bluuebunny/crossref_metadata_2025_split huggingface dataset:
Inheritance of chloroplast and mitochondrial genomes in cucumber revealed by four reciprocal F1 hybrid combinations
Authors: Park Hyun-Seung , Lee Won Kyung , Lee Sang-Choon , Lee Hyun Oh , Joh Ho Jun , Park Jee Young , Kim Sunggil , Song Kihwan , Yang Tae-Jin 
Published: January 2021

AbstractBoth genomes in chloroplasts and mitochondria of plant cell are usually inherited from maternal parent, with rare exceptions. To characterize the inheritance patterns of the organelle genomes in cucumber (Cucumis sativus var. sativus), two inbred lines and their reciprocal F1 hybrids were analyzed using an next generation whole genome sequencing data. Their complete chloroplast genome sequences were de novo assembled, and a single SNP was identified between the parental lines. Two reciprocal F1 hybrids have the same chloroplast genomes with their maternal parents. Meanwhile, 292 polymorphic sites were identified between mitochondrial genomes of the two parental lines, which showed the same genotypes with their paternal parents in the two reciprocal F1 hybrids, without any recombination. The inheritance patterns of the chloroplast and mitochondria genomes were also confirmed in four additional cucumber accessions and their six reciprocal F1 hybrids using molecular markers derived from the identified polymorphic sites. Taken together, our results indicate that the cucumber chloroplast genome is maternally inherited, as is typically observed in other plant species, whereas the large cucumber mitochondrial genome is paternally inherited. The combination of DNA markers derived from the chloroplast and mitochondrial genomes will provide a convenient system for purity test of F1 hybrid seeds in cucumber breeding.
A correlation propagation model for nonlinear fourier transform of second order solitons
Authors: Zhang Wen Qi , Chan Terence H. , Afshar V. Shahraam 
Published: January 2021

AbstractInverse scattering transform or nonlinear Fourier transform (NFT) has been proposed for optic communication to increase channel capacity beyond the well known Shannon limit. Within NFT, solitons, as discrete outputs of the transform, can be a type of resource to carry information. Second-order solitons as the most basic higher order solitons show correlations among their parameters in the nonlinear Fourier domain as they propagate along a fibre. In this work, we report, for the first time, a correlation propagation model for second-order soliton pulses in the nonlinear Fourier domain. The model can predict covariance matrices of soliton pulses at any propagation distance using only the covariance matrices calculated at the input of the fibre with different phases in the nonlinear Fourier domain without the need of propagating the pulses.
Socioeconomic factors predicting outcome in surgically treated carpal tunnel syndrome: a national registry-based study
Authors: Zimmerman Malin , Hall Evelina , Carlsson Katarina Steen , Nyman Erika , Dahlin Lars B. 
Published: January 2021

AbstractThe study aimed to investigate socioeconomic factors in patients with carpal tunnel syndrome (CTS) and to evaluate their impact on outcome following open carpal tunnel release (OCTR). Data from the National Quality Register for Hand Surgery were combined with socioeconomic data (marital status, education level, earnings, migrant status, occupation, sick leave, unemployment, and social assistance) from Statistics Sweden to evaluate OCTRs performed from 2010 to 2016 (total 10,746 OCTRs). Patients completed QuickDASH (short version of Disabilities of Arm, Shoulder and Hand) questionnaires preoperatively (n = 3597) and at three (n = 2824) and 12 months (n = 2037) postoperatively. The effect of socioeconomic factors on QuickDASH scores was analyzed with linear regression analysis. Socioeconomically deprived patients scored higher on the QuickDASH on all occasions than patients with higher socioeconomic status. Being widowed, having a low education level, low earnings, immigrant status, frequent sick leave and dependence on social assistance all increased the postoperative QuickDASH score at 12 months. The change in total score for QuickDASH between preoperative and 12 months postoperatively did not vary between the groups. We conclude that such factors as being widowed, having a lower education level, low earnings, immigrant status, frequent sick leave and social assistance dependence are associated with more symptoms both before and after OCTR for CTS, but these factors do not affect the relative improvement in QuickDASH.
Quantitative imaging and automated fuel pin identification for passive gamma emission tomography
Authors: Fang Ming , Altmann Yoann , Della Latta Daniele , Salvatori Massimiliano , Di Fulvio Angela 
Published: January 2021

