bluuebunny/crossref_metadata_2025 huggingface dataset:
TGF-β1-mediated exosomal lnc-MMP2-2 increases blood–brain barrier permeability via the miRNA-1207-5p/EPB41L5 axis to promote non-small cell lung cancer brain metastasis
Authors: Wu Dongming , Deng Shihua , Li Li , Liu Teng , Zhang Ting , Li Jing , Yu Ye , Xu Ying
Published: July 2021

Brain metastases remain a major problem in patients with advanced non-small cell lung cancer (NSCLC). The permeability of the blood–brain barrier (BBB) is highly increased during lung cancer brain metastasis; however, the underlying mechanism remains largely unknown. We previously found that lnc-MMP2-2 is highly enriched in tumor growth factor (TGF)-β1-mediated exosomes and regulates the migration of lung cancer cells. This study aimed to explore the role of exosomal lnc-MMP2-2 in the regulation of BBB and NSCLC brain metastasis. Here, using endothelial monolayers and mouse models, we found that TGF-β1-mediated NSCLC-derived exosomes efficiently destroyed tight junctions and the integrity of these natural barriers. Overexpression of lnc-MMP2-2 in human brain microvascular endothelial cells increased vascular permeability in endothelial monolayers, whereas inhibition of lnc-MMP2-2 alleviated these effects. Furthermore, lnc-MMP2-2 knockdown markedly reduced NSCLC brain metastasis in vivo. Mechanistically, through luciferase reporter assays, RNA pull-down assay, and Ago2 RNA immunoprecipitation assay, we showed that lnc-MMP2-2 served as a microRNA sponge or a competing endogenous RNA for miR-1207-5p and consequently modulated the derepression of EPB41L5. In conclusion, TGF-β1-mediated exosomal lnc-MMP2-2 increases BBB permeability to promote NSCLC brain metastasis. Thus, exosomal lnc-MMP2-2 may be a potential biomarker and therapeutic target against lung cancer brain metastasis.
Comparable radiation sensitivity in p53 wild-type and p53 deficient tumor cells associated with different cell death modalities
Authors: Li Ping , Liu Xiongxiong , Zhao Ting , Li Feifei , Wang Qiqi , Zhang Pengcheng , Hirayama Ryoichi , Chen Weiqiang , Jin Xiaodong , Zheng Xiaogang , Wang Zhen , Li Qiang
Published: July 2021

Studies of radiation interaction with tumor cells often take apoptosis as the desired results. However, mitotic catastrophe and senescence are also promoted by clinically relevant doses of radiation. Furthermore, p53 is a well-known transcription factor that is closely associated with radiosensitivity and radiation-induced cell death. Therefore, we aimed to investigate the involvement of radiosensitivity, cell death modalities and p53 status in response to carbon-ion radiation (CIR) here. Isogenic human colorectal cancer cell lines HCT116 (p53+/+ and p53−/−) were irradiated with high-LET carbon ions. Cell survival was determined by the standard colony-forming assay. 53BP1 foci were visualized to identify the repair kinetics of DNA double-strand breaks (DSBs). Cellular senescence was measured by SA-β-Gal and Ki67 staining. Mitotic catastrophe was determined with DAPI staining. Comparable radiosensitivities of p53+/+ and p53−/− HCT116 colorectal cells induced by CIR were demonstrated, as well as persistent 53BP1 foci indicated DNA repair deficiency in both cell lines. Different degree of premature senescence in isogenic HCT116 colorectal cancer cells suggested that CIR-induced premature senescence was more dependent on p21 but not p53. Sustained upregulation of p21 played multifunctional roles in senescence enhancement and apoptosis inhibition in p53+/+ cells. p21 inhibition further increased radiosensitivity of p53+/+ cells. Complex cell death modalities rather than single cell death were induced in both p53+/+ and p53−/− cells after 5 Gy CIR. Mitotic catastrophe was predominant in p53−/− cells due to inefficient activation of Chk1 and Chk2 phosphorylation in combination with p53 null. Senescence was the major cell death mechanism in p53+/+ cells via p21-dependent pathway. Taken together, p21-mediated premature senescence might be used by tumor cells to escape from CIR-induced cytotoxicity, at least for a time.
A boronate gel-based synthetic platform for closed-loop insulin delivery systems
Authors: Matsumoto Akira , Chen Siyuan
Published: July 2021

Diabetes is one of the most devastating global diseases with an ever-increasing number of patients. Achieving persistent glycemic control in a painless and convenient way is an unmet goal for diabetes management. Insulin therapy is commonly utilized for diabetes treatment and usually relies on patient self-injection. This not only impairs a patient’s quality of life and fails to precisely control the blood glucose level but also brings the risk of life-threatening hypoglycemia. “closed-loop” insulin delivery systems could avoid these issues by providing on-demand insulin delivery. However, safety concerns limit the application of currently developed electronics-derived or enzyme-based systems. Phenylboronic acid (PBA), with the ability to reversibly bind glucose and a chemically tailored binding specificity, has attracted substantial attention in recent years. This focus review provides an overview of PBA-based versatile insulin delivery platforms developed in our group, including new PBA derivatives, glucose-responsive gels, and gel-combined medical devices, with a unique “skin layer” controlled diffusion feature.
Development and implementation of a scalable and versatile test for COVID-19 diagnostics in rural communities
Authors: Ceci A. , Muñoz-Ballester C. , Tegge A. N. , Brown K. L. , Umans R. A. , Michel F. M. , Patel D. , Tewari B. , Martin J. , Alcoreza O. , Maynard T. , Martinez-Martinez D. , Bordwine P. , Bissell N. , Friedlander M. J. , Sontheimer H. , Finkielstein C. V.
Published: July 2021

