bluuebunny/crossref_metadata_2025 huggingface dataset:
18F-FDG-PET/CT in measuring volume and global metabolic activity of thigh muscles: a novel CT-based tissue segmentation methodology
Authors: Kothekar Esha , Yellanki Dani , Borja Austin J. , Al-zaghal Abdullah , Werner Thomas J. , Revheim Mona-Elisabeth , Gerke Oke , Saboury Babak , Gholamrezanezad Ali , Høilund-Carlsen Poul F. , Alavi Abass
Published: December 2019

Purpose

We present a novel computed tomography-based tissue segmentation methodology for determining volume and global uptake of FDG of the thigh muscles and correlate these parameters with age.

Materials and methods

A total of 71 subjects from a prospective clinical trial (NCT01724749) were included. PET/CT scans were acquired 180 minutes after intravenous injection of FDG. A 3D growing region algorithm with neighborhood Hounsfield unit threshold between one and 150 was used to highlight the muscle. FDG uptake was expressed as the average mean standardized uptake value normalized for lean body mass (average SULmean). Femur volume was used to normalize thigh muscle volume to calculate normalized volume and correlate with age.

Results

We found a significant negative correlation between normalized volume and age (left side r = −0.262,P= 0.02; right side r = −0.286,P= 0.01). No statistically significant difference was found between SUL and age or between SUL and BMI. There was no statistically significant difference in muscle volume on the two sides. Statistically significant difference was noted in the global metabolic activity (SUL) between the two sides (left 0.39 ± 0.06, right 0.42 ± 0.08,P< 0.001), with 56/71 (78.8%) subjects having higher uptake on the right side.

Conclusion

FDG-PET/CT using CT-based segmentation is a novel imaging modality assessing the volume and global metabolic activity of the thigh muscles. It could be possible to utilize this methodology for the research and understanding of lower limb muscle pathophysiology.
Establishing Meaningful Learning in Online Nursing Postconferences
Authors: Petrovic Kristin A. , Hack Regan , Perry Beth
Published: December 2019

Background

Effective teaching and learning strategies in online postconference can assist students to find meaning within clinical experiences.

Purpose

To explore this, we completed a literature review about meaningful learning in online clinical postconferencing in prelicensure nursing education.

Methods

Articles that were peer-reviewed, published within the last 10 years, written in English, and addressed online learning in clinical postconferences in prelicensure nursing programs were included.

Results

Analysis revealed the following themes: connecting theory to practice, reflective practice, impact on future practice, peer and instructor support, mentoring and leadership development, giving and receiving feedback effectively, critical thinking, and engagement of active learners. Gaps were evident with minimal evidence-based practice described related to postconferences in general. Additionally, there is limited discussion of online postconferencing.

Conclusions

Understanding the nuances of meaningful learning in online postconference is critical to facilitating students' ability to connect theory to practice.
Patient Preferences for Attributes of Primary Surgical Debulking Versus Neoadjuvant Chemotherapy for Treatment of Newly Diagnosed Ovarian Cancer
Authors: Havrilesky Laura J. , Yang Jui-Chen , Lee Paula S. , Secord Angeles Alvarez , Ehrisman Jessie A. , Davidson Brittany , Berchuck Andrew , Darcy Kathleen M. , Maxwell G. Larry , Reed Shelby D.
Published: December 2019

(Abstracted from Cancer 2019;125:4399–4406)

Retrospective analyses have found that optimal tumor debulking after a new diagnosis of ovarian cancer results in significantly greater progression-free survival (PFS) and overall survival (OS) compared with those who are suboptimally debulked. Primary debulking surgery (PDS) has become a common first line of therapy in patients with ovarian cancer.
Two-Dose Versus Single-Dose Methotrexate for Treatment of Ectopic Pregnancy: A Meta-analysis
Authors: Alur-Gupta Snigdha , Cooney Laura G. , Senapati Suneeta , Sammel Mary D. , Barnhart Kurt T.
Published: December 2019

(Abstracted from Am J Obstet Gynecol 2019;221:95–108.e2)

A number of studies have demonstrated comparable efficacy of medical and surgical management for treatment of stable ectopic pregnancies. Methotrexate, a folate antagonist, has been the mainstay of medical management.
A Review of CONSORT Guidelines About Comparison Groups With a Focused Discussion on Implications for Rehabilitation Clinical Trials
Authors: Levack William M. M. , Engkasan Julia P. , Heinemann Allen W. , Negrini Stefano
Published: December 2019

Objective

We examined and appraised the Consolidated Standards of Reporting Trials (CONSORT) 2010 Statement and its extension from the perspective of the reporting of comparison groups (ie, interventions or control conditions against which an experimental intervention is compared) in clinical trials on rehabilitation topics.

Design

We downloaded the CONSORT 2010 Statement and all endorsed and unofficial extensions reported on the CONSORT and EQUATOR Web sites. We extracted all statements on the selection, design, delivery, or interpretation of data from comparison groups in clinical trials. We discussed preliminary findings during the Cochrane Rehabilitation Methodology Meeting in Kobe and then further by email before finalizing results.

Results

We identified 23 standards reported across the CONSORT 2010 Statement and 10 extensions. Overall, these standards address many, but not all, issues related to reporting of comparison groups in rehabilitation trials.

