bluuebunny/crossref_metadata_2025_split huggingface dataset:
The disubstituted adamantyl derivative LW1564 inhibits the growth of cancer cells by targeting mitochondrial respiration and reducing hypoxia-inducible factor (HIF)-1α accumulation
Authors: Kim Inhyub , Kim Minkyoung , Park Min Kyung , Naik Ravi , Park Jae Hyung , Kim Bo-Kyung , Choi Yongseok , Chang Kwan Young , Won Misun , Ban Hyun Seung , Lee Kyeong 
Published: November 2020

AbstractTargeting cancer metabolism has emerged as an important cancer therapeutic strategy. Here, we describe the synthesis and biological evaluation of a novel class of hypoxia-inducible factor (HIF)-1α inhibitors, disubstituted adamantyl derivatives. One such compound, LW1564, significantly suppressed HIF-1α accumulation and inhibited the growth of various cancer cell lines, including HepG2, A549, and HCT116. Measurements of the oxygen consumption rate (OCR) and ATP production rate revealed that LW1564 suppressed mitochondrial respiration, thereby increasing the intracellular oxygen concentration to stimulate HIF-1α degradation. LW1564 also significantly decreased overall ATP levels by inhibiting mitochondrial electron transport chain (ETC) complex I and downregulated mammalian target of rapamycin (mTOR) signaling by increasing the AMP/ATP ratio, which increased AMP-activated protein kinase (AMPK) phosphorylation. Consequently, LW1564 promoted the phosphorylation of acetyl-CoA carboxylase, which inhibited lipid synthesis. In addition, LW1564 significantly inhibited tumor growth in a HepG2 mouse xenograft model. Taken together, the results indicate that LW1564 inhibits the growth of cancer cells by targeting mitochondrial ETC complex I and impairing cancer cell metabolism. We, therefore, suggest that LW1564 may be a potent therapeutic agent for a subset of cancers that rely on oxidative phosphorylation for ATP generation.
Systems identification and characterization of β-glucuronosyltransferase genes involved in arabinogalactan-protein biosynthesis in plant genomes
Authors: Ajayi Oyeyemi Olugbenga , Showalter Allan M. 
Published: November 2020

AbstractUtilizing plant biomass for bioethanol production requires an understanding of the molecular mechanisms involved in plant cell wall assembly. Arabinogalactan-proteins (AGPs) are glycoproteins that interact with other cell wall polymers to influence plant growth and developmental processes. Glucuronic acid, which is transferred to the AGP glycan by β-glucuronosyltransferases (GLCATs), is the only acidic sugar in AGPs with the ability to bind calcium. We carried out a comprehensive genome-wide analysis of a putative GLCAT gene family involved in AGP biosynthesis by examining its sequence diversity, genetic architecture, phylogenetic and motif characteristics, selection pressure and gene expression in plants. We report the identification of 161 putative GLCAT genes distributed across 14 plant genomes and a widely conserved GLCAT catalytic domain. We discovered a phylogenetic clade shared between bryophytes and higher land plants of monocot grass and dicot lineages and identified positively selected sites that do not result in functional divergence of GLCATs. RNA-seq and microarray data analyses of the putative GLCAT genes revealed gene expression signatures that likely influence the assembly of plant cell wall polymers which is critical to the overall growth and development of edible and bioenergy crops.
Bromalites from the Upper Triassic Polzberg section (Austria); insights into trophic interactions and food chains of the Polzberg palaeobiota
Authors: Lukeneder Alexander , Surmik Dawid , Gorzelak Przemysław , Niedźwiedzki Robert , Brachaniec Tomasz , Salamon Mariusz A. 
Published: November 2020

AbstractA rich assemblage of various types of bromalites from the lower Carnian “Konservat-Lagerstätte” from the Reingraben Shales in Polzberg (Northern Calcareous Alps, Lower Austria) is described for the first time in detail. They comprise large regurgitalites consisting of numerous entire shells of ammonoid Austrotrachyceras or their fragments and rare teuthid arm hooks, and buccal cartilage of Phragmoteuthis. Small coprolites composed mainly of fish remains were also found. The size, shape and co-occurrence with vertebrate skeletal remains imply that regurgitalites were likely produced by large durophagous fish (most likely by cartilaginous fish Acrodus). Coprolites, in turn, were likely produced by medium-sized piscivorous actinopterygians. Our findings are consistent with other lines of evidence suggesting that durophagous predation has been intense during the Triassic and that the so-called Mesozoic marine revolution has already started in the early Mesozoic.
Single cell profiling of capillary blood enables out of clinic human immunity studies
Authors: Dobreva Tatyana , Brown David , Park Jong Hwee , Thomson Matt 
Published: November 2020