Rapid and widespread testing of severe acute respiratory coronavirus 2 (SARS-CoV-2) is essential for an effective public health response aimed at containing and mitigating the coronavirus disease 2019 (COVID-19) pandemic. Successful health policy implementation relies on early identification of infected individuals and extensive contact tracing. However, rural communities, where resources for testing are sparse or simply absent, face distinctive challenges to achieving this success. Accordingly, we report the development of an academic, public land grant University laboratory-based detection assay for the identification of SARS-CoV-2 in samples from various clinical specimens that can be readily deployed in areas where access to testing is limited. The test, which is a quantitative reverse transcription polymerase chain reaction (RT-qPCR)-based procedure, was validated on samples provided by the state laboratory and submitted for FDA Emergency Use Authorization. Our test exhibits comparable sensitivity and exceeds specificity and inclusivity values compared to other molecular assays. Additionally, this test can be re-configured to meet supply chain shortages, modified for scale up demands, and is amenable to several clinical specimens. Test development also involved 3D engineering critical supplies and formulating a stable collection media that allowed samples to be transported for hours over a dispersed rural region without the need for a cold-chain. These two elements that were critical when shortages impacted testing and when personnel needed to reach areas that were geographically isolated from the testing center. Overall, using a robust, easy-to-adapt methodology, we show that an academic laboratory can supplement COVID-19 testing needs and help local health departments assess and manage outbreaks. This additional testing capacity is particularly germane for smaller cities and rural regions that would otherwise be unable to meet the testing demand.
Fully automated fast-flow synthesis of antisense phosphorodiamidate morpholino oligomers
Authors: Li Chengxi , Callahan Alex J. , Simon Mark D. , Totaro Kyle A. , Mijalis Alexander J. , Phadke Kruttika-Suhas , Zhang Genwei , Hartrampf Nina , Schissel Carly K. , Zhou Ming , Zong Hong , Hanson Gunnar J. , Loas Andrei , Pohl Nicola L. B. , Verhoeven David E. , Pentelute Bradley L.
Published: July 2021

Rapid development of antisense therapies can enable on-demand responses to new viral pathogens and make personalized medicine for genetic diseases practical. Antisense phosphorodiamidate morpholino oligomers (PMOs) are promising candidates to fill such a role, but their challenging synthesis limits their widespread application. To rapidly prototype potential PMO drug candidates, we report a fully automated flow-based oligonucleotide synthesizer. Our optimized synthesis platform reduces coupling times by up to 22-fold compared to previously reported methods. We demonstrate the power of our automated technology with the synthesis of milligram quantities of three candidate therapeutic PMO sequences for an unserved class of Duchenne muscular dystrophy (DMD). To further test our platform, we synthesize a PMO that targets the genomic mRNA of SARS-CoV-2 and demonstrate its antiviral effects. This platform could find broad application not only in designing new SARS-CoV-2 and DMD antisense therapeutics, but also for rapid development of PMO candidates to treat new and emerging diseases.
A low-noise photonic heterodyne synthesizer and its application to millimeter-wave radar
Authors: Kittlaus Eric A. , Eliyahu Danny , Ganji Setareh , Williams Skip , Matsko Andrey B. , Cooper Ken B. , Forouhar Siamak
Published: July 2021

Microwave photonics offers transformative capabilities for ultra-wideband electronic signal processing and frequency synthesis with record-low phase noise levels. Despite the intrinsic bandwidth of optical systems operating at ~200 THz carrier frequencies, many schemes for high-performance photonics-based microwave generation lack broadband tunability, and experience tradeoffs between noise level, complexity, and frequency. An alternative approach uses direct frequency down-mixing of two tunable semiconductor lasers on a fast photodiode. This form of optical heterodyning is frequency-agile, but experimental realizations have been hindered by the relatively high noise of free-running lasers. Here, we demonstrate a heterodyne synthesizer based on ultralow-noise self-injection-locked lasers, enabling highly-coherent, photonics-based microwave and millimeter-wave generation. Continuously-tunable operation is realized from 1-104 GHz, with constant phase noise of -109 dBc/Hz at 100 kHz offset from carrier. To explore its practical utility, we leverage this photonic source as the local oscillator within a 95-GHz frequency-modulated continuous wave (FMCW) radar. Through field testing, we observe dramatic reduction in phase-noise-related Doppler and ranging artifacts as compared to the radar’s existing electronic synthesizer. These results establish strong potential for coherent heterodyne millimeter-wave generation, opening the door to a variety of future applications including high-dynamic range remote sensing, wideband wireless communications, and THz spectroscopy.
A synthetic tubular molecular transport system
Authors: Stömmer Pierre , Kiefer Henrik , Kopperger Enzo , Honemann Maximilian N. , Kube Massimo , Simmel Friedrich C. , Netz Roland R. , Dietz Hendrik
Published: July 2021

