gebhart/patrepeval huggingface dataset:
Omnipose: a high-precision morphology-independent solution for bacterial cell segmentation (2022)

Advances in microscopy hold great promise for allowing quantitative and precise measurement of morphological and molecular phenomena at the single-cell level in bacteria; however, the potential of this approach is ultimately limited by the availability of methods to faithfully segment cells independent of their morphological or optical characteristics. Here, we present Omnipose, a deep neural network image-segmentation algorithm. Unique network outputs such as the gradient of the distance field allow Omnipose to accurately segment cells on which current algorithms, including its predecessor, Cellpose, produce errors. We show that Omnipose achieves unprecedented segmentation performance on mixed bacterial cultures, antibiotic-treated cells and cells of elongated or branched morphology. Furthermore, the benefits of Omnipose extend to non-bacterial subjects, varied imaging modalities and three-dimensional objects. Finally, we demonstrate the utility of Omnipose in the characterization of extreme morphological phenotypes that arise during interbacterial antagonism. Our results distinguish Omnipose as a powerful tool for characterizing diverse and arbitrarily shaped cell types from imaging data.
The Case of the Strangerationist (2016)

We describe a method for critically informed development of new technical systems by combining analysis of historical discourse with critical technical practice. We take the case of social recommender systems, a class of algorithms that calculate which people should be recommended to whom. We demonstrate similarities between limitations of "social network" rhetoric in contemporary social matching algorithms and discourse on planning in Artificial Intelligence. We develop an algorithm for social matching that recombines "lost" ideas from the history of AI, orienting around situated behavior and algorithmic transparency. By implementing this approach in a functioning prototype called "the Strangerationist", we examine directly how conceptual commitments inform low-level technical decisions, and how available technologies shape conceptual vision. Our goal is not to design a "better" algorithm but to explore the challenges and opportunities of weaving together historical discourse and critical analysis of values embedded in technology with the experience of designing it.
Joint Investment and Operation Optimization of a Distribution System in a Market Environment (2019)

A generation expansion planning strategy for distribution systems is proposed in this paper to derive the optimal generation mix considering decentralized storage units, variable generation units, dispatchable generation units and demand response. To better exploit the economic value of these investments, participation in reserve and energy markets is considered. As the investment and market bidding decisions are made sequentially, a multi-stage stochastic programming model is formulated to minimize the sum of long-term investment costs and short-term costs, which include fixed operation costs, variable operation and maintenance costs, emission costs, discomfort costs minus the market participation revenue. A case study based on modified Swiss data demonstrates the effectiveness of the proposed model, analyzes the impact of demand response and forecast errors and shows the importance of market participation.
State and Role of Hydrogen in Amorphous Oxide Semiconductors (2022)

Hydrogen is an unavoidable impurity species in oxide semiconductor thin films. The concentration of H-impurity in conventional sputtering-deposited AOS (amorphous oxide semiconductor) thin films goes up to 10 20 –10 21 cm −3 . These hydrogen species are incorporated during vacuum deposition processes through reactions with residual gas species, H 2 O and H 2 , in the vacuum chamber. This chapter describes the current understanding of hydrogen-related impurities and defects in AOS materials, focusing on their chemical states, energy levels, and influence on carrier generation and annihilation.
Reaction of Octachlorodirhenate with a Redox-Active Tetrathiafulvalene Phosphine Ligand:  Spectroscopic, Magnetic, and Structural Characterization of the Unusual Paramagnetic Salt [ReCl2(o-P2)2][Re2Cl6(o-P2)] (o-P2 =o-{P(C6H5)2}2(CH3)2TTF) (1998)