Conclusions

We recommend that additional standards be created for the selection of types of comparisons, choices around reporting of “usual care,” reporting of intended “mechanisms of control,” and reporting a rationale for the hypothesized superiority of one intervention over another when superiority trial design are used. Rehabilitation research would benefit from development of a specific checklist and guidelines to help researchers make best use of existing extensions.
Resilience After Spinal Cord Injury
Authors: McDonald Scott D. , Pugh Mickeal , Mickens Melody N.
Published: December 2019

Rehabilitation medicine has recently embraced resilience, and research in this area has surged within the past decade. Several systematic reviews of resilience research have been conducted in traumatic brain injury, chronic diseases, and stroke populations. A decade into research into the role of resilience in the lives of individuals with spinal cord injury, a review of the current state of the research literature is needed to identify trends and knowledge gaps. The aims of this scoping review were (a) to classify study methods and designs used for resilience research in spinal cord injury to date, (b) to describe how researchers have defined “resilience,” and (c) to identify knowledge gaps and suggest future directions for research. Literature searches were conducted to identify English-language, peer-reviewed articles on resilience and spinal cord injury. Most of the 40 studies reviewed were correlational using cross-sectional data, although descriptive, longitudinal, qualitative, test development, and intervention studies and review articles were found as well. As is the case outside of rehabilitation medicine, there is considerable definitional and conceptual heterogeneity that limits our ability to apply resilience research to clinical practice. Moving forward, the field needs model-driven, longitudinal research that offers clear, conceptual distinctions between risk and protective factors, processes, and outcomes.
Mini Nutritional Assessment Score as a Potential Predictor of Pressure Ulcers in Elderly Nursing Home Patients With Dementia
Authors: Jones Amy , Pope Janet , Osei-Boadi Anguah Katherene , Erickson Dawn
Published: December 2019

This retrospective study compared the presence and severity of pressure ulcers in long-term care residents with dementia based on Mini Nutritional Assessment (MNA) scores. Participants included 50 older adults with pressure ulcers and 50 matched controls. MNA scores for subjects with and without ulcers were significantly different (8.34 ± 2.67 vs 9.98 ± 2.32, P = .001). Scores based on ulcer stage did not follow a linear pattern; however, subjects with stage 4 ulcers had significantly lower scores (6.33 ± 2.55) than subjects with stages 1 to 3 ulcers (8.90 ± 2.70, P = .009; 9.64 ± 2.16, P = .001; and 9.08 ± 2.02, P = .004, respectively). Results show a relationship between low MNA scores and pressure ulcers. Thus, MNA has the potential for use in implementation of preventive measures and mitigation of ulcer progression.
Micro-structured medium with large isotropic negative thermal expansion
Authors: Cabras Luigi , Brun Michele , Misseroni Diego
Published: December 2019

A challenge in nano- and micro-mechanics is the realization of innovative materials exploiting auxetic behaviour to tailor thermal expansion properties. For this purpose, a new class of micro-structured media possessing an extremely wide range of tunable (positive, negative or even zero) thermal expansion is proposed and analytically and experimentally assessed. For this class of isotropic
Mechanical-Auxetic Thermal-Shrinking
media, the effective coefficient of thermal expansion is explicitly linked to two microstructural variables via a simple relation, allowing the design with desired values. The theoretical predictions for the negative thermal properties are fully validated by the experimental and numerical outcomes. The simplicity of the proposed structure makes the design useful for the production of a new generation of advanced media, with applications ranging from micromechanical devices to large civil and space structures.
Periodic particle arrangements using standing acoustic waves
Authors: Guevara Vasquez Fernando , Mauck China
Published: December 2019

We determine crystal-like materials that can be fabricated by using a standing acoustic wave to arrange small particles in a non-viscous liquid resin, which is cured afterwards to keep the particles in the desired locations. For identical spherical particles with the same physical properties and small compared to the wavelength, the locations where the particles are trapped correspond to the minima of an acoustic radiation potential which describes the net forces that a particle is subject to. We show that the global minima of spatially periodic acoustic radiation potentials can be predicted by the eigenspace of a small real symmetric matrix corresponding to its smallest eigenvalue. We relate symmetries of this eigenspace to particle arrangements composed of points, lines or planes. Since waves are used to generate the particle arrangements, the arrangement’s periodicity is limited to certain Bravais lattice classes that we enumerate in two and three dimensions.
Metabolic theory of ecology successfully predicts distinct scaling of ectoparasite load on hosts
Authors: Hechinger Ryan F. , Sheehan Kate L. , Turner Andrew V.
Published: December 2019

The impacts of parasites on hosts and the role that parasites play in ecosystems must be underlain by the load of parasites in individual hosts. To help explain and predict parasite load across a broad range of species, quantitative theory has been developed based on fundamental relationships between organism size, temperature and metabolic rate. Here, we elaborate on an aspect of that ‘scaling theory for parasitism’, and test a previously unexplored prediction, using new data for total ectoparasite load from 263 wild birds of 42 species. We reveal that, despite the expected substantial variation in parasite load among individual hosts, (i) the theory successfully predicts the distinct increase of ectoparasite load with host body size, indicating the importance of geometric scaling constraints on access to host resources, (ii) ectoparasite load appears ultimately limited by access—not to host space—but to host energy, and (iii) there is a currency-dependent shift in taxonomic dominance of parasite load on larger birds. Hence, these results reveal a seemingly new macroecological pattern, underscore the utility of energy flux as a currency for parasitism and highlight the promise of using scaling theory to provide baseline expectations for parasite load for a diversity of host species.
A Cretaceous peak in family-level insect diversity estimated with mark–recapture methodology
Authors: Schachat Sandra R. , Labandeira Conrad C. , Clapham Matthew E. , Payne Jonathan L.
Published: December 2019

