bluuebunny/crossref_metadata_2025_split huggingface dataset:
Tuberculous meningitis in children is characterized by compartmentalized immune responses and neural excitotoxicity
Authors: Rohlwink Ursula K. , Figaji Anthony , Wilkinson Katalin A. , Horswell Stuart , Sesay Abdul K. , Deffur Armin , Enslin Nico , Solomons Regan , Van Toorn Ronald , Eley Brian , Levin Michael , Wilkinson Robert J. , Lai Rachel P. J. 
Published: August 2019

AbstractTuberculous meningitis (TBM) is the most severe form of TB with high rates of mortality and morbidity. Here we conduct RNA-sequencing on whole blood as well as on ventricular and lumbar cerebrospinal fluid (CSF) of pediatric patients treated for TBM. Differential transcript expression of TBM cases are compared with healthy controls in whole blood and with non-TB cerebral infection controls in CSF. Whole blood RNA-Seq analysis demonstrates a distinct immune response pattern in TBM, with significant increase in both canonical and non-canonical inflammasome activation and decrease in T-cell activation. In ventricular CSF, a significant enrichment associated with neuronal excitotoxicity and cerebral damage is detected in TBM. Finally, compartmental comparison in TBM indicates that the ventricular profile represents brain injury whereas the lumbar profile represents protein translation and cytokine signaling. Together, transcriptomic analysis shows that disease processes differ between the periphery and the central nervous system, and within brain compartments.
Programmable biomolecular switches for rewiring flux in Escherichia coli
Authors: Gao Cong , Hou Jianshen , Xu Peng , Guo Liang , Chen Xiulai , Hu Guipeng , Ye Chao , Edwards Harley , Chen Jian , Chen Wei , Liu Liming 
Published: August 2019

AbstractSynthetic biology aims to develop programmable tools to perform complex functions such as redistributing metabolic flux in industrial microorganisms. However, development of protein-level circuits is limited by availability of designable, orthogonal, and composable tools. Here, with the aid of engineered viral proteases and proteolytic signals, we build two sets of controllable protein units, which can be rationally configured to three tools. Using a protease-based dynamic regulation circuit to fine-tune metabolic flow, we achieve 12.63 g L−1 shikimate titer in minimal medium without inducer. In addition, the carbon catabolite repression is alleviated by protease-based inverter-mediated flux redistribution under multiple carbon sources. By coordinating reaction rate using a protease-based oscillator in E. coli, we achieve d-xylonate productivity of 7.12 g L−1 h−1 with a titer of 199.44 g L−1. These results highlight the applicability of programmable protein switches to metabolic engineering for valuable chemicals production.
A rapid access to aliphatic sulfonyl fluorides
Authors: Xu Ruting , Xu Tianxiao , Yang Mingcheng , Cao Tianpeng , Liao Saihu 
Published: August 2019

AbstractThe past few years have witnessed a fast-growing research interest on the study of sulfonyl fluorides as reactive probes in chemical biology and molecular pharmacology, which raises an urgent need for the development of effective synthetic methods to expand the toolkit. Herein, we present the invention of a facile and general approach for the synthesis of aliphatic sulfonyl fluorides via visible-light-mediated decarboxylative fluorosulfonylethylation. The method is based on abundant carboxylic acid feed stock, applicable to various alkyl carboxylic acids including primary, secondary, and tertiary acids, and is also suitable for the modification of natural products like amino acids, peptides, as well as drugs, forging a rapid, metal-free approach to build sulfonyl fluoride compound libraries of considerable structural diversity. Further diversification of the SO2F-containing products is also demonstrated, which allows for access to a range of pharmaceutically important motifs such as sultam, sulfonate, and sulfonamide.
High possibility of hepatocarcinogenesis in HBV genotype C1 infected Cambodians is indicated by 340 HBV C1 full-genomes analysis from GenBank
Authors: Chuon Channarena , Takahashi Kazuaki , Matsuo Junko , Katayama Keiko , Yamamoto Chikako , Ko Ko , Hok Sirany , Nagashima Shintaro , Akbar Sheikh Mohammad Fazle , Tanaka Junko 
Published: August 2019

