bluuebunny/crossref_metadata_2025 huggingface dataset:
Patient–prosthesis mismatch in mitral annuloplasty for degenerative mitral regurgitation: an ignored issue
Authors: Ma Wenrui , Shi Wei , Wu Weihua , Ma Xinyu , Kong Ye , Zhu Dan , Zhang Wei
Published: February 2019

OBJECTIVES

Elevated postoperative transmitral gradient (TMG), partially induced by a small annuloplasty ring, is associated with late atrial fibrillation (AF) after mitral valve repair. Here, we aimed to provide the optimal cut-off of prosthetic ring size to reduce patient–prosthesis mismatch (PPM) after mitral annuloplasty.

METHODS

From 2006 to 2017, 262 patients who underwent mitral valve repair for degenerative pathologies were retrospectively studied. The relationships of body surface area (BSA)–indexed prosthetic orifice area (POAi)–postoperative TMG and POAi–late AF were tested using regression curves and receiver operating characteristic curves, respectively. The optimal cut-off of POAi predictive of late AF was used to define PPM. Baseline and follow-up data of patients with and without PPM were compared in propensity score-matched cohorts.

RESULTS

In-hospital mortality was 0. Late AF was observed in 9.2% (24/262) patients during a median follow-up of 3.8 years. An exponential model was best fitted based on the POAi–postoperative TMG relationship (P < 0.001). Using late AF as the dependent variable, the optimal cut-off for PPM was POAi ≤2.28 cm2/m2 (c-statistic 0.71; sensitivity 0.61; specificity 0.80; P < 0.001). PPM was identified in 113 (43.1%) patients. After propensity score matching, the estimated 5-year rate of late AF was significantly higher in PPM patients than in non-PPM patients (24% vs 5%; P < 0.001).

CONCLUSIONS

Postoperative TMG increases significantly with a small POAi for full ring annuloplasty. A patient’s BSA should be considered in addition to valvular dimensions during the selection of a proper ring size to reduce PPM-related AF.
Carotid Intima–Media Thickness and Markers of Brain Health in a Biracial Middle-Aged Cohort: CARDIA Brain MRI Sub-study
Authors: Cermakova Pavla , Ding Jie , Meirelles Osorio , Reis Jared , Religa Dorota , Schreiner Pamela J , Jacobs David R , Bryan R Nick , Launer Lenore J
Published: February 2019

Background

We investigated whether carotid intima–media thickness is associated with measures of cerebral blood flow (CBF), white matter hyperintensities, and brain volume in a biracial cohort of middle-aged individuals.

Methods

We performed a cross-sectional cohort study based on data from a multicenter, population-based study Coronary Artery Risk Development in Young Adults. Using linear and logistic regression, we estimated the association of the composite intima–media thickness measured in three segments of carotid arteries (common carotid artery, carotid artery bulb, and internal carotid artery) with volume (cm3) and CBF (mL/100 g/min) in the total brain and gray matter as well as volume of white matter hyperintensities (cm3).

Results

In the analysis, 461 participants (54% women, 34% African Americans) were included. Greater intima–media thickness was associated with lower CBF in gray matter (β=−1.36; p = .04) and total brain (β=−1.26; p = .04), adjusting for age, sex, race, education, and total brain volume. The associations became statistically nonsignificant after further controlling for cardiovascular risk factors. Intima–media thickness was not associated with volumes of total brain, gray matter, and white matter hyperintensities.

Conclusions

This study suggests that lower CBF in middle age is associated with markers of atherosclerosis in the carotid arteries. This association may reflect early long-term exposure to traditional cardiovascular risk factors. Early intervention on atherosclerotic risk factors may modulate the trajectory of CBF as people age and develop brain pathology.
Whole Exome Sequencing of Ulcerative Colitis–associated Colorectal Cancer Based on Novel Somatic Mutations Identified in Chinese Patients
Authors: Yan Pengguang , Wang Yanan , Meng Xiangchen , Yang Hong , Liu Zhanju , Qian Jiaming , Zhou Weixun , Li Jingnan
Published: February 2019

Background

Carcinogenesis is a severe consequence of chronic ulcerative colitis. We investigated the somatic mutations and pathway alterations in ulcerative colitis–associated colorectal cancer (CRC) in Chinese patients compared with sporadic CRCs to reveal potential therapeutic targets in ulcerative colitis–associated CRC.

Methods

Whole exome sequencing was performed on archival tumor tissues and paired adjacent nondysplastic mucosa from 10 ulcerative colitis–associated CRC patients at a high risk of carcinogenesis. Genomic alteration profiles from 223 primary CRCs from The Cancer Genome Atlas served as sporadic CRC controls. A meta-analysis was performed to investigate differences in major genetic mutations between ulcerative colitis–associated and Crohn’s disease–associated CRCs.

Results

We identified 44 nonsilent recurrent somatic mutations via whole exome sequencing, including 25 deleterious mutations involved in apoptosis and the PI3K-Akt pathway (COL6A3, FN1), autophagy (ULK1), cell adhesion (PODXL, PTPRT, ZFHX4), and epigenetic regulation (ARID1A, NCOR2, KMT2D, NCOA6, MECP2, SUPT6H). In total, 11 of the 25 mutated genes significantly differed between ulcerative colitis–associated CRC and sporadic CRC (APC, APOB, MECP2, NCOR2, NTRK2, PODXL, RABGAP1, SIK3, SUPT6H, ULK1, USP48). Somatic TP53 mutations occurred in 33% of ulcerative colitis–associated CRCs. Subsequent meta-analysis revealed distinct mutation profiles for Crohn’s disease– and ulcerative colitis–associated CRCs. Mutations involving the NF-kB pathway and epigenetic regulation were more common in ulcerative colitis–associated CRCs than in sporadic CRCs.

