bluuebunny/crossref_metadata_2025_split huggingface dataset:
Classism in Pain Care: The Role of Patient Socioeconomic Status on Nurses’ Pain Assessment and Management Practices
Authors: Brandão Tânia , Campos Lúcia , de Ruddere Lies , Goubert Liesbet , Bernardes Sónia F 
Published: June 2019

Abstract

Objective
Research on social disparities in pain care has been mainly focused on the role of race/racism and sex/sexism. Classism in pain assessment and management practices has been much less investigated. We aimed to test the effect of patient socioeconomic status (SES; a proxy of social class) on nurses’ pain assessment and management practices and whether patient SES modulated the effects of patient distress and evidence of pathology on such practices.

Design
Two experimental studies with a two (patient SES: low/high) by two (patient distress or evidence of pathology: absent/present) between-subject design.

Subjects
Female nurses participated in two experimental studies (N = 150/N = 158).

Methods
Nurses were presented with a vignette/picture depicting the clinical case of a female with chronic low back pain, followed by a video of the patient performing a pain-inducing movement. Afterwards, nurses reported their pain assessment and management practices.

Results
The low-SES patient’s pain was assessed as less intense, more attributed to psychological factors, and considered less credible (in the presence of distress cues) than the higher-SES patient’s pain. Higher SES buffered the detrimental impact of the presence of distress cues on pain assessment. No effects were found on management practices.

Conclusions
Our findings point to the potential buffering role of SES against the detrimental effect of certain clinical cues on pain assessments. This study contributes to highlighting the need for further investigation of the role of SES/social class on pain care and its underlying meanings and processes.
Directed evolution of a bacterial WS/DGAT acyltransferase: improving tDGAT from Thermomonospora curvata
Authors: Santín Omar , Galié Serena , Moncalián Gabriel 
Published: June 2019

Abstract
Some bacteria belonging to the actinobacteria and proteobacteria groups can accumulate neutral lipids expressing enzymes of the wax ester synthase/acyl coenzyme A: diacylglycerol acyltransferase (WS/DGAT) family. tDGAT is a WS/DGAT-like enzyme from Thermomonospora curvata able to produce TAGs and WEs when heterologously expressed in Escherichia coli. In this study, a protocol for the directed evolution of bacterial lipid-producing enzymes based on fluorimetry is developed and tested. tDGAT has been successfully evolved towards the improvement of TAG production with an up to 2.5 times increase in TAG accumulation. Mutants with no ability to produce TAGs but able to accumulate waxes were also selected during the screening. The localization of the mutations that enhance TAG production in the outer surface of tDGAT points out possible new mechanisms that contribute to the activity of this family of enzymes. This Nile red-based high throughput screening provides an evolution platform for other WS/DGAT-like enzymes.
Using a Multi-Stage hESC Model to Characterize BDE-47 Toxicity During Neurogenesis
Authors: Chen Hao , Seifikar Helia , Larocque Nicholas , Kim Yvonne , Khatib Ibrahim , Fernandez Charles J , Abello Nicomedes , Robinson Joshua F 
Published: June 2019

AbstractAlthough the ramifications associated with polybrominated diphenyl ethers (PBDEs) exposures during human pregnancy have yet to be determined, increasing evidence in humans and animal models suggests that these compounds cause neurodevelopmental toxicity. Human embryonic stem cells (hESCs) models can be used to study the effects of environmental chemicals throughout the successive stages of neuronal development. Here, using a hESC differentiation model, we investigated the effects of common PBDE congeners (BDE-47 or -99) on the successive stages of early neuronal development. First, we determined the points of vulnerability to PBDEs across 4 stages of in vitro neural development by using assays to assess for cytotoxicity. Differentiated neural progenitors were identified to be more sensitive to PBDEs than their less differentiated counterparts. In follow-up investigations, we observed BDE-47 to inhibit functional processes critical for neurogenesis (eg, proliferation, expansion) in hESC-derived neural precursor cells (NPCs) at sub-lethal concentrations. Finally, to determine the mechanism(s) underlying PBDE-toxicity, we conducted global transcriptomic and methylomic analyses of BDE-47. We identified 589 genes to be differentially expressed due to BDE-47 exposure, including molecules involved in oxidative stress mediation, cell cycle, hormone signaling, steroid metabolism, and neurodevelopmental pathways. In parallel analyses, we identified a broad significant increase in CpG methylation. In summary our results suggest, on a cellular level, PBDEs induce human neurodevelopmental toxicity in a concentration-dependent manner and sensitivity to these compounds is dependent on the developmental stage of exposure. Proposed mRNA and methylomic perturbations may underlie toxicity in early embryonic neuronal populations.
Epigenetic regulation of a mouse PPARγ splicing variant, Pparγ1sv, during adipogenesis in 3T3-L1 cells
Authors: Takenaka Yasuhiro , Nakano Takanari , Ikeda Masaaki , Kakinuma Yoshihiko , Inoue Ikuo 
Published: June 2019

