Top 10 Biorxiv Papers Today in Bioengineering


2.009 Mikeys
#1. Design principles for open source bioinstrumentation: the poseidon syringe pump system as an example
A. Sina Booeshaghi, Eduardo da Veiga Beltrame, Dylan Bannon, Jase Gehring, Lior Pachter
The poseidon syringe pump and microscope system is an open source alternative to commercial systems. It costs less than $400 and can be assembled in under an hour using the instructions and source files available at https://pachterlab.github.io/poseidon. We describe the poseidon system and use it to illustrate design principles that can facilitate the adoption and development of open source bioinstruments. The principles are functionality, robustness, simplicity, modularity, benchmarking, and documentation.
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biorxivpreprint: Design principles for open source bioinstrumentation: the poseidon syringe pump system as an example https://t.co/iscp6Ft8iU #bioRxiv
lpachter: There is a lot of talk in genomics about open source software. But how about hardware? Thanks to the leadership of Jase Gehring and exceptional work by @sinabooeshaghi & @VeigaBeltrame we've developed an OS syringe pump/microscope system for microfluidics. https://t.co/13BpK9oNa5
FritzPreusser: https://t.co/XZAFuc17ly Exciting preprint by the @lpachter lab, highlighting challenges and possibilities of open bioinstrumentation! Poseidon pump and microfluidics microscopy station are presented. Comes with a website and detailed instruction videos! Can't wait to build it! https://t.co/Yau3LKGuCz
PromPreprint: Design principles for open source bioinstrumentation: the poseidon syringe pump system as an example https://t.co/zwrm9EW9GS
preibischs: RT @FritzPreusser: https://t.co/XZAFuc17ly Exciting preprint by the @lpachter lab, highlighting challenges and possibilities of open bioins…
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poseidon system - open source syringe pumps and microscope for laboratories

Repository: poseidon
User: pachterlab
Language: Python
Stargazers: 12
Subscribers: 6
Forks: 5
Open Issues: 5
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Authors: 5
Total Words: 4150
Unqiue Words: 1546

1.998 Mikeys
#2. Differential Effector Response of Amnion- and Adipose-Derived Mesenchymal Stem Cells to Inflammation; Implications for Intradiscal Therapy
Ryan Borem, Allison Madeline, Mackenzie Bowman, Sanjitpal Gill, John Tokish, Jeremy Mercuri
Intervertebral disc degeneration (IVDD) is a progressive condition marked by inflammation and tissue destruction. The effector functions of mesenchymal stem cells (MSCs) make them an attractive therapy for patients with IVDD. While several sources of MSCs exist, the optimal choice for use in the inflamed IVD remains a significant question. Adipose (AD)- and amnion (AM)-derived MSCs have several advantages compared to other sources, however, no study has directly compared the impact of IVDD inflammation on their effector functions. Human MSCs were cultured in media with or without supplementation of interleukin-1β and tumor necrosis factor-α at concentrations produced by IVDD cells. MSC proliferation and production of pro- and anti-inflammatory cytokines were quantified following 24- and 48-hours of culture. Additionally, the osteogenic and chondrogenic potential of AD- and AM-MSCs was characterized via histology and biochemical analysis following 28 days of culture. In inflammatory culture, AM-MSCs produced significantly more...
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Sample Sizes : [3, 3, 3, 3, 3, 3, 3, 3, 3]
Authors: 6
Total Words: 9372
Unqiue Words: 2528

1.997 Mikeys
#3. Ultra-fast fit-free analysis of complex fluorescence lifetime imaging via deep learning
Jason T. Smith, Ruoyang Yao, Nattawut Sinsuebphon, Alena Rudkouskaya, Joseph Mazurkiewicz, Margarida Barroso, Pingkun Yan, Xavier Intes
Fluorescence lifetime imaging (FLI) provides unique quantitative information in biomedical and molecular biology studies, but relies on complex data fitting techniques to derive the quantities of interest. Herein, we propose a novel fit-free approach in FLI image formation that is based on Deep Learning (DL) to quantify complex fluorescence decays simultaneously over a whole image and at ultra-fast speeds. Our deep neural network (DNN), named FLI-Net, is designed and model-based trained to provide all lifetime-based parameters that are typically employed in the field. We demonstrate the accuracy and generalizability of FLI-Net by performing quantitative microscopic and preclinical experimental lifetime-based studies across the visible and NIR spectra, as well as across the two main data acquisition technologies. Our results demonstrate that FLI-Net is well suited to quantify complex fluorescence lifetimes, accurately, in real time in cells and intact animals without any parameter settings. Hence, it paves the way to reproducible...
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Authors: 8
Total Words: 9834
Unqiue Words: 3218

