bluuebunny/crossref_metadata_2025_split huggingface dataset:
On the stability of sequences inserted into viral genomes
Authors: Willemsen Anouk , Zwart Mark P 
Published: October 2019

AbstractViruses are widely used as vectors for heterologous gene expression in cultured cells or natural hosts, and therefore a large number of viruses with exogenous sequences inserted into their genomes have been engineered. Many of these engineered viruses are viable and express heterologous proteins at high levels, but the inserted sequences often prove to be unstable over time and are rapidly lost, limiting heterologous protein expression. Although virologists are aware that inserted sequences can be unstable, processes leading to insert instability are rarely considered from an evolutionary perspective. Here, we review experimental work on the stability of inserted sequences over a broad range of viruses, and we present some theoretical considerations concerning insert stability. Different virus genome organizations strongly impact insert stability, and factors such as the position of insertion can have a strong effect. In addition, we argue that insert stability not only depends on the characteristics of a particular genome, but that it will also depend on the host environment and the demography of a virus population. The interplay between all factors affecting stability is complex, which makes it challenging to develop a general model to predict the stability of genomic insertions. We highlight key questions and future directions, finding that insert stability is a surprisingly complex problem and that there is need for mechanism-based, predictive models. Combining theoretical models with experimental tests for stability under varying conditions can lead to improved engineering of viral modified genomes, which is a valuable tool for understanding genome evolution as well as for biotechnological applications, such as gene therapy.
A Machine Learning Algorithm to Predict the Probability of (Occult) Posterior Malleolar Fractures Associated With Tibial Shaft Fractures to Guide “Malleolus First” Fixation
Authors: Hendrickx Laurent A. M. , Sobol Garret L. , Langerhuizen David W. G. , Bulstra Anne Eva J. , Hreha Jeremy , Sprague Sheila , Sirkin Michael S. , Ring David , Kerkhoffs Gino M. M. J. , Jaarsma Ruurd L. , Doornberg Job N. ,   Machine Learning Consortium
Published: October 2019

Objectives:
To develop an accurate machine learning (ML) predictive model incorporating patient, fracture, and trauma characteristics to identify individual patients at risk of an (occult) PMF.

Methods:
Databases of 2 studies including patients with TSFs from 2 Level 1 trauma centers were combined for analysis. Using ten-fold cross-validation, 4 supervised ML algorithms were trained in recognizing patterns associated with PMFs: (1) Bayes point machine; (2) support vector machine; (3) neural network; and (4) boosted decision tree. Performance of each ML algorithm was evaluated and compared based on (1) C-statistic; (2) calibration slope and intercept; and (3) Brier score. The best-performing ML algorithm was incorporated into an online open-access prediction tool.

Results:
Total data set included 263 patients, of which 28% had a PMF. Training of the Bayes point machine resulted in the best-performing prediction model reflected by good C-statistic, calibration slope, calibration intercept, and Brier score of 0.89, 1.02, −0.06, and 0.106, respectively. This prediction model was deployed as an open-access online prediction tool.

Conclusion:
A ML-based prediction model accurately predicted the probability of a (occult) PMF in patients with a TSF based on patient- and fracture-specific characteristics. This prediction model can guide surgeons in their diagnostic workup and preoperative planning. Further research is required to externally validate the model before implementation in clinical practice.

Level of Evidence:
Prognostic Level III. See Instructions for Authors for a complete description of levels of evidence.
Identification of predictors for acute postoperative pain after gynecological laparoscopy (STROBE-compliant article)
Authors: Joo Jin , Moon Hyun Kyung , Moon Young Eun 
Published: October 2019