AbstractWe have previously reported the abundant and ubiquitous expression of a newly identified splicing variant of mouse peroxisome proliferator-activated receptor-γ (Pparγ), namely Pparγ1sv that encodes PPARγ1 protein, and plays an important role in adipogenesis. Pparγ1sv has a unique 5’UTR sequence, compared to those of mouse Pparγ1 and Pparγ2 mRNAs. This implies the presence of a novel transcriptional initiation site and promoter for Pparγ1sv. We found that DNA methylation of 42 CpG sites in the proximal promoter region (−733 to −76) of Pparγ1sv was largely unchanged five days after adipocyte differentiation, whereas chromatin immunoprecipitation-quantitative PCR (ChIP-qPCR) using antibodies against H3K4me3 and H3K27ac revealed that these modifications significantly elevated at the transcription start sites of Pparγ1sv and Pparγ2 after differentiation.
Chemical Impacts of the Microbiome Across Scales Reveal Novel Conjugated Bile Acids
Authors: Quinn Robert A. , Vrbanac Alison , Melnik Alexey V. , Patras Kathryn A. , Christy Mitchell , Nelson Andrew T. , Aksenov Alexander , Tripathi Anupriya , Humphrey Greg , da Silva Ricardo , Bussell Robert , Thron Taren , Wang Mingxun , Vargas Fernando , Gauglitz Julia M. , Meehan Michael J. , Poulsen Orit , Boland Brigid S. , Chang John T. , Sandborn William J. , Lim Meerana , Garg Neha , Lumeng Julie , Kazmierczak Barbara I. , Jain Ruchi , Egan Marie , Rhee Kyung E. , Haddad Gabriel G. , Siegel Dionicio , Mazmanian Sarkis , Nizet Victor , Knight Rob , Dorrestein Pieter C. 
Published: June 2019

AbstractA mosaic of cross-phyla chemical interactions occurs between all metazoans and their microbiomes. In humans, the gut harbors the heaviest microbial load, but many organs, particularly those with a mucosal surface, associate with highly adapted and evolved microbial consortia1. The microbial residents within these organ systems are increasingly well characterized, yielding a good understanding of human microbiome composition, but we have yet to elucidate the full chemical impact the microbiome exerts on an animal and the breadth of the chemical diversity it contributes2. A number of molecular families are known to be shaped by the microbiome including short-chain fatty acids, indoles, aromatic amino acid metabolites, complex polysaccharides, and host lipids; such as sphingolipids and bile acids3–11. These metabolites profoundly affect host physiology and are being explored for their roles in both health and disease. Considering the diversity of the human microbiome, numbering over 40,000 operational taxonomic units12, a plethora of molecular diversity remains to be discovered. Here, we use unique mass spectrometry informatics approaches and data mapping onto a murine 3D-model13–15to provide an untargeted assessment of the chemical diversity between germ-free (GF) and colonized mice (specific-pathogen free, SPF), and report the finding of novel bile acids produced by the microbiome in both mice and humans that have evaded characterization despite 170 years of research on bile acid chemistry16.
Comparative analyses of 3654 chloroplast genomes unraveled new insights into the evolutionary mechanism of green plants
Authors: Yang Ting , Liao Xuezhu , Yang Lingxiao , Liu Yang , Mu Weixue , Sahu Sunil Kumar , Liu Xin , Strube Mikael Lenz , Zhong Bojian , Liu Huan 
Published: June 2019

