bluuebunny/crossref_metadata_2025_split huggingface dataset:
Abstract IA23: Phospho-RNA-seq: A liquid biopsy approach for cell-free mRNA/lncRNA profiling
Authors: Giraldez Maria D. , Spengler Ryan M. , Etheridge Alton , Goicochea Annika J. , Tuck Missy , Choi Sung W. , Galas David J. , Tewari Muneesh 
Published: June 2020

Abstract
Measuring disease biomarkers in biofluids to detect and monitor pathophysiologic events in tissues has enormous appeal. While detecting specific DNA sequences in blood plasma has been successful in informing about the presence of cancers, viruses, and a range of pathogens, this approach does not provide gene expression information, which could reveal more detailed information about disease activity. Measuring cell-free RNA in plasma would provide such information and has the potential to be more sensitive, given that one DNA molecule in a cell gives rise often to thousands or more RNA molecules.
However, with the exception of microRNAs, broad sequencing of cell-free messenger RNA (mRNA) profiles in plasma has been generally challenging. We discovered that a major barrier to cell-free RNA sequencing from plasma is that the large majority of mRNAs are both fragmented and have modified phosphorylation states at their 5’ and 3’ ends that make them invisible to standard small RNA-seq methods. We present a modified RNA-seq methodology, called phospho-RNA-seq, which revealed thousands of mRNA in blood plasma. The key to this approach is (i) the incorporation of T4-polynucleotide kinase treatment to change the phosphorylation states at the RNA ends, and (ii) a stringent bioinformatics analysis pipeline to reduce false positive alignments.
Phospho-RNA-seq identified cohorts of gene transcripts in plasma, including ones expressed in a tissue-specific manner. As proof-of-concept validation of the approach for biomarker identification, we used phospho-RNA-seq to longitudinally profile plasma specimens collected from patients undergoing hematopoietic stem cell transplantation. We detected bone marrow-enriched and liver-enriched transcript sets in plasma, which tracked with bone marrow recovery and hepatic injury, respectively. By providing expanded access to the transcriptome in plasma and potentially other biofluids, phospho-RNA-seq enables the discovery of new cell-free RNA biomarker signatures for a wide variety of liquid biopsy applications.
Citation Format: Maria D. Giraldez, Ryan M. Spengler, Alton Etheridge, Annika J. Goicochea, Missy Tuck, Sung W. Choi, David J. Galas, Muneesh Tewari. Phospho-RNA-seq: A liquid biopsy approach for cell-free mRNA/lncRNA profiling [abstract]. In: Proceedings of the AACR Special Conference on Advances in Liquid Biopsies; Jan 13-16, 2020; Miami, FL. Philadelphia (PA): AACR; Clin Cancer Res 2020;26(11_Suppl):Abstract nr IA23.
Abstract PR14: Sub-nucleosomal fragmentation in urine cell-free DNA
Authors: Markus Havell , Zhao Jun , Contente-Cuomo Tania , Raupach Elizabeth , Odenheimer-Bergman Ahuva , Connor Sydney , McDonald Bradon , Hutchins Elizabeth , McGilvrey Marissa , de la Maza Michelina C. , Van Jensen Kendall Van Keuren-Jensen , Pirrotte Patrick Pirrotte , Goel Ajay , Becerra Carlos , Von Hoff Daniel D. , Celinski Scott , Hingorani Pooja , Murtaza Muhammed 
Published: June 2020

