bluuebunny/crossref_metadata_2025_split huggingface dataset:
Data analytics approach to predict high-temperature cyclic oxidation kinetics of NiCr-based Alloys
Authors: Peng Jian , Pillai Rishi , Romedenne Marie , Pint Bruce A. , Muralidharan Govindarajan , Allen Haynes J. , Shin Dongwon 
Published: August 2021

AbstractAlthough of practical importance, there is no established modeling framework to accurately predict high-temperature cyclic oxidation kinetics of multi-component alloys due to the inherent complexity. We present a data analytics approach to predict the oxidation rate constant of NiCr-based alloys as a function of composition and temperature with a highly consistent and well-curated experimental dataset. Two characteristic oxidation models, i.e., a simple parabolic law and a statistical cyclic oxidation model, have been chosen to numerically represent the high-temperature oxidation kinetics of commercial and model NiCr-based alloys. We have successfully trained machine learning (ML) models using highly ranked key input features identified by correlation analysis to accurately predict experimental parabolic rate constants (kp). This study demonstrates the potential of ML approaches to predict oxidation kinetics of alloys over wide composition and temperature ranges. This approach can also serve as a basis for introducing more physically meaningful ML input features to predict the comprehensive cyclic oxidation behavior of multi-component high-temperature alloys with proper constraints based on the known underlying mechanisms.
Quantum-enhanced analysis of discrete stochastic processes
Authors: Blank Carsten , Park Daniel K. , Petruccione Francesco 
Published: August 2021

AbstractDiscrete stochastic processes (DSP) are instrumental for modeling the dynamics of probabilistic systems and have a wide spectrum of applications in science and engineering. DSPs are usually analyzed via Monte-Carlo methods since the number of realizations increases exponentially with the number of time steps, and importance sampling is often required to reduce the variance. We propose a quantum algorithm for calculating the characteristic function of a DSP, which completely defines its probability distribution, using the number of quantum circuit elements that grows only linearly with the number of time steps. The quantum algorithm reduces the Monte-Carlo sampling to a Bernoulli trial while taking all stochastic trajectories into account. This approach guarantees the optimal variance without the need for importance sampling. The algorithm can be further furnished with the quantum amplitude estimation algorithm to provide quadratic speed-up in sampling. The Fourier approximation can be used to estimate an expectation value of any integrable function of the random variable. Applications in finance and correlated random walks are presented. Proof-of-principle experiments are performed using the IBM quantum cloud platform.
CcrZ is a pneumococcal spatiotemporal cell cycle regulator that interacts with FtsZ and controls DNA replication by modulating the activity of DnaA
Authors: Gallay Clement , Sanselicio Stefano , Anderson Mary E. , Soh Young Min , Liu Xue , Stamsås Gro A. , Pelliciari Simone , van Raaphorst Renske , Dénéréaz Julien , Kjos Morten , Murray Heath , Gruber Stephan , Grossman Alan D. , Veening Jan-Willem 
Published: August 2021

AbstractMost bacteria replicate and segregate their DNA concomitantly while growing, before cell division takes place. How bacteria synchronize these different cell cycle events to ensure faithful chromosome inheritance by daughter cells is poorly understood. Here, we identify Cell Cycle Regulator protein interacting with FtsZ (CcrZ) as a conserved and essential protein in pneumococci and related Firmicutes such as Bacillus subtilis and Staphylococcus aureus. CcrZ couples cell division with DNA replication by controlling the activity of the master initiator of DNA replication, DnaA. The absence of CcrZ causes mis-timed and reduced initiation of DNA replication, which subsequently results in aberrant cell division. We show that CcrZ from Streptococcus pneumoniae interacts directly with the cytoskeleton protein FtsZ, which places CcrZ in the middle of the newborn cell where the DnaA-bound origin is positioned. This work uncovers a mechanism for control of the bacterial cell cycle in which CcrZ controls DnaA activity to ensure that the chromosome is replicated at the right time during the cell cycle.
High-quality genome assembly and resequencing of modern cotton cultivars provide resources for crop improvement
Authors: Ma Zhiying , Zhang Yan , Wu Liqiang , Zhang Guiyin , Sun Zhengwen , Li Zhikun , Jiang Yafei , Ke Huifeng , Chen Bin , Liu Zhengwen , Gu Qishen , Wang Zhicheng , Wang Guoning , Yang Jun , Wu Jinhua , Yan Yuanyuan , Meng Chengsheng , Li Lihua , Li Xiuxin , Mo Shaojing , Wu Nan , Ma Limei , Chen Liting , Zhang Man , Si Aijun , Yang Zhanwu , Wang Nan , Wu Lizhu , Zhang Dongmei , Cui Yanru , Cui Jing , Lv Xing , Li Yang , Shi Rongkang , Duan Yihong , Tian Shilin , Wang Xingfen 
Published: August 2021