Creating artificial macromolecular transport systems that can support the movement of molecules along defined routes is a key goal of nanotechnology. Here, we report the bottom-up construction of a macromolecular transport system in which molecular pistons diffusively move through micrometer-long, hollow filaments. The pistons can cover micrometer distances in fractions of seconds. We build the system using multi-layer DNA origami and analyze the structures of the components using transmission electron microscopy. We study the motion of the pistons along the tubes using single-molecule fluorescence microscopy and perform Langevin simulations to reveal details of the free energy surface that directs the motions of the pistons. The tubular transport system achieves diffusivities and displacement ranges known from natural molecular motors and realizes mobility improvements over five orders of magnitude compared to previous artificial random walker designs. Electric fields can also be employed to actively pull the pistons along the filaments, thereby realizing a nanoscale electric rail system. Our system presents a platform for artificial motors that move autonomously driven by chemical fuels and for performing nanotribology studies, and it could form a basis for future molecular transportation networks.
Self-healing polyurethane-elastomer with mechanical tunability for multiple biomedical applications in vivo
Authors: Jiang Chenyu , Zhang Luzhi , Yang Qi , Huang Shixing , Shi Hongpeng , Long Qiang , Qian Bei , Liu Zenghe , Guan Qingbao , Liu Mingjian , Yang Renhao , Zhao Qiang , You Zhengwei , Ye Xiaofeng
Published: July 2021

The unique properties of self-healing materials hold great potential in the field of biomedical engineering. Although previous studies have focused on the design and synthesis of self-healing materials, their application in in vivo settings remains limited. Here, we design a series of biodegradable and biocompatible self-healing elastomers (SHEs) with tunable mechanical properties, and apply them to various disease models in vivo, in order to test their reparative potential in multiple tissues and at physiological conditions. We validate the effectiveness of SHEs as promising therapies for aortic aneurysm, nerve coaptation and bone immobilization in three animal models. The data presented here support the translation potential of SHEs in diverse settings, and pave the way for the development of self-healing materials in clinical contexts.
High-depth spatial transcriptome analysis by photo-isolation chemistry
Authors: Honda Mizuki , Oki Shinya , Kimura Ryuichi , Harada Akihito , Maehara Kazumitsu , Tanaka Kaori , Meno Chikara , Ohkawa Yasuyuki
Published: July 2021

In multicellular organisms, expression profiling in spatially defined regions is crucial to elucidate cell interactions and functions. Here, we establish a transcriptome profiling method coupled with photo-isolation chemistry (PIC) that allows the determination of expression profiles specifically from photo-irradiated regions of interest. PIC uses photo-caged oligodeoxynucleotides for in situ reverse transcription. PIC transcriptome analysis detects genes specifically expressed in small distinct areas of the mouse embryo. Photo-irradiation of single cells demonstrated that approximately 8,000 genes were detected with 7 × 104 unique read counts. Furthermore, PIC transcriptome analysis is applicable to the subcellular and subnuclear microstructures (stress granules and nuclear speckles, respectively), where hundreds of genes can be detected as being specifically localised. The spatial density of the read counts is higher than 100 per square micrometre. Thus, PIC enables high-depth transcriptome profiles to be determined from limited regions up to subcellular and subnuclear resolutions.
Fundamental limitations on distillation of quantum channel resources
Authors: Regula Bartosz , Takagi Ryuji
Published: July 2021

Quantum channels underlie the dynamics of quantum systems, but in many practical settings it is the channels themselves that require processing. We establish universal limitations on the processing of both quantum states and channels, expressed in the form of no-go theorems and quantitative bounds for the manipulation of general quantum channel resources under the most general transformation protocols. Focusing on the class of distillation tasks — which can be understood either as the purification of noisy channels into unitary ones, or the extraction of state-based resources from channels — we develop fundamental restrictions on the error incurred in such transformations, and comprehensive lower bounds for the overhead of any distillation protocol. In the asymptotic setting, our results yield broadly applicable bounds for rates of distillation. We demonstrate our results through applications to fault-tolerant quantum computation, where we obtain state-of-the-art lower bounds for the overhead cost of magic state distillation, as well as to quantum communication, where we recover a number of strong converse bounds for quantum channel capacity.
TEM8 marks neovasculogenic tumor-initiating cells in triple-negative breast cancer
Authors: Xu Jiahui , Yang Xiaoli , Deng Qiaodan , Yang Cong , Wang Dong , Jiang Guojuan , Yao Xiaohong , He Xueyan , Ding Jiajun , Qiang Jiankun , Tu Juchuanli , zhang Rui , Lei Qun-Ying , Shao Zhi-min , Bian Xiuwu , Hu Ronggui , Zhang Lixing , Liu Suling
Published: July 2021

Enhanced neovasculogenesis, especially vasculogenic mimicry (VM), contributes to the development of triple-negative breast cancer (TNBC). Breast tumor-initiating cells (BTICs) are involved in forming VM; however, the specific VM-forming BTIC population and the regulatory mechanisms remain undefined. We find that tumor endothelial marker 8 (TEM8) is abundantly expressed in TNBC and serves as a marker for VM-forming BTICs. Mechanistically, TEM8 increases active RhoC level and induces ROCK1-mediated phosphorylation of SMAD5, in a cascade essential for promoting stemness and VM capacity of breast cancer cells. ASB10, an estrogen receptor ERα trans-activated E3 ligase, ubiquitylates TEM8 for degradation, and its deficiency in TNBC resulted in a high homeostatic level of TEM8. In this work, we identify TEM8 as a functional marker for VM-forming BTICs in TNBC, providing a target for the development of effective therapies against TNBC targeting both BTIC self-renewal and neovasculogenesis simultaneously.
Appropriate sampling methods and statistics can tell apart fraud from pesticide drift in organic farming
Authors: Benzing Albrecht , Piepho Hans-Peter , Malik Waqas Ahmed , Finckh Maria R. , Mittelhammer Manuel , Strempel Dominic , Jaschik Johannes , Neuendorff Jochen , Guamán Liliana , Mancheno José , Melo Luis , Pavón Omar , Cangahuamín Roberto , Ullauri Juan-Carlos
Published: July 2021

