bluuebunny/crossref_metadata_2025 huggingface dataset:
Author Correction: Probing nanomechanical responses of cell membranes
Authors: Kim Jichul
Published: January 2021

An amendment to this paper has been published and can be accessed via a link at the top of the paper.
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

Pseudomonas 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

It 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

Prostate 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

The 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

In 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

This 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

We 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

Executive 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

Methamphetamine (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

T 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

Genetic 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

The 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.
Dissecting the interaction between HSP70 and vascular contraction: role of $$\hbox{Ca}^{2+}$$ handling mechanisms
Authors: de Oliveira Amanda A. , Priviero Fernanda , Tostes Rita C. , Webb R. Clinton , Nunes Kenia P.
Published: January 2021

Heat-shock protein 70 (HSP70) is a ubiquitously expressed molecular chaperone with various biological functions. Recently, we demonstrated that HSP70 is key for adequate vascular reactivity. However, the specific mechanisms targeted by HSP70 to assist in this process remain elusive. Since there is a wealth of evidence connecting HSP70 to calcium ($$\hbox {Ca}^{2+}$$

Ca

2
+

), a master regulator of contraction, we designed this study to investigate whether blockade of HSP70 disrupts vascular contraction via impairment of $${\text{Ca}}^{2+}$$

Ca

2
+

handling mechanisms. We performed functional studies in aortas isolated from male Sprague Dawley rats in the presence or absence of exogenous $$\hbox {Ca}^{2+}$$

Ca

2
+

, and we determined the effects of VER155008, an inhibitor of HSP70, on $$\hbox {Ca}^{2+}$$

Ca

2
+

handling as well as key mechanisms that regulate vascular contraction. Changes in the intracellular concentration of $$\hbox {Ca}^{2+}$$

Ca

2
+

were measured with a biochemical assay kit. We report that blockade of HSP70 leads to $$\hbox {Ca}^{2+}$$

Ca

2
+

mishandling in aorta stimulated with phenylephrine, decreasing both phasic and tonic contractions. Importantly, in $$\hbox {Ca}^{2+}$$

Ca

2
+

free Krebs’ solution, inhibition of HSP70 only reduced the $$\hbox {E}_{\mathrm{max}}$$

E
max

of the phasic contraction if the protein was blocked before IP3r-mediated $$\hbox {Ca}^{2+}$$

Ca

2
+

release, suggesting that HSP70 has a positive effect towards this receptor. Corroborating this statement, VER155008 did not potentiate an IP3r inhibitor’s outcomes, even with partial blockade. In another set of experiments, the inhibition of HSP70 attenuated the amplitude of the tonic contraction independently of the moment VER155008 was added to the chamber (i.e., whether it was before or after IP3r-mediated phasic contraction). More compelling, following re-addition of $$\hbox {Ca}^{2+}$$

Ca

2
+

, VER155008 amplified the inhibitory effects of a voltage-dependent $$\hbox {Ca}^{2+}$$

Ca

2
+

channel blocker, but not of a voltage-independent $$\hbox {Ca}^{2+}$$

Ca

2
+

channel inhibitor, indicating that HSP70 has a positive impact on the latter. Lastly, the mechanism by which HSP70 modulates vascular contraction does not involve the $$\hbox {Ca}^{2+}$$

Ca

2
+

sensitizer protein, Rho-kinase, nor the SERCA pump, as blockade of these proteins in the presence of VER155008 almost abolished contraction. In summary, our findings shed light on the processes targeted by HSP70 during vascular contraction and open research avenues for potential new mechanisms in vascular diseases.
The impact of delayed surgical intervention following high velocity maxillofacial injuries
Authors: Oren Daniel , Dror Amiel A. , Zoabi Adeeb , Kasem Adi , Tzadok Lior , Kablan Fares , Morozov Nicole G. , Safory Enssaf , Sela Eyal , Srouji Samer
Published: January 2021

