bluuebunny/crossref_metadata_2025_split huggingface dataset:
The RLR/NLR expression and pro-inflammatory activity of tissue mast cells are regulated by cathelicidin LL-37 and defensin hBD-2
Authors: Agier Justyna , Różalska Sylwia , Wiktorska Magdalena , Żelechowska Paulina , Pastwińska Joanna , Brzezińska-Błaszczyk Ewa 
Published: July 2018

AbstractConsidering the significance of mast cells (MCs) in the course of various physiological and pathological processes, and the pivotal role of endogenous molecules, i.e., cathelicidins and defensins as multifunctional modulators, the study examines the constitutive and cathelicidin LL-37/defensin hBD-2-induced expression of certain NLRs and RLRs, i.e., NOD1, NOD2, and RIG-I, in fully-mature tissue MCs, and the impact of LL-37 and hBD-2 on MC pro-inflammatory activity. All experiments were carried outin vitroon freshly-isolated peritoneal (P)MCs. qRT-PCR, western blotting, flow cytometry, and confocal microscopy were used to evaluate both constitutive and LL-37/hBD-2-induced expression of NOD1, NOD2, and RIG-I receptors. ROS was determined using H2DCFDA, and Boyden microchamber assay was used to define the migratory response. Standard techniques assessed histamine, cysLT, and chemokine generation. PMCs express NOD1, NOD2, and RIG-I constitutively. LL-37 and hBD-2 enhance the expression and induce translocation of the studied receptors and directly activate the pro-inflammatory and migratory responses of PMCs. Observations demonstrate that LL-37 and hBD-2 might augment MC capability and sensitivity to NLR and RLR ligands and strengthen the role of MCs in inflammation.
A coevolution-guided model for the rotor of the bacterial flagellar motor
Authors: Khan Shahid , Guo Tai Wei , Misra Saurav 
Published: July 2018

AbstractThe Salmonella typhimurium trans-membrane FliF MS ring templates assembly of the rotary bacterial flagellar motor, which also contains a cytoplasmic C-ring. A full-frame fusion of FliF with the rotor protein FliG assembles rings in non-motile expression hosts. 3D electron microscopy reconstructions of these FliFFliG rings show three high electron-density sub-volumes. 3D-classification revealed heterogeneity of the assigned cytoplasmic volume consistent with FliG lability. We used residue coevolution to construct homodimer building blocks for ring assembly, with X-ray crystal structures from other species and injectisome analogs. The coevolution signal validates folds and, importantly, indicates strong homodimer contacts for three ring building motifs (RBMs), initially identified in injectisome structures. It also indicates that the cofolded domains of the FliG N-terminal domain (FliG_N) with embedded α-helical FliF carboxy-terminal tail homo-oligomerize. The FliG middle and C-terminal domains (FliG_MC) have a weak signal for homo-dimerization but have coevolved to conserve their stacking contact. The homodimers and their ring models fit well into the 3D reconstruction. We hypothesize that a stable FliF periplasmic hub provides a platform for FliG ring self-assembly, but the FliG_MC ring has only limited stability without the C-ring. We also present a mechanical model for torque transmission in the FliFFliG ring.
Expression map of 78 brain-expressed mouse orphan GPCRs provides a translational resource for neuropsychiatric research
Authors: Ehrlich Aliza T. , Maroteaux Grégoire , Robe Anne , Venteo Lydie , Nasseef Md. Taufiq , van Kempen Leon C. , Mechawar Naguib , Turecki Gustavo , Darcq Emmanuel , Kieffer Brigitte L. 
Published: July 2018

AbstractOrphan G-protein-coupled receptors (oGPCRs) possess untapped potential for drug discovery. In the brain, oGPCRs are generally expressed at low abundance and their function is understudied. Expression profiling is an essential step to position oGPCRs in brain function and disease, however public databases provide only partial information. Here, we fine-map expression of 78 brain-oGPCRs in the mouse, using customized probes in both standard and supersensitive in situ hybridization. Images are available at http://ogpcr-neuromap.douglas.qc.ca. This searchable database contains over 8000 coronal brain sections across 1350 slides, providing the first public mapping resource dedicated to oGPCRs. Analysis with public mouse (60 oGPCRs) and human (56 oGPCRs) genome-wide datasets identifies 25 oGPCRs with potential to address emotional and/or cognitive dimensions of psychiatric conditions. We probe their expression in postmortem human brains using nanoString, and included data in the resource. Correlating human with mouse datasets reveals excellent suitability of mouse models for oGPCRs in neuropsychiatric research.
Activated protein C reverses epigenetically sustained p66Shc expression in plaque-associated macrophages in diabetes
Authors: Shahzad Khurrum , Gadi Ihsan , Nazir Sumra , Al-Dabet Moh’d Mohanad , Kohli Shrey , Bock Fabian , Breitenstein Lukas , Ranjan Satish , Fuchs Tina , Halloul Zuhir , Nawroth Peter. P. , Pelicci Pier Giuseppe , Braun-Dullaeus Ruediger C. , Camerer Eric , Esmon Charles T. , Isermann Berend 
Published: July 2018

