bluuebunny/crossref_metadata_2025 huggingface dataset:
PROGRESSION OF ABCA4-RELATED RETINOPATHY
Authors: Müller Philipp L. , Pfau Maximilian , Treis Tim , Pascual-Camps Isabel , Birtel Johannes , Lindner Moritz , Herrmann Philipp , Holz Frank G.
Published: January 2020

Purpose:

To investigate the prognostic value of demographic, functional, genetic, and imaging parameters on retinal pigment epithelium atrophy progression secondary to ABCA4-related retinopathy.

Methods:

Patients with retinal pigment epithelium atrophy secondary to ABCA4-related retinopathy were examined longitudinally with fundus autofluorescence imaging. Lesion area, perimeter, circularity, caliper diameters, and focality of areas with definitely decreased autofluorescence were determined. A model was used to predict the lesion enlargement rate based on baseline variables. Sample size calculations were performed to model the power in a simulated interventional study.

Results:

Sixty-eight eyes of 37 patients (age range, 14–78 years) with a follow-up time of 10 to 100 months were included. The mean annual progression of retinal pigment epithelium atrophy was 0.89 mm2. The number of atrophic areas, the retina-wide functional impairment, and the age-of-onset category constituted significant predictors for future retinal pigment epithelium atrophy growth, explaining 25.7% of the variability. By extension of a simulated study length and/or specific patient preselection based on these baseline characteristics, the required sample size could significantly be reduced.

Conclusion:

Trial design based on specific shape-descriptive factors and patients' baseline characteristics and the adaption of the trial duration may provide potential benefits in required cohort size and absolute number of visits.
The dichotomous role of epiregulin in pain
Authors: Verma Vivek , Khoury Samar , Parisien Marc , Cho Chulmin , Maixner William , Martin Loren J. , Diatchenko Luda
Published: January 2020

It has recently been shown that epidermal growth factor receptor (EGFR) contributes to the pathogenesis of pain. We scanned genetic markers within genes coding for receptors of the EGFR family (EGFR, ERBB2, ERBB3, and ERBB4) and their ligands (AREG, BTC, EGF, EPGN, EREG, HBEGF, MUC4, NRG1, NRG2, NRG3, NRG4, and TGFA) for association with self-reported pain intensity in patients with chronic facial pain who participated in the Orofacial Pain: Prospective Evaluation and Risk Assessment (OPPERA) cohort. We found that only epiregulin(EREG)was associated with pain. The strongest effect was observed for a minor allele at rs6836436 inEREG, which was associated with lower chronic pain intensity. However, the same allele was associated with higher facial pain intensity among cases with recent onset of facial pain. Similar trends were observed in an independent cohort of UK Biobank (UKB) where the minor allele at rs6836436 was associated with a higher number of acute pain sites but a lower number of chronic pain sites. Expression quantitative trait loci analyses established rs6836436 as a loss-of-function variant of EREG. Finally, we investigated the functional role of EREG using mouse models of chronic and acute pain. Injecting mice with an EREG monoclonal antibody reversed established mechanosensitivity in the complete Freund's adjuvant and spared nerve injury models of chronic pain. However, the EREG monoclonal antibody prolonged allodynia when administered during the development of complete Freund's adjuvant–induced mechanosensitivity and enhanced pain behavior in the capsaicin model of acute pain.
Cochlear Implant Mapping Through Telemedicine—A Feasibility Study
Authors: Luryi Alexander L. , Tower Jacob I. , Preston Jessica , Burkland Adam , Trueheart Cyndi E. , Hildrew Douglas M.
Published: January 2020

Objective:

Access to postoperative aural rehabilitation limits cochlear implant (CI) penetration to the candidate population. The purpose of this study was to evaluate the effectiveness of remote CI programming and aural rehabilitation via telehealth.

Study Design and Setting:

Retrospective study of one cochlear implant center.

Patients and Intervention:

Patients undergoing cochlear implantation from 2015 to 2018 undergoing remote programming as part of routine audiologic follow up.

Main Outcome Measures:

AzBio scores, impedances, comfort and threshold levels, and responses to the International Outcome Inventory for Hearing Aids questionnaire modified for CIs (IOI-CI).

Results:

A total of 22 CIs in 20 patients were included during the study period. Threshold, comfort, and impedance levels were readily obtained via telehealth and were not significantly different between telehealth and live sessions. AzBio scores and warble tone pure tone averages were also similar and acceptable in both session modalities. Based on IOI-CI scores, patients were very satisfied with their hearing outcomes.

Conclusions:

Using telemedicine, reliable measurements were readily obtained and hearing outcomes after remote programming were comparable to those expected after in-person programming sessions. Patients were overall satisfied with their remote programming sessions. Telehealth is a cost-effective and safe way to deliver post-CI audiologic care, particularly to patients with limited mobility or those in remote locations.
Deconstructing the Reconstruction: Evaluation of Process and Efficiency in Deep Inferior Epigastric Perforator Flaps
Authors: Haddock Nicholas T. , Teotia Sumeet S.
Published: January 2020

Background:

With advances in technology and technique, the goal of microvascular breast reconstruction has transitioned from flap success to minimizing complications and maximizing aesthetic outcome and efficiency. In an effort to evaluate efficiency, the authors implemented a rigorous process analysis in their practice to evaluate deep inferior epigastric perforator (DIEP) flap breast reconstruction.

