Multi-omics network characterization reveals novel microRNA biomarkers and mechanisms for diagnosis and subtyping of kidney transplant rejection
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Abstract The purpose of subtyping is to differentiate bacterial isolates beyond the classification of species or subspecies. Subtyping methods can be grouped into two broad categories based on the cellular components targeted: (1) phenotypic subtyping methods that differentiate isolates by the enzymes, proteins, or other metabolites expressed by the cell, and (2) molecular subtyping methods that discriminate isolates based on interrogation of nucleic acid sequences. The two major types of molecular subtyping methods include band-based methods based on fragment pattern data or DNA fingerprints, and methods that generate DNA sequence data. Molecular subtyping methods have shown that Listeria monocytogenes isolates can be classified into four genetic lineages or divisions. Although band-based molecular subtyping methods continue to serve as the gold standard for routine molecular subtyping of most clinically important foodborne pathogens, including L. monocytogenes, the explosion of recently completed and ongoing DNA sequencing projects, and thus available DNA sequence data, have stimulated efforts to develop highly discriminatory and high-throughput DNA sequence-based subtyping methods for L. monocytogenes. L. monocytogenes represents one of the most highly sequenced human pathogens; more than 20 genome sequences are currently available for this organism. This review provides an overview of the concepts behind subtyping and discusses the application of molecular subtyping methods, with an emphasis on DNA sequence-based subtyping methods to characterize L. monocytogenes.
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Bacteria subtyping methods not only improve our ability to detect and track human listeriosis outbreaks, but also provide useful tools to track sources of L.monocytogenes contamination throughout the food system. Additionally, the use of subtyping methods provide an opportunity to better understand the population genetics, epidemiology, and the ecology of L.monocytogenes.The last five years have seen tremendous advancements in the development of sensitive,rapid,automated,and increasingly easy to use molecular subtyping methods for L.monocytogenes This review focused on the the different subtyping methods of L.monocytogenes and it's applications.
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Racial disparities in kidney transplantation continue to persist despite voluminous studies attempting to address this problem. We conducted 26 semi-structured, one-on-one interviews with African-American and Caucasian dialysis patients to analyze whether or not there is a difference in attitudes toward kidney transplantation and whether or not this contributes to these disparities. Pre-dialysis education strongly correlates with a person’s willingness to get listed, while fear of surgery and care of the transplanted kidney, and interaction with peers who have gone through a failed kidney transplant, decrease the chances of getting listed. Subjects did not report racial bias in being referred or worked up for transplant. African Americans were more likely to weigh the pros and cons of transplants while Caucasians were more likely to see dialysis as temporary and viewed transplant as the default treatment for their kidney failure. All dialysis patients, but especially African Americans, may benefit from transplant education tailored to address specific patient concerns.
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Background/Aims: Kidney transplantation (KT) is the best treatment for end-stage renal disease patients.Although previous studies have demonstrated that the clinical outcome following living related (LR) KT is better than that following unrelated (LUR) KT in ABO-compatible KT recipients, recent studies showed no differences in clinical outcomes between the two treatments.In this study, we compared the clinical outcomes of LR and LUR KT in ABO-incompatible KT recipients.Methods: From January 2011 to August 2013, 19 cases of ABO-incompatible KT were analyzed retrospectively.Eight kidneys (7 cases of parent-offspring and 1 case of siblings, Group 1) were donated from living-related donors and 11 (all spousal donors, Group 2) from living-unrelated donors.We investigated patient survival, graft survival, acute rejection, graft function, and complications.Results: On Kaplan-Meier analysis, patient and graft survival during follow-up were 87.5% and 87.5% in Group 1; both were 100% in Group 2. Acute rejection, graft function, and medical and surgical complications were not significantly different between the two groups.Conclusions: The short-term clinical outcomes between LR and LUR KT in ABO-incompatible KT recipients were equivalent.Most domestic cases of LUR KT are from spousal donors and the spousal donor will be a major donor in ABO-incompatible KT patients.(
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Consistent subtyping is employed in some gradual type systems to validate type conversions. The original definition by Siek and Taha serves as a guideline for designing gradual type systems with subtyping. Polymorphic types à la System F also induce a subtyping relation that relates polymorphic types to their instantiations. However Siek and Taha's definition is not adequate for polymorphic subtyping. The first goal of this paper is to propose a generalization of consistent subtyping that is adequate for polymorphic subtyping, and subsumes the original definition by Siek and Taha. The new definition of consistent subtyping provides novel insights with respect to previous polymorphic gradual type systems, which did not employ consistent subtyping. The second goal of this paper is to present a gradually typed calculus for implicit (higher-rank) polymorphism that uses our new notion of consistent subtyping. We develop both declarative and (bidirectional) algorithmic versions for the type system. We prove that the new calculus satisfies all static aspects of the refined criteria for gradual typing, which are mechanically formalized using the Coq proof assistant.
