bluuebunny/crossref_metadata_2025_split huggingface dataset:
In-vacuum active colour sensor and wireless communication across a vacuum-air interface
Authors: Sakai Osamu , Kitagawa Takayuki , Sakurai Keiji , Itami Go , Miyagi Shigeyuki , Noborio Kazuyuki , Taguchi Kohshi 
Published: January 2021

AbstractIn situ sensing with wireless digital-data transfer is a potential processing scheme that works very closely to the location of an event monitored by a sensor and converts the sensor’s raw output into digitized and informative small-volume bits, as suggested by recent proposals for edge computing and the Internet of Things (IoT). Colour perception may be a target of in situ sensor data acquisition; however, in contrast to from other sensing devices, colour sensors that detect visible light signals are usually located away from light-emitting sources, collecting light transmitting through the space and attenuating it in some manner. For example, in a vacuum chamber whose gas pressure is much less than the ambient atmosphere in which the sensors usually work, there are many veiled light sources, such as discharge plasma, for various industrial purposes including nanoscale manufacturing. In this study, we designed an in-vacuum colour sensor that can work with analogue-to-digital conversion and transfer data by wireless communication; this sensor is active in a low-pressure plasma chamber, detecting light signals and transferring them to a personal computer located outside the vacuum chamber. In addition to detecting lights with controlled spectra from outside successfully, we achieved complete operation of our in-vacuum active sensor for plasma emissions generated at 100 Pa. Comparing the signals with data from simultaneous monitoring by a monochromator, we established that the recorded signals arose from the plasma, confirming successful direct detection of low-pressure plasma emissions without any filtering effects between the sensor and the target object.
Pseudomonas aeruginosa reverse diauxie is a multidimensional, optimized, resource utilization strategy
Authors: McGill S. Lee , Yung Yeni , Hunt Kristopher A. , Henson Michael A. , Hanley Luke , Carlson Ross P. 
Published: January 2021

AbstractPseudomonas aeruginosa is a globally-distributed bacterium often found in medical infections. The opportunistic pathogen uses a different, carbon catabolite repression (CCR) strategy than many, model microorganisms. It does not utilize a classic diauxie phenotype, nor does it follow common systems biology assumptions including preferential consumption of glucose with an ‘overflow’ metabolism. Despite these contradictions, P. aeruginosa is competitive in many, disparate environments underscoring knowledge gaps in microbial ecology and systems biology. Physiological, omics, and in silico analyses were used to quantify the P. aeruginosa CCR strategy known as ‘reverse diauxie’. An ecological basis of reverse diauxie was identified using a genome-scale, metabolic model interrogated with in vitro omics data. Reverse diauxie preference for lower energy, nonfermentable carbon sources, such as acetate or succinate over glucose, was predicted using a multidimensional strategy which minimized resource investment into central metabolism while completely oxidizing substrates. Application of a common, in silico optimization criterion, which maximizes growth rate, did not predict the reverse diauxie phenotypes. This study quantifies P. aeruginosa metabolic strategies foundational to its wide distribution and virulence including its potentially, mutualistic interactions with microorganisms found commonly in the environment and in medical infections.
Long-term risk of primary liver cancers in entecavir versus tenofovir treatment for chronic hepatitis B
Authors: Chang Te-Sheng , Yang Yao-Hsu , Chen Wei-Ming , Shen Chien-Heng , Tung Shui-Yi , Yen Chih-Wei , Hsieh Yung-Yu , Lee Chuan-Pin , Tsai Meng-Ling , Hung Chao-Hung , Lu Sheng-Nan 
Published: January 2021