Abstract
Cell-free DNA (cfDNA) in plasma has been shown to be a promising analyte for noninvasive diagnostics. The collection of blood plasma requires venipuncture, and plasma volume obtainable at a single point is limited. In contrast, cfDNA in urine can be collected noninvasively, with minimal assistance and in larger volumes. However, so far there has been limited success in diagnostic development using urine cfDNA as urine cfDNA is highly fragmented, and whether the characteristics of these fragments reflect underlying genomic architecture is unknown. Here, we perform a comprehensive characterization of fragmentation patterns in urine cfDNA using high-depth whole-genome sequencing from 30 healthy volunteers. We show the distribution of fragment sizes and genome-wide distribution of urine cfDNA fragments are consistent with transient protection from complete degradation by stable intermediates of nucleosome disassembly. Genome-wide nucleosome occupancy and fragment sizes in urine cfDNA are informative of the cell of origin and renal epithelial cells are among the highest contributors in urine. Based on a reference nucleosome map for urine cfDNA positioning, we developed a computational method to measure the fraction of urine cfDNA fragments with aberrant ends at unexpected genomic loci. We observe a higher fraction of fragments with aberrant ends in pediatric and adult cancer patients, distinguishing cancer samples with an area under the curve of 0.89. Our results demonstrate genomic architecture is preserved to an unexpected degree in urine cfDNA and are proof of principle that genome-wide fragmentation analysis of urine cfDNA can enable cancer diagnostics.
This abstract is also being presented as Poster B12.
Citation Format: Havell Markus, Jun Zhao, Tania Contente-Cuomo, Elizabeth Raupach, Ahuva Odenheimer-Bergman, Sydney Connor, Bradon McDonald, Elizabeth Hutchins, Marissa McGilvrey, Michelina C. de la Maza, Kendall Van Keuren-Jensen Van Jensen, Patrick Pirrotte Pirrotte, Ajay Goel, Carlos Becerra, Daniel D. Von Hoff, Scott Celinski, Pooja Hingorani, Muhammed Murtaza. Sub-nucleosomal fragmentation in urine cell-free DNA [abstract]. In: Proceedings of the AACR Special Conference on Advances in Liquid Biopsies; Jan 13-16, 2020; Miami, FL. Philadelphia (PA): AACR; Clin Cancer Res 2020;26(11_Suppl):Abstract nr PR14.
Large Extracellular Vesicle-Associated Rap1 Accumulates in Atherosclerotic Plaques, Correlates With Vascular Risks and Is Involved in Atherosclerosis
Authors: Perdomo Liliana , Vidal-Gómez Xavier , Soleti Raffaella , Vergori Luisa , Duluc Lucie , Chwastyniak Maggy , Bisserier Malik , Le Lay Soazig , Villard Alexandre , Simard Gilles , Meilhac Olivier , Lezoualc’h Frank , Khantalin Ilya , Veerapen Reuben , Dubois Séverine , Boursier Jérôme , Henni Samir , Gagnadoux Frédéric , Pinet Florence , Andriantsitohaina Ramaroson , Martínez M. Carmen ,   on behalf of Metabol study Group
Published: June 2020

Rationale:
Metabolic syndrome (MetS) is a cluster of interrelated risk factors for cardiovascular diseases and atherosclerosis. Circulating levels of large extracellular vesicles (lEVs), submicrometer-sized vesicles released from plasma membrane, from MetS patients were shown to induce endothelial dysfunction, but their role in early stage of atherosclerosis and on vascular smooth muscle cells (SMC) remain to be fully elucidated.

Objective:
To determine the mechanisms by which lEVs lead to the progression of atherosclerosis in the setting of MetS.

Methods and Results:

Proteomic analysis revealed that the small GTPase, Rap1 was overexpressed in lEVs from MetS patients compared with those from non-MetS subjects. Rap1 was in GTP-associated active state in both types of lEVs, and Rap1-lEVs levels correlated with increased cardiovascular risks, including stenosis. MetS-lEVs, but not non-MetS-lEVs, increased Rap1-dependent endothelial cell permeability. MetS-lEVs significantly promoted migration and proliferation of human aortic SMC and increased expression of proinflammatory molecules and activation of ERK (extracellular signal-regulated kinase) 5/p38 pathways. Neutralization of Rap1 by specific antibody or pharmacological inhibition of Rap1 completely prevented the effects of lEVs from MetS patients. High-fat diet-fed ApoE
−/−
mice displayed an increased expression of Rap1 both in aortas and circulating lEVs. lEVs accumulated in plaque atherosclerotic lesions depending on the progression of atherosclerosis. lEVs from high-fat diet-fed ApoE
−/−
mice, but not those from mice fed with a standard diet, enhanced SMC proliferation. Human atherosclerotic lesions were enriched in lEVs expressing Rap1.

Conclusions:
These data demonstrate that Rap1 carried by MetS-lEVs participates in the enhanced SMC proliferation, migration, proinflammatory profile, and activation of ERK5/p38 pathways leading to vascular inflammation and remodeling, and atherosclerosis. These results highlight that Rap1 carried by MetS-lEVs may be a novel determinant of diagnostic value for cardiometabolic risk factors and suggest Rap1 as a promising therapeutic target against the development of atherosclerosis.

