gebhart/patrepeval huggingface dataset:
Label-free fingerprinting of tumor cells in bulk flow using inline digital holographic microscopy (2017)

Large-scale and label-free phenotyping of cells holds great promise in medicine, especially in cancer diagnostics and prognosis. Here, we introduce inline digital holography microscopy for volumetric imaging of cells in bulk flow and fingerprinting of flowing tumor cells based on two metrics, in-focus scattered intensity and cell diameter. Using planar distribution of immobilized particles, we identify the optimal recording distance and microscope objective magnification that minimizes the error in measurement of particle position, size and scattered intensity. Using the optimized conditions and the two metrics, we demonstrate the capacity to enumerate and fingerprint more than 100,000 cells. Finally, we highlight the power of our label-free and high throughput technology by characterizing breast tumor cell lines with different metastatic potentials and distinguishing drug resistant ovarian cancer cells from their parental cell line.
Neural Face Editing with Intrinsic Image Disentangling (2017)

Traditional face editing methods often require a number of sophisticated and task specific algorithms to be applied one after the other --- a process that is tedious, fragile, and computationally intensive. In this paper, we propose an end-to-end generative adversarial network that infers a face-specific disentangled representation of intrinsic face properties, including shape (i.e. normals), albedo, and lighting, and an alpha matte. We show that this network can be trained on "in-the-wild" images by incorporating an in-network physically-based image formation module and appropriate loss functions. Our disentangling latent representation allows for semantically relevant edits, where one aspect of facial appearance can be manipulated while keeping orthogonal properties fixed, and we demonstrate its use for a number of facial editing applications.
General Scope of 1,4-Diastereoselective Additions to a 2(3<i>H</i>)-Quinazolinone:  Practical Preparation of HIV Therapeutics (2002)

The practical and highly diastereoselective syntheses of CF(3)-substituted dihydroquinazolinones via 1,4-additions of nucleophiles to chiral auxiliary substituted 2(3H)-quinazolinones is described. This methodology is applied to the syntheses of the NNRTIs (nonnucleoside reverse transcriptase inhibitors) DPC 961 (1) and DPC 083 (2), which are useful for the treatment of HIV (human immunodeficiency virus). The synthesis of DPC 961 (1) requires three steps, proceeds in >55% overall yield from the keto-aniline 9, and gives synthetic access to DPC 083 (2). In addition, the scope of the new diastereoselective 1,4-addition chemistry is investigated. The first preparation of DPC 961 (1) described in this paper is a derivatization fractional crystallization protocol.
Multi-locus transcranial magnetic stimulation—theory and implementation (2018)

Already with two coils, we can adjust the location of the induced electric field maximum along one dimension, which is sufficient to study, for example, the primary motor cortex.
An Autoregressive Exogenous Neural Network to Model Fire Behavior via a Naïve Bayes Filter (2020)

This work presents an artificial neural network-based linearly regressive technique for the prediction of a temperature rise event caused by a fire in enclosed building environments. The method predicts temperature range in a burning compartment based on the historic fire behavior data modelled via a neural network algorithm. The approach further extends the method by transforming the regression outcome as actionable information for firefighters via a self-organising feature map (SOM) fire-stage-clustering algorithm which categorises the predicted temperature range to provide warnings of any imminent and catastrophic temperature variations. The methodology implements a linear regression artificial neural model to model and predicts catastrophic temperature variations that are a threat to fire-and-rescue personnel in enclosed burning compartments via a ceiling gas-layer temperature acting as an exogenous variable. Based on the predicted temperature window, the SOM classifier maps the output in distinct clusters while isolating spurious prediction spikes and categorising the output to various self-organising threat/warning levels. The model was trained on temperature data captured with pole-mounted sensors in controlled fire training exercises. Tests carried out in actual fire-settings showed the capability of the SOM classifier to generate evacuation warnings for forecasted temperatures exceeding 300 C in 5 - 30 seconds ahead of the occurrences. Tests on these short-term and long-term prediction ranged from 78.31% to 96.27% in accuracy whereas the SOM classifier generated an overall accuracy of 76.92% to 100%. The techniques also showed a high resilience against both false-positives and false-negatives.
Balanced Antipodal Vivaldi Antenna With Dielectric Director for Near-Field Microwave Imaging (2010)

