bluuebunny/crossref_metadata_2025 huggingface dataset:
Determination of the Ratio of the Decantation Time and the Separation of Components in Lipoaspirate
Authors: Mecott Gabriel A. , Cueto-Ramos Rubén G. , González-Martínez Adrian , Perez-Trujillo José J. , Chacon-Martinez Hernán , de Oca Roberto Montes , Garcia-Perez Mauricio M.
Published: February 2020

Decantation of the lipoaspirate is one of the most common techniques used to prepare the fat graft. The aim of the study was to determine the ideal time of decantation that provides the best separation of the components without compromising the viability of the adipocytes.

Methods

Thirty milliliters of fat were obtained from 11 healthy adults and decanted at room temperature for 0, 30, and 60 minutes. After decantation, the infiltration liquid and the remnant fat were measured with a volumetric pipette. Once the solution was removed, the remnant fat was centrifuged at 3000 rpm for 5 minutes to separate any residual solution, to measure the amount of actual fat obtained at that time point. Viability was determined with trypan blue staining for all the samples.

Results

After decantation, 9.4 ± 0.79 mL of fat was obtained at time 0, whereas 7.7 ± 1.56 mL was obtained at 30 minutes and 6.9 ± 0.92 mL at 60 minutes. Actual fat volume was 6.6 ± 1.56 mL, 5.5 ± 1.39, and 5.26 ± 1.3 mL, respectively. Viability at time 0 was 73.33 ± 0.06%, 72.57 ± 0.1% at 30 minutes, and 59.3 ± 0.09% at 60 minutes (P = 0.004).

Results

The fat grafting, processed by decantation, will have the best performance within a period of 30 minutes after harvesting, where the best rate of viability and separation of components will be achieved.
Clinical Applications of Allograft Skin in Burn Care
Authors: Wang Chunyang , Zhang Feng , Lineaweaver William C.
Published: February 2020

Allograft skin has been widely used for wound management in burn centers. Functional as biologic dressing, it can not only provide ideal temporary wound coverage in extensive burns when autograft is not immediately available but also prepare the wound bed for definitive autografting. In this article, the up-to-date clinical application of allograft in burn care was reviewed, including coverage of extensive burn wounds, combined use with meshed autograft, template for delayed application of cultured epidermal autografts, and the use of human acellular dermal matrix. Although it has potential disadvantages of rejection and disease transmission, allograft skin remains a workhorse in treatment of severe burn wounds.
Incomplete Cleft Palate, Bifid Tongue, and Oral Hamartomas: A Rare Congenital Anomaly
Authors: Yin Shilu , Zhao Zhenmin
Published: February 2020

Congenital bifid tongue is a rare malformation, which is usually present in association with other oral findings such as cleft palate and tongue mass. The authors present a rare case of congenital bifid tongue together with cleft palate, labial-buccal frenulum deformity, absence of lingual frenulum, and 3 hamartomas in the oral cavity. The authors excised oral hamartomas and repaired the palate and tongue with satisfactory results.
Pediatric Mandibular Condylar Fractures With Concomitant Cervical Spine Injury: A Treatment Protocol for Prevention of Temporomandibular Joint Ankylosis
Authors: Marji Fady P. , Anstadt Erin , Davit Alexander , Goldstein Jesse A. , Losee Joseph E.
Published: February 2020

In pediatric patients with mandible fractures and concomitant cervical spine injury (CSI), treatment strategies may occasionally compete: condylar fractures require functional therapy with range of motion exercises of the temporomandibular joint (TMJ), while CSI requires neck immobilization. The authors report the case of a child presenting with bilateral condylar head fractures, a right parasymphyseal fracture, and concomitant CSI treated with cervical collar immobilization, who ultimately developed TMJ ankylosis. Here, the authors review mandibular condylar fracture management and suggest an approach for the pediatric patient presenting with condylar fractures and concomitant CSI requiring immobilization. To preserve range of motion at the TMJ, it is critical to prevent external restriction by prolonged cervical collar use. Instead, these patients benefit from a protocol utilizing conventional halo or noninvasive, pinless halo cervical spine stabilization. Without limitation of the TMJ, condylar fracture rehabilitation and healing may proceed unhindered.
Surgical Planning for Mandibular Distraction Osteogenesis Using Low-Cost Three-Dimensional–Printed Anatomic Models
Authors: Telich-Tarriba José E. , Chávez-Serna Enrique , Rangel-Rangel Edna , Gorostieta-Esperon Miguel Angel , Andrade Delgado Laura , Fuente del Campo Antonio
Published: February 2020

Mandibular distraction osteogenesis (MDO) is a fairly common procedure in specialized craniofacial surgery centers. The MDO is a minimally invasive technique that is able to generate new bone in patients with a severe hypoplastic ascending ramus, while also expanding the overlying soft tissues; therefore, it has become the treatment of choice for the surgical correction of mandibular hypoplasias. One of the most common postoperative complications involves misplacement of the distractor and/or corticotomy, which can result in the creation of an erroneous distraction vector. The introduction of 3-dimensional (3D) printing has revolutionized preoperative planning in several surgical fields; however, cost can hinder its application in developing nations, specially in public institutions. The aim of this work is present our experience using low-cost 3D-printed anatomic models for preoperative planning and surgical simulation in patients requiring MDO.
Effects of Rhinoplasty on Smile Esthetic and Gingival Appearance
Authors: Arli Cengiz , Bilgic Fundagul , Kaya Abdullah , Arpag Osman Fatih
Published: February 2020

