Top 10 Biorxiv Papers Today


2.143 Mikeys
#1. Opposing functions for retromer and Rab11 in extracellular vesicle cargo traffic at synapses
Rylie B Walsh, Agata N Becalska, Matthew J Zunitch, Shiyu Wang, Berith Isaac, Anna Yeh, Kate Koles, Avital A Rodal
Neuronal extracellular vesicles (EVs) play critical roles in intercellular communication and in propagation of pathogenic proteins in neurological disease. However, little is known about how cargoes are selectively packaged into neuronal EVs. Here, we examined the intracellular traffic and release of the EV cargoes Amyloid Precursor Protein (APP) and Synaptotagmin-4 (Syt4) at presynaptic nerve terminals of Drosophila motor neurons. We found that loss of the endosomal retromer complex leads to increased EV cargo levels both presynaptically and in EVs, and that this function is separable from previously identified roles of neuronal retromer. Conversely, EV cargo levels are reduced in rab11 mutants, and EV cargo sorting depends on a balance between Rab11-mediated recycling and retromer-dependent removal from the EV pathway. Rab11 and retromer have previously been implicated in Alzheimer's Disease, suggesting that these competing pathways may serve as therapeutic targets for limiting accumulation and release of toxic EV cargoes.
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biorxivpreprint: Opposing functions for retromer and Rab11 in extracellular vesicle cargo traffic at synapses https://t.co/UiMEOodOFm #bioRxiv
biorxiv_cellbio: Opposing functions for retromer and Rab11 in extracellular vesicle cargo traffic at synapses https://t.co/w0w2vlKYsL #biorxiv_cellbio
sbotlite: RT @biorxivpreprint: Opposing functions for retromer and Rab11 in extracellular vesicle cargo traffic at synapses https://t.co/UiMEOodOFm…
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Sample Sizes : [8]
Authors: 8
Total Words: 16803
Unqiue Words: 4918

2.121 Mikeys
#2. Directional stepping model for yeast dynein: Longitudinal- and side- step distributions
Rony Granek, Itay Fayer
We deduce the directional step distribution of yeast dynein motor protein on the microtubule surface by combing intrinsic features of the dynein and microtubule. These include the probability distribution of the separation vector between the two microtubule binding domains (MTBDs), the angular probability distribution of a single MTBD translation, the existence of a microtubule seam defect, microtubule binding sites, and theoretical extension that accounts for a load force on the motor. Our predictions are in excellent accord with the measured longitudinal step size distributions at various load forces. Moreover, we predict the side-step distribution and its dependence on longitudinal load forces, which shows a few surprising features. First, the distribution is broad. Second, in the absence of load, we find a small right-hand bias. Third, the side-step bias is susceptible to the longitudinal load force; it vanishes at a load equal to the motor stalling force and changes to a left-hand bias above that value. Fourth, our results...
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biorxivpreprint: Directional stepping model for yeast dynein: Longitudinal- and side- step distributions https://t.co/nS7L6wgsHB #bioRxiv
biorxiv_biophys: Directional stepping model for yeast dynein: Longitudinal- and side- step distributions https://t.co/6fhIcqR8PQ #biorxiv_biophys
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Authors: 2
Total Words: 6378
Unqiue Words: 1711

2.089 Mikeys
#3. Quantification of bioagressors induced yield gap for grain crops in France
Nathan Devaud, Corentin Mario Barbu
Analyzing yield losses of crops is instrumental in sustaining high productivity. Here, we develop statistical modelling of yield losses by French department based on weather, soil and epidemiological data for 13 diseases and 12 insect pests of grain crops over 8 years. Those environmental factors explain up to 90% of yield variations (wheat). Weather and soil quality are first order determinants as manifested both by direct assessment and by strongly correlated yields of even taxonomically very different crops. Bioagressors are important second order determinants: losses of 5 qx/ha (~7%) on wheat and 2 qx/ha (~15%) on winter oilseed rape. Across models based on conceptually different achievable yields, only Septoria tritici and Sitobion avenae on wheat, and Ceutorhynchus picitarsis and Ceutorhynchus assimilis on winter oilseed rape are consistently and significantly detrimental to yield. Those bioagressors seem not fully controlled which is compatible with empirical observations in the non academical litterature.