1.997 Mikeys
#4. Spatial control of oxygen delivery to 3D cultures alters cancer cell growth and gene expression
William W. Wulftange, Michelle A. Rose, Marcial Garmendia-Cedillos, Davi da Silva, Joanna E. Poprawski, Dhruv Srinivasachar, Taylor Sullivan, Langston Lim, Valery V. Bliskovsky, Matthew D. Hall, Thomas J. Pohida, Robert W. Robey, Nicole Y. Morgan, Michael Gottesman
Commonly used monolayer cancer cell cultures fail to provide a physiologically relevant environment in terms of oxygen delivery. Here, we describe a three-dimensional bioreactor system where cancer cells are grown in Matrigel in modified 6-well plates. Oxygen is delivered to the cultures through a polydimethylsiloxane (PDMS) membrane at the bottom of the wells, with microfabricated PDMS pillars to control oxygen delivery. The plates receive 3% oxygen from below and 0% oxygen at the top surface of the media, providing a gradient of 3% to 0% oxygen. We compared growth and transcriptional profiles for cancer cells grown in Matrigel in the bioreactor, 3D cultures grown in 21% oxygen, and cells grown in a standard hypoxia chamber at 3% oxygen. Additionally, we compared gene expression of conventional 2D monolayer culture and 3D Matrigel culture in 21% oxygen. We conclude that controlled oxygen delivery may provide a more physiologically relevant 3D system.
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Authors: 14
Total Words: 13018
Unqiue Words: 3458

0.0 Mikeys
#5. Real-time three-dimensional MRI for the assessment of dynamic carpal instability
Calvin B Shaw, Brent H Foster, Marissa Borgese, Robert D Boutin, Cyrus Bateni, Christopher O Bayne, Robert M Szabo, Krishna S Nayak, Abhijit Chaudhari
Carpal instability is defined as a condition where wrist motion or loading creates mechanical dysfunction, resulting in weakness, pain and decreased function. Often the diagnosis is made late when malalignment is visualized on static radiography, CT, or MRI. When conventional imaging methods do not identify the instability patterns, yet clinical signs associated with instability exist, the diagnosis of dynamic instability is often suggested to describe carpal derangement manifested only during the wrist's active motion or stress. We addressed the question: can advanced MRI techniques provide quantitative measures for evaluating dynamic carpal instability and supplement standard static MRI acquisition? Our objectives were to [1] develop a real-time, three-dimensional MRI method to image the carpal joints during their active, uninterrupted motion; and [2] demonstrate feasibility of the method for assessing metrics relevant to dynamic carpal instability, thus overcoming limitations of conventional MRI. Twenty wrists (bilateral wrists...
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Authors: 9
Total Words: 7592
Unqiue Words: 2389

