bluuebunny/crossref_metadata_2025 huggingface dataset:
Germination biology of three populations of Navua sedge (Cyperus aromaticus)
Authors: Chadha Aakansha , Florentine Singarayer K. , Dhileepan Kunjithapatham , Dowling Kim , Turville Christopher
Published: November 2020

Navua sedge [Cyperus aromaticus(Ridley) Mattf. & Kük.] is an aggressive perennial sedge native to equatorial Africa that has become problematic in many Pacific islands and wet, tropical Queensland, Australia. It has had a significant impact on the livestock-grazing industry, sugarcane (Saccharum officinarumL.) and banana (Musa acuminataColla) plantations, and various other ecosystems. A laboratory-based research investigation was conducted to understand germination and emergence requirements under various environmental conditions of three geographically varied populations sourced from South Johnstone (SJ), Mackay (M) and Nyleta Creek (NC) in Queensland. Germination was identified to be stimulated by light, with no germination recorded under darkness. Populations SJ and NC had optimal germination at alternating temperatures of 25/15, 30/20, and 35/25 C, whereas population M had optimal germination at 25/15 and 30/20 C. All populations recorded greater than 85% germination at all pH levels tested. Seeds of population SJ were more sensitive to salinity compared with populations M and NC, with SJ showing no germination at 100 mM, whereas populations M and NC had 23% and 9% germination, respectively. An inverse relationship was observed between osmotic potential and germination, with no germination recorded at osmotic potentials below −0.8 MPa in any population, indicating moisture availability is a critical requirement for germination. Exposing seeds to 120 C radiant heat completely inhibited germination in populations M and NC, whereas 3% of population SJ germinated following a 180-s exposure at 120 C. Seedling emergence decreased as planting depth increased. Emergence was greatest for seeds on the soil surface or at 0.5-cm burial depth, consistent with germination being stimulated by light. Knowledge of these biological characteristics ofC. aromaticusseed germination will assist in investigation of suitable control actions for this species, particularly in the early stage of its invasion into new areas, and will contribute to significant reduction in the soil seedbank.
Through Their Own Eyes: The Implications of COVID-19 for PhD Students
Authors: Haas Nicholas , Gureghian Aida , Jusino Díaz Cristel , Williams Abby
Published: November 2020

COVID-19 is expected to radically alter higher education in the United States and to further limit the availability of tenure-track academic positions. How has the pandemic and its associated fallout affected doctoral students’ career aspirations and priorities? We investigate this question by comparing responses to a PhD career survey prior to and following significant developments in the pandemic. We find little evidence that the pandemic caused substantial shifts in PhD students’ aspirations and priorities. However, some differences emerge when considering later dates in our survey period, particularly among more senior students who express a greater interest in some non-academic careers and job characteristics. Contrary to expectation, we also find evidence that the pandemic improved some students’ perceptions of their academic departments. In our conclusion, we speculate whether steps taken by the comparatively well-resourced institution that we study helped to mitigate some of the more negative consequences of the pandemic.
Magnetic plasmon resonances in nanostructured topological insulators for strongly enhanced light–MoS2 interactions
Authors: Lu Hua , Yue Zengji , Li Yangwu , Zhang Yinan , Zhang Mingwen , Zeng Wei , Gan Xuetao , Mao Dong , Xiao Fajun , Mei Ting , Zhao Weiyao , Wang Xiaolin , Gu Min , Zhao Jianlin
Published: November 2020

Magnetic resonances not only play crucial roles in artificial magnetic materials but also offer a promising way for light control and interaction with matter. Recently, magnetic resonance effects have attracted special attention in plasmonic systems for overcoming magnetic response saturation at high frequencies and realizing high-performance optical functionalities. As novel states of matter, topological insulators (TIs) present topologically protected conducting surfaces and insulating bulks in a broad optical range, providing new building blocks for plasmonics. However, until now, high-frequency (e.g. visible range) magnetic resonances and related applications have not been demonstrated in TI systems. Herein, we report for the first time, to our knowledge, a kind of visible range magnetic plasmon resonances (MPRs) in TI structures composed of nanofabricated Sb2Te3 nanogrooves. The experimental results show that the MPR response can be tailored by adjusting the nanogroove height, width, and pitch, which agrees well with the simulations and theoretical calculations. Moreover, we innovatively integrated monolayer MoS2 onto a TI nanostructure and observed strongly reinforced light–MoS2 interactions induced by a significant MPR-induced electric field enhancement, remarkable compared with TI-based electric plasmon resonances (EPRs). The MoS2 photoluminescence can be flexibly tuned by controlling the incident light polarization. These results enrich TI optical physics and applications in highly efficient optical functionalities as well as artificial magnetic materials at high frequencies.
Marine Dadabacteria exhibit genome streamlining and phototrophy-driven niche partitioning
Authors: Graham Elaina D , Tully Benjamin J
Published: November 2020

