gebhart/patrepeval huggingface dataset:
Are those bugs reflective? non-destructive biofilm imaging with white light interferometry (2016)

White light interferometry (WLI) is not typically used to image bacterial biofilms that are immersed in water because there is insufficient refractive index contrast to induce reflection from the biofilm’s interface. The soft structure and water-like bulk properties of hydrated biofilms make them difficult to characterize <i>in situ</i> by any means, especially in a non-destructive manner. Here we describe a new method for measuring and monitoring the thickness and topology of live biofilms using a WLI microscope. A microfluidic system was used to create a reflective interface on the surface of biofilms. Live biofilm samples were monitored non-destructively over time. The method enables surface metrology measurements (roughness, surface area) and a novel approach to measuring thickness of the thin hydrated biofilms. Increase in surface roughness preceded observable increase in biofilm thickness, indicating that this measure may be used to predict future development of biofilms. We have also developed a flow cell that enables WLI biofilm imaging in a dynamic environment. We have used this flow cell to observe changes in biofilm structure in response to changes in environmental conditions - flow velocity, availability of nutrients, and presence of biocides.
Progress on photonic tensor processors based on time multiplexing and photoelectric multiplication (2021)

Optical approaches to machine learning rely heavily on programmable linear photonic circuits. Since the performance and energy efficiency scale with size, a major challenge is overcoming scaling roadblocks to the photonic technology. Recently, we proposed an optical neural network architecture based on coherent detection. This architecture has several scaling advantages over competing approaches, including linear (rather than quadratic) chip-area scaling and constant circuit depth. We review the fundamental and technological limits to the energy consumption in this architecture, which shed light on the quantum limits to analog computing, which are distinct from the thermodynamic (e.g. Landauer) limits to digital computing. Lastly, we highlight a recent "digital" implementation of our architecture, which sheds light on the scaling challenges associated with controlling aberrations in the free-space optical propagation.
Immunodeterminant specificity of human immunity to type III group B streptococcus. (1979)

The type III polysaccharides of group B Streptococcus in its native state chemically consists of glucose, galactose, glucosamine, and sialic acid. The core of this polysaccharide lacks sialic acid and precipitates with type III antiserum to give a partial identity with the precipitate between the native antigen and this serum. The core determinant is immunochemically similar to the capsular polysaccharide of type XIV Streptococcus pneumoniae, while the native type III group B streptococcal polysaccharide does not cross-react with type XIV pneumococcal antiserum. In human sera, it is antibody directed to the native antigen which correlates very highly with opsonic immunity (r = 0.94) while a poorer correlation exists between antibody to the core antigen and opsonins (r = 0.51 P less than 0.001). In natural infections, as association exists between low levels of maternal antibody to the native antigen and risk of disease in the infant. This association is not true for antibody to the core structure, where both infected infants and their mothers have much higher levels of antibody to the core than the native antigens. Infected infants are also more likely to respond to infection by developing antibody to the native antigen. Immunization of 12 adults with multivalent pneumococcal polysaccharide induced significantly better antibody response to the core antigen than to the native, and this vaccine induced opsonic activity in only one recipient. Immunization of adults with type III group B streptococcal antigens induced antibody to the native determinant which correlated with opsonic activity. Therefore, it would appear that native group B streptococcal polysaccharides will provide the best candidate antigens for immunization.
Novel Online Sensor Technology for Continuous Monitoring of Milk Coagulation and Whey Separation in Cheesemaking (2007)

The cheese industry has continually sought a robust method to monitor milk coagulation. Measurement of whey separation is also critical to control cheese moisture content, which affects quality. The objective of this study was to demonstrate that an online optical sensor detecting light backscatter in a vat could be applied to monitor both coagulation and syneresis during cheesemaking. A prototype sensor having a large field of view (LFV) relative to curd particle size was constructed. Temperature, cutting time, and calcium chloride addition were varied to evaluate the response of the sensor over a wide range of coagulation and syneresis rates. The LFV sensor response was related to casein micelle aggregation and curd firming during coagulation and to changes in curd moisture and whey fat contents during syneresis. The LFV sensor has potential as an online, continuous sensor technology for monitoring both coagulation and syneresis during cheesemaking.
The Conversion of Fibrinogen to Fibrin: Recombinant Fibrinogen Typifies Plasma Fibrinogen (1997)