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biorxivpreprint: Quantification of bioagressors induced yield gap for grain crops in France https://t.co/wKKgRoW7rs #bioRxiv
biorxiv_plants: Quantification of bioagressors induced yield gap for grain crops in France https://t.co/rXwA1W35pP #biorxiv_plants
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2.088 Mikeys
#4. Changes in the expression of mitochondrial morphology-related genes during the differentiation of murine embryonic stem cells
Jeong Eon Lee, Bong Jong Seo, Min Ji Han, Yean Ju Hong, Kwonho Hong, Hyuk Song, Jeong Woong Lee, Jeong Tae Do
During embryonic development, cells undergo changes in gene expression, signaling pathway activation/inactivation, metabolism, and intracellular organelle structures, which are mediated by mitochondria. Mitochondria continuously switch their morphology between elongated tubular and fragmented globular via mitochondrial fusion and fission. Mitochondrial fusion is mediated by proteins encoded by Mfn1, Mfn2, and Opa1, whereas mitochondrial fission is mediated by proteins encoded by Fis1 and Dmn1L. Here, we investigated the expression patterns of mitochondria-related genes during the differentiation of mouse embryonic stem cells (ESCs) in response to leukemia inhibitory factor (LIF) withdrawal. The expression of Mfn2 and Dnm1L was, as expected, increased and decreased, respectively. By comparing gene expression and mitochondrial morphology, we proposed an index that could precisely represent mitochondrial changes during the differentiation of pluripotent stem cells by analyzing the expression ratios of three fusion- and two...
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biorxivpreprint: Changes in the expression of mitochondrial morphology-related genes during the differentiation of murine embryonic stem cells https://t.co/EOG5ExxcXh #bioRxiv
biorxiv_cellbio: Changes in the expression of mitochondrial morphology-related genes during the differentiation of murine embryonic stem cells https://t.co/55OCTuy7oz #biorxiv_cellbio
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2.068 Mikeys
#5. Inverted encoding models estimate sensible channel responses for sensible models
Thomas C Sprague, Geoffrey M Boynton, John Serences
In a commentary published in eNeuro, Gardner & Liu (2019) discuss the role of model specification in interpreting the output of complex models of neural data. As a case study, they suggest that one variant of such analyses, the inverted encoding model (IEM) analysis framework, should not be used to assay properties of "stimulus representations" because the ability to apply linear transformations at various stages of the analysis procedure renders results 'arbitrary'. As we discuss, the specification of all models is arbitrary to the extent that an experimenter makes choices based on current knowledge of the model system. However, the results derived from any given model, such as the reconstructed channel response profiles obtained from an IEM analysis, are uniquely defined and are arbitrary only in the sense that changes in the model can predictably change results. Moreover, with knowledge of the model used for IEM analyses, the results remain informative as comparisons between reconstructed channel response profiles across task...
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biorxivpreprint: Inverted encoding models estimate sensible channel responses for sensible models https://t.co/LOw5TSzdof #bioRxiv
biorxiv_neursci: Inverted encoding models estimate sensible channel responses for sensible models https://t.co/HThQYlDqaL #biorxiv_neursci
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Repository: iem_sim
User: JohnSerences
Language: MATLAB
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Total Words: 6152
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2.056 Mikeys
#6. Cellular and Molecular Probing of Intact Transparent Human Organs
Shan Zhau, Mihail Ivilinov Todorov, Ruiyao Cai, Hanno Steinke, Elisabeth Kemter, Eckhard Wolf, Jan Lipfert, Ingo Bechmann, Ali Erturk
Optical tissue transparency permits cellular and molecular investigation of complex tissues in 3D, a fundamental need in biomedical sciences. Adult human organs are particularly challenging for this approach, owing to the accumulation of dense and sturdy molecules in decades-aged human tissues. Here, we introduce SHANEL method utilizing a new tissue permeabilization approach to clear and label stiff human organs. We used SHANEL to generate the first intact transparent adult human brain and kidney, and perform 3D histology using antibodies and dyes in centimeters depth. Thereby, we revealed structural details of the sclera, iris and suspensory ligament in the human eye, and the vessels and glomeruli in the human kidney. We also applied SHANEL on transgenic pig organs to map complex structures of EGFP expressing beta cells in >10 cm size pancreas. Overall, SHANEL is a robust and unbiased technology to chart the cellular and molecular architecture of intact large mammalian organs.
