bluuebunny/crossref_metadata_2025 huggingface dataset:
Lichen-like association of Chlamydomonas reinhardtii and Aspergillus nidulans protects algal cells from bacteria
Authors: Krespach Mario K C , García-Altares María , Flak Michal , Schoeler Hanno , Scherlach Kirstin , Netzker Tina , Schmalzl Anica , Mattern Derek J , Schroeckh Volker , Komor Anna , Mittag Maria , Hertweck Christian , Brakhage Axel A
Published: August 2020

Organismal interactions within microbial consortia and their responses to harmful intruders remain largely understudied. An important step toward the goal of understanding functional ecological interactions and their evolutionary selection is the study of increasingly complex microbial interaction systems. Here, we discovered a tripartite biosystem consisting of the fungus Aspergillus nidulans, the unicellular green alga Chlamydomonas reinhardtii, and the algicidal bacterium Streptomyces iranensis. Genetic analyses and MALDI-IMS demonstrate that the bacterium secretes the algicidal compound azalomycin F upon contact with C. reinhardtii. In co-culture, A. nidulans attracts the motile alga C. reinhardtii, which becomes embedded and surrounded by fungal mycelium and is shielded from the algicide. The filamentous fungus Sordaria macrospora was susceptible to azalomycin F and failed to protect C. reinhardtii despite chemotactically attracting the alga. Because S. macrospora was susceptible to azalomycin F, this data imply that for protection the fungus needs to be resistant. Formation of the lichen-like association between C. reinhardtii and A. nidulans increased algal growth. The protection depends on the increased amounts of membrane lipids provided by resistant fungi, thereby generating a protective shelter against the bacterial toxin. Our findings reveal a strategy whereby algae survive lethal environmental algicides through cooperation with fungi.
The influence of a priori grouping on inference of genetic clusters: simulation study and literature review of the DAPC method
Authors: Miller Joshua M. , Cullingham Catherine I. , Peery Rhiannon M.
Published: August 2020

Inference of genetic clusters is a key aim of population genetics, sparking development of numerous analytical methods. Within these, there is a conceptual divide between finding de novo structure versus assessment of a priori groups. Recently developed, Discriminant Analysis of Principal Components (DAPC), combines discriminant analysis (DA) with principal component (PC) analysis. When applying DAPC, the groups used in the DA (specified a priori or described de novo) need to be carefully assessed. While DAPC has rapidly become a core technique, the sensitivity of the method to misspecification of groups and how it is being empirically applied, are unknown. To address this, we conducted a simulation study examining the influence of a priori versus de novo group designations, and a literature review of how DAPC is being applied. We found that with a priori groupings, distance between genetic clusters reflected underlying FST. However, when migration rates were high and groups were described de novo there was considerable inaccuracy, both in terms of the number of genetic clusters suggested and placement of individuals into those clusters. Nearly all (90.1%) of 224 studies surveyed used DAPC to find de novo clusters, and for the majority (62.5%) the stated goal matched the results. However, most studies (52.3%) omit key run parameters, preventing repeatability and transparency. Therefore, we present recommendations for standard reporting of parameters used in DAPC analyses. The influence of groupings in genetic clustering is not unique to DAPC, and researchers need to consider their goal and which methods will be most appropriate.
Recycled arc mantle recovered from the Mid-Atlantic Ridge
Authors: Urann B. M. , Dick H. J. B. , Parnell-Turner R. , Casey J. F.
Published: August 2020

Plate tectonics and mantle dynamics necessitate mantle recycling throughout Earth’s history, yet direct geochemical evidence for mantle reprocessing remains elusive. Here we present evidence of recycled supra-subduction zone mantle wedge peridotite dredged from the Mid-Atlantic Ridge near 16°30′N. Peridotite trace-element characteristics are inconsistent with fractional anhydrous melting typically associated with a mid-ocean ridge setting. Instead, the samples are best explained by hydrous flux melting which changed the melting reactions such that clinopyroxene was not exhausted at high degrees of melting and was retained in the residuum. Based on along-axis ridge depth variations, this buoyant refractory arc mantle is likely compensated at depth by denser, likely garnet-rich, lithologies within the mantle column. Our results suggest that highly refractory arc mantle relicts are entrained in the upper mantle and may constitute >60% of the upper mantle by volume. These highly refractory mantle domains, which contribute little to mantle melting, are under-represented in compilations of mantle composition that rely on inverted basalt compositions alone.
Lipo-chitooligosaccharides as regulatory signals of fungal growth and development
Authors: Rush Tomás Allen , Puech-Pagès Virginie , Bascaules Adeline , Jargeat Patricia , Maillet Fabienne , Haouy Alexandra , Maës Arthur QuyManh , Carriel Cristobal Carrera , Khokhani Devanshi , Keller-Pearson Michelle , Tannous Joanna , Cope Kevin R. , Garcia Kevin , Maeda Junko , Johnson Chad , Kleven Bailey , Choudhury Quanita J. , Labbé Jessy , Swift Candice , O’Malley Michelle A. , Bok Jin Woo , Cottaz Sylvain , Fort Sébastien , Poinsot Verena , Sussman Michael R. , Lefort Corinne , Nett Jeniel , Keller Nancy P. , Bécard Guillaume , Ané Jean-Michel
Published: August 2020

