bluuebunny/crossref_metadata_2025 huggingface dataset:
The influence of stocking levels, clone, fertilization, and weed control on surface CO2 efflux in a mid-rotation Pinus radiata D. Don plantation in Canterbury, New Zealand
Authors: KC Mohan , Mason Euan G. , Bown Horacio E.
Published: February 2021

Silvicultural practices applied in managed forest plantations may help counteract the effects of climate change by influencing soil surface CO2 efflux (Fs). Understanding the effects of silvicultural practices on Fs will provide unbiased estimates of carbon fluxes and allow better silvicultural decisions for carbon sequestration. Therefore, we assessed how Fs differed seasonally across silvicultural practices (i.e., stocking levels, clone, fertilization and weed control treatments) and evaluated the effects of soil temperature (Ts) and soil volumetric water content (θv) on Fs across these practices for a mid-rotation (14 year-old) Pinus radiata plantation in the Canterbury region of New Zealand. There were significant differences in Fs (p < 0.05) over the four seasons, three levels of stocking, and five clones. The effects of fertilization and weed control applied 12 years previously on Fs were insignificant. Annual estimate of Fs (mean ± 1 standard deviation) from the study site was 22.7 ± 7.1 t ha−1 a−1 in the form of CO2 (6.2 ± 2.1 t ha−1 a−1 in the form of C). Fs values were consistently higher in plots with 1250 stems ha−1 compared to 2500 stems ha−1, which may be related to a strong soil resource limitation because of the close spacing in the latter plantation. Significant differences in Fs across clones suggest that variations in carbon partitioning might explain their growth performance. Silvicultural treatments influenced Fs response to soil temperature (p < 0.05), resulting in models explaining 28–49% of the total variance in Fs. These findings provide insights into how silvicultural management decisions may impact Fs in mid-rotation radiata pine plantations, contributing towards developing more precise and unbiased plantation carbon budgets.
Vom Sprechenkönnen und Gehörtwerden
Authors: Herrmann Peter , Szynka Peter
Published: February 2021

Dienste allgemein und speziell die Dienste für Wohnungslose sind immer auch dadurch gekennzeichnet, dass es Kommunikationsschwierigkeiten zwischen den unterschiedlichen Akteur_innen gibt. Diese Einleitung in den Schwerpunkt „Wohnungslosigkeit“ problematisiert diesen Umstand und weist nicht zuletzt darauf hin, dass alle Beteiligten den gesellschaftlich gleichen Status als Bürger haben.
Impact of COVID-19 lockdown on physical activity and sedentary behaviour in Dutch cardiovascular disease patients
Authors: van Bakel B. M. A. , Bakker E. A. , de Vries F. , Thijssen D. H. J. , Eijsvogels T. M. H.
Published: February 2021

Background

Coronavirus disease 2019 (COVID-19) lockdown restrictions may impact lifestyle and therefore also physical (in)activity patterns in patients with cardiovascular disease (CVD). This study aimed to evaluate the effect of lockdown on physical activity and sedentary behaviour.

Methods

A total of 1565 Dutch CVD patients participated in this prospective cohort study, in which we compared physical activity and sedentary behaviour before and during the COVID-19 lockdown period. Baseline measures were assessed in 2018 and data on follow-up measures were collected between 17 and 24 April 2020 (5 weeks after the introduction of COVID-19 lockdown restrictions). Validated questionnaires were used to assess physical activity and sedentary behaviour.

Results

Moderate-to-vigorous physical activities increased from 1.6 (0.9, 2.8) to 2.0 (1.0, 3.5) h/day [median (interquartile range)] (p < 0.001) during the COVID-19 lockdown, mainly due to an increase in time spent walking and doing odd jobs. In contrast, time spent exercising significantly declined [1.0 (0.0, 2.3) to 0.0 (0.0, 0.6) h/week], whereas sedentary time increased from 7.8 (6.1, 10.4) to 8.9 (6.8, 11.4) h/day (p < 0.001). The absolute increase in physical activity was 13 (−36, 81) min/day, whereas sedentary behaviour increased by 55 (−72, 186) min/day.

Conclusion

Despite a small increase in physical activities, the larger increase in sedentary time induced a net reduction in habitual physical activity levels in Dutch CVD patients during the first-wave COVID-19 lockdown. Since a more inactive lifestyle is strongly associated with disease progression and mortality, we encourage CVD patients and their caregivers to explore novel solutions to increase physical activity levels and reduce sedentary time during (and beyond) the COVID-19 pandemic.
Humane Driving
Authors: Black Vaughan , Fenton Andrew
Published: February 2021

The advent of fully autonomous vehicles (AVs) raises many questions. While some appear purely technical, others engage matters of public policy, sometimes with a prominent ethical component. Our expertise lies in law and applied ethics, and so our inquiry will focus heavily on legal or ethical issues arising from a widespread adoption of AVs and their response in emergency situations involving animals. By “animals” we do not mean all other animals than humans. We will concentrate on interest-bearing animals. These are animals who possess a welfare or wellbeing, animals whose lives can fare well or badly from their perspective.
Transforming American Prosecution
Authors: Bazelon Emily
Published: February 2021

My goal in this paper is to tell you a story, a story about race, about crime, about discretion, and about hope. I want to suggest that mass incarceration in the United States is not necessary or wise. It is the product of a criminal justice system that has ballooned beyond reason or recognition from its design.
Gaussian process approximations for multicolor Pólya urn models
Authors: Borovkov Konstantin
Published: February 2021

