bluuebunny/crossref_metadata_2025_split huggingface dataset:
Environmental stress perception activates structural remodeling of extant Streptococcus mutans biofilms
Authors: Marx Patrick , Sang Yu , Qin Hua , Wang Qingjing , Guo Rongkai , Pfeifer Carmem , Kreth Jens , Merritt Justin 
Published: March 2020

AbstractTranscription regulators from the LexA-like Protein Superfamily control a highly diverse assortment of genetic pathways in response to environmental stress. All characterized members of this family modulate their functionality and stability via a strict coordination with the coprotease function of RecA. Using the LexA-like protein IrvR from Streptococcus mutans, we demonstrate an exception to the RecA paradigm and illustrate how this evolutionary innovation has been coopted to diversify the stress responsiveness of S. mutans biofilms. Using a combination of genetics and biophysical measurements, we demonstrate how non-SOS stresses and SOS stresses each trigger separate regulatory mechanisms that stimulate production of a surface lectin responsible for remodeling the viscoelastic properties of extant biofilms during episodes of environmental stress. These studies demonstrate how changes in the external environment or even anti-biofilm therapeutic agents can activate biofilm-specific adaptive mechanisms responsible for bolstering the integrity of established biofilm communities. Such changes in biofilm community structure are likely to play central roles in the notorious recalcitrance of biofilm infections.
A unidirectional on-chip photonic interface for superconducting circuits
Authors: Guimond P.-O. , Vermersch B. , Juan M. L. , Sharafiev A. , Kirchmair G. , Zoller P. 
Published: March 2020

AbstractWe propose and analyze a passive architecture for realizing on-chip, scalable cascaded quantum devices. In contrast to standard approaches, our scheme does not rely on breaking Lorentz reciprocity. Rather, we engineer the interplay between pairs of superconducting transmon qubits and a microwave transmission line, in such a way that two delocalized orthogonal excitations emit (and absorb) photons propagating in opposite directions. We show how such cascaded quantum devices can be exploited to passively probe and measure complex many-body operators on quantum registers of stationary qubits, thus enabling the heralded transfer of quantum states between distant qubits, as well as the generation and manipulation of stabilizer codes for quantum error correction.
A hybrid stochastic model of the budding yeast cell cycle
Authors: Ahmadian Mansooreh , Tyson John J. , Peccoud Jean , Cao Yang 
Published: March 2020

AbstractThe growth and division of eukaryotic cells are regulated by complex, multi-scale networks. In this process, the mechanism of controlling cell-cycle progression has to be robust against inherent noise in the system. In this paper, a hybrid stochastic model is developed to study the effects of noise on the control mechanism of the budding yeast cell cycle. The modeling approach leverages, in a single multi-scale model, the advantages of two regimes: (1) the computational efficiency of a deterministic approach, and (2) the accuracy of stochastic simulations. Our results show that this hybrid stochastic model achieves high computational efficiency while generating simulation results that match very well with published experimental measurements.
A bivalent vaccine confers immunogenicity and protection against Shigella flexneri and enterotoxigenic Escherichia coli infections in mice
Authors: Medeiros Pedro Henrique Q. S. , Bolick David T. , Ledwaba Solanka E. , Kolling Glynis L. , Costa Deiziane V. S. , Oriá Reinaldo B. , Lima Aldo Ângelo M. , Barry Eileen M. , Guerrant Richard L. 
Published: March 2020

AbstractVaccine studies for Shigella flexneri and enterotoxigenic Escherichia coli have been impaired by the lack of optimal animal models. We used two murine models to show that a S. flexneri 2a bivalent vaccine (CVD 1208S-122) expressing enterotoxigenic Escherichia coli colonization factor antigen-I (CFA/I) and the binding subunits A2 and B of heat labile-enterotoxin (LTb) is immunogenic and protects against weight loss and diarrhea. These findings document the immunogenicity and pre-clinical efficacy effects of CVD 1208S-122 vaccine and suggest that further work can help elucidate relevant immune responses and ultimately its clinical efficacy in humans.
Online characterization of bacterial processes in drinking water systems
Authors: Farhat Nadia , Kim Lan Hee , Vrouwenvelder Johannes S. 
Published: March 2020