Lipo-chitooligosaccharides (LCOs) are signaling molecules produced by rhizobial bacteria that trigger the nodulation process in legumes, and by some fungi that also establish symbiotic relationships with plants, notably the arbuscular and ecto mycorrhizal fungi. Here, we show that many other fungi also produce LCOs. We tested 59 species representing most fungal phyla, and found that 53 species produce LCOs that can be detected by functional assays and/or by mass spectroscopy. LCO treatment affects spore germination, branching of hyphae, pseudohyphal growth, and transcription in non-symbiotic fungi from the Ascomycete and Basidiomycete phyla. Our findings suggest that LCO production is common among fungi, and LCOs may function as signals regulating fungal growth and development.
Identifying the nature of the active sites in methanol synthesis over Cu/ZnO/Al2O3 catalysts
Authors: Laudenschleger Daniel , Ruland Holger , Muhler Martin
Published: August 2020

The heterogeneously catalysed reaction of hydrogen with carbon monoxide and carbon dioxide (syngas) to methanol is nearly 100 years old, and the standard methanol catalyst Cu/ZnO/Al2O3 has been applied for more than 50 years. Still, the nature of the Zn species on the metallic Cu0 particles (interface sites) is heavily debated. Here, we show that these Zn species are not metallic, but have a positively charged nature under industrial methanol synthesis conditions. Our kinetic results are based on a self-built high-pressure pulse unit, which allows us to inject selective reversible poisons into the syngas feed passing through a fixed-bed reactor containing an industrial Cu/ZnO/Al2O3 catalyst under high-pressure conditions. This method allows us to perform surface-sensitive operando investigations as a function of the reaction conditions, demonstrating that the rate of methanol formation is only decreased in CO2-containing syngas mixtures when pulsing NH3 or methylamines as basic probe molecules.
A hybrid achromatic metalens
Authors: Balli F. , Sultan M. , Lami Sarah K. , Hastings J. T.
Published: August 2020

Metalenses, ultra-thin optical elements that focus light using subwavelength structures, have been the subject of a number of recent investigations. Compared to their refractive counterparts, metalenses offer reduced size and weight, and new functionality such as polarization control. However, metalenses that correct chromatic aberration also suffer from markedly reduced focusing efficiency. Here we introduce a Hybrid Achromatic Metalens (HAML) that overcomes this trade-off and offers improved focusing efficiency over a broad wavelength range from 1000–1800 nm. HAMLs can be designed by combining recursive ray-tracing and simulated phase libraries rather than computationally intensive global search algorithms. Moreover, HAMLs can be fabricated in low-refractive index materials using multi-photon lithography for customization or using molding for mass production. HAMLs demonstrated diffraction limited performance for numerical apertures of 0.27, 0.11, and 0.06, with average focusing efficiencies greater than 60% and maximum efficiencies up to 80%. A more complex design, the air-spaced HAML, introduces a gap between elements to enable even larger diameters and numerical apertures.
Single-site pyrrolic-nitrogen-doped sp2-hybridized carbon materials and their pseudocapacitance
Authors: Tian Kesong , Wang Junyan , Cao Ling , Yang Wei , Guo Wanchun , Liu Shuhu , Li Wei , Wang Fengyan , Li Xueai , Xu Zhaopeng , Wang Zhenbo , Wang Haiyan , Hou Yanglong
Published: August 2020

Integrating nitrogen species into sp2-hybridized carbon materials has proved an efficient means to improve their electrochemical performance. Nevertheless, an inevitable mixture of nitrogen species in carbon materials, due to the uncontrolled conversion among different nitrogen configurations involved in synthesizing nitrogen-doped carbon materials, largely retards the precise identification of electrochemically active nitrogen configurations for specific reactions. Here, we report the preparation of single pyrrolic N-doped carbon materials (SPNCMs) with a tunable nitrogen content from 0 to 4.22 at.% based on a strategy of low-temperature dehalogenation-induced and subsequent alkaline-activated pyrolysis of 3-halogenated phenol-3-aminophenol-formaldehyde (X-APF) co-condensed resins. Additionally, considering that the pseudocapacitance of SPNCMs is positively dependent on the pyrrolic nitrogen content, it could be inferred that pyrrolic nitrogen species are highly active pseudocapacitive sites for nitrogen-doped carbon materials. This work gives an ideal model for understanding the contribution of pyrrolic nitrogen species in N-doped carbon materials.
Evolving cooperation in multichannel games
Authors: Donahue Kate , Hauser Oliver P. , Nowak Martin A. , Hilbe Christian
Published: August 2020

Humans routinely engage in many distinct interactions in parallel. Team members collaborate on several concurrent projects, and even whole nations interact with each other across a variety of issues, including trade, climate change and security. Yet the existing theory of direct reciprocity studies isolated repeated games. Such models cannot account for strategic attempts to use the vested interests in one game as a leverage to enforce cooperation in another. Here we introduce a general framework of multichannel games. Individuals interact with each other over multiple channels; each channel is a repeated game. Strategic choices in one channel can affect decisions in another. With analytical equilibrium calculations for the donation game and evolutionary simulations for several other games we show that such linkage facilitates cooperation. Our results suggest that previous studies tend to underestimate the human potential for reciprocity. When several interactions occur in parallel, people often learn to coordinate their behavior across games to maximize cooperation in each of them.
Publisher Correction: The mutational impact of culturing human pluripotent and adult stem cells
Authors: Kuijk Ewart , Jager Myrthe , van der Roest Bastiaan , Locati Mauro D. , Van Hoeck Arne , Korzelius Jerome , Janssen Roel , Besselink Nicolle , Boymans Sander , van Boxtel Ruben , Cuppen Edwin
Published: August 2020