The remineralization of organic material via heterotrophy in the marine environment is performed by a diverse and varied group of microorganisms that can specialize in the type of organic material degraded and the niche they occupy. The marine Dadabacteria are cosmopolitan in the marine environment and belong to a candidate phylum for which there has not been a comprehensive assessment of the available genomic data to date. Here in, we assess the functional potential of the marine pelagic Dadabacteria in comparison to members of the phylum that originate from terrestrial, hydrothermal, and subsurface environments. Our analysis reveals that the marine pelagic Dadabacteria have streamlined genomes, corresponding to smaller genome sizes and lower nitrogen content of their DNA and predicted proteome, relative to their phylogenetic counterparts. Collectively, the Dadabacteria have the potential to degrade microbial dissolved organic matter, specifically peptidoglycan and phospholipids. The marine Dadabacteria belong to two clades with apparent distinct ecological niches in global metagenomic data: a clade with the potential for photoheterotrophy through the use of proteorhodopsin, present predominantly in surface waters up to 100 m depth; and a clade lacking the potential for photoheterotrophy that is more abundant in the deep photic zone.
Correction: Advances and potential pitfalls of oncolytic viruses expressing immunomodulatory transgene therapy for malignant gliomas
Authors: Zhang Qing , Liu Fusheng
Published: November 2020

A Correction to this paper has been published: https://doi.org/10.1038/s41419-020-2696-5.
Surveying biomolecular frustration at atomic resolution
Authors: Chen Mingchen , Chen Xun , Schafer Nicholas P. , Clementi Cecilia , Komives Elizabeth A. , Ferreiro Diego U. , Wolynes Peter G.
Published: November 2020

To function, biomolecules require sufficient specificity of interaction as well as stability to live in the cell while still being able to move. Thermodynamic stability of only a limited number of specific structures is important so as to prevent promiscuous interactions. The individual interactions in proteins, therefore, have evolved collectively to give funneled minimally frustrated landscapes but some strategic parts of biomolecular sequences located at specific sites in the structure have been selected to be frustrated in order to allow both motion and interaction with partners. We describe a framework efficiently to quantify and localize biomolecular frustration at atomic resolution by examining the statistics of the energy changes that occur when the local environment of a site is changed. The location of patches of highly frustrated interactions correlates with key biological locations needed for physiological function. At atomic resolution, it becomes possible to extend frustration analysis to protein-ligand complexes. At this resolution one sees that drug specificity is correlated with there being a minimally frustrated binding pocket leading to a funneled binding landscape. Atomistic frustration analysis provides a route for screening for more specific compounds for drug discovery.
Sensory substitution reveals a manipulation bias
Authors: Zai Anja T. , Cavé-Lopez Sophie , Rolland Manon , Giret Nicolas , Hahnloser Richard H. R.
Published: November 2020

Sensory substitution is a promising therapeutic approach for replacing a missing or diseased sensory organ by translating inaccessible information into another sensory modality. However, many substitution systems are not well accepted by subjects. To explore the effect of sensory substitution on voluntary action repertoires and their associated affective valence, we study deaf songbirds to which we provide visual feedback as a substitute of auditory feedback. Surprisingly, deaf birds respond appetitively to song-contingent binary visual stimuli. They skillfully adapt their songs to increase the rate of visual stimuli, showing that auditory feedback is not required for making targeted changes to vocal repertoires. We find that visually instructed song learning is basal-ganglia dependent. Because hearing birds respond aversively to the same visual stimuli, sensory substitution reveals a preference for actions that elicit sensory feedback over actions that do not, suggesting that substitution systems should be designed to exploit the drive to manipulate.
Common and distinct neural representations of aversive somatic and visceral stimulation in healthy individuals
Authors: Van Oudenhove Lukas , Kragel Philip A. , Dupont Patrick , Ly Huynh Giao , Pazmany Els , Enzlin Paul , Rubio Amandine , Delon-Martin Chantal , Bonaz Bruno , Aziz Qasim , Tack Jan , Fukudo Shin , Kano Michiko , Wager Tor D.
Published: November 2020

Different pain types may be encoded in different brain circuits. Here, we examine similarities and differences in brain processing of visceral and somatic pain. We analyze data from seven fMRI studies (N = 165) and five types of pain and discomfort (esophageal, gastric, and rectal distension, cutaneous thermal stimulation, and vulvar pressure) to establish and validate generalizable pain representations. We first evaluate an established multivariate brain measure, the Neurologic Pain Signature (NPS), as a common nociceptive pain system across pain types. Then, we develop a multivariate classifier to distinguish visceral from somatic pain. The NPS responds robustly in 98% of participants across pain types, correlates with perceived intensity of visceral pain and discomfort, and shows specificity to pain when compared with cognitive and affective conditions from twelve additional studies (N = 180). Pre-defined signatures for non-pain negative affect do not respond to visceral pain. The visceral versus the somatic classifier reliably distinguishes somatic (thermal) from visceral (rectal) stimulation in both cross-validation and independent cohorts. Other pain types reflect mixtures of somatic and visceral patterns. These results validate the NPS as measuring a common core nociceptive pain system across pain types, and provide a new classifier for visceral versus somatic pain.
Extreme anti-reflection enhanced magneto-optic Kerr effect microscopy
Authors: Kim Dongha , Oh Young-Wan , Kim Jong Uk , Lee Soogil , Baucour Arthur , Shin Jonghwa , Kim Kab-Jin , Park Byong-Guk , Seo Min-Kyo
Published: November 2020

