bluuebunny/crossref_metadata_2025 huggingface dataset:
The Observed Agulhas Retroflection Behaviors During 1993–2018
Authors: Zhu Yanan , Li Yuanlong , Zhang Zhengguang , Qiu Bo , Wang Fan
Published: December 2021

Near the southern tip of the African continent, the Agulhas Current retroflects eastward to feed the Agulhas Return Current, giving rise to the Agulhas Retroflection (AR). The AR is dynamically unstable and radiates eddies and rings that constitute a portion of the Agulhas leakage. In this study, by analyzing 26 years (1993–2018) of updated satellite altimetry data, the spatial and temporal characteristic of the surface AR point are revisited. By adopting a refined identification algorithm of the AR point, we show that the AR longitude (XAR) fluctuates widely between 7° and 27°E on timescales ranging from days to months, without a stable seasonal cycle. The XAR variability also shows evident temporal asymmetry with shorter residence time at western positions. The retreat of the AR from the western to eastern positions tends to be swift, with 46% of the events completed in one day. In comparison, the intrusion from the eastern to western positions is much slower, with 32% of the events taking more than one month. The energy transfer from the mean flow to mesoscale eddies is likely the primary regime underlying the AR variability. Further analysis suggests that the AR variability causes sea surface temperature anomalies of ∼0.5°C through anomalous advection and thereby gives rise to turbulent heat flux anomalies of ∼10 W m−2, exerting potential impacts on the local climate.
Investigating the Influence of Ethical and Epistemic Values on Decisions in the Watershed Modeling Process
Authors: Deitrick Autumn R. , Torhan Sarah A. , Grady Caitlin A.
Published: December 2021

Throughout the watershed modeling process, modelers, collaborators, and stakeholders make decisions about how to study various challenges that impact watersheds. To understand these decisions, we investigated values held by modelers who have worked or collaborated on projects within the Chesapeake Bay Watershed and their influence on decisions made during the modeling process. Using a mixed‐methodological approach, we designed an online survey and semistructured interviews to evaluate these complexities. In total, we received 27 survey responses from Chesapeake Bay Watershed modelers and conducted four semistructured interviews. The results indicate that ethical and epistemic values impact every stage of the watershed modeling process. These values occur alongside decisions, motivations, outcomes, and objectives that often involve collaborators and stakeholders in addition to the modelers. Therefore, including these values in scientific discourse can increase transparency around watershed modeling that guides policy decision making processes. Our results articulate that a discussion of the ethical and epistemic values present throughout the watershed modeling process should be incorporated into model documentation to clearly explain assumptions and decisions.
Phage co-transport with hyphal-riding bacteria fuels bacterial invasion in a water-unsaturated microbial model system
Authors: You Xin , Kallies René , Kühn Ingolf , Schmidt Matthias , Harms Hauke , Chatzinotas Antonis , Wick Lukas Y
Published: December 2021

Nonmotile microorganisms often enter new habitats by co-transport with motile microorganisms. Here, we report that also lytic phages can co-transport with hyphal-riding bacteria and facilitate bacterial colonization of a new habitat. This is comparable to the concept of biological invasions in macroecology. In analogy to invasion frameworks in plant and animal ecology, we tailored spatially organized, water-unsaturated model microcosms using hyphae of Pythium ultimum as invasion paths and flagellated soil-bacterium Pseudomonas putida KT2440 as carrier for co-transport of Escherichia virus T4. P. putida KT2440 efficiently dispersed along P. ultimum to new habitats and dispatched T4 phages across air gaps transporting ≈0.6 phages bacteria−1. No T4 displacement along hyphae was observed in the absence of carrier bacteria. If E. coli occupied the new habitat, T4 co-transport fueled the fitness of invading P. putida KT2440, while the absence of phage co-transport led to poor colonization followed by extinction. Our data emphasize the importance of hyphal transport of bacteria and associated phages in regulating fitness and composition of microbial populations in water-unsaturated systems. As such co-transport seems analogous to macroecological invasion processes, hyphosphere systems with motile bacteria and co-transported phages could be useful models for testing hypotheses in invasion ecology.
Understanding X-ray absorption spectra by means of descriptors and machine learning algorithms
Authors: Guda A. A. , Guda S. A. , Martini A. , Kravtsova A. N. , Algasov A. , Bugaev A. , Kubrin S. P. , Guda L. V. , Šot P. , van Bokhoven J. A. , Copéret C. , Soldatov A. V.
Published: December 2021

X-ray absorption near-edge structure (XANES) spectra are the fingerprint of the local atomic and electronic structures around the absorbing atom. However, the quantitative analysis of these spectra is not straightforward. Even with the most recent advances in this area, for a given spectrum, it is not clear a priori which structural parameters can be refined and how uncertainties should be estimated. Here, we present an alternative concept for the analysis of XANES spectra, which is based on machine learning algorithms and establishes the relationship between intuitive descriptors of spectra, such as edge position, intensities, positions, and curvatures of minima and maxima on the one hand, and those related to the local atomic and electronic structure which are the coordination numbers, bond distances and angles and oxidation state on the other hand. This approach overcoms the problem of the systematic difference between theoretical and experimental spectra. Furthermore, the numerical relations can be expressed in analytical formulas providing a simple and fast tool to extract structural parameters based on the spectral shape. The methodology was successfully applied to experimental data for the multicomponent Fe:SiO2system and reference iron compounds, demonstrating the high prediction quality for both the theoretical validation sets and experimental data.
Statin Use and In-hospital Mortality in Patients with COVID-19 and Coronary Heart Disease
Authors: Shen Lan , Qiu Lin , Wang Li , Huang Hengye , Liu Dong , Xiao Ying , Liu Yi , Jin Jingjin , Liu Xiulan , Wang Dao Wen , He Ben , Zhou Ning
Published: December 2021

