bluuebunny/crossref_metadata_2025_split huggingface dataset:
Reservoir computing based on a silicon microring and time multiplexing for binary and analog operations
Authors: Borghi Massimo , Biasi Stefano , Pavesi Lorenzo 
Published: August 2021

AbstractPhotonic implementations of reservoir computing (RC) promise to reach ultra-high bandwidth of operation with moderate training efforts. Several optoelectronic demonstrations reported state of the art performances for hard tasks as speech recognition, object classification and time series prediction. Scaling these systems in space and time faces challenges in control complexity, size and power demand, which can be relieved by integrated optical solutions. Silicon photonics can be the disruptive technology to achieve this goal. However, the experimental demonstrations have been so far focused on spatially distributed reservoirs, where the massive use of splitters/combiners and the interconnection loss limits the number of nodes. Here, we propose and validate an all optical RC scheme based on a silicon microring (MR) and time multiplexing. The input layer is encoded in the intensity of a pump beam, which is nonlinearly transferred to the free carrier concentration in the MR and imprinted on a secondary probe. We harness the free carrier dynamics to create a chain-like reservoir topology with 50 virtual nodes. We give proof of concept demonstrations of RC by solving two nontrivial tasks: the delayed XOR and the classification of Iris flowers. This forms the basic building block from which larger hybrid spatio-temporal reservoirs with thousands of nodes can be realized with a limited set of resources.
Foraging behavior of the sea urchin Mesocentrotus nudus exposed to conspecific alarm cues in various conditions
Authors: Chi Xiaomei , Yang Mingfang , Hu Fangyuan , Huang Xiyuan , Yu Yushi , Chang Yaqing , Wang Qingzhi , Zhao Chong 
Published: August 2021

AbstractConspecific alarm cues crushed from Mesocentrotus nudus prevent sea urchins from foraging the kelp, but do not repel them far away from the kelp. However, it remains largely unknown of whether this phenomenon was affected by conspecific alarm cues or by the attraction of the kelp. The present study found no significant difference in the duration in the danger area with or without the kelp around conspecific alarm cues. This suggests that the phenomenon is the strategy of sea urchins but not by the attraction of kelp. We found that conspecific alarm cues appearing between the kelp and sea urchins significantly affected foraging behavior of sea urchins fasted for 21 days. This indicates that conspecific alarm cues can effectively prevent fasted sea urchins from foraging the kelp. Further, there was no correlation between foraging velocity and the duration in the danger area. Pearson correlation analysis revealed no significant correlation between foraging velocity and the duration in the safety area close to different amounts of conspecific alarm cues, suggesting that conspecific alarm cues prevent sea urchins with strong foraging ability to forage. Collectively, the present results indicate that conspecific alarm cues as highly available biological barriers are cost-effective approaches to preventing overgrazing of sea urchins in the protection of kelp beds ecosystems. Notably, the present study is a short-term laboratory investigation that does not consider the complexity of natural conditions. Future studies are essential to test the present findings in the field.
Effect of skin–capsular distance on controlled attenuation parameter for diagnosing liver steatosis in patients with nonalcoholic fatty liver disease
Authors: Kimura Syunichiro , Tanaka Kenichi , Oeda Satoshi , Inoue Kaori , Inadomi Chika , Kubotsu Yoshihito , Yoshioka Wataru , Okada Michiaki , Isoda Hiroshi , Kuwashiro Takuya , Akiyama Takumi , Kurashige Aya , Oshima Ayaka , Oshima Mayumi , Matsumoto Yasue , Kawaguchi Atsushi , Anzai Keizo , Sueoka Eisaburo , Aishima Shinichi , Takahashi Hirokazu 
Published: August 2021

