The discovery of antibiotics marked a golden age in the revolution of human medicine. However,decades later, bacterial infections remain a global healthcare threat, and a return to the pre-antibiotic era seems inevita...The discovery of antibiotics marked a golden age in the revolution of human medicine. However,decades later, bacterial infections remain a global healthcare threat, and a return to the pre-antibiotic era seems inevitable if stringent measures are not adopted to curb the rapid emergence and spread of multidrug resistance and the indiscriminate use of antibiotics. In hospital settings, multidrug resistant(MDR) pathogens, including carbapenem-resistant Pseudomonas aeruginosa, vancomycin-resistant enterococci(VRE), methicillin-resistant Staphylococcus aureus(MRSA), and extendedspectrum β-lactamases(ESBL) bearing Acinetobacter baumannii, Escherichia coli, and Klebsiella pneumoniae are amongst the most problematic due to the paucity of treatment options,increased hospital stay, and exorbitant medical costs. Antimicrobial peptides(AMPs) provide an excellent potential strategy for combating these threats. Compared to empirical antibiotics, they show low tendency to select for resistance, rapid killing action, broad-spectrum activity, and extraordinary clinical efficacy against several MDR strains. Therefore, this review highlights multidrug resistance among nosocomial bacterial pathogens and its implications and reiterates the importance of AMPs as next-generation antibiotics for combating MDR superbugs.展开更多
1 Introduction In[5]we investigated the significance of some truth-functional three valued logics of ill-known sets described by pairs of disjoint(or pairs of nested) subsets.In particular,we referred to the case of r...1 Introduction In[5]we investigated the significance of some truth-functional three valued logics of ill-known sets described by pairs of disjoint(or pairs of nested) subsets.In particular,we referred to the case of rough sets showing that if from a mathematical standpoint we obtain sound results,the interpretation with respect展开更多
Graphene-coated silicon carbide(SiC@C)core-shell nanostructures have attracted attention in the fields of energy storage and nanoelectronics.In this study,multilayer graphene-coated silicon carbide(SiC)nanowires were ...Graphene-coated silicon carbide(SiC@C)core-shell nanostructures have attracted attention in the fields of energy storage and nanoelectronics.In this study,multilayer graphene-coated silicon carbide(SiC)nanowires were obtained through the laser irradiation of a mixture target of graphite powder and silicon(Si)grinding sludge discharged from Si wafer manufacturing.Laser irradiation was performed using an ytterbium(Yb)fiber pulsed laser with a pulse width of 10 ms and a wavelength of 1070 nm with various defocus distances.The effect of laser defocusing on the morphology of the generated nanostructures was investigated.Results showed that nanowires were produced under the defocused conditions,and nanoparticles were observed at the on-focus position.The products obtained under all defocused conditions showed a core-shell structure,and the SiC nanowires were covered by graphene layers.The aspect ratio of the nanowires increased with the defocus distance.Observation of the laser-induced plume using a high-speed camera showed that when the laser was defocused,the plume propagation speed slowed down,and the shape of the plume changed to a swirling vortex.The nanowire formation was closely related to the propagation speed and shape variation of the plume.This successful production of SiC@C core-shell nanowires from Si waste opens up the possibility of the sustainable development of new materials for energy storage and nanoelectronics.展开更多
Dysfunctions of ATP-binding cassette,subfamily D,member 1(ABCD1)cause X-linked adrenoleukodystrophy,a rare neurodegenerative disease that affects all human tissues.Residing in the peroxisome membrane,ABCD1 plays a rol...Dysfunctions of ATP-binding cassette,subfamily D,member 1(ABCD1)cause X-linked adrenoleukodystrophy,a rare neurodegenerative disease that affects all human tissues.Residing in the peroxisome membrane,ABCD1 plays a role in the translocation of very long-chain fatty acids for theirβ-oxidation.Here,the six cryo-electron microscopy structures of ABCD1 in four distinct conformational states were presented.In the transporter dimer,two transmembrane domains form the substrate translocation pathway,and two nucleotide-binding domains form the ATP-binding site that binds and hydrolyzes ATP.The ABCD1 structures provide a starting point for elucidating the substrate recognition and translocation mechanism of ABCD1.Each of the four inward-facing structures of ABCD1 has a vestibule that opens to the cytosol with variable sizes.Hexacosanoic acid(C26:0)-CoA substrate binds to the transmembrane domains(TMDs)and stimulates the ATPase activity of the nucleotide-binding domains(NBDs).W339 from the transmembrane helix 5(TM5)is essential for binding substrate and stimulating ATP hydrolysis by substrate.ABCD1 has a unique C-terminal coiled-coil domain that negatively modulates the ATPase activity of the NBDs.Furthermore,the structure of ABCD1 in the outward-facing state indicates that ATP molecules pull the two NBDs together and open the TMDs to the peroxisomal lumen for substrate release.The five structures provide a view of the substrate transport cycle and mechanistic implication for disease-causing mutations.展开更多