Pesticide residues are much lower in organic than in conventional food. The article summarizes the available residue data from the EU and the U.S. organic market. Differences between samples from several sources suggest that organic products are declared conventional, when they have residues—but the origin of the residues is not always investigated. A large number of samples are being tested by organic certifiers, but the sampling methods often do not allow to determine if such residues stem from prohibited pesticide use by organic farmers, from mixing organic with conventional products, from short-range spray-drift from neighbour farms, from the ubiquitous presence of such substances due to long-distance drift, or from other sources of contamination. Eight case studies from different crops and countries are used to demonstrate that sampling at different distances from possible sources of short-distance drift in most cases allows differentiating deliberate pesticide application by the organic farmer from drift. Datasets from 67 banana farms in Ecuador, where aerial fungicide spraying leads to a heavy drift problem, were subjected to statistical analysis. A linear discriminant function including four variables was identified for distinguishing under these conditions application from drift, with an accuracy of 93.3%.
Noise reduction in X-ray photon correlation spectroscopy with convolutional neural networks encoder–decoder models
Authors: Konstantinova Tatiana , Wiegart Lutz , Rakitin Maksim , DeGennaro Anthony M. , Barbour Andi M.
Published: July 2021

Like other experimental techniques, X-ray photon correlation spectroscopy is subject to various kinds of noise. Random and correlated fluctuations and heterogeneities can be present in a two-time correlation function and obscure the information about the intrinsic dynamics of a sample. Simultaneously addressing the disparate origins of noise in the experimental data is challenging. We propose a computational approach for improving the signal-to-noise ratio in two-time correlation functions that is based on convolutional neural network encoder–decoder (CNN-ED) models. Such models extract features from an image via convolutional layers, project them to a low dimensional space and then reconstruct a clean image from this reduced representation via transposed convolutional layers. Not only are ED models a general tool for random noise removal, but their application to low signal-to-noise data can enhance the data’s quantitative usage since they are able to learn the functional form of the signal. We demonstrate that the CNN-ED models trained on real-world experimental data help to effectively extract equilibrium dynamics’ parameters from two-time correlation functions, containing statistical noise and dynamic heterogeneities. Strategies for optimizing the models’ performance and their applicability limits are discussed.
Development and validation of HPLC-MS2 methodology for the accurate determination of C4–C8 B-type flavanols and procyanidins
Authors: Bussy Ugo , Olanrewaju Yusuf , Crozier Alan , Ottaviani Javier , Kwik-Uribe Catherine
Published: July 2021

Cocoa flavanols and procyanidins (CFs), natural dietary bioactives, have been studied extensively over the past two decades for their potential health benefits. Research on their safety and efficacy is critically dependent upon on the ability to reliably characeterize the research materials that are utilized, and with growing consumer availability of CF-based products, reliable methods for the detection of potential adulteration are of increasing importance. This research focused on the development of a high performance liquid chromatography-tandem mass spectrometry method (HPLC-MS2) using primary standards and 13C-labelled procyanidins as internal standards. The ability of MS2 detection to discriminate A- and B-type procyanidins was demonstrated. Method performances were validated for degrees of polymerization up to four in seven model food matrices. Accuracy ranged from 90.9 to 125.4% and precision was < 10% at lower concentrations. Finally, the method was applied to cocoa-based samples and compared to the AOAC 2020.05 analytical protocol, supporting the use of NIST 8403 as reference material for HPLC-MS2 analysis.
Multi-omics integration of methyltransferase-like protein family reveals clinical outcomes and functional signatures in human cancer
Authors: Campeanu Ion John , Jiang Yuanyuan , Liu Lanxin , Pilecki Maksymilian , Najor Alvina , Cobani Era , Manning Morenci , Zhang Xiaohong Mary , Yang Zeng-Quan
Published: July 2021

Human methyltransferase-like (METTL) proteins transfer methyl groups to nucleic acids, proteins, lipids, and other small molecules, subsequently playing important roles in various cellular processes. In this study, we performed integrated genomic, transcriptomic, proteomic, and clinicopathological analyses of 34 METTLs in a large cohort of primary tumor and cell line data. We identified a subset of METTL genes, notably METTL1, METTL7B, and NTMT1, with high frequencies of genomic amplification and/or up-regulation at both the mRNA and protein levels in a spectrum of human cancers. Higher METTL1 expression was associated with high-grade tumors and poor disease prognosis. Loss-of-function analysis in tumor cell lines indicated the biological importance of METTL1, an m7G methyltransferase, in cancer cell growth and survival. Furthermore, functional annotation and pathway analysis of METTL1-associated proteins revealed that, in addition to the METTL1 cofactor WDR4, RNA regulators and DNA packaging complexes may be functionally interconnected with METTL1 in human cancer. Finally, we generated a crystal structure model of the METTL1–WDR4 heterodimeric complex that might aid in understanding the key functional residues. Our results provide new information for further functional study of some METTL alterations in human cancer and might lead to the development of small inhibitors that target cancer-promoting METTLs.
Quantification of pedogenic particles masked by geogenic magnetic fraction
Authors: Szuszkiewicz Marcin , Grison Hana , Petrovský Eduard , Szuszkiewicz Maria Magdalena , Gołuchowska Beata , Łukasik Adam
Published: July 2021