Methods:

A prospective implementation of process analysis was instituted on 147 DIEP flaps. The eight critical maneuvers for a DIEP flap are (1) skin to perforator identification, (2) perforator decision making, (3) perforator dissection, (4) pedicle dissection, (5) flap harvest, (6) preparation for microsurgery, (7) venous anastomosis, and (8) arterial anastomosis. Surgeons with variable experiences (faculty, faculty with senior resident/fellow, and supervised chief resident) used these eight steps to perform DIEP flap reconstruction. The outcomes and time of each maneuver were tracked.

Results:

The total flap harvest time among the three groups was 54.8 minutes for faculty surgeons, 98.3 minutes for senior resident/fellow working with faculty, and 178.8 minutes for supervised chief resident (p < 0.001). The largest difference was seen in perforator dissection. Increasing the number of perforators resulted in longer flap harvest times. Perforator location did not have an impact on times, but harvesting multiple rows took longer for less experienced surgeons. Body mass index and flap weight did not have an impact on time.

Conclusions:

The authors share their experience using process analysis for DIEP flap reconstruction. They defined eight critical maneuvers to maximize efficiency and safety. By communicating efficient processes and integrating them into the workflow of a given operation, surgeons can continue to improve throughout the arc of their careers.
Brachioplasty Refinements
Authors: Rohrich Rod J. , Mohan Raja , Durand Paul D.
Published: January 2020

With a growing massive weight loss population, upper arm contouring continues to rise in popularity. Refinements in technique, such as modification of skin excision patterns and the adjunct use of liposuction, have allowed for safe and reproducible results. This article helps to understand the evolution of upper arm contouring and provides an update on the limited-incision medial brachioplasty. Details of preoperative markings and operative technique are clearly illustrated in the video included.
Ultrafast Brain Magnetic Resonance Imaging in Acute Neurological Emergencies
Authors: Kazmierczak Philipp M. , Dührsen Max , Forbrig Robert , Patzig Maximilian , Klein Matthias , Pomschar Andreas , Kunz Wolfgang G. , Puhr-Westerheide Daniel , Ricke Jens , Solyanik Olga , Cyran Clemens C.
Published: January 2020

Objectives

The aim of this study was to investigate diagnostic accuracy and impact on patient management of an ultrafast (4:33 minutes/5 sequences) brain magnetic resonance imaging (MRI) protocol for the detection of intracranial pathologies in acute neurological emergencies.

Materials and Methods

Four hundred forty-nine consecutive emergency patients with acute nontraumatic neurological symptoms were evaluated for this institutional review board–approved prospective single-center trial. Sixty patients (30 female, 30 male; mean age, 61 years) with negative head CT were included and underwent emergency brain MRI at 3 T subsequent to CT. MRI included the ultrafast protocol (ultrafast-MRI; sag T1 GRE, ax T2 TSE, ax T2 TSE Flair, ax T2* EPI-GRE, ax DWI SS-EPI; TA, 5 minutes) and an equivalent standard-length protocol (TA, 15 minutes) as reference standard. Two blinded board-certified neuroradiologists independently analyzed the MRI with regard to image quality (1, nondiagnostic; 2, substantial artifacts; 3, satisfactory; 4, minor artifacts; 5, no artifacts) and intracranial pathologies. Sensitivity and specificity for the detection of intracranial pathologies were calculated accordingly.

Results

Ninety-three additional intracranial lesions (acute ischemia, n = 21; intracranial hemorrhage/microbleeds, n = 27; edema, n = 2; white matter lesion, n = 38; chronic infarction, n = 3; others, n = 2) were detected by ultrafast-MRI, whereas 101 additional intracranial lesions were detected by the standard-length protocol (acute ischemia, n = 24; intracranial hemorrhage/microbleeds, n = 32; edema, n = 2; white matter lesion, n = 38; chronic infarction, n = 3; others, n = 2). Image quality was equivalent to the standard-length protocol. Ultrafast-MRI demonstrated high diagnostic accuracy (sensitivity, 0.939 [0.881–0.972]; specificity, 1.000 [0.895–1.000]) for the detection of intracranial pathologies. MRI led to a change in patient management in 10% compared with the initial CT.

Conclusions

Ultrafast-MRI enables time-optimized diagnostic workup in acute neurological emergencies at high sensitivity and specificity compared with a standard-length protocol, with direct impact on patient management. Ultrafast MRI protocols are a powerful tool in the emergency setting and may be implemented on various scanner types based on the optimization of individual acquisition parameters.
Is Rural Plastic Surgery Feasible and Important?
Authors: Meaike Jesse D. , Cantwell Sean , Mills Andrew , Singh Kuldeep , Moran Steven L.
Published: January 2020

Background

There is little written about the scope of rural plastic surgery within the United States. Approximately 25 million people do not have immediate access to a plastic surgeon. Most areas are designated as rural, and this lack of specialty care can result in suboptimal care. Physicians are more likely to move to a rural area if they have prior life experience with rural areas, but exposure to rural plastic surgery in residency training is scarce. We attempted to examine the practice characteristics of rural plastic surgeons within the United States to (a) to better define the average rural plastic surgery practice and (b) to highlight the broad scope of practice of the rural plastic surgeon to educate both hospital administrators and our physician colleagues of the impact and benefit a plastic surgeon can have on a health system.