AbstractThe use of traditional drinking water microbial quality monitoring methods, including heterotrophic plate counts (HPCs) and total coliform counts, are not only laborious and time-consuming but also do not readily allow identification of risk areas in the network. Furthermore, if areas of concern are identified, and mitigation measures are taken, it takes days before the effectiveness of these measures is known. This study identified flow cytometry (FCM) as an online sensor technology for bacterial water quality monitoring in the distribution network. We monitored the total bacterial cell numbers and biodiversity in a drinking water distribution system (DWDS) using an online FCM. Two parallel online FCM monitoring systems were installed on two different locations at a drinking water treatment plant (DWTP; Saudi Arabia) supplying chlorinated water to the distribution and in the network 3.6 km away from the DWTP. The FCMs were operated at the same time in parallel to assess the biological stability in DWDSs. The flow cytometric data was compared with the conventional water quality detection methods (HPC and total coliforms). HPC and total coliforms were constantly below the detection limits, while the FCM provided detectable total cell count data and enabled the quantification of changes in the drinking water both with time and during distribution. Results demonstrate the value of FCM as a tool for compliance monitoring and risk assessment of DWDSs.
Sinking flux of particulate organic matter in the oceans: Sensitivity to particle characteristics
Authors: Omand Melissa M. , Govindarajan Rama , He Jing , Mahadevan Amala 
Published: March 2020

AbstractThe sinking of organic particles produced in the upper sunlit layers of the ocean forms an important limb of the oceanic biological pump, which impacts the sequestration of carbon and resupply of nutrients in the mesopelagic ocean. Particles raining out from the upper ocean undergo remineralization by bacteria colonized on their surface and interior, leading to an attenuation in the sinking flux of organic matter with depth. Here, we formulate a mechanistic model for the depth-dependent, sinking, particulate mass flux constituted by a range of sinking, remineralizing particles. Like previous studies, we find that the model does not achieve the characteristic ‘Martin curve’ flux profile with a single type of particle, but instead requires a distribution of particle sizes and/or properties. We consider various functional forms of remineralization appropriate for solid/compact particles, and aggregates with an anoxic or oxic interior. We explore the sensitivity of the shape of the flux vs. depth profile to the choice of remineralization function, relative particle density, particle size distribution, and water column density stratification, and find that neither a power-law nor exponential function provides a definitively superior fit to the modeled profiles. The profiles are also sensitive to the time history of the particle source. Varying surface particle size distribution (via the slope of the particle number spectrum) over 3 days to represent a transient phytoplankton bloom results in transient subsurface maxima or pulses in the sinking mass flux. This work contributes to a growing body of mechanistic export flux models that offer scope to incorporate underlying dynamical and biological processes into global carbon cycle models.
Preventive effect of fluvastatin on the development of medication-related osteonecrosis of the jaw
Authors: Adachi Naomi , Ayukawa Yasunori , Yasunami Noriyuki , Furuhashi Akihiro , Imai Mikio , Sanda Koma , Atsuta Ikiru , Koyano Kiyoshi 
Published: March 2020

AbstractMedication-related osteonecrosis of the jaw (MRONJ) occurs in patients undergoing oral surgery while medicated with bisphosphonate, denosumab or anti-angiogenic agents. We employed a MRONJ-like rat model to investigate whether injecting fluvastatin at extraction sites prevents MRONJ-like lesion. A MRONJ-like model was created by treating rats with zoledronate and dexamethasone, extracting teeth, and immediately injecting fluvastatin at the extraction site. The experimental group comprised three subgroups treated with low (0.1 mg/kg; FS-L), medium (1.0 mg/kg; FS-M) and high concentrations (10 mg/kg; FS-H) of fluvastatin. Necrotic bone exposure was significantly lower in the FS-M (p = 0.028) and FS-H (p = 0.041) groups than in the MRONJ group. The distance between the edges of the epithelial surfaces was significantly shorter in the FS-M (p = 0.042) and FS-H (p = 0.041) groups. The area of necrotic bone and the necrotic bone ratio were significantly smaller in the FS-H group (p = 0.041 and p = 0.042 respectively). Bone volume fraction calculated on μ-CT images was significantly larger in the FS-H group than in the MRONJ group (p = 0.021). Our findings suggest that a single local injection of fluvastatin following tooth extraction can potentially reduce the chance of developing MRONJ-like lesion in rats.
Potential impacts of high-sensitivity creatine kinase-MB on long-term clinical outcomes in patients with stable coronary heart disease
Authors: Wu Yen-Wen , Ho Sing Kong , Tseng Wei-Kung , Yeh Hung-I , Leu Hsin-Bang , Yin Wei-Hsian , Lin Tsung-Hsien , Chang Kuan-Cheng , Wang Ji-Hung , Wu Chau-Chung , Chen Jaw-Wen 
Published: March 2020