An amendment to this paper has been published and can be accessed via a link at the top of the paper.
X-ray microtomography is a novel method for accurate evaluation of small-bowel mucosal morphology and surface area
Authors: Virta Johannes , Hannula Markus , Tamminen Ilmari , Lindfors Katri , Kaukinen Katri , Popp Alina , Taavela Juha , Saavalainen Päivi , Hiltunen Pauliina , Hyttinen Jari , Kurppa Kalle
Published: August 2020

The often poorly orientated small-bowel mucosal biopsies taken for the diagnostics of celiac disease and other intestinal disorders are prone to misinterpretation. Furthermore, conventional histopathology has suboptimal sensitivity for early histopathological changes observed in short-term challenge studies. X-ray microtomography (micro-CT) is a promising new method for accurate imaging of human-derived biological samples. Here, we report that micro-CT could be utilized to create virtual reconstructions of endoscopically obtained intestinal biopsies. The formed digital 3D images enabled selection of always optimal cutting angles for accurate measurement of the mucosal damage and revealed diagnostic lesions in cases interpreted as normal with conventional histomorphometry. We also demonstrate that computer-assisted point cloud analysis can be used to calculate biologically meaningful surface areas of the biopsies in different stages of mucosal damage with excellent replicability and correlation with other disease parameters. We expect the improved diagnostic accuracy and capability to measure the surface areas to provide a powerful tool for the diagnostics of intestinal diseases and for future clinical and pharmaceutical trials.
Decisions and disease: a mechanism for the evolution of cooperation
Authors: Karlsson Carl-Joar , Rowlett Julie
Published: August 2020

In numerous contexts, individuals may decide whether they take actions to mitigate the spread of disease, or not. Mitigating the spread of disease requires an individual to change their routine behaviours to benefit others, resulting in a ‘disease dilemma’ similar to the seminal prisoner’s dilemma. In the classical prisoner’s dilemma, evolutionary game dynamics predict that all individuals evolve to ‘defect.’ We have discovered that when the rate of cooperation within a population is directly linked to the rate of spread of the disease, cooperation evolves under certain conditions. For diseases which do not confer immunity to recovered individuals, if the time scale at which individuals receive accurate information regarding the disease is sufficiently rapid compared to the time scale at which the disease spreads, then cooperation emerges. Moreover, in the limit as mitigation measures become increasingly effective, the disease can be controlled; the number of infections tends to zero. It has been suggested that disease spreading models may also describe social and group dynamics, indicating that this mechanism for the evolution of cooperation may also apply in those contexts.
Publisher Correction: Genomic analyses of early responses to radiation in glioblastoma reveal new alterations at transcription, splicing, and translation levels
Authors: Choudhary Saket , Burns Suzanne C. , Mirsafian Hoda , Li Wenzheng , Vo Dat T. , Qiao Mei , Lei Xiufen , Smith Andrew D. , Penalva Luiz O.
Published: August 2020

An amendment to this paper has been published and can be accessed via a link at the top of the paper.
The prostaglandin synthases, COX-2 and L-PGDS, mediate prostate hyperplasia induced by low-dose bisphenol A
Authors: Wu Shuangshuang , Huang Dongyan , Su Xin , Yan Han , Ma Aicui , Li Lei , Wu Jianhui , Sun Zuyue
Published: August 2020

This study aimed to identify prostaglandin synthases (PGS) that mediate bisphenol A (BPA)-induced prostatic hyperplasia and explore their underlying mechanisms. In an in vivo study, male adult Sprague–Dawley rats were treated with different concentrations of BPA (10, 30, 90, or 270 μg/kg, i.g., daily), or with vehicle for 4 weeks. Results revealed that low-dose BPA induced prostatic hyperplasia with increased PCNA/TUNEL ratio. It significantly upregulated the expression of cyclooxygenase-2 (COX-2) and NF-κB in the dorsolateral prostate (P < 0.05) and the expression of lipocalin-type prostaglandin D synthase (L-PGDS) in ventral prostate (P < 0.05). The level of estradiol (E2)/testosterone (T) and expression of androgen receptor (AR) and estrogen receptor α (ERα) were also altered. In vitro studies showed that low-dose BPA (0.1–10 nM) promoted the proliferation of human prostate fibroblasts and epithelial cells, and significantly upregulated the expression of COX-2 and L-PGDS in the cells. The two types of cell proliferation induced by BPA were inhibited by COX-2 inhibitor (NS398) and L-PGDS inhibitor (AT56), with increased apoptosis level. These findings suggested that COX-2 and L-PGDS could mediate low-dose BPA-induced prostatic hyperplasia through pathways involved in cell proliferation and apoptosis, which might be related to the functions of ERα and AR. The role of COX-2/NF-κB pathway in dorsolateral prostate requires further research.
Selective dysregulation of ROCK2 activity promotes aberrant transcriptional networks in ABC diffuse large B-cell lymphoma
Authors: Ricker Edd , Verma Akanksha , Marullo Rossella , Gupta Sanjay , Ye Chao , Pannellini Tania , Manni Michela , Tam Wayne , Inghirami Giorgio , Elemento Olivier , Cerchietti Leandro , Pernis Alessandra B.
Published: August 2020

