bluuebunny/crossref_metadata_2025_split huggingface dataset:
MRI of the sacroiliac joints in athletes: recognition of non-specific bone marrow oedema by semi-axial added to standard semi-coronal scans
Authors: Weber Ulrich , Jurik Anne Grethe , Zejden Anna , Larsen Ejnar , Jørgensen Steen Hylgaard , Rufibach Kaspar , Schioldan Christian , Schmidt-Olsen Søren 
Published: September 2019

Abstract

Objective
Assessment of combined semi-axial and semi-coronal SI joint MRI in two cohorts of young athletes to explore frequency and topography of non-specific bone marrow oedema (BMO), its association with four constitutional SI joint features, and potential restriction of false-positive assignments of Assessment of SpondyloArthritis International Society-defined sacroiliitis on standard semi-coronal scans alone.

Methods
Combined semi-axial and semi-coronal SI joint MRI scans of 20 recreational runners before/after running and 22 elite ice-hockey players were evaluated by three blinded readers for BMO and its association with four constitutional SI joint features: vascular partial volume effect, deep iliac ligament insertion, fluid-filled bone cyst and lumbosacral transitional anomaly. Scans of TNF-treated spondyloarthritis patients served to mask readers. We analysed distribution and topography of BMO and SI joint features across eight anatomical SI joint regions (upper/lower ilium/sacrum, subdivided in anterior/posterior slices) descriptively, as concordantly recorded by ⩾2/3 readers on both MRI planes. BMO confirmed on both scans was compared with previous evaluation of semi-coronal MRI alone, which met the Assessment of SpondyloArthritis International Society definition for active sacroiliitis.

Results
Perpendicular semi-axial and semi-coronal MRI scans confirmed BMO in the SI joint of every fourth young athlete, preferentially in the anterior upper sacrum. BMO associated with four constitutional SI joint features was observed in 20–36% of athletes, clustering in the posterior lower ilium. The proportion of Assessment of SpondyloArthritis International Society-positive sacroiliitis recorded on the semi-coronal plane alone decreased by 33–56% upon amending semi-axial scans.

Conclusion
Semi-axial combined with standard semi-coronal scans in MRI protocols for sacroiliitis facilitated recognition of non-specific BMO, which clustered in posterior lower ilium/anterior upper sacrum.
OCCUPATIONAL RADIATION DOSE PERFORMING HEPATOBILIARY MINIMALLY INVASIVE PROCEDURES IN CHILDREN WEIGHING LESS THAN 20 kg
Authors: Gerasia Roberta , Cannataci Christine , Maruzzelli Luigi , Caruso Calogero , Liotta Ferdinanda , Cucchiara Antonino , Cortis Kelvin , Miraglia Roberto 
Published: September 2019

Abstract
Our objective is to retrospectively evaluate the effective dose (E) of operators performing pediatric Hepatobiliary Minimally Invasive Procedures (HMIP). Between October 2015 and December 2017, 58 consecutive HMIP were performed on 26 children weighing less than 20 kg (mean 12.3 kg, median 13 kg, range 2.4–20 kg). About 31 vascular procedures (n = 9 hepatic venograms with/without stenting; n = 9 retrograde wedge portography; n = 8 transhepatic portography with angioplasty and/or stenting and n = 5 hepatic arteriography/embolization) and 27 non-vascular procedures (n = 6 percutaneous transhepatic biliary drainage (PTBD); n = 3 bilioplasty; n = 15 biliary catheter change and n = 3 cholangiogram) were performed. Electronic personal dosimeters were used to measure radiation doses to the interventional radiologist, radiographer and anesthesia nurse. The results shows the highest mean effective dose: interventional radiologist’s in PTBD (1.18 μSv); radiographer’s in hepatic veins phlebography with/without stenting (0.25 μSv) and nurse’s in hepatic arteriography/embolization (0.26 μSv). Operators’ E can vary depending on the complexity of procedure performed and the position of the operators within the angiosuite.
Contentions over World Culture: The Rise of Legal Restrictions on Foreign Funding to NGOs, 1994–2015
Authors: Bromley Patricia , Schofer Evan , Longhofer Wesley 
Published: September 2019

