bluuebunny/crossref_metadata_2025_split huggingface dataset:
Modeling a population of retinal ganglion cells with restricted Boltzmann machines
Authors: Volpi Riccardo , Zanotto Matteo , Maccione Alessandro , Di Marco Stefano , Berdondini Luca , Sona Diego , Murino Vittorio 
Published: October 2020

AbstractThe retina is a complex circuit of the central nervous system whose aim is to encode visual stimuli prior the higher order processing performed in the visual cortex. Due to the importance of its role, modeling the retina to advance in interpreting its spiking activity output is a well studied problem. In particular, it has been shown that latent variable models can be used to model the joint distribution of Retinal Ganglion Cells (RGCs). In this work, we validate the applicability of Restricted Boltzmann Machines to model the spiking activity responses of a large a population of RGCs recorded with high-resolution electrode arrays. In particular, we show that latent variables can encode modes in the RGC activity distribution that are closely related to the visual stimuli. In contrast to previous work, we further validate our findings by comparing results associated with recordings from retinas under normal and altered encoding conditions obtained by pharmacological manipulation. In these conditions, we observe that the model reflects well-known physiological behaviors of the retina. Finally, we show that we can also discover temporal patterns, associated with distinct dynamics of the stimuli.
Effects of sodium citrate on the structure and microbial community composition of an early-stage multispecies biofilm model
Authors: Yao Yuan , Pu Yang , Ngan Wing Yui , Kan Karin , Pan Jie , Li Meng , Habimana Olivier 
Published: October 2020

AbstractIn recent years, most biofilm studies have focused on fundamental investigations using multispecies biofilm models developed preferentially in simulated naturally occurring low-nutrient medium than in artificial nutrient-rich medium. Because biofilm development under low-nutrient growth media is slow, natural media are often supplemented with an additional carbon source to increase the rate of biofilm formation. However, there are knowledge gaps in interpreting the effects of such supplementation on the resulting biofilm in terms of structure and microbial community composition. We investigated the effects of supplementation of a simulated freshwater medium with sodium citrate on the resulting structure, bacterial community composition, and microbial network interactions of an early-stage multispecies biofilm model. Qualitative and quantitative analyses of acquired confocal laser scanning microscopy data confirmed that sodium citrate supplementation distinctly increased biofilm biomass. Sequencing data revealed that the microbial community structure of biofilms grown in sodium citrate-supplemented conditions was characterized with increased relative abundance and dominance of Proteobacteria compared with that of biofilms grown in sodium citrate-free conditions. Our findings suggest that the supplementation of a low-nutrient medium with a carbon source in experiments involving multispecies biofilms may lead to structural and compositional biases of the microbial community, causing changes in biofilm phenotype.
Beyond MHz image recordings using LEDs and the FRAME concept
Authors: Kornienko Vassily , Kristensson Elias , Ehn Andreas , Fourriere Antoine , Berrocal Edouard 
Published: October 2020

AbstractMany important scientific questions in physics, chemistry and biology rely on high-speed optical imaging techniques for their investigations. These techniques are either passive, relying on the rapid readout of photoactive elements, or active, relying on the illumination properties of specially designed pulse trains. Currently, MHz imaging speeds are difficult to realize; passive methods, being dictated by electronics, cause the unification of high spatial resolution with high frame rates to be very challenging, while active methods rely on expensive and complex hardware such as femto- and picosecond laser sources. Here we present an accessible temporally resolved imaging system for shadowgraphy based on multiplexed LED illumination that is capable of producing four images at MHz frame rates. Furthermore as the LEDs are independent of each other, any light burst configuration can be obtained, allowing for instance the simultaneous determination of low- and high speed events in parallel. To the best of the authors’ knowledge, this is the fastest high speed imaging system that does not rely on pulsed lasers or fast detectors, in this case reaching up to 4.56 MHz.
Using Bayesian spatial models to map and to identify geographical hotspots of multidrug-resistant tuberculosis in Portugal between 2000 and 2016
Authors: Oliveira Olena , Ribeiro Ana Isabel , Krainski Elias Teixeira , Rito Teresa , Duarte Raquel , Correia-Neves Margarida 
Published: October 2020