AbstractAn individual’s immune system is driven by both genetic and environmental factors that vary over time. To better understand the temporal and inter-individual variability of gene expression within distinct immune cell types, we developed a platform that leverages multiplexed single-cell sequencing and out-of-clinic capillary blood extraction to enable simplified, cost-effective profiling of the human immune system across people and time at single-cell resolution. Using the platform, we detect widespread differences in cell type-specific gene expression between subjects that are stable over multiple days.
Micro-contextual identification of archaeological lipid biomarkers using resin-impregnated sediment slabs
Authors: Rodríguez de Vera Caterina , Herrera-Herrera Antonio V. , Jambrina-Enríquez Margarita , Sossa-Ríos Santiago , González-Urquijo Jesús , Lazuen Talia , Vanlandeghem Marine , Alix Claire , Monnier Gilliane , Pajović Goran , Tostevin Gilbert , Mallol Carolina 
Published: November 2020

AbstractCharacterizing organic matter preserved in archaeological sediment is crucial to behavioral and paleoenvironmental investigations. This task becomes particularly challenging when considering microstratigraphic complexity. Most of the current analytical methods rely on loose sediment samples lacking spatial and temporal resolution at a microstratigraphic scale, adding uncertainty to the results. Here, we explore the potential of targeted molecular and isotopic biomarker analysis on polyester resin-impregnated sediment slabs from archaeological micromorphology, a technique that provides microstratigraphic control. We performed gas chromatography–mass spectrometry (GC–MS) and gas chromatography–isotope ratio mass spectromety (GC–IRMS) analyses on a set of samples including drill dust from resin-impregnated experimental and archaeological samples, loose samples from the same locations and resin control samples to assess the degree of interference of polyester resin in the GC–MS and Carbon-IRMS signals of different lipid fractions (n-alkanes, aromatics, n-ketones, alcohols, fatty acids and other high polarity lipids). The results show that biomarkers within the n-alkane, aromatic, n-ketone, and alcohol fractions can be identified. Further work is needed to expand the range of identifiable lipid biomarkers. This study represents the first micro-contextual approach to archaeological lipid biomarkers and contributes to the advance of archaeological science by adding a new method to obtain behavioral or paleoenvironmental proxies.
Tracking COVID-19 using taste and smell loss Google searches is not a reliable strategy
Authors: Asseo Kim , Fierro Fabrizio , Slavutsky Yuli , Frasnelli Johannes , Niv Masha Y. 
Published: November 2020

AbstractWeb search tools are widely used by the general public to obtain health-related information, and analysis of search data is often suggested for public health monitoring. We analyzed popularity of searches related to smell loss and taste loss, recently listed as symptoms of COVID-19. Searches on sight loss and hearing loss, which are not considered as COVID-19 symptoms, were used as control. Google Trends results per region in Italy or state in the US were compared to COVID-19 incidence in the corresponding geographical areas. The COVID-19 incidence did not correlate with searches for non-symptoms, but in some weeks had high correlation with taste and smell loss searches, which also correlated with each other. Correlation of the sensory symptoms with new COVID-19 cases for each country as a whole was high at some time points, but decreased (Italy) or dramatically fluctuated over time (US). Smell loss searches correlated with the incidence of media reports in the US. Our results show that popularity of symptom searches is not reliable for pandemic monitoring. Awareness of this limitation is important during the COVID-19 pandemic, which continues to spread and to exhibit new clinical manifestations, and for potential future health threats.
Improving existing analysis pipeline to identify and analyze cancer driver genes using multi-omics data
Authors: Nguyen Quang-Huy , Le Duc-Hau 
Published: November 2020