Abstract
While the pain after gynecological laparoscopy is assumed to be minor, many women suffer from unexpected postoperative pain in the post-anesthesia care unit (PACU). Prior identification of these patients is significant for effective analgesia. Therefore, we sought to determine the predictors for acute postoperative pain after gynecological laparoscopy. The data of 280 patients undergoing gynecological laparoscopy were analyzed. Data included demographic characteristics, previous obstetric/gynecologic surgical history, menstruation pattern including dysmenorrhea severity, gynecological hormone administration history, and surgical data (surgical time, endometriosis severity, adhesion, drainage insertion, and surgery type). Univariate analysis and binary logistic regression were used to evaluate predictors for substantial pain in the PACU after gynecologic laparoscopy. Among the 280 patients, 115 (41%) suffered from substantial postoperative pain in the PACU. Whenever the level of dysmenorrhea became more severe (none → mild → moderate → severe), the risk of substantial pain in the PACU increased 2.9-fold (odds ratio [OR] 2.92, 95% confidence interval [CI] 2.11–4.03, P < .001). Moreover, patients undergoing laparoscopy for ectopic pregnancy had a higher risk of substantial pain compared with the others (OR 3.11, 95% CI 1.36–7.12, P = .007). Other factors did not show a significant association with substantial pain. Patients with preoperative severe dysmenorrhea and those undergoing laparoscopy for ectopic pregnancy should be considered to have a high risk of substantial postoperative pain in the PACU so that they receive prompt and aggressive analgesic intervention. In particular, dysmenorrhea severity is clinically valuable as a useful predictor for substantial pain after gynecological laparoscopy.
Measuring chromosome conformation by fluorescence microscopy
Authors: Ross Brian C. , Anaclerio Fabio , Lorusso Nicola , Ventura Mario , Costello Jim 
Published: October 2019

AbstractMeasurement of in-vivo chromosome conformations (structures) in single cells is a major technological goal of structural biology. If one could identify many genetic loci in a microscope image despite the limited palette of fluorescent colors used to label them, then the conformation could be solved at some resolution by ‘connecting the dots’. Computational tools for making this reconstruction are expected to produce near-perfect reconstructions when the number of fluorescent colors is high enough, irrespective of the number of loci assayed. Here we report the first experimental test of the performance of these reconstruction algorithms and check their ability to reconstruct experimentally-measured conformations. We also demonstrate the experimental metrics needed to assess reconstruction quality. Our results indicate that current sequential FISH experiments may be close to the point where the reconstructions are nearly flawless at some distance scales.
Flow-cytometric microglial sorting coupled with quantitative proteomics identifies moesin as a highly-abundant microglial protein with relevance to Alzheimer’s disease
Authors: Rayaprolu Sruti , Gao Tianwen , Xiao Hailian , Ramesha Supriya , Weinstock Laura D. , Shah Jheel , Duong Duc M. , Dammer Eric B. , Webster James A. , Lah James J. , Wood Levi B. , Betarbet Ranjita , Levey Allan I. , Seyfried Nicholas T. , Rangaraju Srikant 
Published: October 2019

AbstractBackgroundProteomic characterization of microglia provides the most proximate assessment of functionally relevant molecular mechanisms of neuroinflammation. However, microglial proteomics studies have been limited by low cellular yield and contamination by non-microglial proteins using existing enrichment strategies.MethodsWe coupled magnetic-activated cell sorting (MACS) and fluorescence activated cell sorting (FACS) of microglia with tandem mass tag-mass spectrometry (TMT-MS) to obtain a highly-pure microglial proteome and identified a core set of highly-abundant microglial proteins in adult mouse brain. We interrogated existing human proteomic data for Alzheimer’s disease (AD) relevance of highly-abundant microglial proteins and performed immuno-histochemical andin-vitrovalidation studies.ResultsQuantitative multiplexed proteomics by TMT-MS of CD11b+ MACS-enriched (N= 5 mice) and FACS-isolated (N= 5 mice), from adult wild-type mice, identified 1,791 proteins. A total of 203 proteins were highly abundant in both datasets, representing a core-set of highly abundant microglial proteins. In addition, we found 953 differentially enriched proteins comparing MACS and FACS-based approaches, indicating significant differences between both strategies. The FACS-isolated microglia proteome was enriched with cytosolic, endoplasmic reticulum, and ribosomal proteins involved in protein metabolism and immune system functions, as well as an abundance of canonical microglial proteins. Conversely, the MACS-enriched microglia proteome was enriched with mitochondrial and synaptic proteins and higher abundance of neuronal, oligodendrocytic and astrocytic proteins. From the 203 consensus microglial proteins with high abundance in both datasets, we confirmed microglial expression of moesin (Msn) in wild-type and 5xFAD mouse brains as well as in human AD brains. Msn expression is nearly exclusively found in microglia that surround Aβ plaques in 5xFAD brains. Inin-vitroprimary microglial studies, Msn silencing by siRNA decreased Aβ phagocytosis and increased lipopolysaccharide-induced production of the pro-inflammatory cytokine, tumor necrosis factor (TNF). In network analysis of human brain proteomic data, Msn was a hub protein of an inflammatory co-expression module positively associated with AD neuropathological features and cognitive dysfunction.ConclusionsUsing FACS coupled with TMT-MS as the method of choice for microglial proteomics, we define a core set of highly-abundant adult microglial proteins. Among these, we validate Msn as highly-abundant in plaque-associated microglia with relevance to human AD.
Energy-based and energy-free food-consumption are correlated in captive non-human-primates: A novel dispenser for feeding and behavioral enrichment
Authors: Shohat Yosef , Paz Rony , Pryluk Raviv , Taub Aryeh H. 
Published: October 2019

