bluuebunny/crossref_metadata_2025_split huggingface dataset:
Bifidobacterial biofilm formation is a multifactorial adaptive phenomenon in response to bile exposure
Authors: Kelly Sandra M. , Lanigan Noreen , O’Neill Ian J. , Bottacini Francesca , Lugli Gabriele Andrea , Viappiani Alice , Turroni Francesca , Ventura Marco , van Sinderen Douwe 
Published: July 2020

AbstractIn the current study, we show that biofilm formation by various strains and species belonging to Bifidobacterium, a genus that includes gut commensals with reported health-promoting activities, is induced by high concentrations of bile (0.5% (w/v) or higher) and individual bile salts (20 mM or higher), rather than by acid or osmotic stress. The transcriptomic response of a bifidobacterial prototype Bifidobacterium breve UCC2003 to such high bile concentrations was investigated and a random transposon bank of B. breve UCC2003 was screened for mutants that affect biofilm formation in order to identify genes involved in this adaptive process. Eleven mutants affected in their ability to form a biofilm were identified, while biofilm formation capacity of an insertional mutation in luxS and an exopolysaccharide (EPS) negative B. breve UCC2003 was also studied. Reduced capacity to form biofilm also caused reduced viability when exposed to porcine bile. We propose that bifidobacterial biofilm formation is an adaptive response to high concentrations of bile in order to avoid bactericidal effects of high bile concentrations in the gastrointestinal environment. Biofilm formation appears to be a multi-factorial process involving EPS production, proteins and extracellular DNA release, representing a crucial strategy in response to bile stress in order to enhance fitness in the gut environment.
Multiple cryoinjuries modulate the efficiency of zebrafish heart regeneration
Authors: Bise Thomas , Sallin Pauline , Pfefferli Catherine , Jaźwińska Anna 
Published: July 2020

AbstractZebrafish can regenerate their damaged hearts throughout their lifespan. It is, however, unknown, whether regeneration remains effective when challenged with successive cycles of cardiac damage in the same animals. Here, we assessed ventricular restoration after two, three and six cryoinjuries interspaced by recovery periods. Using transgenic cell-lineage tracing analysis, we demonstrated that the second cryoinjury damages the regenerated area from the preceding injury, validating the experimental approach. We identified that after multiple cryoinjuries, all hearts regrow a thickened myocardium, similarly to hearts after one cryoinjury. However, the efficiency of scar resorption decreased with the number of repeated cryoinjuries. After six cryoinjuries, all examined hearts failed to completely resolve the fibrotic tissue, demonstrating reduced myocardial restoration. This phenotype was associated with enhanced recruitment of neutrophils and decreased cardiomyocyte proliferation and dedifferentiation at the early regenerative phase. Furthermore, we found that each repeated cryoinjury increased the accumulation of collagen at the injury site. Our analysis demonstrates that the cardiac regenerative program can be successfully activated many times, despite a persisting scar in the wounded area. This finding provides a new perspective for regenerative therapies, aiming in stimulation of organ regeneration in the presence of fibrotic tissue in mammalian models and humans.
Functionalization and antimicrobial evaluation of ampicillin, penicillin and vancomycin with Pyrenacantha grandiflora Baill and silver nanoparticles
Authors: Murei Arinao , Ayinde Wasiu B. , Gitari Mugera W. , Samie Amidou 
Published: July 2020

AbstractSome antibiotics have lost their efficacy over common infections and this has led to the search for new antibiotics and chemically altering existing ones for a better control of infectious diseases. In the present study, Pyrenacantha grandiflora tubers extracts were conjugated with ampicillin, penicillin, vancomycin and silver nanoparticles and their antimicrobial activity was evaluated against Escherichia coli, Staphylococcus aureus and Klebsiella Pneumoniae. The reactions were confirmed by formation of new functional groups that were identified by Fourier transmission infrared spectroscopy (FTIR). Minimum inhibitory concentrations were determined using the microdilution assay. Minimum bactericidal concentrations and the fractional inhibition concentration index were also determined. FTIR analysis indicated different functional group associated with conjugation. The activity of ampicillin was improved when conjugated with silver nanoparticles against K. pneumonia and E. coli. Vancomycin showed improvement of activity when conjugated to silver nanoparticles against K. pneumonia. Penicillin was improved by acetone extracts and vancomycin showed to be more effective when conjugated with silver nanoparticles and water extracts. The conjugation of P. grandiflora with penicillin, ampicillin and vancomycin in the presence of silver nanoparticles improved their biological activities. Therefore, the conjugates are medicinally important and can be used to improve the activity of existing antibiotics.
Comparison of single- and multi-trait approaches to identify best wild candidates for aquaculture shows that the simple way fails
Authors: Toomey Lola , Lecocq Thomas , Bokor Zoltán , Espinat Laurent , Ferincz Árpád , Goulon Chloé , Vesala Sami , Baratçabal Margot , Barry Mamadou-Diouhe , Gouret Mélanie , Gouron Camille , Staszny Ádám , Mauduit Emilie , Mean Vicheka , Muller Iris , Schlick Nicolas , Speder Kévin , Thumerel Romain , Piatti Clémentine , Pasquet Alain , Fontaine Pascal 
Published: July 2020