The history of insects’ taxonomic diversity is poorly understood. The two most common methods for estimating taxonomic diversity in deep time yield conflicting results: the ‘range through’ method suggests a steady, nearly monotonic increase in family-level diversity, whereas ‘shareholder quorum subsampling’ suggests a highly volatile taxonomic history with family-level mass extinctions occurring repeatedly, even at the midpoints of geological periods. The only feature shared by these two diversity curves is a steep increase in standing diversity during the Early Cretaceous. This apparent diversification event occurs primarily during the Aptian, the pre-Cenozoic interval with the most described insect occurrences, raising the possibility that this feature of the diversity curves reflects preservation and sampling biases rather than insect evolution and extinction. Here, the capture–mark–recapture (CMR) approach is used to estimate insects’ family-level diversity. This method accounts for the incompleteness of the insect fossil record as well as uneven sampling among time intervals. The CMR diversity curve shows extinctions at the Permian/Triassic and Cretaceous/Palaeogene boundaries but does not contain any mass extinctions within geological periods. This curve also includes a steep increase in diversity during the Aptian, which appears not to be an artefact of sampling or preservation bias because this increase still appears when time bins are standardized by the number of occurrences they contain rather than by the amount of time that they span. The Early Cretaceous increase in family-level diversity predates the rise of angiosperms by many millions of years and can be better attributed to the diversification of parasitic and especially parasitoid insect lineages.
Cost effective, experimentally robust differential-expression analysis for human/mammalian, pathogen and dual-species transcriptomics
Authors: Shetty Amol C. , Mattick John , Chung Matthew , McCracken Carrie , Mahurkar Anup , Filler Scott G. , Fraser Claire M. , Rasko David A. , Bruno Vincent M. , Dunning Hotopp Julie C.
Published: December 2019

As sequencing read length has increased, researchers have quickly adopted longer reads for their experiments. Here, we examine 14 pathogen or host–pathogen differential gene expression data sets to assess whether using longer reads is warranted. A variety of data sets was used to assess what genomic attributes might affect the outcome of differential gene expression analysis including: gene density, operons, gene length, number of introns/exons and intron length. No genome attribute was found to influence the data in principal components analysis, hierarchical clustering with bootstrap support, or regression analyses of pairwise comparisons that were undertaken on the same reads, looking at all combinations of paired and unpaired reads trimmed to 36, 54, 72 and 101 bp. Read pairing had the greatest effect when there was little variation in the samples from different conditions or in their replicates (e.g. little differential gene expression). But overall, 54 and 72 bp reads were typically most similar. Given differences in costs and mapping percentages, we recommend 54 bp reads for organisms with no or few introns and 72 bp reads for all others. In a third of the data sets, read pairing had absolutely no effect, despite paired reads having twice as much data. Therefore, single-end reads seem robust for differential-expression analyses, but in eukaryotes paired-end reads are likely desired to analyse splice variants and should be preferred for data sets that are acquired with the intent to be community resources that might be used in secondary data analyses.
Characterization of 100 extended major histocompatibility complex haplotypes in Indonesian cynomolgus macaques
Authors: Shortreed Cecilia G. , Wiseman Roger W. , Karl Julie A. , Bussan Hailey E. , Baker David A. , Prall Trent M. , Haj Amelia K. , Moreno Gage K. , Penedo Maria Cecilia T. , O’Connor David H.
Published: December 2019

Many medical advancements – including improvements to anti-rejection therapies in transplantation and vaccine development – rely on pre-clinical studies conducted in cynomolgus macaques (Macaca fascicularis). Major histocompatibility complex (MHC) class I and class II genes of cynomolgus macaques are orthologous to human leukocyte antigen complex (HLA) class I and class II genes, respectively. Both encode cell-surface proteins involved in cell recognition and rejection of non-host tissues. MHC class I and class II genes are highly polymorphic, so comprehensive genotyping requires the development of complete databases of allelic variants. Our group used PacBio circular consensus sequencing of full-length cDNA amplicons to characterize MHC class I and class II transcript sequences for a cohort of 295 Indonesian cynomolgus macaques (ICM) in a large, pedigreed breeding colony. These studies allowed us to expand the existing database ofMacaca fascicularis(Mafa) alleles by identifying an additional 141 MHC class I and 61 class II transcript sequences. In addition, we defined co-segregating combinations of allelic variants as regional haplotypes for 70 Mafa-A, 78 Mafa-B and 45 Mafa-DRB gene clusters. Finally, we defined class I and class II transcripts that are associated with 100 extended MHC haplotypes in this breeding colony by combining our genotyping analyses with short tandem repeat (STR) patterns across the MHC region. Our sequencing analyses and haplotype definitions improve the utility of these ICM for transplantation studies as well as infectious disease and vaccine research.
Accurate and simultaneous identification of differential expression and splicing using hierarchical Bayesian analysis
Authors: Karlebach Guy , Hansen Peter , Veiga Diogo F.T. , Steinhaus Robin , Danis Daniel , Li Sheng , Anczukow Olga , Robinson Peter N.
Published: December 2019

