bluuebunny/crossref_metadata_2025 huggingface dataset:
Comammox Nitrospira within the Yangtze River continuum: community, biogeography, and ecological drivers
Authors: Liu Shufeng , Wang Haiying , Chen Liming , Wang Jiawen , Zheng Maosheng , Liu Sitong , Chen Qian , Ni Jinren
Published: June 2020

The recent discovery of comammox Nitrospira as complete nitrifiers has fundamentally renewed perceptions of nitrogen cycling in natural and engineered systems, yet little is known about the environmental controls on these newly recognized bacteria. Based on improved phylogenetic resolution through successful assembly of ten novel genomes (71–96% completeness), we provided the first biogeographic patterns for planktonic and benthic comammox Nitrospira in the Yangtze River over a 6030 km continuum. Our study revealed the widespread distributions and relative abundance of comammox Nitrospira in this large freshwater system, constituting 30 and 46% of ammonia-oxidizing prokaryotes (AOPs) and displaying 30.4- and 17.9-fold greater abundances than canonical Nitrospira representatives in water and sediments, respectively. Comammox Nitrospira contributed more to nitrifier abundances (34–87% of AOPs) in typical oligotrophic environments with a higher pH and lower temperature, particularly in the plateau (clade B), mountain and foothill (clade A) areas of the upper reach. The dominant position of planktonic comammox Nitrospira was replaced by canonical Nitrospira sublineages I/II and ammonia-oxidizing bacteria from the plateau to downstream plain due to environmental selection, while the dissimilarity of benthic comammox Nitrospira was moderately associated with geographic distance. A substantial decrease (83%) in benthic comammox Nitrospira abundance occurred immediately downstream of the Three Gorges Dam, consistent with a similarly considerable decrease in overall sediment bacterial taxa. Together, this study highlights the previously unrecognized dominance of comammox Nitrospira in major river systems and underlines the importance of revisiting the distributions of and controls on nitrification processes within global freshwater environments.
Induction of ASC pyroptosis requires gasdermin D or caspase-1/11-dependent mediators and IFNβ from pyroptotic macrophages
Authors: Zhang Cuiping , Zhao Caiqi , Chen Xiaoyan , Tao Rujia , Wang Sijiao , Meng Guangxun , Liu Xing , Shao Changzhou , Su Xiao
Published: June 2020

Mesenchymal stem cells (MSCs) have been used in cell-based therapies for a variety of disorders. Some factors such as inflammatory mediators in the diseased area might damage the survival of MSCs and affect their efficacy. Pyroptosis is a form of programmed necrosis as a response for immune cells to cytosolic pathogenic stimuli. Whether MSCs develop pyroptosis under pathological stimulation, its underlying mechanism and biological significance are still unclear. Here, we found that LPS, flagellin, dsDNA, nigericin (NIG), or LPS combined with nigericin (LPS/NIG) could not induce pyroptosis in adipose-tissue-derived mesenchymal stem cells (ASCs). However, when applied the culture media collected from LPS/NIG-induced pyroptotic bone marrow-derived macrophages (BMDMs) to incubate ASCs, ASCs developed pyroptosis. Inhibition of caspases or deletion of Caspase-1/11 in ASCs did not affect the pyroptotic macrophage media-triggered ASC pyroptosis while ablation of Caspase-1/11 abolished BMDM pyroptosis induced by LPS/NIG. Media collected from LPS/NIG stimulated Gsdmd−/− or Caspase-1/11−/− BMDMs could not induce pyroptosis of ASCs. In addition, RNA-seq analysis showed that interferon (IFN)-stimulated genes were upregulated in pyroptotic ASCs. Adding IFNβ could boost LPS/NIG stimulated BMDM media-induced ASC pyroptosis. Surprisingly, the pyroptotic ASCs had a lower bactericidal ability to P. Aeruginosa. Taken together, induction of ASC pyroptosis requires gasdermin D or caspase-1/11-dependent mediators and IFNβ from pyroptotic macrophages.
Control of electrical resistance and magnetoresistance by electric-field-driven oxygen ion migration in a single GdOx wire
Authors: Kang Jun-Ho , Lee Soogil , Lee Taek-Hyeon , Yang Ji-Seok , Lee Jae Wook , Tae Cheong Cheon , Jeong Jong-Ryul , Park Seung-Young , Park Byong-Guk , Kim Kab-Jin
Published: June 2020

Electric-field-driven ion migration can significantly modulate the electric and magnetic properties of solids, creating novel functionalities useful for advanced electromagnetic devices. Earlier works have used vertically stacked structures for this purpose, in which the redox process results from ion migration driven by a vertical electric field through the interfaces. However, the existence of the interfaces between the dissimilar layers causes the oxidation and reduction processes to have high and asymmetric energy barriers, which means that a large electric field is required to control the devices. Here, we show that in a partially oxidized single GdOx wire using a lateral electric field configuration, low and symmetric energy barriers for the oxidation and reduction processes can be achieved. We provide evidence that the redox process is the result of the lateral motion of oxygen ions by directly visualizing the electric-field-driven real-time ionic motion using an optical microscope. An electric field as low as 105 V/m was able to drive oxygen ions at room temperature, allowing controllable modulation of the electrical resistance using a lateral electric field. A large negative magnetoresistance was also observed in the GdOx wire, and its magnitude was significantly enhanced up to 20% at 9 T through oxygen ion control. Our results suggest that the electrical and magnetic properties of single GdOx can be efficiently controlled through oxygen ion motion driven by a lateral electric field, which paves the way for fully functional electromagnetic devices such as artificial synapses.
Globalization and the rise and fall of cognitive control
Authors: Mosleh Mohsen , Kyker Katelynn , Cohen Jonathan D. , Rand David G.
Published: June 2020