Reaction of [(n-Bu)(4)N](2)[Re(2)Cl(8)] with the tetrathiafulvalene phosphine ligand o-{P(C(6)H(5))(2)}(2)(CH(3))(2)TTF (o-P2) in refluxing ethanol produces the mixed-nuclearity salt [ReCl(2)(o-P2)(2)][Re(2)Cl(6)(o-P2)] (1.2), composed of the mononuclear Re(III) complex (1) and the mixed-valence Re(II)-Re(III) dinuclear anion (2). The complex crystallizes as a CH(2)Cl(2) solvate in the triclinic space group P&onemacr;, a = 13.4559(1) Å, b = 20.4015(3) Å, c = 21.5538(1) Å, alpha = 88.261(1) degrees, beta = 72.987(1) degrees, gamma = 84.933(1) degrees, and Z = 2. The molecular cation consists of two trans o-P2 ligands in the equatorial plane and axial chloride ligands. The dinuclear anion adopts an eclipsed geometry with an unsymmetrical coordination environment for the two metal atoms; one Re(II) center is coordinated to a chelating o-P2 ligand and two chlorides while the other Re atom is coordinated to four chloride ligands. The dinuclear portion of the salt is a monoanion which leads to a formal bond order assignment of 3.5, based on the fact that the molecule possesses an Re(2)(5+) core. The salt was further characterized by infrared and electronic spectroscopies, electrochemistry, and variable temperature magnetic susceptibility; the presence of the individual ions in bulk samples was verified by positive and negative FAB mass spectrometry. Isolation of the two separate ions was achieved by treatment of the salt with Co(C(5)H(5))(2), which reduces the Re(III) cation to the Re(II) complex ReCl(2)(o-P2)(2) (3). This neutral compound was separated from the byproduct salt [Co(C(5)H(5))(2)][Re(2)Cl(6)(o-P2)] and reoxidized with CCl(4)/CH(2)Cl(2) or NOBF(4) to produce [ReCl(2)(o-P2)(2)][Cl] (1.[Cl]) and [ReCl(2)(o-P2)(2)][BF(4)] (1.[BF(4)]), respectively. Compounds 3, 1.[Cl], and 1.[BF(4)] were identified by a combination of infrared spectroscopy, mass spectrometry, and cyclic voltammetric measurements. Variable temperature dc susceptibility studies of [ReCl(2)(o-P2)(2)][Re(2)Cl(6)(o-P2)] (1.2) revealed classical Curie paramagnetic behavior (with a Curie constant equal to 0.395) and a large temperature independent paramagnetic contribution (chi(TIP) = 9.64 x 10(-)(3) emu/mol). The EPR spectrum of 1.2 consists of a broad, complex signal due to hyperfine interactions to both isotopes (185,187)Re (I = (5)/(2)) and (31)P (I = (1)/(2)) which is typical for paramagnetic metal-metal bonded dirhenium phosphine compounds.
A Reconfigurable On-die Traffic Generator in 45nm CMOS for a 48 iA-32 Core Network-on-Chip (2012)

A reconfigurable on-die Traffic Generator (TG) is proposed to test the packet switched 2D-mesh network of a 48 iA-32 core Single-chip Cloud Computer. The Single-chip Cloud Computer (SCC) is an experimental processor created by Intel Labs. The 24-tile Network-on-Chip (NoC) consists of a Traffic Generator per tile which can be programmed to generate deterministic and random traffic patterns. It also consists of reconfigurable activity control, (non)-cacheable reads and writes, message class and route control bits to feed synthetic traffic to the network to investigate NoC functional, protocol issues and to measure the key power-performance metrics. In this paper, we present the architecture and design details of the Traffic Generator, operating modes, re-configurability and the testing procedures. This semi-custom design has a transistor count of 54K, which is 0.1% of tile transistor count, and occupies 0.3mm2 area which is 0.9% of tile area. The estimated power consumption is only 23mW at 1.1V and at 500C, 0.02% of the total chip power in 45nm high-K nine metal CMOS process.
Investigation of 20S-hydroxyvitamin D3 analogs and their 1α-OH derivatives as potent vitamin D receptor agonists with anti-inflammatory activities (2018)