Graphical Abstract:
A graphical abstract is available for this article.
Comparative Safety and Effectiveness of Oral Anticoagulants in Nonvalvular Atrial Fibrillation
Authors: Van Ganse Eric , Danchin Nicolas , Mahé Isabelle , Hanon Olivier , Jacoud Flore , Nolin Maëva , Dalon Faustine , Lefevre Cinira , Cotté François-Emery , Gollety Sabrina , Falissard Bruno , Belhassen Manon , Steg Ph. Gabriel 
Published: June 2020

Background and Purpose:
The effects of direct oral anticoagulants in nonvalvular atrial fibrillation should be assessed in actual conditions of use. France has near-universal healthcare coverage with a unified healthcare information system, allowing large population-based analyses. NAXOS (Evaluation of Apixaban in Stroke and Systemic Embolism Prevention in Patients With Nonvalvular Atrial Fibrillation) aimed to compare the safety, effectiveness, and mortality of apixaban with vitamin K antagonists (VKAs), rivaroxaban, and dabigatran, in oral anticoagulant-naive patients with nonvalvular atrial fibrillation.

Methods:
This was an observational study using French National Health System claims data and including all adults with nonvalvular atrial fibrillation who initiated oral anticoagulant between 2014 and 2016. Outcomes of interest were major bleeding events leading to hospitalization (safety), stroke and systemic thromboembolic events (effectiveness), and all-cause mortality. Four approaches were used for comparative analyses: matching on propensity score (PS; 1:n); as a sensitivity analysis, matching on high-dimensional PS; adjustment on PS; and adjustment on known confounders. For each outcome, cumulative incidence rates accounting for competing risks of death were estimated.

Results:
Overall, 321 501 patients were analyzed, of whom 35.0%, 27.2%, 31.1%, and 6.6% initiated VKAs, apixaban, rivaroxaban, and dabigatran, respectively. Apixaban was associated with a lower PS–matched risk of major bleeding compared with VKAs (hazard ratio [HR], 0.43 [95% CI, 0.40–0.46]) and rivaroxaban (HR, 0.67 [95% CI, 0.63–0.72]), but not dabigatran (HR, 0.93 [95% CI, 0.81–1.08]). Apixaban was associated with a lower risk of stroke and systemic thromboembolic event compared with VKAs (HR, 0.60 [95% CI, 0.56–0.65]), but not rivaroxaban (HR, 1.05 [95% CI, 0.97–1.15]) or dabigatran (HR, 0.93 [95% CI, 0.78–1.11]). All-cause mortality was lower with apixaban than with VKAs, but not lower than with rivaroxaban or dabigatran.

Conclusions:
Apixaban was associated with superior safety, effectiveness, and lower mortality than VKAs; with superior safety than rivaroxaban and similar safety to dabigatran; and with similar effectiveness when compared with rivaroxaban or dabigatran. These observational data suggest potentially important differences in outcomes between direct oral anticoagulants, which should be explored in randomized trials.
Salinity effects on egg production, hatching, and survival of Eurytemora affinis (Copepoda, Calanoida)
Authors: Kuismanen Lauri , Forsblom Louise , Engström-Öst Jonna , Båmstedt Ulf , Glippa Olivier 
Published: June 2020

Abstract
Salinity is an important biodiversity regulating factor in the Baltic Sea, forming a physiological dispersal barrier for species. The salinity in the Baltic Sea has been predicted to decline due to increased precipitation and fewer saline water inflows from the ocean. This causes stress to species already living on the edge of their tolerances and can alter species compositions and interactions in ecosystems. Calanoid copepod resting eggs, originating from a known egg bank on the seabed in the western Gulf of Finland, were incubated in the laboratory. We monitored the hatching of the calanoid copepods Acartia sp. and Eurytemora affinis, as well as the survival to maturity of hatched Eurytemora affinis nauplii in salinities ranging from 0 to 25. Further, we also investigated salinity-related effects on body size and egg production. Based on the results of our generalized linear mixed model, peak hatching occurred within the salinity range 5-20 (6.3 at the study site). Body size was not affected by salinity and most eggs were produced in salinities of 5, 7.5 and 15. The results suggest that E. affinis lives on the edge of an optimal salinity and that a decline of salinity could affect the fitness of the local populations of the species.
Occupational Therapy Roles in an Indigenous Context: An Integrative Review
Authors: White Tara , Beagan Brenda L. 
Published: June 2020

Background. Indigenous peoples experience health inequities linked in part to lack of access to culturally-relevant health care. The Truth and Reconciliation Commission of Canada (TRC) calls on all health professionals, including occupational therapists, to reduce health inequities through improved work with Indigenous communities. Purpose. This integrative review of the literature explores how occupational therapists can improve their work with Indigenous peoples. Key issues. Communication and building relationships are central to effective work with Indigenous communities, along with reciprocity regarding knowledge exchange. Issues surrounding service provision are a significant concern, yet improvements are unlikely to be effective unless therapists can critically examine the (mainstream) Western cultural assumptions that infuse the profession and their own practices. Implications. Though nascent, there are identified directions for occupational therapists to meet the TRC’s calls for more competent health care. Researchers should explore best ways for therapists to critically interrogate taken-for-granted professional assumptions mired in Western colonialism.
A Poultry Project in the Connecticut School for the Blind
Authors: Barrett Florence 
Published: June 2020

