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"Jin, Xu"
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SBMLKinetics: a tool for annotation-independent classification of reaction kinetics for SBML models
Background
Reaction networks are widely used as mechanistic models in systems biology to reveal principles of biological systems. Reactions are governed by kinetic laws that describe reaction rates. Selecting the appropriate kinetic laws is difficult for many modelers. There exist tools that attempt to find the correct kinetic laws based on annotations. Here, I developed annotation-independent technologies that assist modelers by focusing on finding kinetic laws commonly used for similar reactions.
Results
Recommending kinetic laws and other analyses of reaction networks can be viewed as a classification problem. Existing approaches to determining similar reactions rely heavily on having good annotations, a condition that is often unsatisfied in model repositories such as BioModels. I developed an annotation-independent approach to find similar reactions via reaction classifications. I proposed a two-dimensional kinetics classification scheme (2DK) that analyzed reactions along the dimensions of kinetics type (K type) and reaction type (R type). I identified approximately ten mutually exclusive K types, including zeroth order, mass action, Michaelis–Menten, Hill kinetics, and others. R types were organized by the number of distinct reactants and the number of distinct products in reactions. I constructed a tool, SBMLKinetics, that inputted a collection of SBML models and then calculated reaction classifications as the probability of each 2DK class. The effectiveness of 2DK was evaluated on BioModels, and the scheme classified over 95% of the reactions.
Conclusions
2DK had many applications. It provided a
data-driven
annotation-independent approach to recommending kinetic laws by using type common for the kind of models in combination with the R type of the reactions. Alternatively, 2DK could also be used to alert users that a kinetic law was unusual for the K type and R type. Last, 2DK provided a way to analyze groups of models to compare their kinetic laws. I applied 2DK to BioModels to compare the kinetics of signaling networks with the kinetics of metabolic networks and found significant differences in K type distributions.
Journal Article
Highly efficient eco-friendly X-ray scintillators based on an organic manganese halide
Scintillation based X-ray detection has received great attention for its application in a wide range of areas from security to healthcare. Here, we report highly efficient X-ray scintillators with state-of-the-art performance based on an organic metal halide, ethylenebis-triphenylphosphonium manganese (II) bromide ((C
38
H
34
P
2
)MnBr
4
), which can be prepared using a facile solution growth method at room temperature to form inch sized single crystals. This zero-dimensional organic metal halide hybrid exhibits green emission peaked at 517 nm with a photoluminescence quantum efficiency of ~ 95%. Its X-ray scintillation properties are characterized with an excellent linear response to X-ray dose rate, a high light yield of ~ 80,000 photon MeV
−1
, and a low detection limit of 72.8 nGy s
−1
. X-ray imaging tests show that scintillators based on (C
38
H
34
P
2
)MnBr
4
powders provide an excellent visualization tool for X-ray radiography, and high resolution flexible scintillators can be fabricated by blending (C
38
H
34
P
2
)MnBr
4
powders with polydimethylsiloxane.
Scintillation-based X-ray detection is promising for applications in various areas ranging from security to healthcare, and low-cost and eco-friendly scintillation materials would be beneficial. Here the authors report a facile solution growth of organic manganese halide for efficient X-ray scintillation.
Journal Article
وجوه لا تلتقيها مرتين : حكايات غير عادية عن أبطال عاديين
\"وجوه لا تلتقيها مرتين\" يروي حكايات غير عادية عن أبطال عاديين، ربما تجدهم في مجتمعك بغض النظر عن طبيعة تكوين هذا المجتمع أو نطاقه الجغرافي أو خلفياته الثقافية والاقتصادية، وهو كتاب واقعي غير مثالي، تعرض فيه الصحفية الشهيرة لي يوان تشنغ الأحداث الخفية والتفاصيل المبهمة التي أفرزت التنمية الصينية الهائلة، والنقلة الاجتماعية كتجربة غير مسبوقة، ولكن من منظور إنساني، فهو لا يتطرق إلى استراتيجيات ولا سياسات ولا خطط خمسية، بل يركز على الفرد، كونه إنسانا فحسب.