The scale of human interaction is larger than ever before—people regularly interact with and learn from others around the world, and everyone impacts the global environment. We develop an evolutionary game theory model to ask how the scale of interaction affects the evolution of cognition. Our agents make decisions using automatic (e.g., reflexive) versus controlled (e.g., deliberative) cognition, interact with each other, and influence the environment (i.e., game payoffs). We find that globalized direct contact between agents can either favor or disfavor control, depending on whether controlled agents are harmed or helped by contact with automatic agents; globalized environment disfavors cognitive control, while also promoting strategic diversity and fostering mesoscale communities of more versus less controlled agents; and globalized learning destroys mesoscale communities and homogenizes the population. These results emphasize the importance of the scale of interaction for the evolution of cognition, and help shed light on modern challenges.
Metallic nanocrystals with low angle grain boundary for controllable plastic reversibility
Authors: Zhu Qi , Huang Qishan , Guang Cao , An Xianghai , Mao Scott X. , Yang Wei , Zhang Ze , Gao Huajian , Zhou Haofei , Wang Jiangwei
Published: June 2020

Advanced nanodevices require reliable nanocomponents where mechanically-induced irreversible structural damage should be largely prevented. However, a practical methodology to improve the plastic reversibility of nanosized metals remains challenging. Here, we propose a grain boundary (GB) engineering protocol to realize controllable plastic reversibility in metallic nanocrystals. Both in situ nanomechanical testing and atomistic simulations demonstrate that custom-designed low-angle GBs with controlled misorientation can endow metallic bicrystals with endurable cyclic deformability via GB migration. Such fully reversible plasticity is predominantly governed by the conservative motion of Shockley partial dislocation pairs, which fundamentally suppress damage accumulation and preserve the structural stability. This reversible deformation is retained in a broad class of face-centred cubic metals with low stacking fault energies when tuning the GB structure, external geometry and loading conditions over a wide range. These findings shed light on practical advances in promoting cyclic deformability of metallic nanomaterials.
General route to design polymer molecular weight distributions through flow chemistry
Authors: Walsh Dylan J. , Schinski Devin A. , Schneider Robert A. , Guironnet Damien
Published: June 2020

The properties of a polymer are known to be intrinsically related to its molecular weight distribution (MWD); however, previous methodologies of MWD control do not use a design and result in arbitrary shaped MWDs. Here we report a precise design to synthesis protocol for producing a targeted MWD design with a simple to use, and chemistry agnostic computer-controlled tubular flow reactor. To support the development of this protocol, we constructed general reactor design rules by combining fluid mechanical principles, polymerization kinetics, and experiments. The ring opening polymerization of lactide, the anionic polymerization of styrene, and the ring opening metathesis polymerization are used as model polymerizations to develop the reactor design rules and synthesize MWD profiles. The derivation of a mathematical model enables the quantitative prediction of the experimental results, and this model provides a tool to explore the limits of any MWD design protocol.
Evolution of generalist resistance to herbicide mixtures reveals a trade-off in resistance management
Authors: Comont David , Lowe Claudia , Hull Richard , Crook Laura , Hicks Helen L. , Onkokesung Nawaporn , Beffa Roland , Childs Dylan Z. , Edwards Robert , Freckleton Robert P. , Neve Paul
Published: June 2020

Intense selection by pesticides and antibiotics has resulted in a global epidemic of evolved resistance. In agriculture and medicine, using mixtures of compounds from different classes is widely accepted as optimal resistance management. However, this strategy may promote the evolution of more generalist resistance mechanisms. Here we test this hypothesis at a national scale in an economically important agricultural weed: blackgrass (Alopecurus myosuroides), for which herbicide resistance is a major economic issue. Our results reveal that greater use of herbicide mixtures is associated with lower levels of specialist resistance mechanisms, but higher levels of a generalist mechanism implicated in enhanced metabolism of herbicides with diverse modes of action. Our results indicate a potential evolutionary trade-off in resistance management, whereby attempts to reduce selection for specialist resistance traits may promote the evolution of generalist resistance. We contend that where specialist and generalist resistance mechanisms co-occur, similar trade-offs will be evident, calling into question the ubiquity of resistance management based on mixtures and combination therapies.
The phytopathogenic fungus Sclerotinia sclerotiorum detoxifies plant glucosinolate hydrolysis products via an isothiocyanate hydrolase
Authors: Chen Jingyuan , Ullah Chhana , Reichelt Michael , Beran Franziska , Yang Zhi-Ling , Gershenzon Jonathan , Hammerbacher Almuth , Vassão Daniel G.
Published: June 2020

Brassicales plants produce glucosinolates and myrosinases that generate toxic isothiocyanates conferring broad resistance against pathogens and herbivorous insects. Nevertheless, some cosmopolitan fungal pathogens, such as the necrotrophic white mold Sclerotinia sclerotiorum, are able to infect many plant hosts including glucosinolate producers. Here, we show that S. sclerotiorum infection activates the glucosinolate-myrosinase system, and isothiocyanates contribute to resistance against this fungus. S. sclerotiorum metabolizes isothiocyanates via two independent pathways: conjugation to glutathione and, more effectively, hydrolysis to amines. The latter pathway features an isothiocyanate hydrolase that is homologous to a previously characterized bacterial enzyme, and converts isothiocyanate into products that are not toxic to the fungus. The isothiocyanate hydrolase promotes fungal growth in the presence of the toxins, and contributes to the virulence of S. sclerotiorum on glucosinolate-producing plants.
Organic NIR-II molecule with long blood half-life for in vivo dynamic vascular imaging
Authors: Li Benhao , Zhao Mengyao , Feng Lishuai , Dou Chaoran , Ding Suwan , Zhou Gang , Lu Lingfei , Zhang Hongxin , Chen Feiya , Li Xiaomin , Li Guangfeng , Zhao Shichang , Jiang Chunyu , Wang Yan , Zhao Dongyuan , Cheng Yingsheng , Zhang Fan
Published: June 2020