AbstractImpaired activated protein C (aPC) generation is associated with atherosclerosis and diabetes mellitus. Diabetes-associated atherosclerosis is characterized by the hyperglycaemic memory, e.g., failure of disease improvement despite attenuation of hyperglycaemia. Therapies reversing the hyperglycaemic memory are lacking. Here we demonstrate that hyperglycaemia, but not hyperlipidaemia, induces the redox-regulator p66Shc and reactive oxygen species (ROS) in macrophages. p66Shc expression, ROS generation, and a pro-atherogenic phenotype are sustained despite restoring normoglycemic conditions. Inhibition of p66Shc abolishes this sustained pro-atherogenic phenotype, identifying p66Shc-dependent ROS in macrophages as a key mechanism conveying the hyperglycaemic memory. The p66Shc-associated hyperglycaemic memory can be reversed by aPC via protease-activated receptor-1 signalling. aPC reverses glucose-induced CpG hypomethylation within the p66Shc promoter by induction of the DNA methyltransferase-1 (DNMT1). Thus, epigenetically sustained p66Shc expression in plaque macrophages drives the hyperglycaemic memory, which—however—can be reversed by aPC. This establishes that reversal of the hyperglycaemic memory in diabetic atherosclerosis is feasible.
Nanocarbon and nanodiamond for high performance phenolics sensing
Authors: Jiang Luyun , Santiago Ibon , Foord John 
Published: July 2018

AbstractPhenolic compounds are pollutants of major concern, and effective monitoring is essential to reduce exposure. Electrochemical sensors offer rapid and accurate detection of phenols but suffer from two main shortcomings preventing their widespread use: electrode fouling and signal interference from co-existing isomers. Here we demonstrate a potential solution based on environmentally friendly and biocompatible carbon nanomaterials to detect monophenols (phenol and cresol) and biphenols (hydroquinone and catechol). Electrode fouling is tackled in two ways: by introducing electrochemically resistant nanodiamond electrodes and by developing single-use nanocarbon electrodes. We provide a comprehensive analysis of the electrochemical performance of three distinct carbon materials (graphene, nanodiamond and nanocarbon). Nanocarbon exhibits the lowest detection limit below 10−8 M, and one order of magnitude higher sensitivity than the other carbon nanomaterials. We detect co-existing phenol isomers with nanocarbon electrodes and apply it in river water and green tea samples, which may pave the way towards low-cost industrial scale monitoring of phenolic compounds.
Phenotypic trait variation measured on European genetic trials of Fagus sylvatica L
Authors: Robson T. Matthew , Garzón Marta Benito ,   BeechCOSTe52 database consortium, Alia Miranda Ricardo , Barba Egido Diana , Bogdan Saša , Borovics Attila , Božič Gregor , Brendel Oliver , Clark Jo , De Vries Sven M.G , Delehan Ivan I , Ducousso Alexis , Fady Bruno , Fennessy John , Forstreuter Manfred , Frýdl Josef , Geburek Thomas , Gömöry Dušan , Hauke-Kowalska Maria , Huber Gerhard , Ibañez Juan-Ignacio , Ioniţă Lucia , Ivankovič Mladen , Hansen Jon Kehlet , Kóczán- Horváth Anikó , Kraigher Hojka , Lee Steve , Liesebach Mirko , Mátyás Csaba , Mertens Patrick , Muhs Hans-Jakob , Novotný Petr , Parnuţa Gheorghe , Paule Ladislav , Picardo Alvaro , Rasztovics Ervin , Rogge Martin , Stener Lars-Göran , Sułkowska Małgorzata , Urban Otmar , Wuehlisch Georg Von , Vendramin Giovanni G , Vettori Cristina , Wesoły Wojciech 
Published: July 2018

