bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evaluation of MICROANAUT-S Anaerobes MIC broth microdilution panels for antibiotic susceptibility testing of anaerobes
Authors: Cordovana Miriam , Ambretti Simone 
Published: October 2019

Background
Accurate and routine-friendly methods for MIC determination of anaerobes are demanded. Here, we evaluate the performance of a commercially available microdilution panel in comparison to a gradient MIC Strip test.

Methods
N=163 anaerobes clinical isolates (60 species, 23 genera) were tested with the MICRONAUT-S Anaerobes MIC panel (MERLIN Diagnostika, Germany). The same bacterial suspension was used for the panel inoculum, and for testing by MIC Strips (Liofilchem, Italy). The panels were incubated at 37 °C in anaerobic conditions for ≥24 h, and read visually. In case of no bacterial growth for the growth control, incubation was prolonged to 48-72 h. Results were interpreted according to EUCAST guidelines. Comparison was performed in terms of essential agreement, category agreement and error rates.

Results
Category agreement with MIC strips resulted overall 95% (from 95.6% to 100%). Essential agreement resulted 91.1% for piperacillin/tazobactam, and 95% for all the otherantibiotics.Overall, n=15 minor errors, n=2 major errors and n=5 very major errors were observed. For doxycycline, tigecycline and moxifloxacin (for which no breakpoints are available), MICRONAUT results diverged for ≤1 dilution fold from MIC Strips results. For most isolates (117/163) the panels were readable after overnight incubation, in 42 cases after 48 h, in 4 cases after 72 h.

Conclusions
The MICRONAUT-S Anaerobes MIC panels proved to be a reliable microdilution method for antibiotic susceptibility testing of anaerobes, providing results consistent with gradient methodology, with both fast and slow growing species. The ease-of-handling and -result interpretation makes this method suitable for routine implementation.
Improving the surveillance of antimicrobial resistance trends amongst anaerobic oral pathogens
Authors: Thomas Dafydd , Scotford Selina , Thomas James , Crossland James , Kelly Grace , Morris Trefor , Lewis Michael , Wilson Melanie 
Published: October 2019

Background
Orofacial infections when treated by dental practitioners are not routinely sampled for culture and susceptibility testing. Consequently, antimicrobial resistant rates amongst the causative bacteria are unknown, hindering efforts to appropriately manage these infections and undertake surveillance of resistant rates. As part of the Cardiff health board leadership in patient safety quality improvement programme a multidisciplinary group was tasked with the aim of improving sampling practices.

Methods
Dental professionals' limited knowledge regarding the role of diagnostic support and an associated lack of confidence in sampling procedures was addressed by the creation and distribution of training aids. Sampling and transportation kits were developed and transport routes identified enabling dentists within the community setting to send samples to the specialist microbiology services based at Cardiff University Dental Hospital [UDH]. All significant anaerobes were identified and antibiotic susceptibility testing undertaken via agar dilution through referral of isolates to the UK Anaerobic Reference Unit.

Results
A 10% increase was seen in the proportion of pus aspirates being received in comparison to pus swabs. For the first time, pus aspirate samples have been received from community dental clinics. A vast diversity of anaerob species and susceptibility profiles have been identified. Increasing rates of resistance amongst Prevotella species to amoxicillin and clindamycin is of concern.

Conclusion
This project has shown that through educational interventions and support the barriers to the sampling of orofacial infections can be overcome. The ultimate aim is for all dentists in Wales to have access to diagnostic support.
Discovering a novel resistance gene for carbapenem resistance in Parabacteroides timonensis using Whole Genome Sequencing
Authors: Boiten Kathleen , Veloo Alida 
Published: October 2019

