Small Strands Research Articles

PENGEMBANGAN LONGEST PATH ALGORITHM (LPA) DALAM RANGKA PENCARIAN LINTASAN TERPANJANG PADA GRAF BERSAMBUNG BERARAH BERUNTAI

The longest distance in a graph that has a number of vertices, arcs and small strands easily done manually. However, if the graph has a number of vertices, arcs and strands of many, the determination of the distance and the longest path will be difficult. Research has developed Longest Path Algorithm (LPA) in order to search for the longest distance and trajectory continued trending stranded on a graph. LPA enables application development and search distance of the longest path in the graph continued trending quickly and accurately. LPA in the development of a solution to help solve the problem of finding the longest path in a directed graph stranded concatenated.

烘丝机设备参数与叶丝质量关系研究—以红河卷烟厂某牌号叶丝为例

烘丝机设备参数直接影响着烘后叶丝物理指标、卷烟后序加工质量及卷烟内在品质。本文采用回归设计试验，系统探讨了红河某牌号烟丝生丝含水率、工艺流量、HT蒸湿压力、烘丝机筒壁温度、热风温度、排潮风门开度6个设备参数与烘后叶丝的含水率、填充值、整丝率、碎丝率、化学成分等质量特性的关系，建立了烘丝机设备参数与烘后叶丝含水率、填充值、叶丝绿原酸和糖碱比的统计模型。结果表明：为保障烘后叶丝含水率均匀一致，应重点关注生丝含水率的波动；为提高叶丝填充值，可适当降低生丝含水率，同时增加HT蒸汽压力和筒壁温度。 Cut tobacco drier equipment parameters directly affect the leaf silk physical indicators, the quality of cigarette after drying processing and cigarette inner quality. Using regression design experiment, this paper systematically discusses the relationship of the tobacco moisture content, process flow, steam pressure of HT, the temperature of hot-air and cylinder wall, the opening of the exhausted valve among the tobacco moisture contents, filling power, the proportion of long strands, the proportion of small strands, and chemical component. Statistical model of cut tobacco drier equipment parameters and silk moisture content after drying, filling power, leaf silk chlorogenic acid, and ratios of total sugar to betaine is established. Results show that in order to ensure silk moisture content after drying uniformity, we should focus on the fluctuation of raw silk moisture content; in order to improve the leaf silk filling power, we should reduce the moisture content of raw silk appropriately and increase the steam pressure of HT and the temperature of cylinder wall at the same time.

The effect of protein aggregate morphology on phase separation in mixtures with polysaccharides

The morphology of aggregates formed by heating the globular protein β-lactoglobulin ( β-lg) changes with the addition of a small amount of CaCl2, from small strands to larger spherical aggregates (microgels). We investigated the effect of this morphological transition on the structure of mixtures of β-lg aggregates with the polysaccharide κ-carrageenan (κ-car), using confocal laser scanning microscopy and dynamic light scattering. The change in the morphology of the β-lg aggregates strongly reduced the κ-car concentration at which the system phase separated. As a consequence a dramatic change in the structure of the mixtures occurred over a narrow range of the CaCl2 concentration. Phase separation leads to the formation of micron-sized protein rich domains that have a tendency to stick together in large flocs. There is a big difference between the protein concentrations in the two phases, but the κ-car concentration is only weakly lower in the protein rich phase. A comparison is made between mixtures prepared at room temperature, after separately heating β-lg, and heated mixtures of native β-lg and κ-car. The micro-phase separated structure of the two systems is similar, but the aggregates disperse upon dilution in the former case, while they are covalently bound within the domains in the latter case. Other, more subtle, differences were also observed. The results explain the very high sensitivity of the structure of β-lg/κ-car mixtures to calcium ions.