AbstractIt remains controversial whether entecavir (ETV) and tenofovir disoproxil fumarate (TDF) is associated with different clinical outcomes for chronic hepatitis B (CHB). This study aimed to compare the long-term risk of ETV versus TDF on hepatocellular carcinoma (HCC) and intrahepatic cholangiocarcinoma (ICC) in CHB patients from a large multi-institutional database in Taiwan. From 2011 to 2018, a total of 21,222 CHB patients receiving ETV or TDF were screened for eligibility. Patients with coinfection, preexisting cancer and less than 6 months of follow-up were excluded. Finally, 7248 patients (5348 and 1900 in the ETV and TDF groups, respectively) were linked to the National Cancer Registry database for the development of HCC or ICC. Propensity score matching (PSM) (2:1) analysis was used to adjust for baseline differences. The HCC incidence between two groups was not different in the entire population (hazard ratio [HR] 0.82; 95% confidence interval [CI] 0.66–1.02, p = 0.078) and in the PSM population (HR 0.83; 95% CI 0.65–1.06, p = 0.129). Among decompensated cirrhotic patients, a lower risk of HCC was observed in TDF group than in ETV group (HR 0.54; 95% CI 0.30–0.98, p = 0.043, PSM model). There were no differences between ETV and TDF groups in the ICC incidence (HR 1.84; 95% CI 0.54–6.29, p = 0.330 in the entire population and HR 1.04; 95% CI 0.31–3.52, p = 0.954 in the PSM population, respectively). In conclusion, treatment with ETV and TDF showed a comparable long-term risk of HCC and ICC in CHB patients.
Clinical characteristics and overall survival nomogram of second primary malignancies after prostate cancer, a SEER population-based study
Authors: Liu Yi , Zhang Peipei , Zhang Yinghao , Zheng Lichuan , Xu Wenbo , Hou Dongtao , Kang Zhengjun 
Published: January 2021

AbstractProstate cancer (PCa) is the most prevalent cancer among males and the survival period of PCa has been significantly extended. However, the probability of suffering from second primary malignancies (SPMs) has also increased. Therefore, we downloaded SPM samples from the SEER database and then retrospectively analyzed the general characteristics of 34,891 PCa patients diagnosed between 2000 and 2016. After excluding cases with unknown clinical information, 2203 patients were used to construct and validate the overall survival (OS) nomogram of SPM patients after PCa. We found that approximately 3.69% of PCa patients were subsequently diagnosed with SPMs. In addition, the three most prevalent sites of SPM were respiratory and intrathoracic organs, skin, and hematopoietic system. The top three histological types of SPMs were squamous cell carcinoma, adenoma and adenocarcinoma, nevi and melanoma. Through univariate and multivariate Cox regression analysis, we found that the site of SPM, age, TNM stage, SPM surgery history, and PCa stage were associated with the OS of SPM. By virtue of these factors, we constructed a nomogram to predict the OS of SPM. The C-index in the training set and validation set were 0.824 (95CI, 0.806–0.842) and 0.862 (95CI, 0.840–0.884), respectively. Furthermore, we plotted the receiver operating characteristic curve (ROC) and the area under curve (AUC) which showed that our model performed well in assessing the 3-year (0.861 and 0.887) and 5-year (0.837 and 0.842) OS of SPMs in the training and validation set. In summary, we investigated the general characteristics of SPMs and constructed a nomogram to predict the prognosis of SPM following PCa.
Estimation of pathogenic potential of an environmental Pseudomonas aeruginosa isolate using comparative genomics
Authors: Berger Carola , Rückert Christian , Blom Jochen , Rabaey Korneel , Kalinowski Jörn , Rosenbaum Miriam A. 
Published: January 2021

AbstractThe isolation and sequencing of new strains ofPseudomonas aeruginosacreated an extensive dataset of closed genomes. Many of the publicly available genomes are only used in their original publication while additional in silico information, based on comparison to previously published genomes, is not being explored. In this study, we defined and investigated the genome of the environmental isolateP. aeruginosaKRP1 and compared it to more than 100 publicly available closedP. aeruginosagenomes. By using different genomic island prediction programs, we could identify a total of 17 genomic islands and 8 genomic islets, marking the majority of the accessory genome that covers ~ 12% of the total genome. Based on intra-strain comparisons, we are able to predict the pathogenic potential of this environmental isolate. It shares a substantial amount of genomic information with the highly virulent PSE9 and LESB58 strains. For both of these, the increased virulence has been directly linked to their accessory genome before. Hence, the integrated use of previously published data can help to minimize expensive and time consuming wetlab work to determine the pathogenetic potential.
Temperature driven hibernation site use in the Western barbastelle Barbastella barbastellus (Schreber, 1774)
Authors: De Bruyn Luc , Gyselings Ralf , Kirkpatrick Lucinda , Rachwald Alek , Apoznański Grzegorz , Kokurewicz Tomasz 
Published: January 2021