0.0 Mikeys
#6. A 3D-printed hand-powered centrifuge for molecular biology
Gaurav Byagathvalli, Aaron Pomerantz, Soham Sinha, Janet Standeven, M. Saad Bhamla
The centrifuge is an essential tool for many aspects of research and medical diagnostics. However, conventional centrifuges are often inaccessible outside of conventional laboratory settings, such as remote field sites, require a constant external power source, and can be prohibitively costly in resource-limited settings and STEM-focused programs. Here we present the 3D-Fuge, a 3D-printed hand-powered centrifuge, as a novel alternative to standard benchtop centrifuges. Based on the design principles of a paper-based centrifuge, this 3D-printed instrument increases the volume capacity to 2 mL and can reach hand-powered centrifugation speeds up to 6,000 rpm. The 3D-Fuge devices presented here are capable of centrifugation of a wide variety of different solutions such as spinning down samples for biomarker applications and performing nucleotide extractions as part of a portable molecular lab setup. We introduce the design and proof-of-principle trials that demonstrate the utility of low-cost 3D printed centrifuges for use in remote...
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strnr: A 3D-printed hand-powered centrifuge for molecular biology https://t.co/RcU0MrE4yo https://t.co/K4hovZZiH7
AaronPomerantz: Ever wanted to extract DNA on-the-go? How about a low-cost alternative to pelleting cells in a class? Maybe just itching to use your portable @nanopore sequencer but tired of lugging around extra bulky tools? Then you might enjoy our 3D-printed centrifuge! https://t.co/0pm0SUsnfs https://t.co/sMPmS32tRt
AaronPomerantz: 3D-printed centrifuges hot off the preprint! In collaboration with a fantastic group of researchers (including high school student Gaurav Byagathvalli, @BhamlaLab & teacher @jastandeven) we present a low-cost centrifuge for molecular biology applications https://t.co/0pm0SUsnfs
minouye271: Woah. Designing a 3D-printed hand-powered centrifuge to do @nanopore sequencing in the Amazon rainforest. https://t.co/zQzFmXYjhs https://t.co/ZyEBcN1PHU
BhamlaLab: Encouraging feedback for our latest pre-print. See paper here https://t.co/k70ETckLIA https://t.co/82GsSnYfO1
jamimmunology: Building on the wonderful paperfuge idea, here's a 3d printable upgrade! https://t.co/uFiG55NUI1 Thanks for pointing this out to me @MazlinaIsm !
Jeew333T: Based on the design principles of a paper-based centrifuge, this 3D-printed instrument increases the volume capacity to 2 mL and can reach hand-powered centrifugation speeds up to 6,000 rpm. https://t.co/1fLi8nlnSo https://t.co/MWhqZ4wDvC
aviseka: @BhamlaLab Making science for everyone!Again a awesome tool using 3D printing technology developed a hand powered centrifuge for molecular biology.I am sure It motivates not-only me but also to many to creat such tool by using basic principles of science https://t.co/8VkzTULnKA https://t.co/Jy9knZvwXc
Shohael1: Really people have great ideas. https://t.co/ZBxg1YLo0y
swathiha1: Amazing technology where this kind of centrifuge can be used in field for dna and rna extractions. https://t.co/vHxJWVa2E8
srghaffari: Hand powered centrifuge! https://t.co/FawyvinT57
PromPreprint: A 3D-printed hand-powered centrifuge for molecular biology https://t.co/14nWfpT8cG
Umasi1981: A 3D-printed hand-powered centrifuge for molecular biology https://t.co/gFBy3viWMX
OceanMelodyBlog: A 3D-printed hand-powered centrifuge for molecular biology https://t.co/Ntgqej4veB
puma_catherine: A 3D-printed hand-powered centrifuge for molecular biology https://t.co/9SRdEsCsOV
AaronPomerantz: RT @BhamlaLab: Encouraging feedback for our latest pre-print. See paper here https://t.co/k70ETckLIA https://t.co/82GsSnYfO1
BhamlaLab: RT @OceanMelodyBlog: A 3D-printed hand-powered centrifuge for molecular biology https://t.co/Ntgqej4veB
BhamlaLab: RT @jamimmunology: Building on the wonderful paperfuge idea, here's a 3d printable upgrade! https://t.co/uFiG55NUI1 Thanks for pointing th…
Jeew333T: RT @biorxivpreprint: A 3D-printed hand-powered centrifuge for molecular biology https://t.co/7cZPOXw1qU #bioRxiv
mehrshmali: RT @PromPreprint: A 3D-printed hand-powered centrifuge for molecular biology https://t.co/14nWfpT8cG
jastandeven: RT @jamimmunology: Building on the wonderful paperfuge idea, here's a 3d printable upgrade! https://t.co/uFiG55NUI1 Thanks for pointing th…
jastandeven: RT @BhamlaLab: Encouraging feedback for our latest pre-print. See paper here https://t.co/k70ETckLIA https://t.co/82GsSnYfO1
campanarostef: RT @biorxivpreprint: A 3D-printed hand-powered centrifuge for molecular biology https://t.co/7cZPOXw1qU #bioRxiv
SmallThingsLab: RT @biorxivpreprint: A 3D-printed hand-powered centrifuge for molecular biology https://t.co/7cZPOXw1qU #bioRxiv
DrStagiaire: RT @biorxivpreprint: A 3D-printed hand-powered centrifuge for molecular biology https://t.co/7cZPOXw1qU #bioRxiv
tito_tasks: RT @biorxivpreprint: A 3D-printed hand-powered centrifuge for molecular biology https://t.co/7cZPOXw1qU #bioRxiv
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Authors: 5
Total Words: 5498
Unqiue Words: 1881

0.0 Mikeys
#7. The effect of stride length on lower extremity joint kinetics at various gait speeds
Robert Levin McGrath, Melissa L. Ziegler, Margaret Pires-Fernandes, Brian A. Knarr, Jill S. Higginson, Fabrizio Sergi
Robot-assisted training is a promising tool under development for rehabilitation of walking function following neurological injury. The challenges in developing the controllers for gait rehabilitation devices that promote desired changes in gait is complicated by the limited understanding of the human response to robotic input. A possible method of controller formulation can be based on the principle of bio-inspiration, where a robot is controlled to apply the change in joint moment applied by human subjects when they achieve a gait feature of interest. However, it is currently unclear how lower extremity joint moments are modulated by even basic gait spatio-temporal parameters. In this study, we investigated how sagittal plane joint moments are affected by a factorial modulation of two important gait parameters: gait speed and stride length. We present the findings obtained from 20 healthy control subjects walking at various treadmill-imposed speeds and instructed to modulate stride length utilizing real-time visual feedback....
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biorxivpreprint: The effect of stride length on lower extremity joint kinetics at various gait speeds https://t.co/P2NNmxKVpS #bioRxiv
HuRoLab: Our recent work on gait analysis for robot-assisted training is now on bioRxiv: https://t.co/SFAdzJmC2P
KillianLab: RT @HuRoLab: Our recent work on gait analysis for robot-assisted training is now on bioRxiv: https://t.co/SFAdzJmC2P
beefstewKLIK: RT @HuRoLab: Our recent work on gait analysis for robot-assisted training is now on bioRxiv: https://t.co/SFAdzJmC2P
jf86phythe: RT @HuRoLab: Our recent work on gait analysis for robot-assisted training is now on bioRxiv: https://t.co/SFAdzJmC2P
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Authors: 6
Total Words: 11279
Unqiue Words: 2992

