bluuebunny/crossref_metadata_2025 huggingface dataset:
LncRNA MALAT1 regulates inflammatory cytokine production in lipopolysaccharide‐stimulated human gingival fibroblasts through sponging miR‐20a and activating TLR4 pathway
Authors: Li Jiashan , Wang Minwei , Song Liting , Wang Xiangpu , Lai Wen , Jiang Shaoyun
Published: September 2019

Background and Objective

It has been reported that long non‐coding RNAs (lncRNAs), such as metastasis‐associated lung adenocarcinoma transcript 1 (MALAT1), act as key regulators of the development of inflammatory diseases. However, it is unclear whether MALAT1 regulates the function of human gingival fibroblasts (HGFs) in periodontitis. This study is to explore the role of MALAT1 on inflammatory cytokine production of HGFs.

Material and Methods

Primary HGFs were harvested from human gingiva. MALAT1 was detected in inflammatory and healthy gingival tissues via quantitative real‐time PCR (qRT‐PCR). Bioinformatics analysis, dual‐luciferase reporter assay, and RNA‐binding protein immunoprecipitation (RIP) were used to detect the relationship among MALAT1, toll‐like receptor 4 (TLR4), and microRNA (miR) ‐20a. After transfection LPS‐treated HGFs with MALAT1 siRNA (si‐MALAT1), miR‐20a mimic or overexpression MALAT1 plasmid (sno‐MALAT1), the levels of MALAT1, miR‐20a, TLR4, IL‐6 and IL‐8 were analyzed by qRT‐PCR, enzyme‐linked immunosorbent assay, or western blot assay.

Results

MALAT1 up‐regulated in inflammatory gingival tissues of chronic periodontitis. MiR‐20a was bound with MALAT1 and TLR4 3′‐UTR in RNA‐protein complex with Ago2, respectively. Moreover, MALAT1, TLR4, IL‐6, and IL‐8 increased while miR‐20a decreased after 1 μg/mL Porphyromonas gingivalis lipopolysaccharide (LPS) or Escherichia coli LPS stimulation. MiR‐20a inhibited the expression of proinflammatory cytokines via binding to TLR4 3′‐UTR. In addition, MALAT1 increased TLR4 level and the secretion of inflammatory cytokines.

Conclusion

MALAT1 enhances inflammatory cytokine production through sponging miR‐20a and releasing TLR4, indicating a regulatory role of MALAT1 in periodontal inflammation.
Using machine learning to understand neuromorphological change and image‐based biomarker identification in Cavalier King Charles Spaniels with Chiari‐like malformation‐associated pain and syringomyelia
Authors: Spiteri Michaela , Knowler Susan P. , Rusbridge Clare , Wells Kevin
Published: September 2019

Background

Chiari‐like malformation (CM) is a complex malformation of the skull and cranial cervical vertebrae that potentially results in pain and secondary syringomyelia (SM). Chiari‐like malformation‐associated pain (CM‐P) can be challenging to diagnose. We propose a machine learning approach to characterize morphological changes in dogs that may or may not be apparent to human observers. This data‐driven approach can remove potential bias (or blindness) that may be produced by a hypothesis‐driven expert observer approach.

Hypothesis/Objectives

To understand neuromorphological change and to identify image‐based biomarkers in dogs with CM‐P and symptomatic SM (SM‐S) using a novel machine learning approach, with the aim of increasing the understanding of these disorders.

Animals

Thirty‐two client‐owned Cavalier King Charles Spaniels (CKCSs; 11 controls, 10 CM‐P, 11 SM‐S).

Methods

Retrospective study using T2‐weighted midsagittal Digital Imaging and Communications in Medicine (DICOM) anonymized images, which then were mapped to images of an average clinically normal CKCS reference using Demons image registration. Key deformation features were automatically selected from the resulting deformation maps. A kernelized support vector machine was used for classifying characteristic localized changes in morphology.

Results

Candidate biomarkers were identified with receiver operating characteristic curves with area under the curve (AUC) of 0.78 (sensitivity 82%; specificity 69%) for the CM‐P biomarkers collectively and an AUC of 0.82 (sensitivity, 93%; specificity, 67%) for the SM‐S biomarkers, collectively.

Conclusions and clinical importance

Machine learning techniques can assist CM/SM diagnosis and facilitate understanding of abnormal morphology location with the potential to be applied to a variety of breeds and conformational diseases.
Genetic alterations of KIT during clonal expansion and subsequent acquisition of resistance to toceranib in a canine mast cell tumor cell line
Authors: Kurita Sena , Miyamoto Ryo , Tani Hiroyuki , Kobayashi Masato , Sasaki Takashi , Tamura Kyoichi , Bonkobara Makoto
Published: September 2019

One of the potential mechanisms underlying acquired resistance to toceranib in canine mast cell tumor (MCT) is the emergence of a secondary mutation in the KIT gene. Here, genetic alterations of KIT during clonal expansion and subsequent acquisition of resistance to toceranib were investigated in the toceranib‐susceptible canine MCT cell line VI‐MC, which carries a KIT‐activating mutation resulting in a predicted p.(Asn508Ile) amino acid change in the receptor tyrosine kinase protein KIT. Two sublines were cloned from VI‐MC and toceranib‐resistant sublines then were established by continuous exposure to toceranib. The mutation status of KIT in parental VI‐MC and its sublines was investigated using next‐generation sequencing (NGS). Additionally, effects of secondary mutations on toceranib sensitivity in p.(Asn508Ile)‐mutant KIT were examined. KIT secondary mutations, including those encoding p.(Asn679Lys)‐, p.(Asp819Val)‐, and p.(Asp819Gly)‐mutant KIT, that confer toceranib insensitivity to p.(Asn508Ile)‐mutant KIT emerged only in toceranib‐resistant VI‐MCs. These mutations were not detected by NGS in the parental VI‐MC line or in the toceranib‐naive cloned VI‐MCs, although the parental line and sublines exhibited genetic heterogeneity in KIT that may have been caused by genetic evolution during clonal expansion. VI‐MC clones with these secondary mutations in KIT appear to have arisen from subclones during treatment with toceranib rather than being pre‐existing. However, further study using a higher resolution technique will be needed to confirm the developmental mechanism of KIT secondary mutation in canine MCT cells with acquired resistance to toceranib.
Structure and function of lipid A–modifying enzymes
Authors: Anandan Anandhi , Vrielink Alice
Published: September 2019