A balanced antipodal Vivaldi antenna is designed to be used as a sensor for a microwave breast cancer detection system. The antenna has the ability to send short electromagnetic pulses into the near-field, with low distortion, low loss and in a directional manner. The antenna directivity is further improved by the inclusion of a novel feature in the antenna aperture called a “director” which consists of a profiled piece of higher dielectric constant material. Several simulated results are successfully confirmed with measurements. Reflections of a tumor placed in a breast model are simulated for two cases, namely a balanced antipodal Vivaldi antenna with and without a director. Greater tumor responses are recorded with the director present, demonstrating the potential of this feature for microwave breast imaging.
Poly(Alkyl Glycidate Carbonate)s as Degradable Pressure‐Sensitive Adhesives (2018)

Insertion of CO<sub>2</sub> into the polyacrylate backbone, forming poly(carbonate) analogues, provides an environmentally friendly and biocompatible alternative. The synthesis of five poly(carbonate) analogues of poly(methyl acrylate), poly(ethyl acrylate), and poly(butyl acrylate) is described. The polymers are prepared using the salen cobalt(III) complex catalyzed copolymerization of CO<sub>2</sub> and a derivatized oxirane. All the carbonate analogues possess higher glass-transition temperatures (T<sub>g</sub> =32 to -5 °C) than alkyl acrylates (T<sub>g</sub> =10 to -50 °C), however, the carbonate analogues (T<sub>d</sub> ≈230 °C) undergo thermal decomposition at lower temperatures than their acrylate counterparts (T<sub>d</sub> ≈380 °C). The poly(alkyl carbonates) exhibit compositional-dependent adhesivity. The poly(carbonate) analogues degrade into glycerol, alcohol, and CO<sub>2</sub> in a time- and pH-dependent manner with the rate of degradation accelerated at higher pH conditions, in contrast to poly(acrylate)s.
Amortized Generation of Sequential Counterfactual Explanations for Black-box Models. (2021)

Explainable machine learning (ML) has gained traction in recent years due to the increasing adoption of ML-based systems in many sectors. Counterfactual explanations (CFEs) provide ``what if'' feedback of the form ``if an input datapoint were $x'$ instead of $x$, then an ML-based system's output would be $y'$ instead of $y$.'' CFEs are attractive due to their actionable feedback, amenability to existing legal frameworks, and fidelity to the underlying ML model. Yet, current CFE approaches are single shot -- that is, they assume $x$ can change to $x'$ in a single time period. We propose a novel stochastic-control-based approach that generates sequential CFEs, that is, CFEs that allow $x$ to move stochastically and sequentially across intermediate states to a final state $x'$. Our approach is model agnostic and black box. Furthermore, calculation of CFEs is amortized such that once trained, it applies to multiple datapoints without the need for re-optimization. In addition to these primary characteristics, our approach admits optional desiderata such as adherence to the data manifold, respect for causal relations, and sparsity -- identified by past research as desirable properties of CFEs. We evaluate our approach using three real-world datasets and show successful generation of sequential CFEs that respect other counterfactual desiderata.
Design of a Highly Selective Quenched Activity-Based Probe and Its Application in Dual Color Imaging Studies of Cathepsin S Activity Localization (2015)

The cysteine cathepsins are a group of 11 proteases whose function was originally believed to be the degradation of endocytosed material with a high degree of redundancy. However, it has become clear that these enzymes are also important regulators of both health and disease. Thus, selective tools that can discriminate between members of this highly related class of enzymes will be critical to further delineate the unique biological functions of individual cathepsins. Here we present the design and synthesis of a near-infrared quenched activity-based probe (qABP) that selectively targets cathepsin S which is highly expressed in immune cells. Importantly, this high degree of selectivity is retained both in vitro and in vivo. In combination with a new green-fluorescent pan-reactive cysteine cathepsin qABP we performed dual color labeling studies in bone marrow-derived immune cells and identified vesicles containing exclusively cathepsin S activity. This observation demonstrates the value of our complementary cathepsin probes and provides evidence for the existence of specific localization of cathepsin S activity in dendritic cells.
Membrane Bioreactor With Pressure Cycle (1991)