Our study compares the number of postoperative complications of Syrian patients admitted to the Galilee Medical Center (GMC) over a 5-year period (May 2013–May 2018) for treatment after initial high-velocity maxillofacial injuries sustained during the Syrian civil war. Specifically, we evaluated complication rates of patients arriving “early,” within 24 h, to the GMC versus those who arrived “late,” or 14–28 days following high-velocity maxillofacial injuries. Both groups of patients received definitive surgical treatment within 48 h of admission to our hospital with a total of 60 patients included in this study. The mean age was 26 ± 8 years (range: 9–50) and all except one were male. Postoperative complications in the early group were found to be significantly higher compared to the delayed arrival group (p = 0.006). We found that unintentionally delayed treatment may have contributed to a critical revascularization period resulting in improved healing and decreased postoperative morbidity and complications. We discuss potential mechanisms for complication rate variations, including critical vascularization periods. Our study may add to a growing body of work demonstrating the potential benefit of delayed surgical treatment for high-velocity maxillofacial injuries.
A novel CO2 utilization technology for the synergistic co-production of multi-walled carbon nanotubes and syngas
Authors: Challiwala Mohamed S. , Choudhury Hanif A. , Wang Dingdi , El-Halwagi Mahmoud M. , Weitz Eric , Elbashir Nimir O.
Published: January 2021

Dry reforming of methane (DRM) is a well-known process in which CH4 and CO2 catalytically react to produce syngas. Solid carbon is a well-known byproduct of the DRM but is undesirable as it leads to catalyst deactivation. However, converting CO2 and CH4 into solid carbon serves as a promising carbon capture and sequestration technique that has been demonstrated in this study by two patented processes. In the first process, known as CARGEN technology (CARbon GENerator), a novel concept of two reactors in series is developed that separately convert the greenhouse gases (GHGs) into multi-walled carbon nanotubes (MWCNTs) and syngas. CARGEN enables at least a 50% reduction in energy requirement with at least 65% CO2 conversion compared to the DRM process. The second process presents an alternative pathway for the regeneration/reactivation of the spent DRM/CARGEN catalyst using CO2. Provided herein is the first report on an experimental demonstration of a 'switching' technology in which CO2 is utilized in both the operation and the regeneration cycles and thus, finally contributing to the overall goal of CO2 fixation. The following studies support all the results in this work: physisorption, chemisorption, XRD, XPS, SEM, TEM, TGA, ICP, and Raman analysis.
Classification of malignant tumours in breast ultrasound using unsupervised machine learning approaches
Authors: Shia Wei-Chung , Lin Li-Sheng , Chen Dar-Ren
Published: January 2021

Traditional computer-aided diagnosis (CAD) processes include feature extraction, selection, and classification. Effective feature extraction in CAD is important in improving the classification’s performance. We introduce a machine-learning method and have designed an analysis procedure of benign and malignant breast tumour classification in ultrasound (US) images without a need for a priori tumour region-selection processing, thereby decreasing clinical diagnosis efforts while maintaining high classification performance. Our dataset constituted 677 US images (benign: 312, malignant: 365). Regarding two-dimensional US images, the oriented gradient descriptors’ histogram pyramid was extracted and utilised to obtain feature vectors. The correlation-based feature selection method was used to evaluate and select significant feature sets for further classification. Sequential minimal optimisation—combining local weight learning—was utilised for classification and performance enhancement. The image dataset’s classification performance showed an 81.64% sensitivity and 87.76% specificity for malignant images (area under the curve = 0.847). The positive and negative predictive values were 84.1 and 85.8%, respectively. Here, a new workflow, utilising machine learning to recognise malignant US images was proposed. Comparison of physician diagnoses and the automatic classifications made using machine learning yielded similar outcomes. This indicates the potential applicability of machine learning in clinical diagnoses.
Estimation of stride-by-stride spatial gait parameters using inertial measurement unit attached to the shank with inverted pendulum model
Authors: Mao Yufeng , Ogata Taiki , Ora Hiroki , Tanaka Naoto , Miyake Yoshihiro
Published: January 2021

