bluuebunny/crossref_metadata_2025_split huggingface dataset:
Central-Positive Complexes
Authors: Hogan R. Edward , Trammel Emma R. , Farber Nuri B. , Avidan Michael S. , Palanca Ben Julian A. 
Published: April 2019

Objectives
Electroencephalography (EEG) allows monitoring of generalized seizures induced during electroconvulsive therapy (ECT). Scalp EEG recordings show different phases of electroencephalographic ictal activity during ECT seizures, documenting a pattern of seizures that may vary within and across individuals. In this case series, we used 64-electrode high-density EEG recording to detect topographic electroencephalographic changes not typically evident with conventional limited montages commonly used during ECT.

Methods
The EEG recordings were acquired from 5 participants (24 ECT sessions) during index courses for treatment-resistant depression. Using previously proposed staging criteria, the ictal EEG and simultaneously acquired video were interpreted by an expert reviewer blinded to study treatment parameters.

Results
The EEG recordings of all seizures showed generalized, high-amplitude, central-positive complexes (CPCs), which emerged at the beginning of phase III (polyspike and slow wave activity), with median duration of 47 seconds (interquartile range, 77 seconds), ranging from 14 to 203 seconds. Although individuals showed variability in frequency and amplitude of CPCs, CPCs typically evolved from 4.0 to 1.5 Hz in frequency and decreased in amplitude as the seizure progressed. Elaborating on previously described phases of ECT-induced electrographic seizures, we describe variability in morphology at seizure termination. Initiation of CPCs typically corresponded with clonic movements, but often terminated after motor signs ceased.

Conclusions
Generalized, high-amplitude, CPCs during ECT are a previously uncharacterized ictal waveform during ECT, which may have important scientific and clinical value. These complexes offer a specific marker for correlating clinical outcomes in ECT and greater understanding of generalized tonic-clonic seizures.
Electroconvulsive Therapy for Neuroleptic Malignant Syndrome
Authors: Morcos Nicholas , Rosinski Amy , Maixner Daniel F. 
Published: April 2019

Objectives
Neuroleptic malignant syndrome (NMS) is an uncommon condition associated with significant morbidity and mortality. Data on treatment interventions are limited. In this case series, we sought to describe all NMS cases requiring ECT from a large academic institution over a nearly 2-decade period.

Methods
We retrospectively identified all patients with NMS who were treated with ECT over a 17-year period. Patients were included in the study based on chart review using the International Consensus Diagnostic Criteria for NMS. Data were collected related to clinical findings, treatment course, and response to ECT.

Results
We identified 15 patients meeting the inclusion criteria. Most patients had neurocognitive or schizophrenia spectrum disorders and developed NMS after exposure to multiple antipsychotic drugs. All patients received bitemporal ECT after failed pharmacotherapy for NMS. Electroconvulsive therapy was well tolerated and resulted in a remission rate of 73.3% (n = 11). Patients showed early initial response to ECT (mean of 4.2 treatments), but an average of 17.7 treatments was necessary to minimize recurrence of catatonic signs. One patient died after interruption of the index course of ECT because of severe infection, and another was discharged to hospice care after limited response. These cases highlight the lethality of NMS and its complications despite aggressive treatment measures.

Conclusions
Bitemporal ECT was well tolerated and effective in treating NMS refractory to pharmacotherapy. We suggest that ECT be considered early in cases of NMS that are refractory to pharmacological interventions, especially if the underlying condition is also responsive to ECT.
The Type III CRISPR-Cas system of Mycobacterium tuberculosis
Authors: Grüschow Sabine , Athukoralage Januka , Hoogeboom Tess , White Malcolm F. 
Published: April 2019

Background
Bacteria and archaea have developed a number of strategies to keep the influx of mobile genetic elements (MGEs) such as viruses and plasmids in check. CRISPR-Cas systems provide adaptive immunity; all types of CRISPR-Cas systems have in common the genes for uptake of genetic information from the invading MGE but differ in the composition of the effector complex that directs and enforces the immune response. The genome of Mycobacterium tuberculosis encodes a Class 1, type III-A CRISPR-Cas system that has not been studied in detail.

