bluuebunny/crossref_metadata_2025 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

This 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

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.
Swimming from coast to coast: a novel fixed-gear swimming gait in fish
Authors: Gellman E. D. , Tandler T. R. , Ellerby D. J.
Published: June 2019

Bluegill sunfish use intermittent propulsion during volitional swimming. The function of this propulsive mode during routine swimming has not been well quantified. At low speeds, propulsive cycle frequencies and amplitudes were constant, and average speed and power output were controlled by modulating coasting duration. This fixed-gear gait may accommodate muscle level constraints on power production. At higher speeds bluegills switched to a mixed power-modulation strategy, increasing speed and power through increased propulsive cycle frequency and reduced coasting time.
An objective, sensitive and ecologically valid neural measure of rapid human individual face recognition
Authors: Zimmermann Friederike G. S. , Yan Xiaoqian , Rossion Bruno
Published: June 2019

Humans may be the only species able to rapidly and automatically recognize a familiar face identity in a crowd of unfamiliar faces, an important social skill. Here, by combining electroencephalography (EEG) and fast periodic visual stimulation (FPVS), we introduce an ecologically valid, objective and sensitive neural measure of this human individual face recognition function. Natural images of various unfamiliar faces are presented at a fast rate of 6 Hz, allowing one fixation per face, with variable natural images of a highly familiar face identity, a celebrity, appearing every seven images (0.86 Hz). Following a few minutes of stimulation, a high signal-to-noise ratio neural response reflecting the generalized discrimination of the familiar face identity from unfamiliar faces is observed over the occipito-temporal cortex at 0.86 Hz and harmonics. When face images are presented upside-down, the individual familiar face recognition response is negligible, being reduced by a factor of 5 over occipito-temporal regions. Differences in the magnitude of the individual face recognition response across different familiar face identities suggest that factors such as exposure, within-person variability and distinctiveness mediate this response. Our findings of a biological marker for fast and automatic recognition of individual familiar faces with ecological stimuli open an avenue for understanding this function, its development and neural basis in neurotypical individual brains along with its pathology. This should also have implications for the use of facial recognition measures in forensic science.
Experimental study on diesel engine exhaust gas recirculation performance and optimum exhaust gas recirculation rate determination method
Authors: Zu Xiang-huan , Yang Chuan-lei , Wang He-Chun , Wang Yin-yan
Published: June 2019

In order to study the exhaust gas recirculation (EGR) performance of marine diesel engines, a venturi high-pressure EGR device was established to overcome the exhaust gas reflow problem based on a certain type of turbocharged diesel engine. The EGR performance test is accomplished and an optimal EGR decision-making optimization method based on grey correlation coefficient modified is proposed. The results show that the venturi tube EGR can basically meet the injection requirements of high-pressure exhaust gas and achieve good results. Through the venturi tube EGR, the NO

X

emissions reduce significantly with the maximum drop of 30.6%. The explosive pressure in cylinder reduces with the EGR rate increases and the cylinder pressure curve shows a single peak at low-speed conditions and double peaks at high-speed condition. However, the fuel consumption rate, NO

X

and smoke have been negatively affected. Due to small samples, the traditional evaluation method is difficult to determine the optimal EGR rate reasonably, while the proposed method can effectively solve this problem. It can weaken the shortcomings of subjective judgement and greatly improve the rationality of decision-making results.
Up for grabs: prey herding by penguins facilitates shallow foraging by volant seabirds
Authors: McInnes A. M. , Pistorius P. A.
Published: June 2019

Visual and olfactory signals are commonly used by seabirds to locate prey in the horizontal domain, but foraging success depends on prey depth and the seabird's ability to access it. Facilitation by diving seabirds has long been hypothesized as a mechanism to elevate deep prey to regions more accessible to volant seabirds, but this has never been demonstrated empirically. Footage from animal-borne video loggers deployed on African penguins was analysed to establish if volant seabird encounters involved active cuing by seabirds on penguins to obtain prey and, during mutual prey encounters, if interactions were driven by the vertical displacement of prey by penguins. Independent of prey biomass estimates, we found a strong inverse relationship between penguin group size, a proxy for visibility, and the time elapsed from the start of penguins' dive bouts to their first encounter with other seabirds. Most mutual prey encounters (7 of 10) involved schooling prey elevated from depths greater than 33 m by penguins and only pursued by other seabird species once prey was herded into shallow waters. This is likely to enhance foraging efficiency in volant seabird species. As such, penguins may be integral to important processes that influence the structure and integrity of marine communities.
Local pesticide use intensity conditions landscape effects on biological pest control
Authors: Ricci B. , Lavigne C. , Alignier A. , Aviron S. , Biju-Duval L. , Bouvier J. C. , Choisis J.-P. , Franck P. , Joannon A. , Ladet S. , Mezerette F. , Plantegenest M. , Savary G. , Thomas C. , Vialatte A. , Petit S.
Published: June 2019