Improved class of multilayer membrane bioreactors uses convention forced by differences in pressure to overcome some of diffusional limitations of prior bioreactors. In reactor of new class, flow of nutrient solution reduces adverse gradients of concentration, keeps cells supplied with fresh nutrient, and sweeps away products faster than diffusion alone. As result, overall yield and rate of reaction increased. Pressures in sweeping gas and nutrient alternated to force nutrient liquid into and out of biocatalyst layer through hyrophilic membrane.
Substream Trading: Towards an open P2P live streaming system (2008)

We consider the design of an open P2P live-video streaming system. When designing a live video system that is both open and P2P, the system must include mechanisms that incentivize peers to contribute upload capacity. We advocate an incentive principle for live P2P streaming: a peer’s video quality is commensurate with its upload rate. We propose Substream Trading, a new P2P streaming design which not only enables differentiated video quality commensurate with a peer’s upload contribution but can also accommodate different video coding schemes, including single-layer coding, layered coding, and multiple description coding. Extensive trace-driven simulations show that substream trading has high efficiency, provides differentiated service, low start-up latency, synergies among peers with different Internet access rates, and protection against free-riders.
Green One-Pot Synthesis of Surface Hydrophobized Cellulose Nanocrystals in Aqueous Medium (2016)

The surface hydrophobization of cellulose nanocrystals (CNCs) by fatty acids (FAs), biodiesel, or plant oils was conducted via a green process using an organic solvent less one-pot method. In the process, an aqueous lactic acid syrup served as a reactive solvent to provide a stable and well-dispersed water suspension of CNC and participate in esterification reactions, producing an intermediate product of polylactic acid (PLA) oligomer grafted CNCs (CNC-g-PLA). This reactive solvent and intermediate product system allows for an in situ solvent exchange from water to lactic acid without prior drying of the CNC and a subsequent efficient esterification reaction of CNC with carboxylic acids or esters having a long hydrocarbon chain (FAs). Another advantage of the proposed process is the possibility to reuse the reagents in the subsequent reaction in order to reduce the production cost. The grafting efficiency of the CNC-g-PLA-FA samples covalently grafted with PLA and FAs were characterized by Fourier transform infrared spectroscopy (FT-IR), elemental analysis (EA), and 13C nuclear magnetic resonance spectroscopy (ss-NMR). The change of dimensions and degree of crystallinity of the modified CNC was evaluated by dynamic light scattering (DLS) and X-ray diffraction (XRD). Different organic solvents were used here to investigate the relative hydrophobicity of the modified CNCs comparing the transmittance of their suspensions in the ultraviolet and visible (UV–vis) spectrometer, and evaluating their hydrodynamic radius by dynamic light scattering (DLS) techniques. Grafting of renewable materials on the surface of CNCs was developed by polyesterification that is capable of being environmentally friendly and mass-produced without any organic solvents or toxic reagents.
Porous, High Capacity Coatings for Solid Phase Microextraction by Sputtering (2015)

