bluuebunny/crossref_metadata_2025_split huggingface dataset:
Utilisation of Ambient Laser Desorption Ionisation Mass Spectrometry (ALDI-MS) Improves Lipid-Based Microbial Species Level Identification
Authors: Cameron Simon J. S. , Bodai Zsolt , Temelkuran Burak , Perdones-Montero Alvaro , Bolt Frances , Burke Adam , Alexander-Hardiman Kate , Salzet Michel , Fournier Isabelle , Rebec Monica , Takáts Zoltán 
Published: February 2019

AbstractThe accurate and timely identification of the causative organism of infection is important in ensuring the optimum treatment regimen is prescribed for a patient. Rapid evaporative ionisation mass spectrometry (REIMS), using electrical diathermy for the thermal disruption of a sample, has been shown to provide fast and accurate identification of microorganisms directly from culture. However, this method requires contact to be made between the REIMS probe and microbial biomass; resulting in the necessity to clean or replace the probes between analyses. Here, optimisation and utilisation of ambient laser desorption ionisation (ALDI) for improved speciation accuracy and analytical throughput is shown. Optimisation was completed on 15 isolates of Escherichia coli, showing 5 W in pulsatile mode produced the highest signal-to-noise ratio. These parameters were used in the analysis of 150 clinical isolates from ten microbial species, resulting in a speciation accuracy of 99.4% - higher than all previously reported REIMS modalities. Comparison of spectral data showed high levels of similarity between previously published electrical diathermy REIMS data. ALDI does not require contact to be made with the sample during analysis, meaning analytical throughput can be substantially improved, and further, increases the range of sample types which can be analysed in potential direct-from-sample pathogen detection.
Familiarity revealed by involuntary eye movements on the fringe of awareness
Authors: Rosenzweig Gal , Bonneh Yoram S. 
Published: February 2019

AbstractInvoluntary eye movements during fixation of gaze are typically transiently inhibited following stimulus onset. This oculomotor inhibition (OMI), which includes microsaccades and spontaneous eye blinks, is modulated by stimulus saliency and anticipation, but it is currently unknown whether it is sensitive to familiarity. To investigate this, we measured the OMI while observers passively viewed a slideshow of one familiar and 7 unfamiliar facial images presented briefly at 1 Hz in random order. Since the initial experiments indicated that OMI was occasionally insensitive to familiarity when the facial images were highly visible, and to prevent top-down strategies and potential biases, we limited visibility by backward masking making the faces barely visible or at the fringe of awareness. Under these conditions, we found prolonged inhibition of both microsaccades and eye-blinks, as well as earlier onset of microsaccade inhibition with familiarity. These findings demonstrate, for the first time, the sensitivity of OMI to familiarity. Because this is based on involuntary eye movements and can be measured on the fringe of awareness and in passive viewing, our results provide direct evidence that OMI can be used as a novel physiological measure for studying hidden memories with potential implications for health, legal, and security purposes.
Promoter RNA sequencing (PRSeq) for the massive and quantitative promoter analysis in vitro
Authors: Ohuchi Shoji , Mascher Thorsten , Suess Beatrix 
Published: February 2019

AbstractAnalysis of promoter strength and specificity is important for understanding and engineering gene regulation. Here, we report an in vitro promoter analysis method that can achieve both massiveness and quantitativeness. In this approach, a pool of single-stranded DNA with a partially randomized promoter sequence to be analyzed is chemically synthesized. Through enzymatic reactions, the randomized sequence will be copied to the downstream region, resulting in a template DNA pool that carries its own promoter information on its transcribed region. After in vitro transcription of the DNA pool with an RNA polymerase of interest, the sequences of the resulting transcripts will be analyzed. Since the promoter strength linearly correlates to the copy number of transcript, the strength of each promoter sequence can be evaluated. A model experiment of T7 promoter variants demonstrated the quantitativeness of the method, and the method was applied for the analysis of the promoter of cyanophage Syn5 RNA polymerase. This method provides a powerful approach for analyzing the complexity of promoter specificity and discrimination for highly abundant and often redundant alternative sigma factors such as the extracellular function (ECF) sigma factors.
Distinct online and offline effects of alpha and beta transcranial alternating current stimulation (tACS) on continuous bimanual performance and task-set switching
Authors: Heise Kirstin-Friederike , Monteiro Thiago Santos , Leunissen Inge , Mantini Dante , Swinnen Stephan P. 
Published: February 2019