Lipopolysaccharides are complex molecules found in the cell envelop of many Gram‐negative bacteria. The toxic activity of these molecules has led to the terminology of endotoxins. They provide bacteria with structural integrity and protection from external environmental conditions, and they interact with host signaling receptors to induce host immune responses. Bacteria have evolved enzymes that act to modify lipopolysaccharides, particularly the lipid A region of the molecule, to enable the circumvention of host immune system responses. These modifications include changes to lipopolysaccharide by the addition of positively charged sugars, such as N‐Ara4N, and phosphoethanolamine (pEtN). Other modifications include hydroxylation, acylation, and deacylation of fatty acyl chains. We review the two‐component regulatory mechanisms for enzymes that carry out these modifications and provide details of the structures of four enzymes (PagP, PagL, pEtN transferases, and ArnT) that modify the lipid A portion of lipopolysaccharides. We focus largely on the three‐dimensional structures of these enzymes, which provide an understanding of how their substrate binding and catalytic activities are mediated. A structure–function–based understanding of these enzymes provides a platform for the development of novel therapeutics to treat antibiotic resistance.
On higher direct images of convergent isocrystals
Authors: Xu Daxin
Published: September 2019

Let $k$ be a perfect field of characteristic $p>0$ and let $\operatorname{W}$ be the ring of Witt vectors of $k$. In this article, we give a new proof of the Frobenius descent for convergent isocrystals on a variety over $k$ relative to $\operatorname{W}$. This proof allows us to deduce an analogue of the de Rham complexes comparison theorem of Berthelot [$\mathscr{D}$-modules arithmétiques. II. Descente par Frobenius, Mém. Soc. Math. Fr. (N.S.) 81 (2000)] without assuming a lifting of the Frobenius morphism. As an application, we prove a version of Berthelot’s conjecture on the preservation of convergent isocrystals under the higher direct image by a smooth proper morphism of $k$-varieties.
Identification of key microRNAs and genes associated with abdominal aortic aneurysm based on the gene expression profile
Authors: Yang Pu , Cai Zhou , Wu Kai , Hu Yu , Liu Ling , Liao Mingmei
Published: September 2019

New Findings

What is the central question of this study?

The aim was to identify abdominal aortic aneurysm (AAA)‐associated microRNAs and their target genes in AAA using microarray analysis.

What is the main finding and its importance?

The main finding was that miR‐145 and miR‐30c‐2* were found to be downregulated microRNAs in AAA, which could exert suppressive effects on AAA progression, and that miR‐145 might target RAC2, whereas miR‐30c‐2* might target PIK3CD, IL1B and RAC2. The findings obtained from the study provide an enhanced understanding of microRNA as a therapeutic target to limit AAA.

The aim of the study was to identify abdominal aortic aneurysm (AAA)‐associated microRNAs (miRNAs) and genes potentially contributing to AAA. Differential analysis was performed to screen out differentially expressed genes (DEGs) and miRNAs in expression datasets of AAA‐related miRNAs [GSE51226 (mouse)] and genes [GSE51227 (mouse) and GSE7084 (human)]. Then, gene ontology (GO) enrichment analysis of DEGs was compared with aneurysm‐related GO to screen out DEGs related to the disease. The target genes of differential miRNAs were predicted and used to construct a miRNA–DEG regulatory network, followed by Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis of target genes. Moreover, the protein–protein interaction network of target genes of miRNAs in the core position (hub‐miRNA) with AAA‐related genes was constructed to screen out hub genes. Finally, the target relationship between hub‐miRNAs and their target genes was verified. There were 20 upregulated miRNAs and 20 downregulated miRNAs in AAA screened from the GSE51226 dataset (mouse). In addition, there were 1154 upregulated genes and 821 downregulated genes in the GSE51227 dataset (mouse), of which 246 DEGs were enriched in aneurysm‐related GO entries in AAA. miR‐145 and miR‐30c‐2* were the key miRNAs of AAA, both of which were downregulated in AAA and influenced pathways so as to affect AAA by regulating their respective target genes. The disease‐related gene ACTA2 was downregulated, whereas DEGs including PIK3CD, IL1B, RAC2 and SELL were upregulated in AAA. Finally, it was proved that miR‐145 targeted RAC2 and SELL, whereas miR‐30c‐2* targeted PIK3CD, IL1B and RAC2. Taken together, miR‐145 and miR‐30c‐2*, downregulated in AAA, could potentially affect AAA, and miR‐145 might target RAC2, whereas miR‐30c‐2* might target PIK3CD, IL1B and RAC2.
Highly Active Electrode With Efficiently Added Surface Oxygen Groups for a Vanadium Redox Flow Battery
Authors: Ishitobi Hirokazu , Sugawara Satoshi , Oba Kosuke , Hirano Takumi , Doki Honoka , Handa Yusuke , Sato Yuma , Yamamoto Shunya , Nakagawa Nobuyoshi
Published: September 2019

