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On the Importance of Gradients for Detecting Distributional Shifts in the Wild [article]

Rui Huang, Andrew Geng, Yixuan Li
2021 arXiv   pre-print
Our key idea is that the magnitude of gradients is higher for in-distribution (ID) data than that for OOD data, making it informative for OOD detection.  ...  Detecting out-of-distribution (OOD) data has become a critical component in ensuring the safe deployment of machine learning models in the real world.  ...  Acknowledgement Research is supported by the Office of the Vice Chancellor for Research and Graduate Education (OVCRGE) with funding from the Wisconsin Alumni Research Foundation (WARF).  ... 
arXiv:2110.00218v2 fatcat:46z5yfxmgvh7lhaa2vqembxbby

The Vacuolar Import and Degradation Pathway Merges with the Endocytic Pathway to Deliver Fructose-1,6-bisphosphatase to the Vacuole for Degradation

C. Randell Brown, Allison B. Wolfe, Dongying Cui, Hui-Ling Chiang
2008 Journal of Biological Chemistry  
After fusion, Sec28p is distributed on the vacuolar membrane, where it concentrates on vesicles that pinch off from this organelle.  ...  Here, using biochemical and genetic approaches, we identified a requirement for SEC28 in FBPase degradation. SEC28 encodes the ⑀-COP subunit of COPI (coat protein complex I) coatomer proteins.  ...  Following a 2-h shift to glucose, most of the FBPase-GFP was in the cytosol in ⌬sec28 cells. By contrast, wild type cells degraded FBPase after a glucose shift for 2 h.  ... 
doi:10.1074/jbc.m709922200 pmid:18660504 pmcid:PMC2533773 fatcat:ybixjgszqbfcnlt52lxvvbry3a

Identification of Novel Vesicles in the Cytosol to Vacuole Protein Degradation Pathway

Pei-Hsin Huang, Hui-Ling Chiang
1997 Journal of Cell Biology  
We re-port the purification of novel FBPase-associated vesicles from wild-type cells to near homogeneity.  ...  Several vid mutants defective in the glucose-induced degradation of FBPase in the vacuole have been isolated. In some vid mutants, FBPase is found in punctate structures in the cytoplasm.  ...  We thank Maria Ericsson for performing EM work, Kathleen J. Barrett for editing this manuscript, and members in the Chiang laboratory for helpful discussions.  ... 
doi:10.1083/jcb.136.4.803 pmid:9049246 pmcid:PMC2132494 fatcat:7hmt2ua2hbfozbafgmnjnqqnm4

Relationship between Yeast Polyribosomes and Upf Proteins Required for Nonsense mRNA Decay

Audrey L. Atkin, Laura R. Schenkman, Margot Eastham, Jeffrey N. Dahlseid, Michael J. Lelivelt, Michael R. Culbertson
1997 Journal of Biological Chemistry  
Density gradient profiles for Upf1p were unchanged in the absence of Upf3p, and although similar, were modestly shifted to fractions lighter than those containing polyribosomes in the absence of Upf2p.  ...  Our results suggest that the association of Upf2p with polyribosomes typically found in a wild-type strain depends on the presence and opposing effects of Upf1p and Upf3p.  ...  Acknowledgments-We thank John Puziss and Phil Hieter for providing yeast strain YJP121 and plasmid pUZ178. We thank Leanne Olds for preparation of figures.  ... 
doi:10.1074/jbc.272.35.22163 pmid:9268361 fatcat:3qgmpvnbtngvxmncqrkxatfale

Demonstration of Lysosomal Localization for the Mammalian Ependymin-related Protein Using Classical Approaches Combined with a Novel Density Shift Method

Maria Cecilia Della Valle, David E. Sleat, Istvan Sohar, Ting Wen, John E. Pintar, Michel Jadot, Peter Lobel
2006 Journal of Biological Chemistry  
EPDR, in parallel with lysosomal markers, shows this density shift in gradient centrifugation experiments comparing mutant and wild type mice.  ...  For more definitive localization, we have developed a novel approach based upon a selective buoyant density shift of the brain lysosomes in a mutant mouse lacking NPC2, a lysosomal protein involved in  ...  Quantitative analysis of the distribution of protein in shifted versus nonshifted organelles will be an important step in distinguishing true resident lysosomal proteins from the contaminants that inevitably  ... 
doi:10.1074/jbc.m606208200 pmid:16954209 fatcat:4s75drmovjcn7ewfijrtqwwkkm