The regulation of mRNA controls both overall gene expression as well as the distribution of mRNA isoforms encoded by the gene. Current algorithmic approaches focus on characterization of significant differential expression or alternative splicing events or isoform distribution without integrating both events. Here, we present Hierarchical Bayesian Analysis of Differential Expression and ALternative SPlicing (HBA-DEALS), which simultaneously characterizes differential expression and splicing in cohorts. HBA-DEALS attains state of the art or better performance for both expression and splicing, and allows genes to be characterized as having differential gene expression (DGE), differential alternative splicing (DAST), both, or neither. Based on an analysis of Genotype-Tissue Expression (GTEx) data we demonstrate the existence of sets of genes that show predominant DGE or DAST across a comparison of 20 tissue types, and show that these sets have pervasive differences with respect to gene structure, function, membership in protein complexes, and promoter architecture.
Molecular structures and mechanisms of DNA break processing in mouse meiosis
Authors: Yamada Shintaro , Hinch Anjali Gupta , Kamido Hisashi , Zhang Yongwei , Edelmann Winfried , Keeney Scott
Published: December 2019

Exonucleolytic resection, critical to repair double-strand breaks (DSBs) by recombination, is not well understood, particularly in mammalian meiosis. Here, we define structures of resected DSBs in mouse spermatocytes genome-wide at nucleotide resolution. Resection tracts averaged 1100 nucleotides, but with substantial fine-scale heterogeneity at individual hotspots. Surprisingly, EXO1 is not the major 5′→3′ exonuclease, but the DSB-responsive kinase ATM proved a key regulator of both initiation and extension of resection. In wild type, apparent intermolecular recombination intermediates clustered near to but offset from DSB positions, consistent with joint molecules with incompletely invaded 3′ ends. Finally, we provide evidence for PRDM9-dependent chromatin remodeling leading to increased accessibility at recombination sites. Our findings give insight into the mechanisms of DSB processing and repair in meiotic chromatin.
EPIGENE: genome wide transcription unit annotation using a multivariate probabilistic model of histone modifications
Authors: Sahu Anshupa , Li Na , Dunkel Ilona , Chung Ho-Ryun
Published: December 2019

Background

Understanding transcriptome is critical for explaining functional as well as regulatory roles of genomic regions. Current methods for the identification of transcription unit (TU) uses RNA-seq which, however, requires large quantities of mRNA limiting the identification of inherently unstable TUs e.g. for miRNA precursors. This problem can be resolved by chromatin based approaches due to a correlation between histone modifications and transcription.

Results

Here we introduce EPIGENE, a novel chromatin segmentation method for the identification of active TUs using transcription associated histone modifications. Unlike existing chromatin segmentation approaches, EPIGENE uses a constrained, semi-supervised multivariate hidden markov model (HMM) that models the observed combination of histone modifications using a product of independent Bernoulli random variables, to identify active TUs. Our results show that EPIGENE can identify genome-wide TUs unbiasedly. EPIGENE predicted TUs showed an enrichment of RNA Polymerase II in transcription start site and gene body indicating that they have been transcribed. Comprehensive validation with existing annotations revealed that 93% of EPIGENE TUs can be explained by existing gene annotations and 5% of EPIGENE TUs in HepG2 can be explained by microRNA annotations. EPIGENE outperforms existing RNA-Seq based approaches in TU prediction precision across human cell lines. Finally, we identify 381 novel TUs in K562 and 43 novel cell-specific TUs all of which are supported by RNA Polymerase II data.

Conclusions

We demonstrate the applicability of HMM to identify genome-wide active TUs and provides valuable information about unannotated TUs. EPIGENE is an open-source method and is freely available at:https://github.com/imbeLab/EPIGENE.
SurA is a “Groove-y” Chaperone That Expands Unfolded Outer Membrane Proteins
Authors: Marx Dagan C. , Plummer Ashlee M. , Faustino Anneliese M. , Devlin Taylor , Roskopf Michaela A. , Leblanc Mathis J. , Lessen Henry J. , Amann Barbara T. , Fleming Patrick J. , Krueger Susan , Fried Stephen D. , Fleming Karen G.
Published: December 2019

The periplasmic chaperone network ensures the biogenesis of bacterial outer membrane proteins (OMPs) and has recently been identified as a promising target for antibiotics. SurA is the most important member of this network both due to its genetic interaction with the β-barrel assembly machinery complex as well as its ability to prevent unfolded OMP (uOMP) aggregation. Using only binding energy, the mechanism by which SurA carries out these two functions is not well understood. Here we use a combination of photo-crosslinking, mass spectrometry, solution scattering, and molecular modeling techniques to elucidate the key structural features that define how SurA solubilizes uOMPs. Our experimental data support a model in which SurA binds uOMPs in a groove formed between the core and P1 domains. This binding event results in a drastic expansion of the rest of the uOMP, which has many biological implications. Using these experimental data as restraints, we adopted an integrative modeling approach to create a sparse ensemble of models of a SurA•uOMP complex. We validated key structural features of the SurA•uOMP ensemble using independent scattering and chemical crosslinking data. Our data suggest that SurA utilizes three distinct binding modes to interact with uOMPs and that more than one SurA can bind a uOMP at a time. This work demonstrates that SurA operates in a distinct fashion compared to other chaperones in the OMP biogenesis network.