Complex landscapes including semi-natural habitats are expected to favour natural enemies thereby enhancing natural pest biocontrol in crops. However, when considering a large number of situations, the response of natural biocontrol to landscape properties is globally inconsistent, a possible explanation being that local agricultural practices counteract landscape effects. In this study, along a crossed gradient of pesticide use intensity and landscape simplification, we analysed the interactive effects of landscape characteristics and local pesticide use intensity on natural biocontrol. During 3 years, using a set of sentinel prey (weed seeds, aphids and Lepidoptera eggs), biocontrol was estimated in 80 commercial fields located in four contrasted regions in France. For all types of prey excepted weed seeds, the predation rate was influenced by interactions between landscape characteristics and local pesticide use intensity. Proportion of meadow and length of interface between woods and crops had a positive effect on biocontrol of aphids where local pesticide use intensity was low but had a negative effect elsewhere. Moreover, the landscape proportion of suitable habitats for crop pests decreased the predation of sentinel prey, irrespectively of the local pesticide use intensity for weed seeds, but only in fields with low pesticide use for Lepidoptera eggs. These results show that high local pesticide use can counteract the positive expected effects of semi-natural habitats, but also that the necessary pesticide use reduction should be associated with semi-natural habitat enhancement to guarantee an effective natural biocontrol.
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

The 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

Investigating 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

Cardiac 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 Statement

Coexpressed 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

ABSRACT

Tracking 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

Alternative 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

Magnetic 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

Clinical 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

As 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.
Autophosphorylation of the CK1 kinase domain regulates enzyme activity and function
Authors: Cullati Sierra N. , Chen Jun-Song , Gould Kathleen L.
Published: June 2019

CK1 enzymes are conserved, acidophilic serine/threonine kinases with a variety of critical cellular functions; misregulation of CK1 contributes to cancer, neurodegenerative diseases, and sleep phase disorders. Despite this, little is known about how CK1 activity is controlled. Here, we describe a new mechanism of CK1 autoregulation that is conserved in CK1 enzymes from yeast to human – the autophosphorylation of a threonine in the mobile L-EF loop proximal to the active site. Phosphorylation at this site inhibits kinase activity, in contrast to well-characterized T-loop autophosphorylation in other kinase families. Consequently, yeast and human enzymes with phosphoablating mutations at this site are hyperactive. InS. pombe, hyperactive CK1 causes defects in cell growth and morphology at a high level but protection from heat shock at a low level, highlighting the necessity of regulated CK1 function. We propose that phosphorylation on the L-EF loop prevents substrate docking with the kinase domain by shielding the positively charged binding pocket and/or sterically hindering the active site. Due to the strong sequence conservation of this autophosphorylation site and the functional importance of the L-EF loop, which is unique to the CK1 family of kinases, this mechanism is likely to regulate the majority of CK1 enzymes in vivo.

Significance Statement

Kinases in the CK1 family are important signaling enzymes, and they function in multiple pathways within the same cell. Misregulation of CK1 activity contributes to human disease, including cancer, neurodegenerative disease, and sleep phase disorders, yet the mechanisms that control CK1 activity are not well understood. We have identified a conserved autophosphorylation site in the CK1 kinase domain that inhibits substrate phosphorylation. We hypothesize that by using kinase domain autophosphorylation in combination with other regulatory mechanisms, CK1 enzymes can coordinate the phosphorylation of their substrates in different pathways.
Aquila: diploid personal genome assembly and comprehensive variant detection based on linked reads
Authors: Zhou Xin , Zhang Lu , Weng Ziming , Dill David L. , Sidow Arend
Published: June 2019

