gebhart/patrepeval huggingface dataset:
Autonomous lab-on-a-chip generic architecture for disposables with integrated actuation (2019)

The integration of actuators within disposable lab-on-a-chip devices is a demanding goal that requires reliable mechanisms, systematic fabrication procedures and marginal costs compatible with single-use devices. In this work an affordable 3D printed prototype that offers a compact and modular configuration to integrate actuation in autonomous lab-on-a-chip devices is demonstrated. The proposed concept can handle multiple step preparation protocols, such as the enzyme-linked immunosorbent assay (ELISA) configuration, by integrating reagents, volume metering capabilities with performance comparable to pipettes (e.g. 2.68% error for 5 μL volume), arbitrary dilution ratio support, effective mixing and active control of the sample injection. The chosen architecture is a manifold served by multiple injectors ending in unidirectional valves, which exchange a null dead volume when idle, thus isolating reagents until they are used. Functionalization is modularly provided by a plug-in element, which together with the selection of reagents can easily repurpose the platform to diverse targets, and this work demonstrates the systematic fabrication of 6 injectors/device at a development cost of USD$ 0.55/device. The concept was tested with a commercial ELISA kit for tumor necrosis factor (TNF), a marker for infectious, inflammatory and autoimmune disorders, and its performance satisfactorily compared with the classical microplate implementation.
rPCR: a powerful tool for random amplification of whole RNA sequences. (1993)

T h e polymerase chain reaction (PCR), at first used to amplify known DNA sequences present at very low levels in genomic DNA samples, ~1-3) was rapidly extended to amplif icat ion of RNA sequences by the use of cDNA. ~4's) The PCR method, which requires mult iple heat-denaturation steps and was originally established with the Klenow fragment of Escherichia coli DNA polymerase I, now employs thermostable forms of DNA polymerase and two gene-specific primers (GSP) that flank the DNA segment to be amplified. Although PCR is the most widely utilized amplif icat ion protocol, known RNA sequences can be amplified alternatively with a RNA transcription-based amplif icat ion system (TAS), ~6'7) changing the final product from double-stranded DNA to singlestranded RNA. The TAS reaction needs two GSP, with the downstream GSP linked to a RNA polymerase (T7, T3, or SP6) b inding site, and is carried out by using sequential cDNA synthesis and RNA transcription, which are displayed as seven steps, including three heat-denaturation steps. Since the original description of the TAS protocol, the reaction conditions have been modif ied to achieve more productive and quantitative amplification. Thus, the self-sustained sequence replication (3SR) ~8,9) reaction was modeled after the general scheme employed during retroviral replication and does not require heat-denaturation; 108 copies of each target molecule can be produced in less than 1 hr with all three enzyme activities from avian myeloblastosis virus reverse transcriptase, Escherichia coli RNase H, and T7 RNA polymerase operating in an efficient and concerted manner . Other protocols such as rapid amplification of cDNA ends (RACE) ~°-12) use only one GSP and permit amplif icat ion of a region between a single known short sequence in a cDNA molecule and its unknown 3' or 5' end. Also described as one-sided PCR ~13) or anchored PCR, ~4) RACE 3'-end and 5'-end procedures are performed by using a homopolymer ic nucleotide containing an adapter primer that anneals to the cDNA's 3' or 5' termin i and one GSP. RACE using a randomly primed first-strand cDNA has also been reported recently, ~1s,16) with the 3' extension technique assuming the amplification of DNA fragments localized both in large 3' unsequenced regions and downstream to a 5' known sequence. Last, an elegant method that employs head-to-tail ligation of specifically primed, single-stranded, firststrand cDNAs with RNA ligase followed by PCR amplification ~17) was developed to yield 5' double-stranded cDNA copies in sufficient abundance for cloning; although there is actually no available data about the efficiency of this technique, it has the potential advantage of c ircumventing the usual problems associated with the homopolymeric tailing.
Applications of physical performance measures to routine diabetes care for frailty prevention concept: fundamental data with grip strength, gait speed, timed chair stand speed, standing balance, and knee extension strength (2020)