AbstractIn agriculture, diversifying production implies picking up, in the wild biodiversity, species or populations that can be domesticated and fruitfully produced. Two alternative approaches are available to highlight wild candidate(s) with high suitability for aquaculture: the single-trait (i.e. considering a single phenotypic trait and, thus, a single biological function) and multi-trait (i.e. considering multiple phenotypic traits involved in several biological functions) approaches. Although the former is the traditional and the simplest method, the latter could be theoretically more efficient. However, an explicit comparison of advantages and pitfalls between these approaches is lacking to date in aquaculture. Here, we compared the two approaches to identify best candidate(s) between four wild allopatric populations of Perca fluviatilis in standardised aquaculture conditions. Our results showed that the single-trait approach can (1) miss key divergences between populations and (2) highlight different best candidate(s) depending on the trait considered. In contrast, the multi-trait approach allowed identifying the population with the highest domestication potential thanks to several congruent lines of evidence. Nevertheless, such an integrative assessment is achieved with a far more time-consuming and expensive study. Therefore, improvements and rationalisations will be needed to make the multi-trait approach a promising way in the aquaculture development.
Photon fluence and dose estimation in computed tomography using a discrete ordinates Boltzmann solver
Authors: Norris Edward T. , Liu Xin 
Published: July 2020

AbstractIn this study, cone-beam single projection and axial CT scans are modeled with a software package—DOCTORS, which solves the linear Boltzmann equation using the discrete ordinates method. Phantoms include a uniform 35 cm diameter water cylinder and a non-uniform abdomen phantom. Series simulations were performed with different simulation parameters, including the number of quadrature angles, the order of Legendre polynomial expansions, and coarse and fine mesh grid. Monte Carlo simulations were also performed to benchmark DOCTORS simulations. A quantitative comparison was made between the simulation results obtained using DOCTORS and Monte Carlo methods. The deterministic simulation was in good agreement with the Monte Carlo simulation on dose estimation, with a root-mean-square-deviation difference of around 2.87%. It was found that the contribution of uncollided photon fluence directly from the source dominates the local absorbed dose in the diagnostic X-ray energy range. The uncollided photon fluence can be calculated accurately using a ‘ray-tracing’ algorithm. The accuracy of collided photon fluence estimation is largely affected by the pre-calculated multigroup cross-sections. The primary benefit of DOCTORS lies in its rapid computation speed. Using DOCTORS, parallel computing with GPU enables the cone-beam CT dose estimation nearly in real-time.
Characterizing transition-metal dichalcogenide thin-films using hyperspectral imaging and machine learning
Authors: Shevitski Brian , Chen Christopher T. , Kastl Christoph , Kuykendall Tevye , Schwartzberg Adam , Aloni Shaul , Zettl Alex 
Published: July 2020

AbstractAtomically thin polycrystalline transition-metal dichalcogenides (TMDs) are relevant to both fundamental science investigation and applications. TMD thin-films present uniquely difficult challenges to effective nanoscale crystalline characterization. Here we present a method to quickly characterize the nanocrystalline grain structure and texture of monolayer WS2 films using scanning nanobeam electron diffraction coupled with multivariate statistical analysis of the resulting data. Our analysis pipeline is highly generalizable and is a useful alternative to the time consuming, complex, and system-dependent methodology traditionally used to analyze spatially resolved electron diffraction measurements.
Novel theoretical approach to the GISAXS issue: the Green function formalism using the q-Eigenwaves propagating through a twofold rough-surfaced medium
Authors: Chukhovskii F. N. , Roshchin B. S. 
Published: July 2020