AbstractBackgroundChloroplast are believed to arise from a cyanobacterium through endosymbiosis and they played vital roles in photosynthesis, oxygen release and metabolites synthesis for the plant. With the advent of next-generation sequencing technologies, until December 2018, about 3,654 complete chloroplast genome sequences have been made available. It is possible to compare the chloroplast genome structure to elucidate the evolutionary history of the green plants.ResultsWe compared the 3654 chloroplast genomes of the green plants and found extreme conservation of gene orders and gene blocks in the green plant such as ATP synthase cluster, Phytosystem, Cytochrome cluster, and Ribosomal cluster. For the chloroplast-based phylogenomics, we used three different data sets to recover the relationships within green plants which accounted for biased GC content and could mitigate the bias in molecular data sets by increasing taxon sampling. The main topology results include: I) Chlorokybales + Mesostigmatales as the earliest-branching lineage and a clade comprising Zygnematales+ Desmidiales formed a grade as the sister group to the land plants, II) Based on matrix AA data, Bryophytes was strongly supported as monophyletic but for matrix nt123 data, hornworts, mosses and liverworts were placed as successive sister lineages of Tracheophytes with strong support, III) Magnoliids were placed in the outside of Monocots using the matrix nt123 data and the matrix AA data, IV) Ceratophyllales + Chloranthales as sister to the Eudicots using matrix nt123 data, but when using matrix nt12 data and AA data, only Ceratophyllales sister to the Eudicots.ConclusionWe present the first of its kind large scale comparative analyses of the chloroplast coding gene constitution for 3654 green plants. Some important genes likely showed co-occurrence and formed gene cluster and gene blocks in Streptophyta. We found a clear expansion of IRs (Inverted Repeats) among seed plants. The comprehensive taxon sampling and different data sets recovered a strong relationship for green plants.
A single-parasite transcriptional atlas of Toxoplasma gondii reveals novel control of antigen expression
Authors: Xue Yuan , Theisen Terence C. , Rastogi Suchita , Ferrel Abel , Quake Stephen R. , Boothroyd John C. 
Published: June 2019

AbstractToxoplasma gondii, a protozoan parasite, undergoes a complex and poorly understood developmental process that is critical for establishing a chronic infection in its intermediate hosts. Here, we applied single-cell RNA-sequencing (scRNA-seq) on >5,400 Toxoplasma in both tachyzoite and bradyzoite stages using three widely studied strains to construct a comprehensive atlas of cell-cycle and asexual development, revealing hidden states and transcriptional factors associated with each developmental stage. Analysis of SAG1-related sequence (SRS) antigenic repertoire reveals a highly heterogeneous, sporadic expression pattern unexplained by measurement noise, cell cycle, or asexual development. Furthermore, we identified AP2IX-1 as a transcription factor that controls the switching from the ubiquitous SAG1 to rare surface antigens not previously observed in tachyzoites. In addition, comparative analysis between Toxoplasma and Plasmodium scRNA-seq results reveals concerted expression of gene sets, despite fundamental differences in cell division. Lastly, we built an interactive data-browser for visualization of our atlas resource.
Enhanced polar auxin transport in tomato polycotyledon mutant seems to be related to glutathione levels
Authors: Nongmaithem Sapana , Ponukumatla Rachana , Sreelakshmi Yellamaraju , Frasse Pierre , Bouzayen Mondher , Sharma Rameshwar 
Published: June 2019

AbstractGlutathione-dependent root growth in Arabidopsis is linked to polar auxin transport (PAT). Arabidopsis mutants with reduced glutathione (GSH) levels also show reduced PAT. To gain an insight into the relationship between PAT and GSH level, we analysed tomato polycotyledon mutant, pct1-2, which has enhanced PAT. Microarray analysis of gene expression in pct1-2 mutant revealed underexpression of several genes related to glutamate and glutathione metabolism. In consonance with microarray analysis, enzymatic as well as in-vivo assay revealed higher glutathione level in the early phase of pct1-2 seedling growth than WT. The inhibition of auxin transport by 2,3,5-triiodobenzoic acid (TIBA) reduced both GSH level and PIN1 expression in pct1-2 root tips. The reduction of in vivo GSH accumulation in pct1-2 root tips by buthionine sulfoximine (BSO) stimulated elongation of the short root of pct1-2 mutant akin to TIBA. The rescue of short root phenotype of pct1-2 mutant was restricted to TIBA and BSO. The other auxin transport inhibitors 1-N-naphthylphthalamic acid (NPA), 2-[4-(diethylamino)-2-hydroxybenzoyl] benzoic acid (BUM), 3-chloro-4-hydroxyphenylacetic acid (CHPAA), brefeldin and gravacin inhibited root elongation in both WT and pct1-2 mutant. Our results indicate a relationship between PAT and GSH level in tomato akin to Arabidopsis. Our work also highlights that TIBA rescues short root phenotype of the pct1-2 mutant by acting on a PAT component distinct from the site of action of other PAT inhibitors.
Epidermal Growth Factor signaling acts directly and through a sedation neuron to depolarizes a sleep-active neuron following cellular stress
Authors: Konietzka Jan , Fritz Maximilian , Spiri Silvan , McWhirter Rebecca , Leha Andreas , Palumbos Sierra , Costa Wagner Steuer , Oranth Alexandra , Gottschalk Alexander , Miller David M. , Hajnal Alex , Bringmann Henrik 
Published: June 2019

