Miracle-dz/UniFAR-FTUs huggingface dataset:
Lymph Node Ratio-Based Staging System for Gallbladder Cancer With Fewer Than Six Lymph Nodes Examined

Purpose The 8th edition of the American Joint Committee on Cancer (AJCC) tumor-lymph node-metastasis (TNM) staging system for gallbladder cancer (GBC) recommended that at least six lymph nodes (LNs) should be examined. But most patients with GBC had fewer than six LNs resected. This study aimed to establish an alternative index for assessing the LN status during the staging system for GBC patients with fewer than six LNs retrieved. Patients and Methods Patient data was extracted from the Surveillance, Epidemiology, and End Results (SEER) database (cases between 2004 and 2013). X-tile software was used to determine the optimal cutoff value for lymph node ratio (LNR) and a concordance index (C-index) was used to evaluate the discriminatory powers of the two staging systems. Results The majority of GBC patients in our cohort (1353, 78.5%) had fewer than six LNs examined. Among patients with inadequate LN examination, the higher number of LNs examined correlated with a lower proportion of patients. Using the TNM staging system, the C-index for patients with fewer than six LNs and patients with six or more LNs screened were 0.636 and 0.704, respectively. Using the staging system based on LNR (TNrM), the C-index for patients with fewer than six LNs retrieved and patients with six or more LNs retrieved were 0.649 and 0.694, respectively. Similar results were observed in patients with gallbladder adenocarcinoma (GBA). Conclusion TNrM might be superior to the 8th AJCC TNM staging system for stratifying GBC patients with fewer than six LNs examined, and it can complement TNM for more accurate risk stratification. Future prospective studies are needed to validate our findings.
SAMHD1 as the Potential Link Between SARS-CoV-2 Infection and Neurological Complications

The recent pandemic of coronavirus infectious illness 2019 (COVID19) triggered by SARS-CoV-2 has rapidly spread around the globe, generating in severe events an acute, highly lethal pneumonia and death. In the past two hitherto similar CoVs, the severe acute respiratory syndrome CoV (SARS-CoV-1) and Middle East respiratory syndrome CoV (MERS-CoV) also gained universal attention as they produced clinical symptoms similar to those of SARS-CoV-2 utilizing angiotensin-converting enzyme 2 (ACE2) receptor and dipeptidyl peptidase 4 (DPP4) to go into the cells. COVID-19 may also present with overtly neurological symptoms. The proper understanding of the expression and dissemination of ACE2 in central and peripheral nerve systems is crucial to understand better the neurological morbidity caused by COVID-19. Using the STRING bioinformatic tool and references through text mining tools associated to Coronaviruses, we identified SAMHD1 as the probable link to neurological symptoms. Paralleled to the response to influenza A virus and, specifically, respiratory syncytial virus, SARS-CoV-2 evokes a response that needs robust induction of a subclass of cytokines, including the Type I and, obviously, Type III interferons as well as a few chemokines. We correlate ACE2 to the pathogenesis and neurologic complications of COVID-19 and found that SAMHD1 links to NF-κB pathway. No correlation was found with other molecules associated with Coronavirus infection, including ADAR, BST2, IRF3, IFITM3, ISG15, MX1, MX2, RNASEL, RSAD2, and VPRBP. We suggest that SAMHD1 is the molecule that may be behind the mechanisms of the neurological complications associated with COVID-19.
Mapping Value Co-creation Literature in the Technology and Innovation Management Field: A Bibliographic Coupling Analysis

Value co-creation has become a very important topic in several disciplines. It is observed that value co-creation has been analyzed mainly from a perspective of marketing or services. The interest of studying value co-creation in relation to innovation is growing but there are no previous literature reviews that focus on the literature that studies value co-creation from a technology and innovation management perspective. The present research aims to close this gap. This research has two aims. First, we make a descriptive analysis of the evolution of documents published from 2004 to 2020. We analyze the main journals and identify the most prolific authors. In addition, we observe collaborative behavior at three different levels – country, institution, and author. Second, we determine the content structure of this literature through a bibliographic coupling analysis, and characterize the resulting groups. As a result of this analysis, we describe eleven thematic groups and characterize them through different metrics. Based on these metrics and the previous analysis, we classify and explain the studies about co-creation in the technology and innovation management field. We obtained three research streams: open innovation, consumer-centric analysis, and service ecosystem and service innovation, and two new trends: servitization and the sharing economy.
Subsurface Ocean Warming Hotspots and Potential Impacts on Marine Species: The Southwest South Atlantic Ocean Case Study