Rhinoplasty alone or combined with septoplasty is one of the cornerstone management techniques in facial esthetic surgery. The aim of the current study was to evaluate the effects of rhinoplasty maneuvers on facial and smile esthetics. The study included a total of 27 adult patients. Measurements of gingival length (GL), right and left maxillary incisor-upper lip distance (MIULD), right and left inter-lip distance (ILD), and right and left gingival pocket depth (GPD) were performed and rounded to the nearest millimeter in full smile and at rest. All measurements were obtained at baseline and at the postoperative 1st and 6th months by the same clinician. As compared with the baseline values, significant decreases were determined in the left and right GLs in full smile, left and right MIULD, and left ILD at the postoperative 1st month and in the GL, left and right MIULD, and left and right ILD at the postoperative 6th month. In conclusion, rhinoplasty maneuvers can improve smile esthetics by changing the GL thereby increase patient satisfaction.
Prediction of Lower Eyelid Malpositioning After Surgical Correction of Orbital Fracture Using the Subciliary Approach Through the Canthal Area and Orbital Vector Analysis
Authors: Kim Choong Hyeon , Choi Woo Young , Son Kyung Min , Cheon Ji Seon
Published: February 2020

A subciliary incision has been widely used not only for blepharoplasty but also for facial fracture surgery. However, lower eyelid malpositioning is one of the most common complications after fracture surgery. A limited number of studies have been conducted on the relationships among evaluation of the canthal area, orbital vector analysis, and lower eyelid malpositioning following the subciliary approach for surgical repair of fractures. The primary goal of this study was to identify and analyze the possible risk factors, including incidence of lower eyelid malpositioning and orbital vector after surgical correction of the orbital fracture. A total of 241 cases of orbital fracture surgery was retrospectively reviewed. Data related to the patient and surgery were collected. Orbital vector and angle that reflects the vector, distance between soft tissue and bone in the lateral canthal area were measured for orbital vector analysis. The relationship between the prevalence of the malpositioning of the lower eyelid and each factor was statistically analyzed. The distance between the soft tissue and bone at the lateral canthal area was statistically significant (P = 0.031). The distance between the soft tissue and bone at lateral canthal area illustrates the lateral side or periorbital anatomical morphology. It could be inferred that patients with a negative orbital vector were relatively more vulnerable to scar formation or lower eyelid malpositioning caused by iatrogenic factors. Therefore, it could be analyzed as a risk factor to predict the malpositioning of the lower eyelid postoperatively.
Congenital Four Eyelid Ectropion Associated With Clefting Anomaly
Authors: Bagheri Abbas , Shahraki Koroush , Yazdani Shahin
Published: February 2020

An infant with congenital 4 eyelid ectropion associated with cleft lip and palate developed exposure keratopathy. He underwent skin grafting of the upper eyelids and lateral canthal reconstruction. Ectropion and signs of exposure keratopathy improved. Congenital eyelid ectropion is a rare disorder. Surgical repair can successfully correct the condition.
The Critical Role of Cannabinoid Receptor 2 in URB602-Induced Protective Effects Against Renal Ischemia-Reperfusion Injury in the Rat
Authors: Li Xing-Huan , Liu Yu-Qi , Gong De-Ying , Hai Ke-Rong , Ke Bo-Wen , Zuo Yun-Xia
Published: February 2020

Renal ischemia-reperfusion injury (IRI) is a major cause of acute kidney injury (AKI) and even induces remote organ damage. Accumulating proofs demonstrates that the endocannabinoid system may provide a promising access for treatment strategy of renal IRI associated AKI. In the current study, using the established renal IRI model of rat, we tested the hypothesis that pretreatment of URB602, 30 min before renal IRI, alleviates kidney injury and relevant distant organ damage via limiting oxidative stress and inflammation. Using Western blot analysis and LC–MS/MS, renal IRI showed to increase the levels of 2-arachidonoylglycerol (2-AG) in kidneys as well as COX-2, PGE2, TXA2, and decrease N-arachidonoylethanolamine (anandamide, AEA); the expressions of renal cannabinoid receptor 1 (CB1) and cannabinoid receptor 2 (CB2) were unchanged. The URB602 pretreatment in renal IRI, further enhanced renal 2-AG which is high affinity to both CB1 and CB2, and reduced renal COX-2 which is involved in the regulation of renal perfusion and inflammation. AM630 (CB2 antagonist) almost blocked all the antioxidant, anti-inflammatory and nephroprotective effects of URB602, whereas AM251 (CB1 antagonist) showed limited influence, and parecoxib (COX-2 inhibitor) slightly ameliorated renal function at the dose of 10 mg/kg. Taken together, our data indicate that URB602 acts as a reactive oxygen species scavenger and anti-inflammatory media in renal IRI mainly depending on the activation of CB2.
Virtual Simulation in Nursing Education: A Systematic Review Spanning 1996 to 2018
Authors: Foronda Cynthia L. , Fernandez-Burgos Margo , Nadeau Catherine , Kelley Courtney N. , Henry Myrthle N.
Published: February 2020