The worsening progress of coronavirus disease 2019 (COVID-19) is attributed to the proinflammatory state, leading to increased mortality. Statin works with its anti-inflammatory effects and may attenuate the worsening of COVID-19. COVID-19 patients were retrospectively enrolled from two academic hospitals in Wuhan, China, from 01/26/2020 to 03/26/2020. Adjusted in-hospital mortality was compared between the statin and the non-statin group by CHD status using multivariable Cox regression model after propensity score matching. Our study included 3133 COVID-19 patients (median age: 62y, female: 49.8%), and 404 (12.9%) received statin. Compared with the non-statin group, the statin group was older, more likely to have comorbidities but with a lower level of inflammatory markers. The Statin group also had a lower adjusted mortality risk (6.44% vs. 10.88%; adjusted hazard ratio [HR] 0.47; 95% CI, 0.29–0.77). Subgroup analysis of CHD patients showed a similar result. Propensity score matching showed an overall 87% (HR, 0.13; 95% CI, 0.05–0.36) lower risk of in-hospital mortality for statin users than nonusers. Such survival benefit of statin was obvious both among CHD and non-CHD patients (HR = 0.30 [0.09–0.98]; HR = 0.23 [0.1–0.49], respectively). Statin use was associated with reduced in-hospital mortality in COVID-19. The benefit of statin was both prominent among CHD and non-CHD patients. These findings may further reemphasize the continuation of statins in patients with CHD during the COVID-19 era.
Simple phasor-based deep neural network for fluorescence lifetime imaging microscopy
Authors: Héliot Laurent , Leray Aymeric
Published: December 2021

Fluorescence lifetime imaging microscopy (FLIM) is a powerful technique to probe the molecular environment of fluorophores. The analysis of FLIM images is usually performed with time consuming fitting methods. For accelerating this analysis, sophisticated deep learning architectures based on convolutional neural networks have been developed for restrained lifetime ranges but they require long training time. In this work, we present a simple neural network formed only with fully connected layers able to analyze fluorescence lifetime images. It is based on the reduction of high dimensional fluorescence intensity temporal decays into four parameters which are the phasor coordinates, the mean and amplitude-weighted lifetimes. This network called Phasor-Net has been applied for a time domain FLIM system excited with an 80 MHz laser repetition frequency, with negligible jitter and afterpulsing. Due to the restricted time interval of 12.5 ns, the training range of the lifetimes was limited between 0.2 and 3.0 ns; and the total photon number was lower than 106, as encountered in live cell imaging. From simulated biexponential decays, we demonstrate that Phasor-Net is more precise and less biased than standard fitting methods. We demonstrate also that this simple architecture gives almost comparable performance than those obtained from more sophisticated networks but with a faster training process (15 min instead of 30 min). We finally apply successfully our method to determine biexponential decays parameters for FLIM experiments in living cells expressing EGFP linked to mCherry and fused to a plasma membrane protein.
Oligonucleotide conjugated antibody strategies for cyclic immunostaining
Authors: Jones Jocelyn A. , McMahon Nathan P. , Zheng Ting , Eng Jennifer , Chin Koei , Kwon Sunjong , Nederlof Michel A. , Gray Joe W. , Gibbs Summer L.
Published: December 2021

A number of highly multiplexed immunostaining and imaging methods have advanced spatial proteomics of cancer for improved treatment strategies. While a variety of methods have been developed, the most widely used methods are limited by harmful signal removal techniques, difficulties with reagent production and antigen sensitivity. Multiplexed immunostaining employing oligonucleotide (oligos)-barcoded antibodies is an alternative approach that is growing in popularity. However, challenges remain in consistent conjugation of oligos to antibodies with maintained antigenicity as well as non-destructive, robust and cost-effective signal removal methods. Herein, a variety of oligo conjugation and signal removal methods were evaluated in the development of a robust oligo conjugated antibody cyclic immunofluorescence (Ab-oligo cyCIF) methodology. Both non- and site-specific conjugation strategies were assessed to label antibodies, where site-specific conjugation resulted in higher retained binding affinity and antigen-specific staining. A variety of fluorescence signal removal methods were also evaluated, where incorporation of a photocleavable link (PCL) resulted in full fluorescence signal removal with minimal tissue disruption. In summary, this work resulted in an optimized Ab-oligo cyCIF platform capable of generating high dimensional images to characterize the spatial proteomics of the hallmarks of cancer.
Therapeutic interfering particles exploiting viral replication and assembly mechanisms show promising performance: a modelling study
Authors: Fatehi Farzad , Bingham Richard J. , Dechant Pierre-Philippe , Stockley Peter G. , Twarock Reidun
Published: December 2021

Defective interfering particles arise spontaneously during a viral infection as mutants lacking essential parts of the viral genome. Their ability to replicate in the presence of the wild-type (WT) virus (at the expense of viable viral particles) is mimicked and exploited by therapeutic interfering particles. We propose a strategy for the design of therapeutic interfering RNAs (tiRNAs) against positive-sense single-stranded RNA viruses that assemble via packaging signal-mediated assembly. These tiRNAs contain both an optimised version of the virus assembly manual that is encoded by multiple dispersed RNA packaging signals and a replication signal for viral polymerase, but lack any protein coding information. We use an intracellular model for hepatitis C viral (HCV) infection that captures key aspects of the competition dynamics between tiRNAs and viral genomes for virally produced capsid protein and polymerase. We show that only a small increase in the assembly and replication efficiency of the tiRNAs compared with WT virus is required in order to achieve a treatment efficacy greater than 99%. This demonstrates that the proposed tiRNA design could be a promising treatment option for RNA viral infections.
Experimental inoculation of chicken broilers with C. gallinacea strain 15-56/1
Authors: Szymańska-Czerwińska Monika , Jodełko Agnieszka , Zaręba-Marchewka Kinga , Niemczuk Krzysztof
Published: December 2021

