bluuebunny/crossref_metadata_2025_split huggingface dataset:
Designed α-sheet peptides suppress amyloid formation in Staphylococcus aureus biofilms
Authors: Bleem Alissa , Francisco Robyn , Bryers James D. , Daggett Valerie 
Published: June 2017

AbstractNosocomial infections affect hundreds of millions of patients worldwide each year, and ~60% of these infections are associated with biofilm formation on an implanted medical device. Biofilms are dense communities of microorganisms in which cells associate with surfaces and each other using a self-produced extracellular matrix composed of proteins, polysaccharides, and genetic material. Proteins in the extracellular matrix take on a variety of forms, but here we focus on functional amyloid structures. Amyloids have long been associated with protein misfolding and neurodegenerative diseases, but recent research has demonstrated that numerous bacterial species utilize the amyloid fold to fortify the biofilm matrix and resist disassembly. Consequently, these functional amyloids, in particular the soluble oligomeric intermediates formed during amyloidogenesis, represent targets to destabilize the extracellular matrix and interrupt biofilm formation. Our previous studies suggested that these amyloidogenic intermediates adopt a non-standard structure, termed “α-sheet”, as they aggregate into soluble oligomeric species. This led to the design of complementary α-sheet peptides as anti-α-sheet inhibitors; these designs inhibit amyloidogenesis in three unrelated mammalian disease-associated systems through preferential binding of soluble oligomers. Here we show that these anti-α-sheet peptides inhibit amyloid formation in Staphylococcus aureus biofilms. Furthermore, they inhibit aggregation of pure, synthetic phenol soluble modulin α1, a major component of Staphylococcus aureus functional amyloids. As it aggregates phenol soluble modulin α1 adopts α-helix then α-sheet and finally forms β-sheet fibrils. The binding of the designed peptide inhibitors coincides with the formation of α-sheet.
Dislocations interaction induced structural instability in intermetallic Al2Cu
Authors: Zhou Qing , Wang Jian , Misra Amit , Huang Ping , Wang Fei , Xu Kewei 
Published: June 2017

AbstractIntermetallic precipitates are widely used to tailor mechanical properties of structural alloys but are often destabilized during plastic deformation. Using atomistic simulations, we elucidate structural instability mechanisms of intermetallic precipitates associated with dislocation motion in a model system of Al2Cu. Interaction of non-coplanar <001> dislocation dipoles during plastic deformation results in anomalous reactions—the creation of vacancies accompanied with climb and collective glide of <001> dislocation associated with the dislocation core change and atomic shuffle—accounting for structural instability in intermetallic Al2Cu. This process is profound with decreasing separation of non-coplanar dislocations and increasing temperature and is likely to be operative in other non-cubic intermetallic compounds as well.
The role of the FliD C-terminal domain in pentamer formation and interaction with FliT
Authors: Kim Hee Jung , Yoo Woongjae , Jin Kyeong Sik , Ryu Sangryeol , Lee Hyung Ho 
Published: June 2017

AbstractFlagellar biogenesis is controlled by a negative feedback loop. When FliD was secreted at the late step of flagellar assembly, the FliD-FliT complex disassembled and free FliT bound to the FlhDC complex, a master regulator of flagellar biogenesis, subsequently inhibiting the overall expression of flagellar proteins. In this study, we analyzed the role of the FliD C-terminal domain in pentamer formation and interaction with FliT. Our study showed that the FliD L443R mutant exists as a monomer in solution, indicating that the Leu443 residue of FliD, which contributes to its interaction with FliT, plays a crucial role in the pentameric oligomerization of FliD. Consistently, the increased levels of free FliT proteins caused by FliD L443R mutation had negative effects on the gene expression of flagellar synthesis and reduced the expression of flagellar proteins. The lengths of flagella in each cell were significantly reduced in L443R mutant strain, suggesting that normal flagellar biogenesis was impeded. These results suggest that the C-terminal domain of FliD plays a crucial role in the pentameric oligmerization of FliD and the binding of FliT to the C-terminal domain of FliD is critical to inhibit the premature assembly of the FliD pentamer in the cytosol.
Evaluation of muscular changes by ultrasound Nakagami imaging in Duchenne muscular dystrophy
Authors: Weng Wen-Chin , Tsui Po-Hsiang , Lin Chia-Wei , Lu Chun-Hao , Lin Chun-Yen , Shieh Jeng-Yi , Lu Frank Leigh , Ee Ting-Wei , Wu Kuan-Wen , Lee Wang-Tso 
Published: June 2017