Summary Statement

As virtual simulation is burgeoning, faculty and administrators are asking for evidence of its effectiveness. The objective of this systematic review was to identify how virtual simulation impacts nursing student learning outcomes. Applying the Preferred Reporting Items for Systematic Reviews and Meta-analyses guidelines, 80 studies were reviewed. Results indicate that most research (n = 69, 86%) supported virtual simulation as an effective pedagogy to support learning outcomes while highlighting gaps and areas of bias. Adding search terms could have expanded the findings. The body of evidence supports virtual simulation as an effective pedagogy. Future studies should use more robust research designs, prioritize curricular integration of virtual simulation, and determine best practices in virtual simulation methodology.
Three-dimensional–Printed Computed Tomography–Based Bone Models for Spine Surgery Simulation
Authors: Stefan Philipp , Pfandler Michael , Lazarovici Marc , Weigl Matthias , Navab Nassir , Euler Ekkehard , Fürmetz Julian , Weidert Simon
Published: February 2020

Introduction

We present a novel 3-dimensional (3D) printing method for low-cost and widely available reproduction of computed tomography (CT)-based synthetic bone models for spine surgery simulation, optimized to reproduce realistic haptic properties. The method allows reproduction of either normal or abnormal patient anatomy. The models are fluoroscopy compatible and contain deformities and fractures present in the underlying CT data.

Methods

Spine models created from CT data were printed on a 3D printer using 2 different materials for cortical and cancellous bone. Printing parameters were iteratively optimized with surgical experts and 3 candidate spine models were evaluated in a study regarding haptic properties. X-ray images of a spine section printed with final printing parameters were evaluated by surgical experts regarding fluoroscopic properties.

Results

Eleven surgical experts performed a trocar insertion, a typical workflow step in spine surgery procedures, on the models. We observed agreement that cortical structures and strong agreement that cancellous structures of the final model are haptically comparable with human vertebral bone. Ten surgical experts evaluated x-ray images of the model. They expressed strong agreement on the similarity with x-ray images of the human spine and confirmed the presence of a fracture. Material cost of a typical spine model is around US $11.

Conclusions

Models created using the novel methodology realistically reproduce the haptic properties during a trocar placement into the vertebral body. The models are compatible with conventional x-ray imaging. Because the models correspond to real patient CT data, those can alternatively be used in simulation environments that simulate fluoroscopy or CT image guidance to produce highly realistic, radiation-free imaging output.
Simultaneous Liver Kidney Transplant in Elderly Patients With Chronic Kidney Disease: Is There an Appropriate Upper Age Cutoff?
Authors: Goldberg David S. , Vianna Rodrigo M. , Martin Eric Fleming , Martin Paul , Arosemena Benitez Leopoldo Ramon , O’Brien Christopher Blackburn , Bhamidimarri Kalyan R.
Published: February 2020

Background.

The aging of liver transplant (LT) recipients, the weighting of the model for end-stage liver disease score, and the increased prevalence of nonalcoholic steatohepatitis has led to an increased number of older LT recipients with pre-LT chronic kidney disease (CKD). There are limited data on the impact of increased recipient age on post-simultaneous liver-kidney (SLK) transplant outcomes among patients with CKD, leading some centers to employ subjective age cutoffs for potential SLK recipients.

Methods.

We evaluated United Network for Organ Sharing data of adult SLK recipients from February 27, 2002, to December 31, 2018, restricted to recipients with ≥90 days of waiting time and CKD (estimated glomerular filtration rate persistently <60 mL/min/1.73 m2 for ≥90 d using the modification of diet in renal disease-4 equation). We fit mixed-effects Cox regression models (center as random effect) to evaluate the association of recipient age and patient survival.

Results.

Among 3146 SLK recipients with CKD, nearly two-thirds were 50–64 years of age, while 465 (14.8%) and 93 (3.0%) were 65–69 years and ≥70 years, respectively. Compared with nondiabetic SLK recipients aged 50–59 years, SLK recipients ≥70 years of age without diabetes (hazard ratio, 1.97; 95% CI, 1.20-3.23; P = 0.007) and with diabetes (hazard ratio, 1.90; 95% CI, 1.16-3.09; P = 0.01) had higher mortality compared with the reference group. In absolute terms, SLK recipients ≥70 years of age had 25% lower patient survival at 5 years compared to recipients aged 40–49 years.

Conclusions.

Although careful selection is required of any SLK recipient, especially those with increased comorbidities, there are no objective data to justify a specific age cutoff <70 years among potential SLK recipients with CKD.
Association Between Neighborhood-level Socioeconomic Deprivation and the Medication Level Variability Index for Children Following Liver Transplantation
Authors: Wadhwani Sharad I. , Bucuvalas John C. , Brokamp Cole , Anand Ravinder , Gupta Ashutosh , Taylor Stuart , Shemesh Eyal , Beck Andrew F.
Published: February 2020

Background.

Neighborhood socioeconomic deprivation is associated with adverse health outcomes. We sought to determine if neighborhood socioeconomic deprivation was associated with adherence to immunosuppressive medications after liver transplantation.

Methods.