Higher power output by a lower kinetic resistance of the vanadium redox flow battery is needed for its commercialization. In this study, we focused on the air oxidation conditions of carbon paper, which is the electrode material, to reduce the kinetic resistance. The air oxidation is considered to affect the number of surface oxygen groups such as the phenol-type hydroxyl group due to oxidation of the carbon fiber. The surface oxygen groups may correspond to the active sites for the charge/discharge reaction. We quantitatively evaluated the number of surface oxygen groups by temperature-programmed desorption. In addition, we measured the double-layer capacitances of the carbon papers, which may reflect the surface area of the carbon fiber. The single-cell performances, i.e., current–voltage curves and charge–discharge profile, of the electrodes were studied. The air oxidized carbon paper, heat-treated at 500 °C for 3 h (8.4% mass decrease from the pristine sample), showed the highest power density (960 mW cm−2) in this study with thin electrode material (ca., 0.2 mm for one sheet). The negative half-reaction was enhanced by air oxidation. This result could be explained by the reduction of the kinetic resistance by increasing the number of phenol groups, and this power output was relatively high as the vanadium redox flow battery by using a commercial carbon paper and the standard flow field.
Peak selection matters in principal component analysis: A case study of syntrophic microbes
Authors: Yang Cuiyun , Wei Wenchao , Liu Fanghua , Yu Xiao-Ying
Published: September 2019

In situ liquid time-of-flight secondary ion mass spectrometry (ToF-SIMS) is a powerful technique to study surface characterization of living biofilms in hydrated conditions. However, ToF-SIMS data analysis is still a great challenge in complicated bacterial biofilms, because many interference peaks from the medium may result in inaccurate interpretation. In this study, two syntrophic Geobacter populations are investigated using in situ liquid ToF-SIMS to reveal the biofilm surface changes between them due to direct interspecies electron transfer. By comparing spectral principal component analysis (PCA) results of all peaks and selected peaks, the authors find that spectral peak overlay is an effective strategy to reduce the matrix effect in handling complex ToF-SIMS data. Additionally, the spectral PCA results of high intensity and high resolution data obtained from liquid ToF-SIMS are compared. Selected peaks, amino acid peaks, and water cluster peaks spectral PCA produce nice separation among samples in both high intensity and high resolution data sets. However, the high resolution data show better separation between coculture planktonic and coculture aggregates, confirming that the higher mass accuracy is useful in the analysis of microbial samples. In conclusion, the results show that peak selection is critical for acquiring effective microbial information and interpretation of syntrophic Geobacter using spectral data from in situ liquid ToF-SIMS.
Acoustic recordings of rough-toothed dolphin (Steno bredanensis) offshore Eastern Sicily (Mediterranean Sea)
Authors: Caruso Francesco , Sciacca Virginia , Parisi Ignazio , Viola Salvatore , de Vincenzi Giovanni , Bocconcelli Alessandro , Mooney T. Aran , Sayigh Laela , Li Songhai , Filiciotto Francesco , Moulins Aurelie , Tepsich Paola , Rosso Massimiliano
Published: September 2019

Rough-toothed dolphin's abundance and distribution is largely unknown worldwide and evaluation of its conservation status in the Mediterranean Sea is necessary. A rough-toothed dolphin was sighted offshore Eastern Sicily (Mediterranean Sea) in July 2017 and acoustic data were acquired in the same area of Watkins, Tyack, Moore, and Notarbartolo di Sciara [(1987). Mar. Mamm. Sci. 3, 78–82]. An automatic detection algorithm was developed to identify the echolocation clicks recorded within both datasets and a recurrent inter-click interval value was identified during the new encounter. Distinctive whistle classes were also identified with similar contour shapes within both datasets.
The Potential of Optometrists’ Referrals of Older Patients to Community-Based Exercise Programs: Findings From a Mixed-Methods Study
Authors: Miyawaki Christina E. , Mauldin Rebecca L. , Carman Carolyn R.
Published: September 2019

Exercise is important for older adults in order to prevent falls and live safer, healthier lives. Visual impairment is a risk factor for falling. Older adults tend to visit optometrists frequently; however, assessing patients’ physical exercise levels is not a routine practice for optometrists. The purpose of this study was to examine the potential for optometrists’ referrals to exercise programs. This study used a mixed-method, cross-sectional design. In focus groups, optometry patients (N = 42) discussed the acceptability of an optometrist’s prescription for exercise programs. The vast majority of optometry patients (90%) indicated that they would follow such a prescription for exercise from their optometrists. Texas optometrists (N = 268) were surveyed about the potential for exercise program prescriptions, and 97% indicated a willingness to prescribe exercise programs to their patients. The results suggest that there is an opportunity for community–clinical partnerships to prevent falls and to improve the health of older patients.
Providing a Basis for Harmonization of Accelerometer-Assessed Physical Activity Outcomes Across Epidemiological Datasets
Authors: Rowlands Alex V. , Plekhanova Tatiana , Yates Tom , Mirkes Evgeny M. , Davies Melanie , Khunti Kamlesh , Edwardson Charlotte L.
Published: September 2019