AbstractCompliance of member States to the Treaty on the Non-Proliferation of Nuclear Weapons is monitored through nuclear safeguards. The Passive Gamma Emission Tomography (PGET) system is a novel instrument developed within the framework of the International Atomic Energy Agency (IAEA) project JNT 1510, which included the European Commission, Finland, Hungary and Sweden. The PGET is used for the verification of spent nuclear fuel stored in water pools. Advanced image reconstruction techniques are crucial for obtaining high-quality cross-sectional images of the spent-fuel bundle to allow inspectors of the IAEA to monitor nuclear material and promptly identify its diversion. In this work, we have developed a software suite to accurately reconstruct the spent-fuel cross sectional image, automatically identify present fuel rods, and estimate their activity. Unique image reconstruction challenges are posed by the measurement of spent fuel, due to its high activity and the self-attenuation. While the former is mitigated by detector physical collimation, we implemented a linear forward model to model the detector responses to the fuel rods inside the PGET, to account for the latter. The image reconstruction is performed by solving a regularized linear inverse problem using the fast-iterative shrinkage-thresholding algorithm. We have also implemented the traditional filtered back projection (FBP) method based on the inverse Radon transform for comparison and applied both methods to reconstruct images of simulated mockup fuel assemblies. Higher image resolution and fewer reconstruction artifacts were obtained with the inverse-problem approach, with the mean-square-error reduced by 50%, and the structural-similarity improved by 200%. We then used a convolutional neural network (CNN) to automatically identify the bundle type and extract the pin locations from the images; the estimated activity levels finally being compared with the ground truth. The proposed computational methods accurately estimated the activity levels of the present pins, with an associated uncertainty of approximately 5%.
Host-directed therapy in foals can enhance functional innate immunity and reduce severity of Rhodococcus equi pneumonia
Authors: Bordin Angela I. , Cohen Noah D. , Giguère Steve , Bray Jocelyne M. , Berghaus Londa J. , Scott Brenton , Johnson Rena , Hook Magnus 
Published: January 2021

AbstractPneumonia caused by the intracellular bacterium Rhodococcus equi is an important cause of disease and death in immunocompromised hosts, especially foals. Antibiotics are the standard of care for treating R. equi pneumonia in foals, and adjunctive therapies are needed. We tested whether nebulization with TLR agonists (PUL-042) in foals would improve innate immunity and reduce the severity and duration of pneumonia following R. equi infection. Neonatal foals (n = 48) were nebulized with either PUL-042 or vehicle, and their lung cells infected ex vivo. PUL-042 increased inflammatory cytokines in BAL fluid and alveolar macrophages after ex vivo infection with R. equi. Then, the in vivo effects of PUL-042 on clinical signs of pneumonia were examined in 22 additional foals after intrabronchial challenge with R. equi. Foals infected and nebulized with PUL-042 or vehicle alone had a shorter duration of clinical signs of pneumonia and smaller pulmonary lesions when compared to non-nebulized foals. Our results demonstrate that host-directed therapy can enhance neonatal immune responses against respiratory pathogens and reduce the duration and severity of R. equi pneumonia.
Theoretical interpretation of drivers’ gaze strategy influenced by optical flow
Authors: Okafuji Yuki , Fukao Takanori 
Published: January 2021

AbstractDriver analysis, particularly revealing where drivers gaze, is a key factor in understanding drivers’ perception. Several studies have examined drivers’ gaze behavior and the two main hypotheses that have been developed are Tangent Point (TP) and Future Path Point (FP). TP is a point on the inner side of the lane, where the driver’s gaze direction becomes tangential with the lane edge. FP is an arbitrary single point on the ideal future path for an individual driver on the road. The location of this single point is dependent on the individual driver. While these gaze points have been verified and discussed by various psychological experiments, it is unclear why drivers gaze at these points. Therefore, in this study, we used optical flow theory to understand drivers’ gaze strategy. Optical flow theory is a method to quantify the extent to which drivers can perceive the future path of the vehicle. The results of numerical simulations demonstrated that optical flow theory can potentially estimate drivers’ gaze behavior. We also conducted an experiment in which the observed driver gaze behavior was compared to calculated gaze strategy based on optical flow theory. The experimental results demonstrate that drivers’ gaze can be estimated with an accuracy of 70.8% and 65.1% on circular and straight paths, respectively. Thus, these results suggest that optical flow theory can be a determining factor in drivers’ gaze strategy.
Early laparoscopic cholecystectomy after percutaneous transhepatic gallbladder drainage for acute cholecystitis
Authors: Lyu Yunxiao , Li Ting , Wang Bin , Cheng Yunxiao 
Published: January 2021

