bluuebunny/crossref_metadata_2025_split huggingface dataset:
Naive B cells in neuromyelitis optica spectrum disorders: impact of steroid use and relapses
Authors: Janssen Malou , Bruijstens Arlette L , van Langelaar Jamie , Wong YuYi , Wierenga-Wolf Annet F , Melief Marie-José , Rijvers Liza , van Pelt E Daniëlle , Smolders Joost , Wokke Beatrijs H , van Luijn Marvin M 
Published: November 2020

Abstract
Neuromyelitis optica spectrum disorders are a group of rare, but severe autoimmune diseases characterized by inflammation of the optic nerve(s) and/or spinal cord. Although naive B cells are considered key players by escaping central tolerance checkpoints, it remains unclear how their composition and outgrowth differ in patients with neuromyelitis optica spectrum disorders. Under complete treatment-naive circumstances, we found that naive mature/transitional B-cell ratios were reduced in the blood of 10 patients with aquaporin-4 immunoglobulin G-positive disease (neuromyelitis optica spectrum disorders) as compared to 11 both age- and gender-matched healthy controls, eight patients with myelin oligodendrocyte glycoprotein-immunoglobulin G-associated disorders and 10 patients with multiple sclerosis. This was the result of increased proportions of transitional B cells, which were the highest in patients with neuromyelitis optica spectrum disorders with relapses and strongly diminished in a separate group of nine patients with neuromyelitis optica spectrum disorders and myelin oligodendrocyte glycoprotein-immunoglobulin G-associated disorders who received corticosteroid treatment. These findings need to be confirmed in longitudinal studies. For purified naive mature B cells of seven patients with neuromyelitis optica spectrum disorders and myelin oligodendrocyte glycoprotein-immunoglobulin G-associated disorders with relapses, Toll-like receptor 9 ligand synergized with interferon-γ to enhance plasmablast formation during germinal centre-like cultures. This was not seen for 11 patients without relapses and nine healthy controls. In the neuromyelitis optica spectrum disorders group, in vitro plasmablast formation corresponded to total and anti-aquaporin-4 immunoglobulin G secretion, of which the latter was found only for relapsing cases. These data indicate that naive B-cell homoeostasis is different and selectively targeted by corticosteroids in patients with neuromyelitis optica spectrum disorders. This also supports further exploration of naive B cells for their use in Toll-like receptor 9-dependent in vitro platforms in order to predict the activity of neuromyelitis optica spectrum disorders.
Association Between Statin Use and Inflammatory Bowel Diseases: Results from a Swedish, Nationwide, Population-based Case-control Study
Authors: Lochhead Paul , Khalili Hamed , Sachs Michael C , Chan Andrew T , Olén Ola , Ludvigsson Jonas F 
Published: November 2020

Abstract

Background
In addition to their potent lipid-lowering action, statins may modulate inflammation. However, data on statin use and the risk of inflammatory bowel diseases [IBD] have been inconsistent.

Methods
We searched the Nationwide Swedish Patient Register [inpatient and non-primary outpatient care] to identify adults diagnosed with Crohn’s disease [CD, n = 7637] or ulcerative colitis [UC, n = 15 652] from 2006 to 2014. Each case was matched to 10 general population controls [n = 232 890]. Data on dispensed statin prescriptions were extracted from the Prescribed Drug Register. Conditional logistic regression models estimated odds ratios [ORs] for risk of IBD according to statin exposure while controlling for potential confounders, including indications for statin therapy.

Results
In multivariable adjusted models, compared with no statin use, any statin use was associated with a lower risk of CD (OR = 0.71; 95% confidence interval [CI], 0.63–0.79), but not UC [OR = 1.03; 95% CI, 0.96–1.11]. The lowest OR for CD was seen for current statin use [OR = 0.67; 95% CI, 0.60–0.75]. For CD, the lowest category of cumulative statin dose [31–325 defined daily dose, DDD] was associated with an OR of 0.73 [95% CI, 0.61–0.88] and the highest category [&gt;1500 DDD] with an OR of 0.66 [95% CI, 0.55–0.80], ptrend = 0.10. For UC, the lowest and highest dose categories yielded ORs of 1.12 [95% CI, 1.00–1.25] and 0.99 [95% CI, 0.88–1.13], respectively, ptrend = 0.13.