Activated B-cell-like diffuse large B-cell lymphoma (ABC-DLBCL) is an aggressive subtype of lymphoma usually associated with inferior outcomes. ABC-DLBCL exhibits plasmablastic features and is characterized by aberrancies in the molecular networks controlled by IRF4. The signaling pathways that are dysregulated in ABC-DLBCL are, however, not fully understood. ROCK2 is a serine-threonine kinase whose role in lymphomagenesis is unknown. Here we show that ROCK2 activity is constitutively dysregulated in ABC-DLBCL but not in GCB-DLBCL and BL. We furthermore show that ROCK2 phosphorylates IRF4 and that the ROCK2-mediated phosphorylation of IRF4 modulates its ability to regulate a subset of target genes. In addition to its effects on IRF4, ROCK2 also controls the expression of MYC in ABC-DLBCL by regulating MYC protein levels. ROCK inhibition furthermore selectively decreases the proliferation and survival of ABC-DLBCL in vitro and inhibits ABC-DLBCL growth in xenograft models. Thus, dysregulated ROCK2 activity contributes to the aberrant molecular program of ABC-DLBCL via its dual ability to modulate both IRF4- and MYC-controlled gene networks and ROCK inhibition could represent an attractive therapeutic target for the treatment of ABC-DLBCL.
Ruminal volatile fatty acid absorption is affected by elevated ambient temperature
Authors: Bedford Andrea , Beckett Linda , Harthan Laura , Wang Chong , Jiang Ning , Schramm Hollie , Guan Le Luo , Daniels Kristy M. , Hanigan Mark D. , White Robin R.
Published: August 2020

The objective of this study was to investigate the effect of short-term elevated ambient temperature on ruminal volatile fatty acid (VFA) dynamics and rumen epithelium gene expression associated with the transport and metabolism of VFA. Eight ruminally cannulated Holstein heifers (200 kg) were used in a factorial, repeated measures experiment with two treatments and two periods. During the first period, animals were provided with feed ad libitum and housed at 20 °C. During the second period, one group (HS) was housed at 30 °C and fed ad libitum. The other group (PF) was housed at 20 °C and pair-fed to match the intake of the HS group. During each period, animals were kept on treatment for 10 day, with sample collection on the final day. In the second period, indicators of heat stress were significantly different between PF and HS animals (P < 0.05). There was a thermal environment effect on butyrate production (P < 0.01) that was not associated with feed intake (P = 0.43). Butyrate absorption decreased in HS animals (P < 0.05) but increased in PF animals (P < 0.05) from period 1 to period 2. There was a feed intake effect on BHD1 expression (P = 0.04) and a tendency for a thermal environment effect (P = 0.08), with expression increasing in both cases. Expression of MCT4 was affected by feed intake (P = 0.003) as were all NHE genes (NHE1, NHE2, and NHE3; P < 0.05). These results indicate that with low feed intake and heat stress, there are shifts in rumen VFA dynamics and in the capacity of the rumen epithelium to absorb and transport VFA.
Systematized reporter assays reveal ZIC protein regulatory abilities are Subclass-specific and dependent upon transcription factor binding site context
Authors: Ahmed Jehangir N. , Diamand Koula E. M. , Bellchambers Helen M. , Arkell Ruth M.
Published: August 2020

The ZIC proteins are a family of transcription regulators with a well-defined zinc finger DNA-binding domain and there is evidence that they elicit functional DNA binding at a ZIC DNA binding site. Little is known, however, regarding domains within ZIC proteins that confer trans-activation or -repression. To address this question, a new cell-based trans-activation assay system suitable for ZIC proteins in HEK293T cells was constructed. This identified two previously unannotated evolutionarily conserved regions of ZIC3 that are necessary for trans-activation. These domains are found in all Subclass A ZIC proteins, but not in the Subclass B proteins. Additionally, the Subclass B proteins fail to elicit functional binding at a multimerised ZIC DNA binding site. All ZIC proteins, however, exhibit functional binding when the ZIC DNA binding site is embedded in a multiple transcription factor locus derived from ZIC target genes in the mouse genome. This ability is due to several domains, some of which are found in all ZIC proteins, that exhibit context dependent trans-activation or -repression activity. This knowledge is valuable for assessing the likely pathogenicity of variant ZIC proteins associated with human disorders and for determining factors that influence functional transcription factor binding.
Fast Periodic Visual Stimulation indexes preserved semantic memory in healthy ageing
Authors: Milton Alex , Rowland Alesi , Stothart George , Clatworthy Phil , Pennington Catherine M. , Kazanina Nina
Published: August 2020

Behavioural studies investigating the preservation of semantic memory in healthy ageing have reported mixed findings. One suggested reason for this discrepancy is that the processes underpinning lexical access to semantic knowledge may be sensitive to ageing. It is therefore necessary to assess semantic memory utilising tasks that are not explicitly linguistic. In this study, a fast periodic visual stimulation (FPVS) paradigm coupled with EEG was used to assess the ability of younger and older adults to automatically distinguish between images by their semantic category. Participants were presented with a 6 Hz stream of images drawn from one semantic category except every fifth image (occurring at a rate of 1.2 Hz) which was drawn from an alternate semantic category. For both younger and older adults, results demonstrate successful and comparable semantic categorisation. This was detectable at the individual level for 71% and 72% of older and younger adults, respectively. Given the rapid presentation rate and absence of explicit instruction to categorise images, the task is unlikely to utilise linguistic strategies and suggests the maintenance of semantic memory in healthy ageing. Moreover, this study utilised mobile EEG equipment and short presentation times that would be suitable for practical application outside a research setting.
Porcine reproductive and respiratory syndrome virus infection induces endoplasmic reticulum stress, facilitates virus replication, and contributes to autophagy and apoptosis
Authors: Chen Quangang , Men Yanjuan , Wang Dang , Xu Deqin , Liu Suyan , Xiao Shaobo , Fang Liurong
Published: August 2020