AbstractWe presentBeechCOSTe52; a database of European beech (Fagus sylvatica) phenotypic measurements for several traits related to fitness measured in genetic trials planted across Europe. The dataset was compiled and harmonized during the COST-Action E52 (2006–2010), and subsequently cross-validated to ensure consistency of measurement data among trials and provenances. Phenotypic traits (height, diameter at breast height, basal diameter, mortality, phenology of spring bud burst and autumn–leaf discoloration) were recorded in 38 trial sites where 217 provenances covering the entire distribution of European beech were established in two consecutive series (1993/95 and 1996/98). The recorded data refer to 862,095 measurements of the same trees aged from 2 to 15 years old over multiple years. This dataset captures the considerable genetic and phenotypic intra-specific variation present in European beech and should be of interest to researchers from several disciplines including quantitative genetics, ecology, biogeography, macroecology, adaptive management of forests and bioeconomy.
Fragmentierung des Fallmanagements in deutschen Krankenhausabteilungen
Authors: Holderried Martin , Wolpert Stephan , Zenner Hans-Peter , Maschmann Jens 
Published: July 2018

Zusammenfassung
Hintergrund Wesentliche Ziele von Krankenhäusern sind eine hohe Qualität, Sicherheit, Effektivität und Effizienz der Leistungserbringung. Dies erfordert
eine optimale Behandlungssteuerung durch das Fallmanagement auf den Krankenhausstationen (FM).
Methoden Für eine Analyse der Mikro- und Makroprozesse des stationären Fallmanagements wurde ein strukturiertes Interviewinventar entwickelt. Anschließend
wurde mit dem Interviewinventar eine Felduntersuchung als community based participatory research (CBPR) an homogenen Fokusgruppen von 24 deutschen, aus
ökonomischer Sicht als Profitcenter wirkenden, öffentlichen Krankenhausabteilungen der Maximalversorgung durchgeführt.
Ergebnisse Mit der CBPR-Feldstudie konnten 1.682 Mikroprozesse des stationären Fallmanagements der untersuchten Krankenhausabteilungen erfasst und
beurteilt werden. Die Studie zeigt, dass alle Abteilungen zwar ein umfangreiches klinisches Fallmanagement betreiben, die Mikroprozesse des Fallmanagements
allerdings durchgehend weder optimal zur Kostenminimierung noch maximal zur Liquiditäts-, Erlös- und Qualitätsverbesserung durchgeführt werden. Auch zeigt sich,
dass die berufsgruppenübergreifende Durchführung der Prozesse des FM durch Ärzte und Pflegekräfte mit einer erheblichen Fragmentierung des FM verbunden ist.
Schlussfolgerungen Die intensive Fragmentierung der Tätigkeiten des FM auf Krankenhausstationen legt die Erarbeitung von Strategien nahe, die Prozesse des
stationären Fallmanagements zu homogenisieren.
Near-Peer Teaching Outreach Programs to Increase Minority Physician Recruitment
Authors: Linderman Wendy , Apostolopoulos Nicholas , Gopal Anand , Encandela John , Teng Christopher , Nwanyanwu Kristen , Forster Susan 
Published: July 2018

Problem Health disparities among racial and ethnic groups exist in the United States despite improvements in health status and access to care. These inequalities may be reduced by increasing minority physician recruitment; however, how best to recruit these physicians remains unclear.
Approach Near-peer teachers are not professionally trained, but have recently learned material that they themselves teach. Near-peer teaching in minority student outreach programs may be effective in increasing minority physician recruitment. The authors used a near-peer teaching model to promote interest in medicine, specifically ophthalmology, as a potential career path for both volunteer near-peer teachers and minority high school students participating in an educational outreach program. Twenty-one college and graduate-school near-peer teachers of various racial and ethnic backgrounds participated to teach 31 inner-city high school students. The program was evaluated using pre- and posttest surveys assessing students' knowledge about and interest in science, medicine, and ophthalmology; analysis used pairwise t-test comparisons. Qualitative responses and an end-of-training survey also assessed students' and near-peer teachers' satisfaction with the program and perceptions about medicine as a career.
Outcomes Students' knowledge about and interest in medicine and ophthalmology increased significantly after participation. Near-peer teachers agreed that teaching in the program was beneficial to their careers and made it more likely that they would enter medicine and ophthalmology.
Next Steps The authors will track the near-peer teachers' career paths and, in the next iteration, will increase the number of program days. This intervention may serve as a model for outreach for other specialties beyond ophthalmology.
Paving the Path to Value: The Role of Registry Studies in Interventional Radiology
Authors: Wang Melinda , Kohi Maureen 
Published: July 2018

