bluuebunny/crossref_metadata_2025_split huggingface dataset:
PERIPHERAL ISCHEMIC RETINAL PHOTOCOAGULATION IN ADDITION TO INTRAVITREAL BEVACIZUMAB VERSUS INTRAVITREAL BEVACIZUMAB ALONE FOR THE TREATMENT OF MACULAR EDEMA SECONDARY TO CENTRAL RETINAL VEIN OCCLUSION
Authors: Nourinia Ramin , Emamverdi Mehdi , Ramezani Alireza , Amizadeh Yashar , Khorshidifar Milad , Behnaz Nazanin , Safi Sare 
Published: June 2019

Purpose:
To investigate the effects of peripheral ischemic retinal photocoagulation in addition to intravitreal bevacizumab (IVB) in the treatment of macular edema due to ischemic central retinal vein occlusion.

Methods:
Forty-eight eyes of 48 treatment-naive patients were randomly selected and divided into 2 groups. Group A comprised 24 eyes that were treated with three consecutive monthly injections of IVB, and Group B comprised 24 eyes that were treated with IVB plus photocoagulation of the peripheral nonperfused retina. Further IVB injections were administered as needed in both groups. Monthly follow-up was conducted for 9 months after the first injection.

Results:
The data of 46 patients were analyzed. Best-corrected visual acuity changes from the fourth to eighth month follow-up in comparison with the baseline were significantly higher in Group B (P = 0.002–0.044—0.002–0.002—0.012). In addition, significant differences were observed in central macular thickness in Group B throughout the study period (all P < 0.001). Group B required less frequent IVB injections during the 9-month study period.

Conclusion:
Photocoagulation of the retinal nonperfused area in patients with macular edema because of central retinal vein occlusion might amplify the beneficial effects of IVB on best-corrected visual acuity and central macular thickness and reduce the frequency of IVB injection.
Using therapeutic essential oils to support the management of anxiety
Authors: Lowring Lauren Mosshart 
Published: June 2019

ABSTRACTThis brief report explores the adjunctive use of therapeutic essential oils in clinical practice to reduce overall patient anxiety and stress. The use of therapeutic essential oils is becoming increasingly popular among the general population. Studies have validated that these oils have the potential to affect patient health and wellness positively, if used properly in the clinical setting. This report discusses how to incorporate essential aromatic oils safely and efficiently in clinical practice and advocates for more research on the efficacy of aromatic oils to reduce patient anxiety in human populations.
A multidisciplinary approach for improving the outcome of out-of-hospital cardiac arrest in South Korea
Authors: Kim Gi Woon , Lee Dong Keon , Kang Bo Ra , Jeong Won Jung , Lee Choung Ah , Oh Young Taeck , Kim Yu Jin , Park Seung Min 
Published: June 2019

Aim:
Direct medical control using video conferencing capabilities of smartphones has never been conducted in out-of-hospital cardiac arrest patients. This study was conducted to investigate the feasibility and treatment effectiveness of real-time smartphone video conferencing calls for the management of out-of-hospital cardiac arrest.

Methods:
This study was a pre–post-intervention prospective cohort study conducted from January 2013 to July 2015. The intervention was pre-hospital advanced life support under a physician’s direction using a smartphone video call.

Results:
In total, 942 cardiac arrests occurred over the 2-year period; 308 patients were excluded, and 314 (49.5%) and 320 (50.5%) cardiac arrest patients were enrolled during the pre- and post-intervention study periods, respectively. There were 248/320 (77.5%) cases of smartphone video-assisted advanced life support during the post-intervention period. For patients in the pre- and post-intervention groups, the pre-hospital return of spontaneous circulation was 6.7 and 20%, respectively (adjusted odds ratio 3.3, 95% confidence interval 1.6–6.8, P < 0.01), and favourable neurological outcomes were ascertained in 1.9 and 6.9%, respectively (adjusted odds ratio 23.6, 95% confidence interval 3.4–164.0, P < 0.01). The smartphone voice and video quality were rated 8.5 and 8.2 out of 10, respectively, in physician evaluation, while the overall utility was rated 9.1.