Conclusion

Distinct genomic alteration profiles of deleterious somatic mutations were found in ulcerative colitis–associated and sporadic CRCs. Mutations of epigenetic regulators, such as KMT2D and NCOA6, were common, suggesting an epigenetic pathomechanism for colitis-associated carcinoma in Chinese patients.
Faecalibacterium prausnitzii produces butyrate to decrease c-Myc-related metabolism and Th17 differentiation by inhibiting histone deacetylase 3
Authors: Zhang Mingming , Zhou Lixing , Wang Yuming , Dorfman Robert Gregory , Tang Dehua , Xu Lei , Pan Yida , Zhou Qian , Li Yang , Yin Yuyao , Zhao Shimin , Wu Jianlin , Yu Chenggong
Published: February 2019

Decreased levels of Faecalibacterium prausnitzii (F. prausnitzii), whose supernatant plays an anti-inflammatory effect, are frequently found in inflammatory bowel disease (IBD) patients. However, the anti-inflammatory products in F. prausnitzii supernatant and the mechanism have not been fully investigated. Here we found that F. prausnitzii and F. prausnitzii-derived butyrate were decreased in the intestines of IBD patients. Supplementation with F. prausnitzii supernatant and butyrate could ameliorate colitis in an animal model. Butyrate, but not other substances produced by F. prausnitzii, exerted an anti-inflammatory effect by inhibiting the differentiation of T helper 17 (Th17) cells. The mechanism underlying the anti-inflammatory effects of the butyrate produced by F. prausnitzii involved the enhancement of the acetylation-promoted degradation of c-Myc through histone deacetylase 3 (HDAC3) inhibition. In conclusion, F. prausnitzii produced butyrate to decrease Th17 differentiation and attenuate colitis through inhibiting HDAC3 and c-Myc-related metabolism in T cells. The use of F. prausnitzii may be an effective new approach to decrease the level of Th17 cells in the treatment of inflammatory diseases.
Roles of multiple lipid mediators in stress and depression
Authors: Furuyashiki Tomoyuki , Akiyama Satoshi , Kitaoka Shiho
Published: February 2019

Prolonged or excessive stress may induce emotional and cognitive disturbances, and is a risk factor for mental illnesses. Using rodent chronic stress models of depression, roles of multiple lipid mediators related to inflammation have been revealed in chronic stress-induced emotional alterations. Prostaglandin (PG) E2, an arachidonic acid (AA)-derived lipid mediator, and its receptor subtype EP1 mediate depression-like behavior induced by repeated social defeat stress through attenuating prefrontal dopaminergic activity. Repeated social defeat stress activates microglia through innate immune receptors, and induces PGE2 synthesis through cyclooxygenase-1, a prostaglandin synthase enriched in microglia. PGD2, another AA-derived lipid mediator, has been implicated in depression induced by chronic stress, although either pro-depressive or anti-depressive actions have been reported. Chronic stress up-regulates hippocampal expression of 5-lipoxygenase, hence synthesis of cysteinyl leukotrienes, thereby inducing depression through their receptors. Consistent with beneficial effects of n-3 fatty acids in the diet of depressive patients, resolvins—a novel class of pro-resolving lipid mediators—in the brain attenuate neuroinflammation-associated depression. These findings in animal models of depression offer lipid mediators and related molecules as novel therapeutic targets for treating depression. To translate these findings into clinics, translational biomarkers to visualize lipid mediator profiles in depressive patients need to be established.
Unintended Labor Supply Effects of Cash Transfer Programs: New Evidence from South Africa’s Pension†
Authors: Abel Martin
Published: February 2019

Using South Africa’s first nationally representative panel data set, I find that the presence of pension recipients in the household reduces the probability of employment of both previously employed and unemployed prime-aged adults. Exploiting institutional features of the disability grant to isolate the pension’s income effect suggests that the effects operate through the income mechanism. By contrast, there is no evidence that pensioners enable household members to work by providing childcare as concluded by previous studies.
A qualitative framework-based evaluation of radiology clinical decision support initiatives: eliciting key factors to physician adoption in implementation
Authors: Marcial Laura Haak , Johnston Douglas S , Shapiro Michael R , Jacobs Sara R , Blumenfeld Barry , Rojas Smith Lucia
Published: February 2019

Objectives

To illustrate key contextual factors that may have effects on clinical decision support (CDS) adoption and, ultimately, success.

Materials and Methods

We conducted a qualitative evaluation of 2 similar radiology CDS innovations for near-term endpoints affecting adoption and present the findings using an evaluation framework. We identified key contextual factors between these 2 innovations and determined important adoption differences between them.

Results

Degree of electronic health record integration, approach to education and training, key drivers of adoption, and tailoring of the CDS to the clinical context were handled differently between the 2 innovations, contributing to variation in their relative degrees of adoption and use. Attention to these factors had impacts on both near and later-term measures of success (eg, patient outcomes).

Discussion

CDS adoption is a well-studied early-term measure of CDS success that directly impacts outcomes. Adoption requires attention throughout the design phases of an intervention especially to key factors directly affecting it, including how implementation across multiple sites and systems complicates adoption, which prior experience with CDS matters, and that practice guidelines invariably require tailoring to the clinical context.