The investigation of genetic differences among humans has given evidence thatmutations in DNA sequences are responsible for some genetic diseases. The most common mutation isthe one that involves only a single nucleot...The investigation of genetic differences among humans has given evidence thatmutations in DNA sequences are responsible for some genetic diseases. The most common mutation isthe one that involves only a single nucleotide of the DNA sequence, which is called a singlenucleotide polymorphism (SNP). As a consequence, computing a complete map of all SNPs occurring inthe human populations is one of the primary goals of recent studies in human genomics. Theconstruction of such a map requires to determine the DNA sequences that from all chromosomes. Indiploid organisms like humans, each chromosome consists of two sequences called haplotypes.Distinguishing the information contained in both haplotypes when analyzing chromosome sequencesposes several new computational issues which collectively form a new emerging topic of ComputationalBiology known as Haplotyping. This paper is a comprehensive study of some new combinatorialapproaches proposed in this research area and it mainly focuses on the formulations and algorithmicsolutions of some basic biological problems. Three statistical approaches are briefly discussed atthe end of the paper.展开更多
The paper discusses the need of a high-level query language to allow analysts,geographers and,in general,non-programmers to easily cross-analyze multi-source VGI created by means of apps,crowd-sourced data from social...The paper discusses the need of a high-level query language to allow analysts,geographers and,in general,non-programmers to easily cross-analyze multi-source VGI created by means of apps,crowd-sourced data from social networks and authoritative geo-referenced data,usually represented as JSON data sets(nowadays,the de facto standard for data exported by social networks).Since an easy to use high-level language for querying and manipulating collections of possibly geo-tagged JSON objects is still unavailable,we propose a truly declarative language,named J-CO-QL,that is based on a well-defined execution model.A plug-in for a GIS permits to visualize geo-tagged data sets stored in a NoSQL database such as MongoDB;furthermore,the same plug-in can be used to write and execute J-CO-QL queries on those databases.The paper introduces the language by exemplifying its operators within a real study case,the aim of which is to understand the mobility of people in the neighborhood of Bergamo city.Cross-analysis of data about transportation networks and VGI from travelers is performed,by means of J-CO-QL language,capable to manipulate and transform,combine and join possibly geo-tagged JSON objects,in order to produce new possibly geo-tagged JSON objects satisfying users’needs.展开更多
The crop rotation system in organic farming is a determinant factor to accumulate and preserve soil organic matter(SOM),and in depth knowledge on its effects is still lacking.Tillage intensity in particular is crucial...The crop rotation system in organic farming is a determinant factor to accumulate and preserve soil organic matter(SOM),and in depth knowledge on its effects is still lacking.Tillage intensity in particular is crucial to maintain soil aggregates and protect SOM from degradation.The evolution of SOM was tested in two adjacent fields under two different rotation cropping systems(low-intensity tillage and high-intensity tillage),and the effect of a further cultivation of legume in both fields was evaluated using ^(13)carbon(C)-nuclear magnetic resonance(NMR)and elemental analysis of samples isolated through combined aggregate size and density fractionation.The two adjacent fields had been managed using the following organic farming methods for 13 seasons since 1998:i)alfalfa-based,with nitrogen(N)enrichment and low-frequency tillage with alfalfa(Medicago sativa)(9 seasons),winter wheat(Triticum durum)(3 seasons),and broad bean(Vicia faba)(1 season)and ii)cereal-based,with N depletion and annual