Chlamydia gallinacea is one of the new Chlamydia species, encountered predominantly in birds and occasionally in cattle, and its dissemination, pathogenicity and zoonotic potential have not yet been fully elucidated. Until now, no case of clinical infection has been described in poultry, but the number of studies is limited. This study was conducted to evaluate the course of infection and the impact on production parameters in chicken broilers inoculated with the strain 15-56/1 isolated from a Polish flock. The presence of C. gallinacea was confirmed in oropharyngeal and cloacal swabs by real-time PCR from the fifth day post inoculation (dpi). Pathogen DNA was also detected in many internal organs of inoculated chickens. All infected animals remained asymptomatic during the entire experimental period, although statistical analyses showed that broilers in the experimental group exhibited significantly lower body weight gains and feed conversion ratios than animals in the control group. These data indicate that subclinical C. gallinacea infection in broilers may lead to financial losses for poultry farmers.
The long term participation trend for the colorectal cancer screening after the 2011 triple disaster in Minamisoma City, Fukushima, Japan
Authors: Saito Hiroaki , Ozaki Akihiko , Murakami Michio , Nishikawa Yoshitaka , Sawano Toyoaki , Fujioka Sho , Shimada Yuki , Zhao Tianchen , Oikawa Tomoyoshi , Kanazawa Yukio , Tsubokura Masaharu
Published: December 2021

Colorectal cancer (CRC) screening is a well-established cancer screening method, and its effectiveness depends on maintaining a high participation rate in the target population. In this study, we analyzed the trends in CRC screening participation rates over 10 years in Minamisoma City, where residents were forced to evacuate after the 2011 triple disaster in Fukushima, Japan. The immunochemical fecal occult blood test is provided as municipal CRC screening. We calculated the annual CRC screening participation rate and analyzed the factors associated with participation in screening. Overall, 4069 (12.3%) and 3839 (11.7%) persons participated in CRC screening in 2009 and 2010, respectively; however, the number decreased significantly to 1090 (3.4%) in 2011 when the earthquake occurred. Over the following 3 years, the rate gradually recovered. Multivariable logistic analysis showed that age < 65 years, living alone, and evacuation were significant associated factors for non-participation after 2011 (p < 0.05). In conclusion, the CRC screening participation rate decreased significantly during the Great East Japan Earthquake but recovered over the next 3 years. Further analysis of factors preventing CRC screening participation and research on the long-term effects of its post-disaster decline are important to consider in assessing the need for intervention in post-disaster cancer screening.
Full-thickness macular hole formation in proliferative diabetic retinopathy
Authors: Tsui Mei-Chi , Hsieh Yi-Ting , Lai Tso-Ting , Lai Chun-Ting , Lin Hsuan-Chieh , Ho Tzyy-Chang , Yang Chang-Hao , Yang Chung-May , Wang Lu-Chun
Published: December 2021

Twenty-one consecutive patients (21 eyes) having proliferative diabetic retinopathy (PDR) and fibrovascular proliferation (FVP) with optical coherence tomography (OCT) available before and after full-thickness macular hole (FTMH) formation were retrospectively reviewed. Four types of FTMH formation pathways in PDR were identified and were quite different from those in idiopathic conditions. The activity, severity and locations of FVP varied in PDR eyes destined to develop FTMHs. Type 1 was characterized by epiretinal membrane (ERM) and/or vitreomacular traction (VMT) inducing foveoschisis, intraretinal cysts or foveal detachment, followed by formation of a FTMH or macular hole retinal detachment (MHRD). In type 2, ERM and/or FVP induced lamellar macular hole (LMH) with foveoschisis, followed by the formation of FTMH or MHRD. Type 3 was characterized by the initial tractional retinal detachment (TRD) with foveal cysts and/or foveoschisis and the subsequent formation of MHRD. Type 4 was characterized by TRD associated with foveal thinning, ensued by the formation of MHRD. The severity of FVP was grade 2 in 66.7% of eyes in both types 1 and 4, and grade 3 in 75% of eyes in type 3 while the severity of FVP was more evenly distributed in type 2.
Human organ donor-derived vagus nerve biopsies allow for well-preserved ultrastructure and high-resolution mapping of myelinated and unmyelinated fibers
Authors: Havton Leif A. , Biscola Natalia P. , Stern Esther , Mihaylov Plamen V. , Kubal Chandrashekhar A. , Wo John M. , Gupta Anita , Baronowsky Elizabeth , Ward Matthew P. , Jaffey Deborah M. , Powley Terry L.
Published: December 2021

The vagus nerve provides motor, sensory, and autonomic innervation of multiple organs, and electrical vagus nerve stimulation (VNS) provides an adjunctive treatment option for e.g. medication-refractory epilepsy and treatment-resistant depression. The mechanisms of action for VNS are not known, and high-resolution anatomical mapping of the human vagus nerve is needed to better understand its functional organization. Electron microscopy (EM) is required for the detection of both myelinated and unmyelinated axons, but access to well-preserved human vagus nerves for ultrastructural studies is sparse. Intact human vagus nerve samples were procured intra-operatively from deceased organ donors, and tissues were immediately immersion fixed and processed for EM. Ultrastructural studies of cervical and sub-diaphragmatic vagus nerve segments showed excellent preservation of the lamellated wall of myelin sheaths, and the axolemma of myelinated and unmyelinated fibers were intact. Microtubules, neurofilaments, and mitochondria were readily identified in the axoplasm, and the ultrastructural integrity of Schwann cell nuclei, Remak bundles, and basal lamina was also well preserved. Digital segmentation of myelinated and unmyelinated axons allowed for determination of fiber size and myelination. We propose a novel source of human vagus nerve tissues for detailed ultrastructural studies and mapping to support efforts to refine neuromodulation strategies, including VNS.
Exploring the legacy of Central European historical winter wheat landraces
Authors: Cseh András , Poczai Péter , Kiss Tibor , Balla Krisztina , Berki Zita , Horváth Ádám , Kuti Csaba , Karsai Ildikó
Published: December 2021