Real-time monitoring of vessel dysfunction is of great significance in preclinical research. Optical bioimaging in the second near-infrared (NIR-II) window provides advantages including high resolution and fast feedback. However, the reported molecular dyes are hampered by limited blood circulation time (~ 5–60 min) and short absorption and emission wavelength, which impede the accurate long-term monitoring. Here, we report a NIR-II molecule (LZ-1105) with absorption and emission beyond 1000 nm. Thanks to the long blood circulation time (half-life of 3.2 h), the fluorophore is used for continuous real-time monitoring of dynamic vascular processes, including ischemic reperfusion in hindlimbs, thrombolysis in carotid artery and opening and recovery of the blood brain barrier (BBB). LZ-1105 provides an approach for researchers to assess vessel dysfunction due to the long excitation and emission wavelength and long-term blood circulation properties.
Asymmetric one-pot transformation of isoflavones to pterocarpans and its application in phytoalexin synthesis
Authors: Ciesielski Philipp , Metz Peter
Published: June 2020

Phytoalexins have attracted much attention due to their health-promoting effects and their vital role in plant health during the last years. Especially the 6a-hydroxypterocarpans glyceollin I and glyceollin II, which may be isolated from stressed soy plants, possess a broad spectrum of bioactivities such as anticancer activity and beneficial contributions against western diseases by anti-oxidative and anti-cholesterolemic effects. Aiming for a catalytic asymmetric access to these natural products, we establish the asymmetric syntheses of the natural isoflavonoids (−)-variabilin, (−)-homopterocarpin, (−)-medicarpin, (−)-3,9-dihydroxypterocarpan, and (−)-vestitol by means of an asymmetric transfer hydrogenation (ATH) reaction. We successfully adapt this pathway to the first catalytic asymmetric total synthesis of (−)-glyceollin I and (−)-glyceollin II. This eight-step synthesis features an efficient one-pot transformation of a 2′-hydroxyl-substituted isoflavone to a virtually enantiopure pterocarpan by means of an ATH and a regioselective benzylic oxidation under aerobic conditions to afford the susceptible 6a-hydroxypterocarpan skeleton.
Harmonization of quality metrics and power calculation in multi-omic studies
Authors: Tarazona Sonia , Balzano-Nogueira Leandro , Gómez-Cabrero David , Schmidt Andreas , Imhof Axel , Hankemeier Thomas , Tegnér Jesper , Westerhuis Johan A. , Conesa Ana
Published: June 2020

Multi-omic studies combine measurements at different molecular levels to build comprehensive models of cellular systems. The success of a multi-omic data analysis strategy depends largely on the adoption of adequate experimental designs, and on the quality of the measurements provided by the different omic platforms. However, the field lacks a comparative description of performance parameters across omic technologies and a formulation for experimental design in multi-omic data scenarios. Here, we propose a set of harmonized Figures of Merit (FoM) as quality descriptors applicable to different omic data types. Employing this information, we formulate the MultiPower method to estimate and assess the optimal sample size in a multi-omics experiment. MultiPower supports different experimental settings, data types and sample sizes, and includes graphical for experimental design decision-making. MultiPower is complemented with MultiML, an algorithm to estimate sample size for machine learning classification problems based on multi-omic data.
Incidence and risk factors for heat-related illness (heatstroke) in UK dogs under primary veterinary care in 2016
Authors: Hall Emily J. , Carter Anne J. , O’Neill Dan G.
Published: June 2020

As climate change causes global temperatures to rise, heat-related illness, a potentially fatal condition in dogs, will become an ever-greater threat. This study aimed to report the incidence, fatality and canine risk factors of heat-related illness in UK dogs under primary veterinary care in 2016. The VetCompassTMprogramme collects de-identified electronic patient records from UK veterinary practices for research. From the clinical records of 905,543 dogs under veterinary care in 2016, 395 confirmed heat-related illness events were identified. The estimated 2016 incidence of heat-related illness was 0.04% (95% CI 0.04-0.05%), with an event fatality rate of 14.18% (95% CI 11.08 – 17.96%). Multivariable analysis identified significant risk factors including breed (e.g. Chow Chow, Bulldog and French Bulldog), higher bodyweight relative to the breed/sex mean and being over two years of age. Dogs with a brachycephalic skull shape and dogs weighing over 50 kg were also at greater risk. As we move into an ever-warmer world, veterinary professionals may need to include resistance to heat-related illness amongst their rationales when advising owners on breed selection. Breeding for good respiratory function and maintaining a healthy bodyweight should be considered key welfare priorities for all dogs to limit the risk of heat-related illness.
Constructing arrays of nucleosome positioning sequences using Gibson Assembly for single-molecule studies
Authors: Spakman Dian , King Graeme A. , Peterman Erwin J. G. , Wuite Gijs J. L.
Published: June 2020