AbstractThe last two decades have witnessed an unprecedented rise in government restrictions on foreign funding to nongovernmental organizations (NGOs). Often in the name of defending the nation from outside influences, over 60 countries have implemented laws limiting foreign funding to NGOs. We use event history analyses to evaluate domestic and global explanations for the adoption of these policies over the period 1994–2015. Prior work has argued that funding restrictions result from real or perceived threats to political regimes, especially in countries with competitive elections. We add to this story by situating it in a larger global and cultural context: new funding laws are part of a growing backlash against the liberal international order, which has long sponsored international and domestic NGOs devoted to issues such as human rights and the environment. In an era of increasing resistance toward globally linked civil society groups—the primary carriers of liberal world society—NGO funding restrictions are now diffusing widely across the international system. We argue that restriction policies will be most common among countries that are linked to illiberal or anti-Western organizations and discourses in the international community. Moreover, adoption will accelerate as more countries do it, representing a growing “wave” or backlash against the liberal international order. Findings support the prior literature as well as our new arguments regarding illiberal international organizations and global backlash.
Inferring putative transmission clusters with Phydelity
Authors: Han Alvin X , Parker Edyth , Maurer-Stroh Sebastian , Russell Colin A 
Published: September 2019

Abstract
Current phylogenetic clustering approaches for identifying pathogen transmission clusters are limited by their dependency on arbitrarily defined genetic distance thresholds for within-cluster divergence. Incomplete knowledge of a pathogen’s underlying dynamics often reduces the choice of distance threshold to an exploratory, ad hoc exercise that is difficult to standardise across studies. Phydelity is a new tool for the identification of transmission clusters in pathogen phylogenies. It identifies groups of sequences that are more closely related than the ensemble distribution of the phylogeny under a statistically principled and phylogeny-informed framework, without the introduction of arbitrary distance thresholds. Relative to other distance threshold- and model-based methods, Phydelity outputs clusters with higher purity and lower probability of misclassification in simulated phylogenies. Applying Phydelity to empirical datasets of hepatitis B and C virus infections showed that Phydelity identified clusters with better correspondence to individuals that are more likely to be linked by transmission events relative to other widely used non-parametric phylogenetic clustering methods without the need for parameter calibration. Phydelity is generalisable to any pathogen and can be used to identify putative direct transmission events. Phydelity is freely available at https://github.com/alvinxhan/Phydelity.
Diapause is not selected as a bet-hedging strategy in insects: a meta-analysis of reaction norm shapes
Authors: Joschinski Jens , Bonte Dries 
Published: September 2019

AbstractMany organisms escape from lethal climatological conditions by entering a resistant resting stage called diapause, which needs to be optimally timed with seasonal change. As climate change exerts selection pressure on phenology, the evolution of mean diapause timing, but also of phenotypic plasticity and bet-hedging strategies is expected. Especially the latter as a strategy to cope with unpredictability is little considered in the context of climate change.Contemporary patterns of phenological strategies across a geographic range may provide information about their evolvability. We thus extracted 458 diapause reaction norms from 60 studies. First, we correlated mean diapause timing with mean winter onset. Then we partitioned the reaction norm variance into a temporal component (phenotypic plasticity) and among-offspring variance (diversified bet-hedging) and correlated this variance composition with predictability of winter onset. Mean diapause timing correlated reasonably well with mean winter onset, except for populations at high latitudes, which apparently failed to track early onsets. Variance among offspring was, however, limited and correlated only weakly with environmental predictability, indicating little scope for bet-hedging. The apparent lack of phenological bet-hedging strategies may pose a risk in a less predictable climate, but we also highlight the need for more data on alternative strategies.
Single-cell RNA-sequencing reveals profibrotic roles of distinct epithelial and mesenchymal lineages in pulmonary fibrosis
Authors: Habermann Arun C. , Gutierrez Austin J. , Bui Linh T. , Yahn Stephanie L. , Winters Nichelle I. , Calvi Carla L. , Peter Lance , Chung Mei-I , Taylor Chase J. , Jetter Christopher , Raju Latha , Roberson Jamie , Ding Guixiao , Wood Lori , Sucre Jennifer MS , Richmond Bradley W. , Serezani Ana P. , McDonnell Wyatt J. , Mallal Simon B. , Bacchetta Matthew J. , Loyd James E. , Shaver Ciara M. , Ware Lorraine B. , Bremner Ross , Walia Rajat , Blackwell Timothy S. , Banovich Nicholas E. , Kropski Jonathan A. 
Published: September 2019