Motivated by mathematical tissue growth modelling, we consider the problem of approximating the dynamics of multicolor Pólya urn processes that start with large numbers of balls of different colors and run for a long time. Using strong approximation theorems for empirical and quantile processes, we establish Gaussian process approximations for the Pólya urn processes. The approximating processes are sums of a multivariate Brownian motion process and an independent linear drift with a random Gaussian coefficient. The dominating term between the two depends on the ratio of the number of time stepsnto the initial number of ballsNin the urn. We also establish an upper bound of the form$c(n^{-1/2}+N^{-1/2})$for the maximum deviation over the class of convex Borel sets of the step-nurn composition distribution from the approximating normal law.
Habitat preferences of the Critically Endangered greater Bermuda land snail Poecilozonites bermudensis in the wild
Authors: Copeland Alison , Hesselberg Thomas
Published: February 2021

The endemic, Critically Endangered greater Bermuda land snail Poecilozonites bermudensis is known from only two relict subpopulations. Little is known of its habitat preferences in the wild. Observations of released zoo-reared P. bermudensis suggested an affinity for limestone, which we investigated on Port's Island. Previous qualitative observations on Port's Island suggested an aversion to the litter of the invasive tree Casuarina equisetifolia, which we examined. Additionally, we hypothesized that snail abundance would increase with elevation, distance from the sea, and with increased plant species diversity. During 2 May–14 June 2018, we found 558 live P. bermudensis at 70 sites across Port's Island. We found no correlation between the number of live snails at a site and either the number of plant species, elevation or distance from the shoreline, but snails were significantly less abundant at sites dominated by C. equisetifolia. Significantly more snails were found around limestone features, indicating future reintroductions and searches for any undiscovered subpopulations should focus on limestone features where C. equisetifolia is absent.
Spatial dynamics of the COVID-19 pandemic in Brazil
Authors: Castro R. R. , Santos R. S. C. , Sousa G. J. B. , Pinheiro Y. T. , Martins R. R. I. M. , Pereira M. L. D. , Silva R. A. R.
Published: February 2021

The objective of this study was to analyse the dynamics of spatial dispersion of the coronavirus disease 2019 (COVID-19) in Brazil by correlating them to socioeconomic indicators. This is an ecological study of COVID-19 cases and deaths between 26 February and 31 July 2020. All Brazilian counties were used as units of analysis. The incidence, mortality, Bayesian incidence and mortality rates, global and local Moran indices were calculated. A geographic weighted regression analysis was conducted to assess the relationship between incidence and mortality due to COVID-19 and socioeconomic indicators (independent variables). There were confirmed 2 662 485 cases of COVID-19 reported in Brazil from February to July 2020 with higher rates of incidence in the north and northeast. The Moran global index of incidence rate (0.50, P = 0.01) and mortality (0.45 with P = 0.01) indicate a positive spatial autocorrelation with high standards in the north, northeast and in the largest urban centres between cities in the southeast region. In the same period, there were 92 475 deaths from COVID-19, with higher mortality rates in the northern states of Brazil, mainly Amazonas, Pará and Amapá. The results show that there is a geospatial correlation of COVID-19 in large urban centres and regions with the lowest human development index in the country. In the geographic weighted regression, it was possible to identify that the percentage of people living in residences with density higher than 2 per dormitory, the municipality human development index (MHDI) and the social vulnerability index were the indicators that most contributed to explaining incidence, social development index and the municipality human development index contributed the most to the mortality model. We hope that the findings will contribute to reorienting public health responses to combat COVID-19 in Brazil, the new epicentre of the disease in South America, as well as in other countries that have similar epidemiological and health characteristics to those in Brazil.
Cigarette smoking behaviors and the importance of ethnicity and genetic ancestry
Authors: Choquet Hélène , Yin Jie , Jorgenson Eric
Published: February 2021

Cigarette smoking contributes to numerous diseases and is one of the leading causes of death in the United States. Smoking behaviors vary widely across race/ethnicity, but it is not clear why. Here, we examine the contribution of genetic ancestry to variation in two smoking-related traits in 43,485 individuals from four race/ethnicity groups (non-Hispanic white, Hispanic/Latino, East Asian, and African American) from a single U.S. healthcare plan. Smoking prevalence was the lowest among East Asians (22.7%) and the highest among non-Hispanic whites (38.5%). We observed significant associations between genetic ancestry and smoking-related traits. Within East Asians, we observed higher smoking prevalence with greater European (versus Asian) ancestry (P = 9.95 × 10−12). Within Hispanic/Latinos, higher cigarettes per day (CPD) was associated with greater European ancestry (P = 3.34 × 10−25). Within non-Hispanic whites, the lowest number of CPD was observed for individuals of southeastern European ancestry (P = 9.06 × 10−5). These associations remained after considering known smoking-associated loci, education, socioeconomic factors, and marital status. Our findings support the role of genetic ancestry and socioeconomic factors in cigarette smoking behaviors in non-Hispanic whites, Hispanic/Latinos, and East Asians.
Massively parallel sequencing of 25 autosomal STRs including SE33 in four population groups for forensic applications
Authors: Kwon Ye-Lim , Kim Bo Min , Lee Eun Young , Shin Kyoung-Jin
Published: February 2021

