bluuebunny/crossref_metadata_2025_split huggingface dataset:
Effectiveness and safety over 3 years after the 2-year U-Act-Early trial of the strategies initiating tocilizumab and/or methotrexate
Authors: Verhoeven Maxime M A , Tekstra Janneke , Welsing Paco M J , Pethö-Schramm Attila , Borm Michelle E A , Bruyn George A W , Bos Reinhard , Griep Ed N , Klaasen Ruth , van Laar Jacob M , Lafeber Floris P J G , Bijlsma Johannes W J , de Hair Marjolein J H , Jacobs Johannes W G 
Published: November 2019

Abstract

Objectives
U-Act-Early was a 2-year, randomized placebo controlled, double-blind trial, in which DMARD-naïve early RA patients were treated to the target of sustained remission (SR). Two strategies initiating tocilizumab (TCZ), with and without methotrexate (MTX), were more effective than a strategy initiating MTX. The aim of the current study was to determine longer-term effectiveness in daily clinical practice.

Methods
At the end of U-Act-Early, patients were included in a 3-year post-trial follow-up (PTFU), in which treatment was according to standard care and data were collected every 3 months during the first year and every 6 months thereafter. Primary end point was disease activity score assessing 28 joints (DAS28) over time. Mixed effects models were used to compare effectiveness between initial strategy groups, correcting for relevant confounders. Between the groups as randomized, proportions of patients were tested for DMARD use, SR and radiographic progression of joint damage.

Results
Of patients starting U-Act-Early, 226/317 (71%) participated in the PTFU. Over the total 5 years, mean DAS28 was similar between groups (P &gt; 0.20). During U-Act-Early, biologic DMARD use decreased in both TCZ initiation groups and increased in the MTX initiation group, but during follow-up this trend did not continue. SR was achieved at least once in 99% of patients. Of the 226 patients, only 30% had any radiographic progression over 5 years, without significant differences between the groups.

Conclusion
Although in the short-term the strategies initiating TCZ yielded the most clinical benefit, in the longer-term differences in important clinical outcomes between the strategies disappeared, probably due to continuation of the treat-to-target principle.
Chemogenetic modulation of the parafacial respiratory group influences the recruitment of abdominal activity during REM sleep
Authors: Pisanski Annette , Ding Xiuqing , Koch Nils A , Pagliardini Silvia 
Published: November 2019

Abstract
Current theories on respiratory control postulate that the respiratory rhythm is generated by oscillatory networks in the medulla: preBötzinger complex (preBötC) is the master oscillator responsible for generating inspiration, while parafacial respiratory group (pFRG) drives active expiration through recruitment of expiratory abdominal (ABD) muscle activity. Research addressing the role of pFRG in ventilation and rhythm generation across sleep states is limited. We recently reported the occurrence of ABD recruitment occurring despite the induction of muscle paralysis during REM sleep. This ABD recruitment was associated with increased tidal volume and regularization of the respiratory period in rats. As pFRG generates active expiration through the engagement of ABD muscles, we hypothesized that the expiratory oscillator is also responsible for the ABD recruitment observed during REM sleep. To test this hypothesis, we inhibited and activated pFRG using chemogenetics (i.e. designer receptors exclusively activated by designer drugs) while recording EEG and respiratory muscle EMG activities across sleep–wake cycles in male Sprague–Dawley rats. Our results suggest that inhibition of pFRG reduced the number of REM events expressing ABD recruitment, in addition to the intensity and prevalence of these events. Conversely, activation of pFRG resulted in an increase in the number of REM events in which ABD recruitment was observed, as well as the intensity and prevalence of ABD recruitment. Interestingly, modulation of pFRG activity did not affect ABD recruitment during NREM sleep or wakefulness. These results suggest that the occurrence of ABD recruitment during sleep is dependent on pFRG activity and is state dependent.
Nick-seq for single-nucleotide resolution genomic maps of DNA modifications and damage
Authors: Cao Bo , Wu Xiaolin , Zhou Jieliang , Wu Hang , DeMott Michael S. , Gu Chen , Wang Lianrong , You Delin , Dedon Peter C. 
Published: November 2019