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Accurate subtyping or classification of breast cancer is important for ensuring proper treatment of patients and also for understanding the molecular mechanisms driving this disease. While there have been several gene signatures proposed in the literature to classify breast tumours, these signatures show very low overlaps, different classification performance, and not much relevance to the underlying biology of these tumours. Here we evaluate DNA-damage response (DDR) and cell cycle pathways, which are critical pathways implicated in a considerable proportion of breast tumours, for their usefulness and ability in breast tumour subtyping. We think that subtyping breast tumours based on these two pathways could lead to vital insights into molecular mechanisms driving these tumours. Here, we performed a systematic evaluation of DDR and cell-cycle pathways for subtyping of breast tumours into the five known intrinsic subtypes. Homologous Recombination (HR) pathway showed the best performance in subtyping breast tumours, indicating that HR genes are strongly involved in all breast tumours. Comparisons of pathway based signatures and two standard gene signatures supported the use of known pathways for breast tumour subtyping. Further, the evaluation of these standard gene signatures showed that breast tumour subtyping, prognosis and survival estimation are all closely related. Finally, we constructed an all-inclusive super-signature by combining (union of) all genes and performing a stringent feature selection, and found it to be reasonably accurate and robust in classification as well as prognostic value. Adopting DDR and cell cycle pathways for breast tumour subtyping achieved robust and accurate breast tumour subtyping, and constructing a super-signature which contains feature selected mix of genes from these molecular pathways as well as clinical aspects is valuable in clinical practice.
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Biomarker Discovery
Molecular diagnostics
Classification scheme
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Conventional, phenotypic, and DNA-based subtyping methods allow differentiation of Listeria monocytogenes beyond the species and subspecies level. Bacterial subtyping methods not only improve our ability to detect and track human listeriosis outbreaks, but also provide tools to track sources of L. monocytogenes contamination throughout the food system. The use of subtyping methods also provides an opportunity to better understand the population genetics, epidemiology, and ecology of L. monocytogenes. The last 5 years have seen tremendous advancements in the development of sensitive, rapid, automated, and increasingly easy-to-use molecular subtyping methods for L. monocytogenes. This review highlights key aspects of different L. monocytogenes subtyping methods and provides examples of their application in public health, food safety, population genetics, and epidemiology. A significant focus is on the application of subtyping methods to define L. monocytogenes subtypes and clonal groups, which may differ in phenotypic characteristics and pathogenic potential.
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Subspecies
Molecular Epidemiology
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By-name subtyping (or user-defined subtyping) and structural subtyping each have their own strengths and weaknesses. By-name subtyping allows programmers to explicitly express design intent, and, when types are associated with run time tags, enables run-time "type" tests and external/multimethod dispatch. On the other hand, structural subtyping is flexible and compositional, allowing unanticipated reuse. To date, nearly all object-oriented languages fully support only one subtyping paradigm or the other.
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The breast cancer is a usual and serious malignant tumor which threatens the women′s health.Molecular subtyping bases on the molecular level, and provides a new classification method for the breast cancer pathology classification, and plays an important guidance significance for the clinical treatment.At present, the breast cancer molecular subtyping is mainly divided into the following subtypes: the Luminal A type and Luminal B type, HER-2 overexpression and the triple negative breast cancer.Different molecular subtyping has different characteristics in treatment reaction, prognosis and the clinical application situation.
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Breast neoplasms; Molecular subtyping; Clinic Treatment
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Clinical Significance
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