AbstractMultidrug-resistant tuberculosis (MDR-TB) is a major threat to the eradication of tuberculosis. TB control strategies need to be adapted to the necessities of different countries and adjusted in high-risk areas. In this study, we analysed the spatial distribution of the MDR- and non-MDR-TB cases across municipalities in Continental Portugal between 2000 and 2016. We used Bayesian spatial models to estimate age-standardized notification rates and standardized notification ratios in each area, and to delimitate high- and low-risk areas, those whose standardized notification ratio is significantly above or below the country’s average, respectively. The spatial distribution of MDR- and non-MDR-TB was not homogeneous across the country. Age-standardized notification rates of MDR-TB ranged from 0.08 to 1.20 and of non-MDR-TB ranged from 7.73 to 83.03 notifications per 100,000 population across the municipalities. We identified 36 high-risk areas for non-MDR-TB and 8 high-risk areas for MDR-TB, which were simultaneously high-risk areas for non-MDR-TB. We found a moderate correlation (ρ = 0.653; 95% CI 0.457–0.728) between MDR- and non-MDR-TB standardized notification ratios. We found heterogeneity in the spatial distribution of MDR-TB across municipalities and we identified priority areas for intervention against TB. We recommend including geographical criteria in the application of molecular drug resistance to provide early MDR-TB diagnosis, in high-risk areas.
Grain refinement of commercially pure aluminum with addition of Ti and Zr elements based on crystallography orientation
Authors: Chen Zhongwei , Yan Kang 
Published: October 2020

AbstractThe edge-to-edge matching (E2EM) model and electron back-scatter diffraction (EBSD) technique are used to explore the grain refinement mechanism of commercially pure Al through the addition of Ti and Zr elements. EBSD results show that there are favorable crystallography orientation relationships (ORs) between both Al3Ti and Al3Zr particles with α-Al matrix. Due to these ORs Al3Ti and Al3Zr particles act as the heterogeneous nucleation site during solidification nucleation of Al–Ti and Al–Zr alloys, respectively. Furthermore, both Al3Ti and Al3Zr particles have small values of interplanar spacing mismatch and interatomic spacing misfit with respect to α-Al matrix by using E2EM. It shows that micro-addition of Ti and Zr element is efficient heterogeneous nucleation refiner in commercial purity Al or Al alloys. Besides, there may be some other mechanisms in grain refinement of Al alloys with addition of Ti grain refiner.
Potential mechanisms involving the immobilization of Cd, As and Cr during swine manure composting
Authors: Guo Hao-Nan , Wang Li-Xia , Liu Hong-Tao 
Published: October 2020

AbstractThis study aims to investigate the relationship between key physicochemical parameters related to composting process and bioavailability of Cd, As and Cr during swine manure composting through regulating different initial carbon to nitrogen (C/N) ratios (15:1, 20:1, 25:1) and bulking agent types (straw, green waste). Results showed that higher initial C/N ratio of 20:1 or 25:1 and straw as bulking agent were optimal to reduce the bioavailability of Cd, As and Cr (62.4%, 20.6% and 32.2% reduction, respectively). Redundancy analysis implied that the bioavailability of Cd was significantly associated with total phosphorus and total nitrogen, deducing the formation of phosphate precipitation and biosorption might participated in the reaction process, while that of As and Cr were mainly influenced by organic matter (OM), cation exchange capacity (CEC) and OM, CEC, electric conductivity, respectively. A total of 48.5%, 64.6% and 62.2% of Cd, As and Cr redistribution information could be explained by the above parameters. Further correlation analysis revealed that bioavailable As and Cr were negatively correlated with humic acid to fulvic acid ratio. In summary, this study confirms that the mechanisms of phosphate precipitation, biosorption and humification played critical role in reducing Cd, As and Cr bioavailability during swine manure composting.
Benefits of glioma resection in the corpus callosum
Authors: Forster Marie-Therese , Behrens Marion , Lortz Irina , Conradi Nadine , Senft Christian , Voss Martin , Rauch Maximilian , Seifert Volker 
Published: October 2020