AbstractHere we present the Nick-seq platform for quantitative mapping of DNA modifications and damage at single-nucleotide resolution across genomes. Pre-existing breaks are blocked and DNA structures converted to strand-breaks for 3’-extension by nick-translation to produce nuclease-resistant oligonucleotides, and 3’-capture by terminal transferase tailing. Libraries from both products are subjected to next-generation sequencing. Nick-seq is a generally applicable method illustrated with quantitative profiling of single-strand-breaks, phosphorothioate modifications, and DNA oxidation.
Verifying molecular clusters by 2-color localization microscopy and significance testing
Authors: Arnold Andreas M. , Schneider Magdalena C. , Hüsson Christoph , Sablatnig Robert , Brameshuber Mario , Baumgart Florian , Schütz Gerhard J. 
Published: November 2019

AbstractWhile single-molecule localization microscopy (SMLM) offers the invaluable prospect to visualize cellular structures below the diffraction limit of light microscopy, its potential could not be fully capitalized due to its inherent susceptibility to blinking artifacts. Particularly, overcounting of single molecule localizations has impeded a reliable and sensitive detection of biomolecular nanoclusters. Here we introduce a 2-Color Localization microscopy And Significance Testing Approach (2-CLASTA), providing a parameter-free statistical framework for the analysis of SMLM data via significance testing methods. 2-CLASTA yields p-values for the null hypothesis of random biomolecular distributions, independent of the blinking behavior of the chosen fluorescent labels. We validated the method both by computer simulations as well as experimentally, using protein concatemers as a mimicry of biomolecular clustering. As the new approach it is not affected by overcounting artifacts, it is able to detect biomolecular clustering of various shapes at high sensitivity down to a level of dimers.
Phytohormonal cross-talk modulate Bipolaris sorokiniana (Scc.)interaction with Zea mays
Authors: Yousaf Muhammad Junaid , Hussain Anwar , Hamayun Muhammad , Iqbal Amjad , Irshad Muhammad , Ahmad Ayaz , Lee In-Jung 
Published: November 2019

AbstractBesides acting as growth inducing molecule, Gibberellin (GA3) also confers the compatibility of microbial interactions with host. We inoculated 11 days oldZ. maysseedlings grown under hydroponic conditions and high GA3levels withBipolaris sorokiniana(BIPOL) at the spore density (SD) of OD0.6. The high level of GA3negatively affected the growth of the seedlings, accompanied by the high level of stress deducing secondary metabolites (proline, total flavanoids, phenylpropanoids, and glucosinolides). Moreover, high level of GA3produced a hypersensitive response (HR) in the seedlings. The HR developed cross talks with IAA and trans-zeatins and triggered higher production of hypersensitive inducing biomolecules. The other HR co-related biological processes were demonstrated by high phytoalexins level and high protease activities. Such activities ultimately inhibited the colonization of BIPOL on the roots of maize seedlings. The products of the genes expressed at high GA3also conferred the deterrence of BIPOL colonization at SD = OD0.6. Intriguingly, when we inhibited GA3biosynthesis in the seedlings with aerially sprayed uniconizole, prior to BIPOL treatment, the BIPOL colonized and subsequently promoted the seedling growth. This low level of GA3after BIPOL treatment checked the high level of secondary metabolites and hypersensitivity inducing molecules. The results, thus suggested that the aforementioned processes only happened in the BIPOL at SD (OD0.6), whereas the SD at lower levels (OD0.2or OD0.4) neither promoted the growth of uniconizole pre-treated seedlings nor produced HR in control seedlings of maize plant.
Strand asymmetry influences mismatch resolution during single-strand annealing
Authors: Pokusaeva Victoria O. , Diez Aránzazu Rosado , Espinar Lorena , Filion Guillaume J. 
Published: November 2019

ABSTRACTBackgroundBiases of DNA repair can shape the nucleotide landscape of genomes at evolutionary timescales. However, such biases have not yet been measured in chromatin for lack of technologies.ResultsHere we develop a genome-wide assay whereby the same DNA lesion is repaired in different chromatin contexts. We insert thousands of barcoded transposons carrying a reporter of DNA mismatch repair in the genome of mouse embryonic stem cells. Upon inducing a double-strand break between tandem repeats, a mismatch is generated when the single strand annealing repair pathway is used. Regardless of the mismatch, we observed a 60-80% bias in the resolution in favor of one strand. The location of the lesion in the genome and the type of mismatch had little influence on the bias in this context. Instead, changing the position of the double-strand break in the reporter gave a complete reversion of the bias.ConclusionThese results suggest that the processing of the double-strand break has a major influence on the repair of mismatches during single-strand annealing, irrespective of the surrounding chromatin context.
Quantitative high-resolution imaging of live microbial cells at high hydrostatic pressure
Authors: Bourges A. C. , Lazarev A. , Declerck N. , Rogers K. L. , Royer C. A. 
Published: November 2019