AbstractThe cumulative of genes carrying mutations is vital for the establishment and development of cancer. However, this driver gene exploring research line has selected and used types of tools and models of analysis unsystematically and discretely. Also, the previous studies may have neglected low-frequency drivers and seldom predicted subgroup specificities of identified driver genes. In this study, we presented an improved driver gene identification and analysis pipeline that comprises the four most widely focused analyses for driver genes: enrichment analysis, clinical feature association with expression profiles of identified driver genes as well as with their functional modules, and patient stratification by existing advanced computational tools integrating multi-omics data. The improved pipeline's general usability was demonstrated straightforwardly for breast cancer, validated by some independent databases. Accordingly, 31 validated driver genes, including four novel ones, were discovered. Subsequently, we detected cancer-related significantly enriched gene ontology terms and pathways, probable drug targets, two co-expressed modules associated significantly with several clinical features, such as number of positive lymph nodes, Nottingham prognostic index, and tumor stage, and two biologically distinct groups of BRCA patients. Data and source code of the case study can be downloaded athttps://github.com/hauldhut/drivergene.
Antiseptic quaternary ammonium compound tolerance by gram-negative bacteria can be rapidly detected using an impermeant fluorescent dye-based assay
Authors: Gregorchuk Branden S. J. , Reimer Shelby L. , Beniac Daniel R. , Hiebert Shannon L. , Booth Timothy F. , Wuzinski Michelle , Funk Brielle E. , Milner Kieran A. , Cartwright Nicola H. , Doucet Ali N. , Mulvey Michael R. , Khajehpour Mazdak , Zhanel George G. , Bay Denice C. 
Published: November 2020

AbstractBiocides such as quaternary ammonium compounds (QACs) are potentially important contributors towards bacterial antimicrobial resistance development, however, their contributions are unclear due to a lack of internationally recognized biocide testing standards. Methods to detect QAC tolerance are limited to laborious traditional antimicrobial susceptibility testing (AST) methods. Here, we developed a rapid fluorescent dye-based membrane impermeant assay (RFDMIA) to discriminate QAC susceptibility among Gram-negative Enterobacterales and Pseudomonadales species. RFDMIA uses a membrane impermeant fluorescent dye, propidium iodide, in a 30-min 96-well fluorescent microplate-based assay where cell suspensions are exposed to increasing QAC concentrations. Our results demonstrate that RFDMIA can discriminate between QAC-susceptible and QAC-adapted Escherichia coli tolerant phenotypes and predict benzalkonium and cetrimide tolerance in all species tested except for intrinsically fluorescent Pseudomonas aeruginosa. RFDMIA identified a close association to minimum inhibitory concentration values determined by broth microdilution AST and increasing fluorescent dye emission values. RFDMIA emission values and scanning electron microscopy results also suggest that CET-adapted E. coli isolates have a CET dependence, where cells require sub-inhibitory CET concentrations to maintain bacilliform cell integrity. Overall, this study generates a new, rapid, sensitive fluorescent assay capable of detecting QAC-susceptible Gram-negative bacteria phenotypes and cell membrane perturbations.
Multiple myeloma hinders erythropoiesis and causes anaemia owing to high levels of CCL3 in the bone marrow microenvironment
Authors: Liu Lanting , Yu Zhen , Cheng Hui , Mao Xuehan , Sui Weiwei , Deng Shuhui , Wei Xiaojing , Lv Junqiang , Du Chenxing , Xu Jie , Huang Wenyang , Xia Shuang , An Gang , Zhou Wen , Ma Xiaoke , Cheng Tao , Qiu Lugui , Hao Mu 
Published: November 2020

AbstractAnaemia is the most common complication of myeloma and is associated with worse clinical outcomes. Although marrow replacement with myeloma cells is widely considered a mechanistic rationale for anaemia, the exact process has not been fully understood. Our large cohort of 1363 myeloma patients had more than 50% of patients with moderate or severe anaemia at the time of diagnosis. Anaemia positively correlated with myeloma cell infiltration in the bone marrow (BM) and worse patient outcomes. The quantity and erythroid differentiation of HSPCs were affected by myeloma cell infiltration in the BM. The master regulators of erythropoiesis, GATA1 and KLF1, were obviously downregulated in myeloma HSPCs. However, the gene encoding the chemokine CCL3 showed significantly upregulated expression. Elevated CCL3 in the BM plasma of myeloma further inhibited the erythropoiesis of HSPCs via activation of CCL3/CCR1/p38 signalling and suppressed GATA1 expression. Treatment with a CCR1 antagonist effectively recovered GATA1 expression and rescued erythropoiesis in HSPCs. Myeloma cell infiltration causes elevated expression of CCL3 in BM, which suppresses the erythropoiesis of HSPCs and results in anaemia by downregulating the level of GATA1 in HSPCs. Thus, our study indicates that targeting CCL3 would be a potential strategy against anaemia and improve the survival of myeloma patients.
Behavioural and ERP evidence of the self-advantage of online self-relevant information
Authors: Niu Gengfeng , Yao Liangshuang , Kong Fanchang , Luo Yijun , Duan Changying , Sun Xiaojun , Zhou Zongkui 
Published: November 2020