The introduction of massively parallel sequencing (MPS) in forensic investigation enables sequence-based large-scale multiplexing beyond size-based analysis using capillary electrophoresis (CE). For the practical application of MPS to forensic casework, many population studies have provided sequence data for autosomal short tandem repeats (STRs). However, SE33, a highly polymorphic STR marker, has little sequence-based data because of difficulties in analysis. In this study, 25 autosomal STRs were analyzed, including SE33, using an in-house MPS panel for 350 samples from four populations (African–American, Caucasian, Hispanic, and Korean). The barcoded MPS library was generated using a two-step PCR method and sequenced using a MiSeq System. As a result, 99.88% genotype concordance was obtained between length- and sequence-based analyses. In SE33, the most discordances (eight samples, 0.08%) were observed because of the 4 bp deletion between the CE and MPS primer binding sites. Compared with the length-based CE method, the number of alleles increased from 332 to 725 (2.18-fold) for 25 autosomal STRs in the sequence-based MPS method. Notably, additional 129 unique alleles, a 4.15-fold increase, were detected in SE33 by identifying sequence variations. This population data set provides sequence variations and sequence-based allele frequencies for 25 autosomal STRs.
A hybrid deep neural network for classification of schizophrenia using EEG Data
Authors: Sun Jie , Cao Rui , Zhou Mengni , Hussain Waqar , Wang Bin , Xue Jiayue , Xiang Jie
Published: February 2021

Schizophrenia is a serious mental illness that causes great harm to patients, so timely and accurate detection is essential. This study aimed to identify a better feature to represent electroencephalography (EEG) signals and improve the classification accuracy of patients with schizophrenia and healthy controls by using EEG signals. Our research method involves two steps. First, the EEG time series is preprocessed, and the extracted time-domain and frequency-domain features are transformed into a sequence of red–green–blue (RGB) images that carry spatial information. Second, we construct hybrid deep neural networks (DNNs) that combine convolution neural networks and long short-term memory to address RGB images to classify schizophrenic patients and healthy controls. The results show that the fuzzy entropy (FuzzyEn) feature is more significant than the fast Fourier transform (FFT) feature in brain topography. The deep learning (DL) method that we propose achieves an average accuracy of 99.22% with FuzzyEn and an average accuracy of 96.34% with FFT. These results show that the best effect is to extract fuzzy features as input features from EEG time series and then use a hybrid DNN for classification. Compared with the most advanced methods in this field, significant improvements have been achieved.
Electronically steered metasurface antenna
Authors: Boyarsky Michael , Sleasman Timothy , Imani Mohammadreza F. , Gollub Jonah N. , Smith David R.
Published: February 2021

Mobile devices, climate science, and autonomous vehicles all require advanced microwave antennas for imaging, radar, and wireless communications. We propose a waveguide-fed metasurface antenna architecture that enables electronic beamsteering from a lightweight circuit board with varactor-tuned elements. Our approach uses a unique feed structure and layout that enables spatial sampling at the Nyquist limit of half a wavelength. We detail the design of this Nyquist metasurface antenna and experimentally demonstrate electronic beamsteering in two directions. Nyquist metasurface antennas can realize high performance without costly and power hungry phase shifters, making them a compelling technology for future antenna hardware.
A bladder cancer patient-derived xenograft displays aggressive growth dynamics in vivo and in organoid culture
Authors: Cai Elise Y. , Garcia Jose , Liu Yuzhen , Vakar-Lopez Funda , Arora Sonali , Nguyen Holly M. , Lakely Bryce , Brown Lisha , Wong Alicia , Montgomery Bruce , Lee John K. , Corey Eva , Wright Jonathan L. , Hsieh Andrew C. , Lam Hung-Ming
Published: February 2021

Bladder cancer is among the most prevalent cancers worldwide. Currently, few bladder cancer models have undergone thorough characterization to assess their fidelity to patient tumors, especially upon propagation in the laboratory. Here, we establish and molecularly characterize CoCaB 1, an aggressive cisplatin-resistant muscle-invasive bladder cancer patient-derived xenograft (PDX) and companion organoid system. CoCaB 1 was a subcutaneous PDX model reliably transplanted in vivo and demonstrated an acceleration in growth upon serial transplantation, which was reflected in organoid and 2D cell culture systems. Transcriptome analysis revealed progression towards an increasingly proliferative and stem-like expression profile. Gene expression differences between organoid and PDX models reflected expected differences in cellular composition, with organoids enriched in lipid biosynthesis and metabolism genes and deprived of extracellular components observed in PDXs. Both PDX and organoid models maintained the histological fidelity and mutational heterogeneity of their parental tumor. This study establishes the CoCaB 1 PDX and organoid system as companion representative tumor models for the development of novel bladder cancer therapies.
3-D shape reconstruction of non-uniform reflectance surface based on pixel intensity, pixel color and camera exposure time adaptive adjustment
Authors: Wang Jianhua , Yang Yanxi , Zhou Yuguo
Published: February 2021

High dynamic range 3-D shape measurement is a challenge. In this work, we propose a novel method to solve the 3-D shape reconstruction of high-reflection and colored surfaces. First, we propose a method to establish a fast pixel-level mapping between the projected image and the captured image. Secondly, we propose a color texture extraction method using a black-and-white (B/W) camera and a pixel-level projection color adjustment method. Third, we give an optimal projection fringe modulation/background intensity ratio. Fourth, we propose a method for estimating the reflectivity of the object surface and ambient light interference, and a method for adjusting the projection intensity at the pixel level and a method for estimating the optimal exposure time. Experiments show that, compared with the existing methods, the proposed method not only can obtain high-quality captured images, but also has higher measurement efficiency and wider application range.
Salicylic acid and kaolin effects on pomological, physiological, and phytochemical characters of hazelnut (Corylus avellana) at warm summer condition
Authors: Khavari Marziyeh , Fatahi Reza , Zamani Zabihollah
Published: February 2021