Magnetic and spintronic media have offered fundamental scientific subjects and technological applications. Magneto-optic Kerr effect (MOKE) microscopy provides the most accessible platform to study the dynamics of spins, magnetic quasi-particles, and domain walls. However, in the research of nanoscale spin textures and state-of-the-art spintronic devices, optical techniques are generally restricted by the extremely weak magneto-optical activity and diffraction limit. Highly sophisticated, expensive electron microscopy and scanning probe methods thus have come to the forefront. Here, we show that extreme anti-reflection (EAR) dramatically improves the performance and functionality of MOKE microscopy. For 1-nm-thin Co film, we demonstrate a Kerr amplitude as large as 20° and magnetic domain imaging visibility of 0.47. Especially, EAR-enhanced MOKE microscopy enables real-time detection and statistical analysis of sub-wavelength magnetic domain reversals. Furthermore, we exploit enhanced magneto-optic birefringence and demonstrate analyser-free MOKE microscopy. The EAR technique is promising for optical investigations and applications of nanomagnetic systems.
Imaging the coupling between itinerant electrons and localised moments in the centrosymmetric skyrmion magnet GdRu2Si2
Authors: Yasui Yuuki , Butler Christopher J. , Khanh Nguyen Duy , Hayami Satoru , Nomoto Takuya , Hanaguri Tetsuo , Motome Yukitoshi , Arita Ryotaro , Arima Taka-hisa , Tokura Yoshinori , Seki Shinichiro
Published: November 2020

Magnetic skyrmions were thought to be stabilised only in inversion-symmetry breaking structures, but skyrmion lattices were recently discovered in inversion symmetric Gd-based compounds, spurring questions of the stabilisation mechanism. A natural consequence of a recent theoretical proposal, a coupling between itinerant electrons and localised magnetic moments, is that the skyrmions are amenable to detection using even non-magnetic probes such as spectroscopic-imaging scanning tunnelling microscopy (SI-STM). Here SI-STM observations of GdRu2Si2 reveal patterns in the local density of states that indeed vary with the underlying magnetic structures. These patterns are qualitatively reproduced by model calculations which assume exchange coupling between itinerant electrons and localised moments. These findings provide a clue to understand the skyrmion formation mechanism in GdRu2Si2.
Structural basis for assembly of non-canonical small subunits into type I-C Cascade
Authors: O’Brien Roisin E. , Santos Inês C. , Wrapp Daniel , Bravo Jack P. K. , Schwartz Evan A. , Brodbelt Jennifer S. , Taylor David W.
Published: November 2020

Bacteria and archaea employ CRISPR (clustered, regularly, interspaced, short palindromic repeats)-Cas (CRISPR-associated) systems as a type of adaptive immunity to target and degrade foreign nucleic acids. While a myriad of CRISPR-Cas systems have been identified to date, type I-C is one of the most commonly found subtypes in nature. Interestingly, the type I-C system employs a minimal Cascade effector complex, which encodes only three unique subunits in its operon. Here, we present a 3.1 Å resolution cryo-EM structure of the Desulfovibrio vulgaris type I-C Cascade, revealing the molecular mechanisms that underlie RNA-directed complex assembly. We demonstrate how this minimal Cascade utilizes previously overlooked, non-canonical small subunits to stabilize R-loop formation. Furthermore, we describe putative PAM and Cas3 binding sites. These findings provide the structural basis for harnessing the type I-C Cascade as a genome-engineering tool.
Universal light-guiding geometry for on-chip resonators having extremely high Q-factor
Authors: Kim Dae-Gon , Han Sangyoon , Hwang Joonhyuk , Do In Hwan , Jeong Dongin , Lim Ji-Hun , Lee Yong-Hoon , Choi Muhan , Lee Yong-Hee , Choi Duk-Yong , Lee Hansuek
Published: November 2020

By providing an effective way to leverage nonlinear phenomena in integrated devices, high-Q optical resonators have led to recent advances in on-chip photonics. However, developing fabrication processes to shape any new material into a resonator with extremely smooth surfaces on a chip has been an exceptionally challenging task. Here, we describe a universal method to implement ultra-high-Q resonators with any new material having desirable properties that can be deposited by physical vapor deposition. Using this method light-guiding cores with surface roughness on the molecular-scale are created automatically on pre-patterned substrates. Its efficacy has been verified using As2S3, a chalcogenide glass that has high-nonlinearity. The Q-factor of the As2S3 resonator so-developed approached the propagation loss record achieved in chalcogenide fibers which were limited by material losses. Owing to the boosted Q-factor, lasing by stimulated Brillouin scattering has been demonstrated with 100 times lower threshold power than the previous record.
Curved neuromorphic image sensor array using a MoS2-organic heterostructure inspired by the human visual recognition system
Authors: Choi Changsoon , Leem Juyoung , Kim Minsung , Taqieddin Amir , Cho Chullhee , Cho Kyoung Won , Lee Gil Ju , Seung Hyojin , Bae Hyung Jong , Song Young Min , Hyeon Taeghwan , Aluru Narayana R. , Nam SungWoo , Kim Dae-Hyeong
Published: November 2020

Conventional imaging and recognition systems require an extensive amount of data storage, pre-processing, and chip-to-chip communications as well as aberration-proof light focusing with multiple lenses for recognizing an object from massive optical inputs. This is because separate chips (i.e., flat image sensor array, memory device, and CPU) in conjunction with complicated optics should capture, store, and process massive image information independently. In contrast, human vision employs a highly efficient imaging and recognition process. Here, inspired by the human visual recognition system, we present a novel imaging device for efficient image acquisition and data pre-processing by conferring the neuromorphic data processing function on a curved image sensor array. The curved neuromorphic image sensor array is based on a heterostructure of MoS2 and poly(1,3,5-trimethyl-1,3,5-trivinyl cyclotrisiloxane). The curved neuromorphic image sensor array features photon-triggered synaptic plasticity owing to its quasi-linear time-dependent photocurrent generation and prolonged photocurrent decay, originated from charge trapping in the MoS2-organic vertical stack. The curved neuromorphic image sensor array integrated with a plano-convex lens derives a pre-processed image from a set of noisy optical inputs without redundant data storage, processing, and communications as well as without complex optics. The proposed imaging device can substantially improve efficiency of the image acquisition and recognition process, a step forward to the next generation machine vision.
Ni-catalyzed asymmetric hydrogenation of N-aryl imino esters for the efficient synthesis of chiral α-aryl glycines
Authors: Liu Dan , Li Bowen , Chen Jianzhong , Gridnev Ilya D. , Yan Deyue , Zhang Wanbin
Published: November 2020