Conclusion:
We concluded that a multidisciplinary approach including the re-education of basic life support, simulation training for advanced life support, real-time medical direction via video call, and dispatching two teams rather than one team improved the outcome of out-of-hospital cardiac arrest.
Comparison of Three Different Techniques on the Movement of Implants After Evisceration
Authors: Sendul Selam Yekta , Mavi Yildiz Aysegul , Dirim Burcu , Kacar Hakan , Yildiz Ali Atakhan , Demir Atilla Gokce , Karapapak Murat , Guven Dilek 
Published: June 2019

Purpose:
To compare the results of 3 evisceration techniques involving placement of an acrylic implant within the scleral shell without posterior sclerotomy (Group 1), posterior sclerotomy with placement of a porous implant within the intraconal space (Group 2) and posterior sclerotomy with placement of a acrylic implant within the intraconal space (Group 3) with respect to ocular mobility, implant complications and patient satisfaction.

Methods:
Single-center, retrospective, interventional case series. A chart review of 72 patients undergoing evisceration between February 2013 and January 2018 was carried out. Thirty-five patients met the inclusion criteria having a normal or near normal size eye and at least 6 months follow-up. The horizontal movements of the implant and the artificial eye was measured by using a ruler. Data analyses were conducted using the Mann-Whitney U test for 2 independent samples.

Results:
Neither infection nor prolapse of the implant had occurred in any of the patients. The mean implant sizes were 18 mm in Group 1, 20 mm in Group 2 and 20 mm in Group 3. Statistically, a significant difference was assessed between Group 1 and Group 2 in both nasal and temporal movement of the socket; nasal and temporal movement of the prosthesis. Statistically, a significant difference was assessed between Group 1 and Group 3 in both nasal and temporal movement of the socket; nasal and temporal movement of the prosthesis. However, there was no statistically significant difference between Group 2 and Group 3 in neither nasal and temporal movement of the socket nor nasal and temporal movement of the artificial eye.

Conclusion:
Group 1 showed the significantly better movement of both prosthesis and socket in adduction and abduction than Group 2 and 3. The likely explanation for this may be that preserving the scleral shell integrity allows more efficient transmission of muscle contraction to the socket and prosthesis.
Anterior Segmental Osteotomy Using Customized Spider-Plates Based on Computer-aided Surgery System
Authors: Cho Seoung-Won , Kim Ju-Won , Kim Jong-Cheol , Jeong Chun-Gi , Park In-Young , Yang Byoung-Eun 
Published: June 2019

Abstract
Anterior segmental osteotomy (ASO) is considered the treatment modality of choice in patients with the bimaxillary dentoalveolar protrusion. However, this meticulous surgical technique accompanies a number of possible disadvantages. The considerable time required before, during, and after the operation, limited movement of the segment, damage of the mental nerve, loss of tooth vitality, loss of a tooth or teeth, or indeed total loss of the anterior segments are those that affect the result of the surgery. Recently, the authors have devised a computer-aided surgical simulation programme and fabricated the customized osteotomy guides and the spider-shaped plates based on the programme. They were then applied to a 28-year-old patient with the complaint of a bimaxillary dentoalveolar protrusion. This approach helped to overcome several problems related to ASO reported earlier.
Electroencephalographic Reporting for Refractory Status Epilepticus
Authors: Sansevere Arnold J. , Arya Ravindra , Sánchez Fernández Iván , Gaillard William D. , Tasker Robert C. , Lai Yi-Chen , Anderson Anne E. , Tchapyjnikov Dmitry , Chapman Kevin E. , Brenton J. Nicholas , Carpenter Jessica L. , Gaínza-Lein Marina , Goldstein Joshua L. , Goodkin Howard P. , Jackson Michele C. , Kapur Kush , Mikati Mohamad A. , Peariso Katrina , Glauser Tracy A. , Topjian Alexis A. , Wainwright Mark , Wilfong Angus A. , Williams Korwyn L. , Loddenkemper Tobias , Abend Nicholas S. ,   the Pediatric Status Epilepticus Research Group (pSERG)
Published: June 2019

Purpose:
We aimed to determine whether clinical EEG reports obtained from children in the intensive care unit with refractory status epilepticus could provide data for comparative effectiveness research studies.

Methods:
We conducted a retrospective descriptive study to assess the documentation of key variables within clinical continuous EEG monitoring reports based on the American Clinical Neurophysiology Society's standardized EEG terminology for children with refractory status epilepticus from 10 academic centers. Two pediatric electroencephalographers reviewed the EEG reports. We compared reports generated using free text or templates.