The effect of the competition for calcium ions between κ-carrageenan and β-lactoglobulin on the rheology and the structure in mixed gels

Protein aggregates were formed by heating the globular protein β-lactoglobulin (β-lg) in aqueous solution in the presence of CaCl2 leading to small strands at low CaCl2 concentrations and larger spherical microgels at higher CaCl2 concentrations. The structure of mixtures of protein aggregates and the polysaccharide κ-carrageenan (κ-car) was investigated at pH 7 using confocal laser scanning microscopy. Microphase separation in the form of dense protein domains was observed for mixtures with microgels even at very low κ-car concentrations (0.5 g/L). Gelation of κ-car was induced by cooling in the presence of 10 mM KCl. Addition of microgels strongly increased the gelation rate and the elastic modulus of the κ-car gels, while the effect of adding native proteins or strands was small. The effect could be attributed to the presence of calcium ions used to form the microgels. However, the effect was smaller than in pure κ-car gels if the same amount of calcium ions was added in the form of CaCl2. The effect is explained by the competition between κ-car and β-lg for calcium ions. A weaker effect was observed with native β-lg, which can be correlated with the weaker binding of Ca2+ by native β-lg compared to microgels. Gelation of β-lg in the presence of κ-car was induced by heating mixtures of κ-car and native β-lg. The presence of κ-car facilitated gelation of β-lg at lower CaCl2 concentrations. κ-car was gelled within the β-lg gel by cooling. It was found that the elastic modulus of the mixed gel was close to the sum of that of the κ-car gel with native β-lg and the β-lg gel with uncrosslinked κ-car coils.

208: Inhibiting cytokine activity – The use of modified DNA aptamers as an alternative to neutralizing antibodies

In clinical medicine the use of neutralizing antibodies has revolutionized the treatment of a number of diseases and improved the quality of like of thousands of patients. However the use of these antibodies is not with out problems, including the development of an immune response to the antibodies themselves. DNA aptamers may be an alternate approach to antibodies for targeting cytokines where cytokine expression is directly contributing to disease pathogenesis, In this study we report the development and characterization of DNA aptamers for the neutralization of Interferon-gamma (IFN-g). A DNA aptamer has been developed for human IFN-g as reported by Kimoto and co-workers (Kimoto et al. 453–57, 2013 Nature Biotechnology). DNA aptamers are small single strand molecules that have high affinities for their target proteins. Modifying the DNA aptamer, by the addition of a few non-natural hydrophobic bases as a fifth base, greatly increases the affinity to IFN-g (Kd = 38 pM). These modified aptamers demonstrate increased stability in binding to IFN-g in the presence of mouse or human serum and efficiently neutralize the ability of IFN-g to induce the phosphorylation of STAT1. Furthermore, they appear to act by directly binding to IFN-g and preventing the interaction of IFN-g with its cell surface receptor. Thus DNA aptamers offer the intriguing possibility of small molecule inhibitors of cytokine signaling as an alternative to the use of neutralizing antibodies.

Photographing physical activity: using visual methods to ‘grasp at’ the sensual experiences of the ageing body

Within the sociology of sport there is a small but rich strand of literature concerned with understanding the sensual experiences of sport and physical activity. Whilst this work has advanced our understanding of the sensual sporting body, less is known about the mature sporting body and the sensual experiences of older adults. Gaining an insight into the sensual experiences of others is no easy task and this article critically reflects on the methods used to ‘grasp at’ (Hockey and Allen-Collinson, 2007) older adults’ embodied experiences of physical activity. An account of the process and outcomes of the method employed is presented along with visual and textual data to illustrate the problems and possibilities of exploring the sensual experiences of the ageing body within the context of physical activity.

Effect of small interfering RNAs on matrix metalloproteinase 1 expression

Three small double strand siRNAs (506-MMP1, 859-MMP1 and 891-MMP1), each contains 25–26 nucleotides, with high specific to human MMP1 were designed according to mRNA sequence of human MMP1 (NCBI, NM_002421). To monitor the MMP1 gene expression, the total RNAs of human skin fibroblast (Detroit 551, BCRC 60118) were extracted. One human matrix metalloproteinase 1 (MMP1) partial sequence cDNA, included all the three siRNA target sequences, amplified specifically via RT-PCR and PCR reactions, and three synthesized siRNA target DNAs were cloned individually into pAcGFP1-N3 with green fluorescent protein (GFP). These reporter plasmids were then transfected individually into malignant melanoma (MeWo, BCRC 60540) and the GFP was detected after 48h. Fluorescence results indicated that the 859 siRNA revealed highest inhibitory ability (almost 90%), and was, accordingly, transfected into MeWo cells. According to the real-time quantitative PCR and western blot, the exhibition ability to silence MMP1 gene expression was 85–89%.