AbstractDuchenne muscular dystrophy (DMD) is the most common debilitating muscular disorder. Developing a noninvasive measure for monitoring the progression of this disease is critical. The present study tested the effectiveness of using ultrasound Nakagami imaging to evaluate the severity of the dystrophic process. A total of 47 participants (40 with DMD and 7 healthy controls) were recruited. Patients were classified into stage 1 (presymptomatic and ambulatory), stage 2 (early nonambulatory), and stage 3 (late nonambulatory). All participants underwent ultrasound examinations on the rectus femoris, tibialis anterior, and gastrocnemius. The results revealed that the ultrasound Nakagami parameter correlated positively with functional severity in the patients with DMD. The median Nakagami parameter of the gastrocnemius muscle increased from 0.50 to 0.85, corresponding to the largest dynamic range between normal and stage 3. The accuracy, sensitivity, and specificity of diagnosing walking function were 85.52%, 76.31%, and 94.73%, respectively. The Nakagami parameter of the rectus femoris and gastrocnemius muscles correlated negatively with the 6-minute walking distance in the ambulatory patients. Therefore, changes in the Nakagami parameter for the gastrocnemius muscle are suitable for monitoring disease progression in ambulatory patients and for predicting ambulation loss. Ultrasound Nakagami imaging shows potential for evaluating patients with DMD.
Viperin is an important host restriction factor in control of Zika virus infection
Authors: Van der Hoek Kylie H. , Eyre Nicholas S. , Shue Byron , Khantisitthiporn Onruedee , Glab-Ampi Kittirat , Carr Jillian M. , Gartner Matthew J. , Jolly Lachlan A. , Thomas Paul Q. , Adikusuma Fatwa , Jankovic-Karasoulos Tanja , Roberts Claire T. , Helbig Karla J. , Beard Michael R. 
Published: June 2017

AbstractZika virus (ZIKV) infection has emerged as a global health threat and infection of pregnant women causes intrauterine growth restriction, spontaneous abortion and microcephaly in newborns. Here we show using biologically relevant cells of neural and placental origin that following ZIKV infection, there is attenuation of the cellular innate response characterised by reduced expression of IFN-β and associated interferon stimulated genes (ISGs). One such ISG is viperin that has well documented antiviral activity against a wide range of viruses. Expression of viperin in cultured cells resulted in significant impairment of ZIKV replication, while MEFs derived from CRISPR/Cas9 derived viperin−/− mice replicated ZIKV to higher titers compared to their WT counterparts. These results suggest that ZIKV can attenuate ISG expression to avoid the cellular antiviral innate response, thus allowing the virus to replicate unchecked. Moreover, we have identified that the ISG viperin has significant anti-ZIKV activity. Further understanding of how ZIKV perturbs the ISG response and the molecular mechanisms utilised by viperin to suppress ZIKV replication will aid in our understanding of ZIKV biology, pathogenesis and possible design of novel antiviral strategies.
Adiponectin is an endogenous anti-fibrotic mediator and therapeutic target
Authors: Marangoni Roberta G. , Masui Yuri , Fang Feng , Korman Benjamin , Lord Gabriel , Lee Junghwa , Lakota Katja , Wei Jun , Scherer Philipp E. , Otvos Laszlo , Yamauchi Toshimasa , Kubota Naoto , Kadowaki Takashi , Asano Yoshihide , Sato Shinichi , Tourtellotte Warren G. , Varga John 
Published: June 2017

AbstractSkin fibrosis in systemic sclerosis (SSc) is accompanied by attrition of dermal white adipose tissue (dWAT) and reduced levels of circulating adiponectin. Since adiponectin has potent regulatory effects on fibroblasts, we sought to assess adiponectin signaling in SSc skin biopsies, and evaluate fibrosis in mice with adiponectin gain- and loss-of-function mutations. Furthermore, we investigated the effects and mechanism of action of agonist peptides targeting adiponectin receptors in vitro and in vivo. We found that adiponectin pathway activity was significantly reduced in a subset of SSc skin biopsies. Mice lacking adiponectin mounted an exaggerated dermal fibrotic response, while transgenic mice with constitutively elevated adiponectin showed selective dWAT expansion and protection from skin and peritoneal fibrosis. Adiponectin receptor agonists abrogated ex vivo fibrotic responses in explanted normal and SSc fibroblasts and in 3D human skin equivalents, in part by attenuating focal adhesion complex assembly, and prevented and reversed experimentally-induced organ fibrosis in mice. These results implicate aberrant adiponectin pathway activity in skin fibrosis, identifying a novel function for this pleiotropic adipokine in regulation of tissue remodeling. Restoring adiponectin signaling in SSc patients therefore might represent an innovative pharmacological strategy for intractable organ fibrosis.
Diagnostic Performance of Contrast Enhanced Pulmonary Computed Tomography Angiography for the Detection of Angioinvasive Pulmonary Aspergillosis in Immunocompromised Patients
Authors: Henzler C. , Henzler T. , Buchheidt D. , Nance John W. , Weis C. A. , Vogelmann R. , Benck U. , Viergutz T. , Becher T. , Boch T. , Klein S. A. , Heidenreich D. , Pilz L. , Meyer M. , Deckert P. M. , Hofmann W.-K. , Schoenberg S. O. , Reinwald M. 
Published: June 2017

