bluuebunny/crossref_metadata_2025_split huggingface dataset:
Small intestinal microbial dysbiosis underlies symptoms associated with functional gastrointestinal disorders
Authors: Saffouri George B. , Shields-Cutler Robin R. , Chen Jun , Yang Yi , Lekatz Heather R. , Hale Vanessa L. , Cho Janice M. , Battaglioli Eric J. , Bhattarai Yogesh , Thompson Kevin J. , Kalari Krishna K. , Behera Gaurav , Berry Jonathan C. , Peters Stephanie A. , Patel Robin , Schuetz Audrey N. , Faith Jeremiah J. , Camilleri Michael , Sonnenburg Justin L. , Farrugia Gianrico , Swann Jonathan R. , Grover Madhusudan , Knights Dan , Kashyap Purna C. 
Published: May 2019

AbstractSmall intestinal bacterial overgrowth (SIBO) has been implicated in symptoms associated with functional gastrointestinal disorders (FGIDs), though mechanisms remain poorly defined and treatment involves non-specific antibiotics. Here we show that SIBO based on duodenal aspirate culture reflects an overgrowth of anaerobes, does not correspond with patient symptoms, and may be a result of dietary preferences. Small intestinal microbial composition, on the other hand, is significantly altered in symptomatic patients and does not correspond with aspirate culture results. In a pilot interventional study we found that switching from a high fiber diet to a low fiber, high simple sugar diet triggered FGID-related symptoms and decreased small intestinal microbial diversity while increasing small intestinal permeability. Our findings demonstrate that characterizing small intestinal microbiomes in patients with gastrointestinal symptoms may allow a more targeted antibacterial or a diet-based approach to treatment.
Nanoscale self-healing mechanisms in shape memory ceramics
Authors: Zhang Ning , Asle Zaeem Mohsen 
Published: May 2019

AbstractShape memory ceramics, such as yttria-stabilized tetragonal zirconia (YSTZ), offer unique properties including ultra-high operating temperatures and high resistance to oxidation. However, they are susceptible to formation of defects during manufacturing and/or by mechanical deformation. To completely take advantage of their shape memory properties, it is necessary to fully understand the nano-structural evolution of defects under external stimuli. In this study, defect evolution behaviors in YSTZ nanopillars are investigated by atomistic simulations. Two characteristic orientations of$$\left[ {01\bar 1} \right]$$011¯and [001] are selected to represent the dominant deformation mechanisms of phase transformation and dislocation migration, respectively. Volume expansion associated with the tetragonal to monoclinic phase transformation is observed to promote healing of crack and void. Atom stress analyses reveal stress concentrations along the newly formed monoclinic phase bands. A critical crack width is identified, less than which the crack can be fully closed in compression. For [001]-oriented YSTZ nanopillars, dislocation migration leads to formations of an amorphous phase, which also assist the crack and void closure process. The revealed crack/void healing mechanisms may provide a path for mitigating internal defects that influences the mechanical properties and deformation mechanisms of shape memory ceramics.
Impact of lattice relaxations on phase transitions in a high-entropy alloy studied by machine-learning potentials
Authors: Kostiuchenko Tatiana , Körmann Fritz , Neugebauer Jörg , Shapeev Alexander 
Published: May 2019

AbstractRecently, high-entropy alloys (HEAs) have attracted wide attention due to their extraordinary materials properties. A main challenge in identifying new HEAs is the lack of efficient approaches for exploring their huge compositional space. Ab initio calculations have emerged as a powerful approach that complements experiment. However, for multicomponent alloys existing approaches suffer from the chemical complexity involved. In this work we propose a method for studying HEAs computationally. Our approach is based on the application of machine-learning potentials based on ab initio data in combination with Monte Carlo simulations. The high efficiency and performance of the approach are demonstrated on the prototype bcc NbMoTaW HEA. The approach is employed to study phase stability, phase transitions, and chemical short-range order. The importance of including local relaxation effects is revealed: they significantly stabilize single-phase formation of bcc NbMoTaW down to room temperature. Finally, a so-far unknown mechanism that drives chemical order due to atomic relaxation at ambient temperatures is discovered.
Recent practical researches in the development of gluten-free breads
Authors: Yano Hiroyuki 
Published: May 2019