AbstractApproximately 75% of hepatocellular carcinomas (HCC) occur in Asia; core promoter mutations are associated with HCC in HBV genotype C, the dominant genotype in Cambodia. We analyzed these mutations in Cambodian residents and compared them with HBV full genomes registered in GenBank. We investigated the characteristics of 26 full-length HBV genomes among 35 residents positive for hepatitis B surface antigen in Siem Reap province, Cambodia. Genotype C1 was dominant (92.3%, 24/26), with one case of B2 and B4 each. Multiple mutations were confirmed in 24 Cambodian C1 isolates, especially double mutation at A1762T/G1764A in 18 isolates (75.0%), and combination mutation at C1653T and/or T1753V and A1762T/G1764A in 14 isolates (58.3%). In phylogenetic analysis, 16 of 24 isolates were located in the cluster with Laos, Thailand, and Malaysia. In 340 GenBank-registered C1 strains, 113 (33.2%) had combination mutation amongst which 16.5%, 34.2%, and 95.2% were found in ASC, chronic hepatitis, and liver cirrhosis (LC)/HCC respectively (P < 0. 001). Mutations were abundantly found in 24 Cambodian C1 isolates, and 340 C1 strains from GenBank showed mutation in genotype C1 brings high possibility of LC/HCC occurrence. Therefore, we suggest that Cambodian people infected with HBV genotype C1 have high possibility of hepatocarcinogenesis.
Sexual experience has no effect on male mating or reproductive success in house mice
Authors: Thonhauser Kerstin E. , Raffetzeder Alexandra , Penn Dustin J. 
Published: August 2019

AbstractThe ability to learn from experience can improve Darwinian fitness, but few studies have tested whether sexual experience enhances reproductive success. We conducted a study with wild-derived house mice (Mus musculus musculus) in which we manipulated male sexual experience and allowed females to choose between (1) a sexually experienced versus a virgin male, (2) two sexually experienced males, or (3) two virgin males (n = 60 females and 120 males). This design allowed us to test whether females are more likely to mate multiply when they encounter more virgin males, which are known to be infanticidal. We recorded females’ preference and mating behaviours, and conducted genetic paternity analyses to determine male reproductive success. We found no evidence that sexual experience influenced male mating or reproductive success, and no evidence that the number of virgin males influenced female multiple mating. Females always copulated with both males and 58% of the litters were multiple-sired. Females’ initial attraction to a male correlated with their social preferences, but neither of these preference behaviours predicted male reproductive success – raising caveats for using mating preferences as surrogates for mate choice. Male reproductive success was predicted by mating order, but unexpectedly, males that copulated first sired fewer offspring.
Regulation of PDE5 expression in human aorta and thoracic aortic aneurysms
Authors: Cesarini Valeriana , Pisano Calogera , Rossi Gabriele , Balistreri Carmela Rita , Botti Flavia , Antonelli Giorgio , Ruvolo Giovanni , Jannini Emmanuele A. , Dolci Susanna 
Published: August 2019