SummarySleep is induced by sleep-active neurons that depolarize at sleep onset to inhibit wake circuits. Sleep-active neurons are under the control of homeostatic and allostatic mechanisms that determine sleep need. However, little is known about the molecular and circuit mechanisms that translate sleep need into the depolarization of sleep-active neurons. During many conditions inC. eleganssleep induction requires a sleep-active neuron called RIS. Here, we defined the transcriptome of RIS to discover that genes of the Epidermal Growth Factor Receptor (EGFR) signaling pathway are expressed in RIS. With cellular stress, EGFR activates RIS, and RIS induces sleep. Activation of EGFR signaling in the ALA neuron has previously been suggested to promote sleep independently of RIS. Unexpectedly, we found that ALA activation promotes RIS depolarization. Our results suggest that ALA is a sedating neuron with two separable functions. (1) It inhibits specific wakefulness behaviors independently of RIS, (2) and it activates RIS to induce sleep. Whereas ALA plays a strong role in surviving cellular stress, surprisingly, RIS does not. In summary, EGFR signaling can induce sleep-active neuron depolarization by an indirect mechanism through activation of the sedating ALA neuron that acts upstream of the sleep-active RIS neuron as well as through a direct mechanism using EGFR signaling in RIS. Sedation rather than sleep appears to be important for increasing survival following cellular stress, suggesting that sedation and sleep play different roles in restoring health.Highlights-The transcriptome of the sleep-active RIS neuron reveals the presence of the EGFR signaling machinery-EGFR activates RIS directly upon cellular stress to induce sleep bouts-In parallel, EGFR activates RIS indirectly through the sedating ALA neuron-Sedation rather than sleep bouts support survival following cellular stress
Designing viscoelastic mucin-based hydrogels
Authors: Joyner Katherine , Song Daniel , Hawkins Robert F. , Silcott Richard D. , Duncan Gregg A. 
Published: June 2019

AbstractWe report the design of a mucin hydrogel created using a thiol-based cross-linking strategy. By using a cross-linking reagent capable of forming disulfide linkages between mucins, the mucin-based hydrogels possess viscoelastic properties comparable to native mucus as measured by bulk rheology. We confirmed disulfide cross-links mediate gel formation in our system using chemical treatments to block and reduce cysteines where we found mucin hydrogel network formation was inhibited and disrupted, respectively. Particle tracking microrheology was used to investigate the kinetics and evolution of microstructure and viscoelasticity within the hydrogel as it formed. We found that the rate of gel formation could be tuned by varying the mucin to crosslinker ratio, producing network pore sizes in the range measured previously in human mucus. The results of this work provide a new, simple method for creating mucin hydrogels with physiologically relevant properties using readily available reagents.
Prochlorococcusrely on microbial interactions rather than on chlorotic resting stages to survive long-term nutrient starvation
Authors: Roth-Rosenberg Dalit , Aharonovich Dikla , Luzzatto-Knaan Tal , Vogts Angela , Zoccarato Luca , Eigemann Falk , Nago Noam , Grossart Hans-Peter , Voss Maren , Sher Daniel 
Published: June 2019