Methods

A survey was e-mailed to surgeons identified as rural plastic surgeons who practiced in communities with fewer than 50,000 people not located in a metropolitan area. Thirty-four surgeons were identified and 12 responded to the survey.

Results

Respondents on average were 56 years old and had practiced for 14.3 years. At the time of the survey, 33% practiced in a hospital-employed group practice, and 33% operated in a hospital that is part of a health system. Seventy-five percent did not complete fellowship training, but 67% believed that fellowship training would be beneficial to someone interested in rural plastic surgery. Seventy-five percent recommended hand surgery as the most beneficial fellowship. Eighty-three percent had prior experiences with rural surgery before starting their practice. Average case volume ranged from 150 to more than 1000 cases per year and spanned the spectrum of plastic surgery. Potential barriers to practicing rural plastic surgery included call responsibility and facility limitations.

Conclusions

A career in rural plastic surgery offers great variety encompassing the spectrum of plastic surgery. Most agreed that hand fellowship would be the most beneficial fellowship. Most had prior experience with rural surgery before seeking a career in rural plastic surgery, highlighting the importance of increasing awareness of these opportunities.
Risk of Complications in Primary Versus Revision-Type Cranioplasty
Authors: Shay Tamir , Belzberg Micah , Asemota Anthony O. , Mitchell Kerry-Ann , Wolff Amir , Santiago Gabriel F. , Huang Judy , Brem Henry , Gordon Chad R.
Published: January 2020

Introduction:

Cranioplasty (CP) is a multifaceted procedure in a heterogenous patient population, with a high risk for complication. However, no previous large-scale studies have compared outcomes in primary (ie, first attempt) CP versus revision CP (ie, following previous attempts). The authors, therefore, analyzed long-term outcomes of 506 consecutive primary and revision CPs, performed by a single surgeon.

Methods:

All CPs performed between 2012 and 2019 were analyzed under IRB protocol approval. Surgeries were categorized as either primary (no previous CP; n = 279) or revision CP (at least one previous CP; n = 227). Complications were defined as either major or minor. Subgroup analyses investigated whether or not CP complication risk directly correlated with the number of previous neuro-cranial surgeries and/or CP attempts.

Results:

The primary CP group experienced a major complication rate of 9% (26/279). In comparison, the revision CP group demonstrated a major complication rate of 32% (73/227). For the revision CP group, the rate of major complications rose with each additional surgery, from 4% (1 prior surgery) to 17% (2 prior surgeries) to 39% (3–4 prior surgeries) to 47% (≥5 prior surgeries).

Conclusion:

In a review of 506 consecutive cases, patients undergoing revision CP had a 3-fold increase in incidence of major complications, as compared to those undergoing primary CP. These results provide critical insight into overall CP risk stratification and may guide preoperative risk-benefit discussions. Furthermore, these findings may support a center-of-excellence care model, particularly for those patients with a history of previous neuro-cranial surgeries and/or CP attempts.
Anandamide and sucralose change ΔFosB expression in the reward system
Authors: Salaya-Velazquez Nadi F. , López-Muciño Luis A. , Mejía-Chávez Sara , Sánchez-Aparicio Pedro , Domínguez-Guadarrama Andrés A. , Venebra-Muñoz Arturo
Published: January 2020

Food reward has been studied with highly palatable stimuli that come from natural additives such as sucrose. The most common food additive is sucralose, a noncaloric sweetener present in many food products of daily intake. The role of anandamide [N-arachidonylethanolamide (AEA)], an endogenous cannabinoid, has been widely studied in food behavior. Studies have shown that cannabinoids, such as AEA, 2-Arachidonilglycerol, and Tetrahydrocannabinol, can provoke hyperphagia, because they enhance the preference and intake of sweet and high-fat food. Taste perception is mediated by receptors taste type 1 receptor 3 (T1R3); therefore, there could be a synergistic effect between receptors CB1 and T1R3. This could explain why cannabinoids could change sweet taste perception and therefore the activity of neural nuclei involved in taste and reward. In this study, we evaluated the activity of dopaminergic nuclei implicated in food reward after the chronic administration of AEA (0.5 mg/kg bw) and sucralose intake (0.02%). We analyzed the expression of ΔFosB by immunohistochemistry. Our results show that the chronic administration of AEA and sucralose intake induces an overexpression of ΔFosB in the infralimbic cortex (Cx), nucleus accumbens (NAc) core, shell, and central nucleus of amygdala (Amy). These results suggest that the possible interaction between receptors CB1 and T1R3 has consequences not only in taste perception but also that AEA intervenes in the activity of dopaminergic nuclei such as the NAc, and that the chronic administration AEA and sucralose intake induce long-term changes in the reward system.
Low light levels increase avoidance behaviour of diurnal fish species: Implications for road culverts
Authors: Keep John K. , Watson Jabin R. , Cramp Rebecca L. , Jones Matthew J. , Gordos Matthew A. , Ward Patrick , Franklin Craig E.
Published: January 2020