Up to 95% of the human microbiome consists of anaerobic bacteria. However, they are not as well studied as the aerobic bacteria. Among all anaerobes, the Bacteroides group is the best known and most studied. There has been an increase in carbapenem resistance in Bacteroidales strains without a known cause.
We isolated a Parabacteroides timonensis strain, related to Bacteroides, resistant for amoxicillin, clindamycin and meropenem.
The strain was sequenced using the Miseq (Illumina, San Diego, CA), followed by a de novo assembly using CLC workbench to create a draft genome. Resistance genes were detected with ResFinder (https://cge.cbs.dtu.dk/services/ResFinder/). Genome annotation was performed by RAST (http://rast.nmpdr.org/). Protein modeling was performed, on genes of interest, using Phyre2 (http://www.sbg.bio.ic.ac.uk/phyre2/html/page.cgi?id=index) and 3DLigandSite (http://www.sbg.bio.ic.ac.uk/3dligandsite/). FatCat (http://fatcat.burnham.org/) was used to do a pairwise structure alignment to compare protein structures.
The draft genome had a size of 6,356,323 bp, present on 95 contigs. Using Resfinder 1 resistance gene was found, tetQ. A possible novel resistance gene for a metallo β-lactamase related to cfiA was found using RAST. The protein model showed similarities with the model for cfiA and includes several Zn2+ ions, used by metallo β-lactamase to hydrolyze carbapenems.
Our results indicate the presence of a not yet described metallo β-lactamase. There are also indications that a conjugative transposon is present, enabling horizontal gene transfer. No erm genes, encoding for clindamycin resistance, were detected in the draft genome.
Faster diffusive dynamics of histone-like nucleoid structuring proteins in live bacteria caused by silver ions
Authors: Sadoon Asmaa A. , Khadka Prabhat , Freeland Jack , Gundampati Ravi Kumar , Manso Ryan , Ruiz Mason , Krishnamurthi Venkata R. , Thallapuranam Suresh Kumar , Chen Jingyi , Wang Yong 
Published: October 2019

AbstractThe antimicrobial activity and mechanism of silver ions (Ag+) have gained broad attention in recent years. However, dynamic studies are rare in this field. Here, we report our measurement of the effects of Ag+ ions on the dynamics of histone-like nucleoid structuring (H-NS) proteins in live bacteria using single-particle tracking photoactivated localization microscopy (sptPALM). It was found that treating the bacteria with Ag+ ions led to faster diffusive dynamics of H-NS proteins. Several techniques were used to understand the mechanism of the observed faster dynamics. Electrophoretic mobility shift assay on purified H-NS proteins indicated that Ag+ ions weaken the binding between H-NS proteins and DNA. Isothermal titration calorimetry confirmed that DNA and Ag+ ions interact directly. Our recently developed sensing method based on bent DNA suggested that Ag+ ions caused dehybridization of double-stranded DNA (i.e., dissociation into single strands). These evidences led us to a plausible mechanism for the observed faster dynamics of H-NS proteins in live bacteria when subjected to Ag+ ions: Ag+-induced DNA dehybridization weakens the binding between H-NS proteins and DNA. This work highlighted the importance of dynamic study of single proteins in the live cells for understanding the functions of antimicrobial agents to the bacteria.
Does extrinsic mortality accelerate the pace of life? A bare-bones approach
Authors: André Jean-Baptiste , Rousset François 
Published: October 2019

1AbstractIt is commonly asserted that when extrinsic mortality is high, individuals should invest early in reproduction. This intuition thrives in the literature on life-history theory and human behavior, yet it has been criticized repeatedly on the basis of mathematical models. The intuition is indeed wrong; but a recent theoretical criticism has confused the reason why it is wrong, thereby obscuring earlier and sounder criticisms. In the present article, based on the simplest possible model, we sought to clarify these issues. We confirm earlier findings that extrinsic mortality can affect the evolution of pace of life, not because it leaves little time to reproduce, but through its effects on density-dependent competition. This result highlights the importance of accounting for density-dependence in theoretical models and data analyses. Further, we find little support for the recent claim that the direction of selection on a reaction norm in a variable environment cannot be easily inferred from models made in homogeneous environments. In conclusion, although life-history theory is still imperfect, it has provided simple results that deserve to be understood.
Season-specific carry-over of early-life associations in a monogamous bird species
Authors: Kurvers Ralf H.J.M. , Prox Lea , Farine Damien R. , Jongeling Coretta , Snijders Lysanne 
Published: October 2019