Reduced grip strength was associated with glycemic exposure indicators of age-related duration, HbA1c, and vascular complications. The physical performance measures became worse with decreasing grip strength. Measurements of grip strength and physical performance in patients with diabetes may help promote intervention to prevent frailty in future studies.
Investigation of Water Films Shed From an Airfoil in a High-Speed Flow (2022)

Abstract The breakup of liquid films in high-speed flows is found in many applications. These include prefilming air blast atomization found in fuel injectors and shedding of droplet off of airfoils. In this work, a test rig has been developed and applied to study the breakup of water films from the trailing edge of an NACA 0012 airfoil placed in a high-speed air flow. The results provided reflect a new detailed dataset focused on air velocities above 75 m/s. Computational fluid dynamic (CFD) simulations were used to guide the development of the rig and the associated boundary and inlet conditions. In this work, air velocities up to 175 m/s were used with water films between 0.4 cm2/s and 3.6 cm2/s. The water film was introduced onto one surface through a series of 0.5 mm holes separated by 1 mm at a location 35 mm downstream of the leading edge of the vane. High speed video was used to document the sheet breakup behavior from the edge of the airfoil. Image analysis was used to identify the breakup length of ligaments formed. Laser diffraction was used 50 mm downstream of the trailing edge of the vane to determine the droplet size distribution and associated representative average diameters generated. A series of test conditions were run between 50 m/s and 175 m/s using multilevel factorial designed experiments. The results obtained were subjected to analysis of variance to generate correlations for breakup length and droplet representative diameters as a function of the conditions studied. The analysis was conducted on dimensionless versions of the variables studied to help connect the results to the physics of the situation. For example, rather than using air velocity to correlate the behavior, the Weber number (based on gas phase density and velocity) was used owing to its historical ability to describe liquid breakup processes. The results obtained are compared with other studies in the literature, and good agreement was found for the conditions at which a comparison could be made. It is observed that, for the conditions studied, liquid film thickness has little effect on the resulting droplet sizes—especially for the higher air velocity cases studied. The results also illustrate the sensitivity to choice of the characteristic length, which is generally consisted of trailing edge geometry or boundary layer thickness. In contrast, liquid film does influence the ligament breakup length, although the time to break up is less affected. Overall, the correlations developed provide engineering tools to help estimate ligament and drop size behavior for water films shed from airfoils in a high-speed flow.
Softlithographic partial integration of surface‐active nanoparticles in a PDMS matrix for microfluidic biodevices (2010)

Abstract The mergence of microfluidics and nanocomposite materials and their in situ structuring leads to a higher integration level within microsystems technology. Nanoparticles (Cu and Ag) produced via laser radiation were suspended in Poly(dimethylsiloxane) to permanently modify surface material. A microstructuring process was implemented which allows the incorporation of these nanomaterials globally or partially at defined locations within a microbioreactor (MBR) for the determination of their antiseptic and toxic effects on the growth of biomass. magnified image Partially structured PDMS with nanoparticle–PDMS composite.
Kinetic mechanisms of glycine oxidase from Bacillus subtilis (2003)