Conclusion

With better planning for the capture of early-term measures of successful CDS implementation, especially adoption, critical adjustments may be made to ensure that the CDS is effectively implemented to be successful.
Endoscopic Resection of Ampullary Tumours: Long-term Outcomes and Adverse Events
Authors: Alali Ali , Espino Alberto , Moris Maria , Martel Myriam , Schwartz Ingrid , Cirocco Maria , Streutker Catherine , Mosko Jeffrey , Kortan Paul , Barkun Alan , May Gary R
Published: February 2019

Background

The management of ampullary lesions has shifted from surgical approach to endoscopic resection. Previous reports were limited by small numbers of patients and short follow-up. The aim of this study is to describe short- and long-term outcomes in a large cohort of patients undergoing endoscopic ampullectomy.

Methods

Retrospective study of endoscopic ampullectomies performed at a tertiary center from January 1999 to October 2016. Information recorded includes patient demographics, clinical outcomes, lesion pathology, procedural events, adverse events and follow-up data.

Results

Overall, 103 patients underwent endoscopic resection of ampullary tumours (mean age 62.3 ± 14.3 years, 50.5% female, mean lesion size 20.9 mm; 94.9% adenomas, with a majority of lesions exhibiting low-grade dysplasia (72.7%). Complete endoscopic resection was achieved in 82.5% at initial procedure. Final complete endoscopic resection was achieved in all patients with benign pathology on follow-up procedures. Final pathology showed that 11% had previously undiagnosed invasive carcinoma. Delayed postprocedure bleeding occurred in 21.4%, all of which were managed successfully at endoscopy. Acute pancreatitis complicated 15.5% of procedures (mild in 93.8%). Perforation occurred in 5.8%, all treated conservatively except for one patient requiring surgery. Piecemeal resection was associated with significantly higher recurrence compared to en-bloc resection (54.3% versus 26.2%, respectively, P = 0.012). All recurrences were treated endoscopically.

Conclusion

Endoscopic ampullectomy appears both safe and effective in managing patients with ampullary tumours in experienced hands. Most adverse events can be managed conservatively. Many patients develop recurrence during long-term follow-up but can be managed endoscopically. Recurrence rates may be reduced by performing initial en-bloc resection.
An Experimental Study of Nicotine Warning Statements in E-cigarette Tweets
Authors: Guillory Jamie , Kim Annice E , Fiacco Leah , Cress Margaret , Pepper Jessica , Nonnemaker James
Published: February 2019

Introduction

It is unclear whether warnings on electronic cigarette (e-cigarette) advertisements required by the US Food and Drug Administration (FDA) will apply to social media. Given the key role of social media in marketing e-cigarettes, we seek to inform FDA decision making by exploring how warnings on various tweet content influence perceived healthiness, nicotine harm, likelihood to try e-cigarettes, and warning recall.

Methods

In this 2 × 4 between-subjects experiment participants viewed a tweet from a fictitious e-cigarette brand. Four tweet content versions (e-cigarette product, e-cigarette use, e-cigarette in social context, unrelated content) were crossed with two warning versions (absent, present). Adult e-cigarette users (N = 994) were recruited via social media ads to complete a survey and randomized to view one of eight tweets. Multivariable regressions explored effects of tweet content and warning on perceived healthiness, perceived harm, and likelihood to try e-cigarettes, and tweet content on warning recall. Covariates were tobacco and social media use and demographics.

Results

Tweets with warnings elicited more negative health perceptions of the e-cigarette brand than tweets without warnings (p < .05). Tweets featuring e-cigarette products (p < .05) or use (p < .001) elicited higher warning recall than tweets featuring unrelated content.

Conclusions

This is the first study to examine warning effects on perceptions of e-cigarette social media marketing. Warnings led to more negative e-cigarette health perceptions, but no effect on perceived nicotine harm or likelihood to try e-cigarettes. There were differences in warning recall by tweet content. Research should explore how varying warning content (text, size, placement) on tweets from e-cigarette brands influences health risk perceptions.

Implications

FDA’s 2016 ruling requires warnings on advertisements for nicotine-containing e-cigarettes, but does not specify whether this applies to social media. This study is the first to examine how e-cigarette warnings in tweets influence perceived healthiness and harm of e-cigarettes, which is important because e-cigarette brands are voluntarily including warnings on Twitter and Instagram. Warnings influenced perceived healthiness of the e-cigarette brand, but not perceived nicotine harm or likelihood to try e-cigarettes. We also saw higher recall of warning statements for tweets featuring e-cigarettes. Findings suggest that expanding warning requirements to e-cigarette social media marketing warrants further exploration and FDA consideration.
Treatment of Posaconazole-Induced Peripheral Neuropathy With Methylprednisolone and Magnesium Infusions: A Case Report
Authors: Hussain Sadia , Nissen Susan , Holland Steven M , Sandroni Paola , Lionakis Michail S
Published: February 2019

The tolerability of long-term posaconazole use remains poorly defined. We present a patient who developed peripheral neuropathy following long-term exposure to the tablet formulation of posaconazole, which was treated with methylprednisolone and magnesium infusions. The potential role of methylprednisolone and magnesium infusions in managing this potentially irreversible triazole-associated complication requires further study.
Infectious Complications After Umbilical Cord Blood Transplantation for Hematological Malignancy
Authors: Linder Kathleen A , McDonald Philip J , Kauffman Carol A , Revankar Sanjay G , Chandrasekar Pranatharthi H , Miceli Marisa H
Published: February 2019

Background

Umbilical cord blood transplant (UCBT) is used for patients who do not have a matched donor, but engraftment often takes longer than with a standard allogeneic transplant, likely increasing the risk for infection. We characterized specific infections and outcomes in adults undergoing UCBT at our 2 centers.