Variant discovery in personal, whole genome sequence data is critical for uncovering the genetic contributions to health and disease. We introduce a new approach, Aquila, that uses linked-read data for generating a high quality diploid genome assembly, from which it then comprehensively detects and phases personal genetic variation. Assemblies cover >95% of the human reference genome, with over 98% in a diploid state. Thus, the assemblies support detection and accurate genotyping of the most prevalent types of human genetic variation, including single nucleotide polymorphisms (SNPs), small insertions and deletions (small indels), and structural variants (SVs), in all but the most difficult regions. All heterozygous variants are phased in blocks that can approach arm-level length. The final output of Aquila is a diploid and phased personal genome sequence, and a phased VCF file that also contains homozygous and a few unphased heterozygous variants. Aquila represents a cost-effective evolution of whole-genome reconstruction that can be applied to cohorts for variation discovery or association studies, or to single individuals with rare phenotypes that could be caused by SVs or compound heterozygosity.
Artificial intelligence method to design and fold alpha-helical structural proteins from the primary amino acid sequence
Authors: Qin Zhao , Wu Lingfei , Sun Hui , Huo Siyu , Ma Tengfei , Lim Eugene , Chen Pin-Yu , Marelli Benedetto , Buehler Markus J.
Published: June 2019

The development of rational techniques to discover new proteins for use in variety of applications ranging from agriculture to biotechnology remains an outstanding materials design problem. The key barrier is to design a sequence to fold into a predictable structure to achieve a certain material function. Focused on alpha-helical proteins, we report a Multi-scale Neighborhood-based Neural Network (MNNN) model to learn how a specific amino acid sequence folds into a protein structure. The algorithm predicts the protein structure without using a template or co-evolutional information at a maximum error of 2.1 Angstrom. We find that the prediction accuracy is higher than other models and the prediction consumes less than six orders of magnitude time than ab initio folding methods. We demonstrate that MNNN can predict the structure of an unknown protein that agrees with experiments, and our model hence shows a great advantage in the rational design of de novo proteins.
The transcription factor Shox2 shapes thalamocortical neuron firing and synaptic properties
Authors: Yu Diankun , Maroteaux Matthieu , Song Yingnan , Han Xiao , Febbo Isabella , Namboodri Claire , Sun Cheng , Ye Wenduo , Meyer Emily , Rowe Stuart , Chen YP , Schrader LA
Published: June 2019

Thalamocortical neurons (TCNs) transmit information about sensory stimuli from the thalamus to the cortex. In response to different physiological states and demands TCNs can fire in tonic and/or phasic burst modes. These firing properties of TCNs are supported by precisely timed inhibitory synaptic inputs from the thalamic reticular nucleus and intrinsic currents, including T-type Ca2+ and HCN currents. These intrinsic currents are mediated by Cav3.1 and HCN channel subunits, and alterations in expression or modulation of these channels can have dramatic implications on thalamus function. The factors that regulate these currents controlling the firing patterns important for integration of the sensory stimuli and the consequences resulting from the disruption of these firing patterns are not well understood. Shox2 is a transcription factor known to be important for pacemaker activity in the heart. We show here that Shox2 is also expressed in adult mouse thalamus. We hypothesized that genes regulated by Shox2’s transcriptional activity may be important for physiological properties of TCNs. In this study, we used RNA sequencing on control and Shox2 knockout mice to determine Shox2-affected genes and revealed a network of ion channel genes important for neuronal firing properties. Quantitative PCR confirmed that expression of Hcn2, 4 and Cav3.1 genes were affected by Shox2 KO. Western blotting showed expression of the proteins for these channels was decreased in the thalamus, and electrophysiological recordings showed that Shox2 KO impacted the firing and synaptic properties of TCNs. Finally, behavioral studies revealed that Shox2 expression in TCNs play a role in somatosensory function and object recognition memory. Overall, these results reveal Shox2 as a transcription factor important for TCN firing properties and thalamic function.
Tonic resting-state hubness supports high-frequency activity defined verbal-memory encoding network in epilepsy
Authors: Ganne Chaitanya , Hinds Walter , Kragel James , He Xiaosong , Sideman Noah , Ezzyat Youssef , Sperling Michael R , Sharan Ashwini , Tracy Joseph I
Published: June 2019