Role of microRNAs in the immunity process of the flat oyster Ostrea edulis against bonamiosis

MicroRNAs (miRNAs) are small (∼22nt) non-coding regulatory single strand RNA molecules that reduce stability and/or translation of sequence-complementary target. miRNAs are a key component of gene regulatory networks and have been involved in a wide variety of biological processes, such as signal transduction, cell proliferation and apoptosis. Many miRNAs are broadly conserved among the animal lineages and even between invertebrates and vertebrates. The European flat oyster Ostrea edulis is highly susceptible to infection with Bonamia ostreae, an intracellular parasite able to survive and proliferate within oyster haemocytes. Mollusc haemocytes play a key role in the immune response of molluscs as main cellular effectors. The roles of miRNAs in the immune response of O. edulis to bonamiosis were analysed using a commercial microarray platform (miRCURY LNA™ v2, Exiqon) for miRNAs. Expression of miRNAs in haemocytes from oysters with different bonamiosis intensity was compared. Differential expression was detected in 63 and 76 miRNAs when comparing heavily-affected with non-affected oysters and with lightly-affected ones, respectively. Among them, 19 miRNAs are known to be linked to immune response, being responsible of proliferation and activation of macrophages, inflammation, apoptosis and/or oxidative damage, which is consistent with the modulation of their expression in oyster haemocytes due to bonamiosis.

Effects of high pressure processing on the thermal gelling properties of chicken breast myosin containing κ-carrageenan

The effects of high pressure processing (HPP) (0–400 MPa for 10 min, 0–20 min under 300 MPa) on the water holding capacity (WHC) and gel strength of chicken breast myosin containing 0.225% κ-carrageenan (W/V, 2.25 g/L relative to myosin solution) (myosin-K) and the thermal gelling mechanism were investigated. The results revealed that HPP at 100–400 MPa could significantly increase the WHC of myosin-K gels while decreasing the gel strength (P < 0.05). The turbidity, surface hydrophobicity and reactive sulfhydryl contents of the pressurized myosin-K increased significantly at 200–400 MPa (P < 0.05). Dynamic rheological measurements indicated that the thermal gelling ability of the pressurized myosin-K matrix gradually decreased as the pressure increased (100–400 MPa). Low-field nuclear magnetic resonance data suggested that HPP at 100–400 MPa might shorten the water relaxation time of the gel. The Fourier transform infrared spectroscopy data revealed that the hydrogen bonding interactions in the gels might weaken when subjected to 100–300 MPa but could be enhanced at 400 MPa. The scanning electron microscopy images revealed that HPP (300 MPa, 10 min) produced a dense, networked myosin-K gel structure with small cavities and thin cross-linked strands. Moreover, pressure levels were responsible for the above results. The protein in myosin-K could denature, unfold and aggregate under HPP (100–400 MPa), thus decreasing the thermal gelling ability of myosin-K matrix. The high WHC of the pressurized myosin-K gel was attributed to the enhanced hydrogen bonding and hydrophobic interactions, as well as the uniform and dense networked structure; the low gel strength might be ascribed to the low thermal gelling ability of pressurized myosin-K.

Palate Mucocele

Woman, 63, complained of a “wart in the palate” that had developed over 6 months. It was asymptomatic, of normal color, had well-defined edges, and was situated near the median suture. The presumptive diagnosis was mucocele or a minor salivary gland tumor. Histopathological analysis identified adenoid cystic carcinoma. Microscopic analysis revealed numerous hyperchromatic, cuboidal epithelial cells with scanty and clear cytoplasm. Perineural infiltration was scarce. Adjacent to it was a dilated duct with mucus inside that suggested a mucous retention cyst. These cells were arranged in small strands and nests, with tubular and ductal aspects. The patient was treated surgically. This case emphasizes the importance of biopsy in identifying tumors associated with mucocele.