Introduction: To capitalize on the increasing availability of accelerometry data for epidemiological research it is desirable to compare and/or pool data from surveys worldwide. This study aimed to establish whether free-living physical activity outcomes can be considered equivalent between three research-grade accelerometer brands worn on the dominant and non-dominant wrist. Of prime interest were the average acceleration (ACC) and the intensity gradient (IG). These two metrics describe the volume and intensity of the complete activity profile; further, they are comparable across populations making them ideal for comparing and/or pooling activity data. Methods: Forty-eight adults wore a GENEActiv, Axivity, and ActiGraph on both wrists for up to 7-days. Data were processed using open-source software (GGIR) to generate physical activity outcomes, including ACC and IG. Agreement was assessed using pairwise 95% equivalence tests (±10% equivalence zone) and intra-class correlation coefficients (ICC). Results: ACC was equivalent between brands when measured at the non-dominant wrist (ICC ≥ 0.93), but approximately 10% higher when measured at the dominant wrist (GENEActiv and Axivity only, ICC ≥ 0.83). The IG was equivalent irrespective of monitor brand or wrist (ICC ≥ 0.88). After adjusting ACC measured at the dominant wrist by −10% (GENEActiv and Axivity only), ACC was also within (or marginally outside) the 10% equivalence zone for all monitor pairings. Conclusion: If average acceleration is decreased by 10% for studies deploying monitors on the dominant wrist (GENEActiv and Axivity only), ACC and IG may be suitable for comparing and/or collating physical activity outcomes across accelerometer datasets, regardless of monitor brand and wrist.
The Association Between Neighborhood Socioeconomic Deprivation, Cardiorespiratory Fitness, and Physical Activity in US Youth
Authors: Clennin Morgan N. , Pate Russell R.
Published: September 2019

Background: Growing evidence suggests that the broader neighborhood socioeconomic environment is independently associated with cardiometabolic health. However, few studies have examined this relationship among younger populations. Purpose: The purpose of the study was to (1) investigate the association between neighborhood socioeconomic deprivation (SED) and cardiorespiratory fitness and (2) determine the extent to which physical activity mediates this relationship. Methods: Data from 312 youth (aged 12–15 y) were obtained from the 2012 National Health and Nutrition Examination Survey National Youth Fitness Survey. Cardiorespiratory fitness was measured using a standard submaximal treadmill test, and maximal oxygen consumption was estimated. Physical activity was self-reported time spent in moderate to vigorous activity. Neighborhood SED was measured by a composite index score at the census tract of residence. Logistic regression analyses examined relationships between neighborhood SED, physical activity, and cardiorespiratory fitness, adjusting for individual-level characteristics and the complex sampling design. Results: Neighborhood SED was not significantly associated with cardiorespiratory fitness or physical activity among youth in the study sample. Conclusions: While not significant, cardiorespiratory fitness levels were observed to decrease as neighborhood SED increased. Future research is needed to better understand this relationship and to identify underlying mechanisms beyond fitness or physical activity that may drive the relationship between neighborhood SED and health.
IgM in human immunity to
Plasmodium falciparum
malaria
Authors: Boyle M. J. , Chan J. A. , Handayuni I. , Reiling L. , Feng G. , Hilton A. , Kurtovic L. , Oyong D. , Piera K. A. , Barber B. E. , William T. , Eisen D. P. , Minigo G. , Langer C. , Drew D. R. , de Labastida Rivera F. , Amante F. H. , Williams T. N. , Kinyanjui S. , Marsh K. , Doolan D. L. , Engwerda C. , Fowkes F. J. I. , Grigg M. J. , Mueller I. , McCarthy J. S. , Anstey N. M. , Beeson J. G.
Published: September 2019

IgM is an important and long-lived component of anti-malarial immunity in humans and blocks infection of red blood cells.
Lrrk2
alleles modulate inflammation during microbial infection of mice in a sex-dependent manner
Authors: Shutinoski Bojan , Hakimi Mansoureh , Harmsen Irene E. , Lunn Michaela , Rocha Juliana , Lengacher Nathalie , Zhou Yi Yuan , Khan Jasmine , Nguyen Angela , Hake-Volling Quinton , El-Kodsi Daniel , Li Juan , Alikashani Azadeh , Beauchamp Claudine , Majithia Jay , Coombs Kevin , Shimshek Derya , Marcogliese Paul C. , Park David S. , Rioux John D. , Philpott Dana J. , Woulfe John M. , Hayley Shawn , Sad Subash , Tomlinson Julianna J. , Brown Earl G. , Schlossmacher Michael G.
Published: September 2019

The
Lrrk2
gene modulates the course of infections in mice in a sex-dependent manner.
IFN-γ enhances cell-mediated cytotoxicity against keratinocytes via JAK2/STAT1 in lichen planus
Authors: Shao Shuai , Tsoi Lam C. , Sarkar Mrinal K. , Xing Xianying , Xue Ke , Uppala Ranjitha , Berthier Celine C. , Zeng Chang , Patrick Matthew , Billi Allison C. , Fullmer Joseph , Beamer Maria A. , Perez-White Bethany , Getsios Spiro , Schuler Andrew , Voorhees John J. , Choi Sung , Harms Paul , Kahlenberg J. Michelle , Gudjonsson Johann E.
Published: September 2019

IFN-γ enhances keratinocyte death in lichen planus.
A Large-Scale Whole-Genome Comparison Shows that Experimental Evolution in Response to Antibiotics Predicts Changes in Naturally Evolved Clinical Pseudomonas aeruginosa
Authors: Wardell Samuel J. T. , Rehman Attika , Martin Lois W. , Winstanley Craig , Patrick Wayne M. , Lamont Iain L.
Published: September 2019

Pseudomonas aeruginosa
is an opportunistic pathogen that causes a wide range of acute and chronic infections. An increasing number of isolates have mutations that make them antibiotic resistant, making treatment difficult. To identify resistance-associated mutations, we experimentally evolved the antibiotic-sensitive strain
P. aeruginosa
PAO1 to become resistant to three widely used antipseudomonal antibiotics, namely, ciprofloxacin, meropenem, and tobramycin.
Aeschynomene indica
-Nodulating Rhizobia Lacking Nod Factor Synthesis Genes: Diversity and Evolution in Shandong Peninsula, China
Authors: Zhang Zhenpeng , Li Yan , Pan Xiaohan , Shao Shuai , Liu Wei , Wang En-Tao , Xie Zhihong
Published: September 2019