Climate change and population increase are two challenges for crop production in the world. Hazelnut (Corylus avellana L.) is considered an important nut regarding its nutritional and economic values. As a fact, the application of supporting materials as foliage sprays on plants will decrease biotic and abiotic stresses. In this study, the effects of salicylic acid (0, 1 mM and 2.5 mM) and kaolin (0, 3% and 6%) sprays were investigated on morphological, physiological, pomological, and biochemical characteristics of hazelnut. The results showed that 1 mM salicylic acid and 6% kaolin had the best effects on nut and kernel weight compared to control. Biochemical parameters such as chlorophyll a, b, a + b, and carotenoid contents showed that salicylic acid and kaolin improved pigment concentration. Proline and antioxidant contents such as phenolic acids, SOD, APX, and CAT enzyme activities increased by these applications. On the other hand, lipid peroxidation, protein content, and H2O2 content were decreased. Based on the tolerance index result, Merveille de Bollwiller cultivar showed the highest tolerance while 'Fertile de Coutard' had the lowest value. Therefore, hazelnut performance may be improved through exogenous application of the signaling (salicylic acid) and particle film (Kaolin) compounds in warmer climates.
Laser ablation synthesis of metal-doped gold clusters from composites of gold nanoparticles with metal organic frameworks
Authors: Pečinka Lukáš , Peña-Méndez Eladia Maria , Conde-González José Elías , Havel Josef
Published: February 2021

Metal-doped gold clusters, mainly cages, are receiving rapidly increasing attention due to their tunable catalytic properties. Their synthesis is mostly based on complex procedures, including several steps. In this work, via adsorption of gold nanoparticles (AuNPs) from aqueous solution to MOF (metal organic frameworks) of M = Co, Cu, Ni, and Zn with various linkers the {AuNPs, MOF} composites were prepared. These composites were used for laser ablation synthesis (LAS) using a common mass spectrometer. Several series of positively and negatively charged AumMn+/− clusters were observed in mass spectra and their stoichiometry (m = 1–35, n = 1–5) was determined. For each dopant (Co, Cu, Ni, and Zn) ~ 50 different clusters were identified in positive, as well as in negative ion modes. About 100 of these clusters were proposed to be endohedral metal-doped gold cages (for m > 12). The developed approach represents a simple procedure for generating metal-doped gold clusters or endohedral metal-doped gold cages materials with potential applications in medicine and/or electronics.
Integrated analysis of behavioral, epigenetic, and gut microbiome analyses in AppNL-G-F, AppNL-F, and wild type mice
Authors: Kundu Payel , Torres Eileen Ruth S. , Stagaman Keaton , Kasschau Kristin , Okhovat Mariam , Holden Sarah , Ward Samantha , Nevonen Kimberly A. , Davis Brett A. , Saito Takashi , Saido Takaomi C. , Carbone Lucia , Sharpton Thomas J. , Raber Jacob
Published: February 2021

Epigenetic mechanisms occurring in the brain as well as alterations in the gut microbiome composition might contribute to Alzheimer’s disease (AD). Human amyloid precursor protein knock-in (KI) mice contain the Swedish and Iberian mutations (AppNL-F) or those two and also the Arctic mutation (AppNL-G-F). In this study, we assessed whether behavioral and cognitive performance in 6-month-oldAppNL-F,AppNL-G-F, and C57BL/6J wild-type (WT) mice was associated with the gut microbiome, and whether the genotype modulates this association. The genotype effects observed in behavioral tests were test-dependent. The biodiversity and composition of the gut microbiome linked to various aspects of mouse behavioral and cognitive performance but differences in genotype modulated these relationships. These genotype-dependent associations include members of the Lachnospiraceae and Ruminococcaceae families. In a subset of female mice, we assessed DNA methylation in the hippocampus and investigated whether alterations in hippocampal DNA methylation were associated with the gut microbiome. Among other differentially methylated regions, we identified a 1 Kb region that overlapped ing 3′UTR of theTomm40gene and the promoter region of theApoegene that and was significantly more methylated in the hippocampus ofAppNL-G-Fthan WT mice. The integrated gut microbiome hippocampal DNA methylation analysis revealed a positive relationship between amplicon sequence variants (ASVs) within the Lachnospiraceae family and methylation at theApoegene. Hence, these microbes may elicit an impact on AD-relevant behavioral and cognitive performance via epigenetic changes in AD-susceptibility genes in neural tissue or that such changes in the epigenome can elicit alterations in intestinal physiology that affect the growth of these taxa in the gut microbiome.
A KDM6 inhibitor potently induces ATF4 and its target gene expression through HRI activation and by UTX inhibition
Authors: Kitajima Shojiro , Sun Wendi , Lee Kian Leong , Ho Jolene Caifeng , Oyadomari Seiichi , Okamoto Takashi , Masai Hisao , Poellinger Lorenz , Kato Hiroyuki
Published: February 2021