AbstractThe effect of the skin–capsular distance (SCD) on the controlled attenuation parameter (CAP) for diagnosis of liver steatosis in patients with nonalcoholic fatty liver disease (NAFLD) remains unclear. The SCD was measured using B-mode ultrasound, and the CAP was measured using the M probe of FibroScan®. According to the indications of the M probe, 113 patients with an SCD of ≤ 25 mm were included in the present study. The association between the SCD and CAP was investigated, and the diagnostic performance of the SCD-adjusted CAP was tested. The SCD showed the most significant positive correlation with the CAP (ρ = 0.329, p < 0.001). In the multiple regression analysis, the SCD and serum albumin concentration were associated with the CAP, independent of pathological liver steatosis. According to the multivariate analysis, two different formulas were developed to obtain the adjusted CAP using the SCD and serum albumin concentration as follows: adjusted CAP (dB/m) = CAP − (5.26 × SCD) and adjusted CAP (dB/m) = CAP − (5.35 × SCD) − (25.77 × serum albumin concentration). The area under the receiver operating characteristic curve for diagnosis of a steatosis score ≥ 2 of adjusted CAP was 0.678 and 0.684 respectively, which were significantly greater than the original CAP (0.621: p = 0.030 and p = 0.024). The SCD is associated with the CAP independent of liver steatosis. Adjustment of the CAP using the SCD improves the diagnostic performance of the CAP in NAFLD.
Inflammatory markers and risk of cardiovascular mortality in relation to diabetes status in the HUNT study
Authors: Løfblad Lena , Hov Gunhild Garmo , Åsberg Arne , Videm Vibeke 
Published: August 2021

AbstractInflammatory markers have been associated with increased risk of cardiovascular mortality in general populations. We assessed whether these associations differ by diabetes status. From a population-based cohort study (n = 62,237) we included all participants with diabetes (n = 1753) and a control group without diabetes (n = 1818). Cox regression models were used to estimate hazard ratios (HRs) with 95% confidence intervals (CI) for possible associations with cardiovascular mortality of 4 different inflammatory markers; C-reactive protein (CRP), calprotectin, neopterin and lactoferrin. During a median follow-up of 13.9 years, 728 (20.4%) died from cardiovascular disease (CVD). After adjustment for age, sex and diabetes, the associations of all inflammatory markers with risk of cardiovascular mortality were log-linear (all P ≤ 0.017 for trend) and did not differ according to diabetes status (all P ≥ 0.53 for interaction). After further adjustments for established risk factors, only CRP remained independently associated with cardiovascular mortality. HRs were 1.22 (1.12–1.32) per standard deviation higher loge CRP concentration and 1.91 (1.50–2.43) when comparing individuals in the top versus bottom quartile. The associations of CRP, calprotectin, lactoferrin and neopterin with cardiovascular mortality did not differ by diabetes, suggesting that any potential prognostic value of these markers is independent of diabetes status.
Water removal during automated peritoneal dialysis assessed by remote patient monitoring and modelling of peritoneal tissue hydration
Authors: Stachowska-Pietka Joanna , Naumnik Beata , Suchowierska Ewa , Gomez Rafael , Waniewski Jacek , Lindholm Bengt 
Published: August 2021

AbstractWater removal which is a key treatment goal of automated peritoneal dialysis (APD) can be assessed cycle-by-cycle using remote patient monitoring (RPM). We analysed ultrafiltration patterns during night APD following a dry day (APDDD; no daytime fluid exchange) or wet day (APDWD; daytime exchange). Ultrafiltration for each APD exchange were recorded for 16 days using RPM in 14 patients. The distributed model of fluid and solute transport was applied to simulate APD and to explore the impact of changes in peritoneal tissue hydration on ultrafiltration. We found lower ultrafiltration (mL, median [first quartile, third quartile]) during first and second vs. consecutive exchanges in APDDD(−61 [−148, 27], 170 [78, 228] vs. 213 [126, 275] mL; p < 0.001), but not in APDWD(81 [−8, 176], 81 [−4, 192] vs. 115 [4, 219] mL; NS). Simulations in a virtual patient showed that lower ultrafiltration (by 114 mL) was related to increased peritoneal tissue hydration caused by inflow of 187 mL of water during the first APDDDexchange. The observed phenomenon of lower ultrafiltration during initial exchanges of dialysis fluid in patients undergoing APDDDappears to be due to water inflow into the peritoneal tissue, re-establishing a state of increased hydration typical for peritoneal dialysis.
Mueller matrix imaging for collagen scoring in mice model of pregnancy
Authors: Lee Hee Ryung , Saytashev Ilyas , Du Le Vinh Nguyen , Mahendroo Mala , Ramella-Roman Jessica , Novikova Tatiana 
Published: August 2021

