271,859 Works

Predictive Coding Deep Neural Network in Chainer (Simple Version, Front. Psychol., 15 March 2018)

Eiji Watanabe
The simple version has omitted Tensorboard function.
When you want to use the function of Tensorboard,
use New version.
New version is here.https://doi.org/10.6084/m9.figshare.7801154The simple version works faster than The Tensorboard Version.
https://doi.org/10.6084/m9.figshare.7801154


The PredNet*, written in Keras, was ported to Chainer and reconstructed for convenience.Visualization of internal images in the network models was performed using a self-made converter program and Tesorboard in Tensorflow.

*Lotter, W., Kreiman, G., & Cox, D., Deep predictive coding networks for video prediction and unsupervised learning,...

2018 SCEC Proposal

Yu Geng
A proposal submitted for the Southern California Earthquake Center 2018 Science Plan.

Autophagy inhibition promotes SNCA/alpha-synuclein release and transfer via extracellular vesicles with a hybrid autophagosome-exosome-like phenotype

Georgia Minakaki, Stefanie Menges, Agnes Kittel, Evangelia Emmanouilidou, Iris Schaeffner, Katalin Barkovits, Anna Bergmann, Edward Rockenstein, Anthony Adame, Franz Marxreiter, Brit Mollenhauer, Douglas Galasko, Edit Irén Buzás, Ursula Schlötzer-Schrehardt, Katrin Marcus, Wei Xiang, Dieter Chichung Lie, Kostas Vekrellis, Eliezer Masliah, Jürgen Winkler & Jochen Klucken
The autophagy-lysosome pathway (ALP) regulates intracellular homeostasis of the cytosolic protein SNCA/alpha-synuclein and is impaired in synucleinopathies, including Parkinson disease and dementia with Lewy bodies (DLB). Emerging evidence suggests that ALP influences SNCA release, but the underlying cellular mechanisms are not well understood. Several studies identified SNCA in exosome/extracellular vesicle (EV) fractions. EVs are generated in the multivesicular body compartment and either released upon its fusion with the plasma membrane, or cleared via the ALP....

Oncogenic RAS-induced downregulation of ATG12 is required for survival of malignant intestinal epithelial cells

Byong Hoon Yoo, Iman Aftab Khan, Ananda Koomson, Pramod Gowda, Takehiko Sasazuki, Senji Shirasawa, Shashi Gujar & Kirill V. Rosen
Activating mutations of RAS GTPase contribute to the progression of many cancers, including colorectal carcinoma. So far, attempts to develop treatments of mutant RAS-carrying cancers have been unsuccessful due to insufficient understanding of the salient mechanisms of RAS signaling. We found that RAS downregulates the protein ATG12 in colon cancer cells. ATG12 is a mediator of autophagy, a process of degradation and reutilization of cellular components. In addition, ATG12 can kill cells via autophagy-independent mechanisms....

Ion channels in the regulation of autophagy

Artem Kondratskyi, Kateryna Kondratska, Roman Skryma, Daniel J. Klionsky & Natalia Prevarskaya
Autophagy is a cellular process in which the cell degrades and recycles its own constituents. Given the crucial role of autophagy in physiology, deregulation of autophagic machinery is associated with various diseases. Hence, a thorough understanding of autophagy regulatory mechanisms is crucially important for the elaboration of efficient treatments for different diseases. Recently, ion channels, mediating ion fluxes across cellular membranes, have emerged as important regulators of both basal and induced autophagy. However, the mechanisms...

Oncogenic RAS-induced downregulation of ATG12 is required for survival of malignant intestinal epithelial cells

Byong Hoon Yoo, Iman Aftab Khan, Ananda Koomson, Pramod Gowda, Takehiko Sasazuki, Senji Shirasawa, Shashi Gujar & Kirill V. Rosen
Activating mutations of RAS GTPase contribute to the progression of many cancers, including colorectal carcinoma. So far, attempts to develop treatments of mutant RAS-carrying cancers have been unsuccessful due to insufficient understanding of the salient mechanisms of RAS signaling. We found that RAS downregulates the protein ATG12 in colon cancer cells. ATG12 is a mediator of autophagy, a process of degradation and reutilization of cellular components. In addition, ATG12 can kill cells via autophagy-independent mechanisms....