AbstractIn the present study we examined the effect of bihemispheric in-phase synchronization of motor cortical rhythms on complex bimanual coordination. Twenty young healthy volunteers received 10 Hz or 20 Hz tACS in a double-blind crossover design while performing a bimanual task-set switching paradigm. We used a bilateral high-density montage centred over the hand knob representation within the primary motor cortices to apply tACS time-locked to the switching events. Online tACS in either frequency led to faster but more erroneous switching transitions compared to trials without active stimulation. When comparing stimulation frequencies, 10 Hz stimulation resulted in higher error rates and slower switching transitions than 20 Hz stimulation. Furthermore, the stimulation frequencies showed distinct carry-over effects in trials following stimulation trains. Non-stimulated switching transitions were generally faster but continuous performance became more erroneous over time in the 20 Hz condition. We suggest that the behavioural effects of bifocal in-phase tACS are explained by online synchronization of long-range interhemispheric sensorimotor oscillations, which impacts on interhemispheric information flow and the top-down control required for flexible control of complex bimanual actions. Different stimulation frequencies may lead to distinct offline effects, which potentially accumulate over time and therefore need to be taken into account when evaluating subsequent performance.
The effect of sex, season and gametogenic cycle on gonad yield, biochemical composition and quality traits of Paracentrotus lividus along the North Atlantic coast of Portugal
Authors: Rocha Filipa , Baião Luís F. , Moutinho Sara , Reis Bruno , Oliveira Ana , Arenas Francisco , Maia Margarida R. G. , Fonseca António J. M. , Pintado Manuela , Valente Luisa M. P. 
Published: February 2019

AbstractSea urchin population harvest in the North Atlantic coast of Portugal was characterized in terms of gonad yield, nutritional composition and important market-related traits, over one reproductive cycle (March 2016 to March 2017). Most of the quality attributes showed a seasonal variation strongly dependent on sea urchin sex. Maximum gonad yield (18%) was observed in March 2017. A single spawning event occurred between May and July. Gonads are rich sources of protein (12–18% WW) with low fat content (≤6% WW), that increase during the gametogenic stages of recovery and growing (November-December). Polyunsaturated fatty acids were the dominant class in both sexes (4.2–14.7 mg.g−1 WW), being preferentially accumulated in females. Total gonads carotenoid varied seasonally, with the highest level being observed in males during spawning season. Echinenone was the main pigment present in gonads, showing highest concentrations in males during spawning and gonad recovering. During the growing and early maturation period gonads were more reddish, yellowish and brighter, as well as more firm, irrespectively of the sex. Based on all seasonal changes affecting gonad yield and quality, the period between November and February seems the most suitable to harvest high quality gonads in the Atlantic coast of Portugal.
Mycobacterium ulcerans mycolactones-fungi crosstalking
Authors: Hammoudi Nassim , Cassagne Carole , Armstrong Nicholas , Ranque Stéphane , Henrissat Bernard , Drancourt Michel , Bouam Amar 
Published: February 2019

AbstractThe opportunistic pathogen Mycobacterium ulcerans, which is responsible for Buruli ulcer, synthesizes a series of plasmid-encoded macrolide exotoxins termed mycolactones. These toxins destabilize cell membranes and induce apoptosis-associated pleiotropic effects including tissue destruction, analgesic and anti-inflammatory effects. Despite its medical interest, M. ulcerans is primarily an environmental mycobacterium and the primary functions of mycolactones in the natural ecosystems are unknown. High throughput biochemical profiling findings suggested that M. ulcerans may interact with fungi. Here, we report that semi-purified and purified mycolactones significantly enhance spore germination of Scedosporium apiospermum, Fusarium equiseti and Mucor circinelloides; and that M. ulcerans mycolactones significantly attract colonies of M. circinelloides whereas no significant effect was observed on S. apiospermum and F. equiseti. These experimental results suggest that mycolactones exhibit a chemoattractant activity independent of their cytotoxicity. In natural ecosystems, M. ulcerans mycolactones may act as spore germination inducers and chemoattractants for some fungi, suggesting a novel role for this unique class of mycobacterial toxins in natural ecosystems.
Development and validation of an SNP genotyping array and construction of a high-density linkage map in castor
Authors: Senthilvel S. , Ghosh Arpita , Shaik Mobeen , Shaw Ranjan K. , Bagali Prashanth G. 
Published: February 2019