We conducted a secondary analysis of a multicenter, prospective cohort of children enrolled in the medication adherence in children who had a liver transplant study (enrollment 2010–2013). Participants (N = 271) received a liver transplant ≥1 year before enrollment and were subsequently treated with tacrolimus. The primary exposure, connected to geocoded participant home addresses, was a neighborhood socioeconomic deprivation index (range 0–1, higher indicates more deprivation). The primary outcome was the medication level variability index (MLVI), a surrogate measure of adherence to immunosuppression in pediatric liver transplant recipients. Higher MLVI indicates worse adherence behavior; values ≥2.5 are predictive of late allograft rejection.

Results.

There was a 5% increase in MLVI for each 0.1 increase in deprivation index (95% confidence interval, −1% to 11%; P = 0.08). Roughly 24% of participants from the most deprived quartile had an MLVI ≥2.5 compared with 12% in the remaining 3 quartiles (P = 0.018). Black children were more likely to have high MLVI even after adjusting for deprivation (adjusted odds ratio 4.0 95% confidence interval, 1.7-10.6).

Conclusions.

This is the first study to evaluate associations between neighborhood socioeconomic deprivation and an objective surrogate measure of medication adherence in children posttransplant. These findings suggest that neighborhood context may be an important consideration when assessing adherence. Differential rates of medication adherence may partly explain links between neighborhood factors and adverse health outcomes following pediatric liver transplantation.
Application of Hemifield Visual Electrophysiology to Diagnose Functional Vision Loss
Authors: Moss Heather E. , Jabbehdari Sayena
Published: February 2020

Neuro-ophthalmologists frequently see patients who are experiencing vision loss not accounted for by a neuro-ophthalmic disorder. In this article, we describe a case of binasal hemianopia in an otherwise healthy 65-year-old woman who was initially diagnosed with glaucoma but ultimately proved to have functional visual loss. This diagnosis was made by confirming by confirming normal visual pathway function using hemifield visual-evoked potential studies.
Combining formal education and citizen science: A case study on students’ perceptions of learning and interest in an urban rat project
Authors: Aivelo Tuomas , Huovelin Suvi
Published: February 2020

Citizen science is a valuable tool in environmental and formal education in creating scientific knowledge for the researchers and facilitating learning and fostering a positive relationship toward the environment and study species. We present a case study on the Helsinki Urban Rat Project in which students surveyed rat occurrence in their own near environments. According to our results, experientiality, involvement, meaningfulness, freedom to choose, ease of participation, and the rats themselves contributed to students’ increased interest in participation. Furthermore, students described diverse factual, conceptual, procedural, and metacognitive knowledge that they acquired during their participation. In general, students described negative attitudes toward rats, but they described fewer negative views on rats after participation. We reflect on the success of the citizen science project and implications of planning a future citizen science project and incorporating citizen science in formal education.
The Influence of bioRχiv onPLOS ONE’s Peer-Review and Acceptance Time
Authors: Tsunoda Hiroyuki , Sun Yuan , Nishizawa Masaki , Liu Xiaomin , Amano Kou
Published: February 2020

This study examines the relation between acceptance times in preprint publishing and journal publishing. Specifically, we investigated the association between a paper’s posting time to bioRχiv, a preprints server, and journal articles’ peer-review and acceptance time forPLOS ONE. So far, of the total papers published in 1,626 academic journals, the average publication rate of those posted in bioRχiv is 40.67%. Meanwhile,PLOS ONEwas the journal that published more papers. Analysis of peer-review and acceptance time of papers published in journals via preprints showed the time these papers are posted in relation to these intervals. The median of the peer-review and acceptance time of the journal submission date that was later than the date of first posting to bioRχiv was 110.00 days, and in the reverse case, it was 139.50 days. Posting to the preprint server before journal submission shows a better order than vice versa. This study provides us a good understanding of the peer-review process. It also gives us good insights into optimizing this process, which would then facilitate paper publication and knowledge dissemination.
Discovery of 20 novel ribosomal leaders in bacteria and archaea
Authors: Eckert Iris , Weinberg Zasha
Published: February 2020

Background

RNAs perform many functions in addition to supplying coding templates, such as binding proteins. RNA-protein interactions are important in multiple processes in all domains of life, and the discovery of additional protein-binding RNAs expands the scope for studying such interactions. To find such RNAs, we exploited a form of ribosomal regulation. Ribosome biosynthesis must be tightly regulated to ensure that concentrations of rRNAs and ribosomal proteins (r-proteins) match. One regulatory mechanism is a ribosomal leader (r-leader), which is a domain in the 5′ UTR of an mRNA whose genes encode r-proteins. When the concentration of one of these r-proteins is high, the protein binds the r-leader in its own mRNA, reducing gene expression and thus protein concentrations. To date, 35 types of r-leaders have been validated or predicted.

Results

By analyzing additional conserved RNA structures on a multi-genome scale, we identified 20 novel r-leader structures. Surprisingly, these included new r-leaders in the highly studied organismsEscherichia coliandBacillus subtilis. Our results reveal several cases where multiple unrelated RNA structures likely bind the same r-protein ligand, and uncover previously unknown r-protein ligands. Each r-leader consistently occurs upstream of r-protein genes, suggesting a regulatory function. That the predicted r-leaders function as RNAs is supported by evolutionary correlations in the nucleotide sequences that are characteristic of a conserved RNA secondary structure. The r-leader predictions are also consistent with the locations of experimentally determined transcription start sites.