20S-hydroxyvitamin D<sub>3</sub> [20S(OH)D<sub>3</sub>] is anti-inflammatory and not hypercalcemic, suggesting its potential as a lead compound. In this study, side chain modified 20S(OH)D<sub>3</sub> analogs (4, 13, 23 and 33) together with their 1α-OH derivatives were synthesized and their metabolism and biological activities tested. 4, 13 and 23 are good substrates for CYP27B1, enabling enzymatic synthesis of their 1α-OH derivatives 5, 14 and 24. However, 33 could not be hydroxylated by CYP27B1 and acts as an inhibitor. All analogs were poorer substrates for CYP24A1 than calcitriol, indicating improved catabolic stability. While the parent analogs showed minimal VDR stimulating activity, their 1α-OH derivatives were potent VDR agonists. 4, 5, 14 and 24 significantly upregulated the expression of CYP24A1 at the mRNA level, consistent with their VDR activation abilities and indicating that 1α-hydroxylation is required to produce analogs with strong activity. These analogs have anti-inflammatory activities that are influenced by side chain composition and by 1α-hydroxylation. To understand their molecular interactions with the VDR, 20S(OH)D<sub>3</sub>, 4 and 33 were co-crystalized with the VDR ligand binding domain, which revealed subtle differences to the calcitriol-bound receptor. This study demonstrates the potential of the 20S(OH)D<sub>3</sub> scaffold for the development of novel anti-inflammatory agents.
43.63-Gbit/s Multiple-User SC-FDMA PON With Sub-Nyquist Receiver and PAPR Reduction (2018)

In this letter, we propose a novel delay-division-multiplexing (DDM) scheme to enable SC-FDMA PON with a sub-Nyquist sampling rate ADC and lower PAPR, named time-interleaved FDMA (TI-FDMA). The proposed pre-processing method reduces the sampling rate of the ADC to 1/2 ~ 1/32 of the Nyquist sampling rate. The FFT size can be reduced to 1/32 (i.e., from 1024 to 32) due to lower sampling ratio and each user just needs to recover and demodulate their corresponding data without any additional DSP, which greatly reduces the complexity of the receiver. Meanwhile, the proposed TI-FDMA has lower PAPR than traditional localized FDMA (L-FDMA), interleaved FDMA (I-FDMA), and OFDM. Such the PAPR reduction makes TI-FDMA support the modulation format of 1 order higher compared to OFDM, thereby, leading to 12.5% capacity improvement. Employing the proposed scheme, up to 43.63-Gbps PON is experimentally demonstrated, and each of 32 users requires only 0.5-GSample/s ADC.
Battery health prognostic with sensor-free differential temperature voltammetry reconstruction and capacity estimation based on multi-domain adaptation (2023)

Battery health prognostic is a key part of battery management used to ensure safe and optimal usage. A novel method for end-to-end sensor-free differential temperature voltammetry reconstruction and state of health estimation based on the multi-domain adaptation is proposed in this paper. Firstly, the partial charging or discharging curve is used to reconstruct the differential temperature curve, removing the requirement for the temperature sensor measurement. The partial differential capacity curve and the reconstructed differential temperature curve are input and then used in an end-to-end state of health estimation. Finally, to reduce the domain discrepancy between the source and target domains, the maximum mean discrepancy is included as an additional loss to improve the accuracy of both differential temperature curve reconstruction and state of health estimation with unlabeled data from the testing battery. Four data sets containing both experimental data and public data with different battery chemistry and formats, current modes and rates, and external conditions are used for the verification and evaluation. Experimental results indicate the proposed method can satisfy health prognostics under different scenarios with mean errors of less than 0.067 °C/V for differential temperature curves and 1.78% for the state of health. The results show that the error for the differential temperature curve reconstruction is reduced by more than 20% and the error for the state of health estimation is reduced by more than 47% of the proposed method compared to the conventional data-driven method without transfer learning.
Antibacterial Activity of Pepducins, Allosterical Modulators of Formyl Peptide Receptor Signaling (2014)

Pepducins containing a fatty acid linked to an amino acid sequence derived from cytosolic parts of a G-protein-coupled receptor (GPCR) constitute a new group of lipopeptide tools in GPCR studies. Pepducins corresponding to the third intracellular loop of formyl peptide receptor 2 (FPR2) activate human neutrophils, and we show here that, in addition, these allosteric modulators of receptor activity also kill bacteria. The functional dualism of FPR2 pepducins could potentially be explored as a novel class of antibacterial drugs with immunomodulatory properties.
Standardized Solutions for Quantitative and Real‐Time RT‐PCR to Accelerate Biopharmaceutical Development (2013)