AbstractSocial relationships can have important fitness consequences. Although there is increasing evidence that social relationships carry over across contexts, few studies have investigated whether relationships formed early in life are carried over to adulthood. For example, juveniles of monogamous species go through a major life-history stage transition—pair formation—during which the pair bond becomes a central unit of the social organization. At present, it remains unclear if pair members retain their early-life relationships after pair formation. We investigated whether same-sex associations formed early in life carry over into adulthood and whether carry-over was dependent on season, in a monogamous species. Moreover, we investigated the role of familiarity, genetic relatedness and aggression on the perseverance of social associations. We studied the social structure before and after pair formation in captive barnacle geese (Branta leucopsis), a highly social, long-lived, monogamous species. We constructed association networks of groups of geese before pair formation, during the subsequent breeding season, and in the following wintering season. Next, we studied how these associations carried over during seasonal changes. We found that early-life associations in females were lost during the breeding season, but resurfaced during the subsequent wintering season. In males, the early-life associations persisted across both seasons. Association persistence was not mediated by genetic relatedness or familiarity. The high level of aggressiveness of males, but not females, in the breeding season suggests that males may have played a key role in shaping both their own social environment and that of their partners. We show that early-life social relationships can be maintained well into later life. Such relationships can be sustained even if they are temporarily disrupted, for example due to reproductive behaviour. Our findings therefore highlight that the early-life social environment can have life-long consequences on individuals’ social environment.
Model Based Inference of Large Scale Brain Networks with Approximate Bayesian Computation
Authors: West Timothy O. , Berthouze Luc , Farmer Simon F. , Cagnan Hayriye , Litvak Vladimir 
Published: October 2019

AbstractBrain networks and the neural dynamics that unfold upon them are of great interest across the many scales of systems neuroscience. The tools of inverse modelling provide a way of both constraining and selecting models of large scale brain networks from empirical data. Such models have the potential to yield broad theoretical insights in the understanding of the physiological processes behind the integration and segregation of activity in the brain. In order to make inverse modelling computationally tractable, simplifying model assumptions have often been adopted that appeal to steady-state approximations to neural dynamics and thus prevent the investigation of stochastic or intermittent dynamics such as gamma or beta burst activity. In this work we describe a framework that uses the Approximate Bayesian Computation (ABC) algorithm for the inversion of neural models that can flexibly represent any statistical feature of empirically recorded data and eschew the need to assume a locally linearized system. Further, we demonstrate how Bayesian model comparison can be applied to fitted models to enable the selection of competing hypotheses regarding the causes of neural data. This work establishes a validation of the procedures by testing for both the face validity (i.e. the ability to identify the original model that has generated the observed data) and predictive validity (i.e. the consistency of the parameter estimation across multiple realizations of the same data). From the validation and example applications presented here we conclude that the proposed framework provides a novel opportunity to researchers aiming to explain how complex brain dynamics emerge from neural circuits.
DeepMicro: deep representation learning for disease prediction based on microbiome data
Authors: Oh Min , Zhang Liqing 
Published: October 2019