Chiral α-aryl glycines play a key role in the preparation of some bioactive products, however, their catalytic asymmetric synthesis is far from being satisfactory. Herein, we report an efficient nickel-catalyzed asymmetric hydrogenation of N-aryl imino esters, affording chiral α-aryl glycines in high yields and enantioselectivities (up to 98% ee). The hydrogenation can be conducted on a gram scale with a substrate/catalyst ratio of up to 2000. The obtained chiral N-p-methoxyphenyl α-aryl glycine derivatives are not only directly useful chiral secondary amino acid esters but can also be easily deprotected by treatment with cerium ammonium nitrate for further transformations to several widely used molecules including drug intermediates and chiral ligands. Formation of a chiral Ni-H species in hydrogenation is detected by 1H NMR. Computational results indicate that the stereo selection is determined during the approach of the substrate to the catalyst.
Publisher Correction: Parallel evolution in the emergence of highly pathogenic avian influenza A viruses
Authors: Escalera-Zamudio Marina , Golden Michael , Gutiérrez Bernardo , Thézé Julien , Keown Jeremy Russell , Carrique Loic , Bowden Thomas A. , Pybus Oliver G.
Published: November 2020

A Correction to this paper has been published: https://doi.org/10.1038/s41467-020-20006-5
A novel Schmallenberg virus subunit vaccine candidate protects IFNAR-/- mice against virulent SBV challenge
Authors: Boshra Hani , Lorenzo Gema , Charro Diego , Moreno Sandra , Guerra Gabriel Soares , Sanchez Isbene , Garrido Joseba M. , Geijo Marivi , Brun Alejandro , Abrescia Nicola G. A.
Published: November 2020

Schmallenberg virus (SBV), an arthropod-transmitted pathogenic bunyavirus, continues to be a threat to the European livestock industry, causing morbidity and mortality among young ruminant livestock. Here, we describe a novel SBV subunit vaccine, based on bacterially expressed SBV nucleoprotein (SBV-N) administered with a veterinary-grade Saponin adjuvant. When assayed in an IFNAR-/- mouse model, SBV-N with Saponin induced strong non-neutralizing broadly virus-reactive antibodies, decreased clinical signs, as well as significantly reduced viremia. Vaccination assays also suggest that this level of immune protection is cell mediated, as evidenced by the lack of neutralizing antibodies, as well as interferon-γ secretion observed in vitro. Therefore, based on these results, bacterially expressed SBV-N, co-administered with veterinary-grade Saponin adjuvant may serve as a promising economical alternative to current SBV vaccines, and warrant further evaluation in large ruminant animal models. Moreover, we propose that this strategy may be applicable to other bunyaviruses.
Ultradian rhythms in heart rate variability and distal body temperature anticipate onset of the luteinizing hormone surge
Authors: Grant Azure D. , Newman Mark , Kriegsfeld Lance J.
Published: November 2020

The menstrual cycle is characterized by predictable patterns of physiological change across timescales. Although patterns of reproductive hormones across the menstrual cycle, particularly ultradian rhythms, are well described, monitoring these measures repeatedly to predict the preovulatory luteinizing hormone (LH) surge is not practical. In the present study, we explored whether non-invasive measures coupled to the reproductive system: high frequency distal body temperature (DBT), sleeping heart rate (HR), sleeping heart rate variability (HRV), and sleep timing, could be used to anticipate the preovulatory LH surge in women. To test this possibility, we used signal processing to examine these measures in 45 premenopausal and 10 perimenopausal cycles alongside dates of supra-surge threshold LH and menstruation. Additionally, urinary estradiol and progesterone metabolites were measured daily surrounding the LH surge in 20 cycles. Wavelet analysis revealed a consistent pattern of DBT and HRV ultradian rhythm (2–5 h) power that uniquely enabled anticipation of the LH surge at least 2 days prior to its onset in 100% of individuals. Together, the present findings reveal fluctuations in distal body temperature and heart rate variability that consistently anticipate the LH surge, suggesting that automated ultradian rhythm monitoring may provide a novel and convenient method for non-invasive fertility assessment.
The mutualism effector MiSSP7 of Laccaria bicolor alters the interactions between the poplar JAZ6 protein and its associated proteins
Authors: Daguerre Yohann , Basso Veronica , Hartmann-Wittulski Sebastian , Schellenberger Romain , Meyer Laura , Bailly Justine , Kohler Annegret , Plett Jonathan M. , Martin Francis , Veneault-Fourrey Claire
Published: November 2020