AbstractPulmonary fibrosis is a form of chronic lung disease characterized by pathologic epithelial remodeling and accumulation of extracellular matrix. In order to comprehensively define the cell types, mechanisms and mediators driving fibrotic remodeling in lungs with pulmonary fibrosis, we performed single-cell RNA-sequencing of single-cell suspensions from 10 non-fibrotic control and 20 PF lungs. Analysis of 114,396 cells identified 31 distinct cell types. We report a remarkable shift in epithelial cell phenotypes occurs in the peripheral lung in PF, and identify several previously unrecognized epithelial cell phenotypes including a KRT5−/KRT17+, pathologic ECM-producing epithelial cell population that was highly enriched in PF lungs. Multiple fibroblast subtypes were observed to contribute to ECM expansion in a spatially-discrete manner. Together these data provide high-resolution insights into the complexity and plasticity of the distal lung epithelium in human disease, and indicate a diversity of epithelial and mesenchymal cells contribute to pathologic lung fibrosis.One Sentence SummarySingle-cell RNA-sequencing provides new insights into pathologic epithelial and mesenchymal remodeling in the human lung.
Genetic Interaction between RLM1 and F-box Motif Encoding gene SAF1 Contributes to Stress Response inSaccharomyces cerevisiae
Authors: Sharma Meenu , Verma V. , Bairwa Narendra K 
Published: September 2019

AbstractStress response is mediated by transcription of stress responsive genes. F-box motif protein Saf1 involves in SCF-E3 ligase mediated degradation of the adenine deaminase, Aah1 upon nutrient stress. Four transcription regulators, BUR6, MED6, SPT10, SUA7, have been reported for SAF1 gene in genome database ofSaccharomyces cerevisiae.Here in this study anin-silcoanalysis of gene expression and transcription factor databases was carried out to understand the regulation of SAF1 gene expression during stress for hypothesis generation and experimental analysis. The GEO profile database analysis showed increased expression of SAF1 gene when treated with clioquinol, pterostilbene, gentamicin, hypoxia, genotoxic, desiccation, and heat stress, in WT cells. SAF1 gene expression in stress conditions correlated positively whereas AAH1 expression negatively with RLM1 transcription factor, which was not reported earlier. Based on analysis of expression profile and regulatory association of SAF1 and RLM1, we hypothesized that inactivation of both the genes may contribute to stress tolerance. The experimental analysis with the double mutant,saf1Δrlm1Δfor cellular growth response to stress causing agents, showed tolerance to calcofluor white, SDS, and hydrogen peroxide. On the contrary,saf1Δrlm1Δshowed sensitivity to MMS, HU, DMSO, Nocodazole, Benomyl stress. Based on in-silicoand experimental data we suggest that SAF1 and RLM1 both interact genetically in differential response to genotoxic and general stressors.
Learning improves decoding of odor identity with phase-referenced oscillations in the olfactory bulb
Authors: Losacco Justin , Ramirez-Gordillo Daniel , Gilmer Jesse , Restrepo Diego 
Published: September 2019

AbstractLocal field potential oscillations reflect temporally coordinated neuronal ensembles— coupling distant brain regions, gating processing windows, and providing a reference for spike timing-based codes. In phase amplitude coupling (PAC), the amplitude of the envelope of a faster oscillation is larger within a phase window of a slower carrier wave. Here, we characterized PAC, and the related theta phase-referenced high gamma and beta power (PRP), in the olfactory bulb of mice learning to discriminate odorants. PAC changes throughout learning, and odorant-elicited changes in PRP increase for rewarded and decrease for unrewarded odorants. Contextual odorant identity (is the odorant rewarded?) can be decoded from peak PRP in animals proficient in odorant discrimination, but not in naïve mice. As the animal learns to discriminate the odorants the dimensionality of PRP decreases. Therefore, modulation of phase-referenced chunking of information in the course of learning plays a role in early sensory processing in olfaction.SignificanceEarly processing of olfactory information takes place in circuits undergoing slow frequency theta oscillations generated by the interplay of olfactory input modulated by sniffing and centrifugal feedback from downstream brain areas. Studies in the hippocampus and cortex suggest that different information “chunks” are conveyed at different phases of the theta oscillation. Here we show that in the olfactory bulb, the first processing station in the olfactory system, the amplitude of high frequency gamma oscillations encodes for information on whether an odorant is rewarded when it is observed at the peak phase of the theta oscillation. Furthermore, encoding of information by the theta phase-referenced gamma oscillations becomes more accurate as the animal learns to differentiate two odorants.
immuneSIM: tunable multi-feature simulation of B- and T-cell receptor repertoires for immunoinformatics benchmarking
Authors: Weber Cédric R. , Akbar Rahmad , Yermanos Alexander , Pavlović Milena , Snapkov Igor , Sandve Geir Kjetil , Reddy Sai T. , Greiff Victor 
Published: September 2019