Significance Statement

Outer membrane proteins play critical roles in bacterial physiology and increasingly are exploited as antibiotic targets. SurA is the most important chaperone in the OMP biogenesis network and is thought to initiate their folding through an interaction with the BAM complex. We observe an unprecedented expansion of unfolded outer membrane proteins when bound to SurA. This expansion suggests a potential mechanism by which SurA can deliver uOMPs to the BAM complex. In addition, this study highlights the use of an integrative/hybrid structural biology approach and emerging methods to map highly heterogeneous structural ensembles such as that of an unfolded protein bound to a chaperone.
Design of Experiments for Fine-Mapping Quantitative Trait Loci in Livestock Populations
Authors: Wittenburg Dörte , Bonk Sarah , Doschoris Michael , Reyer Henry
Published: December 2019

Single nucleotide polymorphisms (SNPs) which capture a significant impact on a trait can be identified with genome-wide association studies. High linkage disequilibrium (LD) among SNPs makes it difficult to identify causative variants correctly. Thus, often target regions instead of single SNPs are reported. Sample size has not only a crucial impact on the precision of parameter estimates, it also ensures that a desired level of statistical power can be reached. We study the design of experiments for fine-mapping of signals of a quantitative trait locus in such a target region.

A multi-locus model allows to identify causative variants simultaneously, to state their positions more precisely and to account for existing dependencies. Based on the commonly applied SNP-BLUP approach, we determine the z-score statistic for locally testing non-zero SNP effects and investigate its distribution under the alternative hypothesis. This quantity employs the theoretical instead of observed dependence between SNPs; it can be set up as a function of paternal and maternal LD for any given population structure.

We simulated multiple paternal half-sib families and considered a target region of 1 Mbp. A bimodal distribution of estimated sample size was observed, particularly if more than two causative variants were assumed. The median of estimates constituted the final proposal of optimal sample size; it was consistently less than sample size estimated from single-SNP investigations which was used as a baseline approach. The second mode pointed to inflated sample sizes and could be explained by blocks of varying linkage phases leading to negative correlations between SNPs. Optimal sample size increased almost linearly with number of signals to be identified but depended much stronger on the assumption on heritability. For instance, three times as many samples were required if heritability was 0.1 compared to 0.3. These results enable the resource-saving design of future experiments for fine-mapping of candidate variants in structured and unstructured populations.
Spen links RNA-mediated endogenous retrovirus silencing and X chromosome inactivation
Authors: Carter Ava C. , Xu Jin , Nakamoto Meagan Y. , Wei Yuning , Shi Quanming , Broughton James P. , Ransom Ryan C. , Salhotra Ankit , Nagaraja Surya D. , Li Rui , Dou Diana R. , Yost Kathryn E. , Cho Seung Woo , Mistry Anil , Longaker Michael T. , Batey Robert T. , Wuttke Deborah S. , Chang Howard Y.
Published: December 2019

Dosage compensation between the sexes has emerged independently multiple times during evolution, often harnessing long noncoding RNAs (lncRNAs) to alter gene expression on the sex chromosomes. In eutherian mammals, X chromosome inactivation (XCI) in females proceeds via the lncRNAXist, which coats one of the two X chromosomes and recruits repressive proteins to epigenetically silence gene expressionin cis1,2. HowXistevolved new functional RNA domains to recruit ancient, pleiotropic protein partners is of great interest. Here we show that Spen, anXist-binding repressor protein essential for XCI3-7, binds to ancient retroviral RNA, performing a surveillance role to recruit chromatin silencing machinery to these parasitic loci.Speninactivation leads to de-repression of a subset of endogenous retroviral (ERV) elements in embryonic stem cells, with gain of chromatin accessibility, active histone modifications, andERVRNA transcription. Spen binds directly toERVRNAs that show structural similarity to the A-repeat ofXist, a region critical forXist-mediated gene silencing8-9.ERVRNA andXistA-repeat bind the RRM3 domain of Spen in a competitive manner. Insertion of an ERV into an A-repeat deficientXistrescues binding ofXistRNA to Spen and results in local gene silencingin cis. These results suggest that insertion of an ERV element into proto-Xistmay have been a critical evolutionary event, which allowedXistto coopt transposable element RNA-protein interactions to repurpose powerful antiviral chromatin silencing machinery for sex chromosome dosage compensation.
Zika and dengue viruses infecting wild-caught mosquitoes in an environmental protection area in Brazil
Authors: Barrio-Nuevo Karolina Morales , Medeiros-Sousa Antônio Ralph , Ceretti-Junior Walter , Fernandes Aristides , Rocco Iray Maria , Cunha Mariana Sequetin , Luchs Adriana , Mucci Luis Filipe , de Souza Renato Pereira , Marrelli Mauro Toledo
Published: December 2019

