bluuebunny/crossref_metadata_2025_split huggingface dataset:
Prevalence of Mycoplasma genitalium and Azithromycin-resistant Infections Among Remnant Clinical Specimens, Los Angeles
Authors: Allan-Blitz Lao-Tzu , Mokany Elisa , Campeau Shelley , Wee Rachel , Shannon Chelsea , Klausner Jeffrey D. 
Published: March 2018

Background

Mycoplasma genitalium is an important cause of bacterial sexually transmitted diseases. Diagnosis and susceptibility testing of M. genitalium are limited by the fastidious nature of the organism. Therefore, the prevalence of infection and azithromycin resistance are poorly studied.

Methods
We conducted an exploratory study on remnant clinical specimens. We collected remnant DNA from consecutive urine samples and clinical swabs (cervical/vaginal, rectal, and pharyngeal) previously tested for Neisseria gonorrhoeae and Chlamydia trachomatis using the Cobas 4800 CT/NG assay (Roche Molecular Systems, Pleasanton, CA) between March-April 2017 from across the University of California, Los Angeles Health System. We then retrospectively tested all specimens with the ResistancePlus MG (550) kit, a molecular assay for the detection of M. genitalium and genetic mutations associated with azithromycin resistance.

Results
Among 500 specimens, the prevalence of M. genitalium was 1.1% (95% confidence interval [CI], 0.04%–3.0%) in urine samples (n = 362), 17.4% (95% CI, 5.7%–39.6%) in rectal swabs (n = 23), and 1.9% (95% CI, 0.3%–7.3%) in cervical/vaginal swabs (n = 106). The prevalence of N. gonorrhoeae was 0.6% in urine samples and 4.3% in rectal swabs, whereas the prevalence of C. trachomatis was 2.2% in urine samples, 4.3% in rectal swabs and 3.8% in cervical/vaginal swabs. Of the 10 M. genitalium positive specimens, 8 (80.0%) had a mutation associated with azithromycin resistance.

Conclusions
The prevalence of M. genitalium infection in our population varied by anatomic site of infection. Most M. genitalium infections had at least 1 mutation associated with azithromycin resistance.
Penile Metastases From Renal Cell Carcinoma
Authors: Gitto Salvatore , Vaiani Marta , Cascella Tommaso , Lanocita Rodolfo 
Published: March 2018

Abstract
The prostate and bladder are the most common primary cancer sites for penile metastases. Here, we describe an unusual case of metastases from renal cell carcinoma to the penis discovered 1 month after nephrectomy in a 60-year-old man. The diagnosis was achieved using B-mode and contrast-enhanced ultrasound.
Consensus and clustering in opinion formation on networks
Authors: Bujalski Julia , Dwyer Grace , Kapitula Todd , Le Quang-Nhat , Malvai Harjasleen , Rosenthal-Kay Jordan , Ruiter Joshua 
Published: March 2018

Ideas that challenge the status quo either evaporate or dominate. The study of opinion dynamics in the socio-physics literature treats space as uniform and considers individuals in an isolated community, using ordinary differential equation (ODE) models. We extend these ODE models to include multiple communities and their interactions. These extended ODE models can be thought of as being ODEs on directed graphs. We study in detail these models to determine conditions under which there will be consensus and pluralism within the system. Most of the consensus/pluralism analysis is done for the case of one and two cities. However, we numerically show for the case of a symmetric cycle graph that an elementary bifurcation analysis provides insight into the phenomena of clustering. Moreover, for the case of a cycle graph with a hub, we discuss how having a sufficient proportion of zealots in the hub leads to the entire network sharing the opinion of the zealots.
This article is part of the theme issue ‘Stability of nonlinear waves and patterns and related topics’.
The phase structure of grain boundaries
Authors: Ercolani Nicholas M. , Kamburov Nikola , Lega Joceline 
Published: March 2018