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PromPreprint: Cellular and Molecular Probing of Intact Transparent Human Organs https://t.co/0WZ39Yu5qR
JimJohnsonSci: RT @biorxivpreprint: Cellular and Molecular Probing of Intact Transparent Human Organs https://t.co/2UWna3xCXQ #bioRxiv
THebertMcGill: RT @biorxivpreprint: Cellular and Molecular Probing of Intact Transparent Human Organs https://t.co/2UWna3xCXQ #bioRxiv
Astro_Erik: RT @biorxivpreprint: Cellular and Molecular Probing of Intact Transparent Human Organs https://t.co/2UWna3xCXQ #bioRxiv
MathaCMU: RT @biorxivpreprint: Cellular and Molecular Probing of Intact Transparent Human Organs https://t.co/2UWna3xCXQ #bioRxiv
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ozgungokce: RT @biorxivpreprint: Cellular and Molecular Probing of Intact Transparent Human Organs https://t.co/2UWna3xCXQ #bioRxiv
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KomaToug: RT @biorxivpreprint: Cellular and Molecular Probing of Intact Transparent Human Organs https://t.co/2UWna3xCXQ #bioRxiv
LipfertLab: RT @PromPreprint: Cellular and Molecular Probing of Intact Transparent Human Organs https://t.co/0WZ39Yu5qR
cnombela: RT @biorxivpreprint: Cellular and Molecular Probing of Intact Transparent Human Organs https://t.co/2UWna3xCXQ #bioRxiv
jordanyaron: RT @biorxivpreprint: Cellular and Molecular Probing of Intact Transparent Human Organs https://t.co/2UWna3xCXQ #bioRxiv
TatsuyaCunshang: RT @biorxivpreprint: Cellular and Molecular Probing of Intact Transparent Human Organs https://t.co/2UWna3xCXQ #bioRxiv
DenaxaMyrto: RT @biorxivpreprint: Cellular and Molecular Probing of Intact Transparent Human Organs https://t.co/2UWna3xCXQ #bioRxiv
MarikaRuiyao: RT @biorxivpreprint: Cellular and Molecular Probing of Intact Transparent Human Organs https://t.co/2UWna3xCXQ #bioRxiv
ssnaka: RT @biorxivpreprint: Cellular and Molecular Probing of Intact Transparent Human Organs https://t.co/2UWna3xCXQ #bioRxiv
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Total Words: 13486
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2.055 Mikeys
#7. Is it time to replace gzip? Comparison of modern compressors for molecular sequence databases
Kirill Kryukov, Mahoko Takahashi Ueda, So Nakagawa, Tadashi Imanishi
Nearly all molecular sequence databases currently use gzip for data compression. Ongoing rapid accumulation of stored data calls for more efficient compression tool. We systematically benchmarked the available compressors on representative DNA, RNA and Protein datasets. We tested specialized sequence compressors 2bit, BLAST, DNA-COMPACT, DELIMINATE, Leon, MFCompress, NAF, UHT and XM, and general-purpose compressors brotli, bzip2, gzip, lz4, lzop, lzturbo, pbzip2, pigz, snzip, xz, zpaq and zstd. Overall, NAF and zstd performed well in terms of transfer/decompression speed. However, checking benchmark results is necessary when choosing compressor for specific data type and application. Benchmark results database is available at: http://kirr.dyndns.org/sequence-compression-benchmark/.
