gebhart/patrepeval huggingface dataset:
An on-chip imaging droplet-sorting system: a real-time shape recognition method to screen target cells in droplets with single cell resolution (2017)

A microfluidic on-chip imaging cell sorter has several advantages over conventional cell sorting methods, especially to identify cells with complex morphologies such as clusters. One of the remaining problems is how to efficiently discriminate targets at the species level without labelling. Hence, we developed a label-free microfluidic droplet-sorting system based on image recognition of cells in droplets. To test the applicability of this method, a mixture of two plankton species with different morphologies (Dunaliella tertiolecta and Phaeodactylum tricornutum) were successfully identified and discriminated at a rate of 10 Hz. We also examined the ability to detect the number of objects encapsulated in a droplet. Single cell droplets sorted into collection channels showed 91 ± 4.5% and 90 ± 3.8% accuracy for D. tertiolecta and P. tricornutum, respectively. Because we used image recognition to confirm single cell droplets, we achieved highly accurate single cell sorting. The results indicate that the integrated method of droplet imaging cell sorting can provide a complementary sorting approach capable of isolating single target cells from a mixture of cells with high accuracy without any staining.
Ureteral Replacement Using Collagen Sponge Tube Grafts (1985)

The use of a collagen sponge tube graft as a material for segmental ureteral replacement was investigated. The structural design of the collagen sponge graft was achieved by cell culture on the matrix. MGH-U1 cells, derived from bladder cell carcinoma, were grown in vitro on the collagen sponge matrix with excellent biocompatibility and without evidence of cytotoxicity. The collagen sponge demonstrated biodegradability when implanted subcutaneously in dogs. However, a urine exposure test of collagen sponge in rat bladders revealed extensive salt deposits on its surface in some rats, as observed by crystallographic examination. Segmental ureteral replacements by collagen sponge tube grafts, accompanied by ureteral splint catheters, were performed in dogs. There was extensive uro-epithelial cell regeneration on the inner surface of the collagen grafts, without evidence of severe hydronephrosis, 5 to 12 weeks following the procedure. The results indicate the potential for ureteral replacement by collagen sponge tube grafts, which would act as non-toxic, biodegradable scaffolds inducing the regenerative activity of the ureter.
A 9 $\mu$A, Addressable Gen2 Sensor Tag for Biosignal Acquisition (2010)

Biosensors present exciting opportunities in novel medical and scientific applications. However, sensor tags presented to date cannot interface with practical sensors, lack addressability, and/or require a custom (high-cost) interrogator. Our tag provides these features via ultra-low-power circuitry including a low-noise biosignal amplifier, unique tag ID generator, calibration-free 3 MHz oscillator, and EPC C1 Gen2 protocol compatibility. In addition to design details and measurement data from the fabricated IC, we present in vivo muscle temperature measurement from an untethered in-flight hawkmoth.
Envisioning the Bioconversion of Methane to Liquid Fuels (2014)

Advances in enzymatic pathways and bioreactor design could allow microorganisms to transform methane into chemicals and fuels.
A novelgndmutation leading to increased l-lysine production inCorynebacterium glutamicum (2004)

Toward more efficient L-lysine production, we have been challenging genome-based strain breeding by the approach of assembling only relevant mutations in a single wild-type background. Following the creation of a new L-lysine producer Corynebacterium glutamicum AHP-3 that carried three useful mutations (lysC311, hom59, and pyc458) on the relevant downstream pathways, we shifted our target to the pentose phosphate pathway. Comparative genomic analysis for the pathway between a classically derived L-lysine producer and its parental wild-type identified several mutations. Among these mutations, a Ser-361-->Phe mutation in the 6-phosphogluconate dehydrogenase gene (gnd) was defined as a useful mutation for L-lysine production. Introduction of the gnd mutation into strain AHP-3 by allelic replacement led to approximately 15% increased L-lysine production. Enzymatic analysis revealed that the mutant enzyme was less sensitive than the wild-type enzyme to allosteric inhibition by intracellular metabolites, such as fructose 1,6-bisphosphate, D-glyceraldehyde 3-phosphate, phosphoribosyl pyrophosphate, ATP, and NADPH, which were known to inhibit this enzyme. Isotope-based metabolic flux analysis demonstrated that the gnd mutation resulted in 8% increased carbon flux through the pentose phosphate pathway during L-lysine production. These results indicate that the gnd mutation is responsible for diminished allosteric regulation and contributes to redirection of more carbon to the pentose phosphate pathway that was identified as the primary source for NADPH essential for L-lysine biosynthesis, thereby leading to improved product formation.
Coaxial Electrospinning of Self‐Healing Coatings (2009)