Explanatory note: The project described below has grown out of efforts over a period of some years to interest a group of pupils in this school in poultry keeping. Previous to our present scheme we have tried to use the school flock as a basis for practical training. These attempts were only partially successful. We are now convinced that a complete separation is desirable between the pupils’ poultry activities and the institution flock. The 4-H Club organization seemed to us to promise most as a means to this end. We now have, thereby, a definite profit incentive and in addition the stimulation afforded by competition among all similar clubs in the county and state. Close cooperation with and definite help from the State College is also of large value to the enterprise. The author of the article, Miss Florence Barrett, teacher of commercial subjects, modestly refers to the voluntary service rendered by one of the teachers. We realize that the succss of this undertaking is largely due her as it would have been impossible to initiate the project without a paid instructor had it not been for this contribution during its beginnings. I am glad to say that Miss Barrett still continues her interest and efforts in behalf of the venture.—Gordon Hicks, Superintendent, Connecticut School for the Blind.
Double‐Layered (Cartilage Island + Extra Perichondrium) Graft for Type 1 Tympanoplasty
Authors: Ismi Onur , Gorur Kemal , Gur Harun , Ozcan Cengiz , Vayisoglu Yusuf 
Published: June 2020

ObjectiveTo compare the graft success rates and hearing results of single‐layered (composite island) grafting (SLG) vs double‐layered (composite plus second layer of perichondrium) grafting (DLG) for over‐under type 1 tympanoplasty techniques.Study DesignRetrospective chart review.SettingsTertiary center otorhinolaryngology clinic.Subjects and MethodsMedical charts of the patients who underwent type 1 tympanoplasty via the microscopic technique by a single surgeon between 2015 and 2019 were analyzed.ResultsA total of 48 patients were included. The DLG (n = 26) group had higher graft take rates as compared to the SLG group (n = 22) for all patients (P =. 038) and for moderate‐ to high‐risk patients according to Middle Ear Risk Index (MERI) scores (P =. 029) but not for patients with mild disease (P =. 429) or myringosclerotic patients (P =. 242). The DLG group exhibited higher air‐bone gap closure (C‐ABG) values as compared to the SLG group for all patients (P =. 018). However, there was no noticeable difference in C‐ABG values within the patients with successful grafting (P =. 217). Only graft success status had a significant effect on C‐ABG values when the multivariate linear regression was performed. (P =. 016). Higher MERI scores and presence of myringosclerosis were related to the unsuccessful grafting (P <. 01).ConclusionDLG tympanoplasty is encouraged, especially for patients with higher MERI scores, to increase the graft success rates. Better hearing outcomes of DLG tympanoplasty were related to the higher graft success status of this technique; DLG had no additional hearing effect for patients with successful grafting. Higher MERI scores and presence of myringosclerosis were related to graft failure.
Olfactory and Gustatory Dysfunction as an Early Identifier of COVID‐19 in Adults and Children: An International Multicenter Study
Authors: Qiu Chenghao , Cui Chong , Hautefort Charlotte , Haehner Antje , Zhao Jun , Yao Qi , Zeng Hui , Nisenbaum Eric J. , Liu Li , Zhao Yu , Zhang Di , Levine Corinna G. , Cejas Ivette , Dai Qi , Zeng Mei , Herman Philippe , Jourdaine Clement , de With Katja , Draf Julia , Chen Bing , Jayaweera Dushyantha T. , Denneny James C. , Casiano Roy , Yu Hongmeng , Eshraghi Adrien A. , Hummel Thomas , Liu Xuezhong , Shu Yilai , Lu Hongzhou 
Published: June 2020