Inadequately designed culverts are known to pose hydraulic barriers to fish passage, but they may also be behavioural barriers if they adversely affect light levels within them. To test this, we performed a choice experiment and quantified the amount of time individuals of four Australian fish species spent in darkened and illuminated areas of an experimental swimming fume. Behavioural responses were reflective of the species’ diel activity patterns; diurnal species preferred illuminated regions, while nocturnal species preferred the darkened region. We then determined a threshold light level of only ~100-200 lux (c.f. midday sunlight ~100,000 lux) was required to overcome the behavioural barrier in ~ 70% of the diurnal fish tested. Placing these threshold values into field context, 100% of culverts sampled recorded inadequate light levels. Attention is required to better understand the impacts of low light levels in culverts on fish passage and to prioritise restoration.
Increased antibiotic susceptibility inNeisseria gonorrhoeaethrough adaptation to the cervical environment
Authors: Ma Kevin C , Mortimer Tatum D , Hicks Allison L , Wheeler Nicole E , Sánchez-Busó Leonor , Golparian Daniel , Taiaroa George , Rubin Daniel HF , Wang Yi , Williamson Deborah A , Unemo Magnus , Harris Simon R , Grad Yonatan H
Published: January 2020

Neisseria gonorrhoeaeis an urgent public health threat due to rapidly increasing incidence and antibiotic resistance. In contrast with the trend of increasing resistance, clinical isolates that have reverted to susceptibility regularly appear, prompting questions about which pressures compete with antibiotics to shape gonococcal evolution. Here, we used genome-wide association on the largest collection ofN. gonorrhoeaeisolates to date (n=4852) to identify loss-of-function (LOF) mutations in the efflux pumpmtrCDEoperon as a mechanism of increased antibiotic susceptibility and demonstrate that these mutations are overrepresented in cervical isolates relative to urethral isolates (odds ratio (OR) = 3.74, 95% CI [1.98-6.70]). In support of a model in which pump expression incurs a fitness cost in this niche, cervical isolates were also enriched relative to urethral isolates in LOF mutations in themtrCDEactivatormtrA(OR = 8.60, 95% CI [4.96-14.57]) and infarA,a subunit of the FarAB efflux pump (OR = 6.25, 95% CI [3.90-9.83]). In total, approximately 2 in 5 cervical isolates (42.6%) contained a LOF mutation in either the efflux pump componentsmtrCorfarAor the activatormtrA.Our findings extend beyondN. gonorrhoeaeto otherNeisseria:mtrCLOF mutations are rare (<1%) in the primarily nasopharyngeal-colonizingN. meningitidisin a collection of 14,798 genomes but enriched in a heterosexual urethritis-associated lineage (8.6%, p = 9.90×10−5), indicating that efflux pump downregulation contributes broadly to the adaptation of pathogenicNeisseriato the female urogenital tract. Overall, our findings highlight the impact of integrating microbial population genomics with host metadata and demonstrate how host environmental pressures can lead to increased antibiotic susceptibility.
Silencing ofTaCKX1mediates expression of otherTaCKXgenes to increase grain yield in wheat
Authors: Jabłoński Bartosz , Ogonowska Hanna , Szala Karolina , Bajguz Andrzej , Orczyk Wacław , Nadolska-Orczyk Anna
Published: January 2020

TaCKXfamily genes influence development of wheat plants by specific regulation of cytokinin content in different organs. However, their detailed role is not known. TheTaCKX1, highly and specifically expressed in developing spikes and in seedling roots, was silenced by RNAi-mediated gene silencing viaAgrobacteriumand the effect of silencing was investigated in 7 DAP spikes of T1and T2generations. Various levels ofTaCKX1silencing in both generations influence different models of co-expression with otherTaCKXgenes and parameters of yield-related traits. Only a high level of silencing in T2resulted in strong down-regulation ofTaCKX11 (3), up-regulation ofTaCKX2.1,2.2,5and9(10), and a high yielding phenotype. This phenotype is characterised by higher spike number, grain number and grain yield, as well as slightly higher mass of seedling roots, but lower thousand grain weight (TGW) and slightly lower spike length. Content of most of cytokinin forms in 7 DAP spikes of silenced T2lines increased from 40 to 76% compared to the non-silenced control. The CKs cross talk with other phytohormones.

Each of the tested yield-related traits is regulated by various up- or down-regulatedTaCKXgenes and phytohormones. Unexpectedly, increased expression ofTaCKX2.1in silent forTaCKX1T2plants up-regulated trans- and cis-zeatin and trans-zeatin glucosides, determining lower TGW and chlorophyll content in flag leaves but higher grain yield. The coordinated effect ofTaCKX1silencing on expression of otherTaCKXgenes, phytohormone levels in 7 DAP spikes and yield-related traits in silenced T2lines is presented.

One-sentence summary

Different levels ofTaCKX1silencing influence various models of coordinated expression ofTaCKXgenes and phytohormone levels in 7 DAP spikes, as well as yield parameters.
Survey of metaproteomics software tools for functional microbiome analysis
Authors: Sajulga R. , Easterly C. , Riffle M. , Mesuere B. , Muth T. , Mehta S. , Kumar P. , Johnson J. , Gruening B. , Schiebenhoefer H. , Kolmeder C. A. , Fuchs S. , Nunn B. L. , Rudney J. , Griffin T. J. , Jagtap P. D.
Published: January 2020

To gain a thorough appreciation of microbiome dynamics, researchers characterize the functional role of expressed microbial genes/proteins. This can be accomplished through metaproteomics, which characterizes the protein complement of the microbiome. Several software tools exist for analyzing microbiomes at the functional level by measuring their combined proteome-level response to environmental perturbations. In this survey, we explore the performance of six available tools, so that researchers can make informed decisions regarding software choice based on their research goals.