AbstractCotton produces natural fiber for the textile industry. The genetic effects of genomic structural variations underlying agronomic traits remain unclear. Here, we generate two high-quality genomes of Gossypium hirsutum cv. NDM8 and Gossypium barbadense acc. Pima90, and identify large-scale structural variations in the two species and 1,081 G. hirsutum accessions. The density of structural variations is higher in the D-subgenome than in the A-subgenome, indicating that the D-subgenome undergoes stronger selection during species formation and variety development. Many structural variations in genes and/or regulatory regions potentially influencing agronomic traits were discovered. Of 446 significantly associated structural variations, those for fiber quality and Verticillium wilt resistance are located mainly in the D-subgenome and those for yield mainly in the A-subgenome. Our research provides insight into the role of structural variations in genotype-to-phenotype relationships and their potential utility in crop improvement.
Transcriptome profiling reveals potential genes involved in browning of fresh-cut eggplant (Solanum melongena L.)
Authors: Liu Xiaohui , Zhang Aidong , Zhao Jie , Shang Jing , Zhu Zongwen , Wu Xuexia , Zha Dingshi 
Published: August 2021

AbstractFresh-cut processing promotes enzymatic browning of fresh fruits and vegetables, which negatively affects the product appearance and impacts their nutrition. We used RNA-sequencing to analyze the transcriptomic changes occurring during the browning of fresh-cut eggplant fruit samples from both browning-sensitive and browning-resistant cultivars to investigate the molecular mechanisms involved in browning. A total of 8347 differentially expressed genes were identified, of which 62 genes were from six gene families (i.e., PPO, PAL, POD, CAT, APX, and GST) potentially associated with enzymatic browning. Furthermore, using qRT-PCR, we verified 231 differentially regulated transcription factors in fresh-cut eggplant fruits. The enzyme activities of PPO, POD, PAL, and CAT in ‘36’ were significantly higher than those of ‘F’ fresh-cut for 15 min. Both PPO and POD play a major role in the browning of eggplant pulp and might therefore act synergistically in the browning process. Meanwhile, qPCR results of 18 browning related genes randomly screened in 15 eggplant materials with different browning tolerance showed variant-specific expression of genes. Lastly, gene regulatory networks were constructed to identify the browning-related genes. This work provides a basis for future molecular studies of eggplants, and lays a theoretical foundation for the development of browning-resistant fresh-cut fruits and vegetables.
Early combination therapy of empagliflozin and linagliptin exerts beneficial effects on pancreatic β cells in diabetic db/db mice
Authors: Fushimi Yoshiro , Obata Atsushi , Sanada Junpei , Nogami Yuka , Ikeda Tomoko , Yamasaki Yuki , Obata Yoshiyuki , Shimoda Masashi , Nakanishi Shuhei , Mune Tomoatsu , Kaku Kohei , Kaneto Hideaki 
Published: August 2021

AbstractEffects of combination therapy of dipeptidyl peptidase-4 (DPP-4) inhibitor and sodium-glucose co-transporter 2 (SGLT2) inhibitor on β-cells are still unclear, although combination agent of these two drugs has become common in clinical practice. Therefore, we aimed to elucidate the effects of DPP-4 inhibitor and/or SGLT2 inhibitor on β-cell mass and function and compared their effects between in an early and advanced phase of diabetes. We used 7-week-old db/db mice as an early phase and 16-week-old mice as an advanced phase and treated them for 2 weeks with oral administration of linagliptin, empagliflozin, linagliptin + empagliflozin (L + E group), and 0.5% carboxymethylcellulose (Cont group). Blood glucose levels in Empa and L + E group were significantly lower than Cont group after treatment. In addition, β-cell mass in L + E group was significantly larger than Cont group only in an early phase, accompanied by increased Ki67-positive β-cell ratio. In isolated islets, mRNA expression levels of insulin and its transcription factors were all significantly higher only in L + E group in an early phase. Furthermore, mRNA expression levels related to β-cell differentiation and proliferation were significantly increased only in L + E group in an early phase. In conclusion, combination of DPP-4 inhibitor and SGLT2 inhibitor exerts more beneficial effects on β-cell mass and function, especially in an early phase of diabetes rather than an advanced phase.
Rodent host population dynamics drive zoonotic Lyme Borreliosis and Orthohantavirus infections in humans in Northern Europe
Authors: Aminikhah Mahdi , Forsman Jukka T. , Koskela Esa , Mappes Tapio , Sane Jussi , Ollgren Jukka , Kivelä Sami M. , Kallio Eva R. 
Published: August 2021