AbstractHuman microbiota plays a key role in human health and growing evidence supports the potential use of microbiome as a predictor of various diseases. However, the high-dimensionality of microbiome data, often in the order of hundreds of thousands, yet low sample sizes, poses great challenge for machine learning-based prediction algorithms. This imbalance induces the data to be highly sparse, preventing from learning a better prediction model. Also, there has been little work on deep learning applications to microbiome data with a rigorous evaluation scheme. To address these challenges, we propose DeepMicro, a deep representation learning framework allowing for an effective representation of microbiome profiles. DeepMicro successfully transforms high-dimensional microbiome data into a robust low-dimensional representation using various autoencoders and applies machine learning classification algorithms on the learned representation. In disease prediction, DeepMicro outperforms the current best approaches based on the strain-level marker profile in five different datasets. In addition, by significantly reducing the dimensionality of the marker profile, DeepMicro accelerates the model training and hyperparameter optimization procedure with 8X-30X speedup over the basic approach. DeepMicro is freely available at https://github.com/minoh0201/DeepMicro.
Migration of intestinal dendritic cell subsets upon intrinsic and extrinsic TLR3 stimulation
Authors: López Agnès Garcias , Bekiaris Vasileios , Luda Katarzyna Müller , Hütter Julia , Muleta Konjit Getachew , Nakawesi Joy , Ulmert Isabel , Kotarsky Knut , Malissen Bernard , O’Keeffe Meredith , Holzmann Bernhard , Agace William , Lahl Katharina 
Published: October 2019

AbstractInitiation of adaptive immunity to particulate antigens in lymph nodes largely depends on their presentation by migratory dendritic cells (DCs). DC subsets differ in their capacity to induce specific types of immunity, allowing subset-specific DC-targeting to influence vaccination and therapy outcomes. Faithful drug design however requires exact understanding of subset-specific versus global activation mechanisms. cDC1, the subset of DCs that excel in supporting immunity towards viruses, intracellular bacteria and tumors, express uniquely high levels of the pattern recognition receptor TLR3. Using various genetic models, we show here that both the cDC1 and cDC2 subsets of cDCs are activated and migrate equally well in response to TLR3 stimulation in a cell extrinsic and TNFα dependent manner, but that cDC1 show a unique requirement for type I interferon signaling. Our findings reveal common and differing pathways regulating DC subset migration, offering important insights for the design of DC-based vaccination and therapy approaches.
First description of the sexual stage ofVenturia effusa, causal agent of pecan scab
Authors: Charlton Nikki D. , Yi Mihwa , Bock Clive H. , Zhang Minling , Young Carolyn A. 
Published: October 2019

ABSTRACTVenturia effusa, cause of pecan scab, is the most prevalent disease of pecan in the southeastern USA; epidemics of the disease regularly result in economic losses to the pecan industry. Recent characterization of the mating type distribution revealed the frequency of theMATidiomorphs are in equilibrium at various spatial scales, indicative of regular sexual recombination. However, the occurrence of the sexual stage ofV. effusahas never been observed, and the pathogen was previously believed to rely entirely on asexual reproduction. To explore the existence of a sexual cycle, we paired opposite mating types on oatmeal culture media. In initial experiments, cultures were incubated at 24 C for 2 mo for hyphal interactions to occur between mating types and then maintained at 4 C for 4 mo. Immature pseudothecia were initially observed but following exposure to a 12 h photoperiod for 2 weeks at 24 C, asci and ascospores developed. Further experiments explored the effect of time on pseudothecial development with 4 mo at 4 C as the optimal requirement. The results of this study demonstrate the heterothallic nature ofV. effusa.Following experiments investigated progeny from a sexual cross of an albino and a wild-type isolate. Evaluation of isolate pigmentation, mating type, and multilocus genotyping of single ascospore progeny provided evidence that recombination occurred within the sexual crosses. The impact of determining the source of the overwintering ascostroma will aid in management decisions to reduce the primary inoculum in the disease cycle.
Reward timing and its expression by inhibitory interneurons in the mouse primary visual cortex
Authors: Monk Kevin J , Allard Simon , Shuler Marshall G Hussain 
Published: October 2019