As the basic building blocks of chromatin, nucleosomes play a key role in dictating the accessibility of the eukaryotic genome. Consequently, nucleosomes are involved in essential genomic transactions such as DNA transcription, replication and repair. In order to unravel the mechanisms by which nucleosomes can influence, or be altered by, DNA-binding proteins, single-molecule techniques are increasingly employed. To this end, DNA molecules containing a defined series of nucleosome positioning sequences are often used to reconstitute arrays of nucleosomes in vitro. Here, we describe a novel method to prepare DNA molecules containing defined arrays of the ‘601’ nucleosome positioning sequence by exploiting Gibson Assembly cloning. The approaches presented here provide a more accessible and efficient means to generate arrays of nucleosome positioning motifs, and facilitate a high degree of control over the linker sequences between these motifs. Nucleosomes reconstituted on such arrays are ideal for interrogation with single-molecule techniques. To demonstrate this, we use dual-trap optical tweezers, in combination with fluorescence microscopy, to monitor nucleosome unwrapping and histone localisation as a function of tension. We reveal that, although nucleosomes unwrap at ~20 pN, histones (at least histone H3) remain bound to the DNA, even at tensions beyond 60 pN.
RPamide neuropeptides NLP-22 and NLP-2 act through GnRH-like receptors to promote sleep and wakefulness in C. elegans
Authors: Van der Auwera Petrus , Frooninckx Lotte , Buscemi Kristen , Vance Ryan T. , Watteyne Jan , Mirabeau Olivier , Temmerman Liesbet , De Haes Wouter , Fancsalszky Luca , Gottschalk Alexander , Raizen David M. , Nelson Matthew D. , Schoofs Liliane , Beets Isabel
Published: June 2020

Sleep and wakefulness are fundamental behavioral states of which the underlying molecular principles are becoming slowly elucidated. Transitions between these states require the coordination of multiple neurochemical and modulatory systems. In Caenorhabditis elegans sleep occurs during a larval transition stage called lethargus and is induced by somnogenic neuropeptides. Here, we identify two opposing neuropeptide/receptor signaling pathways: NLP-22 promotes behavioral quiescence, whereas NLP-2 promotes movement during lethargus, by signaling through gonadotropin-releasing hormone (GnRH) related receptors. Both NLP-2 and NLP-22 belong to the RPamide neuropeptide family and share sequence similarities with neuropeptides of the bilaterian GnRH, adipokinetic hormone (AKH) and corazonin family. RPamide neuropeptides dose-dependently activate the GnRH/AKH-like receptors GNRR-3 and GNRR-6 in a cellular receptor activation assay. In addition, nlp-22-induced locomotion quiescence requires the receptor gnrr-6. By contrast, wakefulness induced by nlp-2 overexpression is diminished by deletion of either gnrr-3 or gnrr-6. nlp-2 is expressed in a pair of olfactory AWA neurons and cycles with larval periodicity, as reported for nlp-22, which is expressed in RIA. Our data suggest that the somnogenic NLP-22 neuropeptide signals through GNRR-6, and that both GNRR-3 and GNRR-6 are required for the wake-promoting action of NLP-2 neuropeptides.
Mutational analysis of TSC1 and TSC2 in Danish patients with tuberous sclerosis complex
Authors: Rosengren Thomas , Nanhoe Santoesha , de Almeida Luis Gustavo Dufner , Schönewolf-Greulich Bitten , Larsen Lasse Jonsgaard , Hey Caroline Amalie Brunbjerg , Dunø Morten , Ek Jakob , Risom Lotte , Nellist Mark , Møller Lisbeth Birk
Published: June 2020

Tuberous sclerosis complex (TSC) is an autosomal dominant disorder characterized by hamartomas in the skin and other organs, including brain, heart, lung, kidney and bones. TSC is caused by mutations in TSC1 and TSC2. Here, we present the TSC1 and TSC2 variants identified in 168 Danish individuals out of a cohort of 327 individuals suspected of TSC. A total of 137 predicted pathogenic or likely pathogenic variants were identified: 33 different TSC1 variants in 42 patients, and 104 different TSC2 variants in 126 patients. In 40 cases (24%), the identified predicted pathogenic variant had not been described previously. In total, 33 novel variants in TSC2 and 7 novel variants in TSC1 were identified. To assist in the classification of 11 TSC2 variants, we investigated the effects of these variants in an in vitro functional assay. Based on the functional results, as well as population and genetic data, we classified 8 variants as likely to be pathogenic and 3 as likely to be benign.
GlioM&M: Web-based tool for studying circulating and infiltrating monocytes and macrophages in glioma
Authors: Abels Erik R. , Maas Sybren L. N. , Tai Eric , Ting David T. , Broekman Marike L. D. , Breakefield Xandra O. , El Khoury Joseph
Published: June 2020

Monocytes, macrophages and microglia make up a large part of the glioma environment and have an important role in maintaining and propagating glioma progression. Targeting these cells to inhibit their tumor-promoting effect and reprogramming them into an anti-tumor phenotype is a potential therapeutic approach for glioma. In this study we analyzed the transcriptomes of eight different monocyte subgroups derived from the brain and the blood of glioma-bearing mice. We compared the expression profile of blood-derived monocytes versus tumor-infiltrating monocytes and found increased expression of both pro- and anti-inflammatory pathways in tumor infiltrating monocytes. To help disseminate these datasets, we created a user-friendly web-based tool accessible at www.glioma-monocytes.com. This tool can be used for validation purposes and to elucidate gene expression profiles of tumor-interacting monocytes and macrophages as well as blood-derived circulating monocytes. This tool can also be used to identify new markers and targets for therapy in these different cell populations.
RNA sequencing of corneas from two keratoconus patient groups identifies potential biomarkers and decreased NRF2-antioxidant responses
Authors: Shinde Vishal , Hu Nan , Mahale Alka , Maiti George , Daoud Yassine , Eberhart Charles G. , Maktabi Azza , Jun Albert S. , Al-Swailem Samar A. , Chakravarti Shukti
Published: June 2020