AbstractSummaryB- and T-cell receptor repertoires of the adaptive immune system have become a key target for diagnostics and therapeutics research. Consequently, there is a rapidly growing number of bioinformatics tools for immune repertoire analysis. Benchmarking of such tools is crucial for ensuring reproducible and generalizable computational analyses. Currently, however, it remains challenging to create standardized ground truth immune receptor repertoires for immunoinformatics tool benchmarking. Therefore, we developed immuneSIM, an R package that allows the simulation of native-like and aberrant synthetic full length variable region immune receptor sequences. ImmuneSIM enables the tuning of the immune receptor features: (i) species and chain type (BCR, TCR, single, paired), (ii) germline gene usage, (iii) occurrence of insertions and deletions, (iv) clonal abundance, (v) somatic hypermutation, and (vi) sequence motifs. Each simulated sequence is annotated by the complete set of simulation events that contributed to its in silico generation. immuneSIM permits the benchmarking of key computational tools for immune receptor analysis such as germline gene annotation, diversity and overlap estimation, sequence similarity, network architecture, clustering analysis, and machine learning methods for motif detection.AvailabilityThe package is available viahttps://github.com/GreiffLab/immuneSIMand will also be available at CRAN (submitted). The documentation is hosted athttps://immuneSIM.readthedocs.io.Contactvictor.greiff@medisin.uio.no,sai.reddy@ethz.ch
Cytokinin promotes jasmonic acid accumulation in the control of maize leaf growth
Authors: Uyehara Aimee N. , Del Valle-Echevarria Angel R. , Hunter Charles T. , Nelissen Hilde , Demuynck Kirin , Cahill James F. , Jander Georg , Muszynski Michael G. 
Published: September 2019

AbstractGrowth of plant organs results from the combined activity of cell division and cell expansion. The coordination of these two processes depends on the interplay between multiple hormones that determine final organ size. Using the semidominant Hairy Sheath Frayed1 (Hsf1) maize mutant, that hypersignals the perception of cytokinin (CK), we show that CK can reduce leaf size and growth rate by decreasing cell division. Linked to CK hypersignaling, the Hsf1 mutant has increased jasmonic acid (JA) content, a hormone that can inhibit cell division. Treatment of wild type seedlings with exogenous JA reduces maize leaf size and growth rate, while JA deficient maize mutants have increased leaf size and growth rate. Expression analysis revealed increased transcript accumulation of several JA pathway genes in the Hsf1 leaf growth zone. A transient treatment of growing wild type maize shoots with exogenous CK also induced JA pathway gene expression, although this effect was blocked by co-treatment with cycloheximide. Together our results suggest that CK can promote JA accumulation possibly through increased expression of specific JA pathway genes.One sentence summaryCytokinin-signaling upregulates the jasmonate biosynthesis pathway, resulting in jasmonate accumulation and influences on maize leaf growth.
β-HPV 8E6 Dysregulates the Hippo Signaling Pathway and Induces Aneuploidy
Authors: Dacus Dalton , McCallister Tristan X. , Cotton Celeste , Riforgiate Elizabeth , Wallace Nicholas A. 
Published: September 2019