AbstractAneurysms and dissections affecting thoracic aorta are associated with smooth muscle cell (SMC) dysfunction. NO/cGMP signaling pathway in smooth muscle cells has been shown to be affected in sporadic thoracic aortic aneurysms. We analyzed the mRNA levels of PDE5, a cGMP-hydrolyzing enzyme highly expressed in aortic SMCs, that regulates arterious vascular tone by lowering cGMP levels. We found that aortic tissue obtained from Marfan, tricuspid and bicuspid thoracic aneurysms expressed lower levels of PDE5 mRNA compared to control aortas. In particular, we found that affected aortas showed lower levels of all the PDE5A isoforms, compared to control aortas. Transfection of vascular SMCs (VSMCs) with NOTCH3 activated domain (NICD3) induced the expression of PDE5A1 and A3 protein isoforms, but not that of the corresponding mRNAs. VSMC stimulation with GSNO, a nitric oxide analogue or with 8-br-cGMP, but not with 8-br-cAMP, up-regulated PDE5 and NOTCH-3 protein levels, indicating a negative feedback loop to protect the arterial wall from excessive relaxation. Finally, we found that PDE5 is expressed early during human aorta development, suggesting that if loss of function mutations of PDE5 occur, they might potentially affect aortic wall development.
Reconstruction of the lncRNA-miRNA-mRNA network based on competitive endogenous RNA reveal functional lncRNAs in Cerebral Infarction
Authors: Zou Jun-Bo , Chai Hong-Bo , Zhang Xiao-Fei , Guo Dong-Yan , Tai Jia , Wang Yu , Liang Yu-Lin , Wang Fang , Cheng Jiang-Xue , Wang Jing , Shi Ya-Jun 
Published: August 2019

AbstractFunctioning as miRNA sponges, long non-coding RNA (lncRNA) exert its pharmacological action via regulating expression of protein-coding genes. However, the lncRNA-mediated ceRNA in cerebral Infarction (CI) remains unclear. In this study, the expression recordsets of mRNA, lncRNA and miRNA of CI samples were obtained from the NCBI GEO datasets separately. The differentially expressed lncRNAs (DELs), miRNAs (DEMis) and mRNAs (DEMs) were identified by limma package in R platform. A total of 267 DELs, 26 DEMis, and 760 DEMs were identified as differentially expressed profiles, with which we constructed the ceRNA network composed of DELs-DEMis-DEMs. Further, clusterProfiler package in R platform is employed for performing Gene Ontology (GO) and KEGG pathway analysis. An aberrant ceRNA network was constructed according to node degrees in CI, including 28 DELs, 19 DEMs and 12 DEMis, from which we extracted the core network, in which 9 nodes were recognized as kernel genes including Tspan3, Eif4a2, rno-miR-208a-3p, rno-miR-194-5p, Pdpn, H3f3b, Stat3, Cd63 and Sdc4. Finally, with the DELs-DEMis-DEMs ceRNA network provided above, we can improve our understanding of the pathogenesis of CI mediated by lncRNA.
Binding of the protein ICln to α-integrin contributes to the activation of IClswell current
Authors: Schedlbauer Andreas , Tamma Grazia , Rodighiero Simona , Civello Davide Antonio , Tamplenizza Margherita , Ledolter Karin , Nofziger Charity , Patsch Wolfgang , Konrat Robert , Paulmichl Markus , Dossena Silvia 
Published: August 2019

AbstractIClswell is the chloride current induced by cell swelling, and plays a fundamental role in several biological processes, including the regulatory volume decrease (RVD). ICln is a highly conserved, ubiquitously expressed and multifunctional protein involved in the activation of IClswell. In platelets, ICln binds to the intracellular domain of the integrin αIIb chain, however, whether the ICln/integrin interaction plays a role in RVD is not known. Here we show that a direct molecular interaction between ICln and the integrin α-chain is not restricted to platelets and involves highly conserved amino acid motifs. Integrin α recruits ICln to the plasma membrane, thereby facilitating the activation of IClswell during hypotonicity. Perturbation of the ICln/integrin interaction prevents the transposition of ICln towards the cell surface and, in parallel, impedes the activation of IClswell. We suggest that the ICln/integrin interaction interface may represent a new molecular target enabling specific IClswell suppression in pathological conditions when this current is deregulated or plays a detrimental role.
Vertical distribution and radiological risk assessment of 137Cs and natural radionuclides in soil samples
Authors: Ahmad Ayesha Y. , Al-Ghouti Mohammad A. , AlSadig Ibrahim , Abu-Dieyeh Mohammed 
Published: August 2019