UTX/KDM6A encodes a major histone H3 lysine 27 (H3K27) demethylase, and is frequently mutated in various types of human cancers. Although UTX appears to play a crucial role in oncogenesis, the mechanisms involved are still largely unknown. Here we show that a specific pharmacological inhibitor of H3K27 demethylases, GSK-J4, induces the expression of transcription activating factor 4 (ATF4) protein as well as the ATF4 target genes (e.g. PCK2, CHOP, REDD1, CHAC1 and TRIB3). ATF4 induction by GSK-J4 was due to neither transcriptional nor post-translational regulation. In support of this view, the ATF4 induction was almost exclusively dependent on the heme-regulated eIF2α kinase (HRI) in mouse embryonic fibroblasts (MEFs). Gene expression profiles with UTX disruption by CRISPR-Cas9 editing and the following stable re-expression of UTX showed that UTX specifically suppresses the expression of the ATF4 target genes, suggesting that UTX inhibition is at least partially responsible for the ATF4 induction. Apoptosis induction by GSK-J4 was partially and cell-type specifically correlated with the activation of ATF4-CHOP. These findings highlight that the anti-cancer drug candidate GSK-J4 strongly induces ATF4 and its target genes via HRI activation and raise a possibility that UTX might modulate cancer formation by regulating the HRI-ATF4 axis.
Cortical oscillations that underlie visual selective attention are abnormal in adolescents with cerebral palsy
Authors: Hoffman Rashelle M. , Embury Christine M. , Lew Brandon J. , Heinrichs-Graham Elizabeth , Wilson Tony W. , Kurz Max J.
Published: February 2021

Adolescence is a critical period for the development and refinement of several higher-level cognitive functions, including visual selective attention. Clinically, it has been noted that adolescents with cerebral palsy (CP) may have deficits in selectively attending to objects within their visual field. This study aimed to evaluate the neural oscillatory activity in the ventral attention network while adolescents with CP performed a visual selective attention task. Adolescents with CP (N = 14; Age = 15.7 ± 4 years; MACS I–III; GMFCS I–IV) and neurotypical (NT) adolescents (N = 21; Age = 14.3 ± 2 years) performed the Eriksen flanker task while undergoing magnetoencephalographic (MEG) brain imaging. The participants reported the direction of a target arrow that was surrounded by congruent or incongruent flanking arrows. Compared with NT adolescents, adolescents with CP had slower responses and made more errors regarding the direction of the target arrow. The MEG results revealed that adolescents with CP had stronger alpha oscillations in the left insula when the flanking arrows were incongruent. Furthermore, participants that had more errors also tended to have stronger alpha oscillatory activity in this brain region. Altogether these results indicate that the aberrant activity seen in the left insula is associated with diminished visual selective attention function in adolescents with CP.
The time domain numerical method of three-dimensional conductors including radiation with lumped parameter circuit
Authors: Jinno Souma , Kitora Shuji , Toki Hiroshi , Abe Masayuki
Published: February 2021

We formulate a numerical method on the transmission and radiation theory of three-dimensional conductors starting from the Maxwell equations in the time domain. We include the delay effect in the integral equations for the scalar and vector potentials rigorously, which is vital to obtain numerically stable solutions for transmission and radiation phenomena in conductors. We provide a formalism to connect the conductors to any passive lumped-parameter circuits. We show one example of numerical calculations, demonstrating that the new formalism provides stable solutions to the transmission and radiation phenomena.
Selection and validation of reference genes by RT-qPCR under photoperiodic induction of flowering in sugarcane (Saccharum spp.)
Authors: da Silva Santos Paulo H. , Manechini João R. Vieira , Brito Michael S. , Romanel Elisson , Vicentini Renato , Scarpari Maximiliano , Jackson Stephen , Pinto Luciana R.
Published: February 2021

Although reference genes have previously been used in the expression analysis of genes involved in sugarcane flowering they had not been experimentally validated for stability and consistency of expression between different samples over a wide range of experimental conditions. Here we report the analysis of candidate reference genes in different tissue types, at different temporal time-points, in both short and long day photoperiodic treatments. The stability of the candidate reference genes in all conditions was evaluated with NormFinder, BestKeeper, and RefFinder algorithms that complement each other for a more robust analysis. As the Normfinder algorithm was more appropriate for our experimental conditions, greater emphasis was placed on Normfinder when choosing the most stable genes. UBQ1 and TUB were shown to be the most stable reference genes to use for normalizing RT-qPCR gene expression data during floral induction, whilst 25SrRNA1 and GAPDH were the least stable. Their use as a reference gene pair was validated by analyzing the expression of two differentially expressed target genes (PIL5 and LHP1). The UBQ1/TUB reference genes combination was able to reveal small significant differences in gene expression of the two target genes that were not detectable when using the least stable reference gene combination. These results can be used to inform the choice of reference genes to use in the study of the sugarcane floral induction pathway. Our work also demonstrates that both PIL5 and LHP1 are significantly up-regulated in the initial stages of photoperiodic induction of flowering in sugarcane.
Epidermal growth factor alleviates the negative impact of urea on frozen-thawed bovine sperm, but the subsequent developmental competence is compromised
Authors: Kowsar Rasoul , Ronasi Shahrzad , Sadeghi Nima , Sadeghi Khaled , Miyamoto Akio
Published: February 2021