This article discusses numerical and analytical results on grain boundaries, which are line defects that separate roll patterns oriented in different directions. The work is set in the context of a canonical pattern-forming system, the Swift–Hohenberg (SH) equation, and of its phase diffusion equation, the regularized Cross–Newell equation. It is well known that, as the angle made by the rolls on each side of a grain boundary is decreased, dislocations appear at the core of the defect. Our goal is to shed some light on this transition, which provides an example of defect formation in a system that is variational. Numerical results of the SH equation that aim to analyse the phase structure of far-from-threshold grain boundaries are presented. These observations are then connected to properties of the associated phase diffusion equation. Outcomes of this work regarding the role played by phase derivatives in the creation of defects in pattern-forming systems, about the role of harmonic analysis in understanding the phase structure in such systems, and future research directions are also discussed.This article is part of the theme issue ‘Stability of nonlinear waves and patterns and related topics’.
Transcriptional differences between the two host strains ofSpodoptera frugiperda(Lepidoptera: Noctuidae)
Authors: Orsucci Marion , Moné Yves , Audiot Philippe , Gimenez Sylvie , Nhim Sandra , Naït-Saïdi Rima , Frayssinet Marie , Dumont Guillaume , Boudon Jean-Paul , Vabre Marin , Rialle Stéphanie , Koual Rachid , Kergoat Gael J. , Nagoshi Rodney N. , Meagher Robert L. , d’Alençon Emmanuelle , Nègre Nicolas 
Published: March 2018

AbstractSpodoptera frugiperda, the fall armyworm (FAW), is an important agricultural pest in the Americas and an emerging pest in sub-Saharan Africa, India, East-Asia and Australia, causing damage to major crops such as corn, sorghum and soybean. While FAW larvae are considered polyphagous, differences in diet preference have been described between two genetic variants: the corn strain (sf-C) and the rice strain (sf-R). These two strains are sometimes considered as distinct species, raising the hypothesis that ost plant specialization might have driven their divergence. To test this hypothesis, we irst performed controlled reciprocal transplant (RT) experiments to address the impact of plant diet on several traits linked to the fitness of the sf-C and sf-R strains. The phenotypical data suggest that sf-C is specialized to corn. We then used RNA-Se to identify constitutive transcriptional differences between strains, regardless of diet, in laboratory as well as in natural populations. We found that variations in mitochon rial transcription levels are among the most substantial and consistent differences between the two strains. Since mitochondrial genotypes also vary between the strains, we believe the mitochondria may have a significant role in driving strain divergence.
Conjugation factors controlling F-plasmid antibiotic resistance transmission
Authors: Alalam Hanna , Graf Fabrice E. , Palm Martin , Abadikhah Marie , Zackrisson Martin , Mattsson Matilda , Hadjineophytou Chris , Persson Linnéa , Stenberg Simon , Ghiaci Payam , Sunnerhagen Per , Warringer Jonas , Farewell Anne 
Published: March 2018

ABSTRACTThe rapid horizontal transmission of many antibiotic resistance genes between bacterial host cells on conjugative plasmids is a major cause of the accelerating antibiotic resistance crisis. Preventing understanding and targeting conjugation, there currently are no experimental platforms for fast and cost-efficient screening of genetic effects on antibiotic resistance transmission by conjugation. We introduce a novel experimental framework to screen for conjugation based horizontal transmission of antibiotic resistance between >60.000 pairs of cell populations in parallel. Plasmid-carrying donor strains are constructed in high throughput. We then mix the resistance plasmid carrying donors with recipients in a design where only transconjugants can reproduce, measure growth in dense intervals and extract transmission times as the growth lag. As proof-of-principle, we exhaustively explored chromosomal genes controlling F plasmid donation withinE. colipopulations, by screening the Keio deletion collection at high replication. We recover all six known chromosomal gene mutants affecting conjugation and identify >50 novel factors, all of which diminish antibiotic resistance transmission. We verify 10 of the novel genes’ effects in a liquid mating assay. The new framework holds great potential for exhaustive disclosing of candidate targets for helper drugs that delay resistance development in patients and societies and improves the longevity of current and future antibiotics.
Pointing Errors in Non-Metric Virtual Environments
Authors: Muryy Alexander , Glennerster Andrew 
Published: March 2018

AbstractThere have been suggestions that human navigation may depend on representations that have no metric, Euclidean interpretation but that hypothesis remains contentious. An alternative is that observers build a consistent 3D representation of space. Using immersive virtual reality, we measured the ability of observers to point to targets in mazes that had zero, one or three ‘wormholes’ – regions where the maze changed in configuration (invisibly). In one model, we allowed the configuration of the maze to vary to best explain the pointing data; in a second model we also allowed the local reference frame to be rotated through 90, 180 or 270 degrees. The latter model outperformed the former in the wormhole conditions, inconsistent with a Euclidean cognitive map.
A widespread thermodynamic effect, but maintenance of biological rates through space across life’s major domains
Authors: Sørensen Jesper G. , White Craig R. , Duffy Grant A. , Chown Steven L. 
Published: March 2018