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biorxivpreprint: Is it time to replace gzip? Comparison of modern compressors for molecular sequence databases https://t.co/m9OPSPdJjZ #bioRxiv
biorxiv_bioinfo: Is it time to replace gzip? Comparison of modern compressors for molecular sequence databases https://t.co/a5PyFLiFpl #biorxiv_bioinfo
PromPreprint: Is it time to replace gzip? Comparison of modern compressors for molecular sequence databases https://t.co/55VZJvNzDP
BioRxivCurator: Is it time to replace gzip? Comparison of modern compressors for molecular sequence databases https://t.co/QxzcYOCnJE
sabahzero: RT @biorxiv_bioinfo: Is it time to replace gzip? Comparison of modern compressors for molecular sequence databases https://t.co/a5PyFLiFpl…
sjackman: RT @biorxivpreprint: Is it time to replace gzip? Comparison of modern compressors for molecular sequence databases https://t.co/m9OPSPdJjZ…
gau: RT @biorxiv_bioinfo: Is it time to replace gzip? Comparison of modern compressors for molecular sequence databases https://t.co/a5PyFLiFpl…
antiplastics: RT @biorxivpreprint: Is it time to replace gzip? Comparison of modern compressors for molecular sequence databases https://t.co/m9OPSPdJjZ…
andrewjroger: RT @biorxiv_bioinfo: Is it time to replace gzip? Comparison of modern compressors for molecular sequence databases https://t.co/a5PyFLiFpl…
Psy_Fer_: RT @biorxiv_bioinfo: Is it time to replace gzip? Comparison of modern compressors for molecular sequence databases https://t.co/a5PyFLiFpl…
prashbio: RT @biorxiv_bioinfo: Is it time to replace gzip? Comparison of modern compressors for molecular sequence databases https://t.co/a5PyFLiFpl…
sounaka: RT @biorxiv_bioinfo: Is it time to replace gzip? Comparison of modern compressors for molecular sequence databases https://t.co/a5PyFLiFpl…
J_M_Aury: RT @biorxiv_bioinfo: Is it time to replace gzip? Comparison of modern compressors for molecular sequence databases https://t.co/a5PyFLiFpl…
aquaskyline: RT @biorxiv_bioinfo: Is it time to replace gzip? Comparison of modern compressors for molecular sequence databases https://t.co/a5PyFLiFpl…
AdamJOrr: RT @biorxivpreprint: Is it time to replace gzip? Comparison of modern compressors for molecular sequence databases https://t.co/m9OPSPdJjZ…
ChasingMicrobes: RT @biorxiv_bioinfo: Is it time to replace gzip? Comparison of modern compressors for molecular sequence databases https://t.co/a5PyFLiFpl…
sbreiff: RT @biorxivpreprint: Is it time to replace gzip? Comparison of modern compressors for molecular sequence databases https://t.co/m9OPSPdJjZ…
GC_GGCCGC: RT @biorxiv_bioinfo: Is it time to replace gzip? Comparison of modern compressors for molecular sequence databases https://t.co/a5PyFLiFpl…
kundu_ritu: RT @biorxiv_bioinfo: Is it time to replace gzip? Comparison of modern compressors for molecular sequence databases https://t.co/a5PyFLiFpl…
agroppi: RT @biorxiv_bioinfo: Is it time to replace gzip? Comparison of modern compressors for molecular sequence databases https://t.co/a5PyFLiFpl…
Sivico26: RT @biorxiv_bioinfo: Is it time to replace gzip? Comparison of modern compressors for molecular sequence databases https://t.co/a5PyFLiFpl…
shian_su: RT @biorxiv_bioinfo: Is it time to replace gzip? Comparison of modern compressors for molecular sequence databases https://t.co/a5PyFLiFpl…
MTwitteJ: RT @biorxivpreprint: Is it time to replace gzip? Comparison of modern compressors for molecular sequence databases https://t.co/m9OPSPdJjZ…
ilnam_kang: RT @biorxiv_bioinfo: Is it time to replace gzip? Comparison of modern compressors for molecular sequence databases https://t.co/a5PyFLiFpl…
hdeshmuk: RT @biorxiv_bioinfo: Is it time to replace gzip? Comparison of modern compressors for molecular sequence databases https://t.co/a5PyFLiFpl…
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Total Words: 2440
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2.052 Mikeys
#8. Is adaptation limited by mutation? A timescale dependent effect of genetic diversity on the adaptive substitution rate in animals.
Marjolaine Rousselle, Paul Simion, Marie-Ka Tilak, Emeric Figuet, Benoit Nabholz, Nicolas Galtier
Whether adaptation is limited by the supply of beneficial mutations is a long-standing question of evolutionary genetics, which more generally relates to the determination of the adaptive substitution rate and its relationship with the effective population size Ne. The empirical evidence so far is equivocal, with some but not all studies supporting a higher adaptive substitution rate in large-Ne than in small-Ne species. We gathered coding sequence polymorphism data and estimated the adaptive amino-acid substitution rate ωa, in 50 species from ten distant groups of animals with markedly different population mutation rate θ. We reveal the existence of a complex, timescale dependent relationship between species adaptive substitution rate and genetic diversity. On the one hand, we report a positive relationship between ωa and θ among closely related species, indicating that adaptation is indeed limited by the supply of beneficial mutations, but this was only true in relatively low-θ taxa. On the other hand, we uncovered a weak...