Inertial measurement unit (IMU)-based gait analysis systems have become popular in clinical environments because of their low cost and quantitative measurement capability. When a shank is selected as the IMU mounting position, an inverted pendulum model (IPM) can accurately estimate its spatial gait parameters. However, the stride-by-stride estimation of gait parameters using one IMU on each shank and the IPMs has not been validated. This study validated a spatial gait parameter estimation method using a shank-based IMU system. Spatial parameters were estimated via the double integration of the linear acceleration transformed by the IMU orientation information. To reduce the integral drift error, an IPM, applied with a linear error model, was introduced at the mid-stance to estimate the update velocity. the gait data of 16 healthy participants that walked normally and slowly were used. The results were validated by comparison with those extracted from an optical motion-capture system; the results showed strong correlation ($$r>0.9$$

r
>
0.9

) and good agreement with the gait metrics (stride length, stride velocity, and shank vertical displacement). In addition, the biases of the stride length and stride velocity extracted using the motion capture system were smaller in the IPM than those in the previous method using the zero-velocity-update. The error variabilities of the gait metrics were smaller in the IPM than those in the previous method. These results indicated that the reconstructed shank trajectory achieved a greater accuracy and precision than that of previous methods. This was attributed to the IPM, which demonstrates that shank-based IMU systems with IPMs can accurately reflect many spatial gait parameters including stride velocity.
ExoFiT trial at the Atacama Desert (Chile): Raman detection of biomarkers by representative prototypes of the ExoMars/Raman Laser Spectrometer
Authors: Veneranda Marco , Lopez-Reyes Guillermo , Saiz Jesus , Manrique-Martinez Jose Antonio , Sanz-Arranz Aurelio , Medina Jesús , Moral Andoni , Seoane Laura , Ibarmia Sergio , Rull Fernando
Published: January 2021

In this work, the analytical research performed by the Raman Laser Spectrometer (RLS) team during the ExoFiT trial is presented. During this test, an emulator of the Rosalind Franklin rover was remotely operated at the Atacama Desert in a Mars-like sequence of scientific operations that ended with the collection and the analysis of two drilled cores. The in-situ Raman characterization of the samples was performed through a portable technology demonstrator of RLS (RAD1 system). The results were later complemented in the laboratory using a bench top RLS operation simulator and a X-Ray diffractometer (XRD). By simulating the operational and analytical constraints of the ExoMars mission, the two RLS representative instruments effectively disclosed the mineralogical composition of the drilled cores (k-feldspar, plagioclase, quartz, muscovite and rutile as main components), reaching the detection of minor phases (e.g., additional phyllosilicate and calcite) whose concentration was below the detection limit of XRD. Furthermore, Raman systems detected many organic functional groups (–C≡N, –NH2 and C–(NO2)), suggesting the presence of nitrogen-fixing microorganisms in the samples. The Raman detection of organic material in the subsurface of a Martian analogue site presenting representative environmental conditions (high UV radiation, extreme aridity), supports the idea that the RLS could play a key role in the fulfilment of the ExoMars main mission objective: to search for signs of life on Mars.
The nationwide retrospective cohort study by Health Insurance Review and Assessment Service proves that asthma management decreases the exacerbation risk of asthma
Authors: Kim Nam-Eun , Lee Sanghun , Kim Bo Yeon , Hwang Ae Gi , Shin Ji Hyeon , Yang Hyeon-Jong , Won Sungho
Published: January 2021