Methodology
We used heterologous production of the mycobacterial CRISPR-Cas genes. Purification of the enzymes enabled in vitro biochemical characterisation of the adaptation, maturation and interference proteins. Reconstitution of the system in E. coli was used to demonstrate functionality in vivo.

Results
Maturation of crRNA through the action of Cas6 proceeded as expected, generating canonical CRISPR RNAs (crRNAs). The type III effector complex, consisting of Csm1-5, was shown to bind crRNA and cleave target RNA with the typical 6 nt spacing, display ssDNase activity and produce the cyclic oligoadenylate signalling molecule. The latter clearly activated the ribonuclease Csm6, an essential element in type III immunity. The M. tuberculosis type III CRISPR-Cas system was also reconstituted in E. coli where it provided plasmid immunity, demonstrating the functionality in vivo.

Conclusions
All elements of the M. tuberculosis type III CRISPR-Cas system are functional in vitro and in vivo. These studies lay the foundation for further investigations into the mechanism of adaptive immunity and possible applications in biotechnology.
Genome annotation of Poly(lactic acid) degradingPseudomonas aeruginosaandSphingobacterium sp.
Authors: Satti Sadia Mehmood , Shah Aamer Ali , Auras Rafael , Marsh Terence L. 
Published: April 2019

AbstractPseudomonas aeruginosaandSphinogobacterium sp. are well known for their ability to decontaminate many environmental pollutants like PAHs, dyes, pesticides and plastics. The present study reports the annotation of genomes fromP. aeruginosaandSphinogobacterium sp. that were isolated from compost, based on their ability to degrade poly(lactic acid), PLA, at mesophillic temperatures (~30°C). Draft genomes of both the strains were assembled from Illumina reads, annotated and viewed with an aim of gaining insight into the genetic elements involved in degradation of PLA. The draft-assembled genome of strainSphinogobacteriumstrain S2 was 5,604,691 bp in length with 435 contigs (maximum length of 434,971 bp) and an average G+C content of 43.5%. The assembled genome ofP. aeruginosastrain S3 was 6,631,638 bp long with 303 contigs (maximum contig length of 659,181 bp) and an average G+C content 66.17 %. A total of 5,385 (60% with annotation) and 6,437 (80% with annotation) protein-coding genes were predicted for strains S2 and S3 respectively. Catabolic genes for biodegradation of xenobiotic and aromatic compounds were identified on both draft genomes. Both strains were found to have the genes attributable to the establishment and regulation of biofilm, with more extensive annotation for this in S3. The genome ofP. aeruginosaS3 had the complete cascade of genes involved in the transport and utilization of lactate whileSphinogobacterium strainS2 lacked lactate permease, consistent with its inability to grow on lactate. As a whole, our results reveal and predict the genetic elements providing both strains with the ability to degrade PLA at mesophilic temperature.
Cognitive modeling informs interpretation of go/no-go task-related neural activations and their links to externalizing psychopathology
Authors: Weigard Alexander , Soules Mary , Ferris Bailey , Zucker Robert A. , Sripada Chandra , Heitzeg Mary 
Published: April 2019

AbstractBackgroundIndividuals with ADHD and other forms of externalizing psychopathology tend to display poor behavioral performance on the go/no-go task, which is thought to reflect deficits in inhibitory control. However, clinical neuroimaging studies using this paradigm have yielded conflicting results, raising basic questions about what the task measures and which aspects of the task relate to clinical outcomes of interest. We aimed to provide a clearer understanding of how neural activations from this paradigm relate to the cognitive mechanisms that underlie performance and the implications of these relationships for clinical research.Methods143 emerging adults (ages 18-21) performed the go/no-go task during fMRI scanning. We used the diffusion decision model (DDM), a mathematical modeling approach, to quantify distinct neurocognitive processes that underlie go/no-go performance. We then correlated DDM parameters with brain activation across several standard go/no-go contrasts and assessed relationships of DDM parameters and associated neural measures with clinical ratings.ResultsFronto-parietal activations on correct inhibition trials, which have typically been assumed to isolate neural processes involved in inhibition, were unrelated to either individuals’ response biases or their efficiency of task performance. In contrast, responses to false alarms in brain regions putatively responsible for error monitoring were strongly related to more efficient performance on the task and correlated with externalizing behavior and ADHD symptoms.ConclusionsOur findings cast doubt on conventional interpretations of go/no-go task-related activations as reflecting inhibition functioning. We instead find that error-related contrasts provide clinically-relevant information about neural systems involved in monitoring and optimizing cognitive performance.
Inter- and intra-specific variation of spider mite susceptibility to fungal infections: implications for the long-term success of biological control
Authors: Zélé Flore , Altıntaş Mustafa , Santos Inês , Cakmak Ibrahim , Magalhães Sara 
Published: April 2019