Plasma fibrinogen is a mixture of multiple molecular forms arising mainly through alternative mRNA processing and subsequent posttranslational modification. Recombinant fibrinogen is synthesized without alternative mRNA processing in a cultured cell system that may generate novel posttranslational modifications. Thus, to show that recombinant fibrinogen can serve as a functional model for plasma fibrinogen, we have examined the conversion of fibrinogen to fibrin, comparing the recombinant with the plasma protein. We examined the kinetics of (1) thrombin-catalyzed fibrinopeptide release, (2) thrombin-catalyzed polymerization of fibrinogen, (3) the polymerization of fibrin monomers, and (4) FXIIIa-catalyzed cross-link formation. We saw small differences in polymerization, suggesting that the ordered assembly of protofibrils and fibers was not identical. In all other analyses, we found that plasma fibrinogen and recombinant fibrinogen were remarkably similar. Using electron microscopy, we examined the structures of individual fibrinogen molecules and fibrin clots. Individual fibrinogen molecules were predominantly three nodule structures for both recombinant and plasma proteins. Both samples also displayed four nodule structures, but fewer four nodule structures were found with recombinant fibrinogen. Fibrin clot structures were essentially indistinguishable. We concluded that recombinant fibrinogen can serve as a accurate model for plasma fibrinogen.
<title>Integrated thin film fluorescence NOx sensor concept</title> (1997)

A fluorescence sensor system is proposed that integrates emission and detection methods as well as optical and electronic components in a thin film geometry. Predicted properties of this sensor include: increased sensitivity, shielding form unwanted radiation, wavelength filtering, potential operation at high temperatures, and miniaturization. The sensor can be tuned to measure a wide variety of species by varying its thin film corrugation periodicity, in particular, the sensor can be used to detect NO<SUB>x</SUB>.
Intracellular localization and membrane topology of 11-cis retinol dehydrogenase in the retinal pigment epithelium suggest a compartmentalized synthesis of 11-cis retinaldehyde (1999)

11-cis retinol dehydrogenase (EC 1.1.1.105) catalyses the last step in the biosynthetic pathway generating 11-cis retinaldehyde, the common chromophore of all visual pigments in higher animals. The enzyme is abundantly expressed in retinal pigment epithelium of the eye and is a member of the short chain dehydrogenase/reductase superfamily. In this work we demonstrate that a majority of 11-cis retinol dehydrogenase is associated with the smooth ER in retinal pigment epithelial cells and that the enzyme is an integral membrane protein, anchored to membranes by two hydrophobic peptide segments. The catalytic domain of the enzyme is confined to a lumenal compartment and is not present on the cytosolic aspect of membranes. Thus, the subcellular localization and the membrane topology of 11-cis retinol dehydrogenase suggest that generation of 11-cis retinaldehyde is a compartmentalized process.
Ultrasonic hearing in humans: applications for tinnitus treatment. (2003)

Masking of tinnitus is possible using high audio frequencies and low-frequency ultrasound. The mechanisms involved in reception and perception of both audio frequencies and ultrasound are identical, with the exception that ultrasound interacts with an intermediary site, the brain. We proposed brain ultrasonic demodulation as the means of place-mapping ultrasound on the first few millimeters of the basilar membrane. We present modeling and psychoacoustic data in support of this theory.
Cytochrome P450s and chemoprevention (2000)

