bluuebunny/crossref_metadata_2025_split huggingface dataset:
Relationship Between Radiomics and Risk of Lymph Node Metastasis in Pancreatic Ductal Adenocarcinoma
Authors: Bian Yun , Guo Shiwei , Jiang Hui , Gao Suizhi , Shao Chenwei , Cao Kai , Fang Xu , Li Jing , Wang Li , Hua Wenda , Zheng Jianming , Jin Gang , Lu Jianping 
Published: October 2019

Objective
The objective of this study was to explore the exact relationship between the arterial radiomics score (rad-score) and lymph node (LN) metastasis in pancreatic ductal adenocarcinoma (PDAC).

Methods
A total of 225 patients with pathologically confirmed PDAC who underwent multislice computed tomography within 1 month of resection from December 2016 to August 2017 were retrospectively studied. For each patient, 1029 radiomics features of arterial phase were extracted, which were reduced using the least absolute shrinkage and selection operator logistic regression algorithm. Multivariate logistic regression models were used to analyze the association between the arterial rad-score and LN metastasis.

Results
Lymph node–negative and LN-positive patients accounted for 107 (47.56%) and 118 (52.44%) of the cohort, respectively. The rad-score, which consisted of 12 selected features of the arterial phase, was significantly associated with LN status (P < 0.05). Univariate analysis revealed that the arterial rad-score and T stage were independently and positively associated with risk of LN metastasis (P < 0.05). Multivariate analyses revealed a significant association between the arterial rad-score and the LN metastasis (P < 0.0001). Higher arterial rad-score was associated with LN metastasis (P for trend <0.0001).

Conclusions
The arterial rad-score is independently and positively associated with the risk of LN metastasis in PDAC.
Topical Review: Effects of Contact Lens Wear on Corneal, Conjunctival, and Lid Margin Sensitivity
Authors: Stapleton Fiona , Chao Cecilia , Golebiowski Blanka 
Published: October 2019

SIGNIFICANCEContemporary soft contact lenses do not affect mechanical sensitivity of the cornea, whereas conjunctival sensitivity is increased compared with nonwearers. Orthokeratology lens wear, however, reduces corneal sensitivity. The effects of contact lenses on lid margin sensitivity are unclear, and the link between ocular surface sensitivity and discomfort requires further exploration.Although up to 50% of contact lens wearers experience discomfort with varying severity, impact, and frequency, the relationship between ocular surface sensitivity and ocular surface discomfort experienced during contact lens wear is unclear. The purpose of this review is to examine and summarize the current evidence for the impact of both historical and contemporary contact lens wear on ocular surface sensitivity, the etiology of changes in ocular surface sensitivity, contact lens wear–related factors associated with changes in ocular surface sensitivity, and the relationship between sensitivity and discomfort. Despite minimal effects on mechanical corneal sensitivity with contemporary soft contact lens wear, orthokeratology reduces corneal sensitivity through pressure-related effects. This review addresses the relevance of conjunctival and potentially lid margin sensitivity in tolerance and discomfort with contemporary lens wear and the impact of instrument and stimulus characteristics. Less invasive techniques particularly for lid margin sensitivity measurements are required. Given the potential interactions between a contact lens and the varied types of ocular surface nociceptors, instruments that allow for exploration of cold and chemical sensitivity particularly may better allow the effects of lens wear to be elucidated compared with those that explore high-threshold mechanical sensitivity alone. A better understanding of the relationships between lens wear and ocular surface sensitivity may result in improved management of contact lens discomfort.
Association Between Socioeconomic Status Mobility and Inflammation Markers Among White and Black Adults in the United States: A Latent Class Analysis
Authors: Surachman Agus , Rice Cara , Bray Bethany , Gruenewald Tara , Almeida David 
Published: October 2019

ABSTRACT

Objective
This article examines whether multidimensional indicators of objective and subjective socioeconomic status (SES) across the life course can be categorized into latent classes of SES mobility and tests the associations of these categories with inflammation markers among white and black adults.

Methods
Data are from 592 non-Hispanic white and 158 non-Hispanic black participants who completed both the baseline survey and biomarkers assessment of the Midlife in the United States Refresher study. Groups of different SES mobility were examined using latent class analysis.