The kinetic properties of glycine oxidase from Bacillus subtilis were investigated using glycine, sarcosine, and d-proline as substrate. The turnover numbers at saturating substrate and oxygen concentrations were 4.0 s(-1), 4.2 s(-1), and 3.5 s(-1), respectively, with glycine, sarcosine, and D-proline as substrate. Glycine oxidase was converted to a two-electron reduced form upon anaerobic reduction with the individual substrates and its reductive half-reaction was demonstrated to be reversible. The rates of flavin reduction extrapolated to saturating substrate concentration, and under anaerobic conditions, were 166 s(-1), 170 s(-1), and 26 s(-1), respectively, with glycine, sarcosine, and D-proline as substrate. The rate of reoxidation of reduced glycine oxidase with oxygen in the absence of product (extrapolated rate approximately 3 x 10(4) M(-1) x s(-1)) was too slow to account for catalysis and thus reoxidation started from the reduced enzyme:imino acid complex. The kinetic data are compatible with a ternary complex sequential mechanism in which the rate of product dissociation from the reoxidized enzyme form represents the rate-limiting step. Although glycine oxidase and D-amino acid oxidase differ in substrate specificity and amino acid sequence, the kinetic mechanism of glycine oxidase is similar to that determined for mammalian D-amino acid oxidase on neutral D-amino acids, further supporting a close similarity between these two amine oxidases.
ChemInform Abstract: Palladium‐Catalyzed Ring‐Opening of Cyclopropyl Benzamides: Synthesis of Benzo[c]azepine‐1‐ones via C(sp3)—H Functionalization. (2013)

Abstract A new synthesis of biologically relevant benzo[c]azepins is achieved via a novel Pd/Ag‐catalyzed intramolecular cyclization of ortho halogenated N‐cyclopropyl benzamides.
Sensitivity of Providence to antiseptics and disinfectants. (1976)

Seventy isolates of Providence were obtained from urinary tract infections in patients from five hospitals. They were all identified as Providence B (Providencia stuartii). A typing system was devised for these organisms based on their production of and sensitivity to bacteriophage and bacteriocins. Using this system, 27 distinct strains were recognized, and it was clear that many patients had been infected with the same strain. The minimum inhibitory concentrations of six antiseptics and disinfectants for these strains were determined. Many of the strains were up to 300-fold more resistant to the cationic antiseptics chlorhexidine, cetrimide, and Resiguard than the control strain Escherichia coli NCTC 10418. The sensitivities of the Providence strains to Hycolin, glutaraldehyde, and phenyl mercuric nitrate, however, were similar to those of the control organism. There were significant correlations between the sensitivities of the strains to the three cationic antiseptics. The loss of chlorhexidine resistance from a Providence strain after exposure of the cells to N-methyl-N' nitro N nitrosoguanidine resulted in a concomitant loss of resistance to cetrimide and Resiguard, but there was no significant increase in the sensitivity of the mutants to the other three antibacterials.
Compressing ECG signals by piecewise polynomial approximation (2002)

Compression of digital electrocardiogram (ECG) signals has traditionally been tackled by heuristical approaches. It has been demonstrated that exact optimization algorithms outclass these heuristical approaches by a wide margin with respect to the reconstruction error. As opposed to traditional time-domain algorithms, where some heuristic is used to extract representative signal samples from the original signal, the exact optimization algorithm proposed by Haugland, Heber and Husoy (see Medical & Biological Engineering & Computing, vol.35, p.420-24, 1997) formulates the sample selection problem as a graph theory problem. Thus well known optimization theory can be applied in order to yield optimal compression. Haughland et al. applied linear interpolation in the reconstruction of the signal. This paper generalizes the optimization algorithm such that reconstruction can be made by second order polynomial interpolation in the extracted signal samples. The polynomials are fitted in a way that guarantees minimal reconstruction error, and the method proves the good performance compared to the case where linear interpolation is used in the reconstruction of the signal.
Carbon Nano-Onions as Non-Cytotoxic Carriers for Cellular Uptake of Glycopeptides and Proteins (2019)

Carbon nano-onions (CNOs) possess favorable properties that make them suitable for biomedical applications, including their small size, ready surface modification, and good biocompatibility. Here, we report the covalent immobilization of a synthetic glycopeptide and the protein bovine serum albumin (BSA) onto the surface of carbon nano-onions using the maleimide-thiol "addition reaction". The glycopeptide and BSA are readily transported inside different cell lines, together with carbon nano-onions, through the endocytosis pathway. Our results show that carbon nano-onions are excellent scaffolds for glycopeptides and proteins immobilization and act as intracellular carriers for these biomolecules. These findings open new perspectives in the application of carbon nano-onions as intracellular transporters in diverse biomedical applications.
Evolving the Materials Genome: How Machine Learning Is Fueling the Next Generation of Materials Discovery (2020)