In the southwest South Atlantic Ocean (SWAO) strong ocean surface warming hotspots have been observed mainly along the path of the Brazil Current (BC), Brazil-Malvinas Confluence (BMC), and in the Río de la Plata (RdlP). However, there is no knowledge about the signature of ocean hotspots below the surface and the potential effects of ocean warming on marine biota. In this work, we provide initial evidence of how deep the hotspots of the SWAO extend in the water column, in particular at mid-water and bottom layers where two marine species - the green turtle (Chelonia mydas) and the Patagonian scallop (Zygochlamys patagonica) - inhabit. We compare 15 years (2003–2017) of Copernicus Marine Environment Monitoring Service (CMEMS) ARMOR3D high−resolution (1/4°) 3-D temperatures reprocessed from combined satellite and in situ observations with high−resolution (1/12°) Mercator ocean reanalysis. We also use location data of C. mydas and Z. patagonica to discuss the potential impacts of warming on these species in terms of geographic distribution, phenological shifts and thermal tolerance. The potential distribution of C. mydas changes in relation to the sea surface temperature (SST) and the bathymetry. The warming of the whole water column in the RdlP (>0.4°C/decade) and the southward movement of the mean surface isotherms, which likely drove turtle displacements, could enable the opening up of novel optimal thermal habitats and/or a longer seasonal residency for the species. At the BMC, warming is driven by the southward displacement of the BC during the past decades. Ocean model temperature indicates cooling/warming in deep waters along the outer shelf and shelf break regions, which vary according the displacements of the BMC. The expected warming of the waters over the Patagonian scallop largest bed could exceed the thermal tolerance of this species and its survival. Given the lack of long-term monitoring programs to address the impacts of climate change on marine biota in the SWAO, our results provide the first effort to call the attention of stakeholders and decision makers on marine conservation and fishery management to work toward better management strategies in the context of climate change.
Transcriptome Profiles Reveal the Growth-Promoting Mechanisms of Paenibacillus polymyxa YC0136 on Tobacco (Nicotiana tabacum L.)

Paenibacillus polymyxa is an important member of the plant growth-promoting rhizobacteria. P. polymyxa YC0136 inoculation had beneficial effect on growth promotion and biological control of tobacco (Nicotiana tabacum L.) under field conditions. This study aimed to reveal the growth-promoting mechanisms of strain YC0136. In growth-promotion assays, tobacco plant height was increased by 8.42% and 8.25% at 60 and 90 days, respectively, after inoculation with strain YC0136. Strain YC0136 also promoted the accumulation of tobacco biomass in varying degrees. Following inoculation with strain YC0136, 3,525 and 4,368 tobacco genes were up-regulated and down-regulated, respectively. Strain YC0136 induced the expression of plant hormone-related genes in tobacco, including auxin, cytokinin, and gibberellin, as well as transcription factors related to stress resistance such as WRKY and MYB. In addition, strain YC0136 induced the up-regulation of genes in the phenylpropanoid biosynthesis pathway by 1.51–4.59 times. Interaction with tobacco also induced gene expression changes in strain YC0136, with 286 and 223 genes up-regulated and down-regulated, respectively. Tobacco interaction induced up-regulation of the ilvB gene related to auxin biosynthesis in strain YC0136 by 1.72 times and induced expression of some nutrient transport genes. This study contributes to our understanding of the growth-promoting mechanisms of strain YC0136 on tobacco and provides a theoretical basis for the application of P. polymyxa YC0136 as a biological fertilizer.
Isolation and Identification of a Novel Anti-protein Aggregation Activity of Lignin-Carbohydrate Complex From Chionanthus retusus Leaves