Upon insemination, sperm cells are exposed to components of the female reproductive tract (FRT) fluids, such as urea and epidermal growth factor (EGF). It has been shown that both urea and EGF use EGF receptor signaling and produce reactive oxygen species (ROS) that are required at certain levels for sperm capacitation and acrosome reaction. We therefore hypothesized that during bovine sperm capacitation, a high level of urea and EGF could interfere with sperm function through overproduction of ROS. High-level urea (40 mg/dl urea is equal to 18.8 mg/dl of blood urea nitrogen) significantly increased ROS production and TUNEL-positive sperm (sperm DNA fragmentation, sDF) percentage, but decreased HOS test score, progressive motility, acrosome reaction and capacitation. The EGF reversed the negative effects of urea on all sperm parameters, with the exception of ROS production and DNA fragmentation, which were higher in urea-EGF-incubated sperm than in control-sperm. The developmental competence of oocytes inseminated with urea-EGF-incubated sperm was significantly reduced compared to the control. A close association of ROS production or sDF with 0-pronuclear and sperm non-capacitation rates was found in the network analysis. In conclusion, EGF enhanced urea-reduced sperm motility; however, it failed to reduce urea-increased sperm ROS or sDF levels and to enhance subsequent oocyte competence. The data suggests that any study to improve sperm quality should be followed by a follow-up assessment of the fertilization outcome.
Generalization of intrinsic ductile-to-brittle criteria by Pugh and Pettifor for materials with a cubic crystal structure
Authors: Senkov O. N. , Miracle D. B.
Published: February 2021

Two classical criteria, by Pugh and Pettifor, have been widely used by metallurgists to predict whether a material will be brittle or ductile. A phenomenological correlation by Pugh between metal brittleness and its shear modulus to bulk modulus ratio was established more than 60 years ago. Nearly four decades later Pettifor conducted a quantum mechanical analysis of bond hybridization in a series of intermetallics and derived a separate ductility criterion based on the difference between two single-crystal elastic constants, C12–C44. In this paper, we discover the link between these two criteria and show that they are identical for materials with cubic crystal structures.
Study of patterned GaAsSbN nanowires using sigmoidal model
Authors: Johnson Sean , Pokharel Rabin , Lowe Michael , Kuchoor Hirandeep , Nalamati Surya , Davis Klinton , Rathnayake Hemali , Iyer Shanthi
Published: February 2021

This study presents the first report on patterned nanowires (NWs) of dilute nitride GaAsSbN on p-Si (111) substrates by self-catalyzed plasma-assisted molecular beam epitaxy. Patterned NW array with GaAsSbN of Sb composition of 3% as a stem provided the best yield of vertical NWs. Large bandgap tuning of ~ 75 meV, as ascertained from 4 K photoluminescence (PL), over a pitch length variation of 200–1200 nm has been demonstrated. Pitch-dependent axial and radial growth rates show a logistic sigmoidal growth trend different from those commonly observed in other patterned non-nitride III–V NWs. The sigmoidal fitting provides further insight into the PL spectral shift arising from differences in Sb and N incorporation from pitch induced variation in secondary fluxes. Results indicate that sigmoidal fitting can be a potent tool for designing patterned NW arrays of optimal pitch length for dilute nitrides and other highly mismatched alloys and heterostructures.
Rapid in situ quantification of the strobilurin resistance mutation G143A in the wheat pathogen Blumeria graminis f. sp. tritici
Authors: Dodhia Kejal N. , Cox Belinda A. , Oliver Richard P. , Lopez-Ruiz Francisco J.
Published: February 2021

As the incidence of fungicide resistance in plant pathogens continues to increase, control of diseases and the management of resistance would be greatly aided by rapid diagnostic methods. Quantitative allele-specific PCR (ASqPCR) is an ideal technique for the in-field analysis of fungicide resistance as it can quantify the frequency of mutations in fungicide targets. We have applied this technique to the fungal pathogen Blumeria graminis f. sp. tritici (Bgt), the causal agent of wheat powdery mildew. In Australia, strobilurin-resistant Bgt was first discovered in 2016. Molecular analysis revealed a nucleotide transversion in the cytochrome b (cytb) gene in the cytochrome bc1 enzyme complex, resulting in a substitution of alanine for glycine at position 143 (G143A). We have developed an in-field ASqPCR assay that can quantify both the resistant (A143) and sensitive (G143) cytb alleles down to 1.67% in host and Bgt DNA mixtures, within 90 min of sample collection. The in situ analysis of samples collected during a survey in Tasmania revealed A143 frequencies ranging between 9–100%. Validation of the analysis with a newly developed laboratory based digital PCR assay found no significant differences between the two methods. We have successfully developed an in-field quantification method, for a strobilurin-resistant allele, by pairing the ASqPCR assay on a lightweight qPCR instrument with a quick DNA extraction method. The deployment of these type of methodologies in the field can contribute to the effective in-season management of fungicide resistance.
Management of retinopathy of prematurity (ROP) in a Polish cohort of infants
Authors: Chmielarz-Czarnocińska Anna , Pawlak Marta , Szpecht Dawid , Choręziak Aneta , Szymankiewicz-Bręborowicz Marta , Gotz-Więckowska Anna
Published: February 2021