AbstractFor over a century, temperature compensation (maintenance of biological rates with changing temperatures) has remained controversial. An alternative idea, that fitness is greater at higher temperatures (the thermodynamic effect), has gained increasing traction, and is being used to understand large-scale biodiversity responses to environmental change. Yet evidence in favour of each of these contrasting hypotheses continues to emerge. In consequence, the fundamental nature of organismal thermal responses and its implications remain unresolved. Here we investigate these ideas explicitly using a global dataset of 619 observations of four categories of organismal performance, spanning 14 phyla and 403 species. In agreement with both hypotheses, we show a positive relationship between the temperature of maximal performance rate (Topt) and environmental temperature (Tenv) for all traits. Next we demonstrate that relationships between Tenvand the temperature of maximal performance rate (Umax) are rarely significant and positive, as expected if a thermodynamic effect predominates. By contrast, a positive relationship between Toptand Umaxis always present, but markedly weaker than theoretically predicted. These outcomes demonstrate that while some form of thermodynamic effect exists, ample scope is present for biochemical and physiological adaptation to thermal environments in the form of temperature compensation.
An epigenetic biomarker of aging for lifespan and healthspan
Authors: Levine Morgan E. , Lu Ake T. , Quach Austin , Chen Brian H. , Assimes Themistocles L. , Bandinelli Stefania , Hou Lifang , Baccarelli Andrea A. , Stewart James D. , Li Yun , Whitsel Eric A. , Wilson James G , Reiner Alex P , Aviv Abraham , Lohman Kurt , Liu Yongmei , Ferrucci Luigi , Horvath Steve 
Published: March 2018

AbstractIdentifying reliable biomarkers of aging is a major goal in geroscience. While the first generation of epigenetic biomarkers of aging were developed using chronological age as a surrogate for biological age, we hypothesized that incorporation of composite clinical measures of phenotypic age that capture differences in lifespan and healthspan may identify novel CpGs and facilitate the development of a more powerful epigenetic biomarker of aging. Using a innovative two-step process, we develop a new epigenetic biomarker of aging, DNAm PhenoAge, that strongly outperforms previous measures in regards to predictions for a variety of aging outcomes, including all-cause mortality, cancers, healthspan, physical functioning, and Alzheimer’s disease. While this biomarker was developed using data from whole blood, it correlates strongly with age in every tissue and cell tested. Based on an in-depth transcriptional analysis in sorted cells, we find that increased epigenetic, relative to chronological age, is associated increased activation of pro-inflammatory and interferon pathways, and decreased activation of transcriptional/translational machinery, DNA damage response, and mitochondrial signatures. Overall, this single epigenetic biomarker of aging is able to capture risks for an array of diverse outcomes across multiple tissues and cells, and provide insight into important pathways in aging.
DensityPath: a level-set algorithm to visualize and reconstruct cell developmental trajectories for large-scale single-cell RNAseq data
Authors: Chen Ziwei , An Shaokun , Bai Xiangqi , Gong Fuzhou , Ma Liang , Wan Lin 
Published: March 2018

