Spectral clustering algorithm for the allometric extension model

The spectral clustering algorithm is often used as a binary clustering method for unclassified data by applying the principal component analysis. To study theoretical properties of the algorithm, the assumption of conditional homoscedasticity is often supposed in existing studies. However, this assumption is restrictive and often unrealistic in practice. Therefore, in this paper, we consider the allometric extension model, that is, the directions of the first eigenvectors of two covariance matrices and the direction of the difference of two mean vectors coincide, and we provide a non-asymptotic bound of the error probability of the spectral clustering algorithm for the allometric extension model. As a byproduct of the result, we obtain the consistency of the clustering method in high-dimensional settings.Comment: 20 page

Sound and Relatively Complete Belief Hoare Logic for Statistical Hypothesis Testing Programs

We propose a new approach to formally describing the requirement for statistical inference and checking whether a program uses the statistical method appropriately. Specifically, we define belief Hoare logic (BHL) for formalizing and reasoning about the statistical beliefs acquired via hypothesis testing. This program logic is sound and relatively complete with respect to a Kripke model for hypothesis tests. We demonstrate by examples that BHL is useful for reasoning about practical issues in hypothesis testing. In our framework, we clarify the importance of prior beliefs in acquiring statistical beliefs through hypothesis testing, and discuss the whole picture of the justification of statistical inference inside and outside the program logic

Formalizing Statistical Causality via Modal Logic

We propose a formal language for describing and explaining statistical causality. Concretely, we define Statistical Causality Language (StaCL) for expressing causal effects and specifying the requirements for causal inference. StaCL incorporates modal operators for interventions to express causal properties between probability distributions in different possible worlds in a Kripke model. We formalize axioms for probability distributions, interventions, and causal predicates using StaCL formulas. These axioms are expressive enough to derive the rules of Pearl's do-calculus. Finally, we demonstrate by examples that StaCL can be used to specify and explain the correctness of statistical causal inference

Digitisation of Weather Records of Seungjeongwon Ilgi: A Historical Weather Dynamics Dataset of the Korean Peninsula (1623-1910)

Introduction This study has exploited the daily weather records of Seungjeongwon Ilgi from the NIKH database (http://sjw.history.go.kr/main.do). Seungjeongwon Ilgi is a daily record of the Seungjeongwon, the Royal Secretariat of the Joseon Dynasty of Korea. These diaries span from 1623 to 1910 and generally involve daily weather records in the entry header. Their observational site would be located in Seoul (N37°35′, E126°59′). We have exploited the weather records from the NIKH database and classified the daily weather using text mining method. We have also converted the report dates from the traditional lunisolar calendar to the Gregorian calendar, to better contextualise our data into the contemporary daily measurements. Data We provide different formats (csv, xlsx, json) to facilitate the usage of data. The main contents of data are listed as below. ID: The unique identifier of a specific record in the metadata, which can also serve as the identifier to merge with external data in the NIKH digital database. Traditional calendar: The original lunar dates in the NIKH digital database, which are listed in data format "YYYY-MM-DD". More specifically, "L0" implies the leap year and "L1" implies the common year. Leap: The identifier of a leap year. Gregorian calendar: The Gregorian calendar date that converted by the traditional calendar date. Weather Text: The text that describe the weather conditions. Specifically, multiple weather descriptions of the same day have been put together. Flag: The computed value that indicates different combinations of weather conditions. Volume: The volume of text in the original record. Herbal Volume: The volume of text in the herbal record. Sunny: A dummy variable that represents whether the weather description contains the expression of sunny. Cloudy: A dummy variable that represents whether the weather description contains the expression of cloudy. Rainy: A dummy variable that represents whether the weather description contains the expression of rainy. Snow: A dummy variable that represents whether the weather description contains the expression of snow. Wind: A dummy variable that represents whether the weather description contains the expression of wind. Import Data # Python # CSV file import pandas as pd data=pd.read_csv('~/SJWilgi_Seoul_Weather_YR1623_1910.csv',encoding="utf-8") # JSON file data=pd.read_json('~/SJWilgi_Seoul_Weather_YR1623_1910.json',encoding="utf-8") # Excel file data=pd.read_excel('~/SJWilgi_Seoul_Weather_YR1623_1910.xlsx') # Excel file # R # CSV file library(readr) data<- read_csv("~/SJWilgi_Seoul_Weather_YR1623_1910.csv") # Excel file library(readxl) data <- read_excel("~/SJWilgi_Seoul_Weather_YR1623_1910.xlsx"

PCTK3/CDK18 regulates cell migration and adhesion by negatively modulating FAK activity

PCTAIRE kinase 3 (PCTK3) is a member of the cyclin dependent kinase family, but its physiological function remains unknown. We previously reported that PCTK3-knockdown HEK293T cells showed actin accumulation at the leading edge, suggesting that PCTK3 is involved in the regulation of actin reorganization. In this study, we investigated the physiological function and downstream signal transduction molecules of PCTK3. PCTK3 knockdown in HEK293T cells increased cell motility and RhoA/Rho-associated kinase activity as compared with control cells. We also found that phosphorylation at residue Tyr-397 in focal adhesion kinase (FAK) was increased in PCTK3-knockdown cells. FAK phosphorylation at Tyr-397 was increased in response to fibronectin stimulation, whereas its phosphorylation was suppressed by PCTK3. In addition, excessive expression of PCTK3 led to the formation of filopodia during the early stages of cell adhesion in HeLa cells. These results indicate that PCTK3 controls actin cytoskeleton dynamics by negatively regulating the FAK/Rho signaling pathway