Historical wheat landraces are rich sources of genetic diversity offering untapped reservoirs for broadening the genetic base of modern varieties. Using a 20K SNP array, we investigated the accessible genetic diversity in a Central European bread wheat landrace collection with great drought, heat stress tolerance and higher tillering capacity. We discovered distinct differences in the number of average polymorphisms between landraces and modern wheat cultivars, and identified a set of novel rare alleles present at low frequencies in the landrace collection. The detected polymorphisms were unevenly distributed along the wheat genome, and polymorphic markers co-localized with genes of great agronomic importance. The geographical distribution of the inferred Bayesian clustering revealed six genetically homogenous ancestral groups among the collection, where the Central European core bared an admixed background originating from four ancestral groups. We evaluated the effective population sizes (Ne) of the Central European collection and assessed changes in diversity over time, which revealed a dramatic ~ 97% genetic erosion between 1955 and 2015.
Effect of sleeve gastrectomy, Roux-en-Y gastric bypass, and ileal transposition on myocardial ischaemia–reperfusion injury in non-obese non-diabetic rats
Authors: Kornyushin Oleg , Sonin Dmitry , Polozov Alexander , Masley Vitaly , Bulavinova Nika , Chervyak Maria , Istomina Maria , Mukhametdinova Daria , Neimark Alexander , Cheburkin Yuri , Toropova Yana , Derkach Kira , Shpakov Alexander , Galagudza Michael , Shlyakhto Evgenyi
Published: December 2021

Bariatric surgery (BS) improves outcomes in patients with myocardial infarction (MI). Here we tested the hypothesis that BS-mediated reduction in fatal MI could be attributed to its infarct-limiting effect. Wistar rats were randomized into five groups: control (CON), sham (SHAM), Roux-en-Y gastric bypass (RYGB), sleeve gastrectomy (SG), and ileotransposition (IT). Ten weeks later, animals were subjected to 30-min myocardial ischemia plus 120-min reperfusion. Infarct size (IS) and no-reflow area were determined histochemically. Fasting plasma levels of glucagon-like peptide-1 (GLP-1), leptin, ghrelin, and insulin were measured using ELISA. Compared with SHAM, RYGB and SG reduced IS by 22% (p = 0.011) and 10% (p = 0.027), and no-reflow by 38% (p = 0.01) and 32% (p = 0.004), respectively. IT failed to reduce IS and no-reflow. GLP-1 level was increased in the SG and RYGB groups compared with CON. In both the SG and RYGB, leptin level was decreased compared with CON and SHAM. In the SG group, ghrelin level was lower than that in the CON and SHAM. Insulin levels were not different between groups. In conclusion, RYGB and SG increased myocardial tolerance to ischemia–reperfusion injury of non-obese, non-diabetic rats, and their infarct-limiting effect is associated with decreased leptin and ghrelin levels and increased GLP-1 level.
CircFOXM1 promotes proliferation and metastasis of hepatocellular carcinoma via regulating miR-1179/SPAG5 axis
Authors: Wang Gaoqing , Jiang Yin , Lu Caide , Jiang Wei , Wu Shugeng , Hua Yongfei
Published: December 2021

Hepatocellular carcinoma (HCC) predominantly occurs in patients with chronic liver disease, accounting for 70–90% of all liver cancer cases. The role of circFOXM1/miR-1179/SPAG5 axis in HCC has not been reported. This study aimed to explore the regulatory mechanism of circFOXM1 in HCC proliferation and metastasis. RNA polymerase inhibitor actinomycin D and RNase R exonuclease were used to identify circFOXM1 in HCC cells. The qRT-PCR was used to detect circFOXM1 expression. Specific siRNA for circFOXM1 was designed, and the sequence of circFOXM1 was inserted in pLCDH-ciR to overexpress circFOXM. Cell proliferation was detected by CCK8 in vitro, by tumor volume and tumor weight of HCC xenograft in vivo. Cell migration was detected by transwell test. Binding status of circFOXM1 with miR-1179 was detected by luciferase reporter gene assay. Rescue experiments were applied to identify the oncogenic mechanism of circFOXM1 in HCC cells. Actinomycin D assay confirmed the cyclization of circFOXM1. RNase R treatment showed that circFOXM1 was not affected by RNase R exonuclease. CCK8 assay, tumor volume and tumor weight showed that circFOXM1 effectively promoted HCC cell proliferation. Transwell assay showed that circFOXM effectively promoted migration and invasion abilities of HCC cells. Luciferase reporter gene activity assay showed that miR-1179 had complementary binding sites with circFOXM1 and SPAG5. CircFOXM1 silencing inhibited malignant phenotypes in HCC cells were partly rescued by either miR-1179 silencing or SPAG5 overexpression. CircFOXM1 promoted HCC cell proliferation and metastasis by regulating miR-1179/SPAG5 axis.
More DNA and RNA of HBV SP1 splice variants are detected in genotypes B and C at low viral replication
Authors: Luk Ka-Cheung , Gersch Jeffrey , Harris Barbara J. , Holzmayer Vera , Mbanya Dora , Sauleda Silvia , Rodgers Mary A. , Cloherty Gavin
Published: December 2021