AbstractTo describe the 1D and 2D patterns of the grazing-incidence small-angle X-ray scattering (GISAXS) from a rough fractal surface, the novel integral equations for the amplitudes of reflected and transmitted waves are derived. To be specific, the analytical expression for the 2D total intensity distribution $$\frac{{dR_{tot} \left( {\theta ,\phi ;\theta_{0} } \right)}}{d\Omega }$$dRtotθ,ϕ;θ0dΩ is obtained. The latter represents by itself a superposition of terms related to the GISAXS specular $$\frac{{dR_{spec} \left( {\theta ;\theta_{0} } \right)}}{d\Omega }$$dRspecθ;θ0dΩ and diffuse $$\frac{{dR_{dif} \left( {\theta ,\phi ;\theta_{0} } \right)}}{d\Omega }$$dRdifθ,ϕ;θ0dΩ patterns, respectively. Hereafter, $$\theta$$θ is the scattering meridian angle, $$\phi$$ϕ is the scattering azimuth angle; $$\theta_{0}$$θ0 is the angle of incidence. By using the above analytical expressions, the 1D and 2D GISAXS patterns are numerically calculated. Some new experimental measurements of the specular reflectivity curves Rspec($$\theta_{0}$$θ0) related to the fused quartz and crystal Si(111) samples have been carried out. Based on the theoretical approach developed, a direct least-squared procedure in a χ2-fit fashion has been used to determine the corresponding values of the root-mean-square roughness σ from the specular GISAXS reflectivity data.
LncRNA RP11-86H7.1 promotes airway inflammation induced by TRAPM2.5 by acting as a ceRNA of miRNA-9-5p to regulate NFKB1 in HBECS
Authors: Zhao Jun , Pu Jinding , Hao Binwei , Huang Lingmei , Chen Jinglong , Hong Wei , Zhou Yumin , Li Bing , Ran Pixin 
Published: July 2020

AbstractTraffic-related air pollution particulate matter 2.5 (TRAPM2.5), is involved in chronic obstructive pulmonary disease (COPD), which is characterized by airway inflammation. Specifically, these harmful particles or gases can increase chronic airway inflammation. Some recent studies have shown that lncRNAs are closely related to COPD and participate in the regulation of airway inflammation. However, the precise mechanisms remain unknown. In the present study, we investigated the effect of TRAPM2.5 on airway inflammation in human bronchial epithelial cells (HBECs) and the underlying mechanisms mediated by a lncRNA. After exposure to TRAPM2.5, the novel lncRNA RP11-86H7.1 was markedly upregulated in HBECs. Functional assays indicated that the lncRNA RP11-86H7.1 was required for the TRAPM2.5-induced expression of inflammatory factors in HBECs. A mechanistic study demonstrated that lncRNA RP11-86H7.1 might participate in TRAPM2.5-induced inflammatory responses by activating the NF-κB signaling pathway. Moreover, the lncRNA RP11-86H7.1 can promote the inflammatory response by acting as a competing endogenous RNA of miR-9-5p, reversing the inhibitory effect of its target gene NFKB1, and sustaining NF-κB activation. In summary, our study elucidates the pro-inflammatory roles of the lncRNA RP11-86H7.1–miR-9-5p–NFKB1 regulatory network in airway inflammation induced by TRAPM2.5 and indicates that the components of this network might serve as novel diagnostic biomarkers and potential therapeutic targets.
Characterization of non-linear mechanical behavior of the cornea
Authors: Ashofteh Yazdi A. , Melchor J. , Torres J. , Faris I. , Callejas A. , Gonzalez-Andrades M. , Rus G. 
Published: July 2020