Results
White and black participants showed different patterns of SES mobility. Among blacks, the latent classes were as follows: 1) objectively always high (24.71%; high objective SES across the life course), 2) subjectively always high (6.48%; high subjective and low objective SES across the life course), 3) downwardly mobile (35.84%; high childhood SES, low adult SES), and 4) always low (32.97%; low childhood SES, education, and adult SES). Among whites, the latent classes were as follows: 1) always high (52.17%; high childhood SES, high education, high adult SES), 2) upwardly mobile (18.14%; low childhood SES, high education, high adult SES), 3) subjectively downward (27.74%; high childhood SES, high education, high objective adult SES, low subjective adult SES), and 4) always low (1.95%; low childhood SES, education, and adult SES). SES mobility was associated with inflammation in white (Wald χ2 values (3) = 12.89–17.44, p values < .050), but not in black adults (Wald χ2 values (3) = 2.79–7.22, p values > .050).

Conclusion
The lack of SES mobility differentiation on inflammation is an indication of diminished return for the most affluent class among black participants.
Basal Cell Carcinoma Arising over a Venous Malformation of the Forehead Communicating with the Endocranial Veins
Authors: Cucurullo Marco , Colletti Giacomo 
Published: October 2019

Introduction:An increasing number of skin cancer arising over vascular anomaly has been reported in literature. In such cases, the oncologic radicality required to threat skin malignancies may be in contrast with the safety needed when dealing with vascular malformation. As a result, treatment of this association may be insidious and treacherous and imposes a sound knowledge and carefulness.Materials and Methods:The authors report on a case of a 77-years-old woman affected by a basal cell carcinoma (BCC) arising over a vascular malformation of forehead. Preoperative radiological imaging revealed an underlying venous malformation (VM) communicating with intracranial district. Patient underwent sclerotherapy of the VM with gelified ethanol in order to reduce potentially fatal bleeding during surgery and, on the other hand, any leakage of the sclerosant in the intracranial veins. Excision of the BCC was then performed without complications.Results:Neither intra-operative nor post-operative complications were observed. Current 3-years follow-up shows no recurrence of BCC whilst the residual VM is stable and clinically silent.Conclusions:Mechanisms leading to the onset of skin cancers over venous malformations are still unclear. However, association between these 2 conditions may be underestimated with possible catastrophic consequences. Thorough knowledge of vascular malformations and a multidisciplinary approach is of the uttermost importance when dealing with such clinical challenges.
Autoantibodies against the prion protein in individuals with PRNP mutations
Authors: Frontzek Karl , Carta Manfredi , Losa Marco , Epskamp Mirka , Meisl Georg , Anane Alice , Brandel Jean-Philippe , Camenisch Ulrike , Castilla Joaquín , Haïk Stéphane , Knowles Tuomas , Lindner Ewald , Lutterotti Andreas , Minikel Eric Vallabh , Roiter Ignazio , Safar Jiri G. , Sanchez-Valle Raquel , Žáková Dana , Hornemann Simone , Aguzzi Adriano 
Published: October 2019

Structured abstractObjectiveTo determine whether naturally occurring autoantibodies against the prion protein are present in individuals with genetic prion disease mutations and controls, and if so, whether they are protective against prion disease.MethodsIn this case-control study, we collected 124 blood samples from individuals with a variety of pathogenic PRNP mutations and 78 control individuals with a positive family history of genetic prion disease but lacking disease-associated PRNP mutations. Antibody reactivity was measured using an indirect ELISA for the detection of human IgG1-4 antibodies against wild-type human prion protein. Multivariate linear regression models were constructed to analyze differences in autoantibody reactivity between a) PRNP mutation carriers versus controls and b) asymptomatic versus symptomatic PRNP mutation carriers. Robustness of results was examined in matched cohorts.ResultsWe found that antibody reactivity was present in a subset of both PRNP mutation carriers and controls. Autoantibody levels were not influenced by PRNP mutation status nor clinical manifestation of prion disease. Post hoc analyses showed anti-PrPC autoantibody titers to be independent of personal history of autoimmune disease and other immunological disorders, as well as PRNP codon 129 polymorphism.ConclusionsPathogenic PRNP variants do not notably stimulate antibody-mediated anti-PrPC immunity. Anti-PrPC IgG autoantibodies are not associated with the onset of prion disease. The presence of anti-PrPC autoantibodies in the general population without any disease-specific association suggests that relatively high titers of naturally occurring antibodies are well tolerated. Clinicaltrials.gov identifier NCT02837705.
Setting Standards to Promote Artificial Intelligence in Colon Mass Endoscopic Sampling
Authors: Zheng Yueping , Su Ruizhang , Wang Wangyue , Meng Sijun , Xiao Hang , Zhang Wen , Xu Haineng , Bu Yemei , Zhong Yuhuan , Zhang Yi , Qiu Hesong , Qin Wenjuan , Zhang Yongxiu , Xu Wen , Chen Hong , Zhang Changhua , Wu Siqi , Han Zhaofang , Zheng Xiaofang , Zhu Huafen , Wu Shuisheng , Pan Wensheng , He Yulong , Hu Yiqun 
Published: October 2019