AbstractIn temperate regions, winter is characterized by cold temperatures and low food availability. Heterothermic animals can bridge this period by entering a state of torpor characterized by decreased body temperature and reduced metabolic rate. Hibernation site choice is crucial since temperature conditions in the hibernaculum will impact torpor. We analysed temperature-dependent hibernation site use of Barbastella barbastellus. Bats and temperature were monitored in an underground system (1999–2019) and standalone bunkers (2007–2019) in Western Poland. During the winter of 2017–2018 we analysed the thermal variability of the hibernacula. Seasonal variation is higher in bunkers and thus temperatures get colder in winter than in the underground system. On the other hand, short-term variability (thermal variability index) in the bunkers was lower than in the underground system. This makes bunkers a more stable environment to hibernate for cold dwelling bats in warm winters, when temperatures in the bunkers do not get below freezing. Bats use both the warm underground system and the colder bunkers. During the last decade, a continuous series of warm winters occurred and the population of barbastelle bats partly moved from the underground system to the bunkers. These present temperature increases broadened the range of potential hibernation sites for barbastelles. Our study indicates that long-term trends, seasonal variation and short-term variability in temperatures are all important and should be analysed to investigate hibernaculum use by bats. Our study shows that small hibernation sites may become more important in the future.
Antibiotic loaded β-tricalcium phosphate/calcium sulfate for antimicrobial potency, prevention and killing efficacy of Pseudomonas aeruginosa and Staphylococcus aureus biofilms
Authors: Jiang Nan , Dusane Devendra H. , Brooks Jacob R. , Delury Craig P. , Aiken Sean S. , Laycock Phillip A. , Stoodley Paul 
Published: January 2021

AbstractThis study investigated the efficacy of a biphasic synthetic β-tricalcium phosphate/calcium sulfate (β-TCP/CS) bone graft substitute for compatibility with vancomycin (V) in combination with tobramycin (T) or gentamicin (G) evidenced by the duration of potency and the prevention and killing efficacies of P. aeruginosa (PAO1) and S. aureus (SAP231) biofilms in in vitro assays. Antibiotic loaded β-TCP/CS beads were compared with antibiotic loaded beads formed from a well characterized synthetic calcium sulfate (CS) bone void filler. β-TCP/CS antibiotic loaded showed antimicrobial potency against PAO1 in a repeated Kirby-Bauer like zone of inhibition assay for 6 days compared to 8 days for CS. However, both bead types showed potency against SAP231 for 40 days. Both formulations loaded with V + T completely prevented biofilm formation (CFU below detection limits) for the 3 days of the experiment with daily fresh inoculum challenges (P < 0.001). In addition, both antibiotic loaded materials and antibiotic combinations significantly reduced the bioburden of pre-grown biofilms by between 3 and 5 logs (P < 0.001) with V + G performing slightly better against PAO1 than V + T. Our data, combined with previous data on osteogenesis suggest that antibiotic loaded β-TCP/CS may have potential to stimulate osteogenesis through acting as a scaffold as well as simultaneously protecting against biofilm infection. Future in vivo experiments and clinical investigations are warranted to more comprehensively evaluate the use of β-TCP/CS in the management of orthopaedic infections.
Large-scale variations in the dynamics of Amazon forest canopy gaps from airborne lidar data and opportunities for tree mortality estimates
Authors: Dalagnol Ricardo , Wagner Fabien H. , Galvão Lênio S. , Streher Annia S. , Phillips Oliver L. , Gloor Emanuel , Pugh Thomas A. M. , Ometto Jean P. H. B. , Aragão Luiz E. O. C. 
Published: January 2021

AbstractWe report large-scale estimates of Amazonian gap dynamics using a novel approach with large datasets of airborne light detection and ranging (lidar), including five multi-temporal and 610 single-date lidar datasets. Specifically, we (1) compared the fixed height and relative height methods for gap delineation and established a relationship between static and dynamic gaps (newly created gaps); (2) explored potential environmental/climate drivers explaining gap occurrence using generalized linear models; and (3) cross-related our findings to mortality estimates from 181 field plots. Our findings suggest that static gaps are significantly correlated to dynamic gaps and can inform about structural changes in the forest canopy. Moreover, the relative height outperformed the fixed height method for gap delineation. Well-defined and consistent spatial patterns of dynamic gaps were found over the Amazon, while also revealing the dynamics of areas never sampled in the field. The predominant pattern indicates 20–35% higher gap dynamics at the west and southeast than at the central-east and north. These estimates were notably consistent with field mortality patterns, but they showed 60% lower magnitude likely due to the predominant detection of the broken/uprooted mode of death. While topographic predictors did not explain gap occurrence, the water deficit, soil fertility, forest flooding and degradation were key drivers of gap variability at the regional scale. These findings highlight the importance of lidar in providing opportunities for large-scale gap dynamics and tree mortality monitoring over the Amazon.
The developmental trajectories of executive function from adolescence to old age
Authors: Ferguson Heather J. , Brunsdon Victoria E. A. , Bradford Elisabeth E. F. 
Published: January 2021