Keratoconus is a highly prevalent (1 in 2000), genetically complex and multifactorial, degenerative disease of the cornea whose pathogenesis and underlying transcriptomic changes are poorly understood. To identify disease-specific changes and gene expression networks, we performed next generation RNA sequencing from individual corneas of two distinct patient populations - one from the Middle East, as keratoconus is particularly severe in this group, and the second from an African American population in the United States. We conducted a case: control RNA sequencing study of 7 African American, 12 Middle Eastern subjects, and 7 controls. A Principal Component Analysis of all expressed genes was used to ascertain differences between samples. Differentially expressed genes were identified using Cuffdiff and DESeq2 analyses, and identification of over-represented signaling pathways by Ingenuity Pathway Analysis. Although separated by geography and ancestry, key commonalities in the two patient transcriptomes speak of disease - intrinsic gene expression networks. We identified an overwhelming decrease in the expression of anti-oxidant genes regulated by NRF2 and those of the acute phase and tissue injury response pathways, in both patient groups. Concordantly, NRF2 immunofluorescence staining was decreased in patient corneas, while KEAP1, which helps to degrade NRF2, was increased. Diminished NRF2 signaling raises the possibility of NRF2 activators as future treatment strategies in keratoconus. The African American patient group showed increases in extracellular matrix transcripts that may be due to underlying profibrogenic changes in this group. Transcripts increased across all patient samples include Thrombospondin 2 (THBS2), encoding a matricellular protein, and cellular proteins, GAS1, CASR and OTOP2, and are promising biomarker candidates. Our approach of analyzing transcriptomic data from different populations and patient groups will help to develop signatures and biomarkers for keratoconus subtypes. Further, RNA sequence data on individual patients obtained from multiple studies may lead to a core keratoconus signature of deregulated genes and a better understanding of its pathogenesis.
Cell Fate Potential of NG2 Progenitors
Authors: Sánchez-González Rebeca , Bribián Ana , López-Mascaraque Laura
Published: June 2020

Determining the origin of different glial subtypes is crucial to understand glial heterogeneity, and to enhance our knowledge of glial and progenitor cell behavior in embryos and adults. NG2-glia are homogenously distributed in a grid-like manner in both, gray and white matter of the adult brain. While some NG2-glia in the CNS are responsible for the generation of mature oligodendrocytes (OPCs), most of them do not differentiate and they can proliferate outside of adult neurogenic niches. Thus, NG2-glia constitute a heterogeneous population containing different subpopulations with distinct functions. We hypothesized that their diversity emerges from specific progenitors during development, as occurs with other glial cell subtypes. To specifically target NG2-pallial progenitors and to define the NG2-glia lineage, as well as the NG2-progenitor potential, we designed two new StarTrack strategies using the NG2 promoter. These approaches label NG2 expressing progenitor cells, permitting the cell fates of these NG2 progenitors to be tracked in vivo. StarTrack labelled cells producing different neural phenotypes in different regions depending on the age targeted, and the strategy selected. This specific genetic targeting of neural progenitors in vivo has provided new data on the heterogeneous pool of NG2 progenitors at both embryonic and postnatal ages.
ERP mismatch response to phonological and temporal regularities in speech
Authors: Emmendorfer Alexandra K. , Correia Joao M. , Jansma Bernadette M. , Kotz Sonja A. , Bonte Milene
Published: June 2020

Predictions of our sensory environment facilitate perception across domains. During speech perception, formal and temporal predictions may be made for phonotactic probability and syllable stress patterns, respectively, contributing to the efficient processing of speech input. The current experiment employed a passive EEG oddball paradigm to probe the neurophysiological processes underlying temporal and formal predictions simultaneously. The component of interest, the mismatch negativity (MMN), is considered a marker for experience-dependent change detection, where its timing and amplitude are indicative of the perceptual system’s sensitivity to presented stimuli. We hypothesized that more predictable stimuli (i.e. high phonotactic probability and first syllable stress) would facilitate change detection, indexed by shorter peak latencies or greater peak amplitudes of the MMN. This hypothesis was confirmed for phonotactic probability: high phonotactic probability deviants elicited an earlier MMN than low phonotactic probability deviants. We do not observe a significant modulation of the MMN to variations in syllable stress. Our findings confirm that speech perception is shaped by formal and temporal predictability. This paradigm may be useful to investigate the contribution of implicit processing of statistical regularities during (a)typical language development.
Preoperative Vitamin D Levels as a Predictor of Transient Hypocalcemia and Hypoparathyroidism After Parathyroidectomy
Authors: Unsal Ilknur Ozturk , Calapkulu Murat , Sencar Muhammed Erkam , Hepsen Sema , Sakiz Davut , Ozbek Mustafa , Cakal Erman
Published: June 2020