Pedogenic magnetic fraction in soils is attributed to fine-grained particles, i.e. superparamagnetic grains. In the case of a strongly magnetic geogenic fraction, pedogenic magnetic contribution is hard to detect. To the best of our knowledge, detailed research into the masking of pedogenic superparamagnetic grains and quantification of this effect has not yet been carried out. The principal aim of our research is to quantify the influence of coarse-grained ferrimagnetic fraction on the detection of the superparamagnetic grains. In order to describe the masking phenomenon, volume and frequency-dependent magnetic susceptibility were determined on a set of laboratory prepared samples composed of natural substances: a diamagnetic quartz matrix, detrital coarse-grained ferrimagnetic crystals from alkaline and ultra-alkaline igneous rocks, and superparamagnetic soil concretions formed in the Haplic Cambisol. Mineralogy, concentration, type and grain size of the tested material were described by parameters of environmental magnetism. The magnetic parameters distinguish both geogenic multidomain and pedogenic superparamagnetic grains. The magnetic signal of the superparamagnetic grains is gradually masked by the increasing proportion of multidomain grains of magnetite/maghemite. The experiment clearly describes the masking effect and brings new insight to studies dealing with strongly magnetic soils of natural and/or highly contaminated origin as a tool for estimation of superparamagnetic pedogenic contribution.
Probing cerebellar involvement in cognition through a meta-analysis of TMS evidence
Authors: Gatti Daniele , Rinaldi Luca , Cristea Ioana , Vecchi Tomaso
Published: July 2021

Traditionally, the cerebellum has been linked to motor coordination, but growing evidence points to its involvement in a wide range of non-motor functions. Though the number of studies using transcranial magnetic stimulation (TMS) to investigate cerebellar involvement in cognitive processes is growing exponentially, these findings have not yet been synthesized in a meta-analysis. Here, we used meta-analysis to estimate the effects of cerebellar TMS on performance in cognitive tasks for healthy participants. Outcomes included participants’ accuracy and response times (RTs) of several non-motor tasks performed either during or after the administration of TMS. We included overall 41 studies, of which 44 single experiments reported effects on accuracy and 41 on response times (RTs). The meta-analyses showed medium effect sizes (for accuracy: d = 0.61 [95% CI = 0.48, .073]; for RTs: d = 0.40 [95% CI = 0.30, 0.49]), with leave-one-out analyses indicating that cumulative effects were robust, and with moderate heterogeneity. For both accuracy and RTs, the effect of TMS was moderated by the stimulation paradigm adopted but not by the cognitive function investigated, while the timing of the stimulation moderated only the effects on RTs. Further analyses on lateralization revealed no moderation effects of the TMS site. Taken together, these findings indicate that TMS administered over the cerebellum is able to modulate cognitive performance, affecting accuracy or RTs, and suggest that the various stimulation paradigms play a key role in determining the efficacy of cerebellar TMS.
Effects of nitrogen fertilization on protein and carbohydrate fractions of Marandu palisadegrass
Authors: Leite Rhaony Gonçalves , Cardoso Abmael da Silva , Fonseca Natália Vilas Boas , Silva Maria Luisa Curvelo , Tedeschi Luís Orlindo , Delevatti Lutti Maneck , Ruggieri Ana Cláudia , Reis Ricardo Andrade
Published: July 2021

The effects of nitrogen (N) fertilization levels on protein and carbohydrate fractions in Marandu palisadegrass pasture [Urochloa brizantha (Hochst. ex A. Rich.) R.D. Webster] were investigated in a pasture over five years. The experimental design was completely randomized with four levels of N (0, 90, 180, and 270 kg N ha-1, as urea) for five years, and with three replicates. The study was conducted in a continuously stocked pasture during the forage growing season (December to April) in a tropical region. The effects of N fertilization were similar across the five years. With increasing N fertilization, the concentrations of crude protein (CP) increased from 103 to 173 g kg−1 (P < 0.001), soluble fractions (Fraction A + B1) increased from 363 to 434 g kg−1 of total CP (P = 0.006); neutral detergent fiber (NDF) decreased from 609 to 556 g kg−1 (P = 0.037); indigestible NDF (P = 0.046), potentially degradable neutral detergent fiber (P = 0.037), and acid detergent fiber decreased (P = 0.05), and total digestible nutrient (TDN) increased (P < 0.001). Increasing N fertilization decreased the concentrations of Fraction C (P = 0.014) and total carbohydrates (P < 0.0001), and increased CP:organic matter digestibility (P < 0.01). Concentrations of neutral detergent fiber free of ash and protein (P = 0.003), indigestible neutral detergent fiber (P < 0.001), neutral detergent fiber potentially degradable (P = 0.11), CP (P < 0.001), Fraction A + B1 (P < 0.001), Fraction B2 (P < 0.001), Fraction B3 (P < 0.01), and non-structural carbohydrates differed (P < 0.001) across years. Therefore, N fertilization can be used to increase CP, soluble protein, and TDN.
Investigation of single-domain Au silicide nanowires on Si(110) formed for Au coverages in the monolayer regime
Authors: Appelfeller Stephan
Published: July 2021