AbstractThe aims of this study were to investigate the vertical distributions of natural radionuclides 232Th, 226Ra and 40K as well as anthropogenic radionuclide 137Cs in soil samples and to analyze the correlation among the radioactivity of these radionuclides and the physiochemical characteristics of soil samples namely pH, grain size, carbonate content and organic matter. Risk assessment of the radiological hazard has also been estimated. Forty-four soil samples were collected from eleven locations in Qatar at four depth levels from 0 to 16 cm. The average concentrations of 232Th, 226Ra, 40K and 137Cs in the soil depth of 16 cm were 10, 17, 201 and 4 Bq/kg, respectively, which were within the reported world mean. The external absorbed gamma dose rate, the annual effective dose, the mean radium equivalent activity, the external hazard index and the lifetime cancer risk were 22 nGy/h, 0.027 mSv/y, 47 Bq/kg, 0.125 and 0.096 × 10−3, respectively. These values were far below the minimum recommended international values. The level of radioactivity concentrations in the soil was affected by the physiochemical characteristics of the soil. The positive correlation with highest R2 value was found among the radioactivity concentrations of 232Th and 40K and the soil clay content. Total organic carbon was also positively correlated for 226Ra and 137Cs activity concentrations, whereas, carbonate content was negatively correlated with the radioactivity concentrations of 232Th and 40K. As far as soil moisture content is concerned, the positive correlation with highest R2 value was obtained for 226Ra activity concentrations.
How to Hide One’s Relationships from Link Prediction Algorithms
Authors: Waniek Marcin , Zhou Kai , Vorobeychik Yevgeniy , Moro Esteban , Michalak Tomasz P. , Rahwan Talal 
Published: August 2019

AbstractOur private connections can be exposed by link prediction algorithms. To date, this threat has only been addressed from the perspective of a central authority, completely neglecting the possibility that members of the social network can themselves mitigate such threats. We fill this gap by studying how an individual can rewire her own network neighborhood to hide her sensitive relationships. We prove that the optimization problem faced by such an individual is NP-complete, meaning that any attempt to identify an optimal way to hide one’s relationships is futile. Based on this, we shift our attention towards developing effective, albeit not optimal, heuristics that are readily-applicable by users of existing social media platforms to conceal any connections they deem sensitive. Our empirical evaluation reveals that it is more beneficial to focus on “unfriending” carefully-chosen individuals rather than befriending new ones. In fact, by avoiding communication with just 5 individuals, it is possible for one to hide some of her relationships in a massive, real-life telecommunication network, consisting of 829,725 phone calls between 248,763 individuals. Our analysis also shows that link prediction algorithms are more susceptible to manipulation in smaller and denser networks. Evaluating the error vs. attack tolerance of link prediction algorithms reveals that rewiring connections randomly may end up exposing one’s sensitive relationships, highlighting the importance of the strategic aspect. In an age where personal relationships continue to leave digital traces, our results empower the general public to proactively protect their private relationships.
Rapid decrease in titer and breadth of neutralizing anti-HCV antibodies in HIV/HCV-coinfected patients who achieved SVR
Authors: Vigón Lorena , Vázquez-Morón Sonia , Berenguer Juan , González-García Juan , Jiménez-Sousa Ma Ángeles , Guardiola Josep M. , Crespo Manuel , de Los Santos Ignacio , Von Wichmann Miguel A. , Carrero Ana , Yélamos María Belén , Gómez Julián , Resino Salvador , Martínez Isidoro ,   The GESIDA 3603b Cohort Study Group, Miralles P. , López J. C. , Parras F. , Padilla B. , Aldamiz-Echevarría T. , Tejerina F. , Díez C. , Pérez-Latorre L. , Fanciulli C. , Gutiérrez I. , Ramírez M. , Carretero S. , Bellón J. M. , Bermejo J. , Hontañón V. , Arribas J. R. , Montes M. L. , Bernardino I. , Pascual J. F. , Zamora F. , Peña J. M. , Arnalich F. , Díaz M. , Domingo P. , Sanz J. , Bustinduy M. J. , Iribarren J. A. , Rodríguez-Arrondo F. , Eynde E Van den , Pérez M. , Ribera E. , Casado J. L. , Dronda F. , Moreno A. , Pérez-Elías M. J. , Sanfrutos M. A. , Moreno S. , Quereda C. , Arranz A. , Casas E. , Miguel J. de , Schroeder S. , Vergas J. , Téllez M. J. , Vinuesa D. , Muñoz L. , Hernández-Quero J. , Ferrer A. , Galindo M. J. , Ortiz L. , Ortega E. , Montero M. , Blanes M. , Cuellar S. , Lacruz J. , Salavert M. , López-Aldeguer J. , Pérez G. , Gaspar G. , Yllescas M. , Crespo P. , Aznar E. , Esteban H. 
Published: August 2019