Self-healing polymer coatings are formed by electrospinning bead-on-string healing agent filled capsules onto a substrate followed by infilling of a polymer matrix. Upon damage to the self-healing coating, liquid healing agents are released from the ruptured beads passivating the damaged region, preventing it from corroding as shown through microscopy, electrochemistry, and corrosion testing. Detailed facts of importance to specialist readers are published as ”Supporting Information”. Such documents are peer-reviewed, but not copy-edited or typeset. They are made available as submitted by the authors. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Microtubule-stabilising drugs for therapy of Alzheimer’s disease and other neurodegenerative disorders with axonal transport impairments (2005)

Increasing evidence implicates impairments of axonal transport in mechanisms underlying diverse neurodegenerative disease. This evidence includes discoveries of mutations in genes encoding human motor proteins or proteins involved in stabilising the microtubule (MT) network required for maintenance of axonal transport in familial neurodegenerative disorders, as well as data from in vivo and in vitro model systems. Moreover, in sporadic neurodegenerative disorders such as Alzheimer's disease (AD), pathological alterations of the MT-binding protein tau are linked to impaired axonal transport and brain degeneration. Because MT-stabilising compounds hold promise for counteracting the loss of tau function in AD and sustaining effective axonal transport, we conclude that MT-binding/stabilising drugs show potential therapeutic utility for the treatment of AD and other neurodegenerative disorders characterised by altered MTs and impaired axonal transport.
Affinity-Aware Modeling of CPU Usage for Provisioning Virtualized Applications (2011)

While virtualization-based systems become a reality, an important issue is that of virtual machine migration-enabled consolidation and dynamic resource provisioning. Mutually communicating virtual machines, as part of migration and consolidation strategies, may get colocated on the same physical machine or placed on different machines. In this work, we argue the need for network affinity-awareness not only in placement but also in resource provisioning for virtual machines. First, we empirically quantify the resource savings due to colocation of communicating virtual machines. We also discuss the increase in resource usage due to dispersion of previously colocated virtual machines. Next, we build models based on different resource-usage micro-benchmarks to predict the resource usages when transitioning from non-colocated placements to colocated placements and vice-versa. These resource usage prediction models are usable along-with consolidation and migration procedures to determine requirements of VMs in colocated and non colocated scenarios. Via extensive experimentation, we evaluate the applicability of our models for synthetic and benchmark application workloads. We find that the models have high prediction accuracy - 90th percentile prediction error within 3% absolute CPU usage for both synthetic and application workloads.
Heterogeneously Catalyzed Aerobic Cross‐Dehydrogenative Coupling of Terminal Alkynes and Monohydrosilanes by Gold Supported on OMS‐2 (2013)

Cross-dehydrogenative coupling of various terminal alkynes and monohydrosilanes efficiently proceeded in the presence of gold supported on OMS-2 (Au/OMS-2) using O2 as a terminal oxidant, affording the corresponding alkynylsilanes in moderate to high yields (see picture). The observed catalysis was truly heterogeneous, and the catalyst could be reused at least ten times without a significant loss of its high catalytic performance. As a service to our authors and readers, this journal provides supporting information supplied by the authors. Such materials are peer reviewed and may be re-organized for online delivery, but are not copy-edited or typeset. Technical support issues arising from supporting information (other than missing files) should be addressed to the authors. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
<title>Decoupled macro/micro-manipulator for fast and precise assembly operations: design and experiments</title> (1999)