HBV produces unspliced and spliced RNAs during replication. Encapsidated spliced RNA is converted into DNA generating defective virions that are detected in plasma and associated with HCC development. Herein we describe a quantitative real-time PCR detection of splice variant SP1 DNA/RNA in HBV plasma. Three PCR primers/probe sets were designed detecting the SP1 variants, unspliced core, or X gene. Plasmids carrying the three regions were constructed for the nine HBV genotypes to evaluate the three sets, which were also tested on DNA/RNA extracted from 193 HBV plasma with unknown HCC status. The assay had an LOD of 80 copies/ml and was equally efficient for detecting all nine genotypes and three targets. In testing 84 specimens for both SP1 DNA (77.4%) and RNA (82.1%), higher viral loads resulted in increased SP1 levels. Most samples yielded < 1% of SP1 DNA, while the average SP1 RNA was 3.29%. At viral load of ≤ 5 log copies/ml, the detectable SP1 DNA varied by genotype, with 70% for B, 33.3% for C, 10.5% for E, 4% for D and 0% for A, suggesting higher levels of splicing in B and C during low replication. At > 5 log, all samples regardless of genotype had detectable SP1 DNA.
Determination of biomarkers from microarray data using graph neural network and spectral clustering
Authors: Yu Kun , Xie Weidong , Wang Linjie , Zhang Shoujia , Li Wei
Published: December 2021

In bioinformatics, the rapid development of gene sequencing technology has produced an increasing amount of microarray data. This type of data shares the typical characteristics of small sample size and high feature dimensions. Searching for biomarkers from microarray data, which expression features of various diseases, is essential for the disease classification. feature selection has therefore became fundemental for the analysis of microarray data, which designs to remove irrelevant and redundant features. There are a large number of redundant features and irrelevant features in microarray data, which severely degrade the classification effectiveness. We propose an innovative feature selection method with the goal of obtaining feature dependencies from a priori knowledge and removing redundant features using spectral clustering. In this paper, the graph structure is firstly constructed by using the gene interaction network as a priori knowledge, and then a link prediction method based on graph neural network is proposed to enhance the graph structure data. Finally, a feature selection method based on spectral clustering is proposed to determine biomarkers. The classification accuracy on DLBCL and Prostate can be improved by 10.90% and 16.22% compared to traditional methods. Link prediction provides an average classification accuracy improvement of 1.96% and 1.31%, and is up to 16.98% higher than the published method. The results show that the proposed method can have full use of a priori knowledge to effectively select disease prediction biomarkers with high classification accuracy.
Generation of mutant pigs by lipofection-mediated genome editing in embryos
Authors: Hirata Maki , Wittayarat Manita , Namula Zhao , Le Quynh Anh , Lin Qingyi , Takebayashi Koki , Thongkittidilok Chommanart , Mito Taro , Tomonari Sayuri , Tanihara Fuminori , Otoi Takeshige
Published: December 2021

The specificity and efficiency of CRISPR/Cas9 gene-editing systems are determined by several factors, including the mode of delivery, when applied to mammalian embryos. Given the limited time window for delivery, faster and more reliable methods to introduce Cas9-gRNA ribonucleoprotein complexes (RNPs) into target embryos are needed. In pigs, somatic cell nuclear transfer using gene-modified somatic cells and the direct introduction of gene editors into the cytoplasm of zygotes/embryos by microinjection or electroporation have been used to generate gene-edited embryos; however, these strategies require expensive equipment and sophisticated techniques. In this study, we developed a novel lipofection-mediated RNP transfection technique that does not require specialized equipment for the generation of gene-edited pigs and produced no detectable off-target events. In particular, we determined the concentration of lipofection reagent for efficient RNP delivery into embryos and successfully generated MSTN gene-edited pigs (with mutations in 7 of 9 piglets) after blastocyst transfer to a recipient gilt. This newly established lipofection-based technique is still in its early stages and requires improvements, particularly in terms of editing efficiency. Nonetheless, this practical method for rapid and large-scale lipofection-mediated gene editing in pigs has important agricultural and biomedical applications.
The C-shaped root canal systems in mandibular second molars in an Emirati population
Authors: Khawaja Summayah , Alharbi Nouf , Chaudhry Jahanzeb , Khamis Amar Hasan , Abed Rashid El , Ghoneima Ahmed , Jamal Mohamed
Published: December 2021

Our study aimed to describe the root and canal morphology of mandibular second molars in Emirati population and to study the prevalence and types of morphological change in C-shaped canal configuration along the root length in an effort to describe C-shaped molars as a unit. Cone beam computed tomography (CBCT) scans of Emirati patients were analyzed in multiple plans and root and canal configuration of mandibular second molars were evaluated. Moreover, specific types of morphological change in C-shaped canal configuration along root length were studied and reconstructed using 3D reconstruction software. A total of 508 mandibular second molars were evaluated. Among the non-C-shaped mandibular second molars, two separate roots were the most prevalent root morphology (78.3%). The mesial root's most common root canal configuration was Vertucci Type II (46.5%), and in the distal root, Vertucci Type I (90.5%). The prevalence of C-shaped mandibular second molars was 17.9% and was significantly prevalent (P < 0.001) in females. Specific types of morphological change in C-shaped molars along the root length were observed and described for the first time, in which the most common types of morphological change were C1-C2-C3d (18%), C1-C3c-C3d (15.4%), C4-C3c-C3d (7.7%), and C3c-C3c-C3d (7.7%). This study showed wide variations in the root and canal morphology in mandibular second molars in Emirati population with a relatively high prevalence of C-shaped canal configuration (17.9%). Moreover, specific types of morphological change in C-shaped configuration were detected and described for the first time in this population.
Phenol-rich alternatives for Rosa x damascena Mill. Efficient phytochemical profiling using different extraction methods and colorimetric assays
Authors: Piotrowicz Zuzanna , Tabisz Łukasz , Waligórska Marta , Pankiewicz Radosław , Łęska Bogusława
Published: December 2021