Desmoplastic hybrid ameloblastoma presenting as a fibrous epulis

Desmoplastic ameloblastoma (DA) is a rare variant of ameloblastoma with specific clinical, imaging, and histological features. Histologically, it is characterized by extensive stromal desmoplasia with small compressed nests and strands of odontogenic epithelium. The purpose of this article is to present a case of central DA that showed unusual clinical presentation of a classic solid/multicystic ameloblastoma occurring as a peripheral lesion in the form of gingival epulis, arising from extraction site and showed histopathological feature of a hybrid variant.

Fluctuations of perch populations in Lake Geneva from 1984 to 2011 estimated from the number and size of egg strands collected in two locations exposed to different fishing practices

AbstractFluctuations in the number and size of spawning perch (Perca fluviatilis) in Lake Geneva were evaluated and compared each year from 1984 to 2011 in two locations. This evaluation was based on: (1) each mature female lays only one egg strand per year and (2) the number and size of mature females are well correlated with those of their egg strands. Egg strands were counted and measured at two locations in France and in Switzerland. The collection of egg strands from either artificial substrates (France) or by direct sampling of the natural lake bottom by a diver (Switzerland) did not seem to affect the results. In most years the number and mean width of egg strands fluctuated in the same way in both locations. In addition, yearly perch catches were correlated with the number of egg strands at both locations. However, more small egg strands were found in France than in Switzerland, whereas the reverse was true of large egg strands. Fishing pressure concentrated to a greater extent on small perch in France than in Switzerland could explain this difference.

Reconsidering reputation through patronage: Cardinal Napoleone Orsini and Angelo Clareno at the Avignonese papal court

The changeable politics of Cardinal Napoleone Orsini (c.1262/3–1342), negotiator and pope-maker, have been explained for over a century as the expression of his independent character and antagonistic relationships. Significant moments in his early career are interpreted as deliberate opposition to his own family's policies. This generalisation does his political acumen and familial loyalty a disservice. In particular, the rationale for his political decisions has previously been relied upon in explanations for his support of the Spiritual Franciscans, reformers and sometime separatists within the Franciscan Order. The cardinal's impact on the group has likewise been understated, as scholars have largely focused on their spokesmen's intellectual output, with limited investigation of the political support that enabled their survival. Orsini was connected to the group's spokesmen at the papal court at Avignon, including the prolific author Angelo Clareno (c.1250–c.1337). Close examination of Clareno's letters allows for a reinterpretation of the relationship. Orsini family documents reframe the relationship as part of an established familial tradition of Franciscan patronage. In this larger picture, the impetus for the cardinal's idiosyncratic patronage of the Spirituals becomes, instead, a small strand in the much larger network of familial obligations and patronage responsibilities. This also sheds further light on the fourteenth-century papal curia.

Bubble-seq analysis of the human genome reveals distinct chromatin-mediated mechanisms for regulating early- and late-firing origins.

We have devised a method for isolating virtually pure and comprehensive libraries of restriction fragments that contained replication initiation sites (bubbles) in vivo. We have now sequenced and mapped the bubble-containing fragments from GM06990, a near-normal EBV-transformed lymphoblastoid cell line, and have compared origin distributions with a comprehensive replication timing study recently published for this cell line. We find that early-firing origins, which represent ∼32% of all origins, overwhelmingly represent zones, associate only marginally with active transcription units, are localized within large domains of open chromatin, and are significantly associated with DNase I hypersensitivity. Origin “density” falls from early- to mid-S-phase, but rises again in late S-phase to levels only 17% lower than in early S-phase. Unexpectedly, late origin density calculated on the 1-Mb scale increases as a function of increasing chromatin compaction. Furthermore, the median efficiency of origins in late-replicating, heterochromatic domains is only 25% lower than in early-replicating euchromatic loci. Thus, the activation of early- and late-firing origins must be regulated by quintessentially different mechanisms. The aggregate data can be unified into a model in which initiation site selection is driven almost entirely by epigenetic factors that fashion both the long-range and local chromatin environments, with underlying DNA sequence and local transcriptional activity playing only minor roles. Importantly, the comprehensive origin map we have prepared for GM06990 overlaps moderately well with origin maps recently reported for the genomes of four different human cell lines based on the distributions of small nascent strands.