Tandem mass spectrometry-based proteomic data obtained from dental carie plaque samples grown with and without sucrose in paired biofilm reactors were used as representative data for this evaluation. Microbial peptides from one sample pair were identified by the X! Tandem search algorithm via SearchGUI and subjected to functional analysis using software tools including eggNOG-mapper, MEGAN6, MetaGOmics, MetaProteomeAnalyzer (MPA), ProPHAnE, and Unipept to generate functional annotation through Gene Ontology (GO) terms.

Among these software tools, notable differences in functional annotation were detected after comparing differentially expressed protein functional groups. Based on the generated GO terms of these tools we performed a peptide-level comparison to evaluate the quality of their functional annotations. A BLAST analysis against the Universal Protein Knowledgebase revealed that the sensitivity and specificity of functional annotation differed between tools. For example, eggNOG-mapper mapped to the most number of GO terms, while Unipept generated the most precise GO terms. Based on our evaluation, metaproteomics researchers can choose the software according to their analytical needs and developers can use the resulting feedback to further optimize their algorithms. To make more of these tools accessible via scalable metaproteomics workflows, eggNOG-mapper and Unipept 4.0 were incorporated into the Galaxy platform.
Macroevolutionary analysis of discrete traits with rate heterogeneity
Authors: Grundler Michael C. , Rabosky Daniel L.
Published: January 2020

Abstract

Organismal traits show dramatic variation in phylogenetic patterns of origin and loss across the Tree of Life. Understanding the causes and consequences of this variation depends critically on accounting for heterogeneity in rates of trait evolution among lineages. Here, we describe a method for modeling among-lineage evolutionary rate heterogeneity in a trait with two discrete states. The method assumes that the present-day distribution of a binary trait is shaped by a mixture of stochastic processes in which the rate of evolution varies among lineages in a phylogeny. The number and location of rate changes, which we refer to as rate-shift events, are inferred automatically from the data. Simulations reveal that the method accurately reconstructs rates of trait evolution and ancestral character states even when simulated data violate model assumptions. We apply the method to an empirical dataset of mimetic coloration in snakes and find elevated rates of trait evolution in two clades of harmless snakes that are broadly sympatric with dangerously venomous New World coral snakes, recapitulating an earlier analysis of the same dataset. Although the method performed well on many simulated data sets, we caution that overall power for inferring heterogeneous dynamics of single binary traits is low.
Preliminary Evaluation of the Utility of Deep Generative Histopathology Image Translation at a Mid-Sized NCI Cancer Center
Authors: Levy Joshua J. , Jackson Christopher R. , Sriharan Aravindhan , Christensen Brock C. , Vaickus Louis J.
Published: January 2020

Evaluation of a tissue biopsy is often required for the diagnosis and prognostic staging of a disease. Recent efforts have sought to accurately quantitate the distribution of tissue features and morphology in digitized images of histological tissue sections, Whole Slide Images (WSI). Generative modeling techniques present a unique opportunity to produce training data that can both augment these models and translate histologic data across different intra-and-inter-institutional processing procedures, provide cost-effective ways to perform computational chemical stains (synthetic stains) on tissue, and facilitate the creation of diagnostic aid algorithms. A critical evaluation and understanding of these technologies is vital for their incorporation into a clinical workflow. We illustrate several potential use cases of these techniques for the calculation of nuclear to cytoplasm ratio, synthetic SOX10 immunohistochemistry (IHC, sIHC) staining to delineate cell lineage, and the conversion of hematoxylin and eosin (H&E) stain to trichome stain for the staging of liver fibrosis.
Anomalous reverse transcription through chemical modifications in polyadenosine stretches
Authors: Kladwang Wipapat , Topkar Ved V. , Liu Bei , Hodges Tracy L. , Keane Sarah C. , al-Hashimi Hashim , Das Rhiju
Published: January 2020

Thermostable reverse transcriptases are workhorse enzymes underlying nearly all modern techniques for RNA structure mapping and for transcriptome-wide discovery of RNA chemical modifications. Despite their wide use, these enzymes’ behaviors at chemical modified nucleotides remain poorly understood. Wellington-Oguri et al. recently reported an apparent loss of chemical modification within putatively unstructured polyadenosine stretches modified by dimethyl sulfate or 2’ hydroxyl acylation, as probed by reverse transcription. Here, re-analysis of these and other publicly available data, capillary electrophoresis experiments on chemically modified RNAs, and nuclear magnetic resonance spectroscopy on A12and variants show that this effect is unlikely to arise from an unusual structure of polyadenosine. Instead, tests of different reverse transcriptases on chemically modified RNAs and molecules synthesized with single 1-methyladenosines implicate a previously uncharacterized reverse transcriptase behavior: near-quantitative bypass through chemical modifications within polyadenosine stretches. All tested natural and engineered reverse transcriptases (MMLV; SuperScript II, III, and IV; TGIRT-III; and MarathonRT) exhibit this anomalous bypass behavior. Accurate DMS-guided structure modeling of the polyadenylated HIV-1 3’ untranslated region RNA requires taking into account this anomaly. Our results suggest that poly(rA-dT) hybrid duplexes can trigger unexpectedly effective reverse transcriptase bypass and that chemical modifications in poly(A) mRNA tails may be generally undercounted.
Enhanced triacylglycerol (TAG) and protein accumulation in transgenic diatomThalassiosira pseudonanawith altered photosynthetic pigmentation
Authors: Gaidarenko Olga , Yee Daniel P. , Hildebrand Mark
Published: January 2020