AbstractExecutive functions demonstrate variable developmental and aging profiles, with protracted development into early adulthood and declines in older age. However, relatively few studies have specifically included middle-aged adults in investigations of age-related differences in executive functions. This study explored the age-related differences in executive function from late childhood through to old age, allowing a more informed understanding of executive functions across the lifespan. Three hundred and fifty participants aged 10 to 86 years-old completed a battery of tasks assessing the specific roles of inhibitory control, working memory, cognitive flexibility, and planning. Results highlighted continued improvement in working memory capacity across adolescence and into young adulthood, followed by declines in both working memory and inhibitory control, beginning from as early as 30–40 years old and continuing into older age. Analyses of planning abilities showed continued improvement across adolescence and into young adulthood, followed by a decline in abilities across adulthood, with a small (positive) change in older age. Interestingly, a dissociation was found for cognitive flexibility; switch costs decreased, yet mixing costs increased across the lifespan. The results provide a description of the developmental differences in inhibitory control, working memory, cognitive flexibility and planning, above any effects of IQ or SES, and highlight the importance of including middle-aged adults in studies seeking to establish a more comprehensive picture of age-related differences in executive function.
Activation of proline biosynthesis is critical to maintain glutamate homeostasis during acute methamphetamine exposure
Authors: Jones Bobby , Balasubramaniam Muthukumar , Lebowitz Joseph J. , Taylor Anne , Villalta Fernando , Khoshbouei Habibeh , Grueter Carrie , Grueter Brad , Dash Chandravanu , Pandhare Jui 
Published: January 2021

AbstractMethamphetamine (METH) is a highly addictive psychostimulant that causes long-lasting effects in the brain and increases the risk of developing neurodegenerative diseases. The cellular and molecular effects of METH in the brain are functionally linked to alterations in glutamate levels. Despite the well-documented effects of METH on glutamate neurotransmission, the underlying mechanism by which METH alters glutamate levels is not clearly understood. In this study, we report an essential role of proline biosynthesis in maintaining METH-induced glutamate homeostasis. We observed that acute METH exposure resulted in the induction of proline biosynthetic enzymes in both undifferentiated and differentiated neuronal cells. Proline level was also increased in these cells after METH exposure. Surprisingly, METH treatment did not increase glutamate levels nor caused neuronal excitotoxicity. However, METH exposure resulted in a significant upregulation of pyrroline-5-carboxylate synthase (P5CS), the key enzyme that catalyzes synthesis of proline from glutamate. Interestingly, depletion of P5CS by CRISPR/Cas9 resulted in a significant increase in glutamate levels upon METH exposure. METH exposure also increased glutamate levels in P5CS-deficient proline-auxotropic cells. Conversely, restoration of P5CS expression in P5CS-deficient cells abrogated the effect of METH on glutamate levels. Consistent with these findings, P5CS expression was significantly enhanced in the cortical brain region of mice administered with METH and in the slices of cortical brain tissues treated with METH. Collectively, these results uncover a key role of P5CS for the molecular effects of METH and highlight that excess glutamate can be sequestered for proline biosynthesis as a protective mechanism to maintain glutamate homeostasis during drug exposure.
Inhibition of succinate dehydrogenase activity impairs human T cell activation and function
Authors: Nastasi Claudia , Willerlev-Olsen Andreas , Dalhoff Kristoffer , Ford Shayne L. , Gadsbøll Anne-Sofie Østergaard , Buus Terkild Brink , Gluud Maria , Danielsen Morten , Litman Thomas , Bonefeld Charlotte Mennè , Geisler Carsten , Ødum Niels , Woetmann Anders 
Published: January 2021