High-frequency gamma activity of verbal-memory encoding using invasive-electroencephalogram coupled has laid the foundation for numerous studies testing the integrity of memory in diseased populations. Yet, the functional connectivity characteristics of networks subserving these HFA-memory linkages remains uncertain. By integrating this electrophysiological biomarker of memory encoding from IEEG with resting-state BOLD fluctuations, we estimated the segregation and hubness of HFA-memory regions in drug-resistant epilepsy patients and matched healthy controls. HFA-memory regions express distinctly different hubness compared to neighboring regions in health and in epilepsy, and this hubness was more relevant than segregation in predicting verbal memory encoding. The HFA-memory network comprised regions from both the cognitive control and primary processing networks, validating that effective verbal-memory encoding requires multiple functions, and is not dominated by a central cognitive core. Our results demonstrate a tonic intrinsic set of functional connectivity, which provides the necessary conditions for effective, phasic, task-dependent memory encoding.

Highlights

High frequency memory activity in IEEG corresponds to specific BOLD changes in resting-state data.

HFA-memory regions had lower hubness relative to control brain nodes in both epilepsy patients and healthy controls.

HFA-memory network displayed hubness and participation (interaction) values distinct from other cognitive networks.

HFA-memory network shared regional membership and interacted with other cognitive networks for successful memory encoding.

HFA-memory network hubness predicted both concurrent task (phasic) and baseline (tonic) verbal-memory encoding success.
A Novel Antenna Protein Complex in the Life Cycle of Cyanobacterial Photosystem II
Authors: Weisz Daniel A. , Johnson Virginia M. , Niedzwiedzki Dariusz M. , Shinn Min Kyung , Liu Haijun , Klitzke Clécio F. , Gross Michael L. , Blankenship Robert E. , Lohman Timothy M. , Pakrasi Himadri B.
Published: June 2019

In oxygenic photosynthetic organisms, photosystem II (PSII) is a unique membrane protein complex that catalyzes light-driven oxidation of water. PSII undergoes frequent damage due to its demanding photochemistry. However, many facets of its repair and reassembly following photodamage remain unknown. We have discovered a novel PSII subcomplex that lacks five key PSII core reaction center polypeptides: D1, D2, PsbE, PsbF, and PsbI. This pigment-protein complex does contain the PSII core antenna proteins CP47 and CP43, as well as most of their associated low–molecular–mass subunits, and the assembly factor Psb27. Immunoblotting analysis, multiple mass spectrometry techniques, and ultrafast spectroscopic results supported the absence of a functional reaction center in this chlorophyll–protein complex. We therefore refer to it as the ‘no reaction center’ complex (NRC). Additionally, genetic deletion of PsbO on the PSII lumenal side resulted in an increased NRC population, indicative of a faulty PSII repair scheme at the cellular level. Analytical ultracentrifugation studies and clear native acrylamide gel analysis showed that the NRC complex is a stable pigment-protein complex and not a mixture of free CP47 and CP43 proteins. Our finding challenges the current model of the PSII repair cycle and implies an alternative PSII repair strategy. We propose that formation of this pigment-protein complex maximizes PSII repair economy by preserving an intact PSII core antenna shell in a single complex that is available for PSII reassembly, thus minimizing the risk of randomly diluting multiple recycling components in the thylakoid membrane following a photodamage event at the RC.

Significance statement

Photosystem II (PSII) converts sunlight into chemical energy, powering nearly all life on Earth. The efficiency of this process is maximized under various environmental conditions by a frequent repair and reassembly cycle that follows inevitable PSII damage even during normal oxygenic photosynthesis. We have isolated a novel pigment protein PSII subcomplex in which, surprisingly, the reaction center (RC) components of PSII are absent. Formation of this stable chlorophyll-protein complex suggests a protective mechanism whereby longer-lived PSII subunits are ‘unplugged’ from the damaged RC to prevent harmful, aberrant photochemistry during RC repair. This finding provides intriguing new insight into how PSII is assembled and rebuilt to optimize its performance to optimally catalyze one of the most challenging reactions in biology.
Identification of a master regulator of differentiation inToxoplasma
Authors: Waldman Benjamin S. , Schwarz Dominic , Wadsworth Marc H. , Saeij Jeroen P. , Shalek Alex K. , Lourido Sebastian
Published: June 2019