The drug development process relies since many years on genomic technologies supporting patient stratification, assessing safety of potential drug candidates in toxicology or investigating mechanistic aspects of a disease to name only few examples. Real-time polymerase chain reaction (PCR) has become a key technology in pharmaco-genomics being routinely employed for quantitative gene expression analysis, analysis of single nucleotide polymorphisms, and pathogen detection significantly reducing costs and increasing productivity in drug discovery and biomarker programs. However, the impact of real-time PCR is largely dependent on preanalytical methods as well as methods chosen for data analysis. This chapter provides a comprehensive overview on critical steps for the successful use of real-time PCR and introduces the concept of multiplex real-time PCR to increase throughput and accuracy of real-time PCR analysis.
Anisotropic Hydrolysis Susceptibility in Deformed Polydimethylsiloxanes (2019)

Chemical reactions involving the polydimethylsiloxane (PDMS) backbone can induce significant network rearrangements and ultimately degrade macro-scale mechanical properties of silicone components. Using two levels of quantum chemical theory, we identify a possible electronic driver for chemical susceptibility in strained PDMS chains and explore the complicated interplay between hydrolytic chain scissioning reactions, mechanical deformations of the backbone, water attack vector, and chain mobility. Density functional theory (DFT) calculations reveal that susceptibility to hydrolysis varies significantly with the vector for water attacks on silicon backbone atoms, which matches strain-induced anisotropic changes in the backbone electronic structure. Efficient semiempirical density functional tight binding (DFTB) calculations are shown to reproduce DFT predictions for select reaction pathways and facilitate more exhaustive explorations of configuration space. We show that concerted strains of the backbone must occur over at least a few monomer units to significantly increase hydrolysis susceptibility. In addition, we observe that sustaining tension across multiple monomer lengths by constraining molecular degrees of freedom further enhances hydrolysis susceptibility, leading to barrierless scission reactions for less substantial backbone deformations than otherwise. We then compute chain scission probabilities as functions of the backbone degrees of freedom, revealing complicated configurational interdependencies that impact the likelihood for hydrolytic degradation. The trends identified in our study suggest simple physical descriptions for the synergistic coupling between local mechanical deformation and environmental moisture in hydrolytic degradation of silicones.
Stable Two-Mode Emission from Semiconductor Quantum Dot Laser (2013)

A two-wavelength emission laser (two-mode laser) has been fabricated using semiconductor quantum dots as the gain medium in the external cavity configuration. Two-mode laser emission with a separation of 98.8 GHz has been achieved by controlling the etalon and narrow-band filter setting. A 98.4 GHz beat signal was observed using the Michelson interferometer configuration, indicating that these emissions occurred simultaneously.
Initial steps toward the realization of large area arrays of single photon counting pixels based on polycrystalline silicon TFTs (2014)

The thin-film semiconductor processing methods that enabled creation of inexpensive liquid crystal displays based on amorphous silicon transistors for cell phones and televisions, as well as desktop, laptop and mobile computers, also facilitated the development of devices that have become ubiquitous in medical x-ray imaging environments. These devices, called active matrix flat-panel imagers (AMFPIs), measure the integrated signal generated by incident X rays and offer detection areas as large as ~43&times;43 cm<sup>2</sup>. In recent years, there has been growing interest in medical x-ray imagers that record information from X ray photons on an individual basis. However, such photon counting devices have generally been based on crystalline silicon, a material not inherently suited to the cost-effective manufacture of monolithic devices of a size comparable to that of AMFPIs. Motivated by these considerations, we have developed an initial set of small area prototype arrays using thin-film processing methods and polycrystalline silicon transistors. These prototypes were developed in the spirit of exploring the possibility of creating large area arrays offering single photon counting capabilities and, to our knowledge, are the first photon counting arrays fabricated using thin film techniques. In this paper, the architecture of the prototype pixels is presented and considerations that influenced the design of the pixel circuits, including amplifier noise, TFT performance variations, and minimum feature size, are discussed.
Mechanical Search on Shelves using a Novel “Bluction” Tool (2022)