Methods

All adults who underwent UCBT between January 1, 2006 and December 31, 2015 were included. Infectious episodes from 6 months before to 2 years after UCBT were reviewed.

Results

Fifty-seven patients underwent UCBT; 47 had neutrophil engraftment. A total of 179 infectious episodes occurred in 55 patients, 73 (41%) within 30 days post-UCBT. Viruses caused 85 (47%) infections. Cytomegalovirus caused 32 infectious episodes and was most common from day 30 to 100. Human herpesvirus 6 occurred in 28 episodes, was most common within 30 days, and caused 1 death. Bacteria were responsible for 82 (46%) infections, most commonly bacteremias due to Staphylococcus spp, Enterococcus spp, and Enterobacteriaceae. Of 11 invasive fungal infections, 9 were aspergillosis, 4 of which were fatal. Overall mortality was 56% in the first year. Thirteen deaths were from infection; 11 occurred in the first 100 days and 7 in the first 30 days post-UCBT. Of 10 patients who never engrafted, 9 died, 6 from infection, within 100 days post-UCBT.

Conclusions

Infectious complications were common after UCBT, especially in the first 30 days. Deaths from viral infections were fewer than expected. Delayed engraftment and nonengraftment continue to convey increased risk for fatal bacterial and fungal infections post-UCBT.
Identification of 19 Novel Hepatitis C Virus Subtypes—Further Expanding HCV Classification
Authors: Hedskog Charlotte , Parhy Bandita , Chang Silvia , Zeuzem Stefan , Moreno Christophe , Shafran Stephen D , Borgia Sergio M , Asselah Tarik , Alric Laurent , Abergel Armand , Chen Jyh-Jou , Collier Jane , Kapoor Dharmesh , Hyland Robert H , Simmonds Peter , Mo Hongmei , Svarovskaia Evguenia S
Published: February 2019

Background

Hepatitis C virus (HCV) is currently classified into 8 genotypes and 86 subtypes. The objective of this study was to characterize novel HCV subtypes and to investigate the impact of subtypes on treatment outcome.

Methods

Full-genome sequencing was performed on HCV plasma samples with <85% sequence homology of NS3, NS5A, and/or NS5B to HCV genotype (GT) 1–8 reference strains.

Results

A total of 14 653 patients with GT1–6 HCV infection were enrolled in clinical studies of sofosbuvir-based regimens. For the majority of the patients, a specific subtype could be assigned based on a close genetic relationship to previously described subtypes. However, for 19 patients, novel subtypes were identified with <85% homology compared with previously described subtypes. These novel subtypes had the following genotypes: 9 in GT2, 5 in GT4, 2 in GT6, and 1 each in GT1, GT3, and GT5. Despite the presence of polymorphisms at resistance-associated substitution positions, 18 of the 19 patients treated with sofosbuvir-containing therapy achieved SVR12.

Conclusions

Nineteen novel HCV subtypes were identified, suggesting an even greater genetic diversity of HCV subtypes than previously recognized.
Safety and Feasibility of Transcranial Magnetic Stimulation as an Exploratory Assessment of Corticospinal Connectivity in Infants After Perinatal Brain Injury: An Observational Study
Authors: Nemanich Samuel T , Chen Chao-Ying , Chen Mo , Zorn Elizabeth , Mueller Bryon , Peyton Colleen , Elison Jed T , Stinear James , Rao Raghu , Georgieff Michael , Menk Jeremiah , Rudser Kyle , Gillick Bernadette
Published: February 2019

Background

Perinatal brain injuries often impact the corticospinal system, leading to motor impairment and cerebral palsy. Although transcranial magnetic stimulation (TMS) has been widely used to study corticospinal connectivity in adults and older children, similar studies of young infants are limited.

Objectives

The objective was to establish the safety and feasibility of advanced TMS assessments of the corticospinal connectivity of young infants with perinatal brain injury.

Design

This was a pilot, cross-sectional study of 3- to 12-month-old (corrected age) infants with perinatal stroke or intracranial hemorrhage.

Methods

Six participants (2 term, 4 preterm) were assessed with stereotactic neuronavigation-guided TMS. Single-pulse TMS was applied to each hemisphere and responses were recorded simultaneously from both upper limbs. During data collection, vital signs and stress responses were measured to assess safety. Developmental motor outcomes were evaluated using the General Movements Assessment and Bayley Scales of Infant and Toddler Development (3rd edition). A clinical diagnosis of cerebral palsy was recorded, if available.

Results

No adverse events occurred during TMS testing. All sessions were well tolerated. Contralateral motor evoked responses were detected in 4 of 6 participants. Both contralateral and ipsilateral responses were observed in 2 of 6 participants.

Limitations

TMS responses were not obtained in all participants. This could be related to the location of brain injury or developmental stage of the corticospinal system controlling the wrist flexor muscle group from which responses were recorded.