ABSTRACTThe majority of the Earth’s microbial biomass exists in the Deep Biosphere, in the deep ocean and within the Earth’s crust. While other physical parameters in these environments, such as temperature or pH, can differ substantially, they are all under high-pressures. Beyond emerging genomic information, little is known about the molecular mechanisms underlying the ability of these organisms to survive and grow at pressures that can reach over 1000-fold pressure on the Earth’s surface. The mechanisms of pressure adaptation are also important to in food safety, with the increasing use of high-pressure food processing. Advanced imaging represents an important tool for exploring microbial adaptation and response to environmental changes. Here we describe implementation of a high-pressure sample chamber with a 2-photon scanning microscope system allowing for the first time, quantitative high-resolution two-photon imaging at 100 MPa of living microbes from all three kingdoms of life. We adapted this setup for Fluorescence Lifetime Imaging Microscopy with Phasor analysis (FLIM/Phasor) and investigated metabolic responses to pressure of live cells from mesophilic yeast and bacterial strains, as well as the piezophilic archaeon,Archaeoglobus fulgidus. We also monitored by fluorescence intensity fluctuation-based methods (scanning Number and Brightness (sN&B) and Raster scanning Imaging Correlation Spectroscopy (RICS)) the effect of pressure on the chromosome-associated protein HU and on the ParB partition protein inE. coli, revealing partially reversible dissociation of ParB foci and concomitant nucleoid condensation.SIGNIFICANCEThe majority of the Earth’s microbial biomass exists in high-pressure environments where pressures can reach over 100 MPa. The molecular mechanisms that allow microbes to flourish under such extreme conditions remain to be discovered. The high pressure, high resolution imaging system presented here revealed pressure dependent changes in metabolism and protein interactions in live microbial cells, demonstrating great promise for understanding deep life.
An in vivo KRAS allelic series reveals distinct phenotypes of common oncogenic variants
Authors: Zafra Maria Paz , Alonso-Curbelo Direna , Goswami Sukanya , Schatoff Emma M , Han Teng , Wilkinson John E , Dow Lukas E 
Published: November 2019

ABSTRACTKRAS is the most frequently mutated oncogene in cancer. Tumor sequencing has revealed a complex spectrum of KRAS mutations across different cancer types, yet there is little understanding how specific KRAS alterations impact tumor in initiation, progression, or therapy response. Using high-fidelity CRISPR-based engineering, we created an allelic series of new LSL-Kras mutant mice, reflecting codon 12 and 13 mutations that are highly prevalent in lung (KRASG12C), pancreas (KRASG12R) and colon (KRASG13D) cancers. Induction of each mutation in the developing mouse pancreas reveal striking quantitative and qualitative differences in the degree of ductal transformation and pre-malignant progression. Further, using organoid models we show that KRASG13D mutants respond to EGFR inhibition, while the anti-proliferative effect of KRASG12C-selective inhibitors can be overcome by upstream EGFR signaling. Together, these new mouse strains provide an ideal for investigating KRAS biology in vivo, and for developing pre-clinical precision oncology models of KRAS-mutant pancreas (G12R), colon (G13D), and lung (G12C) cancers.
Structural characterization of the N-terminal domain of theDictyostelium discoideummitochondrial calcium uniporter
Authors: Yuan Yuan , Cao Chan , Wen Maorong , Li Min , Dong Ying , Wu Lijie , Wu Jian , Cui Tanxing , Li Dianfan , Chou James J. , OuYang Bo 
Published: November 2019