Lignin-carbohydrate complex (LCC) is the biological macromolecule that has been demonstrated to exert multiple biological functions, including antioxidant, anti-inflammation and anti-tumorigenesis, which support its broad application in the bioengineering field. However, it remains elusive the involvements of LCC in human neurological disorders, especially those with the overproduction of reactive oxygen species (ROS), such as spinocerebellar ataxias (SCAs). In this study, we found a previously undetermined anti-protein aggregation activity of LCC. Initially, two individual LCC preparations and carbohydrate-free lignin were isolated from the water-extracted waste residues of Chionanthus retusus (C. retusus) tender leaves. The chemical compositional analysis revealed that lignin (61.5%) is the predominant constituent in the lignin-rich LCC (LCC-L-CR), whereas the carbohydrate-rich LCC (LCC-C-CR) is mainly composed of carbohydrate (60.9%) with the xylan as the major constituent (42.1%). The NMR structural characterization showed that LCC-L-CR preparation is enriched in benzyl ether linkage, while phenyl glycoside is the predominant type of linkage in LCC-C-CR. Both LCC and lignin preparations showed antioxidant activities as exemplified by their abilities to scavenge free radicals in cultured mammalian cells and ROS in zebrafish. We further demonstrated a pronounced capability of LCC-L-CR in inhibiting the aggregation of expanded Ataxin-3, disease protein of SCA type 3, in human neuronal cells. Taken together, our study highlights the antioxidant and novel anti-protein aggregation activities of the C. retusus tender leaves-derived LCC.
Research Workshop 1: Explorations in sound and visual art

The EVA London Research Workshop is one of the more unique elements of our Conference that we have been keen to develop over many years. Often Postgraduate Students, at Masters or PhD level, or Unaffiliated Artists may feel excluded from prestigious conferences until their research is complete and they can submit a full paper proposal. However apart from their Tutors, Supervisors and Mentors, EVA London provides an almost unique opportunity to submit projects which can be truly described as ‘Work in Progress’. With an audience of International Academics and acknowledged experts in a field, the Research Workshop presentations have often lead to very positive interest and support, and sometimes to future collaborations, or returning to EVA London a year later with a completed piece of Research and a successful Full Conference Proposal. In previous years the presentations have been very popular with our delegates and as Chair of the Research Workshops I can think of a number of occasions where an audience question that began “Have you thought of…” has lead to very exciting new lines of discovery. Sadly in 2020 we will miss that particular interaction, however, we have, as always selected an exciting, ground breaking and quite eclectic group of RW delegates. We hope that by publishing their papers here, either grouped together, around themes, or individually published, you will be keen to contact our RW authors to discuss and develop ideas, as if we had all been able to meet up together in July 2020.
Digging for Stress-Responsive Cell Wall Proteins for Developing Stress-Resistant Maize

As a vital component of plant cell walls, proteins play important roles in stress response by modifying the structure of cell walls and involving in the wall integrity signaling pathway. Recently, we have critically reviewed the predictors, databases, and cross-referencing of the subcellular locations of possible cell wall proteins (CWPs) in plants (Briefings in Bioinformatics 2018;19:1130–1140). Here, we briefly introduce strategies for isolating CWPs during proteomic analysis. Taking maize (Zea mays) as an example, we retrieved 1873 probable maize CWPs recorded in the UniProt KnowledgeBase (UniProtKB). After curation, 863 maize CWPs were identified and classified into 59 kinds of protein families. By referring to gene ontology (GO) annotations and gene differential expression in the Expression Atlas, we have highlighted the potential of CWPs acting in the front line of defense against biotic and abiotic stresses. Moreover, the analysis results of cis-acting elements revealed the responsiveness of the genes encoding CWPs toward phytohormones and various stresses. We suggest that the stress-responsive CWPs could be promising candidates for applications in developing varieties of stress-resistant maize.
Long Non-coding RNA AGAP2-AS1 Silencing Inhibits PDLIM5 Expression Impeding Prostate Cancer Progression via Up-Regulation of MicroRNA-195-5p