Conclusions
Statin use was associated with a lower risk of CD, but not of UC. The association with CD risk appeared strongest for current statin use. Our findings suggest that statin use may influence the development of CD.
The Impact of Youth Engagement on Life Satisfaction: A Quasi-Experimental Field Study of a UK National Youth Engagement Scheme
Authors: Laurence James 
Published: November 2020

Abstract
There is growing interest in the role of organized social participation in clubs, associations and activities in shaping subjective well-being (SWB). However, the field remains contested. This study addresses key questions regarding the participation–SWB link: concerns regarding endogeneity; debate surrounding the mechanisms at work; and the role participation can play in closing inequalities in SWB. Each question is addressed through a quasi-experimental field study into the impact of a large-scale, nationally-implemented youth engagement scheme (UK National Citizen Service) on life satisfaction. Using pre-test/post-test data on a sample of participants and (propensity score matched) controls, results suggest discrete periods of youth engagement can lead to significant improvements in life satisfaction, observable at least 4–6 months after involvement ended. Participation can also help close social inequalities in SWB via a significantly stronger impact on life satisfaction among young people from more economically disadvantaged communities. Although youth from disadvantaged communities join the scheme with lower SWB, post-participation, they have entirely closed the gap in SWB with their less-disadvantaged peers. Improvements in SWB emerge from positive impacts of participation on both social- and psychological-resource pathways. However, stronger participation-effects on psychological-resources become increasingly important for explaining the additional SWB-gains of more disadvantaged young people.
Distinct co-occurrence patterns of prokaryotic community between the waters and sediments in lakes with different salinity
Authors: Yang Jian , Jiang Hongchen , Sun Xiaoxi , Huang Jianrong , Han Mingxian , Wang Beichen 
Published: November 2020

ABSTRACT
Temporal variations and co-occurrence patterns of the prokaryotic community in saline lakes remain elusive. In this study, we investigated the temporal variations of the prokaryotic community in six lakes with different salinity by using Illumina sequencing. The results showed that prokaryotic community compositions exhibited temporal variations in all studied lakes, which may be partially caused by temporal fluctuations of environmental variables (e.g. salinity, temperature, total nitrogen). Salinity fluctuations exhibited stronger influences on temporal variations of prokaryotic community composition in the lakes with low salinity than in those with high salinity. Stochastic factors (i.e. neutral processes) also contributed to temporal variations of prokaryotic community composition, and their contributions decreased with increasing salinity in the studied saline lakes. Network analysis showed that prokaryotic co-occurrence networks of the studied lakes exhibited non-random topology. Salinity affected the phylogenetic composition of nodes in the studied networks. The topological features (e.g. average connectivity and modularity) of the studied networks significantly differed between lake waters and sediments. Collectively, these results expand our knowledge of the mechanisms underlying prokaryotic community assembly and co-occurrence relationships in saline lakes with different salinity.
Anomalous azimuthal variations with 360° periodicity of Rayleigh phase velocities observed in Scandinavia
Authors: Mauerberger Alexandra , Maupin Valérie , Gudmundsson Ólafur , Tilmann Frederik 
Published: November 2020