During viral infection, the host cell synthesizes high amounts of viral proteins, which often causes stress to the endoplasmic reticulum (ER). To manage abnormal ER stress, mammalian cells trigger a response called the unfolded protein response (UPR). Previous studies have indicated that porcine reproductive and respiratory syndrome virus (PRRSV), an Arterivirus that has been devastating the swine industry worldwide, can induce ER stress and activate UPR, however, the activation pathways and the biological significance requires further investigation. In this study, we demonstrated that, among the three types of UPR pathways, PRRSV infection induced PERK and IRE1 pathways, but not the ATF6 pathway. Furthermore, the induction of UPR promoted PRRSV replication. We also found that PRRSV-induced UPR, particularly the PERK pathway, was involved in the induction of autophagy, a cellular degradation process that can alleviate cell stress. Besides, we also provided insights into the ER stress-mediated apoptosis in response to PRRSV infection. PRRSV infection induced the expression of the transcription factor CHOP, which activated caspase 3 and PARP led to ER stress-mediated apoptosis. Using 3-Methyladenine (3-MA) to inhibit autophagy, the increased ER stress and cell apoptosis were observed in the PRRSV infected cell. Taken together, our results revealed the associations of ER stress, autophagy, and apoptosis during PRRSV infection, helping us to further understand how PRRSV interacts with host cells.
Differential effects of ethanol on behavior and GABAA receptor expression in adult zebrafish (Danio rerio) with alternative stress coping styles
Authors: Goodman Alexander C. , Wong Ryan Y.
Published: August 2020

Variation in stress responses between individuals are linked to factors ranging from stress coping styles to sensitivity of neurotransmitter systems. Many anxiolytic compounds (e.g. ethanol) can increase stressor engagement through modulation of neurotransmitter systems and are used to investigate stress response mechanisms. There are two alternative suites of correlated behavioral and physiological responses to stressors (stress coping styles) that differ in exploration tendencies: proactive and reactive stress coping styles. By chronically treating individuals differing in stress coping style with ethanol, a GABA-acting drug, we assessed the role of the GABAergic system on the behavioral stress response. Specifically, we investigated resulting changes in stress-related behavior (i.e. exploratory behavior) and whole-brain GABAA receptor subunits (gabra1, gabra2, gabrd, & gabrg2) in response to a novelty stressor. We found that ethanol-treated proactive individuals showed lower stress-related behaviors than their reactive counterparts. Proactive individuals showed significantly higher expression of gabra1, gabra2, and gabrg2 compared to reactive individuals and ethanol treatment resulted in upregulation of gabra1 and gabrg2 in both stress coping styles. These results suggest that impacts of ethanol on stress-related behaviors vary by stress coping style and that expression of select GABAA receptor subunits may be one of the underlying mechanisms.
Differential proteomics study of postharvest Volvariella volvacea during storage at 4 °C
Authors: Zha Lei , Chen Mingjie , Yu Changxia , Guo Qian , Zhao Xu , Li Zhengpeng , Zhao Yan , Li Chuanhua , Yang Huanling
Published: August 2020

The postharvest storage of Volvariella volvacea is an important factor limiting the industry development. Low-temperature storage is the traditional storage method used for most edible fungi, but V. volvacea undergoes autolysis at low temperature. To understand the molecular mechanism underlying the low-temperature autolysis of V. volvacea after harvesting, fruiting bodies of V. volvacea strain V23 were stored at 4 °C. Based on our previous study, in which the changes of morphological and physiological indexes during storage for 0, 6, 12, 24, 30, 36, 48 and 60 h were measured; four time points, namely, 0, 12, 24 and 60 h, were selected for this differential proteomics study. The proteomic changes in the postharvest storage samples were studied by isobaric tags for relative and absolute quantification-coupled two-dimensional liquid chromatography-tandem mass spectrometry (2D LC–MS/MS). A total of 2,063 proteins were identified, and 192 differentially expressed proteins (DEPs), including 24 up-regulated proteins and 168 down-regulated proteins, were detected after 12 h of storage. After 24 h of storage, 234 DEPs, including 48 up-regulated and 186 down-regulated proteins, were observed, and after 60 h, 415 DEPs, including 65 up-regulated proteins and 350 down-regulated proteins, were observed. An in-depth data analysis showed that the DEPs participated in various cellular processes, particularly metabolic processes. In this study, we combined Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway analyses, and the results focused on oxidative phosphorylation and ubiquitin mediated proteolysis pathways. In addition, sdh2, uba1 and ubc1 was confirmed by quantitative real-time polymerase chain reaction, and the results showed that the expression of these genes were consistent with their protein level. Based on the literature and our results, it is speculated that the identified DEPs, such as ATP1, SDH2, COR1, UBA1, COX4, UBC1 and SKP1 play a key role in the low-temperature autolysis of V. volvacea.
Extreme hyperthermia tolerance in the world’s most abundant wild bird
Authors: Freeman M. T. , Czenze Z. J. , Schoeman K. , McKechnie A. E.
Published: August 2020