AbstractThe present study examined whether individuals experienced the same cognitive advantage for online self-relevant information (nickname) as that experienced for information encountered in real life (real name) through two experiments at both the behavioural and neural levels (event-related potential, ERP). The results indicated that individuals showed the same cognitive advantage for nicknames and real names. At the behavioural level, a nickname was detected as quickly as the real name, and both were detected faster than a famous name; at the neural level, the P300 potential elicited by one’s nickname was similar to that elicited by one’s real name, and both the P300 amplitudes and latencies were larger and more prolonged than those elicited by other name stimuli. These results not only confirmed the cognitive advantage for one’s own nickname and indicated that this self-advantage can be extended to online information, but also indicated that the virtual self could be integrated into the self and further expanded individuals’ self-concept.
Relationship of early acute complications and insertion site in push method percutaneous endoscopic gastrostomy
Authors: Suzuki Hiroshi , Joshita Satoru , Nagaya Tadanobu , Sato Koichi , Ito Akihiro , Suga Tomoaki , Umemura Takeji 
Published: November 2020

AbstractPercutaneous endoscopic gastrostomy (PEG), which is frequently used for nutrition management in patients having difficulty with oral intake, is considered a safe procedure. However, serious complications may occur depending on site of the puncture. This study aimed to clarify whether push method PEG construction at the posterior wall (PW) of the greater curvature (GC) had a higher risk of complications. We retrospectively investigated the relationship between puncture site at the PW of the GC and early acute complications in 540 patients receiving PEG. Early acute complications were defined as bleeding or perforation within 30 days after the PEG procedure. PEG-related complications were observed in 80 patients in total, with early acute complications detected in 42 patients. PEG construction at the PW of the GC in 12 cases exhibited a significantly higher occurrence of early acute complications versus PEG at other sites (41.7% vs. 7.0%, p = 0.001). Further, multivariate analysis revealed PW at the GC to be independently associated with early acute complications (OR 9.59, 95% CI 2.82–32.61; p = 0.0003). It may be desirable to avoid PEG at the PW of the GC. If performed, clinicians should pay careful attention to early acute complications.
Environmental effects on efficacy of herbicides for postemergence goosegrass (Eleusine indica) control
Authors: Shekoofa Avat , Brosnan James T. , Vargas Jose J. , Tuck Daniel P. , Elmore Matthew T. 
Published: November 2020

AbstractExperiments were conducted to understand environmental effects on efficacy of herbicides used to control goosegrass (Eleusine indica L. Gaertn.). Herbicides were applied to goosegrass maintained at soil moisture contents (VMC) of < 12%, 12 to 20%, or > 20%. Herbicides included fenoxaprop-p-ethyl (140 g ha−1), topramezone (25 g ha−1), foramsulfuron (44 g ha−1), 2,4-D + dicamba + MCPP + carfentrazone (860 + 80 + 270 + 28 g ha−1), and thiencarbazone-methyl + foramsulfuron + halosulfuron-methyl (22 + 45 + 69 g ha−1). Goosegrass control increased as VMC increased. Vapor pressure deficit (VPD) and air temperature were manipulated to determine effects of evaporative demand on foramsulfuron. Effects of soil drying were also studied following foramsulfuron application. Reductions in transpiration rate (TR) and leaf area were greatest with foramsulfuron applications to goosegrass in silt-loam under high evaporative demand (3 kPa VPD, 38 °C). Foramsulfuron had no effect on goosegrass in silica-sand regardless of evaporative demand. TR dropped to 0.2 mmh−1 within eight days after application to goosegrass in silt-loam compared to 18 days in silica-sand. Overall, foramsulfuron efficacy on goosegrass was maximized under conditions of high soil moisture and evaporative demand, and may be reduced in sandy soils that hold less water.
Transcriptome analysis of Xanthomonas fragariae in strawberry leaves
Authors: Puławska Joanna , Kałużna Monika , Warabieda Wojciech , Pothier Joël F. , Gétaz Michael , van der Wolf Jan M. 
Published: November 2020