tillage with barley(Hordeum vulgare)(7 seasons),sunflower(Helianthus annuus)(2 seasons),broad bean(Vicia faba)(3 seasons),and bare fallow(1 season).Soil sampling was carried out at the end of the 13-year rotation(T0,November 2011)and after winter wheat and chickpea cultivation in both fields over two subsequent years(T1,July 2013).Bulk organic C was significantly higher in the alfalfa-based system than in the cereal-based system at both T0 and T1,with SOM occluded in soil aggregates and associated with mineral particles.In terms of the macroaggregates heavy fraction at T0,the alfalfa-based field contained twice the organic C of that in the cereal-based field,as well as three times the organic C in the occluded particulate organic matter(POM).The occluded POM(oPOM)had a lower aryl/O-alkyl C ratio in the alfalfa-based system than in the cereal-based system,suggesting that oPOM undergoes a lower degree of decomposition during low-intensity management.The aryl/O-alkyl C ratios of the macro-and microaggregate oPOM decreased from T0 to T1 in the cereal-based system,suggesting increased protection of these fractions by soil aggregates.Thus,including legumes in crop rotation appears to positively affect the accumulation of SOM associated with mineral particles and within soil aggregates.展开更多
Among multiple sclerosis(MS)susceptibility genes,the strongest non-human leukocyte antigen(HLA)signal in the Italian population maps to the TNFSF14 gene encoding LIGHT,a glycoprotein involved in dendritic cell(DC)matu...Among multiple sclerosis(MS)susceptibility genes,the strongest non-human leukocyte antigen(HLA)signal in the Italian population maps to the TNFSF14 gene encoding LIGHT,a glycoprotein involved in dendritic cell(DC)maturation.Through fine-mapping in a large Italian dataset(4,198 patients with MS and3,903 controls),we show that the TNFSF14 intronic SNP rs1077667 is the primarily MS-associated variant in the region.Expression quantitative trait locus(e QTL)analysis indicates that the MS risk allele is significantly associated with reduced TNFSF14 messenger RNA levels in blood cells,which is consistent with the allelic imbalance in RNA-Seq reads(P<0.0001).The MS risk allele is associated with reduced levels of TNFSF14 gene expression(P<0.01)in blood cells from 84 Italian patients with MS and 80 healthy controls(HCs).Interestingly,patients with MS are lower expressors of TNFSF14 compared to HC(P<0.007).Individuals homozygous for the MS risk allele display an increased percentage of LIGHT-positive peripheral blood myeloid DCs(CD11 c+,P=0.035)in 37 HCs,as well as in in vitro monocyte-derived DCs from 22 HCs(P=0.04).Our findings suggest that the intronic variant rs1077667 alters the expression of TNFSF14 in immune cells,which may play a role in MS pathogenesis.展开更多
基金supported by the National Natural Science Foundation of China(21761142002 and 31801975)Chinese Academy of Sciences(XDB31000000,SAJC201606,KFZD-SW-219-2,KFJ-BRP-008,and KGFZD-135-17-011)Yunnan Province Grant(2015HA023)
文摘The discovery of antibiotics marked a golden age in the revolution of human medicine. However,decades later, bacterial infections remain a global healthcare threat, and a return to the pre-antibiotic era seems inevitable if stringent measures are not adopted to curb the rapid emergence and spread of multidrug resistance and the indiscriminate use of antibiotics. In hospital settings, multidrug resistant(MDR) pathogens, including carbapenem-resistant Pseudomonas aeruginosa, vancomycin-resistant enterococci(VRE), methicillin-resistant Staphylococcus aureus(MRSA), and extendedspectrum β-lactamases(ESBL) bearing Acinetobacter baumannii, Escherichia coli, and Klebsiella pneumoniae are amongst the most problematic due to the paucity of treatment options,increased hospital stay, and exorbitant medical costs. Antimicrobial peptides(AMPs) provide an excellent potential strategy for combating these threats. Compared to empirical antibiotics, they show low tendency to select for resistance, rapid killing action, broad-spectrum activity, and extraordinary clinical efficacy against several MDR strains. Therefore, this review highlights multidrug resistance among nosocomial bacterial pathogens and its implications and reiterates the importance of AMPs as next-generation antibiotics for combating MDR superbugs.
文摘1 Introduction In[5]we investigated the significance of some truth-functional three valued logics of ill-known sets described by pairs of disjoint(or pairs of nested) subsets.In particular,we referred to the case of rough sets showing that if from a mathematical standpoint we obtain sound results,the interpretation with respect
基金This study was funded by Japan Society for the Promotion of Science,Grant-in-Aid for Exploratory Research(Project Number 21K18681).