AbstractDue to anticipated postoperative neuropsychological sequelae, patients with gliomas infiltrating the corpus callosum rarely undergo tumor resection and mostly present in a poor neurological state. We aimed at investigating the benefit of glioma resection in the corpus callosum, hypothesizing neuropsychological deficits were mainly caused by tumor presence. Between 01/2017 and 1/2020, 21 patients who underwent glioma resection in the corpus callosum were prospectively enrolled into this study. Neuropsychological function was assessed preoperatively, before discharge and after 6 months. Gross total tumor resection was possible in 15 patients, and in 6 patients subtotal tumor resection with a tumor reduction of 97.7% could be achieved. During a median observation time of 12.6 months 9 patients died from glioblastoma after a median of 17 months. Preoperatively, all cognitive domains were affected in up to two thirds of patients, who presented a median KPS of 100% (range 60–100%). After surgery, the proportion of impaired patients increased in all neurocognitive domains. Most interestingly, after 6 months, significantly fewer patients showed impairments in attention, executive functioning, memory and depression, which are domains considered crucial for everyday functionality. Thus, the results of our study strongly support our hypothesis that in patients with gliomas infiltrating the corpus callosum the benefit of tumor resection might outweigh morbidity.
Predictive factors of selective mineralocorticoid receptor antagonist treatment in chronic central serous chorioretinopathy
Authors: Gergely Róbert , Kovács Illés , Récsán Zsuzsanna , Sándor Gábor László , Czakó Cecília , Nagy Zoltán Zsolt , Ecsedy Mónika 
Published: October 2020

AbstractTo compare the macular morphology of good and poor responders to eplerenone treatment in chronic central serous chorioretinopathy (CSCR) patients. Thirty eyes of 29 patients with chronic CSCR were treated with 50 mg/day oral eplerenone and followed up for 1 year. The integrity of outer retinal layers at baseline was assessed using optical coherence tomography. Patients who showed complete resolution of subretinal fluid at 1 year were assigned to the good responder group (Group 1), whilst those who showed moderate or no resolution were classified as poor responders (Group 2). Ellipsoid zone interruption, ELM interruption and hyperreflective foci in outer segment (OS) and outer nuclear layer (ON layer) was significantly more frequent in Group 2 than in Group 1 (p < 0.05 for all parameteres). Outer segment elongation was significantly more frequently seen in Group 1 than in Group 2 (p < 0.05) Multivariable regression analysis showed that intact ellipsoid zone at baseline is an independent predictor of good therapeutic response, with an odds ratio of 26.00 (95% CI 3.69–183.45; p = 0.001) after controlling for the effect of hyperreflective foci and ELM integrity. There is higher chance of the resolution of subretinal fluid after eplerenone treatment in CSCR patients with intact outer retinal layers at baseline. Baseline morphologic evaluation of the outer retinal layers on OCT scans can be useful in predicting the response to mineralocorticoid antagonist therapy in these patients.
Development of an antibody-dependent cellular cytotoxicity reporter assay for measuring anti-Middle East Respiratory Syndrome antibody bioactivity
Authors: Cao Junxia , Wang Lan , Yu Chuanfei , Wang Kaiqin , Wang Wenbo , Yan Jinghua , Li Yan , Yang Yalan , Wang Xiaomin , Wang Junzhi 
Published: October 2020

AbstractMiddle East Respiratory Syndrome coronavirus (MERS-CoV) is a highly virulent pathogen that causes Middle East Respiratory Syndrome (MERS). Anti-MERS-CoV antibodies play an integral role in the prevention and treatment against MERS-CoV infections. Bioactivity is a key quality attribute of therapeutic antibodies, and high accuracy and precision are required. The major methods for evaluating the antiviral effect of antiviral antibodies include neutralization assays using live viruses or pseudoviruses are highly variable. Recent studies have demonstrated that the antibody-dependent cellular cytotoxicity (ADCC) activity of antiviral antibodies is more consistent with the virus clearance effect in vivo than neutralization activity. However, no reports evaluating the ADCC activity of anti-MERS antibodies have been published to date. Here, we describe the development of a robust and reliable cell-based reporter gene assay for the determination of ADCC activity of anti-MERS antibodies using 293T/MERS cells stably expressing the spike protein of MERS-CoV (MERS-S) as target cells and the engineered Jurkat/NFAT-luc/FcγRIIIa stably expressing FcγRIIIA and NFAT reporter gene as effector cells. According to the ICH-Q2 analytical method guidelines, we carefully optimized the experimental conditions and assessed the performance of our assay. In addition, we found that the ADCC activity of afucosylated anti-MERS antibodies is higher than their fucosylated counterparts. The establishment of this ADCC determination system provides a novel method for evaluating the bioactivity of anti-MERS antibodies and improving ADCC activity through modification of N-glycosylation of the Fc segment.
Predictive factors for effective selection of Interleukin-6 inhibitor and tumor necrosis factor inhibitor in the treatment of rheumatoid arthritis
Authors: Hayashi Shinya , Matsubara Tsukasa , Fukuda Koji , Funahashi Keiko , Hashimoto Marowa , Maeda Toshihisa , Kamenaga Tomoyuki , Takashima Yoshinori , Matsumoto Tomoyuki , Niikura Takahiro , Kuroda Ryosuke 
Published: October 2020