AbstractCastor is a commercially important oilseed crop that provides raw materials for several industries. Currently, the availability of genomic resources for castor is very limited. In this study, genome-wide SNPs were discovered in castor via whole-genome sequencing of 14 diverse lines to an average of 34X coverage. A total of 2,179,759 putative SNPs were detected, and a genotyping array was designed with 6,000 high-quality SNPs representing 2,492 scaffolds of the draft castor genome (87.5% genome coverage). The array was validated by genotyping a panel of 314 inbred castor lines, which resulted in 5,025 scorable SNPs with a high call rate (98%) and reproducibility (100%). Using this array, a consensus linkage map consisting of 1,978 SNP loci was constructed with an average inter-marker distance of 0.55 cM. The genome-wide SNP data, the genotyping array and the dense linkage map are valuable genomic tools for promoting high-throughput genomic research and molecular breeding in castor.
Elevated atmospheric CO2 concentrations alter grapevine (Vitis vinifera) systemic transcriptional response to European grapevine moth (Lobesia botrana) herbivory
Authors: Reineke Annette , Selim Moustafa 
Published: February 2019

AbstractAtmospheric carbon dioxide (CO2) concentrations are among the chief factors shaping the mode and magnitude of interactions between plants and herbivorous insects. Here, we describe the first global analysis of systemic transcriptomic responses of grapevineVitis viniferaplants to feeding of European grapevine mothLobesia botranalarvae at future elevated CO2concentrations. The study was conducted on mature, fruit-bearing grapevine plants under ambient and elevated CO2concentrations in a grapevine free-air carbon dioxide enrichment (FACE) facility. Grapevine transcriptional response to herbivory was clearly dependent on phenological stage, with a higher number of differentially expressed genes identified at fruit development compared to berry ripening. At fruit development, more transcripts were differentially expressed as a response to herbivory under elevated compared to ambient CO2concentrations. Classification of the respective transcripts revealed that in particular genes involved in metabolic pathways, biosynthesis of secondary metabolites and plant-pathogen interactions were significantly enriched. Most of these genes had similar expression patterns under both CO2concentrations, with a higher fold-change under elevated CO2concentrations. Differences in expression levels of a subset of herbivory responsive genes were further validated by RT-qPCR. Our study indicates that future elevated CO2concentrations will affect interactions between grapevine plants and one of its key insect pests, with consequences for future relevance ofL. botranain worldwide viticulture.
High-resolution record reveals climate-driven environmental and sedimentary changes in an active rift
Authors: McNeill Lisa C. , Shillington Donna J. , Carter Gareth D. O. , Everest Jeremy D. , Gawthorpe Robert L. , Miller Clint , Phillips Marcie P. , Collier Richard E. Ll. , Cvetkoska Aleksandra , De Gelder Gino , Diz Paula , Doan Mai-Linh , Ford Mary , Geraga Maria , Gillespie Jack , Hemelsdaël Romain , Herrero-Bervera Emilio , Ismaiel Mohammad , Janikian Liliane , Kouli Katerina , Le Ber Erwan , Li Shunli , Maffione Marco , Mahoney Carol , Machlus Malka L. , Michas Georgios , Nixon Casey W. , Oflaz Sabire Asli , Omale Abah P. , Panagiotopoulos Kostas , Pechlivanidou Sofia , Sauer Simone , Seguin Joana , Sergiou Spyros , Zakharova Natalia V. , Green Sophie 
Published: February 2019