AbstractWheat bread is consumed globally and has played a critical role in the story of civilization since the development of agriculture. While the aroma and flavor of this staple food continue to delight and satisfy most people, some individuals have a specific allergy to wheat or a genetic disposition to celiac disease. To improve the quality of life of these patients from a dietary standpoint, food-processing researchers have been seeking to develop high-quality gluten-free bread. As the quality of wheat breads depends largely on the viscoelastic properties of gluten, various ingredients have been employed to simulate its effects, such as hydrocolloids, transglutaminase, and proteases. Recent attempts have included the use of redox regulation as well as particle-stabilized foam. In this short review, we introduce the ongoing advancements in the development of gluten-free bread, by our laboratory as well as others, focusing mainly on rice-based breads. The social and scientific contexts of these efforts are also mentioned.
A yield-cost tradeoff governs Escherichia coli’s decision between fermentation and respiration in carbon-limited growth
Authors: Mori Matteo , Marinari Enzo , De Martino Andrea 
Published: May 2019

AbstractLiving cells react to changes in growth conditions by re-shaping their proteome. This accounts for different stress-response strategies, both specific (i.e., aimed at increasing the availability of stress-mitigating proteins) and systemic (such as large-scale changes in the use of metabolic pathways aimed at a more efficient exploitation of resources). Proteome re-allocation can, however, imply significant biosynthetic costs. Whether and how such costs impact the growth performance are largely open problems. Focusing on carbon-limited E. coli growth, we integrate genome-scale modeling and proteomic data to address these questions at quantitative level. After deriving a simple formula linking growth rate, carbon intake, and biosynthetic costs, we show that optimal growth results from the tradeoff between yield maximization and protein burden minimization. Empirical data confirm that E. coli growth is indeed close to Pareto-optimal over a broad range of growth rates. Moreover, we establish that, while most of the intaken carbon is diverted into biomass precursors, the efficiency of ATP synthesis is the key driver of the yield-cost tradeoff. These findings provide a quantitative perspective on carbon overflow, the origin of growth laws and the multidimensional optimality of E. coli metabolism.
The influence of spatial and temporal resolutions on the analysis of cell-cell interaction: a systematic study for time-lapse microscopy applications
Authors: Comes M. C. , Casti P. , Mencattini A. , Di Giuseppe D. , Mermet-Meillon F. , De Ninno A. , Parrini M. C. , Businaro L. , Di Natale C. , Martinelli E. 
Published: May 2019

AbstractCell-cell interactions are an observable manifestation of underlying complex biological processes occurring in response to diversified biochemical stimuli. Recent experiments with microfluidic devices and live cell imaging show that it is possible to characterize cell kinematics via computerized algorithms and unravel the effects of targeted therapies. We study the influence of spatial and temporal resolutions of time-lapse videos on motility and interaction descriptors with computational models that mimic the interaction dynamics among cells. We show that the experimental set-up of time-lapse microscopy has a direct impact on the cell tracking algorithm and on the derived numerical descriptors. We also show that, when comparing kinematic descriptors in two diverse experimental conditions, too low resolutions may alter the descriptors’ discriminative power, and so the statistical significance of the difference between the two compared distributions. The conclusions derived from the computational models were experimentally confirmed by a series of video-microscopy acquisitions of co-cultures of unlabelled human cancer and immune cells embedded in 3D collagen gels within microfluidic devices. We argue that the experimental protocol of acquisition should be adapted to the specific kind of analysis involved and to the chosen descriptors in order to derive reliable conclusions and avoid biasing the interpretation of results.
Phosphodiesterase 5 inhibition improves contractile function and restores transverse tubule loss and catecholamine responsiveness in heart failure
Authors: Lawless Michael , Caldwell Jessica L. , Radcliffe Emma J. , Smith Charlotte E. R. , Madders George W. P. , Hutchings David C. , Woods Lori S. , Church Stephanie J. , Unwin Richard D. , Kirkwood Graeme J. , Becker Lorenz K. , Pearman Charles M. , Taylor Rebecca F. , Eisner David A. , Dibb Katharine M. , Trafford Andrew. W. 
Published: May 2019