Conclusions

This work increases the number of known or predicted r-leader structures by more than 50%, providing additional opportunities to study structural and evolutionary aspects of RNA-protein interactions. These results provide a starting point for detailed experimental studies.
Efficacy of therapeutic plasma exchange for the treatment of autoimmune hemolytic anemia: Protocol for a meta-analysis of randomized controlled trials
Authors: Deng Jiawen
Published: February 2020

Autoimmune hemolytic anemia (AIHA) is a rare blood disorder that results in hemolysis of red blood cells (RBCs) due to the presence of autoantibodies in the serum. Previous research has shown that the use of therapeutic plasma exchange therapy (TPE) may be effective at treating AIHA by removing autoimmune antibodies from the intravascular space. However, very little knowledge synthesis is available on the use of TPE in AIHA patients due to the rarity of the disease. We propose a meta-analysis that investigates whether the use of TPE, with or without concurrent treatment regimens, can decrease adverse events, increase remission rate and improve lab results including hemoglobin, RBC, reticulocyte counts, hematocrit and total bilirubin.
KDM6B-dependent chromatin remodelling underpins effective virus-specific CD8+T cell differentiation
Authors: Li Jasmine , Hardy Kristine , Olshansky Moshe , Barugahare Adele , Gearing Linden J. , Prier Julia E. , Sng Xavier Y.X. , Thai Nguyen Michelle Ly , Piovesan Dana , Russ Brendan , La Gruta Nicole L. , Hertzog Paul J. , Rao Sudha , Turner Stephen J.
Published: February 2020

Naive CD8+T cell activation results in an autonomous program of cellular proliferation and differentiation. However, the mechanisms that underpin this process are unclear. Here we profiled genome-wide changes in chromatin accessibility, gene transcription and the deposition of a key chromatin modification (H3K27me3) early after naive CD8+T cell activation. Rapid upregulation of the histone demethylase, KDM6B, prior to first cell division was required for initiating H3K27me3 removal at genes essential for subsequent T cell differentiation and proliferation. Inhibition of KDM6B-dependent H3K27me3 demethylation limited the magnitude of an effective primary virus-specific CD8+T cell response and the formation of memory CD8+T cell populations. Accordingly, we define the early spatio-temporal events underpinning early lineage-specific epigenetic reprogramming that is necessary for autonomous CD8+T cell proliferation and differentiation.
RASSF effectors couple diverse RAS subfamily GTPases to the Hippo pathway
Authors: Thillaivillalan Dhanaraman , Singh Swati , Killoran Ryan C. , Singh Anamika , Xu Xingjian , Shifman Julia , Smith Matthew J.
Published: February 2020

Activated RAS GTPases signal by directly binding effector proteins. Effectors have a folded RAS association (RA) domain that binds exclusively to GTP-loaded RAS, but the specificity of most RA domains for >150 RAS superfamily GTPases is unknown. Ten RAS-association domain family (RASSF) proteins comprise the largest group of effectors, proposed to couple RAS to the pro-apoptotic Hippo pathway. We show that RASSF1-6 complex with Hippo kinase, while RASSF7-10 are a separate family related to p53-regulatory ASPP effectors. Only RASSF5 directly binds activated HRAS and KRAS. Structural modelling reveals that expansion of RASSFs in vertebrates included amino acid substitutions that alter their GTPase binding specificity. We demonstrate that the tumour suppressor RASSF1A complexes with the GTPases GEM, REM1, REM2 and the enigmatic RASL12. Interplay between RASSFs and RAS GTPases can drastically restrict YAP1 nuclear localization. Thus, these simple scaffolds can link activation of diverse RAS proteins to Hippo or p53 regulation.
Protective anti-prion antibodies in human immunoglobulin repertoires
Authors: Senatore Assunta , Frontzek Karl , Emmenegger Marc , Chincisan Andra , Losa Marco , Reimann Regina , Horny Geraldine , Guo Jingjing , Fels Sylvie , Sorce Silvia , Zhu Caihong , George Nathalie , Ewert Stefan , Pietzonka Thomas , Hornemann Simone , Aguzzi Adriano
Published: February 2020

Prion immunotherapy may hold great potential, but antibodies against certain PrP epitopes can be neurotoxic. Here we identified >6000 PrP-binding antibodies in a synthetic human Fab phage display library, 49 of which we characterized in detail. Antibodies directed against the flexible tail of PrP conferred neuroprotection against infectious prions. We then mined published repertoires of circulating B cells from healthy humans and found antibodies similar to the protective phage-derived antibodies. When expressed recombinantly, these antibodies exhibited anti-PrP reactivity. Furthermore, we surveyed 48’718 samples from 37’894 hospital patients for the presence of anti-PrP IgGs, and found 21 high-titer individuals. The clinical files of these individuals did not reveal any enrichment of specific pathologies, suggesting that anti-PrP autoimmunity is innocuous. The existence of protective anti-prion antibodies in unbiased human immunological repertoires, combined with the reported lack of such antibodies in carriers of disease-associatedPRNPmutations, suggests a link to the low incidence of spontaneous prion diseases in human populations.
Short-term heritable variation overwhelms two hundred generations of mutational variance for metabolic traits inCaenorhabditis elegans
Authors: Baer Charles F. , Hahn Dan , Johnson Lindsay M , Smith Olivia J
Published: February 2020