Conclusions

This study provides a summary of the framework for performing novel TMS assessments in infants with perinatal brain injury. Implementing this approach to measure corticospinal connectivity in hypothesis-driven studies in young infants appears to be justified. Such studies could inform the characterization of corticospinal development and the neural mechanisms driving recovery following early interventions.
Lack of Signal for the Impact of Conotoxin Gene Diversity on Speciation Rates in Cone Snails
Authors: Phuong Mark A , Alfaro Michael E , Mahardika Gusti N , Marwoto Ristiyanti M , Prabowo Romanus Edy , von Rintelen Thomas , Vogt Philipp W H , Hendricks Jonathan R , Puillandre Nicolas
Published: February 2019

Understanding why some groups of organisms are more diverse than others is a central goal in macroevolution. Evolvability, or the intrinsic capacity of lineages for evolutionary change, is thought to influence disparities in species diversity across taxa. Over macroevolutionary time scales, clades that exhibit high evolvability are expected to have higher speciation rates. Cone snails (family: Conidae, $>$900 spp.) provide a unique opportunity to test this prediction because their toxin genes can be used to characterize differences in evolvability between clades. Cone snails are carnivorous, use prey-specific venom (conotoxins) to capture prey, and the genes that encode venom are known and diversify through gene duplication. Theory predicts that higher gene diversity confers a greater potential to generate novel phenotypes for specialization and adaptation. Therefore, if conotoxin gene diversity gives rise to varying levels of evolvability, conotoxin gene diversity should be coupled with macroevolutionary speciation rates. We applied exon capture techniques to recover phylogenetic markers and conotoxin loci across 314 species, the largest venom discovery effort in a single study. We paired a reconstructed timetree using 12 fossil calibrations with species-specific estimates of conotoxin gene diversity and used trait-dependent diversification methods to test the impact of evolvability on diversification patterns. Surprisingly, we did not detect any signal for the relationship between conotoxin gene diversity and speciation rates, suggesting that venom evolution may not be the rate-limiting factor controlling diversification dynamics in Conidae. Comparative analyses showed some signal for the impact of diet and larval dispersal strategy on diversification patterns, though detection of a signal depended on the dataset and the method. If our results remain true with increased taxonomic sampling in future studies, they suggest that the rapid evolution of conid venom may cause other factors to become more critical to diversification, such as ecological opportunity or traits that promote isolation among lineages.
Understanding the processes that Federally Qualified Health Centers use to select and implement colorectal cancer screening interventions: a qualitative study
Authors: Leeman Jennifer , Askelson Natoshia , Ko Linda K , Rohweder Catherine L , Avelis Jade , Best Alicia , Friedman Daniela , Glanz Karen , Seegmiller Laura , Stradtman Lindsay , Vanderpool Robin C
Published: February 2019

Colorectal cancer (CRC) screening is highly effective at reducing cancer-related morbidity and mortality, yet screening rates remain suboptimal. Evidence-based interventions can increase screening rates, particularly when they target multiple levels (e.g., patients, providers, health care systems). However, effective interventions remain underutilized. Thus, there is a pressing need to build capacity to select and implement multilevel CRC screening interventions. We report on formative research aimed at understanding how Federally Qualified Health Center (FQHC) staff select and implement CRC screening interventions, which will inform development of capacity-building strategies. We report the qualitative findings from a study that used a mixed methods design, starting with a quantitative survey followed by a qualitative study. In-depth interviews were conducted with 28 staff from 14 FQHCs in 8 states. The Consolidated Framework for Implementation Research (CFIR) guided interview questions and data analysis. Related to the CFIR process domain, few respondents described conducting formal assessments of factors contributing to low screening rates prior to planning their interventions. Many described engaging champions, implementation leaders, and external change agents. Few described a systematic approach to executing implementation plans beyond conducting plan-do-study-act cycles. Reflection and evaluation consisted primarily of reviewing Uniform Data System performance measures. Findings also include themes related to factors influencing these implementation processes. Although FQHCs are implementing CRC screening interventions, they are not actively targeting the multilevel factors influencing their CRC screening rates. Our findings on gaps in FQHCs’ implementation processes will inform development of strategies to build capacity to select and implement multilevel CRC screening interventions.
Leveraging high-powered RNA-Seq datasets to improve inference of regulatory activity in single-cell RNA-Seq data
Authors: Wang Ning , Teschendorff Andrew E.
Published: February 2019

Inferring the activity of transcription factors in single cells is a key task to improve our understanding of development and complex genetic diseases. This task is, however, challenging due to the relatively large dropout rate and noisy nature of single-cell RNA-Seq data. Here we present a novel statistical inference framework called SCIRA (Single Cell Inference of Regulatory Activity), which leverages the power of large-scale bulk RNA-Seq datasets to infer high-quality tissue-specific regulatory networks, from which regulatory activity estimates in single cells can be subsequently obtained. We show that SCIRA can correctly infer regulatory activity of transcription factors affected by high technical dropouts. In particular, SCIRA can improve sensitivity by as much as 70% compared to differential expression analysis and current state-of-the-art methods. Importantly, SCIRA can reveal novel regulators of cell-fate in tissue-development, even for cell-types that only make up 5% of the tissue, and can identify key novel tumor suppressor genes in cancer at single cell resolution. In summary, SCIRA will be an invaluable tool for single-cell studies aiming to accurately map activity patterns of key transcription factors during development, and how these are altered in disease.
Genetic risk score for Alzheimer’s disease is associated with poor hearing
Authors: Brenowitz Willa D. , Filshtein Teresa J. , Yaffe Kristine , Walter Stefan , Hoffmann Thomas J. , Jorgenson Eric , Whitmer Rachel A. , Glymour M. Maria
Published: February 2019

Introduction

Incipient dementia or shared genetics may partly explain the association between hearing loss and dementia. We evaluated whether genetic variants known to increase Alzheimer’s disease (AD) also influence hearing difficulty.