ABSTRACTObjectiveArtificial intelligence (AI) has undeniable values in detection, characterization, and monitoring of tumors during cancer imaging. However, major AI explorations in digestive endoscopy have not been systematically planned, and more important, most AI productions are based on Single-center Studies (ScSs). ScSs result in data scarcity, redundancy as well as island effects, which leads to some limitations in applying it on endoscopy. We investigate the disadvantages of picture processing which may effect the AI detection, and make improvements in AI detection and image recognition accuracy.DesignCurrent investigation aggregates a total of 2,500 gastroenteroscopy samples from various hospitals in multiple regions and carries out deep learning.ResultsIt is found that factors inconducive to AI recognition are common such as: (a) the gastrointestinal tract is not cleaned up completely; (b) shooting angle (from left to right and the top of polyp are unexposed clearly), shooting distance (too close or too far to shoot causes the lump to be unclear), shooting light (insufficient light source or overexposed light source in mass) and unstable shooting lead to poor quality of pictures.ConclusionWe set standards for a multicenter cooperation involving three-level medical institutions from the provincial, municipal and county to improve the recognition accuracy as well as the diagnosis and treatment efficiency meanwhile.
Towards a brain signature of chronic pain using cerebral blood flow spatial covariance analysis in people with chronic knee pain
Authors: Iwabuchi Sarina J. , Xing Yue , Cottam William J. , Drabek Marianne M. , Tadjibaev Arman , Fernandes Gwen S. , Petersen Kristian K , Arendt-Nielsen Lars , Graven-Nielsen Thomas , Valdes Ana M. , Zhang Weiya , Doherty Michael , Walsh David , Auer Dorothee P. 
Published: October 2019

AbstractChronic musculoskeletal pain is a common problem globally. Current evidence suggests that maladaptive modulation of central pain pathways is associated with pain chronicity following e.g. chronic post-operative pain after knee replacement. Other factors such as low mood, anxiety and tendency to catastrophize seem to also be important contributors. We aimed to identify a chronic pain brain signature that discriminates chronic pain from pain-free conditions using cerebral blood flow (CBF) measures, and explore how this signature relates to the chronic pain experience. In 44 chronic knee pain patients and 29 pain-free controls, we acquired CBF data (using arterial spin labelling) and T1-weighted images. Participants completed a series of questionnaires related to affective processes, and pressure and cuff algometry to assess pain sensitization. Two factor scores were extracted from these scores representing negative affect and pain sensitization, respectively. A spatial covariance principal components analysis of CBF identified five components that significantly discriminated chronic pain patients from controls, with the unified network achieving 0.83 discriminatory accuracy (area under the curve). In chronic knee pain, significant patterns of relative hypo-perfusion were evident in anterior regions of the default mode and salience network hubs, while hyperperfusion was seen in posterior default mode regions, the thalamus, and sensory regions. One component was positively correlated to the pain sensitization score (r=.43,p=.006), suggesting that this CBF pattern reflects the neural activity changes encoding pain sensitization. Here, we report the first chronic knee pain-related brain signature, pointing to a brain signature underpinning the central aspects of pain sensitisation.
Bayesian Linear Mixed Models for Motif Activity Analysis
Authors: Lederer Simone , Heskes Tom , van Heeringen Simon J. , Albers Cornelis A. 
Published: October 2019

