarity measures. Using this learned representation as features of the sequential data, our accompanying visual query system enables interactive feedback-driven adjustments of the pattern search to adapt to the users’ perceived similarity. Using an active learning sampling strategy, Peax collects user-generated binary relevance feedback. This feedback is used to train a model for binary classification, to ultimately find other regions that exhibit patterns similar to the search target. We demonstrate Peax’s features through a case study in genomics and report on a user study with eight domain experts to assess the usability and usefulness of Peax. Moreover, we evaluate the effectiveness of the learned feature representation for visual similarity search in two additional user studies. We find that our models retrieve significantly more similar patterns than other commonly used techniques.
To enrich or not to enrich: Enhancing (glyco)peptide ionization using the CaptiveSpray nanoBooster™
Authors: Alagesan Kathirvel , Kolarich Daniel 
Published: April 2019

ABSTRACTThe CaptiveSpray source ensures a stable spray and excellent nano ESI performance facilitated by a vortex gas that sweeps around the emitter spray tip to support liquid desolvation and focus the Taylor cone. Enriching the vortex gas with dopant solvents provides tremendous opportunities to increase ionization efficiency, in particular for hydrophilic compounds such as glycopeptides. How this CaptiveSpray nanobooster benefits their analysis, however, has to date not been systematically studied.We evaluated various dopant solvents such as (i) acetone (ii) acetonitrile (iii) methanol (iv) ethanol and (v) isopropanol for their ability to enhance glycopeptide ionization. Using a synthetic IgG2 glycopeptide as a standard, acetonitrile provided a five-fold increase in signal intensities and resulted in an overall charge state increase compared to conventional CaptiveSpray ionization. This trend remained the same when tryptic IgG (glyco)peptides were analyzed and allowed highly sensitive detection of glycopeptides even without any enrichment. While acetone dopant gas enhanced glycopeptide ionization by doubling glycopeptide signal intensities, all other tested solvents resulted either in ion suppression or adduct formation. This is in agreement with and can be explained by their individual physio-chemical properties of the solvents. Finally, by omitting glycopeptide enrichment steps, we established a bias-free human Immunoglobulin G (IgG) subclass specific glycosylation profile applying the optimized CaptiveSpray nanoBooster nano-LC-ESI-MS/MS analysis conditions.
Identification of viruses with the potential to infect human
Authors: Zhang Zheng , Cai Zena , Tan Zhiying , Lu Congyu , Zhang Gaihua , Peng Yousong 
Published: April 2019

AbstractThe virus has caused much mortality and morbidity to humans, and still posed a serious threat to the global public health. The virome with the human-infection potential is far from complete. Novel viruses have been discovered at an unprecedented pace as the rapid development of viral metagenomics. However, there is still a lack of a method for rapidly identifying the virus with the human-infection potential. This study built several machine learning models for discriminating the human-infecting viruses from other viruses based on the frequency of k-mers in the viral genomic sequences. The k-nearest neighbor (KNN) model could predict the human-infecting virus with an accuracy of over 90%. Even for the KNN models built on the contigs as short as 1kb, they performed comparably to those built on the viral genomes, suggesting that the models could be used to identify the human-infecting virus from the viral metagenomic sequences. This work could help for discovery of novel human-infecting virus in metagenomics studies.