Shelves are common in homes, warehouses, and commercial settings due to their storage efficiency. However, this efficiency comes at the cost of reduced visibility and accessibility. When looking from a side (lateral) view of a shelf, most objects will be fully occluded, resulting in a constrained lateral-access mechanical search problem. To address this problem, we introduce: (1) a novel bluction tool, which combines a thin pushing blade and a suction cup gripper, (2) a simulation pipeline and perception model that combine ray-casting with 2D Minkowski sums to efficiently generate target occupancy distributions, and (3) a novel search policy, which optimally reduces target object distribution support area using the bluction tool. Experimental data from 2000 simulated shelf trials and 18 trials with a physical Fetch robot suggest that a bluction tool can improve the average success rate by 26% in simulation and 67% in physical experiments over the highest-performing push-only policy.
Surrogate fuels for premixed combustion in compression ignition engines (2011)

Simple surrogate fuels are needed to model practical fuels, which are complex mixtures of hydrocarbons. The surrogate fuel should match the combustion and emissions behaviour of the target fuel as much as possible. This paper presents experimental results using a wide range of fuels in both the gasoline and diesel auto-ignition range, but of different volatilities and compositions, in a single cylinder diesel engine. Premixed combustion in a compression ignition engine is defined, in this paper, to occur when the injection event is clearly separated from the combustion and the engine-out smoke is very low – below 0.05 FSN (filter smoke number). Under such circumstances, if the combustion phasing is matched for two fuels at a given operating condition and injection timing, the emissions are also comparable regardless of the differences in composition and volatility. For the experimental conditions considered, combustion phasing at a given operating condition and injection timing depends only on the octane index (OI), OI = (1-K)RON + KMON, where RON and MON are research and motor octane numbers and K is an empirical constant that depends on operating conditions. A mixture of iso-octane, n-heptane and toluene can be found to match the RON and MON of any practical gasoline and will be a very good surrogate for the gasoline since it will have the same OI. If the compression ratio is greater than 14, practical diesel fuels, with DCN (derived cetane number) between 40 and 60, will have comparable ignition delays ton-heptane, which is an adequate surrogate for such fuels. However, premixed combustion can be attained only at much lower loads at a given speed with diesel fuels compared to gasolines.
Optimization of Precursor Injection in an Atmospheric Pressure Plasma Jet System (2009)

Atmospheric Pressure Plasma Enhanced Chemical Vapor Deposition (AP PECVD) of thin films is a recently emerged technology, showing important advantages in comparison with the traditional and well established low pressure plasma enhanced deposition methods. The main benefit of AP-PECVD is the potential of cost efficient in-line production without expensive and bulky vacuum equipment. \nIn this work, an innovative AP plasma jet system is investigated which serves as a pilot system for industrial scale equipment, the VITO PlasmaLine®. Applications include moisture/oxygen diffusion barriers as well as grease barriers, UV curing of coatings or chemical activation of a surface. For industrial application a high throughput (~ 100-1000 m/min) is critical in order to compete with conventional techniques, such as wet chemical coating. Barrier coating deposition by AP-PECVD on polymer substrates has been demonstrated to be superior to wet chemical coating, with less consumption of precursor material [1], though many technical challenges remain to obtain the desired (dynamic) growth rates.\nThe pilot equipment utilizes a 0.5 mm double slit configuration with 1000-2000 W power input at a frequency of 40-50 kHz with N2 as the primary carrier gas. By utilizing the plasma afterglow remote from the source, uniform surface treatment can be achieved despite the filamentary discharge in the slits. Deposition on the electrodes is prevented by injection of precursor into the jet and because of the remote nature of the plasma source the thermal load on the substrate is minimized, making it ideally suited for treatment of polymers and paper. \nA key area for improvement and upscaling of the pilot system for industrial application is optimization of gaseous and liquid (aerosol) precursor injection. To this end, extensive characterization of the plasma jet is undertaken, including current-voltage, fast imaging and optical emission and absorption measurements, with focus on the dynamics of gaseous and aerosol precursor particles in the jet. For optimum control over the gas distribution and precursor injection, Computational Fluid Dynamic models are presented in conjunction with the experimental work.
Selective Sphingosine 1-Phosphate Receptor 1 Agonist Is Protective Against Ischemia/Reperfusion in Mice (2016)

The selective S1P1 agonist LASW1238 reduces infarct volume after ischemia/reperfusion in mice, but only when lymphopenia is sustained for at least 24 hours. S1P1 and lymphocytes are potential targets for drug treatment in stroke. Defining the best drug dosing regimens to control the extent and duration of lymphopenia is critical to achieve the desired effects.