AbstractMotivationCellular identity and behavior is controlled by complex gene regulatory networks. Transcription factors (TFs) bind to specific DNA sequences to regulate the transcription of their target genes. On the basis of these TF motifs in cis-regulatory elements we can model the influence of TFs on gene expression. In such models of TF motif activity the data is usually modeled assuming a linear relationship between the motif activity and the gene expression level. A commonly used method to model motif influence is based on Ridge Regression. One important assumption of linear regression is the independence between samples. However, if samples are generated from the same cell line, tissue, or other biological source, this assumption may be invalid. This same assumption of independence is also applied to different, yet similar, experimental conditions, which may also be inappropriate. In theory, the independence assumption between samples could lead to loss in signal detection. Here we investigate whether a Bayesian model that allows for correlations results in more accurate inference of motif activities.ResultsWe extend the Ridge Regression to a Bayesian Linear Mixed Model, which allows us to model dependence between different samples. In a simulation study, we in-vestigate the differences between the two model assumptions. We show that our Bayesian Linear Mixed Model implementation outperforms Ridge Regression in a simulation scenario where the noise, the signal that can not be explained by TF motifs, is uncorrelated. However, we demonstrate that there is no such gain in performance if the noise has a similar covariance structure over samples as the signal that can be explained by motifs. We give a mathematical explanation to why this is the case. Using two representative real data sets we show that at most∼40% of the signal is explained by motifs using the linear model. With these data there is no advantage to using the Bayesian Linear Mixed Model, due to the similarity of the covariance structure.Availability & ImplementationThe project implementation is available athttps://github.com/Sim19/SimGEXPwMotifs.
PlasClass improves plasmid sequence classification
Authors: Pellow David , Mizrahi Itzik , Shamir Ron 
Published: October 2019

AbstractBackgroundMany bacteria contain plasmids, but separating between contigs that originate on the plasmid and those that are part of the bacterial genome can be difficult. This is especially true in metagenomic assembly, which yields many contigs of unknown origin. Existing tools for classifying sequences of plasmid origin give less reliable results for shorter sequences, are trained using a fraction of the known plasmids, and can be difficult to use in practice.ResultsWe present PlasClass, a new plasmid classifier. It uses a set of standard classifiers trained on the most current set of known plasmid sequences for different sequence lengths. PlasClass outperforms the state-of-the-art plasmid classification tool on shorter sequences, which constitute the majority of assembly contigs, while using less time and memory.ConclusionsPlasClass can be used to easily classify plasmid and bacterial genome sequences in metagenomic or isolate assemblies. It is available from: https://github.com/Shamir-Lab/PlasClass
GiniClust3: a fast and memory-efficient tool for rare cell type identification
Authors: Dong Rui , Yuan Guo-Cheng 
Published: October 2019

AbstractMotivationWith the rapid development of single-cell RNA sequencing technology, it is possible to dissect cell-type composition at high resolution. A number of methods have been developed with the purpose to identify rare cell types. However, existing methods are still not scalable to large datasets, limiting their utility. To overcome this limitation, we present a new software package, called GiniClust3, which is an extension of GiniClust2 and significantly faster and memory-efficient than previous versions.ResultsUsing GiniClust3, it only takes about 7 hours to identify both common and rare cell clusters from a dataset that contains more than one million cells. Cell type mapping and perturbation analyses show that GiniClust3 could robustly identify cell clusters.AvailabilityGiniCluster3 is implemented in the open-source python package, with source code freely available through the Github (https://github.com/rdong08/GiniClust3).Contactgcyuan@jimmy.harvard.eduSupplementary informationSupplementary data are available at Bioinformatics online.
Globins in the marine Annelid Platynereis dumerilii shed new light on hemoglobin evolution in Bilaterians
Authors: Song Solène , Starunov Viktor , Bailly Xavier , Ruta Christine , Kerner Pierre , Cornelissen Annemiek J.M. , Balavoine Guillaume 
Published: October 2019