0.0 Mikeys
#8. Fatiguing Effects of Indirect Vibration Stimulation in Upper Limb Muscles- pre, post and during Isometric Contractions Superimposed on Upper Limb Vibration
Amit N Pujari, Richard D Neilson, Marco Cardinale
Background: Indirect vibration stimulation i.e. whole body vibration and upper limb vibration (ULV), are gaining popularity as exercise intervention for sports and rehabilitation applications. However, the fatiguing effects of indirect vibration stimulation are not yet fully understood. In addition, current vibration stimulation devices have a series of limitations. For this scope, we investigated the effects of ULV superimposed on fatiguing graded isometric contractions using a newly, purpose developed upper limb stimulation device. Twelve healthy volunteers were exposed to both ULV superimposed to fatiguing isometric contractions, at 80% of the maximum voluntary contractions (V) and just isometric contractions performed on a custom designed arm curl/flexion device- Control (C). The stimulation used consisted of 30Hz frequency of 0.4mm amplitude. Surface electromyographic (EMG) activity of the Biceps Brachii (BB), Triceps Brachii (TB), and Flexor Carpi Radialis (Forearm- FCR) were measured during both V and C conditions. EMG...
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Authors: 3
Total Words: 8066
Unqiue Words: 2167

0.0 Mikeys
#9. In vitro and in vivo phasor analysis of stoichiometry and pharmacokinetics using short lifetime near-infrared dyes and time-gated imaging
Sez-Jade Kathleen Chen, Nattawut Sinsuebphon, Alena Rudkouskaya, Margarida Barroso, Xavier Intes, Xavier Michalet
We introduce a simple new approach for time-resolved multiplexed analysis of complex systems using near-infrared (NIR) dyes, applicable to in vitro and in vivo studies. We show that fast and precise in vitro quantification of NIR fluorophores' short (sub-nanosecond) lifetime and stoichiometry can be done using phasor analysis, a computationally efficient and user-friendly representation of complex fluorescence intensity decays obtained with pulsed laser excitation and time-gated camera imaging. We apply this approach to the study of binding equilibria by Förster resonant energy transfer using two different model systems: primary/secondary antibody binding in vitro and ligand/receptor binding in cell cultures. We then extend it to dynamic imaging of the pharmacokinetics of transferrin engagement with the transferrin receptor in live mice, elucidating the kinetics of differential transferrin accumulation in specific organs, straightforwardly differentiating specific from non-specific binding. Our method, implemented in a...
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barrosolab: Phasor analysis for in vivo small animal lifetime imaging: In vitro and in vivo phasor analysis of stoichiometry and pharmacokinetics using short lifetime near-infrared dyes and time-gated imaging https://t.co/vz98FMVn3q
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Authors: 6
Total Words: 11250
Unqiue Words: 3152

0.0 Mikeys
#10. Cardiac myocyte microtissue aggregates broadcast local field potentials
Mijail Demian Serruya, Suradip Das, Kritika S Katiyar, Laura Struzyna, Justin C Burrell, D. Kacy Cullen
Muscle tissue has been exploited as a living biopotential amplifier to facilitate transduction of peripheral nerve signals into prosthetic control in patients with limb amputation. Here we sought to address the question of whether microscopically small volumes of muscle tissue could effectively broadcast field potentials to electrodes not immediately in contact with that tissue. Cardiac myocytes were grown as three-dimensional aggregates containing 105 cells comprising a volume of approximately 0.065 mm3 (~500 μm in diameter) atop multi-electrode arrays. In addition to the expected spontaneous contraction potentials detected using electrodes in direct contact with the myocytes, potentials could also be detected on distant electrodes not contacting the aggregates. Specifically, while both dissociated and aggregated cardiac myocyte cultures generated spontaneous contractions that could easily be recorded from underlying multi-electrode arrays, only aggregated myocyte cultures generated signals detectable several millimeters away by...
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Authors: 6
Total Words: 7659
Unqiue Words: 2991

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