AbstractInvasive pulmonary aspergillosis (IPA) is one of the major complications in immunocompromised patients. The mainstay of diagnostic imaging is non-enhanced chest-computed-tomography (CT), for which various non-specific signs for IPA have been described. However, contrast-enhanced CT pulmonary angiography (CTPA) has shown promising results, as the vessel occlusion sign (VOS) seems to be more sensitive and specific for IPA in hematologic patients. The aim of this study was to evaluate the diagnostic accuracy of CTPA in a larger cohort including non-hematologic immunocompromised patients. CTPA studies of 78 consecutive immunocompromised patients with proven/probable IPA were analyzed. 45 immunocompromised patients without IPA served as a control group. Diagnostic performance of CTPA-detected VOS and of radiological signs that do not require contrast-media were analyzed. Of 12 evaluable radiological signs, five were found to be significantly associated with IPA. The VOS showed the highest diagnostic performance with a sensitivity of 0.94, specificity of 0.71 and a diagnostic odds-ratio of 36.8. Regression analysis revealed the two strongest independent radiological predictors for IPA to be the VOS and the halo sign. The VOS is highly suggestive for IPA in immunocompromised patients in general. Thus, contrast-enhanced CTPA superior over non-contrast_enhanced chest-CT in patients with suspected IPA.
Natural and induced loss of function mutations in SlMBP21 MADS-box gene led to jointless-2 phenotype in tomato
Authors: Roldan Maria Victoria Gomez , Périlleux Claire , Morin Halima , Huerga-Fernandez Samuel , Latrasse David , Benhamed Moussa , Bendahmane Abdelhafid 
Published: June 2017

AbstractAbscission is the mechanism by which plants disconnect unfertilized flowers, ripe fruits, senescent or diseased organs from the plant. In tomato, pedicel abscission is an important agronomic factor that controls yield and post-harvest fruit quality. Two non-allelic mutations, jointless (j) and jointless-2 (j-2), controlling pedicel abscission zone formation have been documented but only j-2 has been extensively used in breeding. J was shown to encode a MADS-box protein. Using a combination of physical mapping and gene expression analysis we identified a positional candidate, Solyc12g038510, associated with j-2 phenotype. Targeted knockout of Solyc12g038510, using CRISPR/Cas9 system, validated our hypothesis. Solyc12g038510 encodes the MADS-box protein SlMBP21. Molecular analysis of j-2 natural variation revealed two independent loss-of-function mutants. The first results of an insertion of a Rider retrotransposable element. The second results of a stop codon mutation that leads to a truncated protein form. To bring new insights into the role of J and J-2 in abscission zone formation, we phenotyped the single and the double mutants and the engineered alleles. We showed that J is epistatic to J-2 and that the branched inflorescences and the leafy sepals observed in accessions harboring j-2 alleles are likely the consequences of linkage drags.
Multiscale studies on the nonlinear vibration of delaminated composite laminates–global vibration mode with micro buckles on the interfaces
Authors: Xue Jianghong , Xia Fei , Ye Jun , Zhang Jianwen , Chen Shuhua , Xiong Ying , Tan Zuyuan , Liu Renhuai , Yuan Hong 
Published: June 2017