This paper presents a high performance single arm robot configuration, based on a macro-manipulator coupled with a micro-manipulator. The system is well suited to fast and precise positioning tasks for repetitive pick and place applications in the manufacturing industry. Firstly, the paper focuses on the design of the micro-manipulator, particularly on the selection of the proper micro-actuator type and location. We show that the micro-manipulator's design with an actuator placed between endpoint and ground and with a flexible suspension system can reduce the dynamic coupling between the macro-manipulator and the micro- manipulator. The overall system performance can then be improved. We describe two different designs of compact and fast micro-manipulators composed of voice coil actuators and a monolithic flexure suspension with notch hinges. Secondly, the paper presents a control strategy that allows both correction of possible misalignments of the end-effector relative to the target and compensation of tip oscillations. The dynamic interaction is analyzed and stability is verified. Finally, experimental results demonstrate significant improvements in acceleration, endpoint accuracy and settling time achieved by the novel configuration of the macro/micro-manipulator.
Yaku’amides A and B, Cytotoxic Linear Peptides Rich in Dehydroamino Acids from the Marine Sponge Ceratopsion sp. (2010)

Two cytotoxic peptides, yaku'amides A (1) and B (2), were isolated from the marine sponge Ceratopsion sp. Their planar structures were elucidated on the basis of spectroscopic data, whereas the absolute configurations were determined by a combination of the Marfey's analysis and dansylation analysis of the total and partial acid hydrolysis products. The growth inhibitory profile of yaku'amide A against a panel of 39 human cancer cell lines was clearly unique and distinguished from other anticancer drugs.
The EDSN Intersatellite Communications Architecture (2014)

The Edison Demonstration of Smallsat Networks (EDSN) is a swarm of eight 1.5U Cubesats developed by the NASA Ames Research Center under the Small Spacecraft Technology Program (SSTP) within NASA Space Technology Mission Directorate (STMD). EDSN, scheduled for launch in late 2014, is designed to explore the use of small spacecraft networks to make synchronized, multipoint scientific measurements, and to organize and pass those data to the ground through their network. Networked swarms of these small spacecraft will open new horizons in astronomy, Earth observations and solar physics. Their range of applications include the formation of synthetic aperture radars for Earth sensing systems, large aperture observatories for next generation telescopes and the collection of spatially distributed measurements of time varying systems, probing the Earth’s magnetosphere, Earth-Sun interactions and the Earth’s geopotential. The EDSN communications network is maintained and operated by a simple set of predefined rules operating independently on all eight spacecraft without direction from ground based systems. One spacecraft serves as a central node, requesting and collecting data from the other seven spacecraft, organizing the data and passing it to a ground station at regular intervals. The central node is rotated among the spacecraft on a regular basis, providing robustness against the failure of a single spacecraft. This paper describes the communication architecture of the EDSN network and its operation with small spacecraft of limited electrical power, computing power and communication range. Furthermore, the problems of collecting and prioritizing data through a system that has data throughput bottlenecks are addressed. Finally, future network enhancements that can be built on top of the current EDSN hardware are discussed.
Cu(OTf)2-Mediated Fluorination of Aryltrifluoroborates with Potassium Fluoride (2013)

This Communication describes the Cu(OTf)2-mediated fluorination of aryltrifluoroborates with KF. The reaction proceeds under mild conditions (at 60 °C over 20 h) and shows a broad substrate scope and functional group tolerance. The Cu is proposed to play two separate roles in this transformation: (1) as a mediator for the aryl–F coupling and (2) as an oxidant for accessing a proposed Cu(III)(aryl)(F) intermediate.
Genetic engineering of cardiac muscle cells: in vitro and in vivo. (1994)

Over the last few years many of the difficulties encountered in applying molecular biology techniques to cardiac muscle have been addressed. Although continuous cardiac cell lines are still, as yet, unavailable, progress in embryonic stem cell systems and in our fundamental understanding of the critical steps that lead to cessation of cardiac myocyte cell division suggests that one may soon emerge. The cis-acting promoter elements and transacting factors responsible for cardiac specificity and inducible expression of cardiac genes are being characterized at a rapid pace. Transgenic models of cardiac disease are being generated and new insights are being made towards the goal of gene therapy in the heart. As the repertoire of techniques for transferring DNA into heart cells continues to expand, so the prospect for efficient and long-term expression of exogenous DNA in heart cells improves. The recent rapid rate of progress promises that ideas once fanciful may ultimately be within our reach.
Identification of the pH-dependent membrane anchor of carboxypeptidase E (EC 3.4.17.10). (1990)