AbstractThis study aimed to investigate the prognostic value of high-sensitivity creatine kinase-myocardial band or fraction (hsCK-MB) in comparison with other well-established biomarkers including heart type-fatty acid binding protein (H-FABP) and N-terminal pro-brain natriuretic peptide (NT-proBNP) in patients with stable coronary heart disease (SCHD). A total of 1,785 patients were enrolled and followed for 36 months. The primary outcome was all-cause mortality. The secondary outcomes included cardiovascular (CV) death, acute myocardial infarction (AMI), angina-related hospitalizations, and hospitalizations for heart failure. The all-cause mortality rate was significantly higher in the high hsCK-MB group compared to the low hsCK-MB group (4.64% vs. 1.88%, p = 0.0026). After adjusting for baseline covariates, there were no significant differences for the secondary outcomes. H-FABP (≥4.226 ng/mL) was the best predictor for all-cause mortality (HR = 2.68, 95% CI = 1.28–5.62, p = 0.009) and CV death (HR = 6.84, 95% CI = 1.89–22.14, p = 0.003). The high NT-proBNP group had a higher AMI-related hospitalization rate (HR = 1.91, 95% CI = 1.00–3.65, p = 0.05). Neither the addition of hsCK-MB to any other markers nor combinations of the three markers improved the prognostic significance of CV outcomes. In conclusion, hsCK-MB was an independent predictor for all-cause mortality but not CV outcomes in patients with SCHD. Combination of hsCK-MB, H-FABP and NT-proBNP failed to improve the prognostic power for all-cause mortality or CV outcomes.
A Randomized Trial Comparing the Bowel Cleansing Efficacy of Sodium Picosulfate/Magnesium Citrate and Polyethylene Glycol/Bisacodyl (The Bowklean Study)
Authors: Hung Shih-Ya , Chen Hong-Chang , Chen William Tzu-Liang 
Published: March 2020

AbstractBowel cleansing is essential for a successful colonoscopy, but the ideal clearing agent and the volume have yet to be determined. A small-volume cleanser is important for patient compliance. This study aimed to compare the bowel cleansing efficacy, safety, tolerability, and acceptability of a 300-mL small-volume sodium picosulfate/magnesium citrate (PSMC) preparation-Bowklean with one 2-L polyethylene glycol (PEG)/bisacodyl-Klean-Prep/Dulcolax preparation under identical dietary recommendations. This multicenter, randomized, parallel-group, pre-specified noninferiority study enrolled 631 outpatients scheduled to undergo colonoscopy (Bowklean = 316 and Klean-Prep/Dulcolax = 315). After bowel preparation, an independent evaluator blinded to the subject’s treatment allocation rated the quality of the colon cleansing. Efficacy was evaluated using the Aronchick Scale and Ottawa Bowel Preparation Scale (OPBS). Safety was assessed by monitoring adverse events. Tolerability and acceptability were measured via a patient questionnaire. Bowklean was non-interior to Klean-Prep/Dulcolax in overall colon cleansing but was associated with significantly better preparation quality. Notably, Bowklean was associated with significantly greater tolerability and acceptability of bowel preparations than Klean-Prep/Dulcolax. Safety profiles did not differ significantly between the groups. Our data indicate that Bowklean is a more effective and better-tolerated bowel cleansing preparation before colonoscopy than Klean-Prep/Dulcolax. Bowklean may therefore increase positive attitudes toward colonoscopies and participation rates.
Fluorescence microscopy tensor imaging representations for large-scale dataset analysis
Authors: Vinegoni Claudio , Fumene Feruglio Paolo , Courties Gabriel , Schmidt Stephen , Hulsmans Maarten , Lee Sungon , Wang Rui , Sosnovik David , Nahrendorf Matthias , Weissleder Ralph 
Published: March 2020