Metabolic disorders have a large heritable component, and have increased over the past few generations. Genome-wide association studies of metabolic traits typically find a substantial unexplained fraction of total heritability, suggesting an important role of spontaneous mutation. An alternative explanation is that epigenetic effects contribute significantly to the heritable variation. Here we report a study designed to quantify the cumulative effects of spontaneous mutation on adenosine metabolism in the nematodeCaenorhabditis elegans, including both the activity and concentration of two metabolic enzymes and the standing pools of their associated metabolites. The only prior studies on the effects of mutation on metabolic enzyme activity, inDrosophila melanogaster, found that total enzyme activity presents a mutational target similar to that of morphological and life-history traits. However, those studies were not designed to account for short-term heritable effects. We find that the short-term heritable variance for most traits is of similar magnitude as the variance among MA lines. This result suggests that the potential heritable effects of epigenetic variation in metabolic disease warrant additional scrutiny.
Multitask learning for Transformers with application to large-scale single-cell transcriptomes
Authors: Pang Minxing , Tegnér Jesper
Published: February 2020

Abstract

Recent progress in machine learning provides competitive methods for bioinformatics in many traditional topics, such as transcriptomes sequence and single-cell analysis. However, discovering biomedical correlation of cells that are present across large-scale data sets remains challenging. Our attention-based neural network module with 300 million parameters is able to capture biological knowledge in a data-driven way. The module contains high-quality embedding, taxonomy analysis and similarity measurement. We tested the model on Mouse Brain Atlas, which consists of 160,000 cells and 25,000 genes. Our module obtained some interesting findings that have been verified by biologists and got better performance when benchmarked against autoencoder and principal components analysis.
GENVISAGE: Rapid Identification of Discriminative and Explainable Feature Pairs for Genomic Analysis
Authors: Huang Silu , Blatti Charles , Sinha Saurabh , Parameswaran Aditya
Published: February 2020

Motivation

A common but critical task in genomic data analysis is finding features thatseparateand thereby help explain differences between two classes of biological objects, e.g., genes that explain the differences between healthy and diseased patients. As lower-cost, high-throughput experimental methods greatly increase the number of samples that are assayed as objects for analysis, computational methods are needed to quickly provide insights into high-dimensional datasets with tens of thousands of objects and features.

Results

We develop an interactive exploration tool called Genvisagethat rapidly discovers the most discriminative feature pairs that best separate two classes in a dataset, and displays the corresponding visualizations. Since quickly finding top feature pairs is computationally challenging, especially when the numbers of objects and features are large, we propose a suite of optimizations to make Genvisagemore responsive and demonstrate that our optimizations lead to a400Xspeedup over competitive baselines for multiple biological data sets. With this speedup, Genvisageenables the exploration of more large-scale datasets and alternate hypotheses in an interactive and interpretable fashion. We apply Genvisageto uncover pairs of genes whose transcriptomic responses significantly discriminate treatments of several chemotherapy drugs.

Availability

Free webserver athttp://genvisage.knoweng.org:443/with source code athttps://github.com/KnowEnG/Genvisage
A micro-PRNT for the detection of Ross River virus antibodies in mosquito blood meals: a useful tool for inferring transmission pathways
Authors: Gyawali Narayan , Murphy Amanda , Hugo Leon E. , Devine Gregor J
Published: February 2020

Introduction Many arboviruses of public health significance are maintained in zoonotic cycles with complex transmission pathways. The presence of serum antibody against arboviruses in vertebrates provides evidence of their historical exposure but reveals nothing about the vector-reservoir relationship. Moreover, collecting blood or tissue samples from vertebrate hosts is ethically and logistically challenging. We developed a novel approach for screening the immune status of vertebrates against Ross River virus that allows us to implicate the vectors that form the transmission pathway for this commonly notified Australian arboviral disease. Methods A micro-plaque reduction neutralisation test (micro-PRNT) was developed and validated on koala ( Phascolarctos cinereus) sera against a standard PRNT. The ability of the micro-PRNT to detect RRV antibodies in mosquito blood meals was then tested using some convenient mosquito models. Laboratory-reared Aedes aegypti were fed, via a membrane, on sheep blood supplemented with RRV seropositive and seronegative human sera. Aedes notoscriptus were fed on RRV seropositive and seronegative human volunteers. Blood-fed mosquitoes were harvested at various time points after feeding and their blood meals analysed for the presence of RRV neutralizing antibodies using the micro-PRNT. Results There was significant agreement of the plaque neutralization resulting from the micro-PRNT and standard PRNT techniques (R 2 =0.65; P<0.0001) when applied to RRV antibody detection in koala sera. Sensitivity and specificity of the micro-PRNT assay were 88.2% and 96%, respectively, in comparison with the standard PRNT. Blood meals from mosquitoes fed on sheep blood supplemented with RRV antibodies neutralised RRV by ≥ 50% until 60 hr post feeding. Similarly, mosquito blood meals from RRV seropositive human volunteers neutralised the virus by ≥ 50% until 48 hr post-blood feeding. Conclusions The small volumes of blood present in mosquito abdomens can be used to identify RRV antibodies and therefore host exposure to arbovirus infection. In tandem with the accurate identification of the mosquito, and diagnostics for the host origin of the blood meal, this technique has tremendous potential for exploring RRV transmission pathways. It can clearly be adapted for similar studies on other mosquito borne zoonoses.
Impact of Cancer-Associated Mutations in Hsh155/SF3b1 HEAT Repeats 9-12 on pre-mRNA Splicing inSaccharomyces cerevisiae
Authors: Kaur Harpreet , Groubert Brent , Paulson Joshua C. , McMillan Sarah , Hoskins Aaron A.
Published: February 2020