AbstractNon-human primates (NHP) provide an important model for studying biological mechanisms that underlie behavior and cognition, and are crucial for supplying translational knowledge that can aid the development of new clinical approaches. At the same time, the importance of the 3Rs to minimize suffering during experiments encouraged the development of environmental enrichment programs. Among them, tools for feeding and foraging are central. However, it remains unclear whether the behavioral enrichment tools are used by the animals only for feeding and to satisfy hunger (and hence for survival), or whether these feeding tools serve also as behavioral enrichment in itself (namely, the animals enjoy it per-se). To answer this, we designed a novel dispenser method – that requires significant yet reasonable energetic effort to obtain food - and tested food consumption via the dispenser compared to free-access, namely that did not require any effort on the animal side. We found that primates consumed food from both the dispenser and when presented in free-access, and importantly, that the consumption via the dispenser was in correlation with the consumption in free-access. This was similar across different subjects, different times during the day, and different types of food. We suggest that monkeys can benefit from using the dispenser for food consumption, but also benefit from it for play (i.e. as behavioral enrichment in itself). Such an approach allows non-human-primates to preserve their natural food procurement activities.
Differences in signalling, trafficking and glucoregulatory properties of glucagon-like peptide-1 receptor agonists exendin-4 and lixisenatide
Authors: Pickford Philip , Lucey Maria , Fang Zijian , Bitsi Stavroula , Broichhagen Johannes , Hodson David J. , Minnion James , Rutter Guy A , Bloom Stephen R , Tomas Alejandra , Jones Ben 
Published: October 2019

AbstractBackground and purposeAmino acid substitutions at the N-termini of glucagon-like peptide-1 receptor agonist (GLP-1RA) peptides result in distinct patterns of intracellular signalling, sub-cellular trafficking and efficacyin vivo. Here we aimed to determine whether sequence differences at the ligand C-termini of clinically approved GLP-1RAs exendin-4 and lixisenatide lead to similar phenomena. We also sought to establish the impact of the C-terminus on signal bias resulting from modifications elsewhere in the molecule.Experimental approachExendin-4, lixisenatide, and N-terminally substituted analogues with biased signalling characteristics were compared across a range ofin vitrotrafficking and signalling assays in different cell types. Fluorescent ligands and new time-resolved FRET approaches were developed to study agonist behaviours at the cellular and sub-cellular level. Anti-hyperglycaemic and anorectic effects of each parent ligand, and their biased derivatives, were assessed in mice.Key resultsLixisenatide and exendin-4 showed equal binding affinity, but lixisenatide was 5-fold less potent for cAMP signalling. Both peptides were rapidly endocytosed, but the GLP-1R recycled more slowly to the plasma membrane after lixisenatide treatment. These combined deficits resulted in reduced maximal sustained insulin secretion and reduced anti-hyperglycaemic and anorectic effects in mice. N-terminal substitutions to both ligands had favourable effects on their pharmacology, resulting in improved insulin release and lowering of blood glucose.Conclusion and implicationsChanges to the C-terminus of exendin-4 affect signalling potency and GLP-1R trafficking via mechanisms unrelated to GLP-1R occupancy. These differences were associated with changes in their ability to control blood glucose and therefore may be therapeutically relevant.
Expression and purification of Protease Activated Receptor 4 (PAR4) and analysis with histidine hydrogen deuterium exchange
Authors: de la Fuente Maria , Han Xu , Miyagi Masaru , Nieman Marvin T. 
Published: October 2019