Hypocalcemia is a common problem after parathyroidectomy and/or thyroidectomy. The complication may be transient or permanent. Most cases occur as a result of removal of the parathyroid glands or damage to the glands during neck surgery. The purpose of this study was to evaluate the effect of preoperative vitamin D deficiency in predicting transient hypocalcemia and hypoparathyroidism after parathyroidectomy.Retrospective evaluation was made of 180 patients with primary hyperparathyroidism in respect of serum 25(OH)D, calcium and parathyroid hormone before and after parathyroidectomy. Transient hypocalcemia was defined as corrected calcium ≤ 8.4 mg/dL, and these cases were then evaluated for preoperative 25(OH)D values. Transient hypoparathyroidism has been described as low PTH level immediately after surgery before beginning any supplementation. Permanent hypoparathyroidism is accepted as the need for medical treatment is necessary over 12 months.Both transient hypocalcemia and hypoparathyroidism developed at statistically significantly higher rates in patients with preoperative vitamin D deficiency and vitamin D insufficiency.Vitamin D deficiency is an independent contributor to transient hypocalcemia and hypoparathyroidism following parathyroidectomy.
Serum hepcidin level, iron metabolism and osteoporosis in patients with rheumatoid arthritis
Authors: Sato Hiroe , Takai Chinatsu , Kazama Junichiro James , Wakamatsu Ayako , Hasegawa Eriko , Kobayashi Daisuke , Kondo Naoki , Nakatsue Takeshi , Abe Asami , Ito Satoshi , Ishikawa Hajime , Kuroda Takeshi , Suzuki Yoshiki , Narita Ichiei
Published: June 2020

Hepcidin, a major regulator of iron metabolism and homeostasis, is regulated by inflammation. Recent studies have suggested that hepcidin and iron metabolism are involved in osteoporosis, and the aim of this study was to determine whether serum hepcidin levels are correlated with the degree of osteoporosis in patients with rheumatoid arthritis (RA). A total of 262 patients with RA (67.5 ± 11.4 years; 77.5% female) were enrolled. Serum iron, ferritin, and hepcidin levels were positively correlated each other. Multiple regression analyses revealed that the serum iron level was positively correlated with femoral T and Z scores, whereas the serum hepcidin level was not. Serum hepcidin level was correlated with the serum 25-hydroxy vitamin D level, which was in turn positively related to the femoral Z score. Serum hepcidin and serum iron were indirectly and directly related to osteoporosis in patients with RA.
Role of Molecular Orbital Energy Levels in OLED Performance
Authors: Yadav Rohit Ashok Kumar , Dubey Deepak Kumar , Chen Sun-Zen , Liang Tzu-Wei , Jou Jwo-Huei
Published: June 2020

Abundant molecules enable countless combinations of device architecture that might achieve the desirable high efficiency from organic light-emitting diodes (OLEDs). Due to the relatively high cost of OLED materials and facilities, simulation approaches have become a must in further advancing the field faster and saver. We have demonstrated here the use of state-of-art simulation approaches to investigate the effect of molecular orbital energy levels on the recombination of excitons in OLED devices. The devices studied are composed of 1,1-bis[(di-4-tolylamino)phenyl]cyclohexane (TAPC) as hole transporting material (HTM), 4,4′-Bis(9-carbazolyl)-1,1′-biphenyl (CBP) as host, 2,2',2”-(1,3,5-benzinetriyl)-tris(1-phenyl-1-H-benzimidazole) (TPBi) or bathophenanthroline (Bphen) as electron transporting materials. The outcomes reveal that exciton recombination highly sensitive to the energy-level alignment, injection barriers, and charge mobilities. A low energy-barrier (<0.4 eV) between the layers is the key to yield high recombination. The lowest unoccupied molecular orbital (LUMO) levels of the organic layers have played a more pivotal role in governing the recombination dynamics than the highest occupied molecular orbital (HOMO) level do. Furthermore, the Bphen based device shows high exciton recombination across the emissive layer, which is >106 times greater than that in the TPBi based device. The high carrier mobility of Bphen whose electron mobility is 5.2 × 10−4 cm2 V−1 s−1 may lead to low charge accumulation and hence high exciton dynamics. The current study has successfully projected an in-depth analysis on the suitable energy-level alignments, which would further help to streamline future endeavours in developing efficient organic compounds and designing devices with superior performance.
Age-associated changes in 4D flow CMR derived Tricuspid Valvular Flow and Right Ventricular Blood Flow Kinetic Energy
Authors: Barker Natasha , Zafar Hamza , Fidock Benjamin , Elhawaz Alaa , Al-Mohammad Abdallah , Rothman Alexander , Kiely David G. , van der Geest R. J. , Westenberg Jos , Swift Andrew J. , Wild James M. , Plein Sven , Garg Pankaj
Published: June 2020

Assessment of right ventricular (RV) diastolic function is not routinely carried out. This is due to standard two-dimensional imaging techniques being unreliable. Four-dimensional flow (4D flow) derived right ventricular blood flow kinetic energy assessment could circumvent the issues of the current imaging modalities. It also remains unknown whether there is an association between right ventricular blood flow kinetic energy (KE) and healthy ageing. We hypothesise that healthy ageing requires maintaining normal RV intra-cavity blood flow as quantified using KE method. The main objective of this study was to investigate the effect of healthy ageing on tricuspid through-plane flow and right ventricular blood flow kinetic energy. In this study, fifty-three healthy participants received a 4D flow cardiovascular magnetic resonance (CMR) scan on 1.5 T Philips Ingenia. Cine segmentation and 4D flow analysis were performed using dedicated software. Standard statistical methods were carried out to investigate the associations. Both RV E-wave KEiEDV (r = −0.3, P = 0.04) and A-wave KEiEDV (r = 0.42, P < 0.01) showed an association with healthy ageing. Additionally, the right ventricular blood flow KEiEDV E/A ratio demonstrated the strongest association with healthy ageing (r = −0.53, P < 0.01) when compared to all RV functional and haemodynamic parameters. Furthermore, in a multivariate regression model, KEiEDV E/A ratio and 4D flow derived tricuspid valve stroke volume demonstrated independent association to healthy ageing (beta −0.02 and 0.68 respectively, P < 0.01). Ageing is independently associated with 4D flow derived tricuspid stroke volume and RV blood flow KE E/A ratio. These novel 4D flow CMR derived imaging markers have future potential for RV diastolic assessment.
Genetic and environmental links between traits of cocoa beans and pods clarify the phenotyping processes to be implemented
Authors: Doaré Fabien , Ribeyre Fabienne , Cilas Christian
Published: June 2020