The thermal tolerances of vertebrates are generally restricted to body temperatures below 45–47 °C, and avian and mammalian critical thermal maxima seldom exceed 46 °C. We investigated thermoregulation at high air temperatures in the red-billed quelea (Quelea quelea), an African passerine bird that occurs in flocks sometimes numbering millions of individuals. Our data reveal this species can increase its body temperature to extremely high levels: queleas exposed to air temperature > 45 °C increased body temperature to 48.0 ± 0.7 °C without any apparent ill-effect, with individual values as high as 49.1 °C. These values exceed known avian lethal limits, with tolerance of body temperature > 48 °C unprecedented among birds and mammals.
Integrated graphene oxide resistive element in tunable RF filters
Authors: Abunahla Heba , Gadhafi Rida , Mohammad Baker , Alazzam Anas , Kebe Mamady , Sanduleanu Mihai
Published: August 2020

Adaptable communication systems are of great interest as they provide dynamic front end to accommodate the tunable spectrum management in advanced wireless systems. Memristor (acronym of memory resistor) is an emerging technology part of resistive RAM (RRAM) that has good potential for application in reconfigurable RF devices. The potentiality of using resistive switches for frequency tuning of high frequency RF filters is successfully explored in this article for the first time. Tunable RF filter is designed with detailed simulation using Ansys HFSS, and then correlated with measured results from experiment. As a proof of concept, a prototype of the tunable RF filter is fabricated by using a graphene oxide (GO) integrated with a conventional microstrip open stub notch filter. The resistor switching ability of the device is exploited for the frequency tuning. The resonating length of the notch filter is varied by changing the resistance of the active GO material between ‘HIGH’ (OFF) and ‘LOW’ (ON) resistance states. The measured results demonstrate the great potential of using RRAM in tunable RF devices. It also proves the possibility of tuning RF devices without any localized surface mount device (SMD) element or complex realization technique.
Neurological disorders-associated anti-glycosphingolipid IgG-antibodies display differentially restricted IgG subclass distribution
Authors: Lardone Ricardo D. , Irazoqui Fernando J. , Nores Gustavo A.
Published: August 2020

Antibodies against several self-glycans on glycosphingolipids are frequently detected in different neurological disorders. Their pathogenic role is profusely documented, but the keys for their origin remain elusive. Additionally, antibodies recognizing non-self glycans appear in normal human serum during immune response to bacteria. Using HPTLC-immunostaining we aimed to characterize IgM and IgG subclass antibody responses against glycosphingolipids carrying self glycans (GM1/GM2/GM3/GD1a/GD1b/GD3/GT1b/GQ1b) and non-self glycans (Forssman/GA1/“A” blood group/Nt7) in sera from 27 randomly selected neurological disorder patients presenting IgG reactivity towards any of these antigens. Presence of IgG2 (p = 0.0001) and IgG1 (p = 0.0078) was more frequent for IgG antibodies against non-self glycans, along with less restricted antibody response (two or more simultaneous IgG subclasses). Contrariwise, IgG subclass distribution against self glycans showed clear dominance for IgG3 presence (p = 0.0017) and more restricted IgG-subclass distributions (i.e. a single IgG subclass,p = 0.0133). Interestingly, anti-self glycan IgG antibodies with simultaneous IgM presence had higher proportion of IgG2 (p = 0.0295). IgG subclass frequencies were skewed towards IgG1 (p = 0.0266) for “anti-self glycan A” subgroup (GM2/GM1/GD1b) and to IgG3 (p = 0.0007) for “anti-self glycan B” subgroup (GM3/GD1a/GD3/GT1b/GQ1b). Variations in players and/or antigenic presentation pathways supporting isotype (M-G) and IgG-subclass pattern differences in the humoral immune response against glycosphingolipids carrying non-selfversusself-glycans are discussed.
25-Hydroxyvitamin D status, vitamin D intake, and skin cancer risk: a systematic review and dose–response meta-analysis of prospective studies
Authors: Mahamat-Saleh Yahya , Aune Dagfinn , Schlesinger Sabrina
Published: August 2020

Sun exposure is a major environmental risk factor for skin cancers and is also an important source of vitamin D. However, while experimental evidence suggests that vitamin D may have a protective effect on skin cancer risk, epidemiologic studies investigating the influence of 25-hydroxyvitamin D (25(OH)D) level and/or vitamin D intake on skin cancer risk are conflicting. A systematic review and dose–response meta-analyses of prospective studies was conducted to clarify these associations. Relevant studies were identified by searching the PubMed database up to 30th August 2019. Random effects dose–response meta-analyses were used to estimate summary relative risks (SRRs) and 95% confidence intervals (CIs). Overall, thirteen prospective studies were included. Circulating level of 25(OH)D was associated with higher risks of melanoma (SRR (95% CI) per 30 nmol = 1.42 (1.17–1.72)) and keratinocyte cancer (KC) (SRR (95% CI) per 30 nmol/L = 1.30 (1.13–1.49)). The SRR (95% CI) per 30 nmol/L increase in 25(OH) D level was 1.41 (1.19–1.67), and 1.57 (0.64–3.86), for basal cell carcinomas (BCCs) and squamous cell carcinomas (SCCs), respectively. However, while we found that vitamin D intake (from diet, supplemental and total) was not associated with risks of melanoma and SCC, vitamin D intake was associated with slightly increased BCC risk, albeit with no heterogeneity across skin cancer type. This meta-analysis suggests positive associations between circulating 25(OH)D level and risk of melanoma and KC, however, this finding is most likely confounded by sun exposure. We found no associations between vitamin D intake skin cancers, except positive associations with BCC risk.
Author Correction: Characteristics of Adolescents and Young adults with HIV in the Republic of Korea from 2010 through 2015
Authors: Yoo Myeongsu , Seong Jaehyun , Yoon Jae-Gyu , Cha Jeong-ok , Chung Yoon-Seok , Kim Kisoon , Kee Mee-Kyung
Published: August 2020