Tuning the Structure of Protein Particles and Gels with Calcium or Sodium Ions

The effect of the addition of NaCl or CaCl2 on the structure of protein particles and gels was investigated in detail for aqueous solutions of the globular milk protein β-lactoglobulin at 40g/L and pH 7.0. When heated in the presence of NaCl or at very low CaCl2 concentrations, the proteins form small strand-like particles, but if more than about two Ca(2+) ions per protein are present, larger spherical particles (microgels) are formed, which increase in size with increasing CaCl2 concentration. The effect of the heating temperature was investigated between 62 and 85 °C. At lower heating temperatures, more Ca(2+) ions per protein are needed to drive the formation of microgels. Particle size measurements done with dynamic light scattering suggest that the aggregation occurs via a nucleation and growth process. The nuclei grow either by fusion or by addition of denatured proteins. If more than three Ca(2+) ions per protein are added, particulate gels are formed by random association of the microgels. Similar particulate gels are also formed at high NaCl concentrations (>200 mM), but by a different mechanism. In this case, the randomly aggregated small strands formed at the early stage of the heating process formed dense spherical domains at a later stage of the heating process by microphase separation that randomly associated to form a particulate gel.

Leishmania Dices Away Cholesterol for Survival

Host lipid alterations are centrally involved in Leishmania donovani infection, and infected patients exhibit hypocholesterolemia. In this issue of Cell Host & Microbe, Ghosh etal. (2013) show that the metalloprotease GP63 released by L.donovani in the liver cleaves DICER1, inhibiting miR-122 maturation, which regulates cholesterol metabolism. These events decrease serum cholesterol and promote parasite growth.

Desmoplastic ameloblastoma with osteoplasia: Review of literature with a case report

Desmoplastic ameloblastoma (DA) is a relatively rare histological variant of ameloblastoma with specific clinical, radiological, and histological features. This tumor is more commonly seen in the anterior region of jaws as a mixed radiopaque-radiolucent lesion resembling benign fibro-osseous lesions. Histologically, DA is characterized by small nests and strands of “compressed” odontogenic epithelium supported by pronounced collagenized stroma. Metaplastic bone formation has been reported in few cases. This report describes a lesion in the left anterior maxilla of a young female patient.

Flow Driven Self-Assembly of Von Willebrand Factor Strands and Cables in Synthetic Blood Vessels

Abstract 261Endothelial activation and microvascular thrombosis are hallmarks of thrombotic microangiopathy—a group of life-threatening disorders that includes thrombotic thrombocytopenic purpura and hemolytic uremic syndrome. Activated endothelial cells release von Willebrand factor (VWF), which can form long strands under flow that remain attached to the endothelium until they are cleaved off by the metalloprotease ADAMTS13. Failure to remove these strands, either because of ADAMTS13 deficiency or oxidation of its cleavage site on VWF, results in microvascular thrombosis.Until now, studies of VWF strands under flow have been performed either in flow chambers with cultured endothelial cells, which does not account for either vessel caliber or geometry, or in live mice, in which it is impossible to study individually the contributions of the various blood components. Recently, we developed a technique to engineer microvessels in vitro that enables us to precisely control several vessel parameters, including lumen diameter and branching architecture, flow patterns, and applied shear stresses, in addition to being able to test individual components of the blood in a system with only human components (PNAS 2012, 109:9342–9347). In the current study, we used this system to examine the effects of a number of variables on the formation of VWF strands from the endothelium of stimulated vessels. We found that VWF fibers can extend across the vessel lumen and attach to opposite sides of the vessel wall in agonist-treated microvessels of up to 200 μm in diameter. Depending on flow conditions, smaller strands can self-associate to form longer and thicker cables. The VWF cables produced solely from VWF contributed by the vessel wall reached lengths up to 5 cm, and became so thick as to be visible, unstained, by light microscopy. When plasma or recombinant VWF was perfused over the VWF cables, the fluid-phase VWF associated with the vessel-bound cables, further thickening them and sometimes inducing web-like structures. The location and structure of the VWF fibers were dependent on vessel geometry and flow pattern; secondary flows that developed at bends or bifurcations in the vessel induced circular clumping of the VWF strands. When whole blood was perfused into the vessels, the transluminal VWF fiber webs caught flowing platelets and leukocytes to form aggregates in the middle of blood stream that sometimes occluded the vessels. The region where the vessel is most likely to occlude also depends on geometry. After this type of trapping, leukocytes were seen to transmigrate across the endothelium. The structure and size of the cables also depended on the agonist employed to stimulate VWF release from the endothelium. Phorbol myristate acetate and shiga-like toxin–2 both produced thicker cables than histamine did, and these were more resistant to ADAMTS13 cleavage. This difference is potentially a result of the former agonists stimulating an endothelial respiratory burst and oxidation of the ADAMTS13 cleavage site on VWF.In summary, our data show that VWF secreted from activated endothelial cells can form transluminal fibers and cables in small vessels. Some of the fibers or cables are resistant to ADAMTS13 cleavage, a likely consequence of their thickness and possibly, oxidation. The webs of VWF fibers or cables in the lumen of small vessels obstruct blood flow by binding to circulating platelets and leukocytes, and are also capable of shredding erythrocytes as they flow past. These findings provide insights into the mechanisms of microangiopathy, and raise the possibility that VWF cables alone, even in the absence of bound platelets, may be capable of occluding small blood vessels and produce many of the characteristic signs of thrombotic microangiopathy. Disclosures:No relevant conflicts of interest to declare.