The self-organized formation of single domain Au silicide nanowires is observed on Si(110). These nanowires are analysed using scanning tunnelling microscopy (STM) and spectroscopy (STS) as well as photoemission spectroscopy (PES). Core-level PES is utilised to confirm the formation of Au silicide and establish its presence as the top most surface structure, i.e., the nanowires. The growth of the Au silicide nanowires and their dimensions are studied by STM. They form for Au coverages of about 1 monolayer and are characterized by widths of about 2 to 3 nm and heights below 1 nm while reaching lengths exceeding 500 nm when choosing appropriate annealing temperatures. Valence band PES and STS indicate a small but finite density of states at the Fermi level typical for compound metals.
Identification of enriched hyperthermophilic microbial communities from a deep-sea hydrothermal vent chimney under electrolithoautotrophic culture conditions
Authors: Pillot Guillaume , Amin Ali Oulfat , Davidson Sylvain , Shintu Laetitia , Godfroy Anne , Combet-Blanc Yannick , Bonin Patricia , Liebgott Pierre-Pol
Published: July 2021

Deep-sea hydrothermal vents are extreme and complex ecosystems based on a trophic chain. We are still unsure of the identities of the first colonizers of these environments and their metabolism, but they are thought to be (hyper)thermophilic autotrophs. Here we investigate whether the electric potential observed across hydrothermal chimneys could serve as an energy source for these first colonizers. Experiments were performed in a two-chamber microbial electrochemical system inoculated with deep-sea hydrothermal chimney samples, with a cathode as sole electron donor, CO2 as sole carbon source, and nitrate, sulfate, or oxygen as electron acceptors. After a few days of culturing, all three experiments showed growth of electrotrophic biofilms consuming the electrons (directly or indirectly) and producing organic compounds including acetate, glycerol, and pyruvate. Within the biofilms, the only known autotroph species retrieved were members of Archaeoglobales. Various heterotrophic phyla also grew through trophic interactions, with Thermococcales growing in all three experiments as well as other bacterial groups specific to each electron acceptor. This electrotrophic metabolism as energy source driving initial microbial colonization of conductive hydrothermal chimneys is discussed.
Rapid and real-time monitoring of bacterial growth against antibiotics in solid growth medium using a contactless planar microwave resonator sensor
Authors: Jain Mandeep Chhajer , Nadaraja Anupama Vijaya , Narang Rakesh , Zarifi Mohammad Hossein
Published: July 2021

Infection diagnosis and antibiotic susceptibility testing (AST) are pertinent clinical microbiology practices that are in dire need of improvement, due to the inadequacy of current standards in early detection of bacterial response to antibiotics and affordability of contemporarily used methods. This paper presents a novel way to conduct AST which hybridizes disk diffusion AST with microwave resonators for rapid, contactless, and non-invasive sensing and monitoring. In this research, the effect of antibiotic (erythromycin) concentrations on test bacterium, Escherichia coli (E. coli) cultured on solid agar medium (MH agar) are monitored through employing a microwave split-ring resonator. A one-port microwave resonator operating at a 1.76 GHz resonant frequency, featuring a 5 mm2 sensitive sensing region, was designed and optimized to perform this. Upon introducing uninhibited growth of the bacteria, the sensor measured 0.005 dB/hr, with a maximum change of 0.07 dB over the course of 15 hours. The amplitude change decreased to negligible values to signify inhibited growth of the bacteria at higher concentrations of antibiotics, such as a change of 0.005 dB in resonant amplitude variation while using 45 µg of antibiotic. Moreover, this sensor demonstrated decisive results of antibiotic susceptibility in under 6 hours and shows great promise to expand automation to the intricate AST workflow in clinical settings, while providing rapid, sensitive, and non-invasive detection capabilities.
Formation and hydration of eco-friendly cement using industrial wastes as raw materials
Authors: Baltakys K. , Dambrauskas T. , Rubinaite D. , Siauciunas R. , Grineviciene A.
Published: July 2021

In this work, the optimal conditions of the synthesis of eco-friendly cement by using industrial wastes as well as the peculiarities of its early stage hydration were investigated. The eco-friendly cement was synthesized within the 1000–1250 °C temperature range when the targeted composition was 60% of belite, 20% of ye’elimite, and 20% of brownmillerite. It was determined that the optimal sintering temperature for eco-friendly cement is 1100 °C because the primary compounds were fully reacted, and hydraulic active compounds were dominant in the products. Microcalorimetry analysis was performed for the investigation of early stage hydration. The best results of hydration were obtained with the eco-friendly cement which was produced by using mixtures with silica gel waste: three exothermic reactions were observed in the heat evolution curve, while the cumulative heat was equal to 264 J/g after 72 h. Additionally, the sequence of compounds formation during the first day of hydration was analyzed. It was determined that the composition of the initial mixture impacts the hydration rate of synthetic eco-friendly cement; however, it did not affect the mineralogical composition of the hydration products. These results were confirmed by XRD, STA, and SEM analysis.
Low hemoglobin levels and an increased risk of psoriasis in patients with chronic kidney disease
Authors: Lee Si-Hyung , Kim Miri , Han Kyung-Do , Lee Ji Hyun
Published: July 2021