AbstractThere is no consensus on the optimal timing of laparoscopic cholecystectomy (LC) after percutaneous transhepatic gallbladder drainage (PTGBD) for patients with acute cholecystitis (AC). We retrospectively evaluated patients who underwent LC after PTGBD between 1 February 2016 and 1 February 2020. We divided patients into three groups according to the interval time between PTGBD and LC as follows: Group I (within 1 week), (Group II, 1 week to 1 month), and Group III (> 1 month) and analyzed patients’ perioperative outcomes. We enrolled 100 patients in this study (Group I, n = 22; Group II, n = 30; Group III, n = 48). We found no significant difference between the groups regarding patients’ baseline characteristics and no significant difference regarding operation time and estimated blood loss (p = 0.69, p = 0.26, respectively). The incidence of conversion to open cholecystectomy was similar in the three groups (p = 0.37), and we found no significant difference regarding postoperative complications (p = 0.987). Group I had shorter total hospital stays and medical costs (p = 0.005, p < 0.001, respectively) vs Group II and Group III. Early LC within 1 week after PTGBD is safe and effective, with comparable intraoperative outcomes, postoperative complications, and conversion rates to open cholecystectomy. Furthermore, early LC could decrease postoperative length of hospital stay and medical costs.
Correlation of surface-enhanced Raman spectroscopic fingerprints of kidney transplant recipient urine with kidney function parameters
Authors: Huang Zhongli , Feng Shijian , Guan Qiunong , Lin Tao , Zhao Jianhua , Nguan Christopher Y. C. , Zeng Haishan , Harriman David , Li Hong , Du Caigan 
Published: January 2021

AbstractRoutine monitoring of kidney transplant function is required for the standard care in post-transplantation management, including frequent measurements of serum creatinine with or without kidney biopsy. However, the invasiveness of these methods with potential for clinically significant complications makes them less than ideal. The objective of this study was to develop a non-invasive tool to monitor the kidney transplant function by using Surface-Enhanced Raman Spectroscopy (SERS). Urine and blood samples were collected from kidney transplant recipients after surgery. Silver nanoparticle-based SERS spectra of the urine were measured and evaluated using partial least squires (PLS) analysis. The SERS spectra were compared with conventional chemical markers of kidney transplant function to assess its predictive ability. A total of 110 kidney transplant recipients were included in this study. PLS results showed significant correlation with urine protein (R2 = 0.4660, p < 0.01), creatinine (R2 = 0.8106, p < 0.01), and urea (R2 = 0.7808, p < 0.01). Furthermore, the prediction of the blood markers of kidney transplant function using the urine SERS spectra was indicated by R2 = 0.7628 (p < 0.01) for serum creatinine and R2 = 0.6539 (p < 0.01) for blood urea nitrogen. This preliminary study suggested that the urine SERS spectral analysis could be used as a convenient method for rapid assessment of kidney transplant function.
Network theoretic analysis of JAK/STAT pathway and extrapolation to drugs and viruses including COVID-19
Authors: Banerjee Arindam , Goswami Rudra Prosad , Chatterjee Moumita 
Published: January 2021