Microalgal productivity in mass cultures is limited by the inefficiency with which available light energy is utilized. In dense cultures, cells closest to the light source absorb more light energy than they can use and dissipate the excess, while light penetrance into the culture is steeply attenuated. Reducing microalgal light harvesting and/or dissipating capacity per cell may improve total light utilization efficiency in mass cultures. In this study, two transgenic lines of the diatomThalassiosira pseudonanawith altered photosynthetic pigment content are evaluated with respect to photosynthetic parameters, growth, and macromolecule accumulation. In one line, violaxanthin de-epoxidase-like 2 (VDL2) is overexpressed (OE), resulting in a reduction of the diadinoxanthin cycle pigments, which are involved in light energy dissipation (non-photochemical quenching, NPQ), accompanied by a stoichiometric increase in the light-harvesting pigment fucoxanthin. No differences in the maximum potential quantum yield of photosystem II (Fv/Fm) or light-limited photosynthetic rate (α) were found. However, when adapted to 30 µmol photons m−2sec−1, the VDL2 OE maximum relative electron transport rate (rETRmax) upon exposure to saturating light intensities was 86-95% of wild type (WT). When adapted to 300 µmol photons m−2sec−1, VDL2 OE saturated photosynthesis at 62-71% of the light intensity needed to saturate WT (Ek). NPQ was substantially lower at and below 300 µmol photons m−2sec−1. VDL2 OE accumulated up to 3.4 times as much triacylglycerol (TAG) as WT during exponential growth, and up to twice as much protein. Growth in terms of culture density was up to 7% slower. TAG and protein accumulation inversely correlated with NPQ. The second line evaluated was obtained by using antisense RNA to simultaneously silence or knock down (KD) both LUT1-like (LTL) genes, hypothesized to catalyze an intermediate carotenoid biosynthesis step of converting β-carotene to zeaxanthin. Overall reduction of photosynthetic pigment content without altering the relative abundance of individual pigments resulted. No significant differences in photosynthetic parameters compared to WT were found. LTL KD grew at a rate comparable to WT and accumulated up to 40% more TAG during exponential growth, while protein content was reduced by 11-19%. LTL KD cells were elongated and 5-10% smaller than WT, and cultures contained auxospores, indicating stress that may relate to a cell cycle progression defect.
TLmutation: predicting the effects of mutations using transfer learning
Authors: Shamsi Zahra , Chan Matthew , Shukla Diwakar
Published: January 2020

A reoccurring challenge in bioinformatics is predicting the phenotypic consequence of amino acid variation in proteins. With the recent advancements in sequencing techniques, sufficient genomic data has become available to train models that predict the evolutionary statistical energies, but there is still inadequate experimental data to directly predict functional effects. One approach to overcome this data scarcity is to apply transfer learning and train more models with available datasets. In this study, we propose a set of transfer learning algorithms we call TLmutation, which implements a supervised transfer learning algorithm that transfers knowledge from survival data of a protein to a particular function of that protein. This is followed by an unsupervised transfer learning algorithm that extends the knowledge to a homologous protein. We explore the application of our algorithms in three cases. First, we test the supervised transfer on 17 previously published deep mutagenesis datasets to complete and refine missing datapoints. We further investigate these datasets to identify which mutations build better predictors of variant functions. In the second case, we apply the algorithm to predict higher-order mutations solely from single point mutagenesis data. Finally, we perform the unsupervised transfer learning algorithm to predict mutational effects of homologous proteins from experimental datasets. These algorithms are generalized to transfer knowledge between Markov random field models. We show the benefit of our transfer learning algorithms to utilize informative deep mutational data and provide new insights into protein variant functions. As these algorithms are generalized to transfer knowledge between Markov random field models, we expect these algorithms to be applicable to other disciplines.
Bayesian cell-type deconvolution and gene expression inference reveals tumor-microenvironment interactions
Authors: Chu Tinyi , Wang Zhong , Pe’er Dana , Danko Charles G.
Published: January 2020

Understanding the interactions between cells in their environment is a major challenge in genomics. Here we developed BayesPrism, a Bayesian method to jointly predict cellular composition and gene expression in each cell type, including heterogeneous malignant cells, from bulk RNA-seq using scRNA-seq as prior information. We conducted an integrative analysis of 1,412 bulk RNA-seq samples in primary glioblastoma, head and neck squamous cell carcinoma, and melanoma using single-cell datasets of 85 patients. We identified cell types correlated with clinical outcomes and explored spatial heterogeneity in malignant cell states and non-malignant cell type composition. We refined subtypes using gene expression in malignant cells, after excluding confounding non-malignant cell types. Finally, we identified genes whose expression in malignant cells correlated with infiltration of macrophages, T cells, fibroblasts, and endothelial cells across multiple tumor types. Our work introduces a new lens that uses scRNA-seq to accurately infer cellular composition and expression in large cohorts of bulk data.
General DNA methylation patterns and environmentally-induced differential methylation in the eastern oyster (Crassostrea virginica)
Authors: Venkataraman Yaamini R. , Downey-Wall Alan M. , Ries Justin , Westfield Isaac , White Samuel J. , Roberts Steven B. , Lotterhos Kathleen E.
Published: January 2020