AbstractTreatment of rheumatoid arthritis (RA) is aimed at long-term remission and inhibition of joint destruction by different biologic drugs. However, the choice of a particular biologic agent based on individual cases of RA remains unestablished. Interleukin-6 (IL-6) inhibitor and tumor necrosis factor (TNF) inhibitor are common biologics used for the treatment of RA. This study aimed to investigate predictive factors for effective selection of tocilizumab (IL-6 inhibitor) and etanercept (TNF inhibitor) in patients with RA. This is a retrospective cohort study. The 196 patients analyzed in this study were divided into four groups: tocilizumab treatment as the first biologic group (TCZ first, 42 patients), tocilizumab as second/ third biologic group (TCZ second, 34 patients), etanercept as the first biologic group (ETN first, 103 patients) and etanercept as second/third group (ETN second, 17 patients). Visual analog scale (VAS), clinical disease activity index (CDAI), and modified health assessment questionnaire (mHAQ) scores at the initiation of biologic treatment and after 6 months of tocilizumab and etanercept therapy were measured and compared to clinical parameters and radiographical parameters among the four groups. CRP, MMP-3, VAS, CDAI, and HAQ were improved after 6 months of treatment in all groups. Improvement of clinical outcomes was correlated with CRP value, duration of RA, and Sharp scores at the initiation of treatment. Multivariate analysis demonstrated improvement in CDAI was significantly associated with the yearly progression of erosion according to the Sharp score in TCZ first group (OR, 1.5; 95% CI, 1.03–2.07) and was negatively associated with the duration of RA (OR, 0.49; 95% CI, 0.29–0.86) at the initiation of treatment with ETN first group. We identified the predictive factors for effective selection of tocilizumab and etanercept treatment and established the effectiveness of tocilizumab for the patients with rapid progressive joint erosion and etanercept for the early administration from diagnosis of RA.
Epenthetic Vowels and Phonemic Vowels: Same or Different?
Authors: Akbari Christina , Aoyama Katsura 
Published: October 2020

PurposeThis study was designed to further investigate epenthetic vowels produced by Persian second language speakers of English. Specifically, the purpose was to compare epenthetic and phonemic vowels to determine if acoustic differences existed or if the epenthetic vowels were quantitative “copies” of their phonemic counterparts.MethodTwenty Persian speakers each produced 120 target words. The target words were composed of two different double cluster compositions (obstruent + glide and obstruent + liquid) as well as obstruent + liquid triple clusters and obstruent + glide triple cluster combinations. The target words occurred in a phonetic environment that was either preceded by a consonant /t/ or occurred in isolation. This resulted in 2400 tokens. The tokens underwent Linear Predictive Coding to determine the F1 and F2 formant measurements as well as the durations of the epenthetic and phonemic vowels. Formants are the resonance of the vocal tract. F1 is the lowest-frequency formant while F2 is the next highest (Kent & Read, 2002). Linear Predictive Coding allows for the acoustic signal to be represented spectrally for analysis.ResultsA total of 236 epenthetic voamp'wels and their phonemic counterparts were acoustically analyzed. The phonemic vowels were found to be significantly longer than the epenthetic vowels. The epenthetic vowels were also found to have significantly lower F1 values. As a group, the mean F2 values were not significantly different from the F2 values of the phonemic vowels. However, significant differences in F2 values were found when specific vowel comparisons were made.ConclusionsThe data indicate that prothetic epenthetic vowels are not copies of the phonemic vowels that they precede. They differ quantitatively in terms of durations, F1, and F2 values. The findings of this study coincide with the findings of other researchers concerning the acoustic characteristics of anaptyctic epenthetic vowels. These results indicate similarities between prothetic and anaptyctic epenthetic vowels.
Reading Outcomes in Elementary School–Age Children With Hearing Loss Who Use Listening and Spoken Language: A Preliminary Report
Authors: Bharadwaj Sneha V. , Barlow Whitney 
Published: October 2020