AbstractBackgroundHow vascular systems and their respiratory pigments evolved is still debated. While many animals present a vascular system, hemoglobin exists as a blood pigment only in a few groups (Vertebrates, Annelids, a few Arthropod and Mollusk species). Hemoglobins are formed of globin sub-units, belonging to multigene families, in various multimeric assemblages. It was so far unclear whether hemoglobin families from different Bilaterian groups had a common origin.ResultsTo unravel globin evolution in Bilaterians, we studied the marine Annelid Platynereis dumerilii, a species with a slow evolving genome. Platynereis exhibits a closed vascular system filled with extracellular hemoglobin. Platynereis genome and transcriptomes reveal a family of 19 globins, nine of which are predicted to be extracellular. Extracellular globins are produced by specialized cells lining the vessels of the segmental appendages of the worm, serving as gills, and thus likely participate in the assembly of the giant hexagonal bilayer hemoglobin of the worm. Extracellular globin mRNAs are absent in smaller juvenile, accumulate considerably in growing and more active worms and peak in swarming adults, as the need for O2 culminates. Next, we conducted a Metazoan-wide phylogenetic analysis of globins using data from complete genomes. We establish that five globin genes (stem globins) were present in the last common ancestor of Bilaterians. Based on these results, we propose a new nomenclature of globins, with five clades. All five ancestral stem-globin clades are retained in some Spiralians, while some clades disappeared early in Deuterostome and Ecdysozoan evolution. All known Bilaterian blood globin families are grouped in a single clade (clade I) together with intracellular globins of Bilaterians devoid of red blood.ConclusionsWe uncover a complex “pre-blood” evolution of globins, with an early gene radiation in ancestral Bilaterians. Circulating hemoglobins in various bilaterian groups evolved convergently, presumably in correlation with animal size and activity. However, all hemoglobins derive from a clade I globin, or cytoglobin, probably involved in intracellular O2 transit and regulation (clade I). The Annelid Platynereis is remarkable in having a large family of extracellular blood globins, while retaining all clades of ancestral Bilaterian globins.
Fine-scale position effects shape the distribution of inversion breakpoints inDrosophila melanogaster
Authors: McBroome Jakob , Liang David , Corbett-Detig Russell 
Published: October 2019

AbstractChromosomal inversions are among the primary drivers of genome structure evolution in a wide range of natural populations. While there is an impressive array of theory and empirical analyses that has identified conditions under which inversions can be positively selected, comparatively little data is available on the fitness impacts of these genome structural rearrangements themselves. Because inversion breakpoints can interrupt functional elements and alter chromatin domains, each rearrangement may in itself have strong effects on fitness. Here, we compared the fine-scale distribution of low frequency inversion breakpoints with those of high frequency inversions and inversions that have fixed betweenDrosophilaspecies. We identified important differences that may influence inversion fitness. In particular, proximity to insulator elements, large tandem duplications adjacent to the breakpoints, and minimal impacts on gene coding spans are more prevalent in high frequency and fixed inversions than in rare inversions. The data suggest that natural selection acts both to preserve both genes and larger cis-regulatory networks in the occurrence and spread of rearrangements. These factors may act to limit the availability of high fitness arrangements when suppressed recombination is favorable.
ProteoClade: a taxonomic toolkit for multi-species and metaproteomic analysis
Authors: Mooradian Arshag D. , van der Post Sjoerd , Naegle Kristen M. , Held Jason M. 
Published: October 2019

AbstractWe present ProteoClade, a Python toolkit that performs taxa-specific peptide assignment, protein inference, and quantitation for multi-species proteomics experiments. ProteoClade scales to hundreds of millions of protein sequences, requires minimal computational resources, and is open source, multi-platform, and accessible to non-programmers. We demonstrate its utility for processing quantitative proteomic data derived from patient-derived xenografts and its speed and scalability enable a novel de novo proteomic workflow for complex microbiota samples.
A polyclonal allelic expression assay for detecting regulatory effects of transcript variants
Authors: Brandt Margot , Gokden Alper , Ziosi Marcello , Lappalainen Tuuli 
Published: October 2019

AbstractWe present an assay to experimentally test regulatory effects of genetic variants within transcripts using CRISPR/Cas9 followed by targeted sequencing. We applied the assay to 35 premature stop-gained variants across the genome and in two Mendelian disease genes, 33 putative causal variants of eQTLs and 65 control variants. We detected significant effects generally in the expected direction, demonstrating the ability of the assay to capture regulatory effects of eQTL variants and nonsense-mediated decay triggered by premature stop-gained variants. The results suggest a utility for validating transcript-level effects of genetic variants.