AbstractYoung rifts are shaped by combined tectonic and surface processes and climate, yet few records exist to evaluate the interplay of these processes over an extended period of early rift-basin development. Here, we present the longest and highest resolution record of sediment flux and paleoenvironmental changes when a young rift connects to the global oceans. New results from International Ocean Discovery Program (IODP) Expedition 381 in the Corinth Rift show 10s–100s of kyr cyclic variations in basin paleoenvironment as eustatic sea level fluctuated with respect to sills bounding this semi-isolated basin, and reveal substantial corresponding changes in the volume and character of sediment delivered into the rift. During interglacials, when the basin was marine, sedimentation rates were lower (excepting the Holocene), and bioturbation and organic carbon concentration higher. During glacials, the basin was isolated from the ocean, and sedimentation rates were higher (~2–7 times those in interglacials). We infer that reduced vegetation cover during glacials drove higher sediment flux from the rift flanks. These orbital-timescale changes in rate and type of basin infill will likely influence early rift sedimentary and faulting processes, potentially including syn-rift stratigraphy, sediment burial rates, and organic carbon flux and preservation on deep continental margins worldwide.
Enhancement of biocatalyst activity and protection against stressors using a microbial exoskeleton
Authors: Sakkos Jonathan K. , Wackett Lawrence P. , Aksan Alptekin 
Published: February 2019

AbstractWhole cell biocatalysts can perform numerous industrially-relevant chemical reactions. While they are less expensive than purified enzymes, whole cells suffer from inherent reaction rate limitations due to transport resistance imposed by the cell membrane. Furthermore, it is desirable to immobilize the biocatalysts to enable ease of separation from the reaction mixture. In this study, we used a layer-by-layer (LbL) self-assembly process to create a microbial exoskeleton which, simultaneously immobilized, protected, and enhanced the reactivity of a whole cell biocatalyst. As a proof of concept, we usedEscherichia coliexpressing homoprotocatechuate 2,3-dioxygenase (HPCD) as a model biocatalyst and coated it with up to ten alternating layers of poly(diallyldimethylammonium chloride) (PDADMAC) and silica. The microbial exoskeleton also protected the biocatalyst against a variety of external stressors including: desiccation, freeze/thaw, exposure to high temperatures, osmotic shock, as well as against enzymatic attack by lysozyme, and predation by protozoa. While we observed increased permeability of the outer membrane after exoskeleton deposition, this had a moderate effect on the reaction rate (up to two-fold enhancement). When the exoskeleton construction was followed by detergent treatment to permeabilize the cytoplasmic membrane, up to 15-fold enhancement in the reaction rate was reached. With the exoskeleton, we increased in the reaction rate constants as much as 21-fold by running the biocatalyst at elevated temperatures ranging from 40 °C to 60 °C, a supraphysiologic temperature range not accessible by unprotected bacteria.
Fast and accurate medication identification
Authors: Larios Delgado Natalia , Usuyama Naoto , Hall Amanda K. , Hazen Rebecca J. , Ma Max , Sahu Siva , Lundin Jessica 
Published: February 2019

AbstractMuch of the AI work in healthcare is focused around disease prediction in clinical settings, which is an important application that has yet to deliver in earnest. However, there are other fundamental aspects like helping patients and care teams interact and communicate in efficient and meaningful ways, which could deliver quadruple-aim improvements. After heart disease and cancer, preventable medical errors are the third leading cause of death in the United States. The largest subset of medical errors is medication error. Providing the right treatment plan for patients includes knowledge about their current medications and drug allergies, an often challenging task. The widespread growth of prescribing and consuming medications has increased the need for applications that support medication reconciliation. We show a deep-learning application that can help reduce avoidable errors with their attendant risk, i.e., correctly identifying prescription medication, which is currently a tedious and error-prone task. We demonstrate prescription-pill identification from mobile images in the NIH NLM Pill Image Recognition Challenge dataset. Our application recognizes the correct pill within the top-5 results at 94% accuracy, which compares favorably to the original competition winner at 83.3% for top-5 under comparable, though not identical configurations. The Institute of Medicine claims that better use of information technology can be an important step in reducing medication errors. Therefore, we believe that a more immediate impact of AI in healthcare will occur with a seamless integration of AI into clinical workflows, readily addressing the quadruple aim of healthcare.
Quantifying Leishmania Metacyclic Promastigotes from Individual Sandfly Bites Reveals the Efficiency of Vector Transmission
Authors: Giraud Emilie , Martin Oihane , Yakob Laith , Rogers Matthew 
Published: February 2019