AbstractUnderstanding complex biological systems requires the system-wide characterization of cellular and molecular features. Recent advances in optical imaging technologies and chemical tissue clearing have facilitated the acquisition of whole-organ imaging datasets, but automated tools for their quantitative analysis and visualization are still lacking. We have here developed a visualization technique capable of providing whole-organ tensor imaging representations of local regional descriptors based on fluorescence data acquisition. This method enables rapid, multiscale, analysis and virtualization of large-volume, high-resolution complex biological data while generating 3D tractographic representations. Using the murine heart as a model, our method allowed us to analyze and interrogate the cardiac microvasculature and the tissue resident macrophage distribution and better infer and delineate the underlying structural network in unprecedented detail.
Inducible Antibacterial Activity in the Bacillales by Triphenyl Tetrazolium Chloride
Authors: Sierra-Zapata Laura , Álvarez Javier C. , Romero-Tabarez Magally , Silby Mark.W. , Traxler Matthew F. , Behie Scott W. , Pessotti Rita de Cassia , Villegas-Escobar Valeska 
Published: March 2020

AbstractThe world is in the midst of an antimicrobial resistance crisis, driving a need to discover novel antibiotic substances. Using chemical cues as inducers to unveil a microorganism’s full metabolic potential is considered a successful strategy. To this end, we investigated an inducible antagonistic behavior in multiple isolates of the order Bacillales, where large inhibition zones were produced against Ralstonia solanacearum only when grown in the presence of the indicator triphenyl tetrazolium chloride (TTC). This bioactivity was produced in a TTC-dose dependent manner. Escherichia coli and Staphylococcus sp. isolates were also inhibited by Bacillus sp. strains in TTC presence, to a lesser extent. Knockout mutants and transcriptomic analysis of B. subtilis NCIB 3610 cells revealed that genes from the L-histidine biosynthetic pathway, the purine, pyrimidine de novo synthesis and salvage and interconversion routes, were significantly upregulated. Chemical space studied through metabolomic analysis, showed increased presence of nitrogenous compounds in extracts from induced bacteria. The metabolites orotic acid and L-phenylalaninamide were tested against R. solanacearum, E. coli, Staphylococcus sp. and B. subtilis, and exhibited activity against pathogens only in the presence of TTC, suggesting a biotransformation of nitrogenous compounds in Bacillus sp. cells as the plausible cause of the inducible antagonistic behavior.
Nanosized Alumina Particle and Proteasome Inhibitor Bortezomib Prevented inflammation and Osteolysis Induced by Titanium Particle via Autophagy and NF-κB Signaling
Authors: Zhang Zhiwei , Fu Xuewei , Xu Ling , Hu Xiaolei , Deng Feng , Yang Zhiqiang , Jiang Lin , Fu Tiwei , Zhou Pengfei , Song Jinlin , Ji Ping , Huang Jiao , Wu Xiaomian 
Published: March 2020

AbstractAutophagy and NF-κB signaling are involving in the process of Particle Disease, which was caused by the particles released from friction interface of artificial joint, implant materials of particle reinforced composite, scaffolds for tissue engineering, or material for drug delivery. However, the biological interaction of different material particles and the mechanism of proteasome inhibitor, Bortezomib (BTZ), against Titanium (Ti) particle-induced Particle Disease remain unclear. In this study, we evaluated effect of nanosized Alumina (Al) particles and BTZ on reducing and treating the Ti particle-induced inflammatory reaction in MG-63 cells and mouse calvarial osteolysis model. We found that Al particles and BTZ could block apoptosis and NF- κB activation in osteoblasts in vitro and in a mouse model of calvarial resorption induced by Ti particles. We found that Al particles and BTZ attenuated the expression of inflammatory cytokines (IL-1β, IL-6, TNF-α). And Al prevented the IL-1β expression induced by Ti via attenuating the NF- κB activation β-TRCP and reducing the expression of Casepase-3. Expressions of autophagy marker LC3 was activated in Ti group, and reduced by Al and/not BTZ. Furthermore, the expressions of OPG were also higher in these groups than the Ti treated group. Collectively, nanosized Al could prevent autophagy and reduce the apoptosis, inflammatory and osteolysis induced by Ti particles. Our data offered a basic data for implant design when it was inevitable to use Ti as biomaterials, considering the outstanding mechanical propertie of Ti. What’s more, proteasome inhibitor BTZ could be a potential therapy for wear particle-induced inflammation and osteogenic activity via regulating the activity of NF- κB signaling pathway.
The cooling mechanism of minuscule ribbed surfaces
Authors: Nishikawa M. , Otomo H. , Yoshida Y. , Deguchi J. , Tsukamoto M. , Yamamoto T. 
Published: March 2020