Species of the genusFlavivirusare widespread in Brazil and are a major public health concern. The city of São Paulo is in a highly urbanized area with some green spaces which are used for recreation and where potential vertebrate hosts and mosquito vectors of these arboviruses can be found, a scenario that can contribute to the transmission of flaviviruses to humans. This study therefore sought to investigate natural flavivirus infection in mosquitoes collected in the Capivari-Monos Environmental Protection Area (EPA) in the south of the city. Monthly mosquito collections were carried out from March 2016 to April 2017 with CO2-baited CDC light traps. Specimens were identified morphologically and grouped in pools. A total of 260 pools of non-engorged females were inoculated into the C6/36 cell lineage after analysis by indirect immunofluorescence assay (IFA). IFA-positive specimens were tested by qRT-PCR with genus-specific primers targeting a region of ~260 nucleotides in the flavivirus NS5 gene, and the PCR products were sequenced to confirm and identify the flavivirus species.Anopheles(Kerteszia)cruziiandWyeomyia(Prosopolepis)confusawere the most frequent species collected. Zika virus (ZIKV) nucleotide sequences were detected in three mosquito species,An. cruzii,Limatus durhamiandWy. confusa, and dengue virus 2 (DENV-2) sequences inCulex. spp. andCulex. (Mel.)vaxus. To our knowledge, this is the first report of natural isolation of DENV-2 and ZIKV in sylvatic species of mosquitoes in the Capivari-Monos EPA. Our findings suggest that DENV-2 is present inCulexmosquitoes, and ZIKV inAnopheles,WyeomyiaandLimatus. The flavivirus species identified here are of medical importance; surveillance is therefore recommended in this EPA, where vertebrates and mosquitoes can act as flavivirus hosts and vectors.
A non-linear system patterns Rab5 GTPase on the membrane
Authors: Cezanne A , Lauer J , Solomatina A , Sbalzarini IF , Zerial M
Published: December 2019

Proteins can self-organize into spatial patterns via non-linear dynamic interactions on cellular membranes. Modelling and simulations have shown that small GTPases can generate patterns by coupling guanine nucleotide exchange factors (GEF) to effector binding, generating a positive feedback of GTPase activation and membrane recruitment. Here, we reconstituted the patterning of the small GTPase Rab5 and its GEF/effector complex Rabex5/Rabaptin5 on supported lipid bilayers as a model system for membrane patterning. We show that there is a “handover” of Rab5 from Rabex5 to Rabaptin5 upon nucleotide exchange. A minimal system consisting of Rab5, RabGDI and a complex of full length Rabex5/Rabaptin5 was necessary to pattern Rab5 into membrane domains. Surprisingly, a lipid membrane composition mimicking that of the early endosome was required for Rab5 patterning. The prevalence of GEF/effector coupling in nature suggests a possible universal system for small GTPase patterning involving both protein and lipid interactions.
Detection of aberrant splicing events in RNA-seq data with FRASER
Authors: Mertes Christian , Scheller Ines , Yépez Vicente A. , Çelik Muhammed H. , Liang Yingjiqiong , Kremer Laura S. , Gusic Mirjana , Prokisch Holger , Gagneur Julien
Published: December 2019

Aberrant splicing is a major cause of rare diseases, yet its prediction from genome sequence remains in most cases inconclusive. Recently, RNA sequencing has proven to be an effective complementary avenue to detect aberrant splicing. Here, we developed FRASER, an algorithm to detect aberrant splicing from RNA sequencing data. Unlike existing methods, FRASER captures not only alternative splicing but also intron retention events. This typically doubles the number of detected aberrant events and identified a pathogenic intron retention inMCOLN1. FRASER automatically controls for latent confounders, which are widespread and substantially affect sensitivity. Moreover, FRASER is based on a count distribution and multiple testing correction, reducing the number of calls by two orders of magnitude over commonly applied z score cutoffs, with a minor sensitivity loss. The application to rare disease diagnostics is demonstrated by reprioritizing a pathogenic aberrant exon truncation inTAZfrom a published dataset. FRASER is easy to use and freely available.
A PI3K-WIPI2 positive feedback loop allosterically activates LC3 lipidation in autophagy
Authors: Fracchiolla Dorotea , Chang Chunmei , Hurley James H. , Martens Sascha
Published: December 2019

Autophagy degrades cytoplasmic cargo by its delivery to lysosomes within double membrane autophagosomes. Synthesis of the phosphoinositide PI(3)P by the autophagic PI 3-kinase complex I (PI3KC3-C1) and conjugation of ATG8/LC3 proteins to phagophore membranes by the ATG12–ATG5-ATG16L1 (E3) complex are two critical steps in autophagosome biogenesis, connected by WIPI2. Here we present a complete reconstitution of these events. On giant unilamellar vesicles (GUVs), LC3 lipidation is strictly dependent on the recruitment of WIPI2, which in turn depends on PI(3)P. Ectopically targeting E3 to membranes in the absence of WIPI2 is insufficient to support LC3 lipidation, demonstrating that WIPI2 allosterically activates the E3 complex. PI3KC3-C1 and WIPI2 mutually promote the recruitment of each other in a positive feedback loop. When both PI 3-kinase and LC3 lipidation reactions were carried out simultaneously, positive feedback between PI3KC3-C1 and WIPI2 led to rapid LC3 lipidation with kinetics similar to those seen in cellular autophagosome formation.