Retinopathy of prematurity (ROP) is potentially blinding, but screening and timely treatment can stop its progression. The data on treatment outcomes of ROP from Central and Eastern Europe are scarce. Therefore, we aimed to analyze the latest results of ROP management in Poznan medical center to update the data from this world region. In the years 2016–2019, 178 patients (350 eyes) received treatment for ROP (6.1% of the screened population). The mean gestational age was 26 weeks (range 22–31 weeks), the mean birth weight was 868 g (range 410–1890 g). The most frequent ROP stage at treatment was zone II, stage 3 + (34.9%). As the first line of treatment, 115 infants (226 eyes, 64.6%) underwent laser photocoagulation (LP); 61 infants (120 eyes, 34.3%) received intravitreal ranibizumab injections (IVR); and 2 infants (4 eyes, 0.6%) were treated simultaneously with LP and IVR. One hundred twenty-six eyes (36%) of 63 patients required retreatment: 20.4% treated with LP and 66.7% treated with IVR. Retinal detachment occurred in 14 eyes (4%). The incidence of ROP, ROP requiring treatment, and reoccurrence rates are higher in the Polish population than in Western Europe and the USA. The identified treatment patterns find increasing use of anti-VEGF agents.
High miR-451 expression in peripheral blood mononuclear cells from subjects at risk of developing rheumatoid arthritis
Authors: Prajzlerová Klára , Kryštůfková Olga , Hánová Petra , Horváthová Veronika , Gregová Monika , Pavelka Karel , Vencovský Jiří , Šenolt Ladislav , Filková Mária
Published: February 2021

Individuals carrying anti-citrullinated protein antibodies (ACPA) are considered at high risk of developing rheumatoid arthritis (RA). The altered expression of miRNAs contributes to the pathogenesis of RA. We aimed to identify differentially expressed miRNAs in the peripheral blood of ACPA-positive individuals with arthralgia at risk of RA compared to healthy controls (HC) and to determine their implications in the preclinical phase of RA. A comprehensive analysis of miRNAs revealed the dysregulation of miR-451 in peripheral blood mononuclear cells (PBMC) and plasma from RA-risk individuals. Higher miR-451 expression in PBMC from RA-risk individuals was further validated. Notably, miR-451 was previously shown to regulate CXCL16, a protein involved in RA pathogenesis. The expression of miR-451 in PBMC positively correlated with the CXCL16 mRNA, which could be secondary to the inflammation-induced expression of miR-451. Transfection of monocytes with pre-miR-451 in vitro resulted in the downregulation of CXCL16. Moreover, flow cytometry revealed a lower count of CXCL16-positive monocytes in RA-risk individuals. We propose that the constitutive or inflammation-induced upregulation of miR-451 in PBMC downregulates the expression of CXCL16, reduces the inflammatory milieu and thereby strives to delay the shift from the preclinical phase to the clinical manifestation of RA. This hypothesis warrants further investigation.
Preparation and characterization of multiphase ceramic designer waste forms
Authors: Clark Braeden M. , Tumurugoti Priyatham , Sundaram Shanmugavelayutham K. , Amoroso Jake W. , Marra James C.
Published: February 2021

The long-term performance, or resistance to elemental release, is the defining characteristic of a nuclear waste form. In the case of multiphase ceramic waste forms, correlating the long-term performance of multiphase ceramic waste forms in the environment to accelerated chemical durability testing in the laboratory is non-trivial owing to their complex microstructures. The fabrication method, which in turn affects the microstructure, is further compounding when comparing multiphase ceramic waste forms. In this work, we propose a “designer waste form” prepared via spark plasma sintering to limit interaction between phases and grain growth during consolidation, leading to monolithic high-density waste forms, which can be used as reference materials for comparing the chemical durability of multiphase waste forms. Designer waste forms containing varying amounts of hollandite in the presence of zirconolite and pyrochlore in a fixed ratio were synthesized. The product consistency test (PCT) and vapor hydration test (VHT) were used to assess the leaching behavior. Samples were unaffected by the VHT after 1500 h. As measured by the PCT, the fractional Cs release decreased as the amount of hollandite increased. Elemental release from the zirconolite and pyrochlore phases did not appear to significantly contribute to the elemental release from the hollandite phase in the designer waste forms.
Monocarboxylate transporter-1 (MCT1) protein expression in head and neck cancer affects clinical outcome
Authors: Leu Martin , Kitz J. , Pilavakis Y. , Hakroush S. , Wolff H. A. , Canis M. , Rieken S. , Schirmer M. A.
Published: February 2021

Treatment of locally advanced, unresectable head and neck squamous cell carcinoma (HNSCC) often yields only modest results with radiochemotherapy (RCT) as standard of care. Prognostic features related to outcome upon RCT might be highly valuable to improve treatment. Monocarboxylate transporters-1 and -4 (MCT1/MCT4) were evaluated as potential biomarkers. A cohort of HNSCC patients without signs for distant metastases was assessed eliciting 82 individuals eligible whereof 90% were diagnosed with locally advanced stage IV. Tumor specimens were stained for MCT1 and MCT4 in the cell membrane by immunohistochemistry. Obtained data were evaluated with respect to overall (OS) and progression-free survival (PFS). Protein expression of MCT1 and MCT4 in cell membrane was detected in 16% and 85% of the tumors, respectively. Expression of both transporters was not statistically different according to the human papilloma virus (HPV) status. Positive staining for MCT1 (n = 13, negative in n = 69) strongly worsened PFS with a hazard ratio (HR) of 3.1 (95%-confidence interval 1.6–5.7, p < 0.001). OS was likewise affected with a HR of 3.8 (2.0–7.3, p < 0.001). Multivariable Cox regression confirmed these findings. We propose MCT1 as a promising biomarker in HNSCC treated by primary RCT.
Redox signaling through zinc activates the radiation response in Deinococcus bacteria
Authors: Magerand Romaric , Rey Pascal , Blanchard Laurence , de Groot Arjan
Published: February 2021