AbstractHeart failure (HF) is characterized by poor survival, a loss of catecholamine reserve and cellular structural remodeling in the form of disorganization and loss of the transverse tubule network. Indeed, survival rates for HF are worse than many common cancers and have not improved over time. Tadalafil is a clinically relevant drug that blocks phosphodiesterase 5 with high specificity and is used to treat erectile dysfunction. Using a sheep model of advanced HF, we show that tadalafil treatment improves contractile function, reverses transverse tubule loss, restores calcium transient amplitude and the heart’s response to catecholamines. Accompanying these effects, tadalafil treatment normalized BNP mRNA and prevented development of subjective signs of HF. These effects were independent of changes in myocardial cGMP content and were associated with upregulation of both monomeric and dimerized forms of protein kinase G and of the cGMP hydrolyzing phosphodiesterases 2 and 3. We propose that the molecular switch for the loss of transverse tubules in HF and their restoration following tadalafil treatment involves the BAR domain protein Amphiphysin II (BIN1) and the restoration of catecholamine sensitivity is through reductions in G-protein receptor kinase 2, protein phosphatase 1 and protein phosphatase 2 A abundance following phosphodiesterase 5 inhibition.
Honey bees increase their foraging performance and frequency of pollen trips through experience
Authors: Klein Simon , Pasquaretta Cristian , He Xu Jiang , Perry Clint , Søvik Eirik , Devaud Jean-Marc , Barron Andrew B. , Lihoreau Mathieu 
Published: May 2019

AbstractHoney bee foragers must supply their colony with a balance of pollen and nectar to sustain optimal colony development. Inter-individual behavioural variability among foragers is observed in terms of activity levels and nectar vs. pollen collection, however the causes of such variation are still open questions. Here we explored the relationship between foraging activity and foraging performance in honey bees (Apis mellifera) by using an automated behaviour monitoring system to record mass on departing the hive, trip duration, presence of pollen on the hind legs and mass upon return to the hive, during the lifelong foraging career of individual bees. In our colonies, only a subset of foragers collected pollen, and no bee exclusively foraged for pollen. A minority of very active bees (19% of the foragers) performed 50% of the colony’s total foraging trips, contributing to both pollen and nectar collection. Foraging performance (amount and rate of food collection) depended on bees’ individual experience (amount of foraging trips completed). We argue that this reveals an important vulnerability for these social bees since environmental stressors that alter the activity and reduce the lifespan of foragers may prevent bees ever achieving maximal performance, thereby seriously compromising the effectiveness of the colony foraging force.
Environmental distribution of certain modified live-virus vaccines with a high safety profile presents a low-risk, high-reward to control zoonotic diseases
Authors: Head Jennifer R. , Vos Ad , Blanton Jesse , Müller Thomas , Chipman Richard , Pieracci Emily G. , Cleaton Julie , Wallace Ryan 
Published: May 2019

AbstractOral vaccines aid immunization of hard to reach animal populations but often contain live-attenuated viruses that pose risks of reversion to virulence or residual pathogenicity. Human risk assessment is crucial prior to vaccine field distribution but there is currently no standardized approach. We mapped exposure pathways by which distribution of oral vaccines may result in inoculation into people and applied a Markov chain to estimate the number of severe adverse events. We simulated three oral rabies vaccination (ORV) campaigns: (1) first generation ORV (SAD-B19) in foxes, (2) SAD-B19 in dogs, and (3) third generation ORV (SPBN GASGAS) in dogs. The risk of SAD-B19-associated human deaths was predicted to be low (0.18 per 10 million baits, 95% CI: 0.08, 0.36) when distributed to foxes, but, consistent with international concern, 19 times greater (3.35 per 10 million baits, 95% CI: 2.83, 3.98) when distributed to dogs. We simulated no deaths from SPBN GAS-GAS. Human deaths during dog campaigns were particularly sensitive to dog bite rate, and during wildlife campaigns to animal consumption rate and human contact rate with unconsumed baits. This model highlights the safety of third generation rabies vaccines and serves as a platform for standardized approaches to inform risk assessments.
Agricultural and Physiological Responses of Tomato Plants Grown in Different Soilless Culture Systems with Saline Water under Greenhouse Conditions
Authors: Rodríguez-Ortega Wilbert M. , Martínez Vicente , Nieves Manuel , Simón I. , Lidón V. , Fernandez-Zapata J. C. , Martinez-Nicolas J. J. , Cámara-Zapata José M. , García-Sánchez Francisco 
Published: May 2019