Methods

UK Biobank participants aged 56+ with Caucasian genetic ancestry self-reported difficulty hearing and hearing with background noise (n=244,915) and underwent objectively measured hearing assessments (n=80,074). Poor objective hearing was defined as >-5.5 dB speech reception threshold on a Digit Triplet Test. We evaluated whether an AD genetic risk score (AD-GRS; range −1.2 to 1.9), the weighted sum of 23 previously identified AD-related polymorphisms, predicted objective or self-reported poor hearing, using age, sex, and genetic ancestry adjusted logistic regression models.

Results

Higher AD-GRS predicted objectively measured poor hearing (OR=1.06; 95% CI: 1.01, 1.11) and self-reported problems hearing with background noise (OR=1.03; 95% CI: 1.00, 1.05).

Discussion

Using novel methods, we found evidence that AD genetic risk influences hearing loss.
The Importance of Anti-Correlations in Graph Theory Based Classification of Autism Spectrum Disorder
Authors: Kazeminejad Amirali , Sotero Roberto C
Published: February 2019

In recent years, there has been a significant growth in the number of applications of machine learning (ML) techniques to the study and identification of neurological disorders. These methods rely heavily on what features are made available to the ML algorithm. Features such as graph theoretical metrics of resting-state fMRI-based brain networks have proven useful. However, the computation of functional brain networks relies on making an arbitrary choice about whether the obtained anti-correlations, representing the strengths of functional connections in the brain, should be discarded or not. In this study, we examine how this choice affects the performance of a support vector machine (SVM) model for classifying autism spectrum disorder. We extracted graph theoretical features using three different pipelines for constructing the functional network graph. These pipelines primarily used positive weights, negative weights (anti-correlations) and only the absolute value of weights of the correlation matrix derived from fMRI time-series. Our results suggest that in the presence of Global Signal Regression (GSR) the features extracted from anti-correlations play a major role in improving model performance. However, this does not undermine the importance of features from other pipelines.
Cooler: scalable storage for Hi-C data and other genomically-labeled arrays
Authors: Abdennur Nezar , Mirny Leonid
Published: February 2019

Most existing coverage-based (epi)genomic datasets are one-dimensional, but newer technologies probing interactions (physical, genetic, etc.) produce quantitative maps with two-dimensional genomic coordinate systems. Storage and computational costs mount sharply with data resolution when such maps are stored in dense form. Hence, there is a pressing need to develop data storage strategies that handle the full range of useful resolutions in multidimensional genomic datasets by taking advantage of their sparse nature, while supporting efficient compression and providing fast random access to facilitate development of scalable algorithms for data analysis. We developed a file format called cooler, based on a sparse data model, that can support genomically-labeled matrices at any resolution. It has the flexibility to accommodate various descriptions of the data axes (genomic coordinates, tracks and bin annotations), resolutions, data density patterns, and metadata. Cooler is based on HDF5 and is supported by a Python library and command line suite to create, read, inspect and manipulate cooler data collections. The format has been adopted as a standard by the NIH 4D Nucleome Consortium. Cooler is cross-platform, BSD-licensed, and can be installed from the Python Package Index or the bioconda repository. The source code is maintained on Github at https://github.com/mirnylab/cooler.
Functional Enrichment and Analysis of Antigen-Specific Memory B Cell Antibody Repertoires in PBMCs
Authors: Waltari Eric , McGeever Aaron , Kim Peter S. , McCutcheon Krista M.
Published: February 2019

Phenotypic screening of antigen-specific antibodies in human blood is a common diagnostic test for infectious agents and a correlate of protection after vaccination. In addition to long-lived antibody secreting plasma cells residing in the bone marrow, memory B cells are a latent source of antigen-experienced, long-term immunity that can be found at low frequencies in circulating PBMCs. Assessing the genotype, clonal frequency, quality, and function of antibodies resulting from an individual’s persistent memory B cell repertoire can help inform the success or failure of immune protection. We have applied ELISPOT cell culture methods to functionally expand the memory repertoire from PBMCs and clonally map monoclonal antibodies from this population. We show that combining deep sequencing of stimulated memory B cell repertoires with retrieving single antigen-specific cells is a promising approach in evaluating the latent, functional B cell memory in PBMCs.
Brassinosteroids Influence Arabidopsis Hypocotyl Graviresponses Through Changes In Mannans And Cellulose
Authors: Somssich Marc , Vandenbussche Filip , Ivakov Alexander , Funke Norma , Ruprecht Colin , Vissenberg Kris , Van Der Straeten Dominique , Persson Staffan , Suslov Dmitry
Published: February 2019