Results:
We reviewed 191 EEG reports. Agreement between the electroencephalographers regarding whether a variable was described in the report ranged from fair to very good. The presence of electrographic seizures (ES) was documented in 46% (87/191) of reports, and these reports documented the time of first ES in 64% (56/87), ES duration in 72% (63/85), and ES frequency in 68% (59/87). Reactivity was documented in 16% (31/191) of reports, and it was more often documented in template than in free-text reports (40% vs. 14%, P = 0.006). Other variables were not differentially reported in template versus free-text reports.

Conclusions:
Many key EEG features are not documented consistently in clinical continuous EEG monitoring reports, including ES characteristics and reactivity assessment. Standardization may be needed for clinical EEG reports to provide informative data for large multicenter observational studies.
Double triage to identify poorly annotated genes in maize: The missing link in community curation
Authors: Tello-Ruiz Marcela K. , Marco Cristina F. , Hsu Fei-Man , Khangura Rajdeep S. , Qiao Pengfei , Sapkota Sirjan , Stitzer Michelle C. , Wasikowski Rachael , Wu Hao , Zhan Junpeng , Chougule Kapeel , Barone Lindsay C. , Ghiban Cornel , Muna Demitri , Olson Andrew C. , Wang Liya C. , Ware Doreen C. , Micklos David A. 
Published: June 2019

AbstractThe sophistication of gene prediction algorithms and the abundance of RNA-based evidence for the maize genome may suggest that manual curation of gene models is no longer necessary. However, quality metrics generated by the MAKER-P gene annotation pipeline identified 17,225 of 130,330 (13%) protein-coding transcripts in the B73 Reference Genome V4 gene set with models of low concordance to available biological evidence. Working with eight graduate students, we used the Apollo annotation editor to curate 86 transcript models flagged by quality metrics and a complimentary method using the Gramene gene tree visualizer. All of the triaged models had significant errors – including missing or extra exons, non-canonical splice sites, and incorrect UTRs. A correct transcript model existed for about 60% of genes (or transcripts) flagged by quality metrics; we attribute this to the convention of elevating the transcript with the longest coding sequence (CDS) to the canonical, or first, position. The remaining 40% of flagged genes resulted in novel annotations and represent a manual curation space of about 10% of the maize genome (~4,000 protein-coding genes). MAKER-P metrics have a specificity of 100%, and a sensitivity of 85%; the gene tree visualizer has a specificity of 100%. Together with the Apollo graphical editor, our double triage provides an infrastructure to support the community curation of eukaryotic genomes by scientists, students, and potentially even citizen scientists.
Transcriptional natural variation at FLM induces synergistic pleiotropy in Arabidopsis thaliana
Authors: Hanemian Mathieu , Vasseur François , Marchadier Elodie , Gilbault Elodie , Bresson Justine , Gy Isabelle , Violle Cyrille , Loudet Olivier 
Published: June 2019

ABSTRACTInvestigating the evolution of complex phenotypes and the underlying molecular bases of their variation is critical to understand how organisms adapt to the environment. We used leaf growth as a model trait as it is highly integrative of internal and external cues and relies on functions at different levels of the plant organization. Applying classical quantitative genetics on a recombinant inbred line population derived from a Can-0 x Col-0 cross, we identified the MADS-box transcription factor FLOWERING LOCUS M (FLM) as a player of the phenotypic variation for leaf growth and colour. Interestingly, we showed that allelic variation at FLM modulates plant growth strategy along the leaf economics spectrum, a trade-off between resource acquisition and resource conservation observable across thousands of plant species. We demonstrated that the functional differences at FLM relies on a single intronic substitution, disturbing transcript splicing and leading to a low expression of the active FLM transcript. Using phenotypic and climatic data across Arabidopsis natural populations, our work shows how noncoding genetic variation of a single gene may be adaptive through synergistic pleiotropy.
Co-expression of calcium channels and delayed rectifier potassium channels protects the heart from proarrhythmic events
Authors: Ballouz Sara , Mangala Melissa M , Perry Matthew D , Heitmann Stewart , Gillis Jesse A , Hill Adam P , Vandenberg Jamie I 
Published: June 2019