AbstractWhenever some phenomenon can be represented as a graph or a network it seems pertinent to explore how much the mathematical properties of that network impact the phenomenon. In this study we explore the same philosophy in the context of immunology. Our objective was to assess the correlation of “size” (number of edges and minimum vertex cover) of the JAK/STAT network with treatment effect in rheumatoid arthritis (RA), phenotype of viral infection and effect of immunosuppressive agents on a system infected with the coronavirus. We extracted the JAK/STAT pathway from Kyoto Encyclopedia of Genes and Genomes (KEGG, hsa04630). The effects of the following drugs, and their combinations, commonly used in RA were tested: methotrexate, prednisolone, rituximab, tocilizumab, tofacitinib and baricitinib. Following viral systems were also tested for their ability to evade the JAK/STAT pathway: Measles, Influenza A, West Nile virus, Japanese B virus, Yellow Fever virus, respiratory syncytial virus, Kaposi’s sarcoma virus, Hepatitis B and C virus, cytomegalovirus, Hendra and Nipah virus and Coronavirus. Good correlation of edges and minimum vertex cover with clinical efficacy were observed (for edge, rho =  − 0.815, R2 = 0.676, p = 0.007, for vertex cover rho =  − 0.793, R2 = 0.635, p = 0.011). In the viral systems both edges and vertex cover were associated with acuteness of viral infections. In the JAK/STAT system already infected with coronavirus, maximum reduction in size was achieved with baricitinib. To conclude, algebraic and combinatorial invariant of a network may explain its biological behaviour. At least theoretically, baricitinib may be an attractive target for treatment of coronavirus infection.
In vitro inactivation of SARS-CoV-2 by commonly used disinfection products and methods
Authors: Xiling Guo , Yin Chen , Ling Wang , Xiaosong Wu , Jingjing Fan , Fang Li , Xiaoyan Zeng , Yiyue Ge , Ying Chi , Lunbiao Cui , Liubo Zhang , Hong Sun , Yan Xu 
Published: January 2021

AbstractSevere acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection is currently a global pandemic, and there are limited laboratory studies targeting pathogen resistance. This study aimed to investigate the effect of selected disinfection products and methods on the inactivation of SARS-CoV-2 in the laboratory. We used quantitative suspension testing to evaluate the effectiveness of the disinfectant/method. Available chlorine of 250 mg/L, 500 mg/L, and 1000 mg/L required 20 min, 5 min, and 0.5 min to inactivate SARS-CoV-2, respectively. A 600-fold dilution of 17% concentration of di-N-decyl dimethyl ammonium bromide (283 mg/L) and the same concentration of di-N-decyl dimethyl ammonium chloride required only 0.5 min to inactivate the virus efficiently. At 30% concentration for 1 min and 40% and above for 0.5 min, ethanol could efficiently inactivate SARS-CoV-2. Heat takes approximately 30 min at 56 °C, 10 min above 70 °C, or 5 min above 90 °C to inactivate the virus. The chlorinated disinfectants, Di-N-decyl dimethyl ammonium bromide/chloride, ethanol, and heat could effectively inactivate SARS-CoV-2 in the laboratory test. The response of SARS-CoV-2 to disinfectants is very similar to that of SARS-CoV.
Charge transport mechanism in the forming-free memristor based on silicon nitride
Authors: Gismatulin Andrei A. , Kamaev Gennadiy N. , Kruchinin Vladimir N. , Gritsenko Vladimir A. , Orlov Oleg M. , Chin Albert 
Published: January 2021

AbstractNonstoichiometric silicon nitride SiNx is a promising material for developing a new generation of high-speed, reliable flash memory device based on the resistive effect. The advantage of silicon nitride over other dielectrics is its compatibility with the silicon technology. In the present work, a silicon nitride-based memristor deposited by the plasma-enhanced chemical vapor deposition method was studied. To develop a memristor based on silicon nitride, it is necessary to understand the charge transport mechanisms in all states. In the present work, it was established that the charge transport in high-resistance states is not described by the Frenkel effect model of Coulomb isolated trap ionization, Hill–Adachi model of overlapping Coulomb potentials, Makram–Ebeid and Lannoo model of multiphonon isolated trap ionization, Nasyrov–Gritsenko model of phonon-assisted tunneling between traps, Shklovskii–Efros percolation model, Schottky model and the thermally assisted tunneling mechanisms. It is established that, in the initial state, low-resistance state, intermediate-resistance state and high-resistance state, the charge transport in the forming-free SiNx-based memristor is described by the space charge limited current model. The trap parameters responsible for the charge transport in various memristor states are determined.
BK virus infection and outcome following kidney transplantation in childhood
Authors: McCaffrey James , Bhute Vijesh J. , Shenoy Mohan 
Published: January 2021