Prediction of postoperative liver failure and evaluation of modifi ed criteria for liver resection with computed volume analysis

Background/Aims: The exact resectable volume corresponding to liver function has never been elucidated for safe resection of a diseased liver. The aim of this study was to evaluate whether modifi ed criteria for safe liver resection could be used to predict postoperative liver failure/dysfunction.Methodology: Consecutive 86 patients who underwent liver resections were assessed. Clinical laboratory tests and liver volume were evaluated. The modifi ed criteria used to determine safe liver resection consisted of indocyanine green retention rate at 15 min (ICGR15), antithrombin III (ATIII), clearance index (HH15), and receptor index (LHL15). We compared clinical outcomes after liver resection using our modifi ed criteria and Makuuchi criteria. Results: There were 78 patients without liver failure and 8 with liver failure/dysfunction. ICGR15 (P < 0.001), ATIII (P = 0.036), operative time (P = 0.014), tumor type (P = 0.047), modifi ed criteria score (P = 0.037), lost liver volume (P = 0.006), and modifi ed criteria (P= 0.007) were signifi cantly different between the groups. Diagnostic probability of modifi ed criteria (P = 0.007) was better than the one of Makuuchi criteria (P = 0.271).Conclusions: Postoperative liver failure/dysfunction could be predicted using the modifi ed criteria. Furthermore, the criteria could be used to provide a putative liver volume for safe removal.departmental bulletin pape

Dysbindin Regulates the Transcriptional Level of Myristoylated Alanine-Rich Protein Kinase C Substrate via the Interaction with NF-YB in Mice Brain

BACKGROUND: An accumulating body of evidence suggests that Dtnbp1 (Dysbindin) is a key susceptibility gene for schizophrenia. Using the yeast-two-hybrid screening system, we examined the candidate proteins interacting with Dysbindin and revealed one of these candidates to be the transcription factor NF-YB. METHODS: We employed an immunoprecipitation (IP) assay to demonstrate the Dysbindin-NF-YB interaction. DNA chips were used to screen for altered expression of genes in cells in which Dysbindin or NF-YB was down regulated, while Chromatin IP and Reporter assays were used to confirm the involvement of these genes in transcription of Myristoylated alanine-rich protein kinase C substrate (MARCKS). The sdy mutant mice with a deletion in Dysbindin, which exhibit behavioral abnormalities, and wild-type DBA2J mice were used to investigate MARCKS expression. RESULTS: We revealed an interaction between Dysbindin and NF-YB. DNA chips showed that MARCKS expression was increased in both Dysbindin knockdown cells and NF-YB knockdown cells, and Chromatin IP revealed interaction of these proteins at the MARCKS promoter region. Reporter assay results suggested functional involvement of the interaction between Dysbindin and NF-YB in MARCKS transcription levels, via the CCAAT motif which is a NF-YB binding sequence. MARCKS expression was increased in sdy mutant mice when compared to wild-type mice. CONCLUSIONS: These findings suggest that abnormal expression of MARCKS via dysfunction of Dysbindin might cause impairment of neural transmission and abnormal synaptogenesis. Our results should provide new insights into the mechanisms of neuronal development and the pathogenesis of schizophrenia

Glial cell line-derived neurotrophic factor and chronic electrical stimulation prevent VIII cranial nerve degeneration following denervation

As with other cranial nerves and many CNS neurons, primary auditory neurons degenerate as a consequence of loss of input from their target cells, the inner hair cells (IHCs). Electrical stimulation (ES) of spiral ganglion cells (SGCs) has been shown to enhance their survival. Glial cell line-derived neurotrophic factor (GDNF) has also been shown to increase survival of SGCs following IHC loss. In this study, the combined effects of the GDNF transgene delivered by adenoviral vectors (Ad- GDNF ) and ES were tested on SGCs after first eliminating the IHCs. Animal groups received Ad- GDNF or ES or both. Ad- GDNF was inoculated into the cochlea of guinea pigs after deafening, to overexpress human GDNF . ES-treated animals were implanted with a cochlear implant electrode and chronically stimulated. A third group of animals received both Ad- GDNF and ES (GDNF/ES). Electrically evoked auditory brainstem responses were recorded from ES-treated animals at the start and end of the stimulation period. Animals were sacrificed 43 days after deafening and their ears prepared for evaluation of IHC survival and SGC counts. Treated ears exhibited significantly greater SGC survival than nontreated ears. The GDNF/ES combination provided significantly better preservation of SGC density than either treatment alone. Insofar as ES parameters were optimized for maximal protection (saturated effect), the further augmentation of the protection by GDNF suggests that the mechanisms of GDNF- and ES-mediated SGC protection are, at least in part, independent. We suggest that GDNF/ES combined treatment in cochlear implant recipients will improve auditory perception. These findings may have implications for the prevention and treatment of other neurodegenerative processes. J. Comp. Neurol. 454:350–360, 2002. © 2002 Wiley-Liss, Inc.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/34465/1/10480_ftp.pd

Spiral Ganglion Neurons Are Protected from Degeneration byGDNF Gene Therapy

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/42436/1/10162-1-4-315_00010315.pd