Autophagy requires the synthesis of PI(3)P and the conjugation of LC3 to the phagophore membrane. We reconstituted these two reactions and their coupling by WIPI2, and showed that positive feedback between PI3KC3-C1 and WIPI2 leads to rapid LC3 lipidation by the ATG16L1 complex.
Prophylactic host behaviour discourages pathogen exploitation
Authors: Mitchell Evan , Wild Geoff
Published: December 2019

Much work has considered the evolution of pathogens, but little is known about how they respond to changes in host behaviour. We build a model where hosts are able to choose to engage in prophylactic measures that reduce the likelihood of disease transmission. This choice is mediated by costs and benefits associated with prophylaxis, but the fraction of hosts engaged in prophylaxis is also affected by population dynamics. We identify a critical cost threshold above which hosts do not engage in prophylaxis. Below the threshold, prophylactic host behaviour does occur and pathogen virulence, measured by the extent to which it exploits its host, is reduced by the action of selection relative to the level that would otherwise be predicted in the absence of prophylaxis. Our work emphasizes the significance of the dual nature of the trade-off faced by the pathogen between balancing transmission and recovery, and creating new infections in hosts engaging or not engaging in prophylaxis.
A Role for the Locus Coeruleus in the Modulation of Feeding
Authors: Sciolino Natale R. , Hsiang Madeline , Mazzone Christopher M. , Wilson Leslie R. , Plummer Nicholas W. , Amin Jaisal , Smith Kathleen G. , McGee Christopher A. , Fry Sydney A. , Yang Cindy X. , Powell Jeanne M. , Bruchas Michael R. , Kravitz Alexxai V. , Cushman Jesse D. , Krashes Michael J. , Cui Guohong , Jensen Patricia
Published: December 2019

Recent data suggest that LC-NE neurons play a role in fear-induced suppression of feeding, but their endogenous activity in naturally behaving animals has not been explored. We found that endogenous activity of LC-NE neurons was enhanced during food approach and suppressed during food consumption, and that these food-evoked LC-NE responses were attenuated in sated mice. Interestingly, visual-evoked LC-NE activity was also attenuated in sated mice, demonstrating that internal satiety state modulates LC-NE encoding of multiple behavioral states. We also found that food intake could be attenuated by brief or longer durations of LC-NE activation. Lastly, we demonstrated that activation of LC neurons suppresses feeding and enhances avoidance and anxiety-like responding through a projection to the lateral hypothalamus. Collectively, our data suggest that LC-NE neurons modulate feeding by integrating both external cues (e.g., anxiogenic environmental cues) and internal drives (e.g., nutritional state).
BioFabric Visualization of Network Alignments
Authors: Desai Rishi M. , Longabaugh William J.R. , Hayes Wayne B.
Published: December 2019

Background

Dozens of global network alignment algorithms have been developed over the past fifteen years. Effective network visualization tools are lacking and would enhance our ability to gain an intuitive understanding of the strengths and weaknesses of these algorithms.

Results

We have created a plugin to the existing network visualization tool BioFabric, calledVISNAB: Visualization of Network Alignments using BioFabric. We leverage BioFabric’s unique approach to layout (nodes are horizontal lines connected by vertical lines representing edges) to improve understanding of network alignment performance. Our visualization tool allows the user to clearly spot deficiencies in alignments that cannot be detected through simply evaluating and comparing standard numerical topological measures such as the Edge Coverage (EC) or Symmetric Substructure Score (S3). Furthermore, we provide new automatic layouts that allow researchers to identify problem areas in an alignment. Finally, our new definitions ofnode groupsandlink groupsthat arise from our visualization technique allows us to also introduce novel numeric measures for assessing alignment quality.

Conclusions

Our new approach to visualize network alignments will allow researchers to gain a new, and better, understanding of the strengths and shortcomings of the many available network alignment algorithms.
Wash and the WASH Regulatory Complex function in Nuclear Envelope budding
Authors: Verboon Jeffrey M. , Nakamura Mitsutoshi , Decker Jacob R. , Davidson Kerri A. , Nandakumar Vivek , Parkhurst Susan M.
Published: December 2019

Nuclear envelope budding is a recently described phenomenon wherein large macromolecular complexes can be packaged inside the nucleus and be extruded through the nuclear membranes, completely bypassing nuclear pores. While factors have been identified both as cargos or actively involved in this process, much remains unknown about the molecules that generate the forces and membrane deformations which appear inherent. Using fluorescence and electron microscopy, biochemical and cell biological assays, and genetic perturbations in theDrosophilamodel, we identify Wash, its regulatory complex, and Arp2/3 as novel players in NE-budding. Surprisingly, Wash’s role in this process is bipotent and, independent of SHRC/Arp2/3, its perturbation disrupts the normal homotypic Lamin A/B meshworks that are necessary for NE-budding to occur. In addition to NE-budding emerging as important in additional cellular processes and organisms, its incredible similarity to herpesvirus egress suggests new avenues for exploration in both normal and disease biology.
Webina: An Open-Source Library and Web App that Runs AutoDock Vina Entirely in the Web Browser
Authors: Kochnev Yuri , Hellemann Erich , Cassidy Kevin C. , Durrant Jacob D.
Published: December 2019