SUMMARY
We use the recently deployed ScanArray network of broad-band stations covering most of Norway and Sweden as well as parts of Finland to analyse the propagation of Rayleigh waves in Scandinavia. Applying an array beamforming technique to teleseismic records from ScanArray and permanent stations in the study region, in total 159 stations with a typical station distance of about 70 km, we obtain phase velocities for three subregions, which collectively cover most of Scandinavia (excluding southern Norway). The average phase dispersion curves are similar for all three subregions. They resemble the dispersion previously observed for the South Baltic craton and are about 1 per cent slower than the North Baltic shield phase velocities for periods between 40 and 80 s. However, a remarkable sin(1θ) phase velocity variation with azimuth is observed for periods &gt;35 s with a 5 per cent deviation between the maximum and minimum velocities, more than the overall lateral variation in average velocity. Such a variation, which is incompatible with seismic anisotropy, occurs in northern Scandinavia and southern Norway/Sweden but not in the central study area. The maximum and minimum velocities were measured for backazimuths of 120° and 300°, respectively. These directions are perpendicular to a step in the lithosphere–asthenosphere boundary (LAB) inferred by previous studies in southern Norway/Sweden, suggesting a relation to large lithospheric heterogeneity. In order to test this hypothesis, we carried out 2-D full-waveform modeling of Rayleigh wave propagation in synthetic models which incorporate a steep gradient in the LAB in combination with a pronounced reduction in the shear velocity below the LAB. This setup reproduces the observations qualitatively, and results in higher phase velocities for propagation in the direction of shallowing LAB, and lower ones for propagation in the direction of deepening LAB, probably due to the interference of forward scattered and reflected surface wave energy with the fundamental mode. Therefore, the reduction in lithospheric thickness towards southern Norway in the south, and towards the Atlantic ocean in the north provide a plausible explanation for the observed azimuthal variations.
Ketamine and Serotonergic Psychedelics: Common Mechanisms Underlying the Effects of Rapid-Acting Antidepressants
Authors: Kadriu Bashkim , Greenwald Maximillian , Henter Ioline D , Gilbert Jessica R , Kraus Christoph , Park Lawrence T , Zarate Carlos A 
Published: November 2020

AbstractBackgroundThe glutamatergic modulator ketamine has created a blueprint for studying novel pharmaceuticals in the field. Recent studies suggest that “classic” serotonergic psychedelics (SPs) may also have antidepressant efficacy. Both ketamine and SPs appear to produce rapid, sustained antidepressant effects after a transient psychoactive period.MethodsThis review summarizes areas of overlap between SP and ketamine research and considers the possibility of a common, downstream mechanism of action. The therapeutic relevance of the psychoactive state, overlapping cellular and molecular effects, and overlapping electrophysiological and neuroimaging observations are all reviewed.ResultsTaken together, the evidence suggests a potentially shared mechanism wherein both ketamine and SPs may engender rapid neuroplastic effects in a glutamatergic activity-dependent manner. It is postulated that, though distinct, both ketamine and SPs appear to produce acute alterations in cortical network activity that may initially produce psychoactive effects and later produce milder, sustained changes in network efficiency associated with therapeutic response. However, despite some commonalities between the psychoactive component of these pharmacologically distinct therapies—such as engagement of the downstream glutamatergic pathway—the connection between psychoactive impact and antidepressant efficacy remains unclear and requires more rigorous research.ConclusionsRapid-acting antidepressants currently under investigation may share some downstream pharmacological effects, suggesting that their antidepressant effects may come about via related mechanisms. Given the prototypic nature of ketamine research and recent progress in this area, this platform could be used to investigate entirely new classes of antidepressants with rapid and robust actions.
Individual and collective impact of Klebsiella pneumoniae carbapenemase (KPC)-producing K. pneumoniae in patients admitted to the ICU
Authors: Kernéis Solen , Lucet Jean Christophe , Santoro Antonella , Meschiari Marianna 
Published: November 2020

Abstract
KPC-producing Klebsiella pneumoniae (KPC-Kp) raises major concerns in the context of intensive care, owing to limited treatment options and the ability to cause outbreaks in this specific setting. The objectives of this review are to give an overview of the burden of KPC-Kp in ICU patients and to discuss methodological issues and limitations regarding the quality of data available. Robust and reliable assessment of the KPC-Kp impact in the ICU should take into consideration not only characteristics of the individuals, but also of the health systems including length of stay, costs and hospital organization issues. Estimates of mortality reported in the current literature are weakened by the poor quality of adjustment for age-specific risks, co-morbidities, and appropriateness of therapy. All these confounding factors should be taken into account in models, with consideration of control groups and competing risks that is currently lacking in the published literature. Since development of antibiotic resistance is an unstoppable phenomenon and economic and human resources are facing progressive limitations due to budget constraints, cost-saving strategies targeted to avoid ICU closure, temporary limitation of admissions or delayed hospital discharge are necessary. The early identification of KPC-Kp-colonized patients through active screening strategies is likely to be the cornerstone of such a cost-saving strategy. However, there are still many open issues concerning which of these strategies are the most effective. Owing to extreme heterogeneity and several methodological flaws in current publications, future studies investigating the long-term sequelae and economic impact of KPC-Kp in the ICU are urgently needed.
Male Linked Genomic Region Determines Sex in DioeciousAmaranthus palmeri
Authors: Neves Cátia José , Matzrafi Maor , Thiele Meik , Lorant Anne , Mesgaran Mohsen B , Stetter Markus G 
Published: November 2020