Despite the pivotal role of jasmonic acid in the outcome of plant-microorganism interactions, JA-signaling components in roots of perennial trees like western balsam poplar (Populus trichocarpa) are poorly characterized. Here we decipher the poplar-root JA-perception complex centered on PtJAZ6, a co-repressor of JA-signaling targeted by the effector protein MiSSP7 from the ectomycorrhizal basidiomycete Laccaria bicolor during symbiotic development. Through protein–protein interaction studies in yeast we determined the poplar root proteins interacting with PtJAZ6. Moreover, we assessed via yeast triple-hybrid how the mutualistic effector MiSSP7 reshapes the association between PtJAZ6 and its partner proteins. In the absence of the symbiotic effector, PtJAZ6 interacts with the transcription factors PtMYC2s and PtJAM1.1. In addition, PtJAZ6 interacts with it-self and with other Populus JAZ proteins. Finally, MiSSP7 strengthens the binding of PtJAZ6 to PtMYC2.1 and antagonizes PtJAZ6 homo-/heterodimerization. We conclude that a symbiotic effector secreted by a mutualistic fungus may promote the symbiotic interaction through altered dynamics of a JA-signaling-associated protein–protein interaction network, maintaining the repression of PtMYC2.1-regulated genes.
Photooxidation of atrazine and its influence on disinfection byproducts formation during post-chlorination: effect of solution pH and mechanism
Authors: Liu Yucan , Zhu Kai , Zhu Huayu , Zhao Min , Huang Lihua , Dong Bin , Liu Qianjin
Published: November 2020

Partial photooxidation of micropollutants may lead to various degradation intermediates, obviously affecting disinfection byproducts (DBPs) formation during the post-chlorination process. The photooxidation of atrazine (ATZ) in aqueous solutions with low-pressure mercury UV lamps in UV, UV/H2O2 and UV/TiO2 treatment system and the formation of chlorinated disinfection byproducts (DBPs) during subsequent chlorination processes including dichloroacetic acid (DCAA), trichloroacetic acid (TCAA), 1,1,1-trichloro-2-propanone (TCP), trichloromethane (TCM) and chloropicrin (CHP) were investigated in this study. The effect of solution pH on the oxidation pathway of ATZ in three UV photooxidation treatment process and the impact of photooxidation on the DBPs formations were assessed. Based on UPLC-ESI–MS/MS analyses, identification of main oxidation intermediates was performed and the plausible degradation pathways of ATZ in photooxidation system were proposed, indicating that photooxidation of ATZ in UV/H2O2 and UV/TiO2 process system was significantly pH-dependent processes. Dichloroacetic acid (DCAA), trichloroacetic acid (TCAA), 1,1,1-trichloro-2-propanone (TCP), trichloromethane (TCM) and chloropicrin (CHP) were detected in photooxidized ATZ solutions. Compared to the other three DBPs, TCM and TCP were the main DBPs formed. The DBPs formations were greatly promoted in oxidized ATZ solutions. Solution pH and UV irradiation time exhibited obvious impact on the DBPs formation on the basis of DBP species. The variation tendency of DBPs observed relates to the combustion of ATZ in photooxidation system and the production oxidation intermediates.
Cardiovascular tissue regeneration system based on multiscale scaffolds comprising double-layered hydrogels and fibers
Authors: Kook Yun-Min , Hwang Soonjae , Kim Hyerim , Rhee Ki-Jong , Lee Kangwon , Koh Won-Gun
Published: November 2020

We report a technique to reconstruct cardiovascular tissue using multiscale scaffolds incorporating polycaprolactone fibers with double-layered hydrogels comprising fibrin hydrogel surrounded by secondary alginate hydrogel. The scaffolds compartmentalized cells into the core region of cardiac tissue and the peripheral region of blood vessels to construct cardiovascular tissue, which was accomplished by a triple culture system of adipose-derived mesenchymal stem cells (ADSCs) with C2C12 myoblasts on polycaprolactone (PCL) fibers along with human umbilical vein endothelial cells (HUVECs) in fibrin hydrogel. The secondary alginate hydrogel prevented encapsulated cells from migrating outside scaffold and maintained the scaffold structure without distortion after subcutaneous implantation. According to in vitro studies, resultant scaffolds promoted new blood vessel formation as well as cardiomyogenic phenotype expression of ADSCs. Cardiac muscle-specific genes were expressed from stem cells and peripheral blood vessels from HUVECs were also successfully developed in subcutaneously implanted cell-laden multiscale scaffolds. Furthermore, the encapsulated stem cells modulated the immune response of scaffolds by secreting anti-inflammatory cytokines for successful tissue construction. Our study reveals that multiscale scaffolds can be promising for the remodeling and transplantation of cardiovascular tissue.
Advantages and limitations of microtiter biofilm assays in the model of antibiofilm activity of Klebsiella phage KP34 and its depolymerase
Authors: Latka Agnieszka , Drulis-Kawa Zuzanna
Published: November 2020

One of the potential antibiofilm strategies is to use lytic phages and phage-derived polysaccharide depolymerases. The idea is to uncover bacteria embedded in the biofilm matrix making them accessible and vulnerable to antibacterials and the immune system. Here we present the antibiofilm efficiency of lytic phage KP34 equipped with virion-associated capsule degrading enzyme (depolymerase) and its recombinant depolymerase KP34p57, depolymerase-non-bearing phage KP15, and ciprofloxacin, separately and in combination, using a multidrug-resistant K. pneumoniae biofilm model. The most effective antibiofilm agents were (1) phage KP34 alone or in combination with ciprofloxacin/phage KP15, and (2) depolymerase KP34p57 with phage KP15 and ciprofloxacin. Secondly, applying the commonly used biofilm microtiter assays: (1) colony count, (2) LIVE/DEAD BacLight Bacterial Viability Kit, and (3) crystal violet (CV) biofilm staining, we unravelled the main advantages and limitations of the above methods in antibiofilm testing. The diverse mode of action of selected antimicrobials strongly influenced obtained results, including a false positive enlargement of biofilm mass (CV staining) while applying polysaccharide degrading agents. We suggest that to get a proper picture of antimicrobials’ effectiveness, multiple examination methods should be used and the results must be read considering the principle of each technique and the antibacterial mechanism.
Breeding progress for pathogen resistance is a second major driver for yield increase in German winter wheat at contrasting N levels
Authors: Zetzsche Holger , Friedt Wolfgang , Ordon Frank
Published: November 2020