AbstractPreterm birth risk is associated with early softening of the uterine cervix in pregnancy due to the accelerated remodeling of collagen extracellular matrix. Studies of mice model of pregnancy were performed with an imaging Mueller polarimeter at different time points of pregnancy to find polarimetric parameters for collagen scoring. Mueller matrix images of the unstained sections of mice uterine cervices were taken at day 6 and day 18 of 19-days gestation period and at different spatial locations through the cervices. The logarithmic decomposition of the recorded Mueller matrices mapped the depolarization, linear retardance, and azimuth of the optical axis of cervical tissue. These images highlighted both the inner structure of cervix and the arrangement of cervical collagen fibers confirmed by the second harmonic generation microscopy. The statistical analysis and two-Gaussians fit of the distributions of linear retardance and linear depolarization in the entire images of cervical tissue (without manual selection of the specific regions of interest) quantified the randomization of collagen fibers alignment with gestation time. At day 18 the remodeling of cervical extracellular matrix of collagen was measurable at the external cervical os that is available for the direct optical observations in vivo. It supports the assumption that imaging Mueller polarimetry holds promise for the fast and accurate collagen scoring in pregnancy and the assessment of the preterm birth risk.
Application of RR-XGBoost combined model in data calibration of micro air quality detector
Authors: Liu Bing , Tan Xianghua , Jin Yueqiang , Yu Wangwang , Li Chaoyang 
Published: August 2021

AbstractGrid monitoring is the current development direction of atmospheric monitoring. The micro air quality detector is of great help to the grid monitoring of the atmosphere, so higher requirements are put forward for the accuracy of the micro air quality detector. This paper presents a model to calibrate the measurement data of the micro air quality detector using the monitoring data of the air quality monitoring station. The concentration of six types of air pollutants is the research object of this study to establish a calibration model for the measurement data of the micro air quality detector. The first step is to use correlation analysis to find out the main factors affecting the concentration of the six types of pollutants. The second step uses Ridge Regression (RR) to select variables, find out the factors that have significant effects on the concentration of pollutants, and give the quantitative relationship between these factors and the pollutants. Finally, the predicted value of the ridge regression model and the measurement data of the micro air quality detector are used as input variables, and the Extreme Gradient Boosting (XGBoost) algorithm is used to give the final pollutant concentration prediction model. We named the combined model of ridge regression and XGBoost algorithm RR-XGBoost model. Relative Mean Absolute Percent Error (MAPE), Mean Absolute Error (MAE), goodness of fit (R2), and Root Mean Square Error (RMSE) were used to evaluate the prediction accuracy of the RR-XGBoost model. The results show that the model is superior to some commonly used pollutant prediction methods such as random forest, support vector machine, and multilayer perceptron neural network in the evaluation of various indicators. The model not only has a good prediction effect on the training set but also on the test set, indicating that the model has good generalization ability. Using the RR-XGBoost model to calibrate the data of the micro air quality detector can make up for the shortcomings of the data monitoring accuracy of the micro air quality detector. The model plays an active role in the deployment of micro air quality detectors and grid monitoring of the atmosphere.
Characterization of the structural forces governing the reversibility of the thermal unfolding of the human acidic fibroblast growth factor
Authors: Agrawal Shilpi , Govind Kumar Vivek , Gundampati Ravi Kumar , Moradi Mahmoud , Kumar Thallapuranam Krishnaswamy Suresh 
Published: August 2021

AbstractHuman acidic fibroblast growth factor (hFGF1) is an all beta-sheet protein that is involved in the regulation of key cellular processes including cell proliferation and wound healing. hFGF1 is known to aggregate when subjected to thermal unfolding. In this study, we investigate the equilibrium unfolding of hFGF1 using a wide array of biophysical and biochemical techniques. Systematic analyses of the thermal and chemical denaturation data on hFGF1 variants (Q54P, K126N, R136E, K126N/R136E, Q54P/K126N, Q54P/R136E, and Q54P/K126N/R136E) indicate that nullification of charges in the heparin-binding pocket can significantly increase the stability of wtFGF1. Triple variant (Q54P/K126N/R136E) was found to be the most stable of all the hFGF1 variants studied. With the exception of triple variant, thermal unfolding of wtFGF1 and the other variants is irreversible. Thermally unfolded triple variant refolds completely to its biologically native conformation. Microsecond-level molecular dynamic simulations reveal that a network of hydrogen bonds and salt bridges linked to Q54P, K126N, and R136E mutations, are responsible for the high stability and reversibility of thermal unfolding of the triple variant. In our opinion, the findings of the study provide valuable clues for the rational design of a stable hFGF1 variant that exhibits potent wound healing properties.
Prognostic significance of the albumin-to-globulin ratio for advanced urothelial carcinoma treated with pembrolizumab: a multicenter retrospective study
Authors: Taguchi Satoru , Kawai Taketo , Nakagawa Tohru , Nakamura Yu , Kamei Jun , Obinata Daisuke , Yamaguchi Kenya , Kaneko Tomoyuki , Kakutani Shigenori , Tokunaga Mayuko , Uemura Yukari , Sato Yusuke , Fujimura Tetsuya , Fukuhara Hiroshi , Enomoto Yutaka , Nishimatsu Hiroaki , Takahashi Satoru , Kume Haruki 
Published: August 2021