Prdx1 (peroxiredoxin 1) deficiency reduces cholesterol efflux via impaired macrophage lipophagic flux

Se-Jin Jeong, Sinai Kim, Jong-Gil Park, In-Hyuk Jung, Mi-Ni Lee, Sejin Jeon, Hyae Yon Kweon, Dae-Yeul Yu, Sang-Hak Lee, Yangsoo Jang, Sang Won Kang, Ki-Hwan Han, Yury I. Miller, Young Mi Park, Cheolho Cheong, Jae-Hoon Choi & Goo Taeg Oh
Oxidative stress activates macroautophagy/autophagy and contributes to atherogenesis via lipophagic flux, a form of lipid removal by autophagy. However, it is not known exactly how endogenous antioxidant enzymes are involved in lipophagic flux. Here, we demonstrate that the antioxidant PRDX1 (peroxiredoxin 1) has a crucial role in the maintenance of lipophagic flux in macrophages. PRDX1 is more highly expressed than other antioxidant enzymes in monocytes and macrophages. We determined that Prdx1 deficiency induced excessive oxidative...

Ion channels in the regulation of autophagy

Artem Kondratskyi, Kateryna Kondratska, Roman Skryma, Daniel J. Klionsky & Natalia Prevarskaya
Autophagy is a cellular process in which the cell degrades and recycles its own constituents. Given the crucial role of autophagy in physiology, deregulation of autophagic machinery is associated with various diseases. Hence, a thorough understanding of autophagy regulatory mechanisms is crucially important for the elaboration of efficient treatments for different diseases. Recently, ion channels, mediating ion fluxes across cellular membranes, have emerged as important regulators of both basal and induced autophagy. However, the mechanisms...

Prdx1 (peroxiredoxin 1) deficiency reduces cholesterol efflux via impaired macrophage lipophagic flux

Se-Jin Jeong, Sinai Kim, Jong-Gil Park, In-Hyuk Jung, Mi-Ni Lee, Sejin Jeon, Hyae Yon Kweon, Dae-Yeul Yu, Sang-Hak Lee, Yangsoo Jang, Sang Won Kang, Ki-Hwan Han, Yury I. Miller, Young Mi Park, Cheolho Cheong, Jae-Hoon Choi & Goo Taeg Oh
Oxidative stress activates macroautophagy/autophagy and contributes to atherogenesis via lipophagic flux, a form of lipid removal by autophagy. However, it is not known exactly how endogenous antioxidant enzymes are involved in lipophagic flux. Here, we demonstrate that the antioxidant PRDX1 (peroxiredoxin 1) has a crucial role in the maintenance of lipophagic flux in macrophages. PRDX1 is more highly expressed than other antioxidant enzymes in monocytes and macrophages. We determined that Prdx1 deficiency induced excessive oxidative...

ESRRA (estrogen-related receptor α) is a key coordinator of transcriptional and post-translational activation of autophagy to promote innate host defense

Soo Yeon Kim, Chul-Su Yang, Hye-Mi Lee, Jin Kyung Kim, Yi-Sak Kim, Ye-Ram Kim, Jae-Sung Kim, Tae Sung Kim, Jae-Min Yuk, Catherine Rosa Dufour, Sang-Hee Lee, Jin-Man Kim, Hueng-Sik Choi, Vincent Giguère & Eun-Kyeong Jo
The orphan nuclear receptor ESRRA (estrogen-related receptor α) is a key regulator of energy homeostasis and mitochondrial function. Macroautophagy/autophagy, an intracellular degradation process, is a critical innate effector against intracellular microbes. Here, we demonstrate that ESRRA is required for the activation of autophagy to promote innate antimicrobial defense against mycobacterial infection. AMP-activated protein kinase pathway and SIRT1 (sirtuin 1) activation led to induction of ESRRA, which is essential for autophagosome formation, in bone marrow-derived macrophages....

Regulation of BECN1-mediated autophagy by HSPB6: Insights from a human HSPB6S10F mutant

Guan-Sheng Liu, Hongyan Zhu, Wen-Feng Cai, Xiaohong Wang, Min Jiang, Kobina Essandoh, Elizabeth Vafiadaki, Kobra Haghighi, Chi Keung Lam, George Gardner, George Adly, Persoulla Nicolaou, Despina Sanoudou, Qiangrong Liang, Jack Rubinstein, Guo-Chang Fan & Evangelia G. Kranias
HSPB6/Hsp20 (heat shock protein family B [small] member 6) has emerged as a novel cardioprotector against stress-induced injury. We identified a human mutant of HSPB6 (HSPB6S10F) exclusively present in dilated cardiomyopathy (DCM) patients. Cardiac expression of this mutant in mouse hearts resulted in remodeling and dysfunction, which progressed to heart failure and early death. These detrimental effects were associated with reduced interaction of mutant HSPB6S10F with BECN1/Beclin 1, leading to BECN1 ubiquitination and its proteosomal...