Carboxypeptidase E (CPE), a peptide hormone-processing enzyme, is present within secretory granules in both a soluble form and a form which is membrane-bound at pH 5.5 but soluble at neutral pH. Antisera raised against a peptide corresponding to the predicted COOH-terminus of CPE bind to the membrane-associated form of CPE but not to the soluble form. This COOH-terminal region is predicted to form an amphiphilic alpha-helix, containing several pairs of hydrophobic residues separated by hydrophilic residues. Synthetic COOH-terminal peptides 11-24 residues in length are able to bind to bovine pituitary membranes and can be extracted by conditions that extract the membrane-bound form of CPE. The influence of pH on the membrane binding of a 21-residue COOH-terminal peptide is similar to the membrane binding of CPE: at pH values less than 6 the majority of the peptide is membrane-bound, while at pH values above 8 less than 20% is membrane-bound. Both the 21-residue COOH-terminal peptide and the purified membrane form of CPE, but not the soluble form, partition into Triton X-114 only at low pH (pH less than 6). Combined polar and hydrophobic interactions of the COOH-terminal peptide appear to be responsible for the reversible, pH-dependent association of CPE with membranes.
Isolation and characterization of murine retinal endothelial cells. (2003)

The retinal endothelial cells can be readily obtained from wild type and transgenic mice, which facilitate the comparison and identification of the physiologic role of specific genes in endothelial cell function.
Highly Multiplexed Genome Engineering Using CRISPR/Cas9 gRNA Arrays (2018)

ABSTRACT The CRISPR/Cas9 system is an RNA guided nuclease system that evolved as a mechanism of adaptive immunity in bacteria. This system has been adopted for numerous genome engineering applications in research and recently, therapeutics. The CRISPR/Cas9 system has been largely implemented by delivery of Cas9 as protein, RNA, or plasmid along with a chimeric crRNA-tracrRNA guide RNA (gRNA) under the expression of a pol III promoter, such as U6. Using this approach, multiplex genome engineering has been achieved by delivering several U6-gRNA plasmids targeting multiple loci. However, this approach is limiting due to the efficiently of delivering multiple plasmids to a single cell at one time. To augment the capability and accessibility of multiplexed genome engineering, we developed an efficient golden gate based method to assemble gRNAs linked by optimal Csy4 ribonuclease sequences to deliver up to 10 gRNAs as a single gRNA array transcript. Here we report the optimal expression of our guide RNA array under a strong pol II promoter. This system can be implemented alongside the myriad of CRISPR applications, allowing users to model complex biological processes requiring numerous gRNAs.
Closed subarachnoid drainage for management of cerebrospinal fluid leakage after an operation on the spine. (1989)

A retrospective review was conducted to assess the effectiveness and safety of a temporary subarachnoid shunt to treat patients who have a leak of cerebrospinal fluid after a spinal operation. The shunt is percutaneously inserted in the lumbar spine and is removed after four days. This technique was used in nineteen patients over a ten-year period. Of the seventeen patients who had the shunt in place for the full four days, fourteen had resolution of the drainage of cerebrospinal fluid from the wound. One of two patients whose shunt was removed early also had a successful result. Eleven of the fifteen patients who were successfully treated were available for follow-up, and none had any adverse effects related to the original cerebrospinal-fluid leak or its treatment. The four patients who had a persistent leak were successfully treated with reoperation and direct repair of the dura. Eleven (58 per cent) of the nineteen patients had transient complaints of nausea and vomiting while being treated with subarachnoid drainage. Two of the nineteen patients had evidence of an intradural infection after placement of the catheter; the infection resolved in both patients after removal of the catheter and treatment with appropriate antibiotics. Closed subarachnoid drainage, when properly performed and monitored, is a reasonably effective and safe method for treating dural-cutaneous cerebrospinal-fluid leaks after a spinal operation. It may be considered as a non-operative alternative to the standard procedure of reoperation and direct repair of the dura. A good result is still possible in patients in whom this technique fails and who eventually need surgical management.
Influence of Osmolarity and the Presence of an Osmoprotectant on Lactococcus lactis Growth and Bacteriocin Production (1999)