Prostate cancer remains a significant cause of cancer-related deaths in male population. More recently, accumulating evidence continues to implicate long non-coding RNAs (lncRNAs), microRNAs (miRNAs), and mRNAs in various types of cancers, including prostate cancer. The current study aimed to elucidate the role of lncRNA AGAP2-AS1/miR-195-5p/PDZ and LIM domain 5 (PDLIM5) in prostate cancer progression. Initially, microarray expression profiles were applied to screen differentially expressed lncRNAs/miRNAs/genes associated with prostate cancer. Dual-luciferase reporter and RNA pull-down/RIP assays were subsequently performed to explore the interactions among lncRNA AGAP2-AS1, miR-195-5p, and PDLIM5, after which their expression was detected in cancer tissues and cells. Next, gain- and loss-of-function approaches were employed to elucidate the mechanism of lncRNA AGAP2-AS1/miR-195-5p/PDLIM5 in the processes of cell proliferation, migration and invasion as well as tumor growth. LncRNA AGAP2-AS1 was found to be highly expressed in prostate cancer. Silencing of lncRNA AGAP2-AS1 contributed to the suppression of proliferation, migration and invasion of cancer cells in vitro. Besides, lncRNA AGAP2-AS1 could bind to miR-195-5p which targeted PDLIM5 and subsequently downregulated its expression, ultimately impeding the progression of prostate cancer. Additionally, lncRNA AGAP2-AS1 inhibition led to an up-regulated expression of miR-195-5p and down-regulated PDLIM5 expression, resulting in delayed tumor growth in vivo. Taken together, the key findings of our study demonstrated that lncRNA AGAP2-AS1 silencing exerted suppressive effects on the development of prostate cancer via the miR-195-5p-dependent downregulation of PDLIM5. Our findings highlighted the potential of lncRNA AGAP2-AS1 as a promising novel molecular target for prostate cancer therapy.
Cross-Modal Correspondences Between Temperature and Taste Attributes

Temperature is an important characteristic of food and drink. In addition to food-intrinsic temperature (i.e., serving temperature), consumers often experience food-extrinsic temperature (e.g., physical warmth). Emerging research on cross-modal correspondence has revealed that people reliably associate temperature with other sensory features. Building on the literature on cross-modal correspondence and sensation transference theory, the present study aimed to reveal mental representations of temperature–taste correspondence and cross-modal mental representations influencing corresponding sensory/hedonic perceptions of beverages, with a focus on manipulating food-extrinsic warmth. To reveal mental representations of temperature–taste correspondence, Experiment 1 investigated whether temperature words (warm, cool) are associated with sensory/hedonic attributes (e.g., sweet, sour, salty, bitter). The results of Experiment 1 demonstrated that warm (vs. cool) was matched more with saltiness, tastiness, healthfulness, and preference (intention to buy), whereas cool (vs. warm) was matched more with sourness and freshness. Experiment 2 assessed whether cross-modal mental representations influence corresponding sensory/hedonic perceptions of beverages. The participants wore hot and cold pads and rated sensory/hedonic attributes of Japanese tea (Experiment 2a) or black coffee (Experiment 2b) before and after tasting it. The results of Experiment 2a demonstrated that physical warmth (vs. coldness) increased healthfulness and the intention to buy Japanese tea. The results of Experiment 2b did not reveal any effects of physical warmth on sensory/hedonic ratings. These findings provide evidence of taste–temperature correspondence and provide preliminary support for the influence of food-extrinsic warmth on taste attributes related to positivity.
The Diapause Lipidomes of Three Closely Related Beetle Species Reveal Mechanisms for Tolerating Energetic and Cold Stress in High-Latitude Seasonal Environments