AbstractDioecy, the separation of reproductive organs on different individuals, has evolved repeatedly in different plant families. Several evolutionary paths to dioecy have been suggested, but the mechanisms behind sex determination is not well understood. The diploid dioecious Amaranthus palmeri represents a well-suited model system to study sex determination in plants. Despite the agricultural importance of the species, the genetic control and evolutionary state of dioecy in A. palmeri is currently unknown. Early cytogenetic experiments did not identify heteromorphic chromosomes. Here, we used whole-genome sequencing of male and female pools from 2 independent populations to elucidate the genetic control of dioecy in A. palmeri. Read alignment to a close monoecious relative and allele frequency comparisons between male and female pools did not reveal significant sex-linked genes. Consequently, we employed an alignment-free k-mer comparison which enabled us to identify a large number of male-specific k-mers. We assembled male-specific contigs comprising a total of almost 2 Mb sequence, proposing a XY sex-determination system in the species. We were able to identify the potential Y chromosome in the A. palmeri draft genome sequence as 90% of our male-specific sequence aligned to a single scaffold. Based on our findings, we suggest an intermediate evolutionary state of dioecy with a young Y chromosome in A. palmeri. Our findings give insight into the evolution of sex chromosomes in plants and may help to develop sustainable strategies for weed management.
Soil microbes weaken the positive effect of an aquatic–terrestrial subsidy on plant performance
Authors: Garcia Alejandra B , Locke Hannah , Crawford Kerri M 
Published: November 2020

AbstractAimsLinkages formed through aquatic–terrestrial subsidies can play an important role in structuring communities and mediating ecosystem functions. Aquatic–terrestrial subsidies may be especially important in nutrient-poor ecosystems, such as the freshwater sand dunes surrounding Lake Michigan. Adult midges emerge from Lake Michigan in the spring, swarm to mate and die. Their carcasses form mounds at the base of plants, where they may increase plant productivity through their nutrient inputs. However, the effect of aquatic–terrestrial subsidies on plant productivity could depend on other biotic interactions. In particular, soil microbes might play a key role in facilitating the conversion of nutrients to plant-available forms or competing for the nutrients with plants.MethodsIn a greenhouse experiment, we tested how carcasses from lake emergent midges (Chironomidae) and soil microbes independently and interactively influenced the performance of a common dune grass, Calamovilfa longifolia. To determine whether midges influenced abiotic soil properties, we measured how midge additions influenced soil nutrients and soil moisture.Important FindingsMidges greatly increased plant biomass, while soil microbes influenced the magnitude of this effect. In the absence of soil microbes plant biomass was seven times greater with midges than without midges. However, in the presence of soil microbes, plant biomass was only three times greater. The effect of midges might be driven by their nutrient inputs into the soil, as midges contained 100 times more N, 10 times more P and 150 times more K than dune soils did. Our results suggest that soil microbes may be competing with plants for these nutrients. In sum, we found that midges can be an important aquatic–terrestrial subsidy that produces strong, positive effects on plant productivity along the shorelines of Lake Michigan, but that the impact of aquatic–terrestrial subsidies must be considered within the context of the complex interactions that take place within ecological communities.
Pilot Executive Functioning Intervention in Epilepsy: Behavioral and Quality of Life Outcomes
Authors: Modi Avani C , Mara Constance A , Schmidt Matthew , Smith Aimee W , Turnier Luke , Wade Shari L 
Published: November 2020

Abstract

Objective
To examine changes in emotional and behavioral functioning and health-related quality of life (HRQOL) following a web-based executive functioning (EF) intervention open pilot trial (e.g., Epilepsy Journey) for adolescents with epilepsy.