AbstractThe objective of this study was to evaluate which hyperelastic model could best describe the non-linear mechanical behavior of the cornea, in order to characterize the capability of the non-linear model parameters to discriminate structural changes in a damaged cornea. Porcine corneas were used, establishing two different groups: control (non-treated) and NaOH-treated (damaged) corneas (n = 8). NaOH causes a chemical burn to the corneal tissue, simulating a disease associated to structural damage of the stromal layer. Quasi-static uniaxial tensile tests were performed in nasal-temporal direction immediately after preparing corneal strips from the two groups. Three non-linear hyperelastic models (i.e. Hamilton-Zabolotskaya model, Ogden model and Mooney-Rivlin model) were fitted to the stress–strain curves obtained in the tensile tests and statistically compared. The corneas from the two groups showed a non-linear mechanical behavior that was best described by the Hamilton-Zabolotskaya model, obtaining the highest coefficient of determination (R2 > 0.95). Moreover, Hamilton-Zabolotskaya model showed the highest discriminative capability of the non-linear model parameter (Parameter A) for the tissue structural changes between the two sample groups (p = 0.0005). The present work determines the best hyperelastic model with the highest discriminative capability in description of the non-linear mechanical behavior of the cornea.
Involved microRNAs in alternative polyadenylation intervene in breast cancer via regulation of cleavage factor “CFIm25”
Authors: Tamaddon Mona , Shokri Gelareh , Hosseini Rad Seyed Mohammad Ali , Rad Iman , Emami Razavi Àmirnader , Kouhkan Fatemeh 
Published: July 2020

AbstractCleavage factor “CFIm25”, as a key repressor at proximal poly (A) site, negatively correlates to cell proliferation and tumorigenicity in various cancers. Hence, understanding CFIm25 mechanism of action in breast cancer would be a great benefit. To this aim four steps were designed. First, potential miRNAs that target 3′-UTR of CFIm25 mRNA, retrieved from Targetscan web server. Second, screened miRNAs were profiled in 100 breast cancer and 100 normal adjacent samples. Third, miRNAs that their expression was inversely correlated to the CFIm25, overexpressed in MDA-MB-231 cell line, and their effect on proliferation and migration monitored via MTT and wound healing assays, respectively. Fourth, interaction of miRNAs of interest with 3′-UTR of CFIm25 confirmed via luciferase assay and western blot. Our results indicate that CFIm25 considerably down-regulates in human breast cancer tissue. qRT-PCR assay, luciferase test, and western blotting confirm that CFIm25 itself could be directly regulated by oncomiRs such as miR-23, -24, -27, -135, -182 and -374. Besides, according to MTT and wound healing assays of cell lines, CFIm25 knockdown intensifies cell growth, proliferation and migration. Our results also confirm indirect impact of CFIm25 on regulation of mRNA’s 3′–UTR length, which then control corresponding miRNAs’ action. miRNAs directly control CFIm25 expression level, which then tunes expression of the oncogenes and tumor proliferation. Therefore, regulation of CFIm25 expression level via miRNAs is expected to improve treatment responses in breast cancer.
Autonomic nervous system changes detected with peripheral sensors in the setting of epileptic seizures
Authors: Vieluf Solveig , Reinsberger Claus , El Atrache Rima , Jackson Michele , Schubach Sarah , Ufongene Claire , Loddenkemper Tobias , Meisel Christian 
Published: July 2020

AbstractA better understanding of the early detection of seizures is highly desirable as identification of an impending seizure may afford improved treatments, such as antiepileptic drug chronotherapy, or timely warning to patients. While epileptic seizures are known to often manifest also with autonomic nervous system (ANS) changes, it is not clear whether ANS markers, if recorded from a wearable device, are also informative about an impending seizure with statistically significant sensitivity and specificity. Using statistical testing with seizure surrogate data and a unique dataset of continuously recorded multi-day wristband data including electrodermal activity (EDA), temperature (TEMP) and heart rate (HR) from 66 people with epilepsy (9.9 ± 5.8 years; 27 females; 161 seizures) we investigated differences between inter- and preictal periods in terms of mean, variance, and entropy of these signals. We found that signal mean and variance do not differentiate between inter- and preictal periods in a statistically meaningful way. EDA signal entropy was found to be increased prior to seizures in a small subset of patients. Findings may provide novel insights into the pathophysiology of epileptic seizures with respect to ANS function, and, while further validation and investigation of potential causes of the observed changes are needed, indicate that epilepsy-related state changes may be detectable using peripheral wearable devices. Detection of such changes with wearable devices may be more feasible for everyday monitoring than utilizing an electroencephalogram.
Structure-based design of gRNA for Cas13
Authors: Bandaru Srinivas , Tsuji Mika Higashide , Shimizu Yurika , Usami Kaya , Lee Suni , Takei Naoko Kumagai , Yoshitome Kei , Nishimura Yasumitsu , Otsuki Takemi , Ito Tatsuo 
Published: July 2020