Chronic diseases, such as chronic kidney disease (CKD), are frequently accompanied by various comorbidities, including anemia, which is considered a surrogate marker of systemic inflammation. Psoriasis is a chronic inflammatory skin disease prevalent in patients with chronic disease. Psoriasis risk in patients with CKD, however, especially in patients with low hemoglobin levels, has never been investigated. In this study, we investigated associations between low hemoglobin levels and psoriasis in patients with CKD using data from the National Health Insurance Service of Korea. During a mean follow-up period of 6.16 ± 1.02 years, psoriasis was recorded in 13,803 patients with CKD (2.39% of CKD patients). The cumulative incidence of psoriasis was significantly higher in CKD patients with anemia (hemoglobin levels < 13 g/dL in men and < 12 g/dL in women) than those without. In multivariate-adjusted Cox proportional hazards regression models, the risk of psoriasis was significantly higher in anemic CKD patients than nonanemic CKD patients (hazard ratio [HR] 1.136, 95% CI 1.089–1.185, p < 0.001). Additionally, we noted that the incidence of psoriasis decreased with increasing hemoglobin levels in CKD patients (HR 0.953, 95% CI 0.942–0.965, p < 0.001). Altogether, our findings indicate that low hemoglobin levels are significantly related to psoriasis risk in patients with CKD. Further study is required to elucidate whether low hemoglobin levels have an impact on the development of psoriasis or are merely a surrogate marker of psoriasis risk in patients with CKD.
Comparison of dural grafts and methods of graft fixation in Chiari malformation type I decompression surgery
Authors: Balasa Artur , Kunert Przemysław , Dziedzic Tomasz , Bielecki Mateusz , Kujawski Sławomir , Marchel Andrzej
Published: July 2021

Suboccipital decompression with duraplasty is a widely accepted method for treating patients with Chiari malformation type I. However, important details of the duraplasty technique are still controversial. This retrospective study analyzes clinical and radiological outcomes after surgery depending upon the type of graft and methods of graft fixation. Seventy consecutive decompressions with duraplasty were analyzed. Two types of grafts, nonautologous (Non-AutoG; 60.0%) and autologous (AutoG; 40.0%), and two methods of graft fixation, suturing (S; 67.1%) and gluing (G; 32.9%), were used in four different combinations: (Non-AutoG+S: 31.4%; Non-AutoG+G: 28.6%; AutoG+S: 35.7%; AutoG+G: 4.3%) according to surgeon preference. The mean follow-up was 63.4 months. According to gestalt and Chicago Chiari Outcome Scales, satisfactory results were obtained in 72.9% and 78.6% of cases, respectively, in the long term. The outcomes were not related to the kind of graft (p = 0.44), fixation method (p = 0.89) or duraplasty pattern (p = 0.32). Decreased syringomyelia was observed in 88.9% of cases, and no associations with the kind of graft (p = 0.84), fixation method (p = 1) or duraplasty pattern were found (p = 0.96). Pseudomeningocele occurred 5 times more often in the Non-AutoG group than in the AutoG group (52.4% vs. 10.7%; p < 0.05), whereas their formations were not related to the fixation method (p = 0.34). Three cases (12.0%) required reoperation with reduraplasty. Autologous and nonautologous dural grafts can be sutured or glued with similar clinical results; however, the use of nonautologous grafts is linked with a much higher risk of pseudomeningocele formation.
Functional expression of the eukaryotic proton pump rhodopsin OmR2 in Escherichia coli and its photochemical characterization
Authors: Kikuchi Masuzu , Kojima Keiichi , Nakao Shin , Yoshizawa Susumu , Kawanishi Shiho , Shibukawa Atsushi , Kikukawa Takashi , Sudo Yuki
Published: July 2021

Microbial rhodopsins are photoswitchable seven-transmembrane proteins that are widely distributed in three domains of life, archaea, bacteria and eukarya. Rhodopsins allow the transport of protons outwardly across the membrane and are indispensable for light-energy conversion in microorganisms. Archaeal and bacterial proton pump rhodopsins have been characterized using an Escherichia coli expression system because that enables the rapid production of large amounts of recombinant proteins, whereas no success has been reported for eukaryotic rhodopsins. Here, we report a phylogenetically distinct eukaryotic rhodopsin from the dinoflagellate Oxyrrhis marina (O. marina rhodopsin-2, OmR2) that can be expressed in E. coli cells. E. coli cells harboring the OmR2 gene showed an outward proton-pumping activity, indicating its functional expression. Spectroscopic characterization of the purified OmR2 protein revealed several features as follows: (1) an absorption maximum at 533 nm with all-trans retinal chromophore, (2) the possession of the deprotonated counterion (pKa = 3.0) of the protonated Schiff base and (3) a rapid photocycle through several distinct photointermediates. Those features are similar to those of known eukaryotic proton pump rhodopsins. Our successful characterization of OmR2 expressed in E. coli cells could build a basis for understanding and utilizing eukaryotic rhodopsins.
Changes in abdominal subcutaneous adipose tissue phenotype following menopause is associated with increased visceral fat mass
Authors: Abildgaard Julie , Ploug Thorkil , Al-Saoudi Elaf , Wagner Thomas , Thomsen Carsten , Ewertsen Caroline , Bzorek Michael , Pedersen Bente Klarlund , Pedersen Anette Tønnes , Lindegaard Birgitte
Published: July 2021