Medical costs have recently increased in South Korea due to the rising rate of asthma. Primary clinics serve an important role in asthma management, as they are the first stop for patients presenting with symptoms. The Health Insurance Review and Assessment Service (HIRA) in South Korea has assessed asthma-management quality since 2013, but studies are lacking on whether these assessments have been performed properly and contribute toward reducing asthma exacerbations. Therefore, we investigated whether the HIRA’s quality assessments have decreased asthma exacerbations using national health insurance claims data from 2013 to 2017 of 83,375 primary-clinic and 15,931 tertiary-hospital patients with asthma. These patients were classified into four groups based on disease severity according to the monthly prescribed amount of asthma medication using K-means clustering. The associations between HIRA assessments and asthma exacerbation were analyzed using a generalized estimating equation. Our results showed that exacerbation odds gradually decreased as the HIRA assessments progressed, especially in the mild-severity group, and that exacerbation risk among patients with asthma decreased in the order of assessment grades: “Unsatisfactory,” “Satisfactory,” and “Tertiary.” Therefore, we may conclude that asthma exacerbations may decrease with high quality asthma management; appropriate quality assessment could be helpful in reducing asthma exacerbations.
Profiling Mannheimia haemolytica infection in dairy calves using near infrared spectroscopy (NIRS) and multivariate analysis (MVA)
Authors: Santos-Rivera Mariana , Woolums Amelia , Thoresen Merrilee , Blair Ellianna , Jefferson Victoria , Meyer Florencia , Vance Carrie K.
Published: January 2021

Bovine respiratory disease (BRD) linked with Mannheimia haemolytica is the principal cause of pneumonia in cattle. Diagnosis of BRD traditionally relies on visual assessment, which can be untimely, insensitive, and nonspecific leading to inadequate treatment and further spread of disease. Near Infrared Spectroscopy (NIRS) is a rapid acquisition vibrational spectroscopy that can profile changes in biofluids, and when used in combination with multivariate analysis, has potential for disease diagnosis. This study characterizes the NIR spectral profile of blood plasma from dairy calves infected with M. haemolytica and validates the spectral biochemistry using standardized clinical and hematological reference parameters. Blood samples were collected for four days prior to (baseline), and 23 days after, a controlled intrabronchial challenge. NIR spectral profiles of blood plasma discriminated and predicted Baseline and Infected states of animal disease progression with accuracy, sensitivity, and specificity ≥ 90% using PCA–LDA models. These results show that physiological and biochemical changes occurring in the bloodstream of dairy calves during M. haemolytica infection are reflected in the NIR spectral profiles, demonstrating the potential of NIRS as a diagnostic and monitoring tool of BRD over time.
Integrating Narcissus-derived galanthamine production into traditional upland farming systems
Authors: Fraser M. D. , Vallin H. E. , Davies J. R. T. , Rowlands G. E. , Chang X.
Published: January 2021

Alzheimer’s disease (AD) is a disorder associated with progressive degeneration of memory and cognitive function. Galantamine is a licenced treatment for AD but supplies of the plant alkaloid that it is produced from, galanthamine, are limited. This three-year system study tested the potential to combineNarcissus-derived galanthamine production with grassland-based ruminant production. Replicate plots of permanent pasture were prepared with and without bulbs ofNarcissus pseudonarcissussown as lines into the sward. Two different fertiliser regimes were imposed. The above-ground green biomass ofN. pseudonarcissuswas harvested in early spring and the galanthamine yield determined. In the second harvest year a split-plot design was implemented with lines ofN. pseudonarcissuscut annually and biennially. All plots were subsequently grazed by ewes and lambs and animal performance recorded. Incorporation ofN. pseudonarcissusinto grazed permanent pasture had no detrimental effects on the health or performance of the sheep which subsequently grazed the pasture. There was no consistency to the effects of fertiliser rates on galanthamine yields. There was no difference in overall galanthamine yield ifN. pseudonarcissuswas cut biennially (1.64 vs. 1.75 kg galanthamine/ha for annual combined vs biennial cuts respectively; s.e.d = 0.117 kg galanthamine/ha; ns). This study verified the feasibility of a dual cropping approach to producing plant-derived galanthamine.
Microstructure and pore structure of polymer-cement composite joint sealants
Authors: Lou Chuanxin , Xu Jinyu , Wang Tengjiao , Ren Weibo
Published: January 2021