Breeding has substantially increased the genetic yield potential, but fungal pathogens are still major constraints for wheat production. Therefore, breeding success for resistance and its impact on yield were analyzed on a large panel of winter wheat cultivars, representing breeding progress in Germany during the last decades, in large scale field trials under different fungicide and nitrogen treatments. Results revealed a highly significant effect of genotype (G) and year (Y) on resistances and G × Y interactions were significant for all pathogens tested, i.e. leaf rust, strip rust, powdery mildew and Fusarium head blight. N-fertilization significantly increased the susceptibility to biotrophic and hemibiotrophic pathogens. Resistance was significantly improved over time but at different rates for the pathogens. Although the average progress of resistance against each pathogen was higher at the elevated N level in absolute terms, it was very similar at both N levels on a relative basis. Grain yield was increased significantly over time under all treatments but was considerably higher without fungicides particularly at high N-input. Our results strongly indicate that wheat breeding resulted in a substantial increase of grain yield along with a constant improvement of resistance to fungal pathogens, thereby contributing to an environment-friendly and sustainable wheat production.
Comparative analyses and structural insights of new class glutathione transferases in Cryptosporidium species
Authors: Mfeka Mbalenhle Sizamile , Martínez-Oyanedel José , Chen Wanping , Achilonu Ikechukwu , Syed Khajamohiddin , Khoza Thandeka
Published: November 2020

Cryptosporidiosis, caused by protozoan parasites of the genus Cryptosporidium, is estimated to rank as a leading cause in the global burden of neglected zoonotic parasitic diseases. This diarrheal disease is the second leading cause of death in children under 5 years of age. Based on the C. parvum transcriptome data, glutathione transferase (GST) has been suggested as a drug target against this pathogen. GSTs are diverse multifunctional proteins involved in cellular defense and detoxification in organisms and help pathogens to alleviate chemical and environmental stress. In this study, we performed genome-wide data mining, identification, classification and in silico structural analysis of GSTs in fifteen Cryptosporidium species. The study revealed the presence three GSTs in each of the Cryptosporidium species analyzed in the study. Based on the percentage identity and comprehensive comparative phylogenetic analysis, we assigned Cryptosporidium species GSTs to three new GST classes, named Vega (ϑ), Gamma (γ) and Psi (ψ). The study also revealed an atypical thioredoxin-like fold in the C. parvum GST1 of the Vega class, whereas C. parvum GST2 of the Gamma class and C. melagridis GST3 of the Psi class has a typical thioredoxin-like fold in the N-terminal region. This study reports the first comparative analysis of GSTs in Cryptosporidium species.
Probing rapid carbon fixation in fast-growing seaweed Ulva meridionalis using stable isotope 13C-labelling
Authors: Tsubaki Shuntaro , Nishimura Hiroshi , Imai Tomoya , Onda Ayumu , Hiraoka Masanori
Published: November 2020

The high growth rate of Ulva seaweeds makes it a potential algal biomass resource. In particular, Ulva meridionalis grows up to fourfold a day. Here, we demonstrated strong carbon fixation by U. meridionalis using 13C stable isotope labelling and traced the 13C flux through sugar metabolites with isotope-ratio mass spectrometry (IR-MS), Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR-MS), 13C-nuclear magnetic resonance spectrometry (13C-NMR), and gas chromatography-mass spectrometry (GC–MS). U. meridionalis was first cultured in 13C-labelled enriched artificial seawater for 0–12 h, and the algae were collected every 4 h. U. meridionalis grew 1.8-fold (dry weight), and the 13C ratio reached 40% in 12 h, whereas 13C incorporation hardly occurred under darkness. At the beginning of the light period, 13C was incorporated into nucleic diphosphate (NDP) sugars in 4 h, and 13C labelled peaks were identified using FT-ICR-MS spectra. Using semiquantitative 13C-NMR measurements and GC–MS, 13C was detected in starch and matrix polysaccharides after the formation of NDP sugars. Moreover, the 14:10 light:dark regime resulted into 85% of 13C labelling was achieved after 72 h of cultivation. The rapid 13C uptake by U. meridionalis shows its strong carbon fixation capacity as a promising seaweed biomass feedstock.
Capuchin and rhesus monkeys show sunk cost effects in a psychomotor task
Authors: Watzek Julia , Brosnan Sarah F.
Published: November 2020