AbstractZoonotic diseases, caused by pathogens transmitted between other vertebrate animals and humans, pose a major risk to human health. Rodents are important reservoir hosts for many zoonotic pathogens, and rodent population dynamics affect the infection dynamics of rodent-borne diseases, such as diseases caused by hantaviruses. However, the role of rodent population dynamics in determining the infection dynamics of rodent-associated tick-borne diseases, such as Lyme borreliosis (LB), caused by Borrelia burgdorferi sensu lato bacteria, have gained limited attention in Northern Europe, despite the multiannual abundance fluctuations, the so-called vole cycles, that characterise rodent population dynamics in the region. Here, we quantify the associations between rodent abundance and LB human cases and Puumala Orthohantavirus (PUUV) infections by using two time series (25-year and 9-year) in Finland. Both bank vole (Myodes glareolus) abundance as well as LB and PUUV infection incidence in humans showed approximately 3-year cycles. Without vector transmitted PUUV infections followed the bank vole host abundance fluctuations with two-month time lag, whereas tick-transmitted LB was associated with bank vole abundance ca. 12 and 24 months earlier. However, the strength of association between LB incidence and bank vole abundance ca. 12 months before varied over the study years. This study highlights that the human risk to acquire rodent-borne pathogens, as well as rodent-associated tick-borne pathogens is associated with the vole cycles in Northern Fennoscandia, yet with complex time lags.
Colored cotton wastes valuation through thermal and catalytic reforming of pyrolysis vapors (Py-GC/MS)
Authors: da Silva Janduir Egito , Calixto Guilherme Quintela , de Araújo Medeiros Rodolfo Luiz Bezerra , de Freitas Melo Marcus Antônio , de Araújo Melo Dulce Maria , de Carvalho Luiz Paulo , Braga Renata Martins 
Published: August 2021

AbstractThis study aims to analyze the products of the catalytic pyrolysis of naturally colored cotton residues, type BRS (seeds from Brazil), called BRS-Verde, BRS-Rubi, BRS-Topázio and BRS-Jade. The energy characterization of biomass was evaluated through ultimate and proximate analysis, higher heating value, cellulose, hemicellulose and lignin content, thermogravimetric analysis and apparent density. Analytical pyrolysis was performed at 500 °C in an analytical pyrolyzer from CDS Analytical connected to a gas chromatograph coupled to the mass spectrometer (GC/MS). The pyrolysis vapors were reformed at 300 and 500 °C through thermal and catalytic cracking with zeolites (ZSM-5 and HZSM-5). It has been noticed that pyrolysis vapor reforming at 500 °C promoted partial deoxygenation and cracking reactions, while the catalytic reforming showed better results for the product deoxygenation. The catalyst reforming of pyrolysis products, especially using HZSM-5 at 500 °C, promoted the formation of monoaromatics such as benzene, toluene, xylene and styrene, which are important precursors of polymers, solvents and biofuels. The main influence on the yields of these aromatic products is due to the catalytic activity of ZSM-5 favored by increased temperature that promotes cracking reactions due expanded zeolites channels.
Quantitative three-dimensional image analysis of the superior canal after surgical plugging to treat superior semicircular canal dehiscence
Authors: Lee Sang-Yeon , Lee Yein , Choi Jun Young , Bae Yun Jung , Kim MinJu , Song Jae-Jin , Choi Byung Yoon , Jeong Won-Ki , Koo Ja-Won 
Published: August 2021