AbstractPrimary sensory cortex has historically been studied as a low-level feature detector, but has more recently been implicated in many higher-level cognitive functions. For instance, after an animal learns that a light predicts water at a fixed delay, neurons in primary visual cortex (V1) can produce “reward timing activity” (i.e., spike modulation of various forms that relate the interval between the visual stimulus and expected reward). The manner by which V1 produces these representations is unknown. Here, we combine behavior, in vivo electrophysiology, and optogenetics to investigate the characteristics of and circuit mechanisms underlying V1 reward timing in the head-fixed mouse. We find that reward timing activity is present in mouse V1, that inhibitory interneurons participate in reward timing, and that these representations are consistent with a theorized network architecture. Together, these results deepen our understanding of V1 reward timing and the manner by which it is produced.
Dietary xanthan gum alters antibiotic efficacy against the murine gut microbiota and attenuatesClostridioides difficilecolonization
Authors: Schnizlein Matthew K. , Vendrov Kimberly C. , Edwards Summer J. , Martens Eric C. , Young Vincent B. 
Published: October 2019

AbstractDietary fiber provides a variety of microbiota-mediated benefits ranging from anti-inflammatory metabolites to pathogen colonization resistance. A healthy gut microbiota protects againstClostridioides difficilecolonization. Manipulation of these microbes through diet may increase colonization resistance to improve clinical outcomes. The primary objective of this study was to identify how the dietary fiber xanthan gum affects the microbiota andC. difficilecolonization.We added 5% xanthan gum to the diet of C57Bl/6 mice and examined its effect on the microbiota through 16S rRNA-gene amplicon sequencing and short-chain fatty acid analysis. Following either cefoperazone or an antibiotic cocktail administration, we challenged mice withC. difficileand measured colonization by monitoring colony-forming units.Xanthan gum administration associates with increases in fiber degrading taxa and short-chain fatty acid concentrations. However, by maintaining both the diversity and absolute abundance of the microbiota during antibiotic treatment, the protective effects of xanthan gum administration on the microbiota were more prominent than the enrichment of these fiber degrading taxa. As a result, mice that were on the xanthan gum diet experienced limited to noC. difficilecolonization.Xanthan gum administration alters mouse susceptibility toC. difficilecolonization by maintaining the microbiota during antibiotic treatment. While antibiotic-xanthan gum interactions are not well understood, xanthan gum has previously been used to bind drugs and alter their pharmacokinetics. Thus, xanthan gum may alter the activity of the oral antibiotics used to make the microbiota susceptible. Future research should further characterize how this and other common dietary fibers interact with drugs.IMPORTANCEA healthy gut bacterial community benefits the host by breaking down dietary nutrients and protecting against pathogens.Clostridioides difficilecapitalizes on the absence of this community to cause diarrhea and inflammation. Thus, a major clinical goal is to find ways to increase resistance toC. difficilecolonization by either supplementing with bacteria that promote resistance or a diet to enrich for those already present in the gut. In this study, we describe an interaction between xanthan gum, a human dietary additive, and the microbiota resulting in an altered gut environment that is protective againstC. difficilecolonization.
Predictive Representations in Hippocampal and Prefrontal Hierarchies
Authors: Brunec Iva K. , Momennejad Ida 
Published: October 2019

AbstractAs we navigate the world, we use learned representations of relational structures to explore and to reach goals. Studies of how relational knowledge enables inference and planning are typically conducted in controlled small-scale settings. It remains unclear, however, how people use stored knowledge in continuously unfolding navigation, e.g., walking long distances in a city. We hypothesized that multiscale predictive representations guide naturalistic navigation, and these scales are organized along posterior-anterior prefrontal and hippocampal hierarchies. We conducted model-based representational similarity analyses of neuroimaging data measured during navigation of realistically long paths in virtual reality. We tested the pattern similarity of each point–along each path–to a weighted sum of its successor points within predictive horizons of different scales. We found that anterior PFC showed the largest predictive horizons, posterior hippocampus the smallest, with the anterior hippocampus and orbitofrontal regions in between. Our findings offer novel insights into how cognitive maps support hierarchical planning at multiple scales.