The force of gravity is a constant environmental factor. Plant shoots respond to gravity through negative gravitropism and gravity resistance. These responses are essential for plants to direct the growth of aerial organs away from the soil surface after germination and to keep an upright posture above ground. We took advantage of the effect of brassinosteroids on the two types of graviresponses inArabidopsis thalianahypocotyls to disentangle functions of cell wall polymers during etiolated shoot growth. The ability of etiolated Arabidopsis seedlings to grow upwards was suppressed in the presence of 24-epibrassinolide (EBL) but enhanced in the presence of brassinazole (BRZ), an inhibitor of brassinosteroid biosynthesis. These effects were accompanied by changes in cell wall mechanics and composition. Cell wall biochemical analyses and confocal microscopy of the cellulose-specific pontamine S4B dye revealed that the EBL and BRZ treatments correlated with changes in cellulose fibre organization and mannan content. Indeed, a longitudinal re-orientation of cellulose fibres supported upright growth whereas the presence of mannans reduced gravitropic bending. The negative effect of mannans on gravitropism is a new function for this class of hemicelluloses, highlighting evolutionary adaptations by which aquatic ancestors of terrestrial plants colonized land.
Short-term consumption of sucralose with, but not without, carbohydrate impairs neural and metabolic sensitivity to sugar
Authors: Dalenberg Jelle R. , Patel Barkha P. , Denis Raphael , Veldhuizen Maria G. , Nakamura Yuko , Vinke Petra C. , Luquet Serge , Small Dana M.
Published: February 2019

There is a general consensus that overconsumption of sugar sweetened beverages contributes to the prevalence of obesity and related comorbidities such as type 2 diabetes (T2D). Whether a similar relationship exists for no, or low-calorie “diet” drinks is a subject of intensive debate and controversy. Here, we show that metabolic dysfunction, coupled with reduced central sensitivity to sweet, but not sour, salty or bitter taste, occurs when sucralose is repeatedly consumed with, but not without, a carbohydrate over a two-week period in healthy humans. A similar exposure to sucralose, with, but not without, a carbohydrate altered substrate utilization in mice. More specifically, greater energy intake was required for the animals to shift from fatty acid to carbohydrate oxidation, indicating a reduced sensitivity to carbohydrate. These findings demonstrate that consumption of sucralose in the presence of a carbohydrate rapidly impairs glucose metabolism and may contribute to the rise in T2D.
Heart rate and its relationship with activity in free-ranging Cheloniidae sea turtles
Authors: Okuyama Junichi , Shiozawa Maika , Shiode Daisuke
Published: February 2019

The primary oxygen stores in Cheloniidae sea turtles are in the lungs. Therefore, management of blood oxygen transportation to peripheral tissues by cardiovascular adjustments while diving is crucial to maximize benefits from dives. However, heart rate, particularly cardiac response to exercise in free-ranging dives, has rarely been examined for sea turtles. In this study, heart rate and its relationship with the amount of activity were determined in six free-ranging green turtles using bio-logging techniques. Our results demonstrated that resting heart rate took 7–11 h to reduce to steady levels after turtles were released in the tank, indicating that turtles may not present normal physiological rates right after release. After heart rate reduction, resting heart rate of green turtles in free-ranging dives was generally low (10.9 ± 2.5 bpm), but they often presented arrhythmia (4–54 bpm) even in resting states. The amount of activity during a dive linearly increased heart rate, but maximum heart rates (39.0–69.8 bpm) were recorded during ventilation at surface. These results indicate that turtles have the capability of cardiac response to increased metabolic demands in their muscles while submerged, and also of cardiovascular adjustment for a rapid renewal of oxygen stores and removal of CO2during ventilation. Such well-organized cardiac adjustments may be because of characteristics of Cheloniidae sea turtles such as ectothermy and oxygen storage in lungs while submerged.

Summary statement

Green sea turtles in free-ranging dive had generally lower heart rate compared to other air-breathing divers and it varied with the amount of exercise. Turtles often showed extreme arrhythmia.
Plasmid-based CRISPR-Cas9 gene editing in multipleCandidaspecies
Authors: Lombardi Lisa , Oliveira-Pacheco João , Butler Geraldine
Published: February 2019

ManyCandidaspecies that cause infection have diploid genomes, and do not undergo classical meiosis. The application of CRISPR-Cas9 gene editing systems have therefore greatly facilitated the generation of gene disruptions, and the introduction of specific polymorphisms. However, CRISPR methods are not yet available for allCandidaspecies. We describe here an adaption of a previously developed CRISPR system inCandida parapsilosisthat uses an autonomously replicating plasmid. Guide RNAs can be introduced in a single cloning step, and are released by cleavage between a tRNA and a ribozyme. The plasmid also containsCAS9and a selectable nourseothricinSAT1marker. It can be used for markerless editing inC. parapsilosis, C. orthopsilosisandC. metapsilosis. We also show that CRISPR can easily be used to introduce molecular barcodes, and to reintroduce wild type sequences into edited strains. Heterozygous mutations can be generated, either by careful selection of the distance between the polymorphism and the Cas9 cut site, or by providing two different repair templates at the same time. In addition, we have constructed a different autonomously replicating plasmid for CRISPR-Cas9 editing inCandida tropicalis. We show that editing can easily be carried out in multipleC. tropicalisisolates. NHEJ repair occurs at a high level inC. metapsilosisandC. tropicalis.

IMPORTANCE

Candidaspecies are a major cause of infection worldwide. The species associated with infection vary with geographical location, and patient population. Infection withCandida tropicalisis particularly common in South America and Asia, andCandida parapsilosisinfections are more common in the very young. Molecular methods for manipulating the genomes of these species are still lacking. We describe a simple and efficient CRISPR-based gene editing system that can be applied in theC. parapsilosisspecies group, including the sister speciesCandida orthopsilosisandCandida metapsilosis. We have also constructed a separate system for gene editing inC. tropicalis.
A comparison of three programming languages for a full-fledged next-generation sequencing tool
Authors: Pascal Costanza , Charlotte Herzeel , Wilfried Verachtert
Published: February 2019

Background

elPrep is an established multi-threaded framework for preparing SAM and BAM files in sequencing pipelines. To achieve good performance, its software architecture makes only a single pass through a SAM/BAM file for multiple preparation steps, and keeps sequencing data as much as possible in main memory. Similar to other SAM/BAM tools, management of heap memory is a complex task in elPrep, and it became a serious productivity bottleneck in its original implementation language during recent further development of elPrep. We therefore investigated three alternative programming languages: Go and Java using a concurrent, parallel garbage collector on the one hand, and C++17 using reference counting on the other hand for handling large amounts of heap objects. We reimplemented elPrep in all three languages and benchmarked their runtime performance and memory use.