AbstractSurgical plugging to treat superior semicircular canal dehiscence (SCD) has been proven to impede the effect of the third mobile window, abating cochleovestibular symptoms. Knowledge of superior semicircular canal (SC)-plugging status has been proposed to serve as a guide for adjuvant treatment. Here, we investigated disturbances in the inner ear fluid space following SC plugging using a novel three-dimensional (3D) reconstruction-based method. This approach used a semi-automatic segmentation algorithm and a direct volume rendering method derived from conventional magnetic resonance images. The variable extents of filling defects at the sites of SC plugging and the positional relation of the defect to the ampulla and common crus were identified. The success group exhibited markedly reduced volumes following surgery, whereas the failure group displayed no changes in volume. These results indicate that the success or failure of SC plugging was related to 3D volume changes in the labyrinth fluid signal. Collectively, this study presents individualized SC-plugging statuses using a novel 3D reconstruction-based method and it facilitates future work regarding easy-to-measure 3D volume changes. This current technology also aids in the exploration of pathologic changes in various targets of interest.
State dependent effects on the frequency response of prestin’s real and imaginary components of nonlinear capacitance
Authors: Santos-Sacchi Joseph , Navaratnam Dhasakumar , Tan Winston J. T. 
Published: August 2021

AbstractThe outer hair cell (OHC) membrane harbors a voltage-dependent protein, prestin (SLC26a5), in high density, whose charge movement is evidenced as a nonlinear capacitance (NLC). NLC is bell-shaped, with its peak occurring at a voltage, Vh, where sensor charge is equally distributed across the plasma membrane. Thus, Vh provides information on the conformational state of prestin. Vh is sensitive to membrane tension, shifting to positive voltage as tension increases and is the basis for considering prestin piezoelectric (PZE). NLC can be deconstructed into real and imaginary components that report on charge movements in phase or 90 degrees out of phase with AC voltage. Here we show in membrane macro-patches of the OHC that there is a partial trade-off in the magnitude of real and imaginary components as interrogation frequency increases, as predicted by a recent PZE model (Rabbitt in Proc Natl Acad Sci USA 17:21880–21888, 2020). However, we find similar behavior in a simple 2-state voltage-dependent kinetic model of prestin that lacks piezoelectric coupling. At a particular frequency, Fis, the complex component magnitudes intersect. Using this metric, Fis, which depends on the frequency response of each complex component, we find that initial Vh influences Fis; thus, by categorizing patches into groups of different Vh, (above and below − 30 mV) we find that Fis is lower for the negative Vh group. We also find that the effect of membrane tension on complex NLC is dependent, but differentially so, on initial Vh. Whereas the negative group exhibits shifts to higher frequencies for increasing tension, the opposite occurs for the positive group. Despite complex component trade-offs, the low-pass roll-off in absolute magnitude of NLC, which varies little with our perturbations and is indicative of diminishing total charge movement, poses a challenge for a role of voltage-driven prestin in cochlear amplification at very high frequencies.
Quantitative analysis of speckle-based X-ray dark-field imaging using numerical wave-optics simulations
Authors: Meyer Sebastian , Shi Serena Z. , Shapira Nadav , Maidment Andrew D. A. , Noël Peter B. 
Published: August 2021