Aeschynomene indica
rhizobia (AIRs) can form both root and stem nodules via Nod factor-independent processes, which distinguishes them from other rhizobia. This study systematically uncovered the diversity and community composition of
A. indica
rhizobia distributed in eastern China. Our results reclassified all the
A. indica
rhizobia across the world and represent a useful contribution to evaluating the diversity and distribution of the symbiont. The presence of novel genospecies specifically distributed in China enriched the
A. indica
rhizobia resources and provided insight into the geographic distribution of rhizobia. The phylogenetic relationship between
nifH
and
pufLM
of
A. indica
rhizobia across the world provides insight into the evolution of their nitrogen fixation and photosynthetic abilities.
Heterologous Expression of a Cryptic Gene Cluster from Streptomyces leeuwenhoekii C34
T
Yields a Novel Lasso Peptide, Leepeptin
Authors: Gomez-Escribano Juan Pablo , Castro Jean Franco , Razmilic Valeria , Jarmusch Scott A. , Saalbach Gerhard , Ebel Rainer , Jaspars Marcel , Andrews Barbara , Asenjo Juan A. , Bibb Mervyn J.
Published: September 2019

Recent developments in genome sequencing combined with bioinformatic analysis have revealed that actinomycetes contain a plethora of unexpected BGCs and thus have the potential to produce many more natural products than previously thought. This reflects the inability to detect the production of these compounds under laboratory conditions, perhaps through the use of inappropriate growth media or the absence of the environmental cues required to elicit expression of the corresponding BGCs. One approach to overcoming this problem is to circumvent the regulatory mechanisms that control expression of the BGC in its natural host by deploying heterologous expression. The generally compact nature of lasso peptide BGCs makes them particularly amenable to this approach, and, in the example given here, analysis revealed a new member of the lasso peptide family of RiPPs. This approach should be readily applicable to other cryptic lasso peptide gene clusters and would also facilitate the design and production of nonnatural variants by changing the sequence encoding the core peptide, as has been achieved with other classes of RiPPs.
Identification and Characterization of a Cell Wall Hydrolase for Sporangiospore Maturation in Actinoplanes missouriensis
Authors: Mitsuyama Kyota , Tezuka Takeaki , Ohnishi Yasuo
Published: September 2019

In streptomycetes, an aerial hypha is compartmentalized by multiple septations into prespores, which become spores through a series of maturation processes. However, little is known about these maturation processes. The rare actinomycete
Actinoplanes missouriensis
produces sporangiospores, which are assumed to be formed also from prespores generated by the compartmentalization of intrasporangium hyphae via septation. The identification of GsmA as a cell wall hydrolase for the separation of adjacent spores sheds light on the almost unknown processes of sporangiospore formation in
A. missouriensis
. Furthermore, the fact that GsmA orthologues are conserved within the genus
Actinoplanes
but not in streptomycetes indicates that
Actinoplanes
has developed an original strategy for the spore maturation in a specific environment, that is, inside a sporangium.
Dissecting the Role of DDX21 in Regulating Human Cytomegalovirus Replication
Authors: Hao Hongyun , Han Tian , Xuan Baoqin , Sun Yamei , Tang Shubing , Yue Nan , Qian Zhikang
Published: September 2019

Previous studies have confirmed that DDX21 is vital for the regulation of various aspects of RNA virus replication. Our research is the first report on the role of DDX21 in HCMV DNA virus replication. We identified that DDX21 knockdown affected HCMV growth and viral late gene transcription. In order to elucidate how DDX21 regulated this transcription, we applied DNA-RNA immunoprecipitation by using the DNA-RNA hybrid-specific S9.6 antibody to test whether more R-loops accumulated on the viral late gene. Consistent with our expectation, more R-loops were detected on the viral late gene at late HCMV infection time points, which demonstrated that the accumulation of R-loops caused by DDX21 knockdown prevented viral late gene transcription and consequently impaired HCMV replication. These results reveal that DDX21 plays an important role in regulating HCMV replication and also provide a basis for investigating the role of DDX21 in regulating other DNA viruses.
Complete Genome Sequence of Klebsiella pneumoniae Myophage Magnus
Authors: Acevedo Ugarriza Laura E. , Michalik-Provasek Jordyn , Newkirk Heather , Liu Mei , Gill Jason J. , Ramsey Jolene
Published: September 2019

Bacteriophage Magnus infects
Klebsiella pneumoniae
, a Gram-negative pathogen whose multidrug-resistant strains are a public health issue. Here, we describe the annotation of the 157,741-bp Magnus genome and its similarity to other myophages.
The effects of a pre-exercise meal on postexercise metabolism following a session of sprint interval training
Authors: Broad Abigail A. , Howe Greg J. , McKie Greg L. , Vanderheyden Luke W. , Hazell Tom J.
Published: September 2019