An amendment to this paper has been published and can be accessed via a link at the top of the paper.
An early Pangaean vicariance model for synapsid evolution
Authors: Brikiatis Leonidas
Published: August 2020

Genetic isolation due to geographic separation (vicariance) is the best understood cause of vertebrate speciation. Nevertheless, it has never been demonstrated in the fossil record across a wide range of taxa. Here, by reviewing in-depth the available data of the Late Palaeozoic (~ 350–250 million years ago), I reconstructed an early Pangaean junction-disjunction palaeogeographic model and showed that it coincides strongly with time-calibrated cladograms of the Late Palaeozoic synapsids (the primitive ancestors of modern mammals). The temporal development of the vicariant topology seems to fit closely with the emergence rhythm of the recovered synapsid taxa, suggesting vicariance due to Pangaean separation as the cause of early amniote evolution. The inferred vicariant topology also accounts for the observed pattern in the North American marine biostratigraphic units. Accordingly, the model demonstrates the link between the evolution of life on Earth and palaeogeographic evolution and strongly supports allopatric speciation through vicariance as the prominent mode of amniote evolution. Furthermore, correlations between state-of-the-art biochronostratigraphic charts and this palaeogeographic model suggest that the arido-eustasy model can explain the mid-Permian biotic extinction event and depositional cycles, such as the pre-Zechstein of the Central European Basin.
Structural dynamics of CH3NH3+ and PbBr3− in tetragonal and cubic phases of CH3NH3PbBr3 hybrid perovskite by nuclear magnetic resonance
Authors: Lim Ae Ran , Kim Sun Ha , Joo Yong Lak
Published: August 2020

Understanding the structural dynamics of lead-halide perovskites is essential for their advanced use as photovoltaics.
Here, the structural dynamics of the CH3NH3 cation and PbBr6 octahedra in the perovskite CH3NH3PbBr3 were studied via nuclear magnetic resonance (NMR) to determine the mechanism of the transition from the tetragonal to cubic phase. The chemical shifts were obtained by 1H, 13C, and 207Pb magic angle spinning NMR and 14N static NMR. The chemical shifts of the 1H nuclei in CH3 and NH3 remained constant with increasing temperature, whereas those of the 13C and 207Pb nuclei varied near the phase transition temperature (TC = 236 K), indicating that the structural environments of 13C and 207Pb change near TC. The spin–lattice relaxation time T1ρ values for 1H, 13C, and 207Pb nuclei increased with increasing temperature and did not exhibit an abrupt change near TC. In addition, the two lines in the 14N NMR spectra superposed into one line near TC, indicating the occurrence of a phase transition to a cubic phase with higher symmetry than tetragonal. Consequently, the main factor causing the phase transition from the tetragonal to cubic phase near TC is a change in the surroundings of the 207Pb nuclei in the PbBr6 octahedra and of the C–N groups in the CH3NH3 cations.
TLR4 896A/G and TLR9 1174G/A polymorphisms are associated with the risk of infectious mononucleosis
Authors: Jabłońska Agnieszka , Studzińska Mirosława , Szenborn Leszek , Wiśniewska-Ligier Małgorzata , Karlikowska-Skwarnik Monika , Gęsicki Tomasz , Paradowska Edyta
Published: August 2020

Toll-like receptors (TLRs) recognize pathogen-associated molecular patterns and activate innate and adaptive immune responses. Single nucleotide polymorphisms (SNPs) within the TLR genes may influence host–pathogen interactions and can have an impact on the progression of infectious diseases. The present study aimed to investigate the genotype distribution of TLR2 (2029C/T, rs121917864; 2258G/A, rs5743708), TLR4 (896A/G, rs4986790), and TLR9 (− 1237T/C, rs5743836; − 1486T/C, rs187084; 1174G/A, rs352139; and 2848C/T, rs352140) polymorphisms in 149 children and adolescents with infectious mononucleosis (IM) and 140 healthy individuals. The potential association of TLR SNPs with the clinical manifestations of EBV infection was also studied. The presence of TLR2, TLR4, and TLR9 SNPs was identified by polymerase chain reaction–restriction fragment length polymorphism (PCR–RFLP). EBV DNA loads were detected by quantitative real-time PCR assay. The TLR4 896 GG and the TLR9 1174 GA genotypes were associated with an increased risk of EBV-related IM in examined patients (p = 0.014 and p = 0.001, respectively). The heterozygous genotype of the TLR4 896A/G SNP was associated with an increased risk of elevated liver enzyme levels and leukocytosis (p < 0.05). Our preliminary study revealed that the TLR4 896A/G and the TLR9 1174G/A polymorphisms seem to be related to the course of acute EBV infection in children and adolescents.
Prognostic nomogram for elderly patients with acute respiratory failure receiving invasive mechanical ventilation: a nationwide population-based cohort study in Taiwan
Authors: Hsu Chun-Hsiang , Hung Yao‐Min , Chu Kuo-An , Chen Chiu-Fan , Yin Chun-Hao , Lee Ching-Chih
Published: August 2020