The cytochrome P450 mono-oxygenase system represents a major defence against chemical challenge from the environment, constituting part of an adaptive response mounted by an organism following exposure to harmful agents. Cytochrome P450s are also able to catalyse the activation of compounds to toxic products, and participate in a variety of essential 'housekeeping' functions, such as biosynthesis of steroid hormones and fatty acid oxidation. It is clear that the modulation of expression of these enzymes can have a significant effect on chemical toxicity, carcinogenicity and mutagenicity. The concept of cancer chemoprevention, i.e. the administration of a (non-toxic) chemical or dietary component in order to prevent neoplastic disease or to inhibit its progression, is an attractive one. Despite this, relatively little work has been done to characterize the ability of putative chemopreventive agents to modulate P450 expression, or to understand the interaction between P450s and chemopreventive agents. Before chemopreventive treatment can become a reality, it is essential that this complex issue is addressed; for instance, it is likely that any single chemopreventive agent will induce more than one P450 isoenzyme, and while altered expression of a particular P450 may attenuate the effects of one toxic agent, the effects of others might well be potentiated. Our laboratory has created a transgenic mouse line in which the rat CYP1A1 promoter drives expression of the beta-galactosidase gene. These mice can be used to define which compounds act via the Ah receptor, in which tissues, and at which stage of development. We are currently developing another mouse line in which beta1-galactosidase expression is controlled by the mouse GstA1 promoter, allowing us to define the role of the antioxidant responsive element in the action of chemopreventive agents. Finally, using cre-loxP transgenic technology, we have generated a mouse line in which P450 reductase can be deleted in a conditional, i.e. tissue-specific, manner, permitting us to investigate the role of P450s in chemoprevention in a more defined manner.
Robust methods for high-quality stills from interlaced video in the presence of dominant motion (1997)

We present robust algorithms which combine global motion compensation and motion adaption for deinterlacing in the presence of both dominant motion, such as camera zoom, pan, or jitter, and local motion, such as object motion. The dominant motion is modeled by a global affine warping and estimated by a gradient-based estimation method. Two alternative algorithms are proposed for compensation of the dominant motion: a bilinear interpolation based on the affine model, and a projections onto convex sets (POCS) based method that takes into account blurring in the image formation. It is important to note that the latter must be used if the blurring is severe enough to act as an anti-alias filter, which imposes an irreversible limit on the resolution improvement ability of any motion-compensated filter. Global motion-compensated images are then input to a motion-adaptive filter to detect and correct for those pixels where there exists local motion. A dynamic thresholding for motion detection is presented, with weighted directional-filtering for regions where motion is detected, to obtain the best results. Experimental results with application to obtaining high quality stills from video camcorders demonstrate the effectiveness of the proposed methods.
Enantioselective α-deprotonation–rearrangement of meso-epoxides (1996)

Enantioselective α-deprotonation–rearrangement of medium-sized (8-, 9- and 10-membered) cycloalkene-derived meso-epoxides using organolithiums in the presence of (–)-sparteine gives bicyclic alcohols in good yields and ees.
Cadaveric and in vivo human joint imaging based on differential phase contrast by X-ray Talbot-Lau interferometry (2012)

We developed an X-ray phase imaging system based on Talbot-Lau interferometry and studied its feasibility for clinical diagnoses of joint diseases. The system consists of three X-ray gratings, a conventional X-ray tube, an object holder, an X-ray image sensor, and a computer for image processing. The joints of human cadavers and healthy volunteers were imaged, and the results indicated sufficient sensitivity to cartilage, suggesting medical significance.
Registration of lung nodules using a semi‐rigid model: Method and preliminary results (2007)