Sprint interval training (SIT) has demonstrated reductions in fat mass through potential alterations in postexercise metabolism. This study examined whether exercising in the fasted or fed state affects postexercise metabolism following acute SIT. Ten active males performed a bout of modified SIT (8 × 15-s sprints; 120 s recovery) in both a fasted (FAST) and fed (FED) state. Gas exchange was collected through 3 h postexercise, appetite perceptions were measured using a visual analog scale, and energy intake was recorded using dietary food logs. There was no difference in energy expenditure between conditions at any time point (p > 0.329) or in total session energy expenditure (FED: 514.8 ± 54.9 kcal, FAST: 504.0 ± 74.3 kcal; p = 0.982). Fat oxidation at 3 h after exercise was higher in FED (0.110 ± 0.04 g·min−1) versus FAST (0.069 ± 0.02 g·min−1; p = 0.013) though not different between conditions across time (p > 0.340) or in total postexercise fat oxidation (FED: 0.125 ± 0.04 g·min−1, FAST: 0.105 ± 0.02 g·min−1; p = 0.154). Appetite perceptions were lower in FED (–4815.0 ± 4098.7 mm) versus FAST (–707.5 ± 2010.4 mm, p = 0.022); however, energy intake did not differ between conditions (p = 0.429). These results demonstrate the fasted or fed state does not augment postexercise metabolism following acute SIT in a way that would favour fat loss following training.

Novelty Energy expenditure was similar between conditions, while fat oxidation was significantly greater in FED at 3 h after exercise. Appetite perceptions were significantly lower in FED; however, energy intake was not different between conditions. Current findings suggest that performing SIT in the fed or fasted state would not affect fat loss following training.
Ultra-narrowband mid-infrared absorber based on Mie resonance in dielectric metamaterials
Authors: Liao Yan-Lin , Zhao Yan
Published: September 2019

Ultra-narrowband absorbers can be applied in many applications. We propose a mid-infrared ultra-narrowband absorber with TM polarization (magnetic field is parallel to grating grooves) based on dielectric metamaterials in this paper. The simulation results show that the absorption rate larger than 0.99 can be achieved at the resonance wavelength, and the absorption bandwidth is less than 10 nm. The simulated field distribution shows that the ultra-narrowband absorption in this absorber originates from Mie resonance. In addition, the absorber preserves high absorption rates up to 4° which means that our absorber has high directivity. Our results show that the ultra-narrowband absorbers can be applied as a thermal emitter.
Non-perturbative determination of improvement coefficients $$b_\mathrm{m}$$ and $$b_\mathrm{A}-b_\mathrm{P}$$ and normalisation factor $$Z_\mathrm{m}Z_\mathrm{P}/Z_\mathrm{A}$$ with $$N_\mathrm{f}= 3$$ Wilson fermions
Authors: de Divitiis Giulia Maria , Fritzsch Patrick , Heitger Jochen , Köster Carl Christian , Kuberski Simon , Vladikas Anastassios
Published: September 2019

We determine non-perturbatively the normalisation parameter $$Z_\mathrm{m}Z_\mathrm{P}/Z_\mathrm{A}$$ZmZP/ZA as well as the Symanzik coefficients $$b_\mathrm{m}$$bm and $$b_\mathrm{A}-b_\mathrm{P}$$bA-bP, required in $$\mathrm{O}(a)$$O(a) improved quark mass renormalisation with Wilson fermions. The strategy underlying their computation involves simulations in $$N_\mathrm{f}=3$$Nf=3 QCD with $$\mathrm{O}(a)$$O(a) improved massless sea and non-degenerate valence quarks in the finite-volume Schrödinger functional scheme. Our results, which cover the typical gauge coupling range of large-volume $$N_\mathrm{f}=2+1$$Nf=2+1 QCD simulations with Wilson fermions at lattice spacings below $$0.1\,\mathrm{fm}$$0.1fm, are of particular use for the non-perturbative calculation of $$\mathrm{O}(a)$$O(a) improved renormalised quark masses.
Collision dynamics of two bright solitons in growth Bose–Einstein condensates with tunable interactions
Authors: Zhang Zhi-Qiang , He Zhang-Ming , Miao Peng , Zhou Y. H.
Published: September 2019

By using the split-step fast Fourier transform (SSFFT) method, we numerically study the collision properties between two bright solitons in the growth Bose–Einstein condensates (BECs) with different interaction strengths under a harmonic potential. It is shown that the soliton’s collision property of the condensates can be controlled by adjusting the gain term, the initial position and the interaction strength between atoms. The number of collisions of the two bright solitons decreases first, then increases, with increasing the values of the gain term. As the initial distance between solitons increases, the number of collisions between the two bright solitons is reduced, and the first collision time is also postponed. The increase in interaction strength between atoms delays the collision time of the two bright solitons. Meanwhile, a critical interaction strength between atoms is found, the amplitude of the soliton’s first collision peak increases slowly when the interaction strength is less than the critical value, but the amplitude increases sharply when the interaction strength is more than the critical value.
A New Date-Balanced Method Based on Adaptive Asymmetric and Diversity Regularization in Person Re-Identification
Authors: Ma Wenjin , Han Hua , Kong Yong , Zhang Yujin
Published: September 2019

Person re-identification (person re-ID) is a challenging task which aims at spotting same persons among disjoint camera views. It has certainly generated a lot of attention in the field of computer vision, but it remains a challenging task due to the complexity of person appearances from different camera views. To solve this challenging problem, many excellent methods have been proposed, especially metric learning-based algorithms. However, most of them suffer from the problem of data imbalance. To solve this problem, in the paper we proposed a new data-balanced method and named it Enhanced Metric Learning (EML) based on adaptive asymmetric and diversity regularization for person re-ID. Metric learning is important for person re-ID because it can eliminate the negative effects caused by camera differences to a certain extent. But most metric learning approaches often neglect the problem of data imbalance caused by too many negative samples but few positive samples. And they often treat all negative samples the same as positive ones, which can lead to the loss of important information. Our approach pays different attention to the positive samples and negative ones. Firstly, we classified negative samples into three groups adaptively, and then paid different attention to them using adaptive asymmetric strategy. By treating samples differently, the proposed method can better exploit the discriminative information between positive and negative samples. Furthermore, we also proposed to impose a diversity regularizer to avoid over-fitting when the training sets are small or medium-sized. Finally, we designed a series of experiments on four challenging databases (VIPeR, PRID450S, CUHK01 and GRID), to compare with some excellent metric learning methods. Experimental results show that the rank-1 matching rate of the proposed method has outperformed the state-of-the-art by 3.64%, 4.2%, 3.13% and 2.83% on the four databases, respectively.
Matrix semigroups over semirings
Authors: Gould Victoria , Johnson Marianne , Naz Munazza
Published: September 2019