Damask rose is a well-established, abundant source of phytochemicals, as well as economically important essential oil—however, its cultivation is demanding and costly. In this paper, extracts from four raw plant materials—Salvia officinalis, Sambucus nigra, Matricaria chamomilla, Calendula officinalis, known to be rich in phenolic compounds, but also far easier to cultivate—were directly compared to those obtained from Rosa × damascena Mill. By combining diverse extraction methodologies (in a Soxhlet apparatus, ultrawave-assisted and microwave-assisted, using supercritical CO2) and complementary in vitro assays (radical scavenging, iron reducing, Folin–Ciocalteau and Al3+ complexation), it was possible to conveniently approximate and compare the phytochemical portfolios of those diverse plants. By factoring in the crop yields of different species, economically important conclusions can be reached—with pot marigold (C. officinalis) seemingly the most viable substitute for damask rose as a source of phenolics. Fatty acid and microelement analyses were also performed, to further enrich the chemical profiles of plant extracts. The paper also aims to collate and redesign multiple colorimetric assays frequently used while studying plant extracts in vitro, but criticized for their lack of correlation to in vivo activity. We show that they remain a viable tool for direct comparison of extraction methodologies, while highlighting their shortcomings.
Use of near-infrared imaging using indocyanine green associates with the lower incidence of postoperative complications for intestinal and mesenteric injury
Authors: Yamaguchi Keishi , Abe Takeru , Nakajima Kento , Watanabe Chikara , Kawamura Yusuke , Suwa Hirokazu , Minami Yuta , Nojiri Kazunori , Ono Hidetaka , Yoshida Kenichi , Masui Hidenobu , Doi Tomoki , Takeuchi Ichiro
Published: December 2021

Anastomotic leakage after intestinal resection is one of the most serious complications of surgical intervention for hollow viscus injury. Adequate vascular perfusion of the anastomotic site is essential to prevent anastomotic leakage. Near-infrared imaging using indocyanine green (NIR-ICG) is useful for the objective assessment of vascular perfusion. The aim of this study was to evaluate the association of NIR-ICG with intestinal and mesenteric injuries. This was a retrospective, single-center study of patients undergoing surgery for intestinal and mesenteric injuries. NIR-ICG was used to evaluate vascular perfusion. Postoperative complications were assessed between NIR-ICG and non-NIR-ICG groups.The use of NIR-ICG was associated with a lower incidence of Clavien-Dindo grade ≥ III complications with a statistical tendency (p = 0.076). When limited to patients that underwent intestinal resection, the use of NIR-ICG was significantly associated with a lower risk of perioperative complications (p = 0.009). The use of NIR-ICG tended to associate with the lower incidence of postoperative complications after intestinal and mesenteric trauma surgery. NIR-ICG was associated with a significantly lower risk of complications in patients undergoing intestinal resection. The NIR-ICG procedure is simple and quick and is expected to be useful for intestinal and mesenteric trauma.
Near infrared spectroscopy accurately detects Trypanosoma cruzi non-destructively in midguts, rectum and excreta samples of Triatoma infestans
Authors: Tátila-Ferreira Aline , Garcia Gabriela A. , dos Santos Lilha M. B. , Pavan Márcio G. , de C. Moreira Carlos José , Victoriano Juliana C. , da Silva-Junior Renato , dos Santos-Mallet Jacenir R. , Verly Thaiane , Britto Constança , Sikulu-Lord Maggy T. , Maciel-de-Freitas Rafael
Published: December 2021

Chagas disease is a neglected tropical disease caused byTrypanosoma cruziparasite with an estimated 70 million people at risk. Traditionally, parasite presence in triatomine vectors is detected through optical microscopy which can be low in sensitivity or molecular techniques which can be costly in endemic countries. The aim of this study was to evaluate the ability of a reagent-free technique, the Near Infrared Spectroscopy (NIRS) for rapid and non-invasive detection ofT. cruziinTriatoma infestansbody parts and in wet/dry excreta samples of the insect. NIRS was 100% accurate for predicting the presence ofT. cruziinfection Dm28c strain (TcI) in either the midgut or the rectum and models developed from either body part could predict infection in the other part. Models developed to predict infection in excreta samples were 100% accurate for predicting infection in both wet and dry samples. However, models developed using dry excreta could not predict infection in wet samples and vice versa. This is the first study to report on the potential application of NIRS for rapid and non-invasive detection ofT. cruziinfection inT. infestansin the laboratory.Future work should demonstrate the capacity of NIRS to detectT. cruziin triatomines originating from the field.
Neurocomputational mechanisms underlying the subjective value of information
Authors: Goh Ariel X.-A. , Bennett Daniel , Bode Stefan , Chong Trevor T.-J.
Published: December 2021