AbstractThe main targets for neutralizing anti-hepatitis C virus (HCV) antibodies (HCV-nAbs) are the E1 and E2 envelope glycoproteins. We have studied the characteristics of HCV-nAbs through a retrospective study involving 29 HIV/HCV-coinfected patients who achieved sustained virological response (SVR) with peg-IFNα + ribavirin anti-HCV therapy. Plasma samples at baseline and week 24 after SVR were used to perform neutralization assays against five JFH1-based HCV recombinant viruses coding for E1 and E2 from genotypes 1a (H77), 1b (J4), 2a (JFH1), 3a (S52) and 4a (ED43). At baseline, the majority of plasma samples neutralized 1a, 1b, 2a, and 4a, but not 3a, genotypes. Twenty-four weeks following SVR, most neutralizing titers declined substantially. Furthermore, titers against 3a and 2a were not detected in many patients. Plasma samples with high HCV-nAb titers neutralized all genotypes, and the highest titers at the starting point correlated with the highest titers at week 24 after SVR. In conclusion, high titers of broad-spectrum HCV-nAbs were detected in HIV/HCV-coinfected individuals, however, those titers declined soon after SVR.
Nano-plasmonic Bundt Optenna for broadband polarization-insensitive and enhanced infrared detection
Authors: Awad Ehab 
Published: August 2019

AbstractInfrared detection devices are becoming miniature with micro or nano-scale size. The advantages of downsizing come on the expense of insufficient collection of infrared radiation. Therefore, utilizing nano-plasmonic optical antennas becomes mandatory. However, it is desirable to develop antennas with broad bandwidth, polarization insensitivity, wide field-of-view, and reasonable plasmonic losses in order to collect most of incident infrared radiation and enhance power absorption efficiency. Here, an innovative optical antenna (optenna) is proposed and demonstrated for the first time. It has a novel shape of Bundt baking-pan. The gold Bundt is arranged in a periodic array that can be placed on top of a thin-film infrared absorbing layer. The developed optenna can squeeze infrared electric and magnetic fields to 50 nm-wide area in order to enhance material absorption efficiency. It demonstrates polarization insensitivity and ultra-broad bandwidth with a large fractional-bandwidth within the near, shortwave, and midwave infrared bands. It shows a remarkable enhanced power absorption efficiency up to 8 orders of magnitude with a reasonable average power loss of −3 dB and 80° field-of-view. It can be promising for future applications in solar-cells, telecommunication photodetectors, shortwave cameras, and midwave microbolometers.
Comparative Transcriptome Analysis of Pinus densiflora Following Inoculation with Pathogenic (Bursaphelenchus xylophilus) or Non-pathogenic Nematodes (B. thailandae)
Authors: Lee Il Hwan , Han Hyerim , Koh Young Ho , Kim In Sik , Lee Seok-Woo , Shim Donghwan 
Published: August 2019