AbstractCell fates are determined by transition-states which occur during complex biological pro-cesses such as proliferation and differentiation. The advance in single-cell RNA sequencing (scRNAseq) provides the snapshots of single cell transcriptomes, thus offering an essential opportunity to study such complex biological processes. Here, we introduce a novel algorithm, DensityPath, which visualizes and reconstructs the underlying cell developmental trajectories for large-scale scRNAseq data. DensityPath has three merits. Firstly, by adopting the nonlinear dimension reduction algorithm elastic embedding, DensityPath reveals the intrinsic structures of the data. Secondly, by applying the powerful level set clustering method, DensityPath extracts the separate high density clusters of representative cell states (RCSs) from the single cell multimodal density landscape of gene expression space, enabling it to handle the heterogeneous scRNAseq data elegantly and accurately. Thirdly, DensityPath constructs cell state-transition path by finding the geodesic minimum spanning tree of the RCSs on the surface of the density landscape, making it more computationally efficient and accurate for large-scale dataset. The cell state-transition path constructed by DensityPath has the physical interpretation as the minimum-transition-energy (least-cost) path. We demonstrate that DensityPath is capable of identifying complex cell development trajectories with bifurcating and trifurcating branches on the human preimplantation embryos. We demonstrate that DensityPath is robust and has high accuracy of pseudotime calculation and branch assignment on the real scRNAseq as well as simulated datasets.
Vulnerability of invasive glioma cells to lysosomal membrane instabilization
Authors: Joncour Vadim Le , Hyvönen Maija , Filppu Pauliina , Turunen Pauliina S. , Sihto Harri , Burghardt Isabel , Joensuu Heikki , Tynninen Olli , Jääskeläinen Juha , Weller Michael , Lehti Kaisa , Laakkonen Pirjo 
Published: March 2018

AbstractDiffusive by nature, glioma challenges clinical care by the impossibility of complete surgical resection of tumor, leaving the radio- and chemoresistant cells responsible for recurrence intact. We identified mammary-derived growth inhibitor (MDGI/FABP3) as invasive glioma biomarker. Here, we show that high MDGI expression associated with poor patient survival and promoted invasive glioma cell growth bothin vitroandin vivo, while MDGI silencing drastically compromised patient-derived tumoroid viability via induction of lysosomal membrane permeabilization (LMP). This alternative cell death pathway provokes release of lysosomal hydrolases into the cytosol leading inevitably to the cell death. Our results show a novel functional role for MDGI in glioma cell invasion, survival, and maintenance of the lysosomal membrane integrity as well as an unsuspected sensitivity of glioma cells to an LMP-inducing drug, anti-histamine clemastine. In a preclinical study, clemastine-treatment significantly prolonged the survival of intracranial glioblastoma-bearing animals due to eradication of invasive glioma cells. This glioma cell vulnerability to LMP-inducing drugs opens new horizons for development of novel treatments and suggest re-positioning of an established drug for new indication.
Epigallocatechin-3-Gallate Improves Facial Dysmorphology Associated with Down Syndrome
Authors: Starbuck John M. , Llambrich Sergi , González Ruben , Albaigès Julia , Sarlé Anna , Wouters Jens , González Alejandro , Sevillano Xavier , Sharpe James , de La Torre Rafael , Dierssen Mara , Velde Greetje Vande , Martínez-Abadías Neus 
Published: March 2018

AbstractIn Down syndrome (DS), the overall genetic imbalance caused by trisomy of chromosome 21 leads to a complex pleiotropic phenotype that involves a recognizable set of facial traits. Several studies have shown the potential of epigallocatechin-3-gallate (EGCG), a green tea flavanol, as a therapeutic tool for alleviating different developmental alterations associated with DS, such as cognitive impairment, skull dysmorphologies, and skeletal deficiencies. Here we provide for the first time experimental and clinical evidence of the potential benefits of EGCG treatment to facial morphology. Our results showed that mouse models treated with low dose of EGCG during pre- and postnatal development improved facial dysmorphology. However, the same treatment at high dose produced disparate facial morphology changes with an extremely wide and abnormal range of variation. Our observational study in humans revealed that EGCG treatment since early in development is associated with intermediate facial phenotypes and significant facial improvement scores. Overall, our findings suggest a potential beneficial effect of ECGC on facial development, which requires further research to pinpoint the optimal dosages of EGCG that reliably improve DS phenotypes. Current evidence warns against the non-prescribed intake of this supplement as a health-promoting measure.
A stress recovery signaling network for enhanced flooding tolerance inArabidopsis thaliana
Authors: Yeung Elaine , Veen Hans van , Vashisht Divya , Sobral Paiva Ana Luiza , Hummel Maureen , Steffens Bianka , Steffen-Heins Anja , Sauter Margret , Vries Michel de , Schuurink Robert , Bazin Jérémie , Bailey-Serres Julia , Voesenek Laurentius A.C.J. , Sasidharan Rashmi 
Published: March 2018