Utilizing methods such as scanning electron microscopy observation and mercury intrusion porosimetry, this paper investigates the basic microstructure and pore structure properties of polymer-cement composite joint sealants for pavements, and analyzes the effects and rules of various material types, ratio parameters and processing conditions. Further, the fractal characteristics and variation rules of pore size distribution are investigated for the joint sealants by introducing the fractal theory. The results show that changes in material type, ratio parameter and processing condition produce insignificant effects on the basic microstructure properties and configuration of joint sealants, with effects reflected primarily in the change of sealant pore structure. Measures like increasing the powder-liquid ratio and cement ratio, blending with sulphoaluminate cement or mica powder, adding latex powder or coupling agent, cold drawing and hot pressing, as well as ultraviolet irradiation treatment are all capable of reducing the total pore volume of joint sealants and refining their pore structure. In contrast, opposite effects are yielded when low-grade cement is used, styrene-acrylic emulsion is blended, or plasticizer is added. Additionally, after blending with talc powder or adding carbon fiber additive, the total pore volume of joint sealants remains basically unchanged or reduced, despite the coarsened pore structure. The total pore volume of joint sealants increases after wet–dry cycling treatment, while no obvious change in the pore size distribution is observed. Pore size distribution of the studied joint sealants presents distinct fractal characteristics, and the corresponding fractal dimension of pore surface area ranges between 2.6 and 2.8.
Action potentials induce biomagnetic fields in carnivorous Venus flytrap plants
Authors: Fabricant Anne , Iwata Geoffrey Z. , Scherzer Sönke , Bougas Lykourgos , Rolfs Katharina , Jodko-Władzińska Anna , Voigt Jens , Hedrich Rainer , Budker Dmitry
Published: January 2021

Upon stimulation, plants elicit electrical signals that can travel within a cellular network analogous to the animal nervous system. It is well-known that in the human brain, voltage changes in certain regions result from concerted electrical activity which, in the form of action potentials (APs), travels within nerve-cell arrays. Electro- and magnetophysiological techniques like electroencephalography, magnetoencephalography, and magnetic resonance imaging are used to record this activity and to diagnose disorders. Here we demonstrate that APs in a multicellular plant system produce measurable magnetic fields. Using atomic optically pumped magnetometers, biomagnetism associated with electrical activity in the carnivorous Venus flytrap, Dionaea muscipula, was recorded. Action potentials were induced by heat stimulation and detected both electrically and magnetically. Furthermore, the thermal properties of ion channels underlying the AP were studied. Beyond proof of principle, our findings pave the way to understanding the molecular basis of biomagnetism in living plants. In the future, magnetometry may be used to study long-distance electrical signaling in a variety of plant species, and to develop noninvasive diagnostics of plant stress and disease.
Freestanding bilayer plasmonic waveguide coupling mechanism for ultranarrow electromagnetic-induced transparency band generation
Authors: Yu Li , Liang Yuzhang , Chu Shuwen , Gao Huixuan , Wang Qiao , Peng Wei
Published: January 2021

Strong electromagnetic coupling among plasmonic nanostructures paves a new route toward efficient manipulation of photons. Particularly, plasmon-waveguide systems exhibit remarkable optical properties by simply tailoring the interaction among elementary elements. In this paper, we propose and demonstrate a freestanding bilayer plasmonic-waveguide structure exhibiting an extremely narrow transmission peak with efficiency up to 92%, the linewidth of only 0.14 nm and an excellent out of band rejection. The unexpected optical behavior considering metal loss is consistent with that of electromagnetic induced transparency, arising from the destructive interference of super-radiative nanowire dipolar mode and transversal magnetic waveguide mode. Furthermore, for slow light application, the designed plasmonic-waveguide structure has a high group index of approximately 1.2 × 105 at the maximum of the transmission band. In sensing application, its lowest sensing figure of merit is achieved up to 8500 due to the ultra-narrow linewidth of the transmission band. This work provides a valuable photonics design for developing high performance nano-photonic devices.
A retrospective study of internal small bowel herniation following pelvic lymphadenectomy for gynecologic carcinomas
Authors: Tanaka Yuji , Shimizu Yusuke , Ikki Ai , Okamoto Kota , Fusegi Atsushi , Nakabayashi Makoto , Omi Makiko , Kurita Tomoko , Tanigawa Terumi , Aoki Yoichi , Netsu Sachiho , Yunokawa Mayu , Nomura Hidetaka , Matoda Maki , Okamoto Sanshiro , Omatsu Kohei , Kanao Hiroyuki
Published: January 2021