Machine learning, applied to chemical and materials data, is transforming the field of materials discovery and design, yet significant work is still required to fully take advantage of machine learning algorithms, tools, and methods. Here, we review the accomplishments to date of the community and assess the maturity of state-of-the-art, data-intensive research activities that combine perspectives from materials science and chemistry. We focus on three major themes—learning to see, learning to estimate, and learning to search materials—to show how advanced computational learning technologies are rapidly and successfully used to solve materials and chemistry problems. Additionally, we discuss a clear path toward a future where data-driven approaches to materials discovery and design are standard practice.
A Pulse Radiolysis Study of Catalytic Superoxide Radical Dismutation by a Manganese(II) Complex with an N‐Tripodal Ligand (Eur. J. Inorg. Chem. 14/2005) (2005)

Abstract The cover picture shows an allegory of bioinorganic chemistry and biomimetic studies. Here, the metalloprotein (human Mn‐SOD, PDB‐code 1MSD) is posing for the painter. As a bioinorganic chemist, he is designing new molecules that would reproduce this protein activity; he is testing the activity of these molecules and deciphering mechanisms. Here, we show the structure of a small Mn II complex that has been studied for its SOD‐like activity by pulsed radiolysis. In the painting, the UV/Vis trace of a multipulse experiment at 300 nm is shown, with successive spikes and plateaus. An overall increase in the absorbance of the successive plateaus is observed. The asterisks indicate irradiations. Simulations of the individual growth of the spikes, of the individual decrease down to the plateau and of the overall increase of the absorbance for the successive plateaus leads to the proposition of a mechanism. This is the triangular cycle shown in the painting, involving an {MnOO} 6 adduct between Mn II and superoxide. This label, {MnOO} 6 , is proposed by analogy with the nomenclature used for iron−nitroxide adducts. Each event indicated in the cycle has been proven. Moreover, this study shows unambiguously that the Mn II compound displays a catalytic activity for superoxide dismutation. Details are presented in the article by J.‐P. Renault, C. Policar et al. on p. 2789 ff. In the original picture by Magritte, the inset in the lower right‐hand corner, is entitled “La clairvoyance” (clear‐sightedness) and was painted in 1936.
Proceedings of the 2015 Design, Automation & Test in Europe Conference & Exhibition (2015)

We proudly present to you the Proceedings of DATE 2015. DATE combines the world's favorite electronic systems design and test conference with an international exhibition for electronic design, automation and test, ranging from advances on system-level hardware and software implementation to integrated circuit design and nano-technology manufacturing technologies.
Switchable release and recovery of nanoparticles via a Pickering-emulsion-templated porous carrier (2013)

A Pickering-emulsion-templated macroporous polymer was utilized as a novel release carrier for switchable controlled release and recovery of nanoparticles. With silica nanoparticles as stabilizers, oil-in-water Pickering high internal phase emulsions were prepared as templates to synthesize porous poly(N-isopropylacrylamide) materials with silica nanoparticles inlaid in the polymer void walls. The porous materials can effectively avoid the diffusion of silica nanoparticles when the release is undesirable, and can resorb the released nanoparticles back from the aqueous solution simply by controlling the temperature. Because a wide range of functional nanoparticles can be used to stabilize Pickering emulsions, the method developed herein provides an alternative to prepare carriers for controlled release and recovery of functional nanoparticles.
Endogenously produced catecholamines improve the regulatory function of TLR9-activated B cells (2021)