Growth inhibition of Lactococcus lactis provoked by increasing osmolarity is reversed when glycine betaine (GB) or its analogs are added to a defined medium. Lacticin 481 production increased sharply with growth medium osmolarity in the absence of osmoprotectant but remained unaffected when GB was supplied in media of increasing osmolarity.
Detection and Tracking of General Movable Objects in Large 3D Maps (2017)

This paper studies the problem of detection and tracking of general objects with long-term dynamics, observed by a mobile robot moving in a large environment. A key problem is that due to the environment scale, it can only observe a subset of the objects at any given time. Since some time passes between observations of objects in different places, the objects might be moved when the robot is not there. We propose a model for this movement in which the objects typically only move locally, but with some small probability they jump longer distances, through what we call global motion. For filtering, we decompose the posterior over local and global movements into two linked processes. The posterior over the global movements and measurement associations is sampled, while we track the local movement analytically using Kalman filters. This novel filter is evaluated on point cloud data gathered autonomously by a mobile robot over an extended period of time. We show that tracking jumping objects is feasible, and that the proposed probabilistic treatment outperforms previous methods when applied to real world data. The key to efficient probabilistic tracking in this scenario is focused sampling of the object posteriors.
Requirements for the inactivation of ribosomes by gelonin (1991)

Inactivation of Artemia salina and rabbit ribosomes by gelonin requires ATP and a high-Mr factor present in the rabbit reticulocyte-lysate post-ribosomal supernatant. The kinetic constants of the gelonin-catalysed release of adenine from A. salina ribosomes are Km = 4.35 microM and Kcat. = 0.1 min-1 in the absence of cofactors, and Km = 1.15 microM and Kcat. = 108 min-1 in their presence. The last two values are similar to those measured for ricin A chain in the absence of cofactors (Km = 2.02 microM and Kcat. = 317 min-1).
Cell cycle‐dependent cytotoxicity and mitotic spindle checkpoint dependency of investigational and approved antimitotic agents (2011)

The mitotic spindle checkpoint (SPC) is a highly regulated mechanism in eukaryotic cells that ensures the even distribution of the duplicated genome between daughter cells. Malfunction of the SPC or deregulated expression of SPC regulatory proteins is frequently associated with a poor response to chemotherapeutic agents. We investigated various approved and investigational mitosis-specific agents, including spindle poisons, an Eg5 kinesin inhibitor, inhibitors of polo-like kinase 1 (Plk1) or Aurora-B kinase, a benzamide class HDAC inhibitor and compounds identified in a chemical genetics screen for their cell cycle-dependent cytotoxicities and for their activities toward SPC deficient (HT29, Caco-2, T47D) and SPC proficient human cell lines (A2780, HCT116, SW480). Using the RKOp27 cell system that allows inducible cell cycle arrest by the tunable expression of the cdk inhibitor p27Kip1, we found an exquisite proliferation-dependent cytotoxicity for all compounds except the aurora kinase inhibitor VX-680. Cytotoxicity of the antimitotic compounds was in general higher on SPC proficient than on deficient cells. We found two exceptions, a benzamide HDAC inhibitor which was effective on SPC proficient and deficient cells and an investigational compound, BYK72767, with a yet unknown mode of action. The degree of increased mitotic index was no predictor of cytotoxicity of the compounds nor was the phosphorylation of BubR1. However, SPC deficient cell lines were able to tolerate mitotic arrest for far longer times than SPC proficient cells. We conclude that targeting of SPC deficient cancers with novel antimitotic principles remains a challenge but certain drug classes may be equally efficacious regardless of SPC status.