Book
Mitogen-activated protein kinase signaling in plant pathogenic fungi
The formation of Mst7 homodimers involves the thioredoxins and is important for Pmk1 activation [6]. Besides its intramolecular self-inhibitory binding, Mst11 also interacts with Ras proteins via the Ras-association domain for Pmk1 activation [7,8]. The Cochliobolus sativus Cshog1 mutant is normal in root infection but significantly reduced in virulence on barley leaves [15]. [...]the function of this MAPK pathway in pathogenesis may be not only species-specific but also tissue-specific. Besides its conserved role in osmoregulation, this pathway has species-specific functions in pathogenesis, vegetative growth, fungicide sensitivity, sexual and asexual development, and responses to oxidative, cell wall, and other stresses in different plant pathogenic fungi. Deletion of MST50 also affects Osm1 activation in response to hyperosmotic stress, and Hik1 interacts with Mst50 [26]. Because the cyclic adenosine monophosphate-protein kinase A (cAMP-PKA) pathway also regulates various developmental and infection processes, cross-talking between cyclic adenosine monophosphate (cAMP) signaling and MAPK cascades must occur and likely involve different mechanisms in plant pathogenic fungi [1,2,27].
Journal Article
Angiogenesis in pancreatic cancer: current research status and clinical implications
Pancreatic cancer is one of the most lethal malignancies worldwide. Although the standard of care in pancreatic cancer has improved, prognoses for patients remain poor with a 5-year survival rate of < 5%. Angiogenesis, namely, the formation of new blood vessels from pre-existing vessels, is an important event in tumor growth and hematogenous metastasis. It is a dynamic and complex process involving multiple mechanisms and is regulated by various molecules. Inhibition of angiogenesis has been an established therapeutic strategy for many solid tumors. However, clinical outcomes are far from satisfying for pancreatic cancer patients receiving anti-angiogenic therapies. In this review, we summarize the current status of angiogenesis in pancreatic cancer research and explore the reasons for the poor efficacy of anti-angiogenic therapies, aiming to identify some potential therapeutic targets that may enhance the effectiveness of anti-angiogenic treatments.
Journal Article
Functional significance of cholesterol metabolism in cancer: from threat to treatment
Cholesterol is an essential structural component of membranes that contributes to membrane integrity and fluidity. Cholesterol homeostasis plays a critical role in the maintenance of cellular activities. Recently, increasing evidence has indicated that cholesterol is a major determinant by modulating cell signaling events governing the hallmarks of cancer. Numerous studies have shown the functional significance of cholesterol metabolism in tumorigenesis, cancer progression and metastasis through its regulatory effects on the immune response, ferroptosis, autophagy, cell stemness, and the DNA damage response. Here, we summarize recent literature describing cholesterol metabolism in cancer cells, including the cholesterol metabolism pathways and the mutual regulatory mechanisms involved in cancer progression and cholesterol metabolism. We also discuss various drugs targeting cholesterol metabolism to suggest new strategies for cancer treatment.
Cancer: Changes in cholesterol metabolism
Emerging evidence suggests that changes in cholesterol metabolism can be involved in the onset and progression of cancer, opening avenues towards better understanding of cancer and new treatment options. Cholesterol is an essential structural component of cell membranes, important for maintaining optimal fluidity of the membrane under varying conditions. Si Shi, Xianjun Yu and colleagues at Fudan University Shanghai Cancer Center, China, review recent research into cholesterol metabolism in cancers, including cellular regulatory pathways involving cholesterol that are also implicated in cancer progression. The influence of cholesterol metabolism on cancer has been linked to effects on several key physiological processes, including the immune response, regulated cell death, recycling of cellular components, DNA repair, and the activities of stem cells. The authors consider the potential of drugs known to influence cholesterol metabolism in anti-cancer therapy.
Journal Article
Genome sequence of Valsa canker pathogens uncovers a potential adaptation of colonization of woody bark
Canker caused by ascomycetous Valsa species are among the most destructive diseases of woody plants worldwide. These pathogens are distinct from other pathogens because they only effectively attack tree bark in the field. To unravel the potential adaptation mechanism of bark colonization, we examined the genomes of Valsa mali and Valsa pyri that preferentially infect apple and pear, respectively. We reported the 44.7 and 35.7 Mb genomes of V. mali and V. pyri, respectively. We also identified the potential genomic determinants of wood colonization by comparing them with related cereal pathogens. Both genomes encode a plethora of pathogenicity‐related genes involved in plant cell wall degradation and secondary metabolite biosynthesis. In order to adapt to the nutrient limitation and low pH environment in bark, they seem to employ membrane transporters associated with nitrogen uptake and secrete proteases predominantly with acidic pH optima. Remarkably, both Valsa genomes are especially suited for pectin decomposition, but are limited in lignocellulose and cutin degradation. Besides many similarities, the two genomes show distinct variations in many secondary metabolism gene clusters. Our results show a potential adaptation of Valsa canker pathogens to colonize woody bark. Secondary metabolism gene clusters are probably responsible for this host specificity.
Journal Article