Human decision-making is often swayed by irrecoverable investments even though it should only be based on future—and not past—costs and benefits. Although this sunk cost effect is widely documented and can lead to devastating losses, the underlying psychological mechanisms are unclear. To tease apart possible explanations through a comparative approach, we assessed capuchin and rhesus monkeys’ susceptibility to sunk costs in a psychomotor task. Monkeys needed to track a moving target with a joystick-controlled cursor for variable durations. They could stop at any time, ending the trial without reward. To minimize the work required for a reward, monkeys should have always persisted for at least 1 s, but should have abandoned the trial if that did not yield a reward. Capuchin monkeys and especially rhesus macaques persisted to trial completion even when it was suboptimal, and were more likely to complete the trial the longer they had already tracked the target. These effects were less pronounced, although still present, when the change in expected tracking duration was signalled visually. These results show that sunk cost effects can arise in the absence of human-unique factors and may emerge, in part, because persisting can resolve uncertainty.
Applicability of minimally invasive surgery for clinically T4 colorectal cancer
Authors: Liao Yu-Tso , Liang Jin-Tung
Published: November 2020

The role of minimally invasive surgery (MIS) to treat clinically T4 (cT4) colorectal cancer (CRC) remains uncertain and deserves further investigation. A retrospective cohort study was conducted between September 2006 and March 2019 recruiting patients diagnosed as cT4 CRC and undergoing MIS at a university hospital and its branch. Patients’ demography, clinicopathology, surgical and oncological outcomes, and radicality were analyzed. A total of 128 patients were recruited with an average follow-up period of 33.8 months. The median time to soft diet was 6 days, and the median postoperative hospitalization periods was 11 days. The conversion and complication (Clavien–Dindo classification ≥ II) rates were 7.8% and 27.3%, respectively. The 30-day mortality was 0.78%. R0 resection rate was 92.2% for cT4M0 and 88.6% for pT4M0 patients. For cT4 CRC patients, the disease-free survival and 3-year overall survival were 86.1% and 86.8% for stage II, 54.1% and 57.9% for stage III, and 10.8% and 17.8% for stage IV. With acceptable conversion, complication and mortality rate, MIS may achieve satisfactory R0 resection rate and thus lead to good oncological outcomes for selected patients with cT4 CRC.
Bimodal microwave and ultrasound phantoms for non-invasive clinical imaging
Authors: Villa Enrique , Arteaga-Marrero Natalia , González-Fernández Javier , Ruiz-Alzola Juan
Published: November 2020

A precise and thorough methodology is presented for the design and fabrication of bimodal phantoms to be used in medical microwave and ultrasound applications. Dielectric and acoustic properties of human soft tissues were simultaneously mimicked. The phantoms were fabricated using polyvinyl alcohol cryogel (PVA-C) as gelling agent at a 10% concentration. Sucrose was employed to control the dielectric properties in the microwave spectrum, whereas cellulose was used as acoustic scatterer for ultrasound. For the dielectric properties at microwaves, a mathematical model was extracted to calculate the complex permittivity of the desired mimicked tissues in the frequency range from 500 MHz to 20 GHz. This model, dependent on frequency and sucrose concentration, was in good agreement with the reference Cole–Cole model. Regarding the acoustic properties, the speed of sound and attenuation coefficient were employed for validation. In both cases, the experimental data were consistent with the corresponding theoretical values for soft tissues. The characterization of these PVA-C phantoms demonstrated a significant performance for simultaneous microwave and ultrasound operation. In conclusion, PVA-C has been validated as gelling agent for the fabrication of complex multimodal phantoms that mimic soft tissues providing a unique tool to be used in a range of clinical applications.
Discriminating pseudoprogression and true progression in diffuse infiltrating glioma using multi-parametric MRI data through deep learning
Authors: Lee Joonsang , Wang Nicholas , Turk Sevcan , Mohammed Shariq , Lobo Remy , Kim John , Liao Eric , Camelo-Piragua Sandra , Kim Michelle , Junck Larry , Bapuraj Jayapalli , Srinivasan Ashok , Rao Arvind
Published: November 2020

Differentiating pseudoprogression from true tumor progression has become a significant challenge in follow-up of diffuse infiltrating gliomas, particularly high grade, which leads to a potential treatment delay for patients with early glioma recurrence. In this study, we proposed to use a multiparametric MRI data as a sequence input for the convolutional neural network with the recurrent neural network based deep learning structure to discriminate between pseudoprogression and true tumor progression. In this study, 43 biopsy-proven patient data identified as diffuse infiltrating glioma patients whose disease progressed/recurred were used. The dataset consists of five original MRI sequences; pre-contrast T1-weighted, post-contrast T1-weighted, T2-weighted, FLAIR, and ADC images as well as two engineered sequences; T1post–T1pre and T2–FLAIR. Next, we used three CNN-LSTM models with a different set of sequences as input sequences to pass through CNN-LSTM layers. We performed threefold cross-validation in the training dataset and generated the boxplot, accuracy, and ROC curve, AUC from each trained model with the test dataset to evaluate models. The mean accuracy for VGG16 models ranged from 0.44 to 0.60 and the mean AUC ranged from 0.47 to 0.59. For CNN-LSTM model, the mean accuracy ranged from 0.62 to 0.75 and the mean AUC ranged from 0.64 to 0.81. The performance of the proposed CNN-LSTM with multiparametric sequence data was found to outperform the popular convolutional CNN with a single MRI sequence. In conclusion, incorporating all available MRI sequences into a sequence input for a CNN-LSTM model improved diagnostic performance for discriminating between pseudoprogression and true tumor progression.
89Zr-pro-MMP-9 F(ab′)2 detects colitis induced intestinal and kidney fibrosis
Authors: Dmochowska Nicole , Tieu William , Keller Marianne D. , Hollis Courtney A. , Campaniello Melissa A. , Mavrangelos Chris , Takhar Prab , Hughes Patrick A.
Published: November 2020