AbstractPredicting how Leishmania will respond to control efforts requires an understanding of their transmission strategy. Using real-time quantitative PCR to quantify infectious metacyclic and non-metacyclic forms in mouse skin from single sandfly bites we show that most transmissions were highly enriched for infectious parasites. However, a quarter of sandflies were capable of transmitting high doses containing more non-infectious promastigotes from the vector’s midgut. Mouse infections replicating “high” to “low” quality, low-dose transmissions confirmed clear differences in the pathology of the infection and their onward transmissibility back to sandflies. Borrowing methods originally developed to account for exposure heterogeneity among hosts, we show how these high-dose, low-quality transmitters act as super-spreading vectors, capable of inflating Leishmania transmission potential by as much as six-fold. These results highlight the hidden potential of transmission of mixed Leishmania promastigote stages on disease prevalence and the role of dose heterogeneity as an underlying strategy for efficient transmission.
Abscisic acid-determined seed vigour differences do not influence redox regulation during ageing
Authors: Schausberger Christina , Roach Thomas , Stöggl Wolfgang , Arc Erwann , Finch-Savage William E. , Kranner Ilse 
Published: February 2019

Abstract
High seed quality is a key trait to achieve successful crop establishment required for optimum yield and sustainable production. Seed storage conditions greatly impact two key seed quality traits; seed viability (ability to germinate and produce normal seedlings) and vigour (germination performance). Accumulated oxidative damage accompanies the loss of seed vigour and viability during ageing, indicating that redox control is key to longevity. Here, we studied the effects of controlled deterioration at 40°C and 75% relative humidity (RH) (‘ageing’) under two different O2 concentrations (21 and 78% O2) in Brassica oleracea. Two B. oleracea genotypes with allelic differences at two QTLs that result in differences in abscisic acid (ABA) signalling and seed vigour were compared. Ageing led to a similar loss in germination speed in both genotypes that was lost faster under elevated O2. In both genotypes, an equal oxidative shift in the glutathione redox state and a minor loss of α-tocopherol progressively occurred before seed viability was lost. In contrast, ABA levels were not affected by ageing. In conclusion, both ABA signalling and seed ageing impact seed vigour but not necessarily through the same biochemical mechanisms.
Effects of Error Experience on Learning to Lower Speech Nasalance Level
Authors: Lo Eric Siu-Chung , Wong Andus Wing-Kuen , Tse Andy Choi-Yeung , Ma Estella Pui-Man , Whitehill Tara L. , Masters Rich 
Published: February 2019

Purpose
This research aims to examine the effects of error experience when learning to speak with lowered nasalance level.

Method
A total of 45 typical speakers were instructed to learn to lower speech nasalance level in either an errorless (restricted possibility for committing errors) or an errorful (unrestricted possibility for committing errors) learning condition. The nasality level of the participants' speech was measured by a nasometer and quantified by nasalance scores (in percent). Errorless learners practiced producing speech with lowered nasalance level with a threshold nasalance score of 50% (the easiest target) at the beginning, which gradually decreased to a threshold of 10% (the most difficult target) at the end. The same set of threshold targets was presented to errorful learners, but in reverse order. Errors were defined by the proportion of speech, with a nasalance score exceeding the threshold. Retention and transfer tests were administered.

Results
Errorless learners displayed fewer errors and lower mean nasalance scores than errorful learners during the acquisition phase. Furthermore, errorless learners achieved lower mean nasalance scores than errorful learners in the retention and transfer tests.

Conclusion
These results suggest that errorless learning is more effective than errorful learning and that error experience has a detrimental effect on the acquisition of a novel speech motor task that requires minimization of the nasality level. Errorless learning may be a useful paradigm for the intervention and management of hypernasality in clinical settings where behavioral treatments are needed.