AbstractBK virus associated nephropathy (BKN) is an important cause of kidney allograft failure. In a cohort of paediatric kidney transplant recipients, we aimed to understand the incidence and clinical outcome associated with BKN, as well as identify risk factors for BKN and BK viraemia development. We retrospectively analysed all patients who received a kidney transplant and received follow up care in our centre between 2009–2019. Among 106 patients included in the study (mean follow up 4.5 years), 32/106 (30.2%) patients experienced BK viraemia. The incidence of BKN was 7/106 (6.6%). The median time of BK viraemia development post-transplant was 279.5 days compared to 90.0 days for BKN. Development of BKN was associated with younger age at transplantation (p = 0.013). Development of BK viraemia was associated with negative recipient serology for cytomegalovirus (CMV) at time of transplantation (p = 0.012) and a higher net level of immunosuppression (p = 0.039). There was no difference in graft function at latest follow up between those who experienced BKN and those without BKN. This study demonstrates that BK virus infection is associated with younger age at transplantation, CMV negative recipient serostatus and higher levels of immunosuppression. Judicious monitoring of BK viraemia in paediatric transplant recipients, coupled with timely clinical intervention can result in similar long-term outcomes for BKN patients compared to controls.
Clinical importance of the absolute count of neutrophils, lymphocytes, monocytes, and platelets in newly diagnosed hepatocellular carcinoma
Authors: Yu Jeong Il , Park Hee Chul , Yoo Gyu Sang , Choi Changhoon , Choi Moon Seok , Nam Heerim , Baek Sun-Young , Park Minsu 
Published: January 2021

AbstractAlthough several studies have confirmed the clinical significance of the systemic inflammation markers in hepatocellular carcinoma (HCC), evaluating the clinical significance of each blood cell remains to be conducted. We aimed to evaluate the clinical importance of absolute counts of blood cells in the overall survival (OS) of patients with newly diagnosed HCC. We recruited patient cohorts from the prospective registry of newly diagnosed and previously untreated HCC at Samsung Medical Center, which included a training set of 6619 patients (2005–2013) and a validation set of 2084 patients (2014–2016). More than three-quarters of all patients had hepatitis B virus (HBV)-related HCC in both training and validation sets. The optimal cutoff values of the absolute counts of neutrophils, lymphocytes, monocytes, and platelets were 3917, 488, 1379, and 22,100, respectively, which correlated significantly with OS. The absolute blood cell counts categorized by each optimal cutoff value significantly correlated with liver function status determined by Child–Pugh class/albumin-bilirubin (ALBI) grade and the HCC burden determined by several staging systems/portal vein tumor thrombosis. Although the prognostic model based on these blood cells (ABC model) showed a lower prognostic ability than the Japan Integrated Staging or ALBI-T staging systems, it provided significant discrimination of survival in the subgroups of ALBI-T and showed the highest prognostic ability in the present study in the training and validation sets. Absolute counts of blood cells are independently associated with OS, though it is also significantly associated with liver function and tumor burden in newly diagnosed HCC.
Spatiotemporal variation of nitrate concentrations in soil and groundwater of an intensely polluted agricultural area
Authors: Nakagawa Kei , Amano Hiroki , Persson Magnus , Berndtsson Ronny 
Published: January 2021

AbstractNitrate pollution in groundwater is a serious problem in many parts of the world. However, due to the diffuse and common spatially over-lapping character of potential several non-point pollution sources, it is often difficult to distinguish main nitrate sources responsible for the pollution. For this purpose, we present a novel methodology applied to groundwater for an intensely polluted area. Groundwater samples were collected monthly from April 2017 to March 2018 in Shimabara City, Nagasaki, Japan. Soil samples were collected seasonally at soil surface and 50 cm depth at 10 locations during the same period. Sequential extraction by water and extract agents was performed using calcium phosphate for anions and strontium chloride for cations. Mean nitrate concentration in groundwater close to a livestock waste disposal site (hereinafter called “LWDS”) was 14.2 mg L−1, which is exceeding Japanese drinking water standards (10 mg L−1). We used coprostanol concentration, which is a fecal pollution indicator, to identify pollution sources related to livestock waste. For this purpose, we measured coprostanol (5β) and cholestanol (5α) and then calculated the sterol ratio (5β/(5β + 5α)). The ratios for three groundwater sampling sites were 0.28, 0.26, and 0.10, respectively. The sterol ratios indicated no pollution (< 0.3). However, the detection of coprostanol originating from animal and human waste showed that groundwater was clearly affected by this pollution source. Nitrate levels in the soil were relatively high in samples collected close to the LWDS and coprostanol contents were affected by livestock waste. Soil and groundwater nitrate concentrations displayed a complex but strong relationship. Nitrate contents were shown to be transported downstream from source areas in both soil and groundwater.