Mass Amplifying Probe for Sensitive Fluorescence Anisotropy Detection of Small Molecules in Complex Biological Samples

Fluorescence anisotropy (FA) is a reliable and excellent choice for fluorescence sensing. One of the key factors influencing the FA value for any molecule is the molar mass of the molecule being measured. As a result, the FA method with functional nucleic acid aptamers has been limited to macromolecules such as proteins and is generally not applicable for the analysis of small molecules because their molecular masses are relatively too small to produce observable FA value changes. We report here a molecular mass amplifying strategy to construct anisotropy aptamer probes for small molecules. The probe is designed in such a way that only when a target molecule binds to the probe does it activate its binding ability to an anisotropy amplifier (a high molecular mass molecule such as protein), thus significantly increasing the molecular mass and FA value of the probe/target complex. Specifically, a mass amplifying probe (MAP) consists of a targeting aptamer domain against a target molecule and molecular mass amplifying aptamer domain for the amplifier protein. The probe is initially rendered inactive by a small blocking strand partially complementary to both target aptamer and amplifier protein aptamer so that the mass amplifying aptamer domain would not bind to the amplifier protein unless the probe has been activated by the target. In this way, we prepared two probes that constitute a target (ATP and cocaine respectively) aptamer, a thrombin (as the mass amplifier) aptamer, and a fluorophore. Both probes worked well against their corresponding small molecule targets, and the detection limits for ATP and cocaine were 0.5 μM and 0.8 μM, respectively. More importantly, because FA is less affected by environmental interferences, ATP in cell media and cocaine in urine were directly detected without any tedious sample pretreatment. Our results established that our molecular mass amplifying strategy can be used to design aptamer probes for rapid, sensitive, and selective detection of small molecules by means of FA in complex biological samples.

The importance of being modular

DNA is the material of choice for making custom-designed, nanoscale shapes and patterns through self-assembly. A new technique revisits old ideas to enable the rapid prototyping of more than 100 such DNA shapes. See Letter p.623 Programmed DNA self-assembly is widely used to create nanometre-sized structures. Modular strategies promise simplicity and versatility, yet cannot easily assemble large numbers of small strands into prescribed and complex shapes. Peng Yin and colleagues overcome this problem by designing a molecular canvas: a rectangle assembled from single-stranded tiles each consisting of a short and unique 42-base DNA strand that folds into a 3-nanometre-by-7-nanometre tile and attaches to 4 neighbouring tiles. A desired shape, drawn on the canvas, is produced by simply mixing those strands that correspond to pixels covered by the target shape, and excluding 'off'-pixel strands. With a master strand collection for a 310-pixel canvas, the team then creates more than 100 distinct and complex two-dimensional shapes that establish the method as a simple, modular and robust framework for assembling short synthetic DNA strands into complex DNA nanostructures.