AbstractThe dark-field signal measures the small-angle scattering strength and provides complementary diagnostic information. This is of particular interest for lung imaging due to the pronounced small-angle scatter from the alveolar microstructure. However, most dark-field imaging techniques are relatively complex, dose-inefficient, and require sophisticated optics and highly coherent X-ray sources. Speckle-based imaging promises to overcome these limitations due to its simple and versatile setup, only requiring the addition of a random phase modulator to conventional X-ray equipment. We investigated quantitatively the influence of sample structure, setup geometry, and source energy on the dark-field signal in speckle-based X-ray imaging with wave-optics simulations for ensembles of micro-spheres. We show that the dark-field signal is accurately predicted via a model originally derived for grating interferometry when using the mean frequency of the speckle pattern power spectral density as the characteristic speckle size. The size directly reflects the correlation length of the diffuser surface and did not change with energy or propagation distance within the near-field. The dark-field signal had a distinct dependence on sample structure and setup geometry but was also affected by beam hardening-induced modifications of the visibility spectrum. This study quantitatively demonstrates the behavior of the dark-field signal in speckle-based X-ray imaging.
Synergistic impact of pre-sensitization and delayed graft function on allograft rejection in deceased donor kidney transplantation
Authors: Lee Hanbi , Park Yohan , Ban Tae Hyun , Song Sang Heon , Song Seung Hwan , Yang Jaeseok , Ahn Curie , Yang Chul Woo , Chung Byung Ha ,   The Korean Organ Transplantation Registry Study Group, Kong Jin Min , Kwon Oh Jung , Kim Deok Gie , Jung Cheol-Woong , Kim Yeong Hoon , Kim Joong Kyung , Kim Chan-Duck , Min Ji Won , Park Sung Kwang , Park Yeon Ho , Berm Park Jae , Park Jung Hwan , Park Jong-Won , Shin Ho Sik , Yoon Hye Eun , Lee Kang Wook , Lee Dong Ryeol , Lee Dong Won , Lee Sam Yeol , Lee Sang-Ho , Lee Su Hyung , Lee Jung Jun , Pyo Lee Jung , Lee Jeong-Hoon , Jeon Jin Seok , Jun Heungman , Jeong Kyunghwan , Chung Ku Yong , Cho Hong Rae , Ki Ju Man , Chae Dong-Wan , Choi Soo Jin Na , Han Duck Jong , Han Seungyeup , Huh Kyu Ha 
Published: August 2021

AbstractThe aim of this study is to investigate whether or not delayed graft function (DGF) and pre-transplant sensitization have synergistic adverse effects on allograft outcome after deceased donor kidney transplantation (DDKT) using the Korean Organ Transplantation Registry (KOTRY) database, the nationwide prospective cohort. The study included 1359 cases between May 2014 and June 2019. The cases were divided into 4 subgroups according to pre-sensitization and the development of DGF post-transplant [non-pre-sensitized-DGF(−) (n = 1097), non-pre-sensitized-DGF(+) (n = 127), pre-sensitized-DGF(−) (n = 116), and pre-sensitized-DGF(+) (n = 19)]. We compared the incidence of biopsy-proven allograft rejection (BPAR), time-related change in allograft function, allograft or patient survival, and post-transplant complications across 4 subgroups. The incidence of acute antibody-mediated rejection (ABMR) was significantly higher in the pre-sensitized-DGF(+) subgroup than in other 3 subgroups. In addition, multivariable cox regression analysis demonstrated that pre-sensitization combined with DGF is an independent risk factor for the development of acute ABMR (hazard ratio 4.855, 95% confidence interval 1.499–15.727). Moreover, DGF and pre-sensitization showed significant interaction (p-value for interaction = 0.008). Pre-sensitization combined with DGF did not show significant impact on allograft function, and allograft or patient survival. In conclusion, the combination of pre-sensitization and DGF showed significant synergistic interaction on the development of allograft rejection after DDKT.
Prevalence of the additional head of quadriceps femoris in the South Indian population: a cadaveric and radiological study
Authors: Sam Femina , Kandagaddala Madhavi , Prithishkumar Ivan James , Mahata Koyeli Mary , Gowri Mahasampath , Rabi Suganthy 
Published: August 2021

AbstractQuadriceps femoris is an extensor muscle in the anterior compartment of thigh and is traditionally taught to be composed of four heads. Recently, there is an increased interest in the occurrence of an additional muscle head of quadriceps femoris. But scientific knowledge regarding its incidence is lacking in the South Indian population. This study was done to confirm the presence of the additional head by routine anatomic dissection and radiological imaging techniques. Forty-one formalin fixed human cadaveric lower limbs were dissected and the morphology of the additional head was noted. Retrospective analysis of 88 MRI images of patients was done. The additional muscle head was present in 43.9% of the cadaveric lower limbs and was consistently located between the vastus lateralis and vastus intermedius. It originated from variable portions of the greater trochanter, intertrochanteric line, lateral lip of linea aspera and lateral surface of the shaft of femur and inserted either as a muscle belly or as an aponeurosis into the vastus intermedius (55.6%), vastus lateralis (22.2%) or directly into the base of the patella. It received its vascular supply from branches of the lateral circumflex femoral artery and was innervated by branches from the posterior division of the femoral nerve. In addition, the additional muscle head was identified by MRI and its incidence was reported to be 30.68% for the first time in living subjects. The result of this study provides additional information in understanding the morphology of the quadriceps femoris muscle.