ObjectiveTo evaluate the prevalence and characteristics of olfactory or gustatory dysfunction in coronavirus disease 2019 (COVID‐19) patients.Study DesignMulticenter case series.SettingFive tertiary care hospitals (3 in China, 1 in France, 1 in Germany).Subjects and MethodsIn total, 394 polymerase chain reaction (PCR)–confirmed COVID‐19‐positive patients were screened, and those with olfactory or gustatory dysfunction were included. Data including demographics, COVID‐19 severity, patient outcome, and the incidence and degree of olfactory and/or gustatory dysfunction were collected and analyzed. The Questionnaire of Olfactory Disorders (QOD) and visual analog scale (VAS) were used to quantify olfactory and gustatory dysfunction, respectively. All subjects at 1 hospital (Shanghai) without subjective olfactory complaints underwent objective testing.ResultsOf 394 screened subjects, 161 (41%) reported olfactory and/or gustatory dysfunction and were included. Incidence of olfactory and/or gustatory disorders in Chinese (n = 239), German (n = 39), and French (n = 116) cohorts was 32%, 69%, and 49%, respectively. The median age of included subjects was 39 years, 92 of 161 (57%) were male, and 10 of 161 (6%) were children. Of included subjects, 10% had only olfactory or gustatory symptoms, and 19% had olfactory and/or gustatory complaints prior to any other COVID‐19 symptom. Of subjects with objective olfactory testing, 10 of 90 demonstrated abnormal chemosensory function despite reporting normal subjective olfaction. Forty‐three percent (44/102) of subjects with follow‐up showed symptomatic improvement in olfaction or gustation.ConclusionsOlfactory and/or gustatory disorders may represent early or isolated symptoms of severe acute respiratory syndrome coronavirus 2 infection. They may serve as a useful additional screening criterion, particularly for the identification of patients in the early stages of infection.
Comparative effectiveness of various treatment strategies for trigger finger by pairwise meta-analysis
Authors: Shen Po-Chih , Chou Shih-Hsiang , Lu Cheng-Chang , Fu Yin-Chih , Lu Chun-Kuan , Liu Wen-Chih , Huang Peng-Ju , Tien Yin-Chun , Shih Chia-Lung 
Published: June 2020

Objective: To compare the efficacy of various strategies in the treatment of trigger finger. Data sources: A systematic literature search for randomized controlled trials to compare treatments for trigger finger was conducted through three online databases, Pubmed, Embase and Cochrane Library, from their inception dates to 22 May 2020. Methods: Relative risk (RR) with 95% confidence interval (CI) was used to evaluate the effect sizes in success rate for included articles. Results: Sixteen articles ( n = 1185) were included in our meta-analysis. The results showed that the efficacy of steroid injection was significantly better than the placebo group at short-term follow-ups (RR = 19.00, 95% CI = 1.17–309.77 for one-week; RR = 3.70, 95% CI = 3.70, 95% CI = 1.61–8.53 for one-month), and then became non-significant at four months (RR = 3.21, 95% CI = 0.88–11.79). There was no significant difference in success rate between steroid injection and nonsteroidal anti-inflammatory drug injection, and between open surgery and percutaneous release at all the follow-ups. Only surgical treatment had significantly better efficacy in success rate than steroid injection at all follow-ups (RR = 0.48, 95% CI = 0.34–0.66 for one-month; RR = 0.87, 95% CI = 0.80–0.96 for three-month; RR = 0.58, 95% CI = 0.48–0.68 for six-month; RR = 0.38, 95% CI = 0.20–0.72 for 12-month). Conclusion: There were no differences in efficacy between steroid injection and shockwave or nonsteroidal anti-inflammatory drug injection. The surgical treatments had the best efficacy among these treatments.
MiR-877 suppresses gastric cancer progression by downregulating AQP3
Authors: Zhu Hongyu , Wu Yulian , Kang Muxing , Zhang Bo 
Published: June 2020

Objectives Gastric cancer (GC) is the leading cause of cancer-related deaths worldwide; however, the underlying molecular mechanisms of GC remain unclear. This study investigated the role of the miR-877–AQP3 axis in GC tumorigenesis. Methods The levels of miR-877 expression were measured in GC tissues and cell lines by qRT-PCR. Functional assays were performed to elucidate the role of miR-877 in GC development. Results Our results showed that miR-877 levels were lower in GC tissues and cell lines compared with the corresponding controls. Additionally, reduced miR-877 levels were associated with unfavorable prognoses. Increased miR-877 expression suppressed proliferation, invasion, and epithelial-mesenchymal transition, while promoting apoptosis in GC cells. Luciferase reporter assays showed that aquaporin 3 (AQP3) was a direct downstream target of miR-877. Overexpression of AQP3 partially rescued the tumor suppressive effects of miR-877 in GC cells. Moreover, miR-877 was negatively correlated with AQP3 mRNA expression in GC tissues. Conclusions This study demonstrated that miR-877 plays a suppressive role in GC tumorigenesis by regulating AQP3.