The average weight of cocoa beans is not generally taken into account during breeding processes, although it is a trait of interest. Several studies indicate that the weight of the beans has a high heritability inTheobroma cacao. However, the values obtained from different countries for the same clone often vary. In this study, we analyzed the effect of different factors on the weight of the beans. Apart from the clone effect, three main factors had an impact: i) the number of beans per pod: a good filling of the pod with beans tended to limit the weight of the beans, ii) the position of the beans in the pod: beans in the apical part of the pod were significantly lighter than the others and iii) the longer the duration of the fructification cycle the heavier the beans were (positive genetics correlation). These results lead us to propose protocols aimed at normalizing the phenotypic values of the genetic material. To obtain a reliable estimate of the bean weight, the following is proposed: either to use beans obtained from manual pollination to saturate the pods with beans, or to systematically use the number beans in the pods as a covariable.
Restriction site-associated DNA sequencing (RAD-seq) analysis in Pacific oyster Crassostrea gigas based on observation of individual sex changes
Authors: Yue Chenyang , Li Qi , Yu Hong , Liu Shikai , Kong Lingfeng
Published: June 2020

The diverse modes of sexual reproduction in Bivalvia make it an excellent clade to understand the evolution of sex and sex determination. The cosmopolitan Pacific oysterCrassostrea gigasis an ideal model for bivalve sex determination studies because of its complicated sexuality, including dioecy, sex change and rare hermaphroditism. A major barrier toC. gigassex determination study has been the lack of information on the type of sex determination. To identify its sex-determining system, sex observation by following the same individual in two consecutive years was conducted on 760 oysters from distinct populations. Stable sexuality and sex reversal in both directions were observed, which provides a case against the protandry ofC. gigas. Restriction site-associated DNA sequencing (RAD-seq) based on 26 samples with unchanged and converted sexualities was carried out for identifying sex-linked marker. One SNP Cgsl-40 was proved to be sex-related, but sex-biased heterozygosity varied between populations for RAD-seq and validation, showing no evidence for sex chromosomes or single-locus models forC. gigasprimary sex determination. Information obtained in our study provides novel insight into sex determination mechanism inC. gigas.
Regional Brain Gray Matter Changes in Patients with Type 2 Diabetes Mellitus
Authors: Roy Bhaswati , Ehlert Luke , Mullur Rashmi , Freeby Matthew J. , Woo Mary A. , Kumar Rajesh , Choi Sarah
Published: June 2020

Patients with Type 2 diabetes mellitus (T2DM) show cognitive and mood impairment, indicating potential for brain injury in regions that control these functions. However, brain tissue integrity in cognition, anxiety, and depression regulatory sites, and their associations with these functional deficits in T2DM subjects remain unclear. We examined gray matter (GM) changes in 34 T2DM and 88 control subjects using high-resolution T1-weighted images, collected from a 3.0-Tesla magnetic resonance imaging scanner, and assessed anxiety [Beck Anxiety Inventory], depressive symptoms [Beck Depression Inventory-II], and cognition [Montreal Cognitive Assessment]. We also investigated relationships between GM status of cognitive and mood control sites and these scores in T2DM. Significantly increased anxiety (p = 0.003) and depression (p = 0.001), and reduced cognition (p = 0.002) appeared in T2DM over controls. Decreased GM volumes appeared in several regions in T2DM patients, including the prefrontal, hippocampus, amygdala, insular, cingulate, cerebellum, caudate, basal-forebrain, and thalamus areas (p < 0.01). GM volumes were significantly associated with anxiety (r = −0.456,p = 0.009), depression (r = −0.465,p = 0.01), and cognition (r = 0.455,p = 0.009) scores in regions associated with those regulations (prefrontal cortices, hippocampus, para hippocampus, amygdala, insula, cingulate, caudate, thalamus, and cerebellum) in T2DM patients. Patients with T2DM show brain damage in regions that are involved in cognition, anxiety, and depression control, and these tissue alterations are associated with functional deficits. The findings indicate that mood and cognitive deficits in T2DM patients has brain structural basis in the condition.
2D materials for spintronic devices
Authors: Ahn Ethan C.
Published: June 2020

2D materials are attractive for nanoelectronics due to their ultimate thickness dimension and unique physical properties. A wide variety of emerging spintronic device concepts will greatly benefit from the use of 2D materials, leading a better way to manipulating spin. In this review, we discuss various 2D materials, including graphene and other inorganic 2D semiconductors, in the context of scientific and technological advances in spintronic devices. Applications of 2D materials in spin logic switches, spin valves, and spin transistors are specifically investigated. We also introduce the spin-orbit and spin-valley coupled properties of 2D materials to explore their potential to address the crucial issues of contemporary electronics. Finally, we highlight major challenges in integrating 2D materials into spintronic devices and provide a future perspective on 2D materials for spin logic devices.
Influence of sodium tripolyphosphate coupled with (−)-epigallocatechin on the in vitro digestibility and emulsion gel properties of myofibrillar protein under oxidative stress
Authors: Chen Jinyu , Zhang Kunsheng , Ren Yunxia , Hu Fangyang , Yan Yijun , Qu Jinping
Published: June 2020