Humans have a striking desire to actively seek new information, even when it is devoid of any instrumental utility. However, the mechanisms that drive individuals’ subjective preference for information remain unclear. Here, we used fMRI to examine the processing of subjective information value, by having participants decide how much effort they were willing to trade-off for non-instrumental information. We showed that choices were best described by a model that accounted for: (1) the variability in individuals’ estimates of uncertainty, (2) their desire to reduce that uncertainty, and (3) their subjective preference for positively valenced information. Model-based analyses revealed the anterior cingulate as a key node that encodes the subjective value of information across multiple stages of decision-making – including when information was prospectively valued, and when the outcome was definitively delivered. These findings emphasise the multidimensionality of information value, and reveal the neurocomputational mechanisms underlying the variability in individuals’ desire to physically pursue informative outcomes.
A small-molecule compound D6 overcomes EGFR-T790M-mediated resistance in non-small cell lung cancer
Authors: Tang Xiaolong , Cheng Lizhi , Li Guo , Yan Yong-Ming , Su Fengting , Huang Dan-Ling , Zhang Shuping , Liu Zuojun , Qian Minxian , Li Ji , Cheng Yong-Xian , Liu Baohua
Published: December 2021

Non-small cell lung cancer (NSCLC) is a deadly and highly prevalent malignancy. Targeting activated-EGFR mutations in NSCLC via EGFR tyrosine kinase inhibitor (EGFR-TKI) initially achieves a profound therapeutic response, but resistance frequently evolves, reducing treatment options. Here, we present a small-molecule compound D6 which selectively inhibits tumor cell growth and migration in NSCLC cells with EGFR-TKI-resistant T790M-EGFR-activated mutations (T790M-EGFR-AM), e.g., L858R/T790M, 19Del/T790M and L858R/T790M/C797S. D6 mimics a natural product isolated from the roots of Codonopsis pilosula and selectively competes with T790M-EGFR-AM to bind to HSP90, thus facilitating the ubiquitination dependent proteasomal degradation of T790M-EGFR-AM. By contrast, D6 has little impact on typical HSP90 chaperone activity, suggesting low systemic toxicity. Promisingly, D6 combined with erlotinib or osimertinib shows efficacy in overcoming the EGFR-TKIs-resistance in NSCLCs. Our study raises an alternative strategy to overcome T790M-mediated EGFR-TKI resistance in NSCLC via targeting the protein–protein interaction of HSP90 and T790M-EGFR by intervention with D6.
Peroxisomal β-oxidation acts as a sensor for intracellular fatty acids and regulates lipolysis
Authors: Ding Lianggong , Sun Wenfei , Balaz Miroslav , He Anyuan , Klug Manuel , Wieland Stefan , Caiazzo Robert , Raverdy Violeta , Pattou Francois , Lefebvre Philippe , Lodhi Irfan J. , Staels Bart , Heim Markus , Wolfrum Christian
Published: December 2021

To liberate fatty acids (FAs) from intracellular stores, lipolysis is regulated by the activity of the lipases adipose triglyceride lipase (ATGL), hormone-sensitive lipase and monoacylglycerol lipase. Excessive FA release as a result of uncontrolled lipolysis results in lipotoxicity, which can in turn promote the progression of metabolic disorders. However, whether cells can directly sense FAs to maintain cellular lipid homeostasis is unknown. Here we report a sensing mechanism for cellular FAs based on peroxisomal degradation of FAs and coupled with reactive oxygen species (ROS) production, which in turn regulates FA release by modulating lipolysis. Changes in ROS levels are sensed by PEX2, which modulates ATGL levels through post-translational ubiquitination. We demonstrate the importance of this pathway for non-alcoholic fatty liver disease progression using genetic and pharmacological approaches to alter ROS levels in vivo, which can be utilized to increase hepatic ATGL levels and ameliorate hepatic steatosis. The discovery of this peroxisomal β-oxidation-mediated feedback mechanism, which is conserved in multiple organs, couples the functions of peroxisomes and lipid droplets and might serve as a new way to manipulate lipolysis to treat metabolic disorders.
Exploring the transformative potential of urban food
Authors: Hebinck A. , Selomane O. , Veen E. , de Vrieze A. , Hasnain S. , Sellberg M. , Sovová L. , Thompson K. , Vervoort J. , Wood A.
Published: December 2021

Urban food is a key lever for transformative change towards sustainability. While research reporting on the urban food practices (UFPs) in support of sustainability is increasing, the link towards transformative potential is lacking. This is because research on urban food is often place-based and contextual. This limits the applicability of insights to large-scale sustainability transformations. This paper describes UFPs that aim to contribute to transformative change. We present signposts for potential change based on the types of intended transformative changes as described in the reviewed literature based on the processes and outcomes of the urban food policies and programmes. Secondly, we classify diverse UFPs to elevate them beyond their local, place-based contexts. We find that UFPs carry a lot of potential to facilitate sustainability transformations. Based on that analysis, we provide insights on how urban food research can further contribute to harnessing the transformative potential of UFPs for actionable purposes.
Cobalt chromium vanadium layered triple hydroxides as an efficient oxygen electrocatalyst for alkaline seawater splitting
Authors: Khatun Sakila , Roy Poulomi
Published: December 2021

Cobalt chromium vanadium layered triple hydroxides have been identified as a promising electrocatalyst for water oxidation by seawater splitting, suppressing the chlorine evolution reaction at the anode.
Asymmetric synthesis of cyclic β-amino carbonyl derivatives by a formal [3 + 2] photocycloaddition
Authors: Mollari Leonardo , Valle-Amores Miguel A. , Martínez-Gualda Ana M. , Marzo Leyre , Fraile Alberto , Aleman José
Published: December 2021

Herein, a visible-light mediated strategy unlocking a family of cyclic β-amino carbonyl derivatives bearing three contiguous stereogenic centres is introduced.
Biophysical andin silicocharacterization of NrtA: a protein-based host for aqueous nitrate and nitrite recognition
Authors: Ji Ke , Baek Kiheon , Peng Weicheng , Alberto Kevin A. , Torabifard Hedieh , Nielsen Steven O. , Dodani Sheel C.
Published: December 2021