AbstractAlthough the albumin-to-globulin ratio (AGR) is a promising biomarker, no study has investigated its prognostic significance for advanced urothelial carcinoma (UC). This study conformed to the REporting recommendations for tumor MARKer prognostic studies (REMARK) criteria. We retrospectively reviewed 176 patients with advanced UC treated with pembrolizumab between 2018 and 2020. We evaluated the associations between pretreatment clinicopathological variables, including the AGR and performance status (PS), with progression-free survival, cancer-specific survival, and overall survival. The Cox proportional hazards model was used for univariate and multivariable analyses. The AGR was dichotomized as < 0.95 and ≥ 0.95 based on receiver operating characteristic curve analysis. After excluding 26 cases with missing data from the total of 176 cases, 109 (73%) patients experienced disease progression, 75 (50%) died from UC, and 6 (4%) died of other causes (median survival = 12 months). Multivariate analyses identified PS ≥ 2 and pretreatment AGR < 0.95 as independent poor prognostic factors for all endpoints. Furthermore, a prognostic risk model incorporating these two variables achieved a relatively high concordance index for all endpoints. This is the first report to evaluate the significance of AGR in advanced UC. Pretreatment AGR < 0.95 may serve as a prognostic marker for advanced UC treated with pembrolizumab.
Implication of specific retinal cell-type involvement and gene expression changes in AMD progression using integrative analysis of single-cell and bulk RNA-seq profiling
Authors: Lyu Yafei , Zauhar Randy , Dana Nicholas , Strang Christianne E. , Hu Jian , Wang Kui , Liu Shanrun , Pan Naifei , Gamlin Paul , Kimble James A. , Messinger Jeffrey D. , Curcio Christine A. , Stambolian Dwight , Li Mingyao 
Published: August 2021

AbstractAge‐related macular degeneration (AMD) is a blinding eye disease with no unifying theme for its etiology. We used single-cell RNA sequencing to analyze the transcriptomes of ~ 93,000 cells from the macula and peripheral retina from two adult human donors and bulk RNA sequencing from fifteen adult human donors with and without AMD. Analysis of our single-cell data identified 267 cell-type-specific genes. Comparison of macula and peripheral retinal regions found no cell-type differences but did identify 50 differentially expressed genes (DEGs) with about 1/3 expressed in cones. Integration of our single-cell data with bulk RNA sequencing data from normal and AMD donors showed compositional changes more pronounced in macula in rods, microglia, endothelium, Müller glia, and astrocytes in the transition from normal to advanced AMD. KEGG pathway analysis of our normal vs. advanced AMD eyes identified enrichment in complement and coagulation pathways, antigen presentation, tissue remodeling, and signaling pathways including PI3K-Akt, NOD-like, Toll-like, and Rap1. These results showcase the use of single-cell RNA sequencing to infer cell-type compositional and cell-type-specific gene expression changes in intact bulk tissue and provide a foundation for investigating molecular mechanisms of retinal disease that lead to new therapeutic targets.
MyD88-dependent BCG immunotherapy reduces tumor and regulates tumor microenvironment in bladder cancer murine model
Authors: de Queiroz Nina M. G. P. , Marinho Fabio V. , de Araujo Ana Carolina V. S. C. , Fahel Julia S. , Oliveira Sergio C. 
Published: August 2021