AbstractPinus densiflora (Korean red pine) is a species of evergreen conifer that is distributed in Korea, Japan, and China, and of economic, scientific, and ecological importance. Korean red pines suffer from pine wilt disease (PWD) caused by Bursaphelenchus xylophilus, the pinewood nematode (PWN). To facilitate diagnosis and prevention of PWD, studies have been conducted on the PWN and its beetle vectors. However, transcriptional responses of P. densiflora to PWN have received less attention. Here, we inoculated Korean red pines with pathogenic B. xylophilus, or non-pathogenic B. thailandae, and collected cambium layers 4 weeks after inoculation for RNA sequencing analysis. We obtained 72,864 unigenes with an average length of 869 bp (N50 = 1,403) from a Trinity assembly, and identified 991 differentially expressed genes (DEGs). Biological processes related to phenylpropanoid biosynthesis, flavonoid biosynthesis, oxidation–reduction, and plant-type hypersensitive response were significantly enriched in DEGs found in trees inoculated with B. xylophilus. Several transcription factor families were found to be involved in the response to B. xylophilus inoculation. Our study provides the first evidence of transcriptomic differences in Korean red pines inoculated with B. xylophilus and B. thailandae, and might facilitate early diagnosis of PWD and selection of PWD-tolerant Korean red pines.
A study of the context in which compact intracloud discharges occur
Authors: Leal Adonis F. R. , Rakov Vladimir A. 
Published: August 2019

AbstractThe occurrence context of compact intracloud discharges (CIDs) is examined using their electric field waveforms and corresponding NLDN data. A total of 1096 CIDs transporting negative charge upward and 8 CIDs transporting positive charge upward were analyzed. The CIDs were categorized based on whether they were isolated or were followed, preceded, or both followed and preceded by other NLDN-reported lightning events. The percentages of isolated CIDs transporting negative charge upward decreased from 92% for 5 km search radius and ±10 ms time window to 31% for 10 km and ±1000 ms, this decrease being accompanied by an increase of the percentage of CIDs preceding (initiating) normal lightning events from 6.8% to 43%. GM NLDN-reported peak currents for isolated CIDs (33 kA) were similar to those initiating normal lightning events (34 kA). Some of our isolated CIDs could be viewed as precursors, because they apparently initiated normal lightning events at essentially the same location after time intervals measured in seconds. CIDs transporting positive charge upward (a) occurred at heights ranging from 16 to 19 km vs. 6 to 16 km for CIDs transporting negative charge upward and (b) had considerably higher NLDN-reported peak currents: 113 kA vs. 33 kA (GM values).
Connective tissue growth factor is correlated with peritoneal lymphangiogenesis
Authors: Kinashi Hiroshi , Toda Naohiro , Sun Ting , Nguyen Tri Q. , Suzuki Yasuhiro , Katsuno Takayuki , Yokoi Hideki , Aten Jan , Mizuno Masashi , Maruyama Shoichi , Yanagita Motoko , Goldschmeding Roel , Ito Yasuhiko 
Published: August 2019

AbstractLymphatic absorption in the peritoneal cavity may contribute to ultrafiltration failure in peritoneal dialysis (PD). Lymphatic vessels develop during PD-related peritoneal fibrosis. Connective tissue growth factor (CTGF, also called CCN2) is an important determinant of fibrotic tissue remodeling, but little is known about its possible involvement in lymphangiogenesis. In this study, we investigated the relationship between CTGF and peritoneal lymphangiogenesis. A positive correlation was observed between vascular endothelial growth factor-C (VEGF-C), a major lymphangiogenic growth factor, and the CTGF concentration in human PD effluents. CTGF expression was positively correlated with expression of lymphatic markers and VEGF-C in human peritoneal biopsies. We found a positive correlation between the increase in CTGF and the increase in VEGF-C in cultured human peritoneal mesothelial cells (HPMCs) treated with transforming growth factor-β1 (TGF-β1). The diaphragm is a central player in peritoneal lymphatic absorption. CTGF expression was also correlated with expression of VEGF-C and lymphatics in a rat diaphragmatic fibrosis model induced by chlorhexidine gluconate (CG). Furthermore, CTGF gene deletion reduced VEGF-C expression and peritoneal lymphangiogenesis in the mouse CG model. Inhibition of CTGF also reduced VEGF-C upregulation in HPMCs treated with TGF-β1. Our results suggest a close relationship between CTGF and PD-associated lymphangiogenesis.