Identification of Cargo for Adaptor Protein (AP) Complexes 3 and 4 by Sucrose Gradient Profiling

Heidi Pertl-Obermeyer, Xu Na Wu, Jens Schrodt, Christina Müdsam, Gerhard Obermeyer, Waltraud X. Schulze
2016 Molecular & Cellular Proteomics  
Thus, we screened for altered distribution profiles across a density gradient of membrane proteins in wild type versus ap-3␤ and ap-4␤ knock-out mutants.  ...  The combination of organelle density gradients with proteome analysis turned out as a suitable experimental strategy for large-scale analyses of protein trafficking. Molecular & Cellular  ...  Salzburg) is acknowledged for excellent technical assistance with the protoplast preparation and swelling assays.  ... 
doi:10.1074/mcp.m116.060129 pmid:27371946 pmcid:PMC5013305 fatcat:37hk6ihs3veoha3spcly36j5um

Vid24p, a Novel Protein Localized to the Fructose-1,6-bisphosphatase–containing Vesicles, Regulates Targeting of Fructose-1,6-bisphosphatase from the Vesicles to the Vacuole for Degradation

Meng-Chieh Chiang, Hui-Ling Chiang
1998 Journal of Cell Biology  
Glucose regulates the degradation of the key  ...  FBPase distribution on the sucrose gradient was detected by Western blotting after a shift of the pep4 cell (a-d) and the vid24-1 mutant (e-h) to glucose for 0, 30, 60, and 90 min. Figure 10 .  ...  The distributions of FBPase on the sucrose gradients at t ϭ 0 min (a), 30 min (b), and 60 min (c), and the distributions of HA-Vid24p on the sucrose gradients at t ϭ 0 min (d), 30 min (e), and 60 min (  ... 
doi:10.1083/jcb.140.6.1347 pmid:9508768 pmcid:PMC2132677 fatcat:elmeqggwabdfpiyru4qr22owia

Implementation of GF-HOG Technique for Effective Commercial and Industrial Load Clustering and Classification for Better Demand Response

Aniruddha Bhattacharya, Madhusudan Singh
2021 International Journal of Electrical and Electronics Research  
The algorithms were tested on a local network which 70% -30 % of load in favor of CIL and found to generate better DR.  ...  residential tariff in India .The present method employed for clustering and classifying Load profile of CIL loads with wild swings will impede effective demand response implementation due to tariff cartelization  ...  used in this research work for detecting distributed density gradient images of CIL Load [12] [13] .  ... 
doi:10.37391/ijeer.090307 fatcat:ardgk5mngba4jlsfzzcqoqrjne

Factors Affecting Nuclear Export of the 60S Ribosomal Subunit In Vivo

Tracy Stage-Zimmermann, Ute Schmidt, Pamela A. Silver, Keith R. Yamamoto
2000 Molecular Biology of the Cell  
In particular, deletion of the previously uncharacterized karyopherin KAP120 caused accumulation of Rpl11b-GFP in the nucleus, whereas ribosomal protein import was not impaired.  ...  A panel of mutant yeast strains was screened for their accumulation of Rpl11b-GFP in the nucleus as an indicator of their involvement in ribosome synthesis and/or transport.  ...  Brodsky, for critical input at the initial phase of the project, Terrence Moy for technical assistance and helpful discussions, Karin Anderson and Anne McBride for critical reading of the manuscript, and  ... 
doi:10.1091/mbc.11.11.3777 pmid:11071906 pmcid:PMC15036 fatcat:ggb4nvsttfbizcsgimtw6bklry

Detection of Genetic Variants of Transthyretin by Liquid Chromatography-Dual Electrospray Ionization Fourier-Transform Ion-Cyclotron-Resonance Mass Spectrometry

A. I. Nepomuceno
2004 Clinical Chemistry  
The [M ؉ 11 H ؉ ] 11؉ charge state for all samples was used to determine the mass accuracies for both wild-type and variant forms of the protein. We correctly assigned seven of seven TTR variants.  ...  One of the numerous proteins causing amyloidosis is transthyretin (TTR), a protein usually responsible for the transport of thyroxine and retinolbinding protein.  ...  detection of novel cis double mutation The [M ϩ 11H ϩ ] 11ϩ charge state of a theoretical wild-type isotopic distribution and an experimental isotopic distribution are shown in Fig. 3A .  ... 
doi:10.1373/clinchem.2004.033274 pmid:15205369 fatcat:guwlfcm4a5bz3aknl4rrriywde