ABSTRACTProtease activated receptors (PARs) are G-protein coupled receptors (GPCRs) that are activated by proteolyis of the N-terminus, which exposes a tethered ligand that interacts with the receptor. Numerous studies have focused on the signaling pathways mediated by PARs. However, the structural basis for initiation of these pathways is unknown. Here, we describe a strategy for the expression and purification of PAR4. This is the first PAR family member to be isolated without stabilizing modifications for biophysical studies. We monitored PAR4 activation with histidine-hydrogen deuterium exchange (His-HDX). PAR4 has 9 histidines that are spaced throughout the protein allowing a global view of solvent accessible and non-accessible regions. Peptides containing each of the 9 His residues were used to determine the t1/2 for each His residue in apo or thrombin activated PAR4. The thrombin cleaved PAR4 had a 2-fold increase (p > 0.01) in t1/2 values observed for four histidine residues (His180, His229, His240, and His380) demonstrating that these regions have decreased solvent accessibility upon thrombin treatment. In agreement, thrombin cleaved PAR4 also was resistant to thermolysin digestion. In contrast, activation with the PAR4 agonist peptide was digested at the same rate as apo PAR4. Further analysis showed the C-terminus is protected in thrombin activated PAR4 compared to uncleaved or agonist peptide treated PAR4. The studies described here are the first to examine the tethered ligand activation mechanism for a PAR family member using biophysically and shed light on the overall conformational changes that follow activation of PARs by a protease.
Architecture of the chromatin remodeler RSC and insights into its nucleosome engagement
Authors: Patel Avinash B. , Moore Camille M. , Greber Basil J. , Luo Jie , Ranish Jeff , Nogales Eva 
Published: October 2019

AbstractEukaryotic DNA is packaged into nucleosome arrays, which are repositioned by chromatin remodeling complexes to control DNA accessibility1,2. The Saccharomyces cerevisiae RSC (Remodeling the Structure of Chromatin) complex, a member of the SWI/SNF chromatin remodeler family, plays critical roles in genome maintenance, transcription, and DNA repair2–4. Here we report cryo-electron microscopy (cryo-EM) and crosslinking mass spectrometry (CLMS) studies of yeast RSC complex and show that RSC is composed of a rigid tripartite core and two flexible lobes. The core structure is scaffolded by an asymmetric Rsc8 dimer and built with the evolutionarily conserved subunits Sfh1, Rsc6, Rsc9 and Sth1. The flexible ATPase lobe, composed of helicase subunit Sth1, Arp7, Arp9 and Rtt102, is anchored through the interactions between the N-terminus of Sth1 and the core. Our cryo-EM analysis also shows that in addition to the expected nucleosome-Sth1 interactions, RSC engages histones and nucleosomal DNA through one arm of the core structure, composed of Rsc8 SWRIM domains, Sfh1 and Npl6. Our findings provide structural insights into the conserved assembly process for all members of the SWI/SNF family of remodelers, and illustrate how RSC selects, engages, and remodels nucleosomes.
Integrative genomic, transcriptomic, and epigenomic analyses of benign prostatic hyperplasia reveal new options for therapy
Authors: Liu Deli , Shoag Jonathan , Poliak Daniel , Goueli Ramy S. , Ravikumar Vaishali , Redmond David , Vosoughi Aram , Fontugne Jacqueline , Pan Heng , Lee Daniel , Thomas Domonique , Salari Keyan , Wang Zongwei , Romanel Alessandro , Te Alexis , Lee Richard , Chughtai Bilal , Olumi Aria F. , Mosquera Juan Miguel , Demichelis Francesca , Elemento Olivier , Rubin Mark A. , Sboner Andrea , Barbieri Christopher E. 
Published: October 2019