Epigenetic modification, specifically DNA methylation, is one possible mechanism for intergenerational plasticity. Before inheritance of methylation patterns can be characterized, we need a better understanding of how environmental change modifies the parental epigenome. To examine the influence of experimental ocean acidification on eastern oyster (Crassostrea virginica) gonad tissue, oysters were cultured in the laboratory under control (491 ± 49 μatm) or high (2550 ± 211 μatm) pCO2 conditions for four weeks. DNA from reproductive tissue was isolated from five oysters per treatment, then subjected to bisulfite treatment and DNA sequencing. Irrespective of treatment, DNA methylation was primarily found in gene bodies with approximately 22% of CpGs (2.7% of total cytosines) in the C. virginica genome predicted to be methylated. In response to elevated pCO2, we found 598 differentially methylated loci primarily overlapping with gene bodies. A majority of differentially methylated loci were in exons (61.5%) with less intron overlap (31.9%). While there was no evidence of a significant tendency for the genes with differentially methylated loci to be associated with distinct biological processes, the concentration of these loci in gene bodies, including genes involved in protein ubiquitination and biomineralization suggests DNA methylation may be important for transcriptional control in response to ocean acidification. Changes in gonad methylation also indicate potential for these methylation patterns to be inherited by offspring. Understanding how experimental ocean acidification conditions modify the oyster epigenome, and if these modifications are inherited, allows for a better understanding of how ecosystems will respond to environmental change.
A validation framework for neuroimaging software: the case of population receptive fields
Authors: Lerma-Usabiaga Garikoitz , Benson Noah , Winawer Jonathan , Wandell Brian A.
Published: January 2020

Neuroimaging software methods are complex, making it a near certainty that some implementations will contain errors. Modern computational techniques (i.e., public code and data repositories, continuous integration, containerization) enable the reproducibility of the analyses and reduce coding errors, but they do not guarantee the scientific validity of the results. It is difficult, nay impossible, for researchers to check the accuracy of software by reading the source code; ground truth test datasets are needed. Computational reproducibility means providing software so that for the same input anyone obtains the same result, right or wrong. Computational validity means obtaining the right result for the ground-truth test data. We describe a framework for validating and sharing software implementations. We apply the framework to an application: population receptive field (pRF) methods for functional MRI data. The framework is composed of three main components implemented with containerization methods to guarantee computational reproducibility: (1) synthesis of fMRI time series from ground-truth pRF parameters, (2) implementation of four public pRF analysis tools and standardization of inputs and outputs, and (3) report creation to compare the results with the ground truth parameters. We identified realistic conditions that lead to imperfect parameter recovery in all four implementations, and we provide means to reduce this problem. The computational validity framework supports scientific rigor and creativity, as opposed to the oft-repeated suggestion that investigators rely upon a few agreed upon packages. The framework and methods can be extended to other critical neuroimaging algorithms. Having validation frameworks help (1) developers to build new software, (2) research scientists to verify the software’s accuracy, and (3) reviewers to evaluate the methods used in publications and grants.

Author Summary

Computer science provides powerful tools and techniques for implementing and deploying software. These techniques support software collaboration, reduce coding errors and enable reproducibility of the analyses. A further question is whether the software estimates are correct (valid). We describe a framework for validating and sharing software implementations based on ground-truth testing. We applied the framework to four separate applications that implemented population receptive field (pRF) estimates for functional MRI data. We quantified the validity, and we also documented limitations with these applications. Finally, we provide ways to mitigate these limitations. Implementing a software validation framework along with sharing and reproducibility is an important step for the complex methods used in neuroscience. Validation will help developers to build new software, researchers verify that the results are valid, and reviewers to evaluate the precision of methods in publications and grants.
Spinal dI2 interneurons regulate the stability of bipedal stepping
Authors: Haimson Baruch , Hadas Yoav , Kania Artur , Daley Monica , Cinnamon Yuval , Lev-Tov Aharon , Klar Avihu
Published: January 2020

Peripheral and intraspinal feedback is required to shape and update the output of spinal networks that execute motor behavior. We report that lumbar dI2 spinal interneurons of the chick receive synaptic input from afferents and pre-motoneurons. They innervate contralateral premotor networks in the lumbar and brachial spinal cord and their ascending projections innervate the cerebellum. These findings suggest that dI2 neurons function as interneurons in local lumbar circuits and involved in lumbo-brachial coupling and that part of them deliver peripheral and intraspinal feedback to the cerebellum. Silencing of dI2 neurons leads to destabilized stepping in P8 hatchlings with occasional collapses, variable step-profiles and wide-base walking, suggesting that the dI2 neurons may contribute to stabilization of the bipedal gait.
The Gene-Rich Genome of the ScallopPecten maximus
Authors: Kenny Nathan J , McCarthy Shane A , Dudchenko Olga , James Katherine , Betteridge Emma , Corton Craig , Dolucan Jale , Mead Dan , Oliver Karen , Omer Arina D , Pelan Sarah , Ryan Yan , Sims Ying , Skelton Jason , Smith Michelle , Torrance James , Weisz David , Wipat Anil , Aiden Erez L , Howe Kerstin , Williams Suzanne T
Published: January 2020

Background

The King Scallop,Pecten maximus, is distributed in shallow waters along the Atlantic coast of Europe. It forms the basis of a valuable commercial fishery and its ubiquity means that it plays a key role in coastal ecosystems and food webs. Like other filter feeding bivalves it can accumulate potent phytotoxins, to which it has evolved some immunity. The molecular origins of this immunity are of interest to evolutionary biologists, pharmaceutical companies and fisheries management.