During winter insects face energetic stress driven by lack of food, and thermal stress due to sub-optimal and even lethal temperatures. To survive, most insects living in seasonal environments such as high latitudes, enter diapause, a deep resting stage characterized by a cessation of development, metabolic suppression and increased stress tolerance. The current study explores physiological adaptations related to diapause in three beetle species at high latitudes in Europe. From an ecological perspective, the comparison is interesting since one species (Leptinotarsa decemlineata) is an invasive pest that has recently expanded its range into northern Europe, where a retardation in range expansion is seen. By comparing its physiological toolkit to that of two closely related native beetles (Agelastica alni and Chrysolina polita) with similar overwintering ecology and collected from similar latitude, we can study if harsh winters might be constraining further expansion. Our results suggest all species suppress metabolism during diapause and build large lipid stores before diapause, which then are used sparingly. In all species diapause is associated with temporal shifts in storage and membrane lipid profiles, mostly in accordance with the homeoviscous adaptation hypothesis, stating that low temperatures necessitate acclimation responses that increase fluidity of storage lipids, allowing their enzymatic hydrolysis, and ensure integral protein functions. Overall, the two native species had similar lipidomic profiles when compared to the invasive species, but all species showed specific shifts in their lipid profiles after entering diapause. Taken together, all three species show adaptations that improve energy saving and storage and membrane lipid fluidity during overwintering diapause. While the three species differed in the specific strategies used to increase lipid viscosity, the two native beetle species showed a more canalized lipidomic response, than the recent invader. Since close relatives with similar winter ecology can have different winter ecophysiology, extrapolations among species should be done with care. Still, range expansion of the recent invader into high latitude habitats might indeed be retarded by lack of physiological tools to manage especially thermal stress during winter, but conversely species adapted to long cold winters may face these stressors as a consequence of ongoing climate warming.
Quantitative Assessment and Driving Force Analysis of Mangrove Forest Changes in China from 1985 to 2018 by Integrating Optical and Radar Imagery

Mangrove ecosystems are valuable, yet vulnerable, and therefore they have been an important subject of protection and restoration in China. Reliable information on long-term China mangrove dynamics is lacking but vital to analyze the driving forces and evaluate the efforts of mangrove conversation. This study aims to quantify the conversions among mangroves and other land covers with high accuracy. The updated mangrove base map for 2018 was produced by integrating Advanced Land Observing Satellite (ALOS) Phased Array type L-band Synthetic Aperture Radar 2 (PALSAR-2) yearly mosaics and Landsat imagery with an overall accuracy of 95.23 ± 6.02%. Then, a novel approach combining map-to-image and image-to-image methods was proposed to detect the changed pixels in mangrove forests from 1985 to 2018. The mangrove base map was adopted to mask the images from other years. To determine the changed pixels, the differencing values in the masked area between two images were calculated and compared with the corresponding thresholds. Based on the changed pixels, the possible driving forces were analyzed and associated with socioeconomic development. The resultant mangrove dynamics demonstrated that mangrove forests in China experienced a tendency of loss first and recovery later during the past 30 years. Most mangrove gains came from aquaculture and mudflat, whilst losses were due to the built-up construction and aquaculture reclamation. These conversions indicated that mangrove deforestations were mainly due to human-induced destruction, while the recoveries were strongly associated with conservation and restoration actions.
Extracellular Vesicle miRNAs in the Promotion of Cardiac Neovascularisation

Cardiovascular disease (CVD) is the leading cause of mortality worldwide claiming almost 17. 9 million deaths annually. A primary cause is atherosclerosis within the coronary arteries, which restricts blood flow to the heart muscle resulting in myocardial infarction (MI) and cardiac cell death. Despite substantial progress in the management of coronary heart disease (CHD), there is still a significant number of patients developing chronic heart failure post-MI. Recent research has been focused on promoting neovascularisation post-MI with the ultimate goal being to reduce the extent of injury and improve function in the failing myocardium. Cardiac cell transplantation studies in pre-clinical models have shown improvement in cardiac function; nonetheless, poor retention of the cells has indicated a paracrine mechanism for the observed improvement. Cell communication in a paracrine manner is controlled by various mechanisms, including extracellular vesicles (EVs). EVs have emerged as novel regulators of intercellular communication, by transferring molecules able to influence molecular pathways in the recipient cell. Several studies have demonstrated the ability of EVs to stimulate angiogenesis by transferring microRNA (miRNA, miR) molecules to endothelial cells (ECs). In this review, we describe the process of neovascularisation and current developments in modulating neovascularisation in the heart using miRNAs and EV-bound miRNAs. Furthermore, we critically evaluate methods used in cell culture, EV isolation and administration.