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biorxivpreprint: Is adaptation limited by mutation? A timescale dependent effect of genetic diversity on the adaptive substitution rate in animals. https://t.co/ISxrZogC5w #bioRxiv
biorxiv_evobio: Is adaptation limited by mutation? A timescale dependent effect of genetic diversity on the adaptive substitution rate in animals. https://t.co/10eT6jjw2a #biorxiv_evobio
GaltierNicolas: Happy that @MarjoRousselle's last PhD paper was released on biorxiv! https://t.co/12W2iRwTZt
nbierne: RT @GaltierNicolas: Happy that @MarjoRousselle's last PhD paper was released on biorxiv! https://t.co/12W2iRwTZt
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BenoitNabholz: RT @GaltierNicolas: Happy that @MarjoRousselle's last PhD paper was released on biorxiv! https://t.co/12W2iRwTZt
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allio_remi: RT @GaltierNicolas: Happy that @MarjoRousselle's last PhD paper was released on biorxiv! https://t.co/12W2iRwTZt
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alan_moan: RT @GaltierNicolas: Happy that @MarjoRousselle's last PhD paper was released on biorxiv! https://t.co/12W2iRwTZt
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Authors: 6
Total Words: 12754
Unqiue Words: 3696

2.048 Mikeys
#9. No evidence for social genetic effects or genetic similarity among friends beyond that due to population stratification: a reappraisal of Domingue et al (2018)
Loic Yengo, Morgan Sidari, Karin J.H. Verweij, Peter Visscher, MATTHEW C. KELLER, Brendan Zietsch
Using data from 5,500 adolescents from the National Longitudinal Study of Adolescent to Adult Health, Domingue et al. (2018) claimed to show that friends are genetically more similar to one another than randomly selected peers, beyond the confounding effects of population stratification by ancestry. The authors also claimed to show "social-genetic" effects, whereby individuals' educational attainment (EA) is influenced by their friends' genes. Neither claim is justified by the data. Mathematically we show that 1) although similarity at causal variants is expected under assortment, the genome-wide relationship between friends (and similarly between mates) is extremely small (an effect that could be explained by subtle population stratification) and 2) significant association between individuals' EA and their friends' polygenic score for EA is expected under homophily with no socio-genetic effects.
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biorxivpreprint: No evidence for social genetic effects or genetic similarity among friends beyond that due to population stratification: a reappraisal of Domingue et al (2018) https://t.co/yF2Hzjrj00 #bioRxiv
biorxiv_genetic: No evidence for social genetic effects or genetic similarity among friends beyond that due to population stratification: a ... https://t.co/K6zcq5S3uh #biorxiv_genetic
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2.046 Mikeys
#10. The minimal behavioral time window for reward conditioning in the nucleus accumbens of mice
Kenji Yamaguchi, Yoshitomo Maeda, Takeshi Sawada, Yusuke Iino, Mio Tajiri, Ryosuke Nakazato, Haruo Kasai, Sho Yagishita
The temporal precision of reward-reinforcement learning is determined by the minimal time window of the reward action-theoretically known as the eligibility trace. In animal studies, however, such a minimal time window and its origin have not been well understood. Here, we used head-restrained mice to accurately control the timing of sucrose water as an unconditioned stimulus (US); we found that the reinforcement effect of the US occurred only within 1 s after a short tone of a conditioned stimulus (CS). The conditioning required the dopamine D1 receptor and CaMKII signaling in the nucleus accumbens (NAc). The time window was not reduced by replacing CS with optogenetic stimulation of the synaptic inputs to the NAc, which is in agreement with previous reports on the effective dopamine timing of NAc synapses. Thus, our data suggest that the minimal reward time window is 1 s, and is formed in the NAc.
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biorxivpreprint: The minimal behavioral time window for reward conditioning in the nucleus accumbens of mice https://t.co/vtb4u9tIMA #bioRxiv
biorxiv_neursci: The minimal behavioral time window for reward conditioning in the nucleus accumbens of mice https://t.co/1S5L1Qrzm4 #biorxiv_neursci
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Authors: 8
Total Words: 11394
Unqiue Words: 3453

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Assert is a website where the best academic papers on arXiv (computer science, math, physics), bioRxiv (biology), BITSS (reproducibility), EarthArXiv (earth science), engrXiv (engineering), LawArXiv (law), PsyArXiv (psychology), SocArXiv (social science), and SportRxiv (sport research) bubble to the top each day.

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