AbstractCardiac electrical activity is controlled by the carefully orchestrated activity of more than a dozen different ion conductances. Yet, there is considerable variability in cardiac ion channel expression levels both within and between subjects. In this study we tested the hypothesis that variations in ion channel expression between individuals are not random but rather there are modules of co-expressed genes and that these modules make electrical signaling in the heart more robust.Meta-analysis of 3653 public RNA-Seq datasets identified a strong correlation between expression of CACNA1C (L-type calcium current, ICaL) and KCNH2 (rapid delayed rectifier K+ current, IKr), which was verified in mRNA extracted from human induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CM). In silico modeling, validated with functional measurements in hiPSC-CM, indicates that the co-expression of CACNA1C and KCNH2 limits the variability in action potential duration and reduces susceptibility to early afterdepolarizations, a surrogate marker for pro-arrhythmia.Impact StatementCoexpressed levels of potassium and calcium ion channel genes in the heart encode more robust cardiac electrophysiology and provide insights into genetic basis of arrhythmic risk
Live cell single molecule tracking and localization microscopy of bioorthogonally labeled plasma membrane proteins
Authors: König Andres I. , Sorkin Raya , Alon Ariel , Nachmias Dikla , Dhara Kalyan , Brand Guy , Yifrach Ofer , Arbely Eyal , Roichman Yael , Elia Natalie 
Published: June 2019

ABSRACTTracking the localization and mobility of individual proteins in live cells is key for understanding how they mediate their function. Such information can be obtained from single molecule imaging techniques such as Single Particle Tracking (SPT) and Single Molecule Localization Microscopy (SMLM). Genetic code expansion (GCE) combined with bioorthogonal chemistry offers an elegant approach for direct labeling of proteins with fluorescent dyes, holding great potential for improving protein labeling in single molecule applications. Here we calibrated conditions for performing SPT and live-SMLM of bioorthogonally labeled plasma membrane proteins in live mammalian cells. Using SPT, the diffusion of bioorthogonally labeled EGF receptor and the prototypical Shaker voltage-activated potassium channel (Kv) was measured and characterized. Applying live-SMLM to bioorthogonally labeled Shaker Kv channels enabled visualizing the plasma membrane distribution of the channel over time with ~30 nm accuracy. Finally, by competitive labeling with two Fl-dyes, SPT and live-SMLM were performed in a single cell and both the density and dynamics of the EGF receptor were measured at single molecule resolution in subregions of the cell. We conclude that GCE and bioorthogonal chemistry is a highly suitable, flexible approach for protein labeling in quantitative single molecule applications that outperforms current protein live-cell labeling approaches.
Asian Zika virus isolate significantly changes the transcriptional profile and alternative RNA splicing events in a neuroblastoma cell line
Authors: Bonenfant Gaston , Meng Ryan , Shotwell Carl , Berglund J. Andrew , Pager Cara T. 
Published: June 2019

AbstractAlternative splicing of pre-mRNAs expands a single genetic blueprint to encode multiple functionally diverse protein isoforms. Viruses have previously been shown to interact with, depend on, and alter host splicing machinery. The consequences however incited by viral infection on the global alternative slicing (AS) landscape are under appreciated. Here we investigated the transcriptional and alternative splicing profile of neuronal cells infected with a contemporary Puerto Rican Zika virus (ZIKVPR) isolate, the prototypical Ugandan ZIKV (ZIKVMR) isolate and dengue virus 2 (DENV2). Our analyses revealed that ZIKVPRinduced significantly more differential changes in expressed genes compared to ZIKVMRor DENV2, despite all three viruses showing equivalent infectivity and viral RNA levels. Consistent with the transcriptional profile, ZIKVPRinduced a higher number of alternative splicing events compared to ZIKVMRor DENV2, and gene ontology analyses highlighted alternative splicing changes in genes associated with mRNA splicing. All three viruses modulated alternative splicing with ZIKVPRhaving the largest impact on splicing. ZIKV alteration of the transcriptomic landscape during infection caused changes in cellular RNA homeostasis, which might dysregulate neurodevelopment and function leading to neuropathologies such as microcephaly and Guillain-Barré syndrome associated with the ZIKV infection.
A frequency-domain machine learning method for dual-calibrated fMRI mapping of oxygen extraction fraction (OEF) and cerebral metabolic rate of oxygen consumption (CMRO2)
Authors: Germuska Michael , Chandler Hannah , Okell Thomas , Fasano Fabrizio , Tomassini Valentina , Murphy Kevin , Wise Richard 
Published: June 2019