ESRRA (estrogen-related receptor α) is a key coordinator of transcriptional and post-translational activation of autophagy to promote innate host defense

Soo Yeon Kim, Chul-Su Yang, Hye-Mi Lee, Jin Kyung Kim, Yi-Sak Kim, Ye-Ram Kim, Jae-Sung Kim, Tae Sung Kim, Jae-Min Yuk, Catherine Rosa Dufour, Sang-Hee Lee, Jin-Man Kim, Hueng-Sik Choi, Vincent Giguère & Eun-Kyeong Jo
The orphan nuclear receptor ESRRA (estrogen-related receptor α) is a key regulator of energy homeostasis and mitochondrial function. Macroautophagy/autophagy, an intracellular degradation process, is a critical innate effector against intracellular microbes. Here, we demonstrate that ESRRA is required for the activation of autophagy to promote innate antimicrobial defense against mycobacterial infection. AMP-activated protein kinase pathway and SIRT1 (sirtuin 1) activation led to induction of ESRRA, which is essential for autophagosome formation, in bone marrow-derived macrophages....

Autophagy inhibition promotes SNCA/alpha-synuclein release and transfer via extracellular vesicles with a hybrid autophagosome-exosome-like phenotype

Georgia Minakaki, Stefanie Menges, Agnes Kittel, Evangelia Emmanouilidou, Iris Schaeffner, Katalin Barkovits, Anna Bergmann, Edward Rockenstein, Anthony Adame, Franz Marxreiter, Brit Mollenhauer, Douglas Galasko, Edit Irén Buzás, Ursula Schlötzer-Schrehardt, Katrin Marcus, Wei Xiang, Dieter Chichung Lie, Kostas Vekrellis, Eliezer Masliah, Jürgen Winkler & Jochen Klucken
The autophagy-lysosome pathway (ALP) regulates intracellular homeostasis of the cytosolic protein SNCA/alpha-synuclein and is impaired in synucleinopathies, including Parkinson disease and dementia with Lewy bodies (DLB). Emerging evidence suggests that ALP influences SNCA release, but the underlying cellular mechanisms are not well understood. Several studies identified SNCA in exosome/extracellular vesicle (EV) fractions. EVs are generated in the multivesicular body compartment and either released upon its fusion with the plasma membrane, or cleared via the ALP....

Signed networks from sociology and political science, systems biology, international relations, finance, and computational chemistry

Samin Aref
This dataset contains a wide range of signed networks from different disciplines. For more information about the data, one may refer to the paper below:
Aref, S., and Wilson, M. C. Balance and frustration in signed networks. Journal of Complex Networks (2019). doi: 10.1093/comnet/cny015.

What Ails Italy: The Competitive Issue of the Italian State

DOMENICO DE MARTINIS
Italy faces a most challenging global financial and economic crisis since the end of World War II. For an economy that grew at a rapid pace between the 1950’s and the 1980’s, Italy has seen slower growth in the last twenty years. Italian policymakers are facing a series of problems that include a contracting gross domestic product (GDP), large unemployment, especially among its young people, high government deficits, large governmental borrowing along with high interest...

What Ails Italy: The Competitive Issue of the Italian State

DOMENICO DE MARTINIS
Italy faces a most challenging global financial and economic crisis since the end of World War II. For an economy that grew at a rapid pace between the 1950’s and the 1980’s, Italy has seen slower growth in the last twenty years. Italian policymakers are facing a series of problems that include a contracting gross domestic product (GDP), large unemployment, especially among its young people, high government deficits, large governmental borrowing along with high interest...

What Ails Italy: The Competitive Issue of the Italian State

DOMENICO DE MARTINIS
Italy faces a most challenging global financial and economic crisis since the end of World War II. For an economy that grew at a rapid pace between the 1950’s and the 1980’s, Italy has seen slower growth in the last twenty years. Italian policymakers are facing a series of problems that include a contracting gross domestic product (GDP), large unemployment, especially among its young people, high government deficits, large governmental borrowing along with high interest...