We study properties determined by idempotents in the following families of matrix semigroups over a semiring [Formula: see text]: the full matrix semigroup [Formula: see text], the semigroup [Formula: see text] consisting of upper triangular matrices, and the semigroup [Formula: see text] consisting of all unitriangular matrices. Il’in has shown that (for [Formula: see text]) the semigroup [Formula: see text] is regular if and only if [Formula: see text] is a regular ring. We show that [Formula: see text] is regular if and only if [Formula: see text] and the multiplicative semigroup of [Formula: see text] is regular. The notions of being abundant or Fountain (formerly, weakly abundant) are weaker than being regular but are also defined in terms of idempotents, namely, every class of certain equivalence relations must contain an idempotent. Each of [Formula: see text], [Formula: see text] and [Formula: see text] admits a natural anti-isomorphism allowing us to characterise abundance and Fountainicity in terms of the left action of idempotent matrices upon column spaces. In the case where the semiring is exact, we show that [Formula: see text] is abundant if and only if it is regular. Our main interest is in the case where [Formula: see text] is an idempotent semifield, our motivating example being that of the tropical semiring [Formula: see text]. We prove that certain subsemigroups of [Formula: see text], including several generalisations of well-studied monoids of binary relations (Hall relations, reflexive relations, unitriangular Boolean matrices), are Fountain. We also consider the subsemigroups [Formula: see text] and [Formula: see text] consisting of those matrices of [Formula: see text] and [Formula: see text] having all elements on and above the leading diagonal non-zero. We prove the idempotent generated subsemigroup of [Formula: see text] is [Formula: see text]. Further, [Formula: see text] and [Formula: see text] are families of Fountain semigroups with interesting and unusual properties. In particular, every [Formula: see text]-class and [Formula: see text]-class contains a unique idempotent, where [Formula: see text] and [Formula: see text] are the relations used to define Fountainicity, but yet the idempotents do not form a semilattice.
Globally Strong Uninvadable Sets of Profiles in Asymmetric Games
Authors: Narang Aradhana , Shaiju A. J.
Published: September 2019

The concept of a globally strong uninvadable set of profiles is studied for asymmetric evolutionary games. After establishing a general result concerning weak [Formula: see text]-limit points of the replicator dynamics trajectories, we prove that globally strong uninvadable sets are weak attracting.
Fine-Grained Air Quality Inference with Remote Sensing Data and Ubiquitous Urban Data
Authors: Xu Yanan , Zhu Yanmin , Shen Yanyan , Yu Jiadi
Published: September 2019

Air quality has gained much attention in recent years and is of great importance to protecting people’s health. Due to the influence of multiple factors, the limited air quality monitoring stations deployed in cities are unable to provide fine-grained air quality information. One cost-effective way is to infer air quality with records from existing monitoring stations. However, the severe data sparsity problem (e.g., only 0.2% data are known) leads to the failure of most inference methods. We observe that remote sensing data are of high quality and have a strong correlation with the air quality. Therefore, we propose to integrate remote sensing data and ubiquitous urban data for the air quality inference. But there are two main challenges, i.e., data heterogeneity and incompleteness of the remote sensing data. To address the challenges, we propose a two-stage approach. In the first stage, we infer and predict air quality conditions of some places leveraging the remote sensing data and meteorological data with two proposed ANN-based methods, respectively. This stage significantly alleviates the data sparsity problem. In the second stage, the records and estimated air quality data are put in a tensor. A tensor decomposition method is applied to complete the tensor. The features extracted from urban data are classified into the spatial features (i.e., road features and POI features) and the temporal features (i.e., meteorological features) as the constraints to further address the data sparsity problem. In addition, an iterative training framework is proposed to improve the inference performance. Experiments on a real-world dataset show that our approach outperforms state-of-the-art methods, such as U-Air.
Density-Friendly Graph Decomposition
Authors: Tatti Nikolaj
Published: September 2019

Decomposing a graph into a hierarchical structure via
k
-core analysis is a standard operation in any modern graph-mining toolkit.
k
-core decomposition is a simple and efficient method that allows to analyze a graph beyond its mere degree distribution. More specifically, it is used to identify areas in the graph of increasing centrality and connectedness, and it allows to reveal the structural organization of the graph.

Despite the fact that
k
-core analysis relies on vertex degrees,
k
-cores do not satisfy a certain, rather natural, density property. Simply put, the most central
k
-core is not necessarily the densest subgraph. This inconsistency between
k
-cores and graph density provides the basis of our study.