After pelvic lymphadenectomy (PLA), pelvic vessels, nerve, and ureter are skeletonized. Internal hernias beneath the skeletonized pelvic structure following pelvic lymphadenectomy (IBSPP) are a rare complication following PLA. To the best of our knowledge, only 12 IBSPP cases have been reported and clinical details on such hernias remain unknown.
The aim of the study was to investigate the incident and etiology of IBSPP. 1313 patients who underwent open or laparoscopic pelvic lymphadenectomy were identified from our database. A retrospective review was performed. Mean follow-up period was 33.9 months. A total of 12 patients had IBSPP. Multivariate analysis of laparoscopic surgeries group as compared to open surgeries group, para-aortic lymphadenectomy rate, number of dissected lymph nodes by PLA, antiadhesive material use rate, and blood loss were lower in laparoscopic surgeries group: odd ratio (OR) = 0.13 [95% confidence interval (CI) 0.08–0.19], and OR = 0.70 [95% CI 0.50–0.99], OR = 0.17 [95% CI 0.10–0.28], OR = 0.93 [95% CI 0.92–0.94]. However, no significant difference was observed in the incidence of IBSPP between laparoscopic surgery (1.0%) and open surgery (0.8%). All IBSPP occurred in the right pelvic space. These findings may contribute to the development of prevention methods for this disease.
Androgen receptor and its splice variant, AR-V7, differentially induce mRNA splicing in prostate cancer cells
Authors: Rana Manjul , Dong Jianrong , Robertson Matthew J. , Basil Paul , Coarfa Cristian , Weigel Nancy L.
Published: January 2021

Prostate cancer (PCa) is dependent on the androgen receptor (AR). Advanced PCa is treated with an androgen deprivation therapy-based regimen; tumors develop resistance, although they typically remain AR-dependent. Expression of constitutively active AR variants lacking the ligand-binding domain including the variant AR-V7 contributes to this resistance. AR and AR-V7, as transcription factors, regulate many of the same genes, but also have unique activities. In this study, the capacity of the two AR isoforms to regulate splicing was examined. RNA-seq data from models that endogenously express AR and express AR-V7 in response to doxycycline were used. Both AR isoforms induced multiple changes in splicing and many changes were isoform-specific. Analyses of two endogenous genes, PGAP2 and TPD52, were performed to examine differential splicing. A novel exon that appears to be a novel transcription start site was preferentially induced by AR-V7 in PGAP2 although it is induced to a lesser extent by AR. The previously described AR induced promoter 2 usage that results in a novel protein derived from TPD52 (PrLZ) was not induced by AR-V7. AR, but not AR-V7, bound to a site proximal to promoter 2, and induction was found to depend on FOXA1.
Anthropogenic warming and intraseasonal summer monsoon variability amplify the risk of future flash droughts in India
Authors: Mishra Vimal , Aadhar Saran , Mahto Shanti Shwarup
Published: January 2021

Flash droughts cause rapid depletion in root-zone soil moisture and severely affect crop health and irrigation water demands. However, their occurrence and impacts in the current and future climate in India remain unknown. Here we use observations and model simulations from the large ensemble of Community Earth System Model to quantify the risk of flash droughts in India. Root-zone soil moisture simulations conducted using Variable Infiltration Capacity model show that flash droughts predominantly occur during the summer monsoon season (June–September) and driven by the intraseasonal variability of monsoon rainfall. Positive temperature anomalies during the monsoon break rapidly deplete soil moisture, which is further exacerbated by the land-atmospheric feedback. The worst flash drought in the observed (1951–2016) climate occurred in 1979, affecting more than 40% of the country. The frequency of concurrent hot and dry extremes is projected to rise by about five-fold, causing approximately seven-fold increase in flash droughts like 1979 by the end of the 21st century. The increased risk of flash droughts in the future is attributed to intraseasonal variability of the summer monsoon rainfall and anthropogenic warming, which can have deleterious implications for crop production, irrigation demands, and groundwater abstraction in India.