AbstractThe mitochondrial calcium uniporter (MCU) plays a critical role in the mitochondrial calcium uptake into the matrix. In metazoans, the uniporter is a tightly regulated multi-component system including the pore-forming subunit MCU and several regulators (MICU1, MICU2, EMRE). The calcium-conducting activity of metazoan MCU requires the single-transmembrane protein EMRE.Dictyostelium discoideum(Dd), however, developed a simplified uniporter for which the pore-forming MCU (DdMCU) alone is necessary and sufficient for calcium influx. Here, we report a crystal structure of the N-terminal domain (NTD) of DdMCU at 1.7 Å resolution. The DdMCU-NTD contains four helices and two strands arranged in a fold that is completely different from the known structures of other MCU-NTD homologs. Biochemical and biophysical analyses of DdMCU-NTD in solution indicated that the domain exists as oligomers, most probably as a pentamer or hexamer. Mutagenesis showed that the acidic residues Asp60, Glu72 and Glu74, which appeared to mediate the parallel interface as observed in the crystal structure, participated in the self-assembly of DdMCU-NTD. Intriguingly, the oligomeric complex readily dissociated to lower-order oligomers in the presence of calcium. We propose that the calcium-triggered dissociation of NTD regulates the channel activity of DdMCU by a yet unknown mechanism.
Effects of dopamine receptor antagonism and amphetamine-induced psychomotor sensitization on sign- and goal-tracking after extended training
Authors: Yon-Seng Khoo Shaun , Uhrig Alexandra , Samaha Anne-Noël , Chaudhri Nadia 
Published: November 2019

AbstractThe dopamine system is important for incentive salience attribution, where motivational value is assigned to conditioned cues that predict appetitive reinforcers. However, the role of dopamine in this process may change with extended training. We tested the effects of dopamine D1-like and D2-like receptor antagonism on the expression of sign-tracking and goal-tracking conditioned responses following extended Pavlovian conditioned approach (PCA) training. We also tested if amphetamine-induced psychomotor sensitization accelerates the enhanced acquisition of sign-tracking that is observed with extended training. In experiment 1, 24 male Long-Evans rats received 20 PCA sessions in which one lever (CS+, 10 s) predicted 0.2 mL sucrose (10%, w/v) delivery and the other lever (CS−) did not. SCH-23390 (D1-like antagonist) or eticlopride (D2-like antagonist) were administered before non-reinforced behavioural tests at doses of 0, 0.01, and 0.1 mg/kg (s.c.). In experiment 2, rats received vehicle or 2 mg/kg amphetamine (i.p.) for 7 days (n = 12/group). Ten days later, they received 16 PCA training sessions. Both doses of SCH-23390 reduced sign- and goal-tracking, but also reduced locomotor behaviour. A low dose of eticlopride (0.01 mg/kg) selectively reduced goal-tracking, without affecting sign-tracking or locomotor behaviour. Amphetamine produced psychomotor sensitization, and this did not affect the acquisition of sign- or goal-tracking. Following extended PCA training, dopamine D2-like receptor activity is required for the expression of goal-tracking but not sign-tracking. Psychomotor sensitization to amphetamine did not impact incentive salience attribution; however, more selective manipulations of the dopamine system may be needed.
Insect egg-killing: a new front on the evolutionary arms-race between Brassicaceae plants and Pierid butterflies
Authors: Griese Eddie , Caarls Lotte , Mohammadin Setareh , Bassetti Niccolò , Bukovinszkine’Kiss Gabriella , Breman Floris C. , Poelman Erik H. , Gols Rieta , Eric Schranz M. , Fatouros Nina E. 
Published: November 2019

AbstractEvolutionary arms-races between plants and herbivores have been proposed to generate key innovations that can drive diversification of the interacting species. Recent studies reveal that plant traits that target herbivore insect eggs are widespread throughout the plant kingdom. Within the Brassicaceae family, some plants express a hypersensitive response (HR)-like necrosis underneath the eggs of specialist cabbage white butterflies (Pieridae) that leads to eggs desiccating or dropping of the leaf. Here, we studied the evolutionary basis of this trait, its egg-killing effect on and elicitation by specialist butterflies, by screening 31 Brassicaceae species and nine Pieridae species. We show that induction of HR-like necrosis by pierid egg deposition is clade-specific in the economically important Brassiceae tribe (Brassica crops and close-relatives) and in the first-branching genus Aethionema. The necrosis is elicited only by pierid butterflies that feed on Brassicaceae plants; four Pieris and Anthocharis cardamines butterflies, of which the larvae are specialists on Brassicaceae, elicited a HR-like necrosis. Eggs of pierid butterflies that feed on Rhamnaceae (Gonepteryx rhamni) or Fabaceae (Colias spp.) however, did not elicit such a leaf necrosis. Finally, eggs of Aglais io, a species of the sister group Nymphalidae, did not elicit any visible response. Counter-adaptations to HR-like necrosis might have evolved by insect deposition of eggs in clusters or on inflorescences. Our findings suggest that the plants’ egg-killing trait is a new front on the evolutionary arms-race between Brassicaceae and pierid butterflies beyond the well-studied chemical defence traits against caterpillars.
Learning of complex auditory patterns changes intrinsic and feedforward effective connectivity between Heschl’s gyrus and planum temporale
Authors: Lumaca Massimo , Dietz Martin J. , Hansen Niels Chr. , Quiroga-Martinez David R. , Vuust Peter 
Published: November 2019

