gebhart/patrepeval huggingface dataset:
Enzyme-based soy processing (2022)

Soybeans contain three major components: protein (ca. 40%), carbohydrate (25–30%) and oil (18–20%). To maximize value and minimize waste in soy processing, all these components should be collected and utilized. Current processing was originally designed to maximize oil extraction. It tends to make protein and carbohydrate separation from the remaining meal more difficult and, as a result, can limit their uses and reduce their value. We have been developing an enzyme-based processing method which, in a single step, enables the recovery of oil, protein, and sugar in separate streams. Further, oil and protein present in soybeans as individually “packaged” oil bodies (oleosomes) and protein bodies. This solvent-free, enzyme-based processing allows collection of intact oleosomes and protein bodies without alteration by heat, solvent, or mechanical pressing. This new processing method can maximize the recovery of nutritional and industrial/economic value of all major soybean components. We also develop and optimize the production of enzyme particularly suitable for soy processing.
Mechanistic and Design Aspects of Transition Metal Nitride Based Supercapacitors (2012)

Abstract not Available.
"