AbstractThe growth rate of interventional radiology (IR) procedures and practitioners has exceeded the pace of evidence development to support evidence-based practice. In the innovative and highly adaptive field of IR, there exists a tremendous need for interventional radiologists to practice evidence-based medicine as a way to maintain and improve quality of health care. Randomized controlled trials (RCTs) are considered to be the gold standard of research, providing level I evidence, but in procedural subspecialties, they remain difficult to design and implement due to challenges in randomization, blinding, and inadequate sample size. To build the foundation of evidence in IR, registry studies can play a complementary role to RCTs. Clinical data registries may offer a more practical approach to gathering outcomes data, important in this era with the advent of the Medicare Access and CHIP Reauthorization Act (MACRA), in comparison with RCTs. Properly designed registries can store an abundance of data with which high-quality observational studies can be performed. Although considered level II evidence, these registry studies will allow the evaluation of both performance and value of IR procedures, particularly in circumstances in which an RCT would not be feasible. This manuscript aims to serve as a guide for developing and participating in IR registry studies.
Osteophytic Iliac Venous Compression: Technical Considerations for a Bony May-Thurner Syndrome Variant
Authors: Shin David , Mokkarala Mahati , Allison Stephen , Monroe Eric 
Published: July 2018

AbstractMay-Thurner syndrome (MTS) results in compression of the left common iliac vein between the spine and right common iliac artery leading to symptomatic venous outflow obstruction. The authors depict a classic case of MTS followed by four variant cases in which the primary culprit lesions causing compression were degenerative vertebral osteophytes. The osteophytic variant of MTS poses distinct diagnostic and therapeutic challenges.
Heterosubtypic influenza protection elicited by double-layered polypeptide nanoparticles in mice
Authors: Deng Lei , Chang Timothy Z. , Wang Ye , Li Song , Wang Shelly , Matsuyama Shingo , Yu Guoying , Compans Richard W. , Li Jian-Dong , Prausnitz Mark R. , Champion Julie A. , Wang Bao-Zhong 
Published: July 2018

Significance
Mismatched seasonal influenza vaccines are low efficacy and provide limited protection against circulating strains. A universal influenza vaccine that can induce broadly cross-protective immunity is urgently needed. Here, we have developed a layered peptide-only nanoparticle vaccine delivered by dissolvable microneedle patches. Immunizations with the vaccine candidates elicited robust long-lasting protective immune responses in mice. We found that the unique in vivo biodistribution feature of the nanoparticles correlated with the long-term immunity. This vaccine approach can be applied to develop peptide-based vaccines for different pathogens.
Functions of the COPII gene paralogs SEC23A and SEC23B are interchangeable in vivo
Authors: Khoriaty Rami , Hesketh Geoffrey G. , Bernard Amélie , Weyand Angela C. , Mellacheruvu Dattatreya , Zhu Guojing , Hoenerhoff Mark J. , McGee Beth , Everett Lesley , Adams Elizabeth J. , Zhang Bin , Saunders Thomas L. , Nesvizhskii Alexey I. , Klionsky Daniel J. , Shavit Jordan A. , Gingras Anne-Claude , Ginsburg David 
Published: July 2018

Significance
In humans, SEC23B deficiency results in congenital dyserythropoietic anemia type II, a disease of abnormal red blood cell development, while SEC23A deficiency results in cranio-lenticulo-sutural-dysplasia, a disease characterized by bone abnormalities due to defective collagen secretion (but no red blood cell defect). In this study, we show that SEC23A and SEC23B overlap in function, and that the disparate phenotypes of SEC23A/SEC23B deficiency within and across species are likely due to evolutionary shifts in gene-expression programs, rather than distinct functions of the SEC23 paralogs. Our studies provide a rationale for increased SEC23A or SEC23B expression as a therapeutic strategy for congenital dyserythropoietic anemia type II or cranio-lenticulo-sutural-dysplasia, respectively.
Evaluation of cross-platform and interlaboratory concordance via consensus modelling of genomic measurements
Authors: Peters Timothy J , French Hugh J , Bradford Stephen T , Pidsley Ruth , Stirzaker Clare , Varinli Hilal , Nair Shalima , Qu Wenjia , Song Jenny , Giles Katherine A , Statham Aaron L , Speirs Helen , Speed Terence P , Clark Susan J 
Published: July 2018