AbstractThis paper presents a multiscale approach to study the nonlinear vibration of fiber reinforced composite laminates containing an embedded, through-width delamination dividing the laminate into four sub-laminates. The equations of motion are established from macroscopic nonlinear mechanics for plates and shells and micro-mechanics of composite material to allow for the influences of large amplitude, membrane stretching in the neutral plane, and the interactions of the sublaminates. Analytical solutions obtained in this paper reveal that the interaction penalty at the interfaces plays a coupling effect between sublaminates, which eventually alters the vibration characters of the four-sublaminate lamina in macroscopic and microscopic mechanism. From a macro perspective, sub-laminates above and below the delamination vibrate in exactly the same mode in spite of their different stiffness and the four-sublaminate lamina has a consistent global vibration mode. In accompanying with the macro vibration, micro buckles occur on the interfaces of the delamination with amplitude about 10−3 times of that of the global mode. It is found that the vibration frequency is an eigenvalue of the delaminated lamina determined only by the geometry of the delamination. Authentication of the multiscale study is fulfilled by comparing the analytical solutions with the FEA results.
Complete genome sequence of the cellulose-producing strain Komagataeibacter nataicola RZS01
Authors: Zhang Heng , Xu Xuran , Chen Xiao , Yuan Fanshu , Sun Bianjing , Xu Yunhua , Yang Jiazhi , Sun Dongping 
Published: June 2017

AbstractKomagataeibacter nataicola is an acetic acid bacterium (AAB) that can produce abundant bacterial cellulose and tolerate high concentrations of acetic acid. To globally understand its fermentation characteristics, we present a high-quality complete genome sequence of K. nataicola RZS01. The genome consists of a 3,485,191-bp chromosome and 6 plasmids, which encode 3,514 proteins and bear three cellulose synthase operons. Phylogenetic analysis at the genome level provides convincing evidence of the evolutionary position of K. nataicola with respect to related taxa. Genomic comparisons with other AAB revealed that RZS01 shares 36.1%~75.1% of sequence similarity with other AAB. The sequence data was also used for metabolic analysis of biotechnological substrates. Analysis of the resistance to acetic acid at the genomic level indicated a synergistic mechanism responsible for acetic acid tolerance. The genomic data provide a viable platform that can be used to understand and manipulate the phenotype of K. nataicola RZS01 to further improve bacterial cellulose production.
Proteomic shifts in multi-species oral biofilms caused by Anaeroglobus geminatus
Authors: Bao Kai , Bostanci Nagihan , Thurnheer Thomas , Belibasakis Georgios N. 
Published: June 2017

AbstractAnaeroglobus geminatus is a relatively newly discovered putative pathogen, with a potential role in the microbial shift associated with periodontitis, a disease that causes inflammatory destruction of the periodontal tissues, and eventually tooth loss. This study aimed to introduce A. geminatus into a polymicrobial biofilm model of relevance to periodontitis, and monitor the proteomic responses exerted to the rest of the biofilm community. A. geminatus was grown together with another 10-species in a well-established “subgingival” in vitro biofilm model. Its effects on the other species were quantitatively evaluated by qPCR and label-free proteomics. A. geminatus caused a significant increase in P. intermedia numbers, but not the other species in the biofilm. Whole cell proteome profiling of the biofilms by LC-MS/MS identified a total of 3213 proteins. Label-free quantitative proteomics revealed that 187 proteins belonging to the other 10 species were differentially abundant when A. geminatus was present in the biofilm. The species with most up-regulated and down-regulated proteins were P. intermedia and S. oralis, respectively. Regulated proteins were of primarily of ribosomal origin, and other affected categories involved proteolysis, carbon metabolism and iron transport. In conclusion, A. geminatus can be successfully grown in a polymicrobial biofilm community, causing quantitative proteomic shifts commensurate with increased virulence properties.
Automatic Detection of Galaxy Type From Datasets of Galaxies Image Based on Image Retrieval Approach
Authors: Abd El Aziz Mohamed , Selim I. M. , Xiong Shengwu 
Published: June 2017

AbstractThis paper presents a new approach for the automatic detection of galaxy morphology from datasets based on an image-retrieval approach. Currently, there are several classification methods proposed to detect galaxy types within an image. However, in some situations, the aim is not only to determine the type of galaxy within the queried image, but also to determine the most similar images for query image. Therefore, this paper proposes an image-retrieval method to detect the type of galaxies within an image and return with the most similar image. The proposed method consists of two stages, in the first stage, a set of features is extracted based on shape, color and texture descriptors, then a binary sine cosine algorithm selects the most relevant features. In the second stage, the similarity between the features of the queried galaxy image and the features of other galaxy images is computed. Our experiments were performed using the EFIGI catalogue, which contains about 5000 galaxies images with different types (edge-on spiral, spiral, elliptical and irregular). We demonstrate that our proposed approach has better performance compared with the particle swarm optimization (PSO) and genetic algorithm (GA) methods.
Effect of boron deficiency on anatomical structure and chemical composition of petioles and photosynthesis of leaves in cotton (Gossypium hirsutum L.)
Authors: Li Mingfeng , Zhao Zhuqing , Zhang Zhihua , Zhang Wei , Zhou Jun , Xu Fangsen , Liu Xinwei 
Published: June 2017