Mutations in the splicing machinery have been implicated in a number of human diseases. Most notably, the U2 small nuclear ribonucleoprotein (snRNP) component SF3b1 has been found to be frequently mutated in blood cancers such as myelodysplastic syndromes (MDS). SF3b1 is a highly conserved HEAT repeat (HR)-containing protein and most of these blood cancer mutations cluster in a hot spot located in HR4-8. Recently, a second mutational hotspot has been identified in SF3b1 located in HR9-12 and is associated with acute myeloid leukemias, bladder urothelial carcinomas, and uterine corpus endometrial carcinomas. The consequences of these mutations on SF3b1 functions during splicing have not yet been tested. We incorporated the corresponding mutations into the yeast homolog of SF3b1 and tested their impact on splicing. We find that all of these HR9-12 mutations can support splicing in yeast, and this suggests that none of them are loss of function alleles in humans. The Hsh155V502Fmutation alters splicing of several pre-mRNA reporters containing weak branch sites as well as a genetic interaction with Prp2 and physical interactions with Prp5 and Prp3. The ability of a single allele of Hsh155 to perturb interactions with multiple factors functioning at different stages of the splicing reaction suggests that some SF3b1-mutant disease phenotypes may have a complex origin on the spliceosome.
RIG-I and PKR, but not stress granules, mediate the pro-inflammatory response to Yellow fever virus
Authors: Beauclair Guillaume , Streicher Felix , Bruni Daniela , Gracias Ségolène , Bourgeau Salomé , Sinigaglia Laura , Fujita Takashi , Meurs Eliane F. , Tangy Frédéric , Jouvenet Nolwenn
Published: February 2020

Yellow fever virus (YFV) is an RNA virus primarily targeting the liver. Severe YF cases are responsible for hemorrhagic fever, plausibly precipitated by excessive pro-inflammatory cytokine response. Pathogen recognition receptors (PRRs), such as the cytoplasmic RIG-I-like receptors (RLRs), and the viral RNA sensor PKR are known to initiate a pro-inflammatory response upon recognition of viral genomes. Here, we sought to reveal the main determinants responsible for the acute cytokine expression occurring in human hepatocytes following YFV infection. Using a RIG-I-defective human hepatoma cell line, we found that RIG-I largely contributes to cytokine secretion upon YFV infection. In infected RIG-I-proficient hepatoma cells, RIG-I was localized in stress granules. These granules are large aggregates of stalled translation preinitiation complexes known to concentrate RLRs and PKR, and are so far recognized as hubs orchestrating RNA virus sensing. Using PKR-deficient hepatoma cells, we found that PKR contributes to both stress granule formation and cytokine induction upon YFV infection. However, stress granules disruption did not affect the cytokine response to YFV infection, as assessed by siRNA-knockdown-mediated inhibition of stress granule assembly. Finally, no viral RNA was detected in stress granules using a fluorescencein situhybridization approach coupled with immunofluorescence. Our findings suggest that both RIG-I and PKR mediate pro-inflammatory cytokine induction in YFV-infected hepatocytes, in a stress granule-independent manner. Therefore, by showing the uncoupling of the early cytokine response from the stress granules formation, our model challenges the current view by which stress granules are required for the mounting of the acute antiviral response.

Importance

Yellow fever is a mosquito-borne acute hemorrhagic disease caused by yellow fever virus (YFV). The mechanisms responsible for its pathogenesis remain largely unknown, although increased inflammation has been linked to worsened outcome. YFV targets the liver, where it primarily infects hepatocytes. We found that two RNA-sensing proteins, RIG-I and PKR, participate in the induction of pro-inflammatory mediators in human hepatocytes infected with YFV. We show that YFV infection promotes the formation of cytoplasmic structures, termed stress granules, in a PKR-, but not RIG-I-dependent manner. Whilst stress granules were previously postulated to be essential platforms for immune activation, we found that they are not required for pro-inflammatory mediators’ production upon YFV infection. Collectively, our work uncovered molecular events triggered by the replication of YFV, which could prove instrumental in clarifying the pathogenesis of the disease, with possible repercussions on disease management.
Soil microbiota influences clubroot disease by modulating Plasmodiophora brassicae and Brassica napus transcriptomes
Authors: Daval Stéphanie , Gazengel Kévin , Belcour Arnaud , Linglin Juliette , Guillerm-Erckelboudt Anne-Yvonne , Sarniguet Alain , Manzanares-Dauleux Maria J , Lebreton Lionel , Mougel Christophe
Published: February 2020