Deinococcus bacteria are extremely resistant to radiation and other DNA damage- and oxidative stress-generating conditions. An efficient SOS-independent response mechanism inducing expression of several DNA repair genes is essential for this resistance, and is controlled by metalloprotease IrrE that cleaves and inactivates transcriptional repressor DdrO. Here, we identify the molecular signaling mechanism that triggers DdrO cleavage. We show that reactive oxygen species (ROS) stimulate the zinc-dependent metalloprotease activity of IrrE in Deinococcus. Sudden exposure of Deinococcus to zinc excess also rapidly induces DdrO cleavage, but is not accompanied by ROS production and DNA damage. Further, oxidative treatment leads to an increase of intracellular free zinc, indicating that IrrE activity is very likely stimulated directly by elevated levels of available zinc ions. We conclude that radiation and oxidative stress induce changes in redox homeostasis that result in IrrE activation by zinc in Deinococcus. We propose that a part of the zinc pool coordinated with cysteine thiolates is released due to their oxidation. Predicted regulation systems involving IrrE- and DdrO-like proteins are present in many bacteria, including pathogens, suggesting that such a redox signaling pathway including zinc as a second messenger is widespread and participates in various stress responses.
Alterations in intestinal microbiota diversity, composition, and function in patients with sarcopenia
Authors: Kang Lin , Li Pengtao , Wang Danyang , Wang Taihao , Hao Dong , Qu Xuan
Published: February 2021

16S rRNA sequencing of human fecal samples has been tremendously successful in identifying microbiome changes associated with both aging and disease. A number of studies have described microbial alterations corresponding to physical frailty and nursing home residence among aging individuals. A gut-muscle axis through which the microbiome influences skeletal muscle growth/function has been hypothesized. However, the microbiome has yet to be examined in sarcopenia. Here, we collected fecal samples of 60 healthy controls (CON) and 27 sarcopenic (Case)/possibly sarcopenic (preCase) individuals and analyzed the intestinal microbiota using 16S rRNA sequencing. We observed an overall reduction in microbial diversity in Case and preCase samples. The genera Lachnospira, Fusicantenibacter, Roseburia, Eubacterium, and Lachnoclostridium—known butyrate producers—were significantly less abundant in Case and preCase subjects while Lactobacillus was more abundant. Functional pathways underrepresented in Case subjects included numerous transporters and phenylalanine, tyrosine, and tryptophan biosynthesis suggesting that protein processing and nutrient transport may be impaired. In contrast, lipopolysaccharide biosynthesis was overrepresented in Case and PreCase subjects suggesting that sarcopenia is associated with a pro-inflammatory metagenome. These analyses demonstrate structural and functional alterations in the intestinal microbiota that may contribute to loss of skeletal muscle mass and function in sarcopenia.
Novel method for screening functional antibody with comprehensive analysis of its immunoliposome
Authors: Hamamichi Shusei , Fukuhara Takeshi , Umeda Izumi O. , Fujii Hirofumi , Hattori Nobutaka
Published: February 2021

Development of monoclonal antibody is critical for targeted drug delivery because its characteristics determine improved therapeutic efficacy and reduced side-effect. Antibody therapeutics target surface molecules; hence, internalization is desired for drug delivery. As an antibody–drug conjugate, a critical parameter is drug-to-antibody ratio wherein the quantity of drugs attached to the antibody influences the antibody structure, stability, and efficacy. Here, we established a cell-based immunotoxin screening system to facilitate the isolation of functional antibodies with internalization capacities, and discovered an anti-human CD71 monoclonal antibody. To overcome the limitation of drug-to-antibody ratio, we employed the encapsulation capacity of liposome, and developed anti-CD71 antibody-conjugated liposome that demonstrated antigen–antibody dependent cellular uptake when its synthesis was optimized. Furthermore, anti-CD71 antibody-conjugated liposome encapsulating doxorubicin demonstrated antigen–antibody dependent cytotoxicity. In summary, this study demonstrates the powerful pipeline to discover novel functional antibodies, and the optimal method to synthesize immunoliposomes. This versatile technology offers a rapid and direct approach to generate antibodies suitable for drug delivery modalities.
Inefficiency of SIR models in forecasting COVID-19 epidemic: a case study of Isfahan
Authors: Moein Shiva , Nickaeen Niloofar , Roointan Amir , Borhani Niloofar , Heidary Zarifeh , Javanmard Shaghayegh Haghjooy , Ghaisari Jafar , Gheisari Yousof
Published: February 2021

The multifaceted destructions caused by COVID-19 have been compared to that of World War II. What makes the situation even more complicated is the ambiguity about the duration and ultimate spread of the pandemic. It is especially critical for the governments, healthcare systems, and economic sectors to have an estimate of the future of this disaster. By using different mathematical approaches, including the classical susceptible-infected-recovered (SIR) model and its derivatives, many investigators have tried to predict the outbreak of COVID-19. In this study, we simulated the epidemic in Isfahan province of Iran for the period from Feb 14th to April 11th and also forecasted the remaining course with three scenarios that differed in terms of the stringency level of social distancing. Despite the prediction of disease course in short-term intervals, the constructed SIR model was unable to forecast the actual spread and pattern of epidemic in the long term. Remarkably, most of the published SIR models developed to predict COVID-19 for other communities, suffered from the same inconformity. The SIR models are based on assumptions that seem not to be true in the case of the COVID-19 epidemic. Hence, more sophisticated modeling strategies and detailed knowledge of the biomedical and epidemiological aspects of the disease are needed to forecast the pandemic.