We start by defining what it means for a subgraph to be
locally dense
, and we show that our definition entails a nested chain decomposition of the graph, similar to the one given by
k
-cores, but in this case the components are arranged in order of increasing density. We show that such a
locally dense decomposition
for a graph
G
=(
V
,
E
) can be computed in polynomial time. The running time of the exact decomposition algorithm is
O
(|
V
|
2
|
E
|) but is significantly faster in practice. In addition, we develop a linear-time algorithm that provides a factor-2 approximation to the optimal locally dense decomposition. Furthermore, we show that the
k
-core decomposition is also a factor-2 approximation, however, as demonstrated by our experimental evaluation, in practice
k
-cores have different structure than locally dense subgraphs, and as predicted by the theory,
k
-cores are not always well-aligned with graph density.
Perinatal nicotine exposure alters Akt/GSK-3β/mTOR/autophagy signaling, leading to development of hypoxic-ischemic-sensitive phenotype in rat neonatal brain
Authors: Li Yong , Song Andrew M. , Fu Yingjie , Walayat Andrew , Yang Meizi , Jian Jie , Liu Bailin , Xia Liang , Zhang Lubo , Xiao Daliao
Published: September 2019

Maternal cigarette smoking is a major perinatal insult that contributes to an increased risk of cardiovascular and neurodevelopmental diseases in offspring. Our previous studies revealed that perinatal nicotine exposure reprograms a sensitive phenotype in neonatal hypoxic-ischemic encephalopathy (HIE), yet the underlying molecular mechanisms remain largely elusive. The present study tested the hypothesis that perinatal nicotine exposure impacts autophagy signaling in the developing brain, resulting in enhanced susceptibility to neonatal HIE. Nicotine was administered to pregnant rats via subcutaneous osmotic minipumps. Neonatal HIE was conducted in 9-day-old male rat pups. Protein kinase B/glycogen synthase kinase- 3β/mammalian target of rapamycin (Akt/GSK-3β/mTOR) signaling and key autophagy markers were determined by Western blotting analysis. Rapamycin and MK2206 were administered via intracerebroventricular injection. Nicotine exposure significantly inhibited autophagy activities in neonatal brain tissues, characterized by an increased ratio of phosphoylated (p-) to total mTOR protein expression but reduced levels of autophagy-related 5, Beclin 1, and LC3βI/II. Treatment with mTOR inhibitor rapamycin effectively blocked nicotine-mediated autophagy deficiency and, more importantly, reversed the nicotine-induced increase in HI brain infarction. In addition, nicotine exposure significantly upregulated p-Akt and p-GSK-3β. Treatment with the Akt selective inhibitor MK2206 reversed the enhanced p-Akt and p-GSK-3β, restored basal autophagic flux, and abolished nicotine-mediated HI brain injury. These findings suggest that perinatal nicotine-mediated alteration of Akt/GSK-3β/mTOR signaling plays a key role in downregulation of autophagic flux, which contributes to the development of hypoxia/ischemia-sensitive phenotype in the neonatal brain.
Intermittent Hypoxic Training at Lactate Threshold Intensity Improves Aiming Performance in Well-Trained Biathletes with Little Change of Cardiovascular Variables
Authors: Czuba Miłosz , Bril Grzegorz , Płoszczyca Kamila , Piotrowicz Zofia , Chalimoniuk Małgorzata , Roczniok Robert , Zembroń-Łacny Agnieszka , Gerasimuk Dagmara , Langfort Józef
Published: September 2019

The main objective of this research was to evaluate the efficacy of intermittent hypoxic training (IHT) on aiming performance and aerobic capacity in biathletes. Fourteen male biathletes were randomly divided into a hypoxia group (H) (n = 7), which trained three times per week in a normobaric hypoxic environment (FiO2 = 16.5%, 2000 m a.s.l.) with lactate threshold intensity (LT) determined in hypoxia, and a control group (C) (n = 7), which exercised under normoxic conditions with LT intensity determined in normoxia. The training program included three weekly microcycles, followed by three days of recovery. The main part of the interval workout consisted of four 7 min (1st week), 8 min (2nd week), or 9 min (3rd week) running bouts at treadmill separated by 2 minutes of active recovery. After the warm-up and during the rest between the bouts, the athletes performed aiming to the target in the standing position with a sporting rifle (20 s). The results showed that the IHT caused a significant (p<0.05) increase in retention time in the target at rest (RT9rest) by 14.4% in hypoxia, whereas RT postincremental test (RT9post) increased by 27.4% in normoxia and 26.7% in hypoxia. No significant changes in this variable were found in group C. Additionally, the capillary oxygen saturation at the end of the maximal effort (SO2capillary max) in hypoxia increased significantly (p<0.001) by ∼4% after IHT. The maximal workload during the incremental test (WRmax) in normoxia also increased significantly (p<0.001) by 6.3% after IHT. Furthermore, in absolute and relative values of VO2max in normoxia, there was a propensity (p<0.07) for increasing this value by 5% in group H. In conclusion, the main findings of this study showed a significant improvement in resting and postexercise aiming performance in normoxia and hypoxia. Furthermore, the results demonstrated beneficial effects of the IHT protocol on aerobic capacity of biathletes.
Dynamic Modeling and Analysis of a Mine Hoisting System with Constant Length and Variable Length
Authors: Wang Guoying , Xiao Xingming , Liu Yunlong
Published: September 2019

A coal mine hoisting system includes two parts, one is a constant‐length cable system, and the other is a variable‐length cable system. In this paper, the nonlinear dynamic modeling of a coal mine hoisting system is established through Hamilton’s principle. The nonlinear partial differential equations of the coal mine hoisting system are discretized into ordinary differential equations by the fourth‐order Galerkin truncation. The nonlinear dynamic responses and four key kinematic and structural parameter analysis of the coal mine hoisting system in the acceleration phases, constant velocity phases, and deceleration phases are given. The results show that the axial vibration displacements of the constant‐length cable are an order of magnitude smaller than that of the variable‐length cable. The load has the greatest effect on the axial vibration displacement of the hoisting cable. Adversely, the speed has the least effect on the axial vibration displacement of the hoisting cable.