Patients in critical care medicine are ageing. There is limited literature evaluating long-term outcomes and prognostic factors for the growing number of elderly patients with acute respiratory failure (ARF) receiving invasive mechanical ventilation (IMV). Data on elderly patients (≧ 65 years old) with ARF receiving intubation and IMV during 2003–2012 were retrospectively collected from the national health database in Taiwan. We included 7,095 elderly patients. The 28-day mortality was 33%, the 60-day mortality was 47.5%, and the 1-year mortality was 70.4%. Patients were divided into groups: young-old (65–74 years), middle-old (75–84 years), and oldest-old (≧ 85 years). Patients in the oldest-old and middle-old groups had higher 1-year mortality than the young-old group (p < 0.001). The multivariate logistic regression revealed 9 significant factors associated with 1-year mortality, and these factors were used to develop a prognostic nomogram. The present study showed that the long-term prognosis of elderly patients with ARF and IMV is very poor. This nomogram can help physicians estimate the 1-year mortality of elderly patients in the early stage of ARF and assist in clinical decision making.
Development of introgression lines in high yielding, semi-dwarf genetic backgrounds to enable improvement of modern rice varieties for tolerance to multiple abiotic stresses free from undesirable linkage drag
Authors: Kumar Arvind , Sandhu Nitika , Venkateshwarlu Challa , Priyadarshi Rahul , Yadav Shailesh , Majumder Ratna Rani , Singh Vikas Kumar
Published: August 2020

Occurrence of multiple abiotic stresses in a single crop season has become more frequent than before. Most of the traditional donors possessing tolerance to abiotic stresses are tall, low-yielding with poor grain quality. To facilitate efficient use of complex polygenic traits in rice molecular breeding research, we undertook development of introgression lines in background of high-yielding, semi-dwarf varieties with good grain quality. The study reports the development and evaluations of over 25,000 introgression lines in eleven elite rice genetic backgrounds for improvement of yield under multiple abiotic-stresses such as drought, flood, high/low temperature. The developed introgression lines within each genetic background are near isogenic/recombinant inbred lines to their recipient recurrent parent with 50 to 98% background recovery and additionally carry QTLs/genes for abiotic stresses. The multiple-stress tolerant pyramided breeding lines combining high yield under normal situation and good yield under moderate to severe reproductive-stage drought, semi-dwarf plant type with good grain quality traits have been developed. The introgression lines in dwarf backgrounds open new opportunity to improve other varieties without any linkage drag as well as facilitate cloning of QTLs, identification and functional characterization of candidate genes, mechanisms associated with targeted QTLs and the genetic networks underlying complex polygenic traits.
Decomposition profile data analysis of multiple drug effects identifies endoplasmic reticulum stress-inducing ability as an unrecognized factor
Authors: Morita Katsuhisa , Mizuno Tadahaya , Kusuhara Hiroyuki
Published: August 2020

Chemicals have multiple effects in biological systems. Because their on-target effects dominate the output, their off-target effects are often overlooked and can sometimes cause dangerous adverse events. Recently, we developed a novel decomposition profile data analysis method, orthogonal linear separation analysis (OLSA), to analyse multiple effects. In this study, we tested whether OLSA identified the ability of drugs to induce endoplasmic reticulum (ER) stress as a previously unrecognized factor. After analysing the transcriptome profiles of MCF7 cells treated with different chemicals, we focused on a vector characterized by well-known ER stress inducers, such as ciclosporin A. We selected five drugs predicted to be unrecognized ER stress inducers, based on their inducing ability scores derived from OLSA. These drugs actually induced X-box binding protein 1 splicing, an indicator of ER stress, in MCF7 cells in a concentration-dependent manner. Two structurally different representatives of the five test compounds exhibited similar results in HepG2 and HuH7 cells, but not in PXB primary hepatocytes derived from human-liver chimeric mice. These results indicate that our decomposition strategy using OLSA uncovered the ER stress-inducing ability of drugs as an unrecognized effect, the manifestation of which depended on the background of the cells.
Comparative effectiveness of pembrolizumab vs. nivolumab in patients with recurrent or advanced NSCLC
Authors: Cui Pengfei , Li Ruixin , Huang Ziwei , Wu Zhaozhen , Tao Haitao , Zhang Sujie , Hu Yi
Published: August 2020

The efficacies of pembrolizumab and nivolumab have never been directly compared in a real-world study. Therefore, we sought to retrospectively evaluate the objective response rate (ORR) and the progression-free survival (PFS) of patients with recurrent or advanced non-small cell lung cancer (NSCLC) in a real-world setting. This study included patients with recurrent or advanced NSCLC diagnosed between September 1, 2015 and August 31, 2019, who were treated with programmed cell death 1 (PD-1) inhibitors at the Cancer Center of the Chinese People’s Liberation Army. PFS was estimated for each treatment group using Kaplan–Meier curves and log-rank tests. The multivariate analysis of PFS was performed with Cox proportional hazards regression models. A total of 255 patients with advanced or recurrent NSCLC treated with PD-1 inhibitors were identified. The ORR was significantly higher in the pembrolizumab group than in the nivolumab group, while PFS was not significantly different between the two groups. Subgroup analysis showed that the ORR was significantly higher for pembrolizumab than for nivolumab in patients in the first-line therapy subgroup and in those in the combination therapy as first-line therapy subgroup. Survival analysis of patients receiving combination therapy as second- or further-line therapy showed that nivolumab had better efficacy than pembrolizumab. However, the multivariate analysis revealed no significant difference in PFS between patients treated with pembrolizumab and those treated with nivolumab regardless of the subgroup. In our study, no significant difference in PFS was noted between patients treated with pembrolizumab and those treated with nivolumab in various clinical settings. This supports the current practice of choosing either pembrolizumab or nivolumab based on patient preferences.