Findings

Here we report the genome sequencing of this species, conducted as part of the Wellcome Sanger 25 Genomes Project. This genome was assembled from PacBio reads and scaffolded with 10x Chromium and Hi-C data, and its 3,983 scaffolds have an N50 of 44.8 Mb (longest scaffold 60.1 Mb), with 92% of the assembly sequence contained in 19 scaffolds, corresponding to the 19 chromosomes found in this species. The total assembly spans 918.3 Mb, and is the best-scaffolded marine bivalve genome published to date, exhibiting 95.5% recovery of the metazoan BUSCO set. Gene annotation resulted in 67,741 gene models. Analysis of gene content revealed large numbers of gene duplicates, as previously seen in bivalves, with little gene loss, in comparison with the sequenced genomes of other marine bivalve species.

Conclusions

The genome assembly ofPecten maximusand its annotated gene set provide a high-quality platform for a wide range of investigations, including studies on such disparate topics as shell biomineralization, pigmentation, vision and resistance to algal toxins. As a result of our findings we highlight the sodium channel geneNav1, known as a gene conferring resistance to saxitoxin and tetrodotoxin, as a candidate for further studies investigating immunity to domoic acid.
Word predictability, prosody, gesture and mouth movements in face-to-face language comprehension
Authors: Zhang Ye , Frassinelli Diego , Tuomainen Jyrki , Skipper Jeremy I , Vigliocco Gabriella
Published: January 2020

The ecology of human language is face-to-face interaction, comprising cues, like prosody, cospeech gestures, and mouth movements. Yet, the multimodal context is usually stripped away in experiments as dominant paradigms focus on linguistic processing only. In two studies we presented video-clips of an actress producing naturalistic passages to participants whose electroencephalographic activity was recorded. We quantified each cue and determined their effect on a well-established electroencephalographic marker of cognitive load in comprehension (N400). We found that brain responses to words were affected by informativeness of co-occurring multimodal cues, indicating that comprehension relies on linguistic and non-linguistic cues. Moreover, brain responses were affected by interactions between the multimodal cues, indicating that the impact of each cue dynamically changes based on the informativeness of other available cues. Thus, results show that multimodal cues are integral to comprehension, hence, our theories must move beyond the limited focus on speech and linguistic processing.
Modeling of Ion and Water Transport in the Biological Nanopore ClyA
Authors: Willems Kherim , Ruić Dino , Lucas Florian , Barman Ujjal , Hofkens Johan , Maglia Giovanni , Van Dorpe Pol
Published: January 2020

In recent years, the protein nanopore cytolysin A (ClyA) has become a valuable tool for the detection, characterization and quantification of biomarkers, proteins and nucleic acids at the single-molecule level. Despite this extensive experimental utilization, a comprehensive computational study of ion and water transport through ClyA is currently lacking. Such a study yields a wealth of information on the electrolytic conditions inside the pore and on the scale the electrophoretic forces that drive molecular transport. To this end we have built a computationally efficient continuum model of ClyA which, together with an extended version of Poison-Nernst-Planck-Navier-Stokes (ePNP-NS) equations, faithfully reproduces its ionic conductance over a wide range of salt concentrations. These ePNP-NS equations aim to tackle the shortcomings of the traditional PNP-NS models by self-consistently taking into account the influence of both the ionic strength and the nanoscopic scale of the pore on all relevant electrolyte properties. In this study, we give both a detailed description of our ePNP-NS model and apply it to the ClyA nanopore. This enabled us to gain a deeper insight into the influence of ionic strength and applied voltage on the ionic conductance through ClyA and a plethora of quantities difficult to assess experimentally. The latter includes the cation and anion concentrations inside the pore, the shape of the electrostatic potential landscape and the magnitude of the electro-osmotic flow. Our work shows that continuum models of biological nanopores—if the appropriate corrections are applied—can make both qualitatively and quantitatively meaningful predictions that could be valuable tool to aid in both the design and interpretation of nanopore experiments.
Conserved and divergent features of DNA methylation in embryonic stem cell-derived neurons
Authors: Martin Sally , Poppe Daniel , Olova Nelly , O’Leary Conor , Ivanova Elena , Pflueger Jahnvi , Dechka Jennifer , Simmons Rebecca K. , Cooper Helen M. , Reik Wolf , Lister Ryan , Wolvetang Ernst J.
Published: January 2020

DNA methylation functions in genome regulation and is implicated in neuronal maturation. Early post-natal accumulation of atypical non-CG methylation (mCH) occurs in neurons of mice and humans, but its precise function remains unknown. Here we investigate mCH deposition in neurons derived from mouse ES-cellsin vitroand in cultured primary mouse neurons. We find that both acquire comparable levels of mCH over a similar period asin vivo. In vitromCH deposition occurs concurrently with a transient increase inDnmt3aexpression, is preceded by expression of the post-mitotic neuronal markerRbfox3(NeuN) and is enriched at the nuclear lamina. Despite these similarities, whole genome bisulfite sequencing reveals that mCH patterning in mESC-derived neurons partially differs fromin vivo. mESC-derived neurons therefore represent a valuable model system for analyzing the mechanisms and functional consequences of correct and aberrantly deposited CG and non-CG methylation in neuronal maturation.