1

Molecular docking is a computational technique for predicting how a small molecule might bind a macromolecular target. Among docking programs, AutoDock Vina is particularly popular. Like many docking programs, Vina requires users to download/install an executable file and to run that file from a Unix- or DOS-like command-line interface. Choosing proper configuration parameters and analyzing Vina output is also sometimes challenging. These issues are particularly problematic for students and novice researchers. We have created Webina, a new version of Vina, to address these challenges. Webina is a JavaScript/WebAssembly library that runs AutoDock Vina entirely in a web browser. To use Webina, users need only visit a Webina-enabled webpage. The docking calculations take place on the user’s own computer rather than a remote server. To encourage use, we have incorporated the Webina library into our own Webina web app. The app includes a convenient interface so users can easily setup their docking runs and analyze the results. Webina will be a useful open-source tool for the research and educational communities. A working version of the app can be accessed free of charge fromhttp://durrantlab.com/webina.
Implications ofTP53Allelic State for Genome Stability, Clinical Presentation and Outcomes in Myelodysplastic Syndromes
Authors: Bernard Elsa , Nannya Yasuhito , Hasserjian Robert P. , Devlin Sean M. , Tuechler Heinz , Medina-Martinez Juan S. , Yoshizato Tetsuichi , Shiozawa Yusuke , Saiki Ryunosuke , Malcovati Luca , Levine Max F. , Arango Juan E. , Zhou Yangyu , Sole Francesc , Cargo Catherine A. , Haase Detlef , Creignou Maria , Germing Ulrich , Zhang Yanming , Gundem Gunes , Sarian Araxe , van de Loosdrecht Arjan A. , Jädersten Martin , Tobiasson Magnus , Kosmider Olivier , Follo Matilde Y. , Thol Felicitas , Pinheiro Ronald F. , Santini Valeria , Kotsianidis Ioannis , Boultwood Jacqueline , Santos Fabio P.S. , Schanz Julie , Kasahara Senji , Ishikawa Takayuki , Tsurumi Hisashi , Takaori-Kondo Akifumi , Kiguchi Toru , Polprasert Chantana , Bennett John M. , Klimek Virginia M. , Savona Michael R. , Belickova Monika , Ganster Christina , Palomo Laura , Sanz Guillermo , Ades Lionel , Porta Matteo Giovanni Della , Smith Alexandra G , Werner Yesenia , Patel Minal , Viale Agnès , Vanness Katelynd , Neuberg Donna S. , Stevenson Kristen E. , Menghrajani Kamal , Bolton Kelly L. , Fenaux Pierre , Pellagatti Andrea , Platzbecker Uwe , Heuser Michael , Valent Peter , Chiba Shigeru , Miyazaki Yasushi , Finelli Carlo , Voso Maria Teresa , Shih Lee-Yung , Fontenay Michaela , Jansen Joop H. , Cervera José , Atsuta Yoshiko , Gattermann Norbert , Ebert Benjamin L. , Bejar Rafael , Greenberg Peter L. , Cazzola Mario , Hellström-Lindberg Eva , Ogawa Seishi , Papaemmanuil Elli
Published: December 2019

TP53mutations are associated with poor clinical outcomes and treatment resistance in myelodysplastic syndromes. However, the biological and clinical relevance of the underlying mono- or bi-allelic state of the mutations is unclear. We analyzed 3,324 MDS patients forTP53mutations and allelic imbalances of theTP53locus and found that 1 in 3TP53-mutated patients had mono-allelic targeting of the gene whereas 2 in 3 had multiple hits consistent with bi-allelic targeting. The established associations forTP53with complex karyotype, high-risk presentation, poor survival and rapid leukemic transformation were specific to patients with multi-hit state only.TP53multi-hit state predicted risk of death and leukemic transformation independently of the Revised International Prognostic Scoring System, while mono-allelic patients did not differ fromTP53wild-type patients. The separation by allelic state was retained in therapy-related MDS. Findings were validated in a cohort of 1,120 patients. Ascertainment ofTP53allelic state is critical for diagnosis, risk estimation and prognostication precision in MDS, and future correlative studies of treatment response should considerTP53allelic state.
Thyroid and androgen receptor signaling are antagonized by CRYM in prostate cancer
Authors: Aksoy Osman , Pencik Jan , Hartenbach Markus , Moazzami Ali A. , Schlederer Michaela , Balber Theresa , Mazumder Bismoy , Whitchurch Jonathan B , Roberts Christopher J. , Susani Martin , Mitterhauser Markus , Marculescu Rodrig , Kramer Gero , Turner Suzanne D. , Hartenbach Sabrina , Tangermann Simone , Egger Gerda , Neubauer Heidi A. , Moriggl Richard , Culig Zoran , Hoermann Gregor , Hacker Marcus , Heery David M. , Merkel Olaf , Kenner Lukas
Published: December 2019

Androgen deprivation therapy (ADT) remains a key approach in the treatment of prostate cancer (PCa). However, PCa inevitably relapses and becomes ADT resistant. Besides androgens, there is evidence that thyroid hormone thyroxine (T4) and its active form 3,5,3’-triiodo-L-thyronine (T3) are involved in the progression of PCa. Epidemiologic evidence indicates a higher incidence of PCa in men with elevated thyroid hormone levels. The thyroid hormone binding protein μ-Crystallin (CRYM) mediates intracellular thyroid hormone action by sequestering T3 and blocks its binding to cognate receptors (TRa/TRb) in target tissues. We show in this study that low CRYM expression levels in PCa patient samples are associated with early BCR and poor prognosis. Moreover, we found a disease stage-specific expression of CRYM in PCa. CRYM counteracted thyroid and androgen signaling and blocked intracellular choline uptake. CRYM inversely correlated with [18F]fluoromethylcholine (FMC) levels in PET/MRI imaging of PCa patients. Our data suggest CRYM as a novel antagonist of T3 and androgen-mediated signalling. The role of CRYM could therefore be an essential control mechanism for the prevention of aggressive PCa growth.

Highlights

Thyroid and androgen hormone driven pathways in prostate cancer (PCa) are antagonized by μ- Crystallin (CRYM).

[18F]fluoromethylcholine uptake and prognostic values in PCa correlate with CRYM protein levels.

Reduced CRYM expression predicts early biochemical recurrence (BCR) in PCa patients.