AbstractMotivationA synoptic view of the human genome benefits chiefly from the application of nucleic acid sequencing and microarray technologies. These platforms allow interrogation of patterns such as gene expression and DNA methylation at the vast majority of canonical loci, allowing granular insights and opportunities for validation of original findings. However, problems arise when validating against a “gold standard” measurement, since this immediately biases all subsequent measurements towards that particular technology or protocol. Since all genomic measurements are estimates, in the absence of a ”gold standard” we instead empirically assess the measurement precision and sensitivity of a large suite of genomic technologies via a consensus modelling method called the row-linear model. This method is an application of the American Society for Testing and Materials Standard E691 for assessing interlaboratory precision and sources of variability across multiple testing sites. Both cross-platform and cross-locus comparisons can be made across all common loci, allowing identification of technology- and locus-specific tendencies.ResultsWe assess technologies including the Infinium MethylationEPIC BeadChip, whole genome bisulfite sequencing (WGBS), two different RNA-Seq protocols (PolyA+ and Ribo-Zero) and five different gene expression array platforms. Each technology thus is characterised herein, relative to the consensus. We showcase a number of applications of the row-linear model, including correlation with known interfering traits. We demonstrate a clear effect of cross-hybridisation on the sensitivity of Infinium methylation arrays. Additionally, we perform a true interlaboratory test on a set of samples interrogated on the same platform across twenty-one separate testing laboratories.Availability and implementationA full implementation of the row-linear model, plus extra functions for visualisation, are found in the R package consensus at https://github.com/timpeters82/consensus.Supplementary informationSupplementary data are available at Bioinformatics online.
Hot-starting software containers for STAR aligner
Authors: Zhang Pai , Hung Ling-Hong , Lloyd Wes , Yeung Ka Yee 
Published: July 2018

Abstract

Background
Using software containers has become standard practice to reproducibly deploy and execute biomedical workflows on the cloud. However, some applications that contain time-consuming initialization steps will produce unnecessary costs for repeated executions.

Findings
We demonstrate that hot-starting from containers that have been frozen after the application has already begun execution can speed up bioinformatics workflows by avoiding repetitive initialization steps. We use an open-source tool called Checkpoint and Restore in Userspace (CRIU) to save the state of the containers as a collection of checkpoint files on disk after it has read in the indices. The resulting checkpoint files are migrated to the host, and CRIU is used to regenerate the containers in that ready-to-run hot-start state. As a proof-of-concept example, we create a hot-start container for the spliced transcripts alignment to a reference (STAR) aligner and deploy this container to align RNA sequencing data. We compare the performance of the alignment step with and without checkpoints on cloud platforms using local and network disks.

Conclusions
We demonstrate that hot-starting Docker containers from snapshots taken after repetitive initialization steps are completed significantly speeds up the execution of the STAR aligner on all experimental platforms, including Amazon Web Services, Microsoft Azure, and local virtual machines. Our method can be potentially employed in other bioinformatics applications in which a checkpoint can be inserted after a repetitive initialization phase.
Risk of health morbidity for the uninsured: 10-year evidence from a large hospital center in Boston, Massachusetts
Authors: Chen Zhaoyi , Min Jae , Bian Jiang , Wang Mo , Zhou Le , Prosperi Mattia 
Published: July 2018

AbstractObjectiveTo investigate the independent contribution of insurance status toward the risk of diagnosis of specific clinical comorbidities for individuals admitted to intensive care unit (ICU).DesignRetrospective analysis of secondary database.SettingTen years of public de-identified ICU electronic medical records from a large hospital in USA.ParticipantsPatients (18–65 years old) who had private insurance or no insurance were extracted from the database.Main outcome measuresIndependent association of insurance status (uninsured vs. privately insured) with the risk of diagnosis of specific clinical comorbidities.ResultsAmong 14 268 (from 11 753 patients) admissions to ICU between 2001 and 2012, 96% of them were covered by private insurance. Patients with private insurance had higher proportion of females, married, White race, longer ICU stay and more procedures during stay, and fewer deaths. A lower CCI was observed in uninsured patients. At multivariable analysis, uninsured patients had higher odds of death and of admissions for accidental falls, substance or alcohol abuse.ConclusionsPatients with no insurance coverage were at higher risk of death and of admission for physical and substance-related injury. We did not observe a higher risk for acute life-threatening diseases such as myocardial infarction or kidney failure. The lower CCI observed in the uninsured may be explained by under diagnosis or voluntary withdrawal from coverage in the pre-Affordable Care Act era. Replication of findings is warranted in other populations, among those with government-subsidized insurance and in the procedure/prescription domains.