AbstractMagnetic resonance imaging (MRI) offers the possibility to non-invasively map the brain’s metabolic oxygen consumption (CMRO2), which is essential for understanding and monitoring neural function in both health and disease. However, in depth study of oxygen metabolism with MRI has so far been hindered by the lack of robust methods. One MRI method of mapping CMRO2 is based on the simultaneous acquisition of cerebral blood flow (CBF) and blood oxygen level dependent (BOLD) weighted images during respiratory modulation of both oxygen and carbon dioxide. Although this dual-calibrated methodology has shown promise in the research setting, current analysis methods are unstable in the presence of noise and/or are computationally demanding. In this paper, we present a machine learning implementation for the multi-parametric assessment of dual-calibrated fMRI data. The proposed method aims to address the issues of stability, accuracy, and computational overhead, removing significant barriers to the investigation of oxygen metabolism with MRI. The method utilizes a time-frequency transformation of the acquired perfusion and BOLD-weighted data, from which appropriate feature vectors are selected for training of machine learning regressors. The implemented machine learning methods are chosen for their robustness to noise and their ability to map complex non-linear relationships (such as those that exist between BOLD signal weighting and blood oxygenation). An extremely randomized trees (ET) regressor is used to estimate resting blood flow and a multi-layer perceptron (MLP) is used to estimate CMRO2 and the oxygen extraction fraction (OEF). Synthetic data with additive noise are used to train the regressors, with data simulated to cover a wide range of physiologically plausible parameters. The performance of the implemented analysis method is compared to published methods both in simulation and with in-vivo data (n=30). The proposed method is demonstrated to significantly reduce computation time, error, and proportional bias in both CMRO2 and OEF estimates. The introduction of the proposed analysis pipeline has the potential to not only increase the detectability of metabolic difference between groups of subjects, but may also allow for single subject examinations within a clinical context.
Genetics of 38 blood and urine biomarkers in the UK Biobank
Authors: Sinnott-Armstrong Nasa , Tanigawa Yosuke , Amar David , Mars Nina J. , Aguirre Matthew , Venkataraman Guhan Ram , Wainberg Michael , Ollila Hanna M. , Pirruccello James P. , Qian Junyang , Shcherbina Anna ,   FinnGen, Rodriguez Fatima , Assimes Themistocles L. , Agarwala Vineeta , Tibshirani Robert , Hastie Trevor , Ripatti Samuli , Pritchard Jonathan K. , Daly Mark J. , Rivas Manuel A. 
Published: June 2019

AbstractClinical laboratory tests are a critical component of the continuum of care and provide a means for rapid diagnosis and monitoring of chronic disease. In this study, we systematically evaluated the genetic basis of 38 blood and urine laboratory tests measured in 358,072 participants in the UK Biobank and identified 1,857 independent loci associated with at least one laboratory test, including 488 large-effect protein truncating, missense, and copy-number variants. We tested these loci for enrichment in specific single cell types in kidney, liver, and pancreas relevant to disease aetiology. We then causally linked the biomarkers to medically relevant phenotypes through genetic correlation and Mendelian randomization. Finally, we developed polygenic risk scores (PRS) for each biomarker and built multi-PRS models using all 38 PRSs simultaneously. We found substantially improved prediction of incidence in FinnGen (n=135,500) with the multi-PRS relative to single-disease PRSs for renal failure, myocardial infarction, liver fat percentage, and alcoholic cirrhosis. Together, our results show the genetic basis of these biomarkers, which tissues contribute to the biomarker function, the causal influences of the biomarkers, and how we can use this to predict disease.
Understanding PCR Processes to Draw Meaningful Conclusions from Environmental DNA Studies
Authors: Kelly Ryan P. , Shelton Andrew Olaf , Gallego Ramón 
Published: June 2019

ABSTRACTAs environmental DNA (eDNA) studies have grown in popularity for use in ecological applications, it has become clear that their results differ in significant ways from those of traditional, non-PCR-based surveys. In general, eDNA studies that rely on amplicon sequencing may detect hundreds of species present in a sampled environment, but the resulting species composition can be idiosyncratic, reflecting species’ true biomass abundances poorly or not at all. Here, we use a set of simulations to develop a mechanistic understanding of the processes leading to the kinds of results common in mixed-template PCR-based (metabarcoding) studies. In particular, we focus on the effects of PCR cycle number and primer amplification efficiency on the results of diversity metrics in sequencing studies. We then show that proportional indices of amplicon reads capture trends in taxon biomass with high accuracy, particularly where amplification efficiency is high (median correlation up to 0.97). Our results explain much of the observed behavior of PCR-based studies, and lead to recommendations for best practices in the field.