Toxoplasma gondiichronically infects a quarter of the world’s population, and its recrudescence can cause life-threatening disease in immunocompromised individuals and recurrent ocular lesions in the immunocompetent. Chronic stages are established by differentiation of rapidly replicating tachyzoites into slow-growing bradyzoites, which form intracellular cysts resistant to immune clearance and existing therapies. Despite its central role in infection, the molecular basis of chronic differentiation is not understood. Through Cas9-mediated genetic screening and single-cell transcriptional profiling, we identify and characterize a putative transcription factor (BFD1) as necessary and sufficient for differentiation. Translation of BFD1 appears to be stress regulated, and its constitutive expression elicits differentiation in the absence of stress. As a Myb-like factor, BFD1 provides a counterpoint to the ApiAP2 factors which dominate our current view of parasite gene regulation. Overall, BFD1 provides a genetic switch to study and controlToxoplasmadifferentiation, and will inform prevention and treatment of chronic infection.
Increase in ribosomal proteins activity: Translational reprogramming inVanilla planifoliaJacks., againstFusariuminfection
Authors: Solano de la Cruz Marco Tulio , Adame-García Jacel , Gregorio-Jorge Josefat , Jiménez-Jacinto Verónica , Vega-Alvarado Leticia , Iglesias-Andreu Lourdes , Escobar-Hernández Esteban Elías , Luna-Rodríguez Mauricio
Published: June 2019

Background

Upon exposure to unfavorable environmental conditions, plants need to respond quickly to maintain their homeostasis. For instance, physiological, biochemical and transcriptomical changes must occur during interactions with pathogens, this causing the triggering of pathogen- and plant-derived molecules. In the case ofVanilla planifoliaJacks., a worldwide economically important crop, it is susceptible toFusarium oxysporumf. sp.vanillae. This pathogen causes root and stem rot in vanilla plants that finally leads to plant death. To further investigate how vanilla plants respond at the transcriptional level upon infection withF.oxysporumf. sp.vanillae, we employed the RNA-Seq approach to analyze the dynamics of whole-transcriptome changes during two-time frames of the infection.

Results

Analysis of global gene expression profiles indicated that a major transcriptional change occurs at 2 dpi, in comparison to 10 dpi, whereas 3420 genes were found with a differential expression at 2 dpi, only 839 were identified at 10 dpi. The analysis of the transcriptional profile at 2 dpi suggests that vanilla plants prepare to counter the infection by gathering a pool of translational regulation-related transcripts.

Conclusions

We propose that the plant-pathogen interaction at early stages causes a transcriptional reprogramming coupled with a translational regulation. Altogether, this study provides the identification of molecular players that could help to fight the most damaging disease of vanilla, where ribosomal proteins and regulation of the translational mechanism are critical. These are insights into the defense responses ofV. planifoliaJacks., providing the basis for the understanding of the plant early response towards biotic stress.
Measuring the distribution of fitness effects in somatic evolution by combining clonal dynamics with dN/dS ratios
Authors: Williams Marc J , Zapata Luiz , Werner Benjamin , Barnes Chris , Sottoriva Andrea , Graham Trevor A
Published: June 2019

The distribution of fitness effects (DFE) defines how new mutations spread through an evolving population. The ratio of non-synonymous to synonymous mutations (dN/dS) has become a popular method to detect selection in somatic cells, however the link, in somatic evolution, between dN/dS values and fitness coefficients is missing. Here we present a quantitative model of somatic evolutionary dynamics that yields the selective coefficients from individual driver mutations from dN/dS estimates, and then measure the DFE for somatic mutant clones in ostensibly normal oesophagus and skin. We reveal a broad distribution of fitness effects, with the largest fitness increases found for TP53 and NOTCH1 mutants (proliferative bias 1-5%). Accurate measurement of the per-gene DFE in cancer evolution is precluded by the quality of currently available sequencing data. This study provides the theoretical link between dN/dS values and selective coefficients in somatic evolution, and reveals the DFE for mutations in human tissues.