The sympathetic nervous system (SNS) contributes to immune balance by promoting anti-inflammatory B cells. However, whether B cells possess a self-regulating mechanism by which they modulate regulatory B cell (Breg) function is not well understood. In this study, we investigated the ability of B cells to synthesize their own catecholamines upon stimulation with different B cell activators and found that expression of the enzyme tyrosine hydroxylase (TH), required to generate catecholamines, is upregulated by TLR9. This TLR9-dependent expression of TH correlated with upregulation of adrenergic receptors, enhanced IL-10 production, and overexpression of the co-inhibitory ligands PD-L1 and FasL. Moreover, concomitant stimulation of ß1-3-adrenergic receptors together with a BCR/TLR9 stimulus clearly enhances the anti-inflammatory potential of Bregs to suppress CD4 T cells, a crucial population in the pathogenesis of autoimmune diseases, like rheumatoid arthritis. Furthermore, TH upregulation was also demonstrated in B cells during the course of collagen-induced arthritis (CIA), a mouse model for the investigation of rheumatoid arthritis. In conclusion, our data show that B cells possess an autonomous mechanism to modulate their regulatory function in an autocrine and/or paracrine manner. These findings help to better understand the function of B cells in the regulation of autoimmune diseases and the interplay of sympathetic nervous system (SNS).
Model Predictive Control: Extension to Coordinated Multi-Vehicle Formations and Real-Time Implementation (2001)

In model predictive control (MPC), the current control action is determined by solving on-line, at each sampling instant, a finite horizon open-loop optimal control problem. Each optimization yields an optimal control sequence and the first control in the sequence is applied to the plant until the next sampling instant. As MPC does not mandate that the control law be pre-computed, it is particularly useful when o#-line computation of such a law is di#cult or impossible. MPC is not a new approach, and has traditionally been applied to plants where the dynamics are slow enough to permit a sampling rate amenable to optimal input computations between samples, e.g. chemical process plants. These systems are usually also governed by strict constraints on states, inputs and/or combinations of both. With the advent of faster modern computers, it has become possible to extend the MPC approach to systems governed by faster dynamics that warrant this type of solution. In the multi-vehicle realm a general objective it to achieve a formation and perform joint maneuvers in formation. In general, the vehicles are individually governed by nonlinear and constrained dynamics. Interest in the multivehicle coordinated control problem has increased in recent years where joint autonomous tasks are of interest, e.g. micro-satellite formations for communications and imaging and unmanned air vehicle (UAV) cooperation in adversarial environments for defense purposes. The objective of this study is to develop a theoretical framework for the application of MPC techniques to the multi-vehicle coordinated control problem. Once the MPC objective is defined in terms of this type of problem, a stability analysis is detailed. Example problems are simulated to study the stability, performance and robus...
Ultrahigh-speed microchannel photomultiplier (1970)

Use of a microchannel-water electron multiplier makes possible a new, compact photomultiplier with time-resolution capabilities better than can be obtained from classical photomultipliers using cascaded dynode structures. The small thickness of the wafer, together with proximity focusing in the electron optics of the input and output of the wafer, results in reduction of the electron transit-time to about 1 ns. The electron transit-time spread is about 10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">-10</sup> seconds. Short pulses from a mode-locked laser were used to measure the impulse response of the photomultiplier. The experimental value of <500 ps (full width at half maximum) is in good agreement with the predictions of a computer analysis. Other salient characteristics of the new tube are: S 20 photocathode diameter of 11 mm; electron gain of about 10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">5</sup> ; dark current <10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">-16</sup> amperes (referred to the cathode); and 50-ohm output impedance.
Presence-Only Geographical Priors for Fine-Grained Image Classification (2019)

Appearance information alone is often not sufficient to accurately differentiate between fine-grained visual categories. Human experts make use of additional cues such as where, and when, a given image was taken in order to inform their final decision. This contextual information is readily available in many online image collections but has been underutilized by existing image classifiers that focus solely on making predictions based on the image contents. We propose an efficient spatio-temporal prior, that when conditioned on a geographical location and time, estimates the probability that a given object category occurs at that location. Our prior is trained from presence-only observation data and jointly models object categories, their spatio-temporal distributions, and photographer biases. Experiments performed on multiple challenging image classification datasets show that combining our prior with the predictions from image classifiers results in a large improvement in final classification performance.