Menopause is associated with a redistribution of adipose tissue towards central adiposity, known to cause insulin resistance. In this cross-sectional study of 33 women between 45 and 60 years, we assessed adipose tissue inflammation and morphology in subcutaneous adipose tissue (SAT) and visceral adipose tissue (VAT) across menopause and related this to menopausal differences in adipose tissue distribution and insulin resistance. We collected paired SAT and VAT biopsies from all women and combined this with anthropometric measurements and estimated whole-body insulin sensitivity. We found that menopause was associated with changes in adipose tissue phenotype related to metabolic dysfunction. In SAT, postmenopausal women showed adipocyte hypertrophy, increased inflammation, hypoxia and fibrosis. The postmenopausal changes in SAT was associated with increased visceral fat accumulation. In VAT, menopause was associated with adipocyte hypertrophy, immune cell infiltration and fibrosis. The postmenopausal changes in VAT phenotype was associated with decreased insulin sensitivity. Based on these findings we suggest, that menopause is associated with changes in adipose tissue phenotype related to metabolic dysfunction in both SAT and VAT. Whereas increased SAT inflammation in the context of menopause is associated with VAT accumulation, VAT morphology is related to insulin resistance.
Visual instrumental learning in blindsight monkeys
Authors: Kato Rikako , Zeghbib Abdelhafid , Redgrave Peter , Isa Tadashi
Published: July 2021

Blindsight is the residual visuo-motor ability without subjective awareness observed after lesions of the primary visual cortex (V1). Various visual functions are retained, however, instrumental visual associative learning remains to be investigated. Here we examined the secondary reinforcing properties of visual cues presented to the hemianopic field of macaque monkeys with unilateral V1 lesions. Our aim was to test the potential role of visual pathways bypassing V1 in reinforcing visual instrumental learning. When learning the location of a hidden area in an oculomotor search task, conditioned visual cues presented to the lesion-affected hemifield operated as an effective secondary reinforcer. We noted that not only the hidden area location, but also the vector of the saccade entering the target area was reinforced. Importantly, when the visual reinforcement signal was presented in the lesion-affected field, the monkeys continued searching, as opposed to stopping when the cue was presented in the intact field. This suggests the monkeys were less confident that the target location had been discovered when the reinforcement cue was presented in the affected field. These results indicate that the visual signals mediated by the residual visual pathways after V1 lesions can access fundamental reinforcement mechanisms but with impaired visual awareness.
Investigation of the activity of transposable elements and genes involved in their silencing in the newt Cynops orientalis, a species with a giant genome
Authors: Carducci Federica , Carotti Elisa , Gerdol Marco , Greco Samuele , Canapa Adriana , Barucca Marco , Biscotti Maria Assunta
Published: July 2021

Caudata is an order of amphibians with great variation in genome size, which can reach enormous dimensions in salamanders. In this work, we analysed the activity of transposable elements (TEs) in the transcriptomes obtained from female and male gonads of the Chinese fire-bellied newt, Cynops orientalis, a species with a genome about 12-fold larger than the human genome. We also compared these data with genomes of two basal sarcopterygians, coelacanth and lungfish. In the newt our findings highlighted a major impact of non-LTR retroelements and a greater total TE activity compared to the lungfish Protopterus annectens, an organism also characterized by a giant genome. This difference in TE activity might be due to the presence of young copies in newt in agreement also with the increase in the genome size, an event that occurred independently and later than lungfish. Moreover, the activity of 33 target genes encoding proteins involved in the TE host silencing mechanisms, such as Ago/Piwi and NuRD complex, was evaluated and compared between the three species analysed. These data revealed high transcriptional levels of the target genes in both newt and lungfish and confirmed the activity of NuRD complex genes in adults. Finally, phylogenetic analyses performed on PRDM9 and TRIM28 allowed increasing knowledge about the evolution of these two key genes of the NuRD complex silencing mechanism in vertebrates. Our results confirmed that the gigantism of the newt genomes may be attributed to the activity and accumulation of TEs.
SpheroidPicker for automated 3D cell culture manipulation using deep learning
Authors: Grexa Istvan , Diosdi Akos , Harmati Maria , Kriston Andras , Moshkov Nikita , Buzas Krisztina , Pietiäinen Vilja , Koos Krisztian , Horvath Peter
Published: July 2021

Recent statistics report that more than 3.7 million new cases of cancer occur in Europe yearly, and the disease accounts for approximately 20% of all deaths. High-throughput screening of cancer cell cultures has dominated the search for novel, effective anticancer therapies in the past decades. Recently, functional assays with patient-derived ex vivo 3D cell culture have gained importance for drug discovery and precision medicine. We recently evaluated the major advancements and needs for the 3D cell culture screening, and concluded that strictly standardized and robust sample preparation is the most desired development. Here we propose an artificial intelligence-guided low-cost 3D cell culture delivery system. It consists of a light microscope, a micromanipulator, a syringe pump, and a controller computer. The system performs morphology-based feature analysis on spheroids and can select uniform sized or shaped spheroids to transfer them between various sample holders. It can select the samples from standard sample holders, including Petri dishes and microwell plates, and then transfer them to a variety of holders up to 384 well plates. The device performs reliable semi- and fully automated spheroid transfer. This results in highly controlled experimental conditions and eliminates non-trivial side effects of sample variability that is a key aspect towards next-generation precision medicine.