A combination of isothermal titration calorimetry experiments and molecular dynamics simulations reveal how the NrtA protein recognizes nitrateversusnitrite in water.
Slippery magnetic track inducing droplet and bubble manipulation
Authors: Chen Wei , Zhang Xiaolin , Zhao Siyang , Huang Jinxia , Guo Zhiguang
Published: December 2021

The prepared slippery magnetic track can realize the conversion between the slippery liquid-infused surfaces and the rough liquid-infused surfaces under the action of a magnetic field.
Functionally modified metal–organic frameworks for the removal of toxic dyes from wastewater
Authors: Yang Ji-Min
Published: December 2021

This review highlights recent advancement in functional modified (FM) MOFs as superior adsorbents for the removal of dyes, classifying them by various modification strategies. The adsorption interactions affected by the FM approach are summarized.
Preparation and investigation of Dy3+/Tm3+-doped NaGd(MoO4)2 with thermal stability and tunable white light emission for LED applications
Authors: Yu Xiaochen , Jiang Yinlin , Li Xiaojie , Song Zeyu , Zhang Xu , Liu Haonan , Zhao Baoyan , Ye Ting , Duan Li , Fan Jibin
Published: December 2021

Combining theoretical calculations and experiments, synthesized NaGd(MoO4)2: 0.06Dy3+zTm3+ phosphors are shown to have good stability. Under 364 nm excitation, the phosphors emit tunable white light and demonstrate good thermal stability.
Enhancement in microwave absorption properties by adjusting the sintering conditions and carbon shell thickness of Ni@C submicrospheres
Authors: Shen Xun , Yang Shu-Hao , Yin Peng-Gang , Li Chao-Qin , Ye Jin-Rui , Wang Guang-Sheng
Published: December 2021

The core–shell Ni@C submicrospheres were fabricated by sintering method and combined with PVDF to prepare Ni@C/PVDF composite, which possessed optimal wave absorption property with RL min of −71.32 dB and EAB of 5.62 GHz at 1.95 mm.
Correction: Challenges for the future of tandem photovoltaics on the path to terawatt levels: a technology review
Authors: Martinho Filipe
Published: December 2021

Correction for ‘Challenges for the future of tandem photovoltaics on the path to terawatt levels: a technology review’ by Filipe Martinho, Energy Environ. Sci., 2021, 14, 3840–3871, DOI: 10.1039/D1EE00540E.
Metal-free visible-light-initiated direct C3 alkylation of quinoxalin-2(1H)-ones and coumarins with unactivated alkyl iodides
Authors: Sun Jun , Yang Hua , Zhang Bo
Published: December 2021

A visible-light-mediated direct C3-alkylation of quinoxalin-2(1H)-ones and coumarins with unactivated alkyl iodides under metal- and external photocatalyst-free conditions is described.
Stepwise benzylic oxygenation via uranyl-photocatalysis
Authors: Hu Deqing , Jiang Xuefeng
Published: December 2021

Stepwise oxygenation of benzylic molecules with uranyl photocatalysis was realized under ambient conditions. The accuracy of the stepwise oxygenation was ensured by the tunability of redox potential in uranyl photocatalysis through solvents and additives.
Shape- and size-dependent desorption kinetics and surface acidity of nano-SnO2
Authors: Cui Zixiang , Xue Yidi , Xue Yongqiang , Wang Mengying , Chen Jiaojiao , Ji Bo Teng , Wang Chenyu , Zhang Lu
Published: December 2021

With the decrease of particle size, Ed and ln A increase, and Ed octahedron > Ed sphere and ln A octahedron > ln A sphere.
Complex supramolecular tessellations with on-surface self-synthesized C60 tiles through van der Waals interaction
Authors: Zhang Xin , Ding Haoxuan , Chen Xiaorui , Lin Haiping , Li Qing , Gao Jianzhi , Pan Minghu , Guo Quanmin
Published: December 2021

Simultaneous on-site synthesis of C60-based hexagonal and rectangular tiles and self-organized tiling through van der Waals interaction.
Enhancing deep-UV emission at 234 nm by introducing a truncated pyramid AlN/GaN nanostructure with fine-tuned multiple facets
Authors: Lu Shiqiang , Jiang Xinjun , Wang Yaozeng , Huang Kai , Gao Na , Cai Duanjun , Zhou Yinghui , Yang C. C. , Kang Junyong , Zhang Rong
Published: December 2021

A unique truncated pyramid nanostructure with fine-tuned multiple facets is fabricated into a (AlN)8/(GaN)2 digital alloy. As reflecting mirrors, the multiple facets can effectively modulate the light extraction patterns and lead to highly efficient 234 nm DUV emission.
Ultrafast and green ionic liquid-mediated controlled cationic polymerization towards amphiphilic diblock copolymers
Authors: Kumar Devendra , Mohammad Sk Arif , Alam Md. Mehboob , Banerjee Sanjib
Published: December 2021

IL-mediated ultrafast ambient temperature living cationic polymerization of styrene (St), yielding well-defined PSt and polystyrene-b-poly(isobutyl vinyl ether) diblock copolymers with acceptable dispersity values (Đ≤ 1.21) is reported.
Novel heterostructure Cu2S/Ni3S2 coral-like nanoarrays on Ni foam to enhance hydrogen evolution reaction in alkaline media
Authors: Peng Yizhi , He Hanwei
Published: December 2021

We fabricated a heterostructure Cu2S/Ni3S2 nanosheet array, which can accelerate charge transfer and provide more active sites. This work provides a promising non-noble metal electrocatalyst for water splitting under alkaline conditions.