AbstractAbiotic stresses in plants are often transient and the recovery phase following stress removal is critical. Flooding, a major abiotic stress that negatively impacts plant biodiversity and agriculture, is a sequential stress where tolerance is strongly dependent on viability underwater and during the postflooding period. Here we show that inArabidopsis thalianaaccessions (Bay-0 and Lp2-6), different rates of submergence recovery correlate with submergence tolerance and fecundity. A genome-wide assessment of ribosome-associated transcripts in Bay-0 and Lp2-6 revealed a signaling network regulating recovery processes. Differential recovery between the accessions was related to the activity of three genes:RESPIRATORY BURST OXIDASE HOMOLOG(RBOHD),SENESCENCE-ASSOCIATED GENE113(SAG113) andORESARA1(ORE1/NAC6) which function in a regulatory network involving a reactive oxygen species (ROS) burst upon de-submergence and the hormones abscisic acid and ethylene. This regulatory module controls ROS homeostasis, stomatal aperture and chlorophyll degradation during submergence recovery. This work uncovers a signaling network that regulates recovery processes following flooding to hasten the return to pre-stress homeostasis.Significance statementFlooding due to extreme weather events can be highly detrimental to plant development and yield. Speedy recovery following stress removal is an important determinant of tolerance, yet mechanisms regulating this remain largely uncharacterized. We identified a regulatory network inArabidopsis thalianathat controls water loss and senescence to influence recovery from prolonged submergence. Targeted control of the molecular mechanisms facilitating stress recovery identified here can potentially improve performance of crops in flood-prone areas.
Metabolic adjustment enhances food web stability
Authors: Quévreux Pierre , Brose Ulrich 
Published: March 2018

AbstractUnderstanding ecosystem stability is one of the greatest challenges of ecology. Over several decades, it has been shown that allometric scaling of biological rates and feeding interactions provide stability to complex food web models. Moreover, introducing adaptive responses of organisms to environmental changes (e.g.like adaptive foraging that enables organisms to adapt their diets depending on resources abundance) improved species per-sistence in food webs. Here, we introduce the concept of metabolic adjustment,i.e.the ability of species to slow down their metabolic rates when facing starvation and to increase it in time of plenty. We study the reactions of such a model to nutrient enrichment and the adjustment speed of metabolic rates. We found that increasing nutrient enrichment leads to a paradox of enrichment (increase in biomasses and oscillation amplitudes and ultimately extinction of species) but metabolic adjustment stabilises the system by dampening the oscillations. Metabolic adjustment also increases the average biomass of the top predator in a tri-trophic food chain. In complex food webs, metabolic adjustment has a stabilising effect as it promotes species survival by creating a large diversity of metabolic rates. However, this stabilising effect is mitigated in enriched ecosystems. Phenotypic plasticity of organisms must be considered in food web models to better understand the response of organisms to their environment. As metabolic rate is central in describing biological rates, we must pay attention to its variations to fully understand the population dynamics of natural communities.
Fusing Mobile Phone Sensing and Brain Imaging to Assess Depression in College Students
Authors: Huckins Jeremy F. , daSilva Alex W. , Wang Rui , Wang Weichen , Hedlund Elin L. , Murphy Eilis I. , Lopez Richard B. , Rogers Courtney , Holtzheimer Paul E. , Kelley William M. , Heatherton Todd F. , Wagner Dylan D. , Haxby James V. , Campbell Andrew T. 
Published: March 2018

AbstractAs smartphone usage has become increasingly prevalent in our society, so have rates of depression, particularly among young adults. Individual differences in smartphone usage patterns have been shown to reflect individual differences in underlying affective processes such as depression (Wang et al., 2018). In the current study, we identified a positive relationship between smartphone screen time (e.g. phone unlock duration) and resting-state functional connectivity (RSFC) between the subgenual cingulate cortex (sgCC), a brain region implicated in depression and antidepressant treatment response, and regions of the ventromedial/orbitofrontal cortex, such that increased phone usage was related to stronger connectivity between these regions. We then used this cluster to constrain subsequent analyses looking at depressive symptoms in the same cohort and observed partial replication in a separate cohort. We believe the data and analyses presented here provide relatively simplistic initial analyses which replicate and provide a first step in combining functional brain activity and smartphone usage patterns to better understand issues related to mental health. Smartphones are a prevalent part of modern life and the usage of mobile sensing data from smartphones promises to be an important tool for mental health diagnostics and neuroscience research.