AbstractThe main symptom of boron (B) deficiency in cotton is the formation of brown rings on leaf petioles. The objective of the present study was to determine the changes in the anatomical structure and chemical composition of petioles and photosynthesis of leaves in cotton under B deficiency. Compared to the control, B deficiency treatment resulted in large increases in the number of petioles with brown rings per plant (160.0%) and the number of rings on the petiole per functional leaf (711.1%) in cotton seedlings. The relative absorbance intensity in the fingerprint region of polysaccharide structure was decreased in petiole rings under B deficiency, while lignin contents were increased. Cotton plants mitigated the impairment of transport function in cotton petioles by increasing the areas of vascular bundles, phloem, xylem, and phloem fiber. Moreover, the stomatal conductance, photosynthetic rate, and transpiration rate in leaves were significantly decreased under B deficiency, thus impeding photosynthesis in cotton plants. Therefore, B deficiency reduces transport function in petioles and photosynthesis in leaves, and leads to the formation of noticeable brown rings on petioles of cotton seedlings.
Near-Zero-Power Temperature Sensing via Tunneling Currents Through Complementary Metal-Oxide-Semiconductor Transistors
Authors: Wang Hui , Mercier Patrick P. 
Published: June 2017

AbstractTemperature sensors are routinely found in devices used to monitor the environment, the human body, industrial equipment, and beyond. In many such applications, the energy available from batteries or the power available from energy harvesters is extremely limited due to limited available volume, and thus the power consumption of sensing should be minimized in order to maximize operational lifetime. Here we present a new method to transduce and digitize temperature at very low power levels. Specifically, two pA current references are generated via small tunneling-current metal-oxide-semiconductor field effect transistors (MOSFETs) that are independent and proportional to temperature, respectively, which are then used to charge digitally-controllable banks of metal-insulator-metal (MIM) capacitors that, via a discrete-time feedback loop that equalizes charging time, digitize temperature directly. The proposed temperature sensor was integrated into a silicon microchip and occupied 0.15 mm2 of area. Four tested microchips were measured to consume only 113 pW with a resolution of 0.21 °C and an inaccuracy of ±1.65 °C, which represents a 628× reduction in power compared to prior-art without a significant reduction in performance.
Co-fermentation using Recombinant Saccharomyces cerevisiae Yeast Strains Hyper-secreting Different Cellulases for the Production of Cellulosic Bioethanol
Authors: Lee Cho-Ryong , Sung Bong Hyun , Lim Kwang-Mook , Kim Mi-Jin , Sohn Min Jeong , Bae Jung-Hoon , Sohn Jung-Hoon 
Published: June 2017

AbstractTo realize the economical production of ethanol and other bio-based chemicals from lignocellulosic biomass by consolidated bioprocessing (CBP), various cellulases from different sources were tested to improve the level of cellulase secretion in the yeast Saccharomyces cerevisiae by screening an optimal translational fusion partner (TFP) as both a secretion signal and fusion partner. Among them, four indispensable cellulases for cellulose hydrolysis, including Chaetomium thermophilum cellobiohydrolase (CtCBH1), Chrysosporium lucknowense cellobiohydrolase (ClCBH2), Trichoderma reesei endoglucanase (TrEGL2), and Saccharomycopsis fibuligera β-glucosidase (SfBGL1), were identified to be highly secreted in active form in yeast. Despite variability in the enzyme levels produced, each recombinant yeast could secrete approximately 0.6–2.0 g/L of cellulases into the fermentation broth. The synergistic effect of the mixed culture of the four strains expressing the essential cellulases with the insoluble substrate Avicel and several types of cellulosic biomass was demonstrated to be effective. Co-fermentation of these yeast strains produced approximately 14 g/L ethanol from the pre-treated rice straw containing 35 g/L glucan with 3-fold higher productivity than that of wild type yeast using a reduced amount of commercial cellulases. This process will contribute to the cost-effective production of bioenergy such as bioethanol and biochemicals from cellulosic biomass.