AbstractBenign prostatic hyperplasia (BPH), a nonmalignant enlargement of the prostate, is one of the most common diseases affecting aging men, but the underlying molecular features of BPH remain poorly understood, and therapeutic options are limited. Here we employed a comprehensive molecular investigation of BPH, including genomic, transcriptomic and epigenetic profiling of 18 BPH cases. At the molecular level, we found no evidence of neoplastic features in BPH: no evidence of driver genomic alterations, including low coding mutation rates, mutational signatures consistent with aging tissues, minimal copy number alterations, and no genomic rearrangements. Similarly at the epigenetic level, we found global hypermethylation was the dominant process (unlike most neoplastic processes). By integrating transcriptional and methylation signatures, we identified two BPH subgroups with distinct clinical features and associated signaling pathways, which were validated in two independent cohorts. Finally, our analyses nominatedmTORinhibitors as a potential subtype-specific therapeutic option. Supporting this, a cohort of men exposed tomTORinhibitors showed a significant decrease in prostate size. Our results demonstrate that BPH consists of distinct molecular subgroups, with potential for subtype-specific precision therapy viamTORinhibition.
Low dose Cold Atmospheric Plasma induces membrane oxidation, stimulates endocytosis and enhances uptake of nanomaterials in Glioblastoma multiforme cells
Authors: He Zhonglei , Liu Kangze , Scally Laurence , Manaloto Eline , Gunes Sebnem , Ng Sing Wei , Maher Marcus , Tiwari Brijesh , Byrne Hugh J , Bourke Paula , Tian Furong , Cullen Patrick J , Curtin James F 
Published: October 2019

AbstractCold atmospheric plasma (CAP) has demonstrated synergistic cytotoxic effects with nanoparticles, especially promoting the uptake and accumulation of nanoparticles inside cells. However, the mechanisms driving the effects need to be explored. In this study, we investigate the enhanced uptake of theranostic nanomaterials by CAP. Numerical modelling of the uptake of gold nanoparticle into U373MG Glioblastoma multiforme (GBM) cells predicts that CAP may introduce a new uptake route. We demonstrate that cell membrane repair pathways play the main role in this stimulated new uptake route, following non-toxic doses of dielectric barrier discharge CAP (30 s, 75 kV). CAP treatment induces cellular membrane damage, mainly via lipid peroxidation as a result of reactive oxygen species (ROS) generation. Membranes rich in peroxidated lipids are then trafficked into cells via membrane repairing endocytosis. We confirm that the enhanced uptake of nanomaterials is clathrin-dependent using chemical inhibitors and silencing of gene expression. Therefore, CAP-stimulated membrane repair increases endocytosis and accelerates the uptake of gold nanoparticles into U373MG cells after CAP treatment. Our data demonstrate the utility of CAP to model membrane oxidative damage in cells and characterise a previously unreported mechanism of membrane repair to trigger nanomaterial uptake which will be useful for developing more efficient deliveries of nanoparticles and pharmaceuticals into cancer cells for tumour therapy and diagnosis. This mechanism of RONS-induced endocytosis will also be of relevance to other cancer therapies that induce an increase in extracellular RONS.
Perceptual Invariance of Words and Other Learned Sounds in Non-human Primates
Authors: Melchor Jonathan , Morán Isaac , Figueroa Tonatiuh , Lemus Luis 
Published: October 2019

AbstractThe ability to invariably identify spoken words and other naturalistic sounds in different temporal modulations and timbres requires perceptual tolerance to numerous acoustic variations. However, the mechanisms by which auditory information is perceived to be invariant are poorly understood, and no study has explicitly tested the perceptual constancy skills of nonhuman primates. We investigated the ability of two trained rhesus monkeys to learn and then recognize multiple sounds that included multisyllabic words. Importantly, we tested their ability to group unexperienced sounds into corresponding categories. We found that the monkeys adequately categorized sounds whose formants were at close Euclidean distance to the learned sounds. Our results indicate that macaques can attend and memorize complex sounds such as words. This ability was not studied or reported before and can be used to study the neuronal mechanisms underlying auditory perception.