We describe a new process for preparing porous solid phase microextraction (SPME) coatings by the sputtering of silicon onto silica fibers. The microstructure of these coatings is a function of the substrate geometry and mean free path of the silicon atoms, and the coating thickness is controlled by the sputtering time. Sputtered silicon structures on silica fibers were treated with piranha solution (a mixture of concd H2SO4 and 30% H2O2) to increase the concentration of silanol groups on their surfaces, and the nanostructures were silanized with octadecyldimethylmethoxysilane in the gas phase. The attachment of this hydrophobic ligand was confirmed by X-ray photoelectron spectroscopy and contact angle goniometry on model, planar silicon substrates. Sputtered silicon coatings adhered strongly to their surfaces, as they were able to pass the Scotch tape adhesion test. The extraction time and temperature for headspace extraction of mixtures of alkanes and alcohols on the sputtered fibers were optimized (5 min and 40 °C), and the extraction performances of SPME fibers with 1.0 or 2.0 μm of sputtered silicon were compared to those from a commercial 7 μm poly(dimethylsiloxane) (PDMS) fiber. For mixtures of alcohols, aldehydes, amines, and esters, the 2.0 μm sputtered silicon fiber yielded signals that were 3-9, 3-5, 2.5-4.5, and 1.5-2 times higher, respectively, than those of the commercial fiber. For the heavier alkanes (undecane-hexadecane), the 2.0 μm sputtered fiber yielded signals that were approximately 1.0-1.5 times higher than the commercial fiber. The sputtered fibers extracted low molecular weight analytes that were not detectable with the commercial fiber. The selectivity of the sputtered fibers appears to favor analytes that have both a hydrophobic component and hydrogen-bonding capabilities. No detectable carryover between runs was noted for the sputtered fibers. The repeatability (RSD%) for a fiber (n = 3) was less than 10% for all analytes tested, and the between-fiber reproducibility (n = 3) was 0-15%, generally 5-10%, for all analytes tested. The repeatabilities of our sputtered fibers and the commercial 7 μm PDMS fiber are essentially the same. Fibers could be used for at least 300 extractions without loss of performance. More than 50 compounds were identified in a gas chromatography-mass spectrometry headspace analysis of a real world botanical sample with the 2.0 μm fiber.
Kerr frequency comb-based K<inf>a</inf>-band RF photonic oscillator (2013)

We report on the realization of a packaged RF photonic oscillator based on Kerr optical frequency comb generated in an ultra-high Q crystalline whispering gallery mode (WGM) resonator. The oscillator produces spectrally pure RF signals in K <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">a</sub> frequency band, characterized with single sideband phase noise of -110 dBc/Hz at 10 kHz. The stability of the free running oscillator is characterized with Allan deviation of 10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">-10</sup> at 1 s. We also argue that usage of hyperparametric gain based on cubic nonlinearity of the host material of an optical microresonator as part of an Opto-Electronic Oscillator (OEO) loop allows achieving generation of low noise RF signals in microrezonator-based OEOs.
Longitudinal determination of total body creatine pool size and skeletal muscle mass in rats by D <sub>3</sub> ‐creatine dilution (2013)

We recently described a new method to determine total body creatine pool size and skeletal muscle mass based on dilution of an oral dose of D 3 ‐creatine in urinary creatinine. Enrichment of D 3 ‐ creatinine was measured by isotope ratio mass spectrometry. Here we adapt the method to LC‐MS/MS, and investigate the potential for repeated application over time. Rats were given an oral tracer dose of D 3 ‐creatine (1.0 mg/kg body weight) at 10 weeks of age. Urine D 3 ‐creatinine enrichment was determined 72 hr after tracer administration and creatine pool size was calculated. Lean body mass (LBM) measured by quantitative magnetic resonance correlated with creatine pool size ( r = 0.92, P = 0.0002). The rate constant for decline in urinary D 3 ‐creatinine enrichment was slow and linear (2.73 ± 0.06 %/day). Subtracting background urinary D 3 ‐creatinine enrichment from the enrichment following a second dose of D 3 ‐creatine at 17 weeks permitted repeat calculations of creatine pool size. As at 10 weeks, 17 week LBM correlated with creatine pool size ( r = 0.98, P < 0.0001). In addition, the change in creatine pool size was correlated with the change in LBM during the 7 weeks of somatic growth between measurements ( r = 0.96, P < 0.0001). Thus, the LC‐MS/MS‐based D 3 ‐creatine dilution method can be applied repeatedly to measure skeletal muscle mass change in longitudinal studies. These studies were funded by GlaxoSmithKline.
Development of Pure Prolactin Receptor Antagonists (2003)