Intestinal fibrosis is a common complication of inflammatory bowel disease but remains difficult to detect. Matrix metalloproteases (MMPs) have key roles in fibrosis and are therefore potential targets for fibrosis detection. We determined whether immunoPET of F(ab′)2 antibody fragments targeting MMPs detects colitis induced colonic fibrosis. Mice were administered 2% dextran sulfate sodium treated water for 1 cycle (inflamed) or 3 cycles (fibrotic), or were untreated (control). Colonic and kidney collagen, innate cytokine, MMPs and fecal MPO concentrations were analyzed by multiplex/ELISA. α-pro-MMP-9 F(ab′)2 fragments were engineered and conjugated to 89Zr for PET imaging, ex-vivo Cherenkov analysis and bio-distribution. Colonic innate cytokine concentrations and fecal myeloperoxidase were increased in inflamed mice but not fibrotic mice, while collagen concentrations were increased in fibrotic mice. MMPs were increased in inflamed mice, but only pro-MMP-9 remained increased in fibrotic mice. 89Zr-pro-MMP-9 F(ab′)2 uptake was increased in the intestine but also in the kidney of fibrotic mice, where collagen and pro-MMP-9 concentrations were increased. 89Zr-pro-MMP-9 F(ab′)2 detects colitis induced intestinal fibrosis and associated kidney fibrosis.
Overexpression of fibulin-3 in tumor tissue predicts poor survival of malignant mesothelioma patients from hand-spinning asbestos exposed area in eastern China
Authors: Jiang Zhaoqiang , Shen Wei , Ying Shibo , Gao Zhibin , He Xianglei , Chen Riping , Xia Hailing , Guo Xinnian , Fang Yuan , Zhang Yixiao , Miao Jianjiang , Zhou Jian , Zhang Xing , Chen Junqiang , Lou Jianlin
Published: November 2020

Fibulin-3 is an extracellular matrix glycoprotein widely expressed in various tissues. Tissue fibulin-3 expression have never been reported in association with prognosis of mesothelioma. Hence, we sought to determine the association between fibulin-3 expression and mesothelioma survival. We made a tissue microarray, which was comprised of cancer and normal tissue from mesothelioma patients (n = 82) during the period 1998–2017 in China. Fibulin-3 and HGMB1 expression were analyzed by immunohistochemistry method. Kaplan–Meier method and Cox proportional hazard models were used for analyzing survival data. Overall, 61 cases (74.4%) were female; 90.2% were of epithelioid type; the median overall survival time was 12.5 months. Fibulin-3 and HMGB1 were highly expressed in tumor tissue rather than adjacent tissue. The expression of fibulin-3 in tissue was correlated with that of HMGB1 (r = 0.32, P = 0.003). High expression of fibulin-3 in tumor tissue could predict poor survival in patients with mesothelioma (P = 0.02). This remained true in a multivariate model, with a significant hazard ratio of 1.91. We demonstrated that fibulin-3 in tumor tissue was a novel biomarker of poor survival of mesothelioma, suggesting it may be a relevant target for therapeutic intervention.
Estimating the population mean for a vertical profile of energy dissipation rate
Authors: Sugiura Nozomi , Kouketsu Shinya , Masuda Shuhei , Osafune Satoshi , Yasuda Ichiro
Published: November 2020

Energy dissipation rates are an important characteristic of turbulence; however, their magnitude in observational profiles can be incorrectly determined owing to their irregular appearance during vertical evolution. By analysing the data obtained from oceanic turbulence measurements, we demonstrate that the vertical sequences of energy dissipation rates exhibit a scaling property. Utilising this property, we propose a method to estimate the population mean for a profile. For scaling in the observed profiles, we demonstrate that our data exhibit a statistical property consistent with that exhibited by the universal multifractal model. Meanwhile, the population mean and its uncertainty can be estimated by inverting the probability distribution obtained by Monte Carlo simulations of a cascade model; to this end, observational constraints from several moments are imposed over each vertical sequence. This approach enables us to determine, to some extent, whether a profile shows an occasionally large mean or whether the population mean itself is large. Thus, it will contribute to the refinement of the regional estimation of the ocean energy budget, where only a small amount of turbulence observation data is available.
The identification of effective welfare indicators for laboratory-housed macaques using a Delphi consultation process
Authors: Truelove Melissa A. , Martin Jessica E. , Langford Fritha M. , Leach Matthew C.
Published: November 2020

Despite the importance for both animal welfare and scientific integrity of effective welfare assessment in non-human primates, there has been little or no consensus as what should be assessed. A Delphi consultation process was undertaken to identify the animal- and environment-based measures of welfare for laboratory-housed macaques and to determine their relative importance in on-site welfare assessments. One-hundred fifteen potential indictors were identified through a comprehensive literature search, followed by a two-round iterative electronic survey process to collect expert opinion. Stable group response and consensus about the validity, reliability, and feasibility of the proposed indicators (67.5% agreement) was achieved by the completion of Round Two. A substantially higher proportion of environment-based measures (72%: n = 44/61) were considered as valid, reliable, and feasible compared to the animal-based measures (22%: n = 12/54). The indicators that ranked most highly for assessing welfare were the presence of self-harm behaviours and the provision of social enrichment. This study provides an empirical basis upon which these indicators can be validated and then integrated into assessment tools developed for macaques and emphasises the need to include both animal- and environment-based indicators for accurate welfare monitoring.