The contribution of surrounding plant microbiota to disease development has led to the postulation of the ‘pathobiome’ concept, which represents the interaction between the pathogen, the host-plant, and the associated biotic microbial community, resulting or not in plant disease. The structure, composition and assembly of different plant-associated microbial communities (soil, rhizosphere, leaf, root) are more and more described, both in healthy and infected plants. A major goal is now to shift from descriptive to functional studies of the interaction, in order to gain a mechanistic understanding of how microbes act on plant growth and defense, and/or on pathogen development and pathogenicity. The aim herein is to understand how the soil microbial environment may influence the functions of a pathogen and its pathogenesis, as well as the molecular response of the plant to the infection, with a dual-RNAseq transcriptomics approach. We address this question using Brassica napus and Plasmodiophora brassicae, the pathogen responsible for clubroot. A time‐course experiment was conducted to study interactions between P. brassicae, two B. napus genotypes, and three soils harboring High (H), Medium (M) or Low (L) microbiota diversities and displaying different levels of richness and diversity. The soil microbial diversity levels had an impact on disease development (symptom levels and pathogen quantity). The P. brassicae and B. napus transcriptional patterns were modulated by these microbial diversities, and the modulations were dependent of the host genotype plant and the kinetic time. The functional analysis of gene expressions allowed the identification of pathogen and plant-host functions potentially involved in the change of plant disease level, such as pathogenicity-related genes (NUDIX effector) in P. brassicae and plant defense-related genes (glucosinolate metabolism) in B. napus.
The versatility of Ascorbate Peroxidase-aided mapping uncovers insights of the nuclear lamina interactions and function
Authors: Tran Joseph R. , Paulson Danielle I. , Moresco James J. , Adam Stephen A. , Yates John R. , Goldman Robert D. , Zheng Yixian
Published: February 2020

The nuclear lamina (NL) is a proteinaceous network found beneath the inner nuclear membrane. The NL is linked to a number of dynamic cellular activities including chromatin organization, transcription and RNA/protein trafficking through nuclear pores. Our understanding of the NL has been hindered in part by the general insolubility and low extractability of proteins from this region. This has spurred the development of proximity ligation methods that label proteins and/or DNA near the NL for systematic identification (Bar et al., 2018; Chen et al., 2018b; Guelen et al., 2008; Roux et al., 2012). To simplify labeling and improve temporal resolution, we fused APEX2 (Hung et al., 2014; Lam et al., 2015) to the nuclear lamina protein lamin-B1 to map proteins, RNA and DNA associated with the NL. We show that APEX2 labeling of the NL is robust and requires as little as 20 seconds. In addition to identifying the NL proteome, this method revealed NL-proximal RNA species that were largely spliced. These NL-proximal RNAs show a bias toward long 3’ UTRs, suggesting an RNA-regulatory role of the NL. This is further supported by the finding of a bias toward longer 3’ UTRs in genes deregulated in lamin-null cells. Interestingly, these RNAs share a sequence motif in their 3’ UTRs. Finally, we demonstrate that the APEX2 method can reliably map lamina-associated domains (LADs) at different stages of the cell cycle, revealing a variability of short LADs regions enriched for histone lysine 27 trimethylation (H3K27me3). Thus the APEX2 method report here is a useful addition to the molecular toolbox for the study of the NL and permits the identification of proteome, transcriptome, and genome elements associated with this nuclear substructure.
Direct Imaging of Liquid Domains in Membranes by Cryo Electron Tomography
Authors: Cornell Caitlin E. , Mileant Alexander , Thakkar Niket , Lee Kelly K. , Keller Sarah L.
Published: February 2020

Images of micron-scale domains in lipid bilayers have provided the gold standard of model-free evidence to understand the domains’ shapes, sizes, and distributions. Corresponding techniques to directly and quantitatively assess smaller (nanoscale and submicron) liquid domains have been lacking, leading to an inability to answer key questions. For example, researchers commonly seek to correlate activities of membrane proteins with attributes of the domains in which they reside; doing so hinges on identification and characterization of membrane domains. Although some features of membrane domains can be probed by indirect methods, these methods are often constrained by the limitation that data must be analyzed in the context of models that require multiple assumptions or parameters. Here, we address this challenge by developing and testing two new methods of identifying submicron domains in biomimetic membranes. Both methods leverage cryo-electron tomograms of ternary membranes under native solution conditions. The first method is optimized for probe-free applications: domains are directly distinguished from the surrounding membrane by their thickness. This technique measures area fractions of domains with quantitative accuracy, in excellent agreement with known phase diagrams. The second method is optimized for applications in which a single label is deployed for imaging membranes by both high-resolution cryo-electron tomography and diffraction-limited optical microscopy. For this method, we test a panel of probes, find that a trimeric mCherry label performs best, and specify criteria for developing future high-performance, dual-use probes. These developments have led to the first direct and quantitative imaging of submicron membrane domains under native conditions.

SIGNIFICANCE STATEMENT

Fluorescence micrographs that capture the sizes, shapes, and distributions of liquid domains in model membranes have provided high standards of evidence to prove (and disprove) theories of how micron-scale domains form and grow. Corresponding theories about smaller domains have remained untested, partly because experimental methods of identifying submicron domains in vesicles under native solvent conditions have not been available. Here we introduce two such methods. Both leverage cryo-electron tomography to observe membrane features far smaller than the diffraction limit of light. The first method is probe-free and identifies differences in thicknesses between liquid domains and their surrounding membranes. The second method identifies membrane regions labeled by an electron-dense, fluorescent protein, which enables direct comparison of fluorescence micrographs with cryo-electron tomograms.