AbstractCas13 endonuclease activity depends on the RNA local secondary structure with strong preference for single-stranded (SS) regions. Hence, it becomes indispensable to identify the SS regions for effective Cas13 mediated RNA knockdown. We herein present rational gRNA design by integrating experimental structure-seq data and predicted structural models. Utilizing structure-seq data for XIST transcript, we observed that gRNAs targeting the SS regions significantly induce transcript knockdown and cleavage than those targeting double-stranded (DS) regions. Further, we identified the “central seed region” in the gRNA that upon targeting the SS regions efficiently facilitates Cas13 mediated cleavage. In our following pursuits, we considered the scenario wherein experimental structure-seq data is not available, hence we used SS18-SSX2 fusion transcript indicated in synovial sarcomas and computationally predicted its structure. We observed that gRNAs targeting the SS regions predicted from the structure, efficiently induced necrosis compared to gRNAs that target the DS regions. In conclusion, for the effective RNA knockdown, the Cas13 mediated targeting strategy presented herein emphasizes the designing of gRNAs specifically targeting SS regions by utilizing structural information. Further, this strategy, in turn, can be anticipated to narrow the search space for gRNA design (by exclusively targeting SS regions) especially when lncRNAs are the targets.
The effect of epinephrine on the perfusion index during ultrasound-guided supraclavicular brachial plexus block: a randomized controlled trial
Authors: Kim Doyeon , Jeong Ji Seon , Park Min Jong , Ko Justin Sangwook 
Published: July 2020

AbstractThe perfusion index (PI) is an objective tool used to assess a successful nerve block. Epinephrine is a widely used adjuvant to local anesthetics, and it may affect PI values because of the vasoconstrictive property. The aim of this study was to investigate the influence of epinephrine on PI as an indicator of a successful block in ultrasound-guided supraclavicular brachial plexus block (SCBPB). In this randomized controlled trial, 82 adult patients underwent upper limb surgery under SCBPB were recruited between July 2018 and March 2019 in a single tertiary care center. Participants were randomly assigned to one of two groups: non-epinephrine group (n = 41) or epinephrine group (5 mcg ml−1, n = 41). The primary outcome was the comparison of the “PI ratio 10,” which was defined as the ratio of the PI 10 to the baseline. Receiver operating characteristic (ROC) curves were constructed to determine the accuracy of the PI in predicting the block success at each time interval. The PI ratio 10 was 2.7 (1.9–4.0) in non-epinephrine group and 3.3 (2.2–4.4) in epinephrine group (median difference: 0.4; 95% confidence interval [CI] − 1.1 to 0.2; P = 0.207). The ROC curves compared without group identification were not significantly different over time. The cut-off value for the PI and PI ratio at 5 min (PI ratio 5) were 7.7 (area under the ROC [AUROC]: 0.89, 95% CI 0.83–0.94) and 1.6 (AUROC: 0.94, 95% CI 0.90–0.98), respectively. The perineural epinephrine did not affect the PI following a SCBPB. The PI ratio 5 > 1.6 might be considered as a relatively accurate predictor of a successful SCBPB.Trial registration: This study was registered at the Clinical Trial Registry of Korea (https://cris.nih.go.kr. CriS No. KCT0003006).
PiDose: an open-source system for accurate and automated oral drug administration to group-housed mice
Authors: Woodard Cameron L. , Nasrallah Wissam B. , Samiei Bahram V. , Murphy Timothy H. , Raymond Lynn A. 
Published: July 2020

AbstractDrug treatment studies in laboratory mice typically employ manual administration methods such as injection or gavage, which can be time-consuming to perform over long periods and cause substantial stress in animals. These stress responses may mask or enhance treatment effects, increasing the risk of false positive or negative results and decreasing reliability. To address the lack of an automated method for drug treatment in group-housed mice, we have developed PiDose, a home-cage attached device that weighs individual animals and administers a daily dosage of drug solution based on each animal’s bodyweight through their drinking water. Group housed mice are identified through the use of RFID tagging and receive both regular water and drug solution drops by licking at a spout within the PiDose module. This system allows animals to be treated over long periods (weeks to months) in a fully automated fashion, with high accuracy and minimal experimenter interaction. PiDose is low-cost and fully open-source and should prove useful for researchers in both translational and basic research.