AbstractLearning of complex auditory sequences such as language and music can be thought of as the continuous optimisation of internal predictive representations of sound-pattern regularities, driven by prediction errors. In predictive coding (PC), this occurs through changes in the intrinsic and extrinsic connectivity of the relevant cortical networks, whereby minimization of precision-weighted prediction error signals improves the accuracy of future predictions. Here, we employed Dynamic Causal Modelling (DCM) on functional magnetic resonance (fMRI) data acquired during the presentation of complex auditory patterns. In an oddball paradigm, we presented 52 volunteers (non-musicians) with isochronous 5-tone melodic patterns (standards), randomly interleaved with rare novel patterns comprising contour or pitch interval changes (deviants). Here, listeners must update their standard melodic models whenever they encounter unexpected deviant stimuli. Contour deviants induced an increased BOLD response, as compared to standards, in primary (Heschl’s gyrus, HG) and secondary auditory cortices (planum temporale, PT). Within this network, we found a left-lateralized increase in feedforward connectivity from HG to PT for deviant responses and a concomitant disinhibition within left HG. Consistent with PC, our results suggest that model updating in auditory pattern perception and learning is associated with specific changes in the excitatory feedforward connections encoding prediction errors and in the intrinsic connections that encode the precision of these errors and modulate their gain.Significance statementThe learning of complex auditory stimuli such as music and speech can be thought of as the continuous optimisation of brain predictive models driven by prediction errors. Using dynamic causal modelling on fMRI data acquired during a melodic oddball paradigm, we here show that brain responses to unexpected sounds were best explained by an increase in excitation within Heschl’s gyrus and an increase in forward connections from Heschl’s gyrus to planum temporale. Our results are consistent with a predictive coding account of sensory learning, whereby prediction error responses to new sounds drive model adjustments via feedforward connections and intrinsic connections encode the confidence of these prediction errors.
The Role of the Ovarian Cancer G -Coupled Receptor (OGR1) in Idiopathic Pulmonary Fibrosis
Authors: Nagel David J. , Clough Ryan , Bell Tyler J. , Ku Wei-Yao , Sime Patricia J. , Kottmann R. M. 
Published: November 2019

AbstractIdiopathic pulmonary fibrosis (IPF) is a disease characterized by irreversible scarring of the lung that is associated with significant mortality and morbidity. The pathophysiology is incompletely understood but it is well-established that fibroblast to myofibroblast differentiation is a key feature of pulmonary fibrosis. Our lab has established that a reduction in extracellular pH is one of several important pathways responsible for the activation of latent TGF-β in the extracellular space. TGF-β activation further decreases extracellular pH and creates a feed-forward mechanism that stimulates myofibroblast differentiation and activation of additional TGF-β. Given the importance of TGF-β and extracellular acidification to the progression of pulmonary fibrosis, we sought to identify novel mechanisms that are involved in pH-dependent fibrotic signaling. The proton sensing G-Protein Coupled family of receptors are activated in acidic environments, but their role in fibrotic signaling has not been studied. Here we report that the Ovarian Cancer G-Protein Coupled Receptor1 (OGR1 or GPR68), a member of the family of proton sensing G-Protein Coupled Receptors, negatively regulates pro-fibrotic signaling. We demonstrate that OGR1 expression is significantly reduced in lung tissue from patients with IPF and TGF-β decreases OGR1 expression. In fibroblasts, a reduction in expression of OGR1 (OGR knockout lung fibroblasts) and knockdown (OGR siRNA), promotes in vitro myofibroblast differentiation. In contrast, OGR1 overexpression inhibits myofibroblast differentiation. Finally, we demonstrate that OGR1 negatively regulates TGF-β stimulation through inhibition of focal adhesion kinase (FAK) phosphorylation. Our results suggest that preserving OGR1 expression may represent a novel therapeutic strategy in pulmonary fibrosis.