ABSTRACTSpider mites are severe pests of several annual and perennial crops worldwide, often causing important economic damages. Moreover, rapid evolution of pesticide resistance in this group hampers the efficiency of chemical control. Alternative control strategies, such as the use of entomopathogenic fungi, are thus being developed. However, while several studies have focussed on the evaluation of the control potential of different fungal species and/or isolates as well as their compatibility with other control methods (e.g. predators or chemical pesticides), knowledge on the extent of inter- and intraspecific variation in spider mite susceptibility to fungal infection is as yet incipient. Here, we measured the mortality induced by two generalist fungi,Beauveria bassianaandMetarhizium brunneum, in 12 spider mite populations belonging to differentTetranychusspecies:T. evansi,T. ludeni, the green form ofT. urticaeand the red form ofT. urticae, within a full factorial experiment. We found that spider mite species differed in their susceptibility to infection to both fungal species. Moreover, we also found important intraspecific variation for this trait. These results draw caution on the development of single strains as biocontrol agents. Indeed, the high level of intraspecific variation suggests that (a) the one-size-fits-all strategy will probably fail to control spider-mite populations and (b) hosts resistance to infection may evolve at a rapid pace. Finally, we propose future directions to better understand this system and improve the long-term success of spider mite control strategies based on entomopathogenic fungi.
Combining multiple data sources in species distribution models while accounting for spatial dependence and overfitting with combined penalised likelihood maximisation
Authors: Renner Ian W. , Louvrier Julie , Gimenez Olivier 
Published: April 2019

SummaryThe increase in availability of species data sets means that approaches to species distribution modelling that incorporate multiple data sets are in greater demand. Recent methodological developments in this area have led to combined likelihood approaches, in which a log-likelihood comprised of the sum of the log-likelihood components of each data source is maximised. Often, these approaches make use of at least one presence-only data set and use the log-likelihood of an inhomogeneous Poisson point process model in the combined likelihood construction. While these advancements have been shown to improve predictive performance, they do not currently address challenges in presence-only modelling such as checking and correcting for violations of the independence assumption of a Poisson point process model or more general challenges in species distribution modelling such as overfitting.In this paper, we present an extension of the combined likelihood frame-work which accommodates alternative presence-only likelihoods in the presence of spatial dependence as well as lasso-type penalties to account for potential overfitting. We compare the proposed combined penalised likelihood approach to the standard combined likelihood approach via simulation and apply the method to modelling the distribution of the Eurasian lynx in the Jura Mountains in eastern France.The simulations show that the proposed combined penalised likelihood approach has better predictive performance than the standard approach when spatial dependence is present in the data. The lynx analysis shows that the predicted maps vary significantly between the model fitted with the proposed combined penalised approach accounting for spatial dependence and the model fitted with the standard combined likelihood.This work highlights the benefits of careful consideration of the presence-only components of the combined likelihood formulation, and allows greater flexibility and ability to accommodate real datasets.
Mapping cell migrations and fates from a gastruloid model to the human primitive streak
Authors: Martyn I. , Siggia E.D. , Brivanlou A.H. 
Published: April 2019