The tracking of lung nodules across computed tomography (CT) scans acquired at different times for the same patient is helpful for the determination of malignancy. We are developing a nodule registration system to facilitate this process. We propose to use a semi-rigid method that considers principal structures surrounding the nodule and allows relative movements among the structures. The proposed similarity metric, which evaluates both the image correlation and the degree of elastic deformation amongst the structures, is maximized by a two-layered optimization method, employing a simulated annealing framework. We tested our method by simulating five cases that represent physiological deformation as well as different nodule shape/size changes with time. Each case is made up of a source and target scan, where the source scan consists of a nodule-free patient CT volume into which we inserted ten simulated lung nodules, and the target scan is the result of applying a known, physiologically based nonrigid transformation to the nodule-free source scan, into which we inserted modified versions of the corresponding nodules at the same, known locations. Five different modification strategies were used, one for each of the five cases: (1) nodules maintain size and shape, (2) nodules disappear, (3) nodules shrink uniformly by a factor of 2, (4) nodules grow uniformly by a factor of 2, and (5) nodules grow nonuniformly. We also matched 97 real nodules in pairs of scans (acquired at different times) from 12 patients and compared our registration to a radiologist's visual determination. In the simulation experiments, the mean absolute registration errors were 1.0+/-0.8 mm (s.d.), 1.1+/-0.7 mm (s.d.), 1.0+/-0.7 mm (s.d.), 1.0+/-0.6 mm (s.d.), and 1.1+/- 0.9 mm (s.d.) for the five cases, respectively. For the 97 nodule pairs in 12 patient scans, the mean absolute registration error was 1.4+/-0.8 mm (s.d.).
RetroFab (2016)

We present RetroFab, an end-to-end design and fabrication environment that allows non-experts to retrofit physical interfaces. Our approach allows for changing the layout and behavior of physical interfaces. Unlike customizing software interfaces, physical interfaces are often challenging to adapt because of their rigidity. With RetroFab, a new physical interface is designed that serves as a proxy interface for the legacy controls that are now operated by actuators. RetroFab makes this concept of retrofitting devices available to non-experts by automatically generating an enclosure structure from an annotated 3D scan. This enclosure structure holds together actuators, sensors as well as components for the redesigned interface. To allow retrofitting a wide variety of legacy devices, the RetroFab design tool comes with a toolkit of 12 components. We demonstrate the versatility and novel opportunities of our approach by retrofitting five domestic objects and exploring their use cases. Preliminary user feedback reports on the experience of retrofitting devices with RetroFab.
Discriminative state tracking for spoken dialog systems (2013)

In spoken dialog systems, statistical state tracking aims to improve robustness to speech recognition errors by tracking a posterior distribution over hidden dialog states. Current approaches based on generative or discriminative models have different but important shortcomings that limit their accuracy. In this paper we discuss these limitations and introduce a new approach for discriminative state tracking that overcomes them by leveraging the problem structure. An offline evaluation with dialog data collected from real users shows improvements in both state tracking accuracy and the quality of the posterior probabilities. Features that encode speech recognition error patterns are particularly helpful, and training requires relatively few dialogs. 1
Novel Cathode Materials for Na‐Ion Batteries Composed of Spoke‐Like Nanorods of Na[Ni<sub>0.61</sub>Co<sub>0.12</sub>Mn<sub>0.27</sub>]O<sub>2</sub> Assembled in Spherical Secondary Particles (2016)

The development of high‐energy and high‐power density sodium‐ion batteries is a great challenge for modern electrochemistry. The main hurdle to wide acceptance of sodium‐ion batteries lies in identifying and developing suitable new electrode materials. This study presents a composition‐graded cathode with average composition Na[Ni 0.61 Co 0.12 Mn 0.27 ]O 2 , which exhibits excellent performance and stability. In addition to the concentration gradients of the transition metal ions, the cathode is composed of spoke‐like nanorods assembled into a spherical superstructure. Individual nanorod particles also possess strong crystallographic texture with respect to the center of the spherical particle. Such morphology allows the spoke‐like nanorods to assemble into a compact structure that minimizes its porosity and maximizes its mechanical strength while facilitating Na + ‐ion transport into the particle interior. Microcompression tests have explicitly verified the mechanical robustness of the composition‐graded cathode and single particle electrochemical measurements have demonstrated the electrochemical stability during Na + ‐ion insertion and extraction at high rates. These structural and morphological features contribute to the delivery of high discharge capacities of 160 mAh (g oxide) −1 at 15 mA g −1 (0.1 C rate) and 130 mAh g −1 at 1500 mA g −1 (10 C rate). The work is a pronounced step forward in the development of new Na ion insertion cathodes with a concentration gradient.
Polyanhydride Nanovaccine Induces Robust Pulmonary B and T Cell Immunity and Confers Protection Against Homologous and Heterologous Influenza A Virus Infections (2018)