ABSTRACTBeta genus human papillomaviruses (β-HPVs) are associated with cutaneous squamous cell carcinomas (cSCCs) in a subset of immunocompromised patients. Although β-HPVs are not necessary for tumor maintenance, they are hypothesized to destabilize the genome in the early stages of cancer development. Supporting this idea, β-HPV’s 8E6 protein attenuates p53 accumulation after failed cytokinesis. This paper identifies the mechanism of this abatement. We show β-HPV 8E6 dysregulates the Hippo signaling pathway (HP). It increases pro-proliferative gene expression, enhances TEAD activity and promotes cell growth. β-HPV 8E6 also reduces LATS activation and p53-mediated apoptosis following unsuccessful division of mitotic cells. These phenotypes are dependent on β-HPV 8E6 binding and destabilizing a cellular histone acetyltransferase, p300. Despite circumventing apoptosis, β-HPV 8E6 caused increased senescence after unsuccessful cytokinesis. We linked this lack of growth to the viral protein’s inability to prevent cytoplasmic sequestration of the HP transcription factor, YAP. We also show that increased telomerase reverse transcriptase activity (a common alteration in cSCCs) acts synergistically with β-HPV 8E6 to promote cellular proliferation after abortive cytokinesis. While β-HPV 8E6 promoted aneuploidy on its own, this genome destabilization is amplified in cells that do not divide after mitosis. Although our group and others have previously described inhibition of DNA repair, to the best of our knowledge this marks the first time that a β-HPV protein has been connected to chromosome level changes in the cellular genome. This represents a substantial escalation in the known genome destabilizing properties likely to occur during a β-HPV infection.IMPORTANCEThere is mounting evidence that β-HPVs contribute to cSCCs development in immunocompromised populations. They may also augment UV’s mutagenic potential, increasing cancer risk in the general population. We demonstrate that β-HPV 8E6 dysregulates the Hippo signaling pathway (HP). HP regulates cell growth and apoptosis in response to a myriad of stimuli, including failed cytokinesis. β-HPV 8E6 attenuates phosphorylation of the HP kinase, LATS, decreasing some but not all downstream signaling events. This allows binucleated cells to avoid apoptosis, however they succumb to senescence. We show that β-HPV 8E6 synergizes with a common cSCC mutation (telomerase activation) to avoid both apoptosis and senescence. We did not find any telomerase immortalized β-HPV 8E6 expressing cells that were not aneuploid after aberrant cytokinesis. This represents a substantial escalation in β-HPV E6’s known mutagenic potential.
Dental emergency: scoping review
Authors: Frichembruder Karla , dos Santos Camila Mello , Hugo Fernando Neves 
Published: September 2019

AbstractPart of the oral health care in the care network encompasses users in cases of emergency. This study proposed to map the determinants of the use of dental care services within the health care network to address dental emergencies of the Brazilian Unified Health System (UHS) and to verify the main gaps in the research in this area. This is a scoping review that took place in 2018 using Andersen’s behavioral model as a reference. A total of 16 studies, out of 3786 original articles identified, were included and reviewed. Two reviewers independently conducted the selection process and the decision was consensually taken. The mapping of the determinants revealed a greater number of enabling factors and a larger gap in results. Greater use of the emergency service was registered by people in pain, women, adults, from an urban area, with a lower income, and less education. In future studies, primary surveys are recommended, which include all ages, analyzing different groups of needs and users that take into account the country’s northern region and the different subjects pointed out in this review.
Can scientists fill the science journalism void? Online public engagement with science stories authored by scientists
Authors: David Yael Barel-Ben , Garty Erez S. , Baram-Tsabari Ayelet 
Published: September 2019

AbstractIn many countries the public’s main source of information about science and technology is the mass media. Unfortunately, in recent years traditional journalism has experienced a collapse, and science journalism has been a major casualty. One potential remedy is to encourage scientists to write for news media about science. On these general news platforms, scientists’ stories would have to compete for attention with other news stories on hard (e.g. politics) and entertaining (e.g. celebrity news) topics written by professional writers. Do they stand a chance?This study aimed to quantitatively characterize audience interactions as an indicator of interest in science news stories authored by early career scientists (henceforth ‘scientists’) trained to function as science reporters, as compared to news items written by reporters and published in the same news outlets.To measure users’ behavior, we collected data on the number of clicks, likes, comments and average time spent on page. The sample was composed of 150 science items written by 50 scientists trained to contribute popular science stories in the Davidson Institute of Science Education reporters’ program and published on two major Israeli news websites -MakoandYnetbetween July 2015 to January 2018. Each science item was paired with another item written by the website’s organic reporter, and published on the same channel as the science story (e.g., tourism, health) and the same close time. Overall significant differences were not found in the public’s engagement with the different items. Although, on one website there was a significant difference on two out of four engagement types, the second website did not have any difference, e.g., people did not click, like or comment more on items written by organic reporters than on the stories written by scientists. This creates an optimistic starting point for filling the science news void by scientists as science reporters.