AbstractBacillus Calmette-Guerin (BCG) is the only FDA approved first line therapy for patients with nonmuscle invasive bladder cancer. The purpose of this study is to better understand the role of innate immune pathways involved in BCG immunotherapy against murine bladder tumor. We first characterized the immunological profile induced by the MB49 mouse urothelial carcinoma cell line. MB49 cells were not able to activate an inflammatory response (TNF-α, IL-6, CXCL-10 or IFN-β) after the stimulus with different agonists or BCG infection, unlike macrophages. Although MB49 cells are not able to induce an efficient immune response, BCG treatment could activate other cells in the tumor microenvironment (TME). We evaluated BCG intratumoral treatment in animals deficient for different innate immune molecules (STING−/−, cGAS−/−, TLR2−/−, TLR3−/−, TLR4−/−, TLR7−/−, TLR9−/−, TLR3/7/9−/−, MyD88−/−, IL-1R−/−, Caspase1/11−/−, Gasdermin-D−/− and IFNAR−/−) using the MB49 subcutaneous mouse model. Only MyD88−/− partially responded to BCG treatment compared to wild type (WT) mice, suggesting a role played by this adaptor molecule. Additionally, BCG intratumoral treatment regulates cellular infiltrate in TME with an increase of inflammatory macrophages, neutrophils and CD8+ T lymphocytes, suggesting an immune response activation that favors tumor remission in WT mice but not in MyD88−/−. The experiments using MB49 cells infected with BCG and co-cultured with macrophages also demonstrated that MyD88 is essential for an efficient immune response. Our data suggests that BCG immunotherapy depends partially on the MyD88-related innate immune pathway.
Comparative analysis of some evolutionary-based models in optimization of dam reservoirs operation
Authors: Sharifi Mohammad Reza , Akbarifard Saeid , Qaderi Kourosh , Madadi Mohamad Reza 
Published: August 2021

AbstractDeriving optimal operation policies for multi-reservoir systems is a complex engineering problem. It is necessary to employ a reliable technique to efficiently solving such complex problems. In this study, five recently-introduced robust evolutionary algorithms (EAs) of Harris hawks optimization algorithm (HHO), seagull optimization algorithm (SOA), sooty tern optimization algorithm (STOA), tunicate swarm algorithm (TSA) and moth swarm algorithm (MSA) were employed, for the first time, to optimal operation of Halilrood multi-reservoir system. This system includes three dams with parallel and series arrangements simultaneously. The results of mentioned algorithms were compared with two well-known methods of genetic algorithm (GA) and particle swarm optimization (PSO) algorithm. The objective function of the optimization model was defined as the minimization of total deficit over 223 months of reservoirs operation. Four performance criteria of reliability, resilience, vulnerability and sustainability were used to compare the algorithms’ efficiency in optimization of this multi-reservoir operation. It was observed that the MSA algorithm with the best value of objective function (6.96), the shortest CPU run-time (6738 s) and the fastest convergence rate (< 2000 iterations) was the superior algorithm, and the HHO algorithm placed in the next rank. The GA, and the PSO were placed in the middle ranks and the SOA, and the STOA placed in the lowest ranks. Furthermore, the comparison of utilized algorithms in terms of sustainability index indicated the higher performance of the MSA in generating the best operation scenarios for the Halilrood multi-reservoir system. The application of robust EAs, notably the MSA algorithm, to improve the operation policies of multi-reservoir systems is strongly recommended to water resources managers and decision-makers.
A CpG island promoter drives the CXXC5 gene expression
Authors: Yaşar Pelin , Kars Gizem , Yavuz Kerim , Ayaz Gamze , Oğuztüzün Çerağ , Bilgen Ecenaz , Suvacı Zeynep , Çetinkol Özgül Persil , Can Tolga , Muyan Mesut 
Published: August 2021

AbstractCXXC5 is a member of the zinc-finger CXXC family that binds to unmethylated CpG dinucleotides. CXXC5 modulates gene expressions resulting in diverse cellular events mediated by distinct signaling pathways. However, the mechanism responsible for CXXC5 expression remains largely unknown. We found here that of the 14 annotated CXXC5 transcripts with distinct 5′ untranslated regions encoding the same protein, transcript variant 2 with the highest expression level among variants represents the main transcript in cell models. The DNA segment in and at the immediate 5′-sequences of the first exon of variant 2 contains a core promoter within which multiple transcription start sites are present. Residing in a region with high G–C nucleotide content and CpG repeats, the core promoter is unmethylated, deficient in nucleosomes, and associated with active RNA polymerase-II. These findings suggest that a CpG island promoter drives CXXC5 expression. Promoter pull-down revealed the association of various transcription factors (TFs) and transcription co-regulatory proteins, as well as proteins involved in histone/chromatin, DNA, and RNA processing with the core promoter. Of the TFs, we verified that ELF1 and MAZ contribute to CXXC5 expression. Moreover, the first exon of variant 2 may contain a G-quadruplex forming region that could modulate CXXC5 expression.