Influenza A virus (IAV) is a major cause of respiratory illness. Given the disease severity, associated economic costs, and recent appearance of novel IAV strains, there is a renewed interest in developing novel and efficacious “universal” IAV vaccination strategies. Recent studies have highlighted that immunizations capable of generating local (i.e., nasal mucosa and lung) tissue-resident memory T and B cells in addition to systemic immunity offer the greatest protection against future IAV encounters. Current IAV vaccines are designed to largely stimulate IAV-specific antibodies, but do not generate the lung-resident memory T and B cells induced during IAV infections. Herein, we report on an intranasally administered biocompatible polyanhydride nanoparticle-based IAV vaccine (IAV-nanovax) capable of providing protection against subsequent homologous and heterologous IAV infections in both inbred and outbred populations. Our findings also demonstrate that vaccination with IAV-nanovax promotes the induction of germinal center B cells within the lungs, both systemic and lung local IAV-specific antibodies, and IAV-specific lung-resident memory CD4 and CD8 T cells. Altogether our findings show that an intranasally administered nanovaccine can induce immunity within the lungs, similar to what occurs during IAV infections, and thus could prove useful as a strategy for providing “universal” protection against IAV.
Patterned waveguide liquid crystal displays (2020)

We report a novel polymer stabilized liquid crystal based light waveguide display whose performance is significantly improved by using patterned photo-polymerization or an electrode. The waveguide display is edge-lit and operates on the light scattering of the polymer stabilized liquid crystal. When no voltage is applied, the liquid crystal is uniformly aligned and is transparent. The incident light is waveguided through the display by total internal reflection and no light comes out of the viewing side of the display. When a voltage is applied, the liquid crystal is switched to a micron-sized poly-domain structure and becomes scattering. The incident light is scattered out of the viewing side of the display. We demonstrated that by using patterned photo-polymerization or an ITO electrode, the scattering efficiency of the liquid crystal in the voltage-on state is significantly enhanced. We have achieved high brightness, low driving voltage, sub-millisecond switching time and high contrast ratio. This new display is suitable for transparent and augmented display applications.
SliceNDice: Mining Suspicious Multi-Attribute Entity Groups with Multi-View Graphs (2019)

Given the reach of web platforms, bad actors have considerable incentives to manipulate and defraud users at the expense of platform integrity. This has spurred research in numerous suspicious behavior detection tasks, including detection of sybil accounts, false information, and payment scams/fraud. In this paper, we draw the insight that many such initiatives can be tackled in a common framework by posing a detection task which seeks to find groups of entities which share too many properties with one another across multiple attributes (sybil accounts created at the same time and location, propaganda spreaders broadcasting articles with the same rhetoric and with similar reshares, etc.) Our work makes four core contributions: Firstly, we posit a novel formulation of this task as a multi-view graph mining problem, in which distinct views reflect distinct attribute similarities across entities, and contextual similarity and attribute importance are respected. Secondly, we propose a novel suspiciousness metric for scoring entity groups given the abnormality of their synchronicity across multiple views, which obeys intuitive desiderata that existing metrics do not. Finally, we propose the SliceNDice algorithm which enables efficient extraction of highly suspicious entity groups, and demonstrate its practicality in production, in terms of strong detection performance and discoveries on Snapchat's large advertiser ecosystem (89% precision and numerous discoveries of real fraud rings), marked outperformance of baselines (over 97% precision/recall in simulated settings) and linear scalability.