AbstractT cell activation is intimately linked to metabolism, as distinct metabolic requirements support the functional and phenotypical differences between quiescent and activated T cells. Metabolic transition from mitochondrial oxidative phosphorylation to aerobic glycolysis is crucial for a proper T cell activation. However, the role of tricarboxylic acid cycle (TCA), and in particular succinate dehydrogenase (SDH) in activated T cells needs further elucidation. Here we show that inhibition of SDH during activation of T cells results in strong impairment of proliferation, expression of activation markers, and production of key inflammatory cytokines, despite a concomitant increase in glycolytic metabolic activity. Similar effect of SDH inhibition were demonstrated in pre-activated T cell. Interestingly, itaconic acid, an endogenous SDH inhibitor released from activated macrophages and dendritic cells, had no immunomodulator effect. Taken together, our findings demonstrate that SDH enzyme fitness is critical for mounting and maintaining appropriate activation and function of human T cells.
Whole-exome sequencing identifies susceptibility genes and pathways for idiopathic pulmonary fibrosis in the Chinese population
Authors: Fang Chuling , Huang Hui , Feng Yujia , Zhang Qian , Wang Na , Jing Xiaoyan , Guo Jian , Ferianc Martin , Xu Zuojun 
Published: January 2021

AbstractGenetic factors play a role in the risk of idiopathic pulmonary fibrosis (IPF). Specifically, MUC5B rs35705950 non-risk alleles and immunologic aberrations were associated with the IPF’s progression. However, rare genetic variants have not been systematically investigated in Chinese IPF patients. In this study, we aimed to improve understanding of the genetic architecture of IPF in the Chinese population and to assess whether rare protein-coding variants in the immunity pathway genes are enriched in the IPF patients with non-risk alleles at rs35705950. A case–control exome-wide study including 110 IPF patients and 60 matched healthy controls was conducted. rs35705950 was genotyped by Sanger sequencing. To identify genes enriched in IPF, gene-based association analyses were performed. Identified genes were included for further pathway analyses using gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG). Associations between rs35705950 and genes enriched in the immunity pathway were also tested. 226 genes that were enriched with deleterious variants were identified in IPF patients. Out of them, 36 genes were significantly enriched in GO and KEGG pathways in the IPF. Pathway analyses implicated that these genes were involved in the immune response and cell adhesion. Rare protein-altering variants in genes related to the immunity pathway did not significantly differ between patients with a MUC5B risk allele and individuals without risk allele. We drafted a comprehensive mutational landscape of rare protein-coding variants in the Chinese IPF and identified genes related to immune response and cell adhesion. These results partially explain changes in gene expression involved in the immunity/inflammatory pathways in IPF patients.
Complexity of the eukaryotic dolichol-linked oligosaccharide scramblase suggested by activity correlation profiling mass spectrometry
Authors: Verchère Alice , Cowton Andrew , Jenni Aurelio , Rauch Monika , Häner Robert , Graumann Johannes , Bütikofer Peter , Menon Anant K. 
Published: January 2021

AbstractThe oligosaccharide required for asparagine (N)-linked glycosylation of proteins in the endoplasmic reticulum (ER) is donated by the glycolipid Glc3Man9GlcNAc2-PP-dolichol. Remarkably, whereas glycosylation occurs in the ER lumen, the initial steps of Glc3Man9GlcNAc2-PP-dolichol synthesis generate the lipid intermediate Man5GlcNAc2-PP-dolichol (M5-DLO) on the cytoplasmic side of the ER. Glycolipid assembly is completed only after M5-DLO is translocated to the luminal side. The membrane protein (M5-DLO scramblase) that mediates M5-DLO translocation across the ER membrane has not been identified, despite its importance for N-glycosylation. Building on our ability to recapitulate scramblase activity in proteoliposomes reconstituted with a crude mixture of ER membrane proteins, we developed a mass spectrometry-based 'activity correlation profiling' approach to identify scramblase candidates in the yeast Saccharomyces cerevisiae. Data curation prioritized six polytopic ER membrane proteins as scramblase candidates, but reconstitution-based assays and gene disruption in the protist Trypanosoma brucei revealed, unexpectedly, that none of these proteins is necessary for M5-DLO scramblase activity. Our results instead strongly suggest that M5-DLO scramblase activity is due to a protein, or protein complex, whose activity is regulated at the level of quaternary structure.