PurposeThis study examined reading outcomes and a comprehensive set of linguistic and cognitive factors considered to be associated with reading outcomes in children with hearing loss who use hearing aids or cochlear implants.MethodSeventeen children with bilateral, prelingual hearing loss who use listening and spoken language and attended Grades 3–5 at a private oral school for the deaf participated in this study. Children were administered 13 subtests from norm-referenced tests pertaining to reading outcomes (reading comprehension and decoding), linguistic factors (vocabulary, background information, literal inferencing, nonliteral inferencing, and grammatical knowledge), and cognitive factors (verbal working memory, short-term memory, phonological short-term memory, and analytical reasoning).ResultsPerformance of children with hearing loss was within normal ranges when compared to the normative means on all factors assessed except for nonword repetition. Furthermore, the performance of children with cochlear implants was comparable to that of the hearing aid users on all measures except for nonword repetition. Decoding was positively correlated with grammatical knowledge, analytical reasoning, and nonword repetition, whereas reading comprehension was positively correlated with grammatical knowledge, analytical reasoning, and inferencing.ConclusionsPreliminary findings from this study suggest that elementary school–age children with hearing loss demonstrated positive outcomes with respect to reading outcomes and other factors assessed except for the nonword repetition task. Findings suggest that a nonword repetition task may be used to flag children with hearing loss who may experience difficulties with decoding. Given that grammatical knowledge and analytical reasoning showed moderate-to-moderately strong correlation with both reading outcome measures, it is recommended that multicomponent reading intervention programs for elementary school–age children with hearing loss incorporate explicit instruction in these domains.
Tango of celestial dancers: A sample of detached eclipsing binary systems containingg-mode pulsating components
Authors: Sekaran S. , Tkachenko A. , Abdul-Masih M. , Prša A. , Johnston C. , Huber D. , Murphy S. J. , Banyard G. , Howard A. W. , Isaacson H. , Bowman D. M. , Aerts C. 
Published: October 2020

Context.Eclipsing binary systems with components that pulsate in gravity modes (gmodes) allow for simultaneous and independent constraints of the chemical mixing profiles of stars. The high precision of the dynamical masses and radii as well as the imposition of identical initial chemical compositions and equivalent ages provide strong constraints during the modelling ofg-mode period-spacing patterns.Aims.We aim to assemble a sample ofg-mode pulsators in detached eclipsing binaries with the purpose of finding good candidates for future evolutionary and asteroseismic modelling. In addition, we present a case study of the eclipsing binary KIC9850387, identified as our most promising candidate, and detail the results of the observational spectroscopic, photometric, and asteroseismic analysis of the system.Methods.We selected all of the detached eclipsing binaries in theKeplereclipsing binary catalogue withKeplerInput Catalogue (KIC) temperatures between 6000 K and 10 000 K, and performed a visual inspection to determine the presence and density ofgmodes, and the presence ofg-mode period-spacing patterns in their frequency spectra. We then characterised our sample based on theirg-mode pulsational parameters and binary and atmospheric parameters. A spectroscopic follow-up of our most promising candidate was then performed, and the orbital elements of the system were extracted. We then performed spectral disentangling followed by atmospheric modelling and abundance analysis for the primary star. We utilised an iterative approach to simultaneously optimise the pulsational and eclipse models, and subsequently performed an analysis of the pressure- (p-) andg-mode pulsational frequencies.Results.We compiled a sample of 93Keplereclipsing binary stars withg-mode pulsating components and identified clearg-mode period-spacing patterns in the frequency spectra of seven of these systems. We also identified 11 systems that contained hybridp- andg-mode pulsators. We found that theg-mode pulsational parameters and the binary and atmospheric parameters of our sample are weakly correlated at best, as expected for detached main-sequence binaries. We find that the eclipsing binary KIC9850387 is a double-lined spectroscopic binary in a near-circular orbit with a hybridp- andg-mode pulsating primary withMp= 1.66−0.01+0.01M⊙andRp= 2.154−0.004+0.002R⊙, and a solar-like secondary withMs= 1.062−0.005+0.003M⊙andRs= 1.081−0.002+0.003R⊙. We findℓ = 1 andℓ = 2 period-spacing patterns in the frequency spectrum of KIC9850387 spanning more than ten radial orders each, which will allow for stringent constraints of stellar structure during future asteroseismic modelling.