Baohuoside-I suppresses cell proliferation and migration by up-regulating miR-144 in melanoma

Ya-Guang Peng & Li Zhang
Context: Baohuoside-I was reported to induce apoptosis in non-small-cell lung cancer and inhibit the growth of multiple myeloma cells. The antitumour potential of baohuoside-I has not been demonstrated in melanoma yet. Objective: To investigate the potential antitumour activity of baohuoside-I against melanoma and elucidate its underlying molecular mechanism. Materials and methods: Cell viability was evaluated by MTT assay. The malignant invasion capacity was measured with trans-well assay. The relative expression change of microRNAs was profiled...

Baohuoside-I suppresses cell proliferation and migration by up-regulating miR-144 in melanoma

Ya-Guang Peng & Li Zhang
Context: Baohuoside-I was reported to induce apoptosis in non-small-cell lung cancer and inhibit the growth of multiple myeloma cells. The antitumour potential of baohuoside-I has not been demonstrated in melanoma yet. Objective: To investigate the potential antitumour activity of baohuoside-I against melanoma and elucidate its underlying molecular mechanism. Materials and methods: Cell viability was evaluated by MTT assay. The malignant invasion capacity was measured with trans-well assay. The relative expression change of microRNAs was profiled...

Gabapentin for Neuropathic Pain: An application to the 21st meeting of the WHO Expert Committee on Selection and Use of Essential Medicines for the inclusion of gabapentin on the WHO Model List of Essential Medicines

Peter Kamerman, Nanna Finnerup, Liliana De Lima, Simon Haroutonian, Srinivasa Raja, Blair Smith, Andrew Rice & Rolf-Detlef Treede
ABOUTThis repository contains all the files required to generate the application (and supporting documents) the International Association for the Study of Pain (IASP) and the International Association of Hospice and Palliative Care (IAHPC) made to the 21st meeting of the WHO Expert Committee on Selection and Use of Essential Medicines (2017) for the inclusion of gabapentin on the WHO Model List of Essential Medicines for the treatment of neuropathic pain.For a brief summary of why...

Data from: Among-species overlap in rodent body size distributions predicts species richness along a temperature gradient

Quentin Read, John Grady, Phoebe Zarnetske, Sydne Record, Benjamin Baiser, Jonathan Belmaker, Mao-Ning Tuanmu, Angela Strecker, Lydia Beaudrot & Katherine Thibault
The associated data files and R script are all that is required to reproduce the analyses in the manuscript "A thermal gradient of trait similarity across North America," published in Ecography: https://onlinelibrary.wiley.com/doi/10.1111/ecog.03641
The following .csv files contain data required to reproduce the analysis, with raw unprocessed small mammal data from NEON, small mammal data that has been put through our QC code, mammal trait data compiled from different sources, and site-level environmental covariates: raw_NEON_mammal_data.csv, final_NEON_mammal_data.csv, mammal_traits.csv,...

Data from: Among-species overlap in rodent body size distributions predicts species richness along a temperature gradient

Quentin Read, John Grady, Phoebe Zarnetske, Sydne Record, Benjamin Baiser, Jonathan Belmaker, Mao-Ning Tuanmu, Angela Strecker, Lydia Beaudrot & Katherine Thibault
The associated data files and R script are all that is required to reproduce the analyses in the manuscript "A thermal gradient of trait similarity across North America," published in Ecography: https://onlinelibrary.wiley.com/doi/10.1111/ecog.03641
The following .csv files contain data required to reproduce the analysis, with raw unprocessed small mammal data from NEON, small mammal data that has been put through our QC code, mammal trait data compiled from different sources, and site-level environmental covariates: raw_NEON_mammal_data.csv, final_NEON_mammal_data.csv, mammal_traits.csv,...

Human Variation Course Syllabus

Melanie Martin
Upper division university course taught in 2015 at the University of California Santa Barbara.

Evolutionary Medicine Course Syllabus

Melanie Martin
Upper division university course in Evolutionary Medicine, taught in 2012 at the University of California Santa Barbara

Evolutionary Medicine Course Syllabus

Melanie Martin
Upper division university course in Evolutionary Medicine, taught in 2012 at the University of California Santa Barbara

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