AbstractXanthomonas fragariae is a quarantine bacterial pathogen that causes angular leaf spot on strawberry. The aim of our study was to analyse the mechanism of interaction of this bacterium with its host plant at the transcriptome level. For this purpose, mRNAs of X. fragariae growing in Wilbrink’s medium and from infected strawberry cv. Elsanta plants were isolated and sequenced using the Illumina MiSeq platform. The expression profiles of the bacteria in Wilbrink’s medium and in planta were very diverse. Of the 3939 CDSs recorded, 1995 had significantly different expression in planta (966 and 1029 genes were down- and upregulated, respectively). Among the genes showing increased expression in planta, those with eggNOG/COG (evolutionary genealogy of genes: Non-supervised Orthologous Groups/Cluster of Orthologous Groups) categories associated with bacterial cell motility, signal transduction, transport and metabolism of inorganic ions and carbohydrates and transcription were overrepresented. Among the genes with the most increased expression in planta, genes primarily associated with flagella synthesis and chemotaxis were found. It is also interesting to note that out of the 31 genes localized on a plasmid, 16 were expressed differently in planta, which may indicate their potential role in plant–pathogen interactions. Many genes with differentiated expression that were localized on chromosome and plasmid encode proteins of unknown function.
Traumatic tracheobronchial injuries: incidence and outcome of 136.389 patients derived from the DGU traumaregister
Authors: Schibilsky David , Driessen Arne , White William James , Lefering Rolf , Paffrath Thomas , Bouillon Bertil , Walker Tobias , Schlensak Christian , Mutschler Manuel 
Published: November 2020

AbstractTo describe the incidence, therapy and outcome of traumatic tracheobronchial injuries (TTBI) in trauma patients with multiple injuries derived from the DGU TraumaRegister. We analyzed the data on all patients listed on the TraumaRegister DGU (TR-DGU) in Germany between 2002 and 2015 aged 16 years or older and with an Injury Severity Score (ISS) of ≥ 9. We analyzed the data on 136,389 trauma patients, 561 of whom had suffered tracheobronchial injuries (0.4%). The majority were male (73.4%) and had a mean age of 43.7 years. In total, 84.0% of all TTBI injuries occurred secondary to blunt trauma, caused mainly by accidents (71.2%). TTBI was accompanied by several concomitant thoracic injuries such as pneumo- (41.2%) and hemothorax (23.2%), lacerations (7.8%) and contusions (32.3%) of the lung, as well as multiple rib fractures (29.6%). The severity of injury was classified via the abbreviated injury scale (AIS): 39.3% with AIS = 3, 51.3% with AIS = 4 and 60% with AIS = 5 patients underwent surgical interventions. The mortality of patients with tracheobronchial injuries was higher: 24.6%, versus 13.7% in all patients (control group). This high percentage reflects their generally severe injury burden through concomitant injuries. The incidence of TTBI in this large cohort of trauma patients is very low. However, its high mortality rate emphasizes its importance. Mortality was associated with higher ISS and AIS scores. Higher rates of concomitant injuries were therefore associated with a higher mortality rate. TTBI injuries revealed a higher rate of progression to surgical management, with 35% undergoing surgery within the first 24 h. This excessive mortality rate demonstrates a high overall injury burden in patients with TTBI and high mortality of associated injuries. A surgical intervention’s impact on mortality cannot be assessed in this study, as it would need to be investigated in a case-matched study.
Secreted sphingomyelins modulate low mammary cancer incidence observed in certain mammals
Authors: Ledet Melissa M. , Harman Rebecca M. , Fan Jennifer C. , Schmitt-Matzen Emily , Diaz-Rubio Maria Elena , Zhang Sheng , Van de Walle Gerlinde R. 
Published: November 2020

AbstractDetermining mechanisms that naturally protect species from developing cancer is critical in order to prevent and treat cancer. Here, we describe a novel cancer-suppressing mechanism, via the secretion of bioactive factors by mammary cells, that is present in domesticated mammals with a low mammary cancer incidence. Specifically, these bioactive factors induced triple-negative breast cancer cell (TNBC) death in vitro and reduced tumorigenicity in a xenograft TNBC mouse model in vivo. RNA deep sequencing showed significant downregulation of genes associated with breast cancer progression in secretome-cultured TNBC cells. Further in-depth multi-omics analysis identified sphingomyelins as key secreted factors, and their role was confirmed via inhibition of the sphingomyelin signaling pathway. We speculate that secreted sphingomyelins in the mammary gland of mammals with a naturally low incidence of mammary cancer mediate the elimination of cancer cells. This study contributes to the growing list of protective mechanisms identified in cancer-proof species.