AbstractMany microorganisms produce resting cells with very low metabolic activity that allow them to survive phases of prolonged nutrient or energy stress. In cyanobacteria and some eukaryotic phytoplankton, the production of resting stages is accompanied by a loss of photosynthetic pigments, a process termed chlorosis. Here, we show that a chlorosis-like process occurs under multiple stress conditions in axenic laboratory cultures ofProchlorococcus, the dominant phytoplankton linage in large regions of the oligotrophic ocean and a global key player in ocean biogeochemical cycles. InProchlorococcusstrain MIT9313, chlorotic cells show reduced metabolic activity, measured as C and N uptake by NanoSIMS. However, unlike many other cyanobacteria, chloroticProchlorococcuscells are not viable and do not re-grow under axenic conditions when transferred to new media. Nevertheless, co-cultures with a heterotrophic bacterium,Alteromonas macleodiiHOT1A3, allowedProchlorococcusto survive nutrient starvation for months. We propose that reliance on co-occurring heterotrophic bacteria, rather than the ability to survive extended starvation as resting cells, underlies the ecological success ofProchlorococcus.ImportanceThe ability of microorganisms to withstand long periods of nutrient starvation is key to their survival and success under highly fluctuating conditions as is common in nature. Therefore, one would expect this trait to be prevalent among organisms in the nutrient-poor open ocean. Here, we show that this is not the case forProchlorococcus, a globally abundant and ecologically impactful marine cyanobacterium. Instead,Prochlorococcusrely on co-occurring heterotrophic bacteria to survive extended phases of nutrient and light starvation. Our results highlight the power of microbial interactions to drive major biogeochemical cycles in the ocean and elsewhere with consequences at the global scale.
Rapid and site-specific deep phosphoproteome profiling by data-independent acquisition (DIA) without the need for spectral libraries
Authors: Bekker-Jensen Dorte B. , Bernhardt Oliver M. , Hogrebe Alexander , del Val Ana Martinez , Verbeke Lynn , Gandhi Tejas , Kelstrup Christian D. , Reiter Lukas , Olsen Jesper V. 
Published: June 2019

ABSTRACTQuantitative phosphoproteomics has in recent years revolutionized understanding of cell signaling, but it remains a challenge to scale the technology for high-throughput analyses. Here we present a rapid and reproducible phosphoproteomics approach to systematically analyze hundreds of samples by fast liquid chromatography tandem mass spectrometry using data independent acquisition (DIA). To overcome the inherent issue of positional phosphopeptide isomers in DIA-based phosphoproteomics, we developed and employed an accurate site localization scoring algorithm, which is incorporated into the Spectronaut software tool. Using a library of synthetic phosphopeptides spiked-in to a yeast phosphoproteome in different ratios we show that it is on par with the top site localization score for data-dependent acquisition (DDA) based phosphoproteomics. Single-shot DIA-based phosphoproteomics achieved an order of magnitude broader dynamic range, higher reproducibility of identification and improved sensitivity and accuracy of quantification compared to state-of-the-art DDA-based phosphoproteomics. Importantly, direct DIA without the need of spectral libraries performed almost on par with analyses using specific project-specific libraries. Moreover, we implemented and benchmarked an algorithm for globally determining phosphorylation site stoichiometry in DIA. Finally, we demonstrate the scalability of the DIA approach by systematically analyzing the effects of thirty different kinase inhibitors in context of epidermal growth factor (EGF) signaling showing that a large proportion of EGF-dependent phospho-regulation is mediated by a specific set of protein kinases.
Untargeted Metabolomic Profiling Identifies Disease-specific Profiles in Food Allergy
Authors: Crestani E , Harb Hani , Charbonnier Louis Marie , Leirer J , Motsinger-Reif A , Rachid Rima , Phipatanakul W , Kaddurah-Daouk R , Chatila T.A. 
Published: June 2019

AbstractBackgroundFood allergy (FA) affects an increasing proportion of children for reasons that remain obscure. Identification of pathogenic mechanisms involved in FA using untargeted metabolomic approaches may provide much needed diagnostic and prognostic disease biomarkers and improved treatment options.MethodsMass spectrometry-based untargeted metabolomic profiling was performed on serum samples of children with either FA alone, asthma alone or both FA and asthma as well as healthy pediatric controls.ResultsFA subjects exhibited a disease-specific metabolomic signature as compared to both control subjects and asthmatics. In particular, FA was uniquely associated with a marked decrease in sphingolipids, as well as a number of other lipid metabolites, in the face of normal frequencies of circulating natural killer T (NKT) cells. Specific comparison of FA and asthmatic subjects revealed differences in the microbiota-sensitive aromatic amino acid and secondary bile acid metabolism. Children with both FA and asthma exhibited a metabolomic profile that aligned with that of FA alone but not asthma. Among children with FA, distinct profiles were associated with history of severe reactions and presence of multiple FA.ConclusionsChildren with FA display a disease-specific metabolomic profile that is informative of disease mechanisms and severity, and which dominates in the presence of asthma. Lower levels of sphingolipids and ceramides and other metabolomic alterations observed in FA children may reflect the interplay between an altered microbiota and immune cell subsets in the gut.