AtPIN4 Mediates Sink-Driven Auxin Gradients and Root Patterning in Arabidopsis

Jiřı́ Friml, Eva Benková, Ikram Blilou, Justyna Wisniewska, Thorsten Hamann, Karin Ljung, Scott Woody, Goran Sandberg, Ben Scheres, Gerd Jürgens, Klaus Palme
2002 Cell  
suggest the involvement of the phytohormone auxin in this process. Here, we characterize a novel member of the PIN family of putative auxin efflux carriers, Arabi-  ...  This was ent and is important for pattern formation in the root tip. confirmed by the expression pattern of a transcriptional Our results suggest a unique role for AtPIN4 in regulating fusion of the AtPIN4  ...  We propose that this basal sink controls the auxin distribution and based on the relative concentrations of a morphogen at specific positions along the gradient may apply in thereby patterning, since chemical  ... 
doi:10.1016/s0092-8674(02)00656-6 pmid:11893337 fatcat:lktx3ervrjhsjalgy42atnwc34

Bicoid Determines Sharp and Precise Target Gene Expression in the Drosophila Embryo

Olivier Crauk, Nathalie Dostatni
2005 Current Biology  
The activity of the Bicoid (Bcd) transcription factor is a useful example of how quantitative information contained in a smooth morphogen gradient is transformed into discrete and precise patterns of target  ...  There are two distinct and important aspects to this process: the "sharpening" of the posterior borders of the expression domains and the "precision" of where the target genes are expressed along the length  ...  We finally show that the bcd mRNA distribution pattern is much more variable in embryos from stau HL females than in wild-type embryos and propose that the effect of the stau HL mutant background on the  ... 
doi:10.1016/j.cub.2005.09.046 pmid:16271865 fatcat:ehvdpwreg5hgfe7yx2wiwywkce

Networked Chemoreceptors Benefit Bacterial Chemotaxis Performance

Vered Frank, Germán E. Piñas, Harel Cohen, John S. Parkinson, Ady Vaknin
2016 mBio  
Motile bacteria use large receptor arrays to detect and follow chemical gradients in their environment.  ...  These advantages proved especially critical for chemotaxis toward an attractant source under conditions in which bacteria are unable to alter the attractant gradient.  ...  FUNDING INFORMATION This work, including the efforts of John S.  ... 
doi:10.1128/mbio.01824-16 pmid:27999161 pmcid:PMC5181776 fatcat:c2qcytm4evbyfohkyj5hbgcztq

Relationships among ecological traits of wild bee communities along gradients of habitat amount and fragmentation

Romain Carrié, Emilie Andrieu, Saul A. Cunningham, Pia E. Lentini, Michel Loreau, Annie Ouin
2016 Ecography  
Le Feon for the provision of part of the French trait data.  ...  ML was supported by the TULIP Laboratory of Excellence (ANR-10-LABX-41). We thank D. Genoud and M. Batley for their help on specimen identification and their expertise on bee species traits.  ...  We also examined the phylogenetic structure of wild bee communities along the landscape gradients (phylogenetic clustering), to detect if changes in some trait distributions were due to a direct effect  ... 
doi:10.1111/ecog.02632 fatcat:bkfvgqefn5hb7n22x5m2g5reb4

Envelope Proteins of Vesicular Stomatitis Virus: Effect of Temperature-Sensitive Mutations in Complementation Groups III and V

Florence Lafay
1974 Journal of Virology  
The distribution of these proteins among cytoplasmic cellular fractions separated on discontinuous sucrose gradients was identical for wild-type and tsllI-infected cells.  ...  Strikingly different patterns were observed for the G protein in gradients from cells infected by tsV mutants; very little, if any, G protein was found in the lightest fraction.  ...  Berkaloff for their interest in this work and for many helpful discussions. I thank L. Prevec for criticism of the manuscript. I am greatly indebted to B. Jaillard, D. Pese, and A.  ... 
doi:10.1128/jvi.14.5.1220-1228.1974 fatcat:kdrqi5kluvb3rb5tzhhrlij2vu
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