AbstractTomato is the most important horticultural crop in the world. The yields for this crop are highest in Southeastern Spain. In this work we studied a commercial variety of tomato, with different soilless culture systems (deep flow technique, nutrient film technique, and the perlite substrate) and three levels of salinity (2.2, 6.3, and 10.2 dS·m−1) typical of Southeastern Spain. The irrigation management was carried out for optimizing the water use efficiency. Alterations in the water status of the plants, Cl− and Na+ toxicity, and nutritional imbalances altered the vegetative growth and physiology of the plants. The marketable yield was affected by both soilless culture system and salinity. Regarding the soilles culture system, yield decreased in the order: deep flow technique > perlite > nutrient film technique. The salinity treatments improved the fruits quality by increasing the total soluble solids and titratable acidity. Plants cultivated with the nutrient film technique had the highest concentrations of Cl− and Na+ and the highest Na+/K+ ratio. The concentrations of Cl− and Na+ in the plants were not related directly to the yield loss. Therefore, the influence of the toxicity, osmotic effect, and nutritional imbalance seems to have been responsible for the yield loss.
A compact acoustic spanner to rotate macroscopic objects
Authors: Toninelli Ermes , Cox Mitchell A. , Gibson Graham M. , Brown Stuart D. , Edgar Matthew P. , Forbes Andrew , Padgett Miles J. 
Published: May 2019

AbstractWaves can carry both linear and angular momentum. When the wave is transverse (e.g. light), the angular momentum can be characterised by the “spin” angular momentum associated with circular polarisation, and the “orbital” angular momentum (OAM) arising from the phase cross-section of the beam. When the wave is longitudinal (e.g. sound) there is no polarization and hence no spin angular momentum. However, a suitably phase-structured sound beam can still carry OAM. Observing the transfer of OAM from sound to a macroscopic object provides an excellent opportunity to study the exchange of energy between waves and matter. In this paper we show how to build a compact free-space acoustic spanner based on a 3D-printed sound-guiding structure and common electronic components. We first characterise the sound fields by measuring both phase and amplitude maps, and then show a video of our free-space acoustic spanner in action, in which macroscopic objects spin in a circular motion and change direction of rotation according to the handedness of the OAM acoustic field.
Association of Anticholinergic Use with Incidence of Alzheimer’s Disease: Population-based Cohort Study
Authors: Joung Kyung-in , Kim Sukil , Cho Yoon Hee , Cho Sung-il 
Published: May 2019

AbstractDrugs with strong anticholinergic properties are used under a variety of conditions; however, they can cause various adverse effects including a negative impact on cognitive functions, with older adults being more susceptible to these effects. We explored whether the use of anticholinergic agents (ACs) affects the risk of Alzheimer’s disease (AD) in terms of incidence by using National Health Insurance Service elderly cohort database (2002–2013). As a result, AD risk was higher in subjects with an increased amount of prescriptions for strong ACs over a long period of time (9–12 years) than that in the least-exposed reference group (0–9 dose/year) [hazard ratio (HR) (95% confidence interval (95% CI)) 0.99 (0.95–1.03), 1.19 (1.12–1.26), 1.39 (1.30–1.50); in the 10–49 doses/year, 50–119 doses/year, and ≥120 doses/year groups]. Hazard ratios were particularly high in the young-old subgroup (60–64 years old in 2002) [HR (95% CI) 1.11 (1.04–1.22), 1.43 (1.25–1.65), 1.83 (1.56–2.14); in the 10–49 doses/year, 50–119 doses/year, and ≥120 doses/year groups]. Use of strong ACs dose-dependently increased the risk of AD in terms of incidence when exposure was followed up for 9 years or more, and the association was greater in the young-old subgroup.
The cell adhesion protein CAR is a negative regulator of synaptic transmission
Authors: Wrackmeyer Uta , Kaldrack Joanna , Jüttner René , Pannasch Ulrike , Gimber Niclas , Freiberg Fabian , Purfürst Bettina , Kainmueller Dagmar , Schmitz Dietmar , Haucke Volker , Rathjen Fritz G. , Gotthardt Michael 
Published: May 2019