Prolactin (PRL) promotes tumor growth in various experimental models and leads to prostate hyperplasia and mammary neoplasia in PRL transgenic mice. Increasing experimental evidence argues for the involvement of autocrine PRL in this process. PRL receptor antagonists have been developed to counteract these undesired proliferative actions of PRL. However, all forms of PRL receptor antagonists obtained to date exhibit partial agonism, preventing their therapeutic use as full antagonists. In the present study, we describe the development of new human PRL antagonists devoid of agonistic properties and therefore able to act as pure antagonists. This was demonstrated using several in vitro bioassays, including highly sensitive assays able to detect extremely low levels of receptor activation. These new compounds also act as pure antagonists in vivo, as assessed by analyzing their ability to competitively inhibit PRL-triggered signaling cascades in various target tissues (liver, mammary gland, and prostate). Finally, by using transgenic mice expressing PRL specifically in the prostate, which exhibit constitutively activated signaling cascades paralleling hyperplasia, we show that these new PRL analogs are able to completely revert PRL-activated events. These second generation human PRL antagonists are good candidates to be used as inhibitors of growth-promoting actions of PRL.
Sol-gel processed cerium oxide and mixed cerium-titanium oxide films as passive counter electrodes for transmissive electrochromic devices (2005)

Thin films of Ce02 and mixed oxide CeOr Ti02 with a CelTi mole ratio of one have been obtained by an alcohol based sol-gel process. The precursor materials for the latter comprises a Ce(lII) salt, CeCI3.7H20 and titanium propoxide in ethanol. The mixed oxide film is characterized by the prevalence of amorphicity, though morphological studies have indicated the presence of Ce02 nanograins. Pure cerium oxide film exhibits crystalline nature with the average grain size in the nanorange. In agreement with the higher levels of Li+ ion intercalation in an amorphous film in comparison to crystallin e film. a superior inserted/extracted charge in the mixed oxide film is revealed from the electrochemical in vestigations . The films prepared from an aged sol are observed to exhibit a much higher ion insertion capacity and transparency as compared to the films deposited using as-prepared sol. The ion insertion capacity obtained for an 800 nm thick film of mixed oxide is of the order of 18.36 mC cm- 2 at a frequency of 0.0011 Hz. The presence of well-defined grains of about 89 nm dimension in the CeOr Ti02 film has been determined by the AFM studies_ The measurements on the films for electrochromic applications such as smart windows reveal fast coloration-bleaching kinetics for W03 in conjunction with the mixed Ce02-Ti02 film and affirm its suitability as passive counter electrode in electrochromic devices. IPC Code: Int. CI. 7 C04B35/0l; C04B35/46; C04B35/624; HO I G9/oo; HO I M4/48
Automatic and exam-type independent algorithm for the segmentation and extraction of foreground, background, and anatomy regions in digital radiographic images (2004)

Processing optimization of digital radiographs requires the knowledge of the location and characteristics of both diagnostically relevant and irrelevant image regions. An algorithm has been developed that can automatically detect and extract foreground, background, and anatomy regions from a digital radiograph. This algorithm is independent of exam-type information and can deal with multiple-exposed computed radiography (CR) images. First, the image is subsampled, and the processing is done on the sub-sampled image to improve subsequent processing efficiency and reduce algorithm dependency on image noise and detector characteristics. Second, an initial background is detected using adaptive thresholding on the cumulative histogram of significant transition pixels and an iterative process, based on background variance. Third, foreground detection is conducted by: (1) classifying all significant transitions using a smart-edge detection, (2) delineating all lines that are possible collimation blades using Hough transform, (3) finding candidate partition blade pairs if the image has several radiation fields, (4) partitioning the image into sub-images containing only one radiation field using a divide-and-conquer process, and (5) identifying the best collimation for each sub-image from a tree-structured hypothesis list. Fourth, the background is regenerated using a region-growing process from identified background “seeds.” Fifth, the background and foreground regions are merged and removed; the rest of the image is labeled and those large, connected regions are identified as anatomy regions. The algorithm has been trained and tested separately with two image sets from a wide variety of exam types. Each set consists of more than 2700 CR images acquired with KODAK DIRECTVIEW CR 800 Systems. The overall success rate in detecting both foreground and background is 97%.