Results

The Go implementation performs best, yielding the best balance between runtime performance and memory use. While the Java benchmarks report a somewhat faster runtime than the Go benchmarks, the memory use of the Java runs is significantly higher. The C++17 benchmarks run significantly slower than both Go and Java, while using somewhat more memory than the Go runs. Our analysis shows that concurrent, parallel garbage collection is better at managing a large heap of objects than reference counting in our case.

Conclusions

Based on our benchmark results, we selected Go as our new implementation language for elPrep, and recommend considering Go as a good candidate for developing other bioinformatics tools for processing SAM/BAM data as well.
Single mRNP analysis by super-resolution microscopy and fluorescence correlation spectroscopy reveals that small mRNP granules represent mRNA singletons
Authors: Mateu-Regué Àngels , Christiansen Jan , Bagger Frederik Otzen , Hellriegel Christian , Nielsen Finn Cilius
Published: February 2019

Small cytoplasmic mRNP granules are implicated in mRNA transport, translational control and decay. Employing Super-resolution Microscopy and Fluorescence Correlation Spectroscopy, we analyzed the molecular composition and dynamics of single cytoplasmic YBX1_IMP1 mRNP granules in live cells. Granules appeared elongated and branched with patches of IMP1 and YBX1 distributed along mRNA, reflecting the attachment of the two RNA-binding proteins incis. Particles form at the nuclear pore and are spatially segregated from translating ribosomes, so the mRNP is a repository for mRNAs awaiting translation. In agreement with the average number of mRNA-binding sites derived from CLIP analyses, individual mRNPs contain 5 to 15 molecules of YBX1 and IMP1 and a single poly(A) tail identified by PABPC1. Taken together, we conclude that small cytoplasmic mRNP granules are mRNA singletons, thus depicting the cellular transcriptome. Consequently, expression of functionally related mRNAs in RNA regulons is unlikely to result from coordinated assembly.
Arabidopsismlo3mutant plants exhibit spontaneous callose deposition and signs of early leaf senescence
Authors: Kusch Stefan , Thiery Susanne , Reinstädler Anja , Gruner Katrin , Zienkiewicz Krzysztof , Feussner Ivo , Panstruga Ralph
Published: February 2019

The family of Mildew resistance Locus O (MLO) proteins is best known for its profound effect on the outcome of powdery mildew infections: when the appropriate MLO protein is absent, the plant is fully resistant to otherwise virulent powdery mildew fungi. However, most members of the MLO protein family remain functionally unexplored. Here, we investigateArabidopsis thaliana MLO3, the closest relative ofAtMLO2, AtMLO6andAtMLO12, which are the ArabidopsisMLOgenes implicated in the powdery mildew interaction. The co-expression network ofAtMLO3suggests association of the gene with plant defense-related processes such as salicylic acid homeostasis. Our extensive analysis shows thatmlo3mutants are unaffected regarding their infection phenotype upon challenge with the powdery mildew fungiGolovinomyces orontiiandErysiphe pisi, the oomyceteHyaloperonospora arabidopsidis, and the bacterial pathogenPseudomonas syringae(the latter both in terms of basal and systemic acquired resistance), indicating that the protein does not play a major role in the response to any of these pathogens. However,mlo3genotypes display spontaneous callose deposition as well as signs of early senescence in six-or seven-week-old rosette leaves in the absence of any pathogen challenge, a phenotype that is reminiscent ofmlo2mutant plants. We hypothesize that de-regulated callose deposition inmlo3genotypes is the result of a subtle transient aberration of salicylic acid-jasmonic acid homeostasis during development.
Pooled CRISPR Inverse PCR sequencing (PCIP-seq): simultaneous sequencing of retroviral insertion points and the associated provirus in thousands of cells with long reads
Authors: Artesi Maria , Hahaut Vincent , Ashrafi Fereshteh , Marçais Ambroise , Hermine Olivier , Griebel Philip , Arsic Natasa , van der Meer Frank , Burny Arsène , Bron Dominique , Charlier Carole , Georges Michel , Van den Broeke Anne , Durkin Keith
Published: February 2019

Retroviral infections create a large population of cells, each defined by a unique proviral insertion site. Methods based on short-read high throughput sequencing can identify thousands of insertion sites, but the proviruses within remain unobserved. We have developed Pooled CRISPR Inverse PCR sequencing (PCIP-seq), a method that leverages long reads on the Oxford Nanopore MinION platform to sequence the insertion site and its associated provirus. We have applied the technique to three exogenous retroviruses, HTLV-1, HIV-1 and BLV, as well as endogenous retroviruses in both cattle and sheep. The long reads of PCIP-seq improved the accuracy of insertion site identification in repetitive regions of the genome. The high efficiency of the method facilitated the identification of tens of thousands of insertion sites in a single sample. We observed thousands of SNPs and dozens of structural variants within proviruses and uncovered evidence of viral hypermutation, recombination and recurrent selection.