AbstractOne reason human beings wear stockings is to warm their legs. Ordinary textile materials are thermally insulative, which prevents body’s heat from dissipating. In contrary to this common sense, it was discovered that some knitted stockings made up of them permanently promote heat release and cool body. This non-intuitive phenomenon emerges when micro-size yarns are knitted to form wide spacing between neighboring yarns. However, the reason why they cool body was unclear because conventional principles of cooling garments cannot account for it. Here, in the basis of fluid-solid conjugate heat transfer analysis of natural convection, we have clarified the cooling mechanism originates from relative relationship between their geometric structure, a periodic alignment of minuscule ribs, and thermal boundary layer. Our novel finding revealed that sufficiently small ribs on the surface are exposed to steep temperature gradient within thermal boundary layer. Thereby, thermal conduction via ribs is enhanced complementarily as they are separated to guide cooler flow onto the surface. Our study provides a general insight into understanding permanent cooling mechanism on micro-size ribbed surfaces in contrast to conventional theory for heat sink, which is applicable not only to other clothes, but also to artificial devices or natural structures.
The risk of twin pregnancies should be minimized in patients with a unicornuate uterus undergoing IVF-ET
Authors: Ouyang Yan , Cai Pei , Gong Fei , Lin Ge , Qin Jiabi , Li Xihong 
Published: March 2020

AbstractUnicornuate uteri are associated with infertility, miscarriage, preterm delivery and even uterine rupture. The aim of this research was to investigate the effects of unicornuate uterine anomaly on twin pregnancies after in vitro fertilization-embryo transfer (IVF-ET). A total of 206 women with unicornuate uteri (A singleton, B selective reduction (SR) of twins to a singleton, C twins) and 314 women with normal uteri (D SR of twins to a singleton, E twins) who delivered at ≥22 weeks were included. C was associated with a significantly lower live birth rate (adjusted odds ratio (aOR) 0.08, 95% confidence interval (CI), 0.01–0.69) and higher risks of preterm delivery (aOR 11.63, 95% CI, 4.85–27.92), perinatal mortality (aOR 11.43, 95% CI, 1.44–90.57) and low birth weight (aOR 5.92, 95% CI 1.94–18.06) than A, a 15-fold greater risk of preterm delivery (aOR 15.54, 95% CI 3.09–78.28) than B and a greater risk of preterm delivery (aOR 2.76, 95% CI 1.33–5.73) than E. After SR to a singleton, the perinatal outcomes were statistically similar between B and D. These results showed that the risk of twin pregnancies should be minimized in patients with unicornuate uterine anomaly undergoing IVF-ET.
Universal scaling of weak localization in graphene due to bias-induced dispersion decoherence
Authors: Somphonsane R. , Ramamoorthy H. , He G. , Nathawat J. , Yin S. , Kwan C.-P. , Arabchigavkani N. , Barut B. , Zhao M. , Jin Z. , Fransson J. , Bird J. P. 
Published: March 2020

AbstractThe differential conductance of graphene is shown to exhibit a zero-bias anomaly at low temperatures, arising from a suppression of the quantum corrections due to weak localization and electron interactions. A simple rescaling of these data, free of any adjustable parameters, shows that this anomaly exhibits a universal, temperature- (T) independent form. According to this, the differential conductance is approximately constant at small voltages (V < kBT/e), while at larger voltages it increases logarithmically with the applied bias. For theoretical insight into the origins of this behaviour, which is inconsistent with electron heating, we formulate a model for weak-localization in the presence of nonequilibrium transport. According to this model, the applied voltage causes unavoidable dispersion decoherence, which arises as diffusing electron partial waves, with a spread of energies defined by the value of the applied voltage, gradually decohere with one another as they diffuse through the system. The decoherence yields a universal scaling of the conductance as a function of eV/kBT, with a logarithmic variation for eV/kBT > 1, variations in accordance with the results of experiment. Our theoretical description of nonequilibrium transport in the presence of this source of decoherence exhibits strong similarities with the results of experiment, including the aforementioned rescaling of the conductance and its logarithmic variation as a function of the applied voltage.