文摘Graphene-coated silicon carbide(SiC@C)core-shell nanostructures have attracted attention in the fields of energy storage and nanoelectronics.In this study,multilayer graphene-coated silicon carbide(SiC)nanowires were obtained through the laser irradiation of a mixture target of graphite powder and silicon(Si)grinding sludge discharged from Si wafer manufacturing.Laser irradiation was performed using an ytterbium(Yb)fiber pulsed laser with a pulse width of 10 ms and a wavelength of 1070 nm with various defocus distances.The effect of laser defocusing on the morphology of the generated nanostructures was investigated.Results showed that nanowires were produced under the defocused conditions,and nanoparticles were observed at the on-focus position.The products obtained under all defocused conditions showed a core-shell structure,and the SiC nanowires were covered by graphene layers.The aspect ratio of the nanowires increased with the defocus distance.Observation of the laser-induced plume using a high-speed camera showed that when the laser was defocused,the plume propagation speed slowed down,and the shape of the plume changed to a swirling vortex.The nanowire formation was closely related to the propagation speed and shape variation of the plume.This successful production of SiC@C core-shell nanowires from Si waste opens up the possibility of the sustainable development of new materials for energy storage and nanoelectronics.
基金We wish to thank the National Facility for Protein Science in Shanghai(NFPS)for enabling the cryo-EM experiments.This work was supported by the National Key Research and Development Project(2017YFA0504300)the National Natural Science Foundation of China(grants 31770897 and 81801294)the International Science and Technology Innovation Cooperation Project of Sichuan(No.2021YFH0141).
文摘Dysfunctions of ATP-binding cassette,subfamily D,member 1(ABCD1)cause X-linked adrenoleukodystrophy,a rare neurodegenerative disease that affects all human tissues.Residing in the peroxisome membrane,ABCD1 plays a role in the translocation of very long-chain fatty acids for theirβ-oxidation.Here,the six cryo-electron microscopy structures of ABCD1 in four distinct conformational states were presented.In the transporter dimer,two transmembrane domains form the substrate translocation pathway,and two nucleotide-binding domains form the ATP-binding site that binds and hydrolyzes ATP.The ABCD1 structures provide a starting point for elucidating the substrate recognition and translocation mechanism of ABCD1.Each of the four inward-facing structures of ABCD1 has a vestibule that opens to the cytosol with variable sizes.Hexacosanoic acid(C26:0)-CoA substrate binds to the transmembrane domains(TMDs)and stimulates the ATPase activity of the nucleotide-binding domains(NBDs).W339 from the transmembrane helix 5(TM5)is essential for binding substrate and stimulating ATP hydrolysis by substrate.ABCD1 has a unique C-terminal coiled-coil domain that negatively modulates the ATPase activity of the NBDs.Furthermore,the structure of ABCD1 in the outward-facing state indicates that ATP molecules pull the two NBDs together and open the TMDs to the peroxisomal lumen for substrate release.The five structures provide a view of the substrate transport cycle and mechanistic implication for disease-causing mutations.
文摘The investigation of genetic differences among humans has given evidence thatmutations in DNA sequences are responsible for some genetic diseases. The most common mutation isthe one that involves only a single nucleotide of the DNA sequence, which is called a singlenucleotide polymorphism (SNP). As a consequence, computing a complete map of all SNPs occurring inthe human populations is one of the primary goals of recent studies in human genomics. Theconstruction of such a map requires to determine the DNA sequences that from all chromosomes. Indiploid organisms like humans, each chromosome consists of two sequences called haplotypes.Distinguishing the information contained in both haplotypes when analyzing chromosome sequencesposes several new computational issues which collectively form a new emerging topic of ComputationalBiology known as Haplotyping. This paper is a comprehensive study of some new combinatorialapproaches proposed in this research area and it mainly focuses on the formulations and algorithmicsolutions of some basic biological problems. Three statistical approaches are briefly discussed atthe end of the paper.
文摘The paper discusses the need of a high-level query language to allow analysts,geographers and,in general,non-programmers to easily cross-analyze multi-source VGI created by means of apps,crowd-sourced data from social networks and authoritative geo-referenced data,usually represented as JSON data sets(nowadays,the de facto standard for data exported by social networks).Since an easy to use high-level language for querying and manipulating collections of possibly geo-tagged JSON objects is still unavailable,we propose a truly declarative language,named J-CO-QL,that is based on a well-defined execution model.A plug-in for a GIS permits to visualize geo-tagged data sets stored in a NoSQL database such as MongoDB;furthermore,the same plug-in can be used to write and execute J-CO-QL queries on those databases.The paper introduces the language by exemplifying its operators within a real study case,the aim of which is to understand the mobility of people in the neighborhood of Bergamo city.Cross-analysis of data about transportation networks and VGI from travelers is performed,by means of J-CO-QL language,capable to manipulate and transform,combine and join possibly geo-tagged JSON objects,in order to produce new possibly geo-tagged JSON objects satisfying users’needs.