AbstractAlthough fate maps of early gastrula embryos exist for nearly all model organisms, a fate map of the gastrulating human embryo remains elusive. Here we use human gastruloids to piece together part of a rudimentary fate map of the human primitive streak (PS). This is possible because stimulation with differing levels of BMP, WNT, and NODAL leads to self-organization of gastruloids into large and homogenous different subpopulations of endoderm and mesoderm, and comparative parallel analysis of these gastruloids, together with the fate map of the mouse embryo, allows the organization of these subpopulations along an anterior-posterior axis. We also developed a novel cell tracking technique that allowed the detection of robust fate-dependent cell migrations in our gastruloids comparable to those found in the mouse embryo. Taken together, our gastruloid derived fate map and recording of cell migrations provides a first coarse view of the embryonic human PS.
Evolution and genetic architecture of disassortative mating at a locus under heterozygote advantage
Authors: Maisonneuve Ludovic , Chouteau Mathieu , Joron Mathieu , Llaurens Violaine 
Published: April 2019

AbstractThe evolution of mate preferences may depend on natural selection acting on the mating cues and on the underlying genetic architecture. While the evolution of assortative mating with respect to locally adapted traits has been well-characterized, the evolution of disassortative mating is poorly characterized. Here we aim at understanding the evolution of disassortative mating for traits under strong balancing selection, by focusing on polymorphic mimicry as an illustrative example. Positive frequency-dependent selection exerted by predators generates local selection on wing patterns acting against rare variants and promoting local monomorphism. This acts across species boundaries, favouring Mullerian mimicry among defended species. In this well-characterized adaptive landscape, polymorphic mimicry is rare but is observed in a butterfly species, associated with polymorphic chromosomal inversions. Because inversions are often associated with recessive deleterious mutations, we hypothesize they may induce heterozygote advantage at the color pattern locus, putatively favoring the evolution of disassortative mating. To explore the conditions underlying the emergence of disassortative mating, we modeled both a trait locus (colour pattern for instance), subject to mutational load, and a preference locus. We confirm that heterozygote advantage favors the evolution of disassortative mating and show that disassortative mating is more likely to emerge if at least one allele at the trait locus is free from any recessive deleterious mutations. We modelled different possible genetic architectures underlying mate choice behaviour, such as self referencing alleles, or specific preference or rejection alleles. Our results showed that self referencing or rejection alleles linked to the color pattern locus can be under positive selection and enable the emergence of disassortative mating. However rejection alleles allow the emergence of disassortative mating only when the color pattern and preference loci are tightly linked. Our results therefore provide relevant predictions on both the selection regimes and the genetic architecture favoring the emergence of disassortative mating and a theoretical framework in which to interprete empirical data on mate preferences in wild populations.
TCR repertoire analysis reveals effector memory T cells differentiation into Th17 cells in rheumatoid arthritis
Authors: Jiang Xu , Wang Shi-yu , Zhou Chen , Wu Jing-hua , Jiao Yu-hao , Lin Li-ya , Lu Xin , Yang Bo , Zhang Wei , Xiao Xin-yue , Li Yue-ting , Wu Xun-yao , Wang Xie , Chen Hua , Zhao Li-dan , Fei Yun-yun , Yang Hua-xia , Zhang Wen , Zhang Feng-chun , Chen Hui , Zhang Jian-min , Li Bin , Yang Huan-ming , Wang Jian , He Wei , Cao Xue-tao , Liu De-pei , Liu Xiao , Zhang Xuan 
Published: April 2019

AbstractThe pathogenesis of rheumatoid arthritis (RA), a systemic autoimmune disease characterized by autoreactive T-cell accumulation and pro-inflammatory cytokine overproduction, is unclear. Systematically addressing T-cell receptor (TCR) repertoires of different CD4+ T-cell subsets could help understand RA pathogenesis. Here, peripheral CD4+ T cells from treatment-naïve RA patients and healthy controls were sorted into seven subsets including naïve, effector, central memory, effector memory (EMT), Th1, Th17, and regulatory T cells. T-cell receptor β chain repertoires were then analyzed by next-generation sequencing. We identified T-cell clonal expansion in EMT and Th17 cells, with highly similar TCR repertoires between them. Ex vivo experiments demonstrated the preferred differentiation from EMT to Th17 cells in RA. Moreover, TCR diversity in subsets including Th17 was negatively correlated with RA disease activity indices such as C-reactive protein and erythrocyte sedimentation rate. Thus, shared and abnormally expanded EMT and Th17 TCR repertoires might be pivotal for RA pathogenesis.
Adaptive Bet-Hedging Revisited: Considerations of Risk and Time Horizon
Authors: Tal Omri , Tran Tat Dat 
Published: April 2019