Methods
Adolescents with an established diagnosis of epilepsy, EF deficits, and without developmental disorders participated in a single-arm trial of Epilepsy Journey. Epilepsy Journey is a gamified, online learning environment comprised of 10 learning modules targeting EF deficits (e.g., working memory, organization) and tailored to epilepsy with accompanying telehealth problem-solving sessions. Adolescents completed questionnaires assessing emotional and behavioral functioning and HRQOL at baseline, posttreatment, and 2 follow-ups . Longitudinal mixed models and logistic regression analyses were used for these secondary analyses.

Results
39 adolescents were recruited for Epilepsy Journey (Mage=15.3 years; 67% female; 87% White: Non-Hispanic; 39% experienced seizures in the past 3 months). Preliminary data indicate significant improvements in caregiver-reported Externalizing symptoms, Behavioral Symptom Index scores and Adaptive Skills from baseline to 5-month follow-up. Significant improvements were observed for caregiver-reported Mood/Behavior and self-reported Impact, Cognitive Functioning, Executive Functioning, and Sleep subscales of the PedsQL Epilepsy Module. Clinically significant improvements (e.g., clinical/at-risk to normative levels) in behavioral and quality of life domains were also noted.

Conclusion
Epilepsy Journey appears to contribute to changes in emotional and behavioral functioning and HRQOL in adolescents with epilepsy. Given the proof of concept trial format of this study, an important future direction is to conduct a randomized controlled trial with a larger, generalizable cohort of adolescents with epilepsy.
Machine learning a model for RNA structure prediction
Authors: Calonaci Nicola , Jones Alisha , Cuturello Francesca , Sattler Michael , Bussi Giovanni 
Published: November 2020

AbstractRNA function crucially depends on its structure. Thermodynamic models currently used for secondary structure prediction rely on computing the partition function of folding ensembles, and can thus estimate minimum free-energy structures and ensemble populations. These models sometimes fail in identifying native structures unless complemented by auxiliary experimental data. Here, we build a set of models that combine thermodynamic parameters, chemical probing data (DMS and SHAPE) and co-evolutionary data (direct coupling analysis) through a network that outputs perturbations to the ensemble free energy. Perturbations are trained to increase the ensemble populations of a representative set of known native RNA structures. In the chemical probing nodes of the network, a convolutional window combines neighboring reactivities, enlightening their structural information content and the contribution of local conformational ensembles. Regularization is used to limit overfitting and improve transferability. The most transferable model is selected through a cross-validation strategy that estimates the performance of models on systems on which they are not trained. With the selected model we obtain increased ensemble populations for native structures and more accurate predictions in an independent validation set. The flexibility of the approach allows the model to be easily retrained and adapted to incorporate arbitrary experimental information.
Tracing and tracking epiallele families in complex DNA populations
Authors: Pezone Antonio , Tramontano Alfonso , Scala Giovanni , Cuomo Mariella , Riccio Patrizia , De Nicola Sergio , Porcellini Antonio , Chiariotti Lorenzo , Avvedimento Enrico V 
Published: November 2020

Abstract
DNA methylation is a stable epigenetic modification, extremely polymorphic and driven by stochastic and deterministic events. Most of the current techniques used to analyse methylated sequences identify methylated cytosines (mCpGs) at a single-nucleotide level and compute the average methylation of CpGs in the population of molecules. Stable epialleles, i.e. CpG strings with the same DNA sequence containing a discrete linear succession of phased methylated/non-methylated CpGs in the same DNA molecule, cannot be identified due to the heterogeneity of the 5′–3′ ends of the molecules. Moreover, these are diluted by random unstable methylated CpGs and escape detection. We present here MethCoresProfiler, an R-based tool that provides a simple method to extract and identify combinations of methylated phased CpGs shared by all components of epiallele families in complex DNA populations. The methylated cores are stable over time, evolve by acquiring or losing new methyl sites and, ultimately, display high information content and low stochasticity. We have validated this method by identifying and tracing rare epialleles and their families in synthetic or in vivo complex cell populations derived from mouse brain areas and cells during postnatal differentiation. MethCoresProfiler is written in R language. The software is freely available at https://github.com/84AP/MethCoresProfiler/.