基金funded by the Department of Agricultural,Food and Environmental Sciences(D3 A),Polytechnic University of Marche,Ancona,Italy。
文摘The crop rotation system in organic farming is a determinant factor to accumulate and preserve soil organic matter(SOM),and in depth knowledge on its effects is still lacking.Tillage intensity in particular is crucial to maintain soil aggregates and protect SOM from degradation.The evolution of SOM was tested in two adjacent fields under two different rotation cropping systems(low-intensity tillage and high-intensity tillage),and the effect of a further cultivation of legume in both fields was evaluated using ^(13)carbon(C)-nuclear magnetic resonance(NMR)and elemental analysis of samples isolated through combined aggregate size and density fractionation.The two adjacent fields had been managed using the following organic farming methods for 13 seasons since 1998:i)alfalfa-based,with nitrogen(N)enrichment and low-frequency tillage with alfalfa(Medicago sativa)(9 seasons),winter wheat(Triticum durum)(3 seasons),and broad bean(Vicia faba)(1 season)and ii)cereal-based,with N depletion and annual tillage with barley(Hordeum vulgare)(7 seasons),sunflower(Helianthus annuus)(2 seasons),broad bean(Vicia faba)(3 seasons),and bare fallow(1 season).Soil sampling was carried out at the end of the 13-year rotation(T0,November 2011)and after winter wheat and chickpea cultivation in both fields over two subsequent years(T1,July 2013).Bulk organic C was significantly higher in the alfalfa-based system than in the cereal-based system at both T0 and T1,with SOM occluded in soil aggregates and associated with mineral particles.In terms of the macroaggregates heavy fraction at T0,the alfalfa-based field contained twice the organic C of that in the cereal-based field,as well as three times the organic C in the occluded particulate organic matter(POM).The occluded POM(oPOM)had a lower aryl/O-alkyl C ratio in the alfalfa-based system than in the cereal-based system,suggesting that oPOM undergoes a lower degree of decomposition during low-intensity management.The aryl/O-alkyl C ratios of the macro-and microaggregate oPOM decreased from T0 to T1 in the cereal-based system,suggesting increased protection of these fractions by soil aggregates.Thus,including legumes in crop rotation appears to positively affect the accumulation of SOM associated with mineral particles and within soil aggregates.
基金supported by the Italian Foundation of Multiple Sclerosis(FISM,2011/R/142015/R/10,2019/R-Multi/033)by the Italian Ministry of Health(RF-2016-02361294)the AGING Project for Department of Excellence at the Department of Translational Medicine(DIMET),Universitàdel Piemonte Orientale,Novara,Italy+1 种基金supported by Consorzio Interuniversitario di Biotecnologie(CIB)partially supported by Multiple MS project(Horizon 2020 European Grant 733161),Stockholm。
文摘Among multiple sclerosis(MS)susceptibility genes,the strongest non-human leukocyte antigen(HLA)signal in the Italian population maps to the TNFSF14 gene encoding LIGHT,a glycoprotein involved in dendritic cell(DC)maturation.Through fine-mapping in a large Italian dataset(4,198 patients with MS and3,903 controls),we show that the TNFSF14 intronic SNP rs1077667 is the primarily MS-associated variant in the region.Expression quantitative trait locus(e QTL)analysis indicates that the MS risk allele is significantly associated with reduced TNFSF14 messenger RNA levels in blood cells,which is consistent with the allelic imbalance in RNA-Seq reads(P<0.0001).The MS risk allele is associated with reduced levels of TNFSF14 gene expression(P<0.01)in blood cells from 84 Italian patients with MS and 80 healthy controls(HCs).Interestingly,patients with MS are lower expressors of TNFSF14 compared to HC(P<0.007).Individuals homozygous for the MS risk allele display an increased percentage of LIGHT-positive peripheral blood myeloid DCs(CD11 c+,P=0.035)in 37 HCs,as well as in in vitro monocyte-derived DCs from 22 HCs(P=0.04).Our findings suggest that the intronic variant rs1077667 alters the expression of TNFSF14 in immune cells,which may play a role in MS pathogenesis.