AbstractModels of adaptive bet-hedging commonly adopt insights from Kelly’s famous work on optimal gambling strategies and the financial value of information. In particular, such models seek evolutionary solutions that maximize long term average growth rate of lineages, even in the face of highly stochastic growth trajectories. Here, we argue for extensive departures from the standard approach to better account for evolutionary contingencies. Crucially, we incorporate considerations of volatility minimization, motivated by interim extinction risk in finite populations, within a finite time horizon approach to growth maximization. We find that a game-theoretic competitive-optimality approach best captures these additional constraints and derive the equilibria solutions under various fitness payoff functions.
Removing zero-lag functional connections can alter EEG-source space networks at rest
Authors: Rizkallah Jennifer , Amoud Hassan , Fraschini Matteo , Wendling Fabrice , Hassan Mahmoud 
Published: April 2019

AbstractElectro-encephalography (EEG) source connectivity is an emerging approach to estimate brain networks with high time/space resolution. Here, we aim to evaluate the effect of different functional connectivity (FC) methods on the EEG-source space networks at rest. The two main families of FC methods tested are: i) the FC methods that do not remove the zero-lag connectivity including the Phase Locking Value (PLV) and the Amplitude Envelope Correlation (AEC) and ii) the FC methods that remove the zero-lag connections such as the Phase Lag Index (PLI) and orthogonalisation approach combined with PLV (PLVorth) and AEC (AECorth). Methods are evaluated on resting state dense-EEG signals recorded from 20 healthy participants. Networks obtained by each FC method are compared with fMRI networks at rest (from the Human Connectome Project -HCP-, N=487). Results show low correlations for all the FC methods, however PLV and AEC networks are significantly correlated with fMRI networks (ρ = 0.12, p = 1.93×10−8 and ρ = 0.06, p = 0.007, respectively), while other methods are not. These observations are consistent for each EEG frequency bands and for different FC matrices threshold. Furthermore, the effect of electrode density was also tested using four EEG montages (dense-EEG 256 electrodes, 128, 64 and 32 electrodes). Results show no significant differences between the four EEG montages in terms of correlations with the fMRI networks. Our main message here is to be careful when selecting the FC methods and mainly those that remove the zero-lag connections as they can affect the network characteristics. More comparative studies (based on simulation and real data) are still needed in order to make EEG source connectivity a mature technique to address questions in cognitive and clinical neuroscience.
Rational programming of history-dependent logic in cellular populations
Authors: Zúñiga Ana , Guiziou Sarah , Mayonove Pauline , Meriem Zachary Ben , Camacho Miguel , Moreau Violaine , Ciandrini Luca , Hersen Pascal , Bonnet Jerome 
Published: April 2019

AbstractGenetic programs operating in an history-dependent fashion are ubiquitous in nature and govern sophisticated processes such as development and differentiation. The ability to systematically and predictably encode such programs would advance the engineering of synthetic organisms and ecosystems with rich signal processing abilities. Here we implement robust, scalable history-dependent programs by distributing the computational labor across a cellular population. Our design is based on recombinase-driven DNA scaffolds expressing different genes according to the order of occurrence of inputs. These multicellular computing systems are highly modular and any program can be built by differential composition of strains containing well-characterized logic scaffolds. We developed an automated workflow that researchers can use to streamline program design and optimization. We anticipate that the history-dependent programs presented here will support many applications using cellular populations for material engineering, biomanufacturing and healthcare.One Sentence SummarySystematic and automated frameworks for implementing robust history-dependent genetic programs in cellular populations.