AbstractThe Coxsackievirus and adenovirus receptor (CAR) is essential for normal electrical conductance in the heart, but its role in the postnatal brain is largely unknown. Using brain specific CAR knockout mice (KO), we discovered an unexpected role of CAR in neuronal communication. This includes increased basic synaptic transmission at hippocampal Schaffer collaterals, resistance to fatigue, and enhanced long-term potentiation. Spontaneous neurotransmitter release and speed of endocytosis are increased in KOs, accompanied by increased expression of the exocytosis associated calcium sensor synaptotagmin 2. Using proximity proteomics and binding studies, we link CAR to the exocytosis machinery as it associates with syntenin and synaptobrevin/VAMP2 at the synapse. Increased synaptic function does not cause adverse effects in KO mice, as behavior and learning are unaffected. Thus, unlike the connexin-dependent suppression of atrioventricular conduction in the cardiac knockout, communication in the CAR deficient brain is improved, suggesting a role for CAR in presynaptic processes.
Impact of ankylosing spondylitis on depression: a nationwide cohort study
Authors: Park Jin-Sung , Jang Hae-Dong , Hong Jae-Young , Park Ye-Soo , Han Kyungdo , Suh Seung-Woo , Park Si-Yong , Kim Bo-Taek 
Published: May 2019

AbstractThe aim of this study is to determine the relationship between AS and subsequent depression. This study was conducted using a nationwide dataset available in Korean National Health Insurance System (KNHIS). We identified 11,465 newly diagnosed AS patients and 57,325 patients without AS in the ratio of 1:5 matched by sex, age, and index date, between 2010 and 2014. We investigated any latent characteristics in the patients’ demographic information and chronic comorbidities that could trigger a depression when diagnosed with AS. By comparing the cohort data, the hazard ratio of developing subsequent depression in AS patients was calculated and adjusted based on several risk factors. Despite the adjustment of demographic variables and chronic comorbidities, the risk of depression was 2.21 times higher in the AS cohort than in the control group. Multivariate analysis showed that AS patients with female gender, old age and low-income status showed higher risks of developing depression. Additionally, the presence of chronic comorbidities including diabetes mellitus, hypertension, hyperlipidemia, cancer, stroke, and chronic kidney disease increased the patients’ risk of depression. The AS patients with stroke were reported to have the highest risk of depression. This population-based cohort study showed that AS significantly increased the subsequent risk of developing depression. Moreover, the development of a depression is influenced by certain demographic variables and different chronic comorbidities.
Mismatch between perceived family and individual chronotype and their association with sleep-wake patterns
Authors: Pereira-Morales Angela J. , Adan Ana , Casiraghi Leandro P. , Camargo Andrés 
Published: May 2019

AbstractWhile social zeitgebers are known to shape diurnal preference, little research has been devoted to determining the contribution of the familiar group chronotype as social zeitgeber on individual circadian rhythms and sleep-wake patterns in adult subjects. The current study aimed to examine the matching between perceived family chronotype and individual chronotype and their relationship with sleep-wake patterns on weekdays and weekends, diurnal subjective somnolence, and substance consumption. Nine hundred and forty-two Colombian adults completed the Composite Scale of Morningness, the Epworth Sleepiness Scale, and responded to a questionnaire about circadian preferences of their family nucleus. We found evidence of a mismatch between perceived family and individual chronotype, mainly for morning-type individuals (Cohen’s Kappa = −0.231; p < 0.001). This mismatch was associated with diurnal subjective somnolence (β = 0.073; p < 0.001) and specific sleep-wake patterns (p < 0.01). In addition, subjects with evening-type families showed higher caffeine and alcohol consumption (p < 0.001). To our knowledge, this is the first study to assess and report the mismatching between perceived family and individual chronotypes, and it adds to the existing body of knowledge regarding the influence of social zeitgebers on circadian rhythms. This is particularly relevant since mismatching between circadian physiology and environmental cues have been shown to lead to diverse pathologies.