This work demonstrates the effects of STP coupled with EGC on the formation of the MP emulsion gel under oxidative stress.
Investigation of the re-dispersion of matrix Cu species in CuxCe1−xO2 nanorod catalysts and its effect on the catalytic performance in CO-PROX
Authors: Guo Xiaolin , Ye Wangxiang , Ma Tingli
Published: June 2020

The CO-PROX catalytic performance is sensitive to the re-dispersion state of matrix copper species, which separate out as highly dispersed CuOx under thermal treatment.
Dipicolinamide and isophthalamide based fluorescent chemosensors: recognition and detection of assorted analytes
Authors: Kumar Pramod , Kumar Vijay , Gupta Rajeev
Published: June 2020

This perspective presents fluorescent chemosensors based on dipicolinamide and isophthalamide groups that participate in the molecular recognition, sensing and detection of assorted analytes either via a “turn-on” or “turn-off” mechanism.
Novel insights into the metal binding ability of ZinT periplasmic protein from Escherichia coli and Salmonella enterica
Authors: Bellotti Denise , Rowińska-Żyrek Magdalena , Remelli Maurizio
Published: June 2020

The characterization of Zn(ii) and Cu(ii) complexes with periplasmic protein ZinT suggests that the N-terminal histidine-rich loop plays a role as a primary metal scavenger and that ZinT can possibly transfer a Zn(ii) ion to ZnuA.
An octabrominated Sn(iv) tetraisopropylporphyrin as a photosensitizer dye for singlet oxygen biomedical applications
Authors: Babu Balaji , Mack John , Nyokong Tebello
Published: June 2020

A readily-synthesized octabrominated Sn(iv) tetraisopropylporphyrin has been prepared which exhibits enhanced properties for use as a photosensitizer dye in biomedical applications.
Room temperature aqueous synthesis of UiO-66 derivatives via postsynthetic exchange
Authors: Kalaj Mark , Prosser Kathleen E. , Cohen Seth M.
Published: June 2020

Herein, we report the room temperature aqueous synthesis of the Zr(iv)-based metal-organic framework (MOF) UiO-66 and a series of functionalized derivatives through postsynthetic exchange (PSE) from a perfluorinated UiO-66-F4.
Allosteric regulation of rotational, optical and catalytic properties within multicomponent machinery
Authors: Saha Suchismita , Ghosh Amit , Paululat Thomas , Schmittel Michael
Published: June 2020

Allosteric regulation of various functions within multicomponent machinery was triggered by the reversible transformation of nanorotors (k298 = 44–61 kHz) to “dimeric” supramolecular structures (k298 = 0.60 kHz) upon adding a stoichiometric chemical stimulus.
Chemical and structural characterization of SeIV biotransformations by Stenotrophomonas bentonitica into Se0 nanostructures and volatiles Se species
Authors: Ruiz-Fresneda Miguel A. , Eswayah Abdurrahman S. , Romero-González María , Gardiner Philip H. E. , Solari Pier L. , Merroun Mohamed L.
Published: June 2020

Microorganisms such as Stenotrophomonas bentonitica could influence the safety of the deep geological repository system by producing nanoparticles and volatile compounds of selenium.
Biarsenical fluorescent probes for multifunctional site-specific modification of proteins applicable in life sciences: an overview and future outlook
Authors: Pomorski Adam , Krężel Artur
Published: June 2020

Fluorescent modification of proteins of interest (POI) in living cells is desired to study their behaviour and functions in their natural environment. In a perfect setting it should be easy to perform, inexpensive, efficient and site-selective. Although multiple chemical and biological methods have been developed, only a few of them are applicable for cellular studies thanks to their appropriate physical, chemical and biological characteristics. One such successful system is a tetracysteine tag/motif and its selective biarsenical binders (e.g. FlAsH and ReAsH). Since its discovery in 1998 by Tsien and co-workers, this method has been enhanced and revolutionized in terms of its efficiency, formed complex stability and breadth of application. Here, we overview the whole field of knowledge, while placing most emphasis on recent reports. We showcase the improvements of classical biarsenical probes with various optical properties as well as multifunctional molecules that add new characteristics to proteins. We also present the evolution of affinity tags and motifs of biarsenical probes demonstrating much more possibilities in cellular applications. We summarize protocols and reported observations so both beginners and advanced users of biarsenical probes can troubleshoot their experiments. We address the concerns regarding the safety of biarsenical probe application. We showcase examples in virology, studies on receptors or amyloid aggregation, where application of biarsenical probes allowed observations that previously were not possible. We provide a summary of current applications ranging from bioanalytical sciences to allosteric control of selected proteins. Finally, we present an outlook to encourage more researchers to use these magnificent probes.
An electrochemical biosensor exploiting binding-induced changes in electron transfer of electrode-attached DNA origami to detect hundred nanometer-scale targets
Authors: Arroyo-Currás Netzahualcóyotl , Sadeia Muaz , Ng Alexander K. , Fyodorova Yekaterina , Williams Natalie , Afif Tammy , Huang Chao-Min , Ogden Nathan , Andresen Eguiluz Roberto C. , Su Hai-Jun , Castro Carlos E. , Plaxco Kevin W. , Lukeman Philip S.
Published: June 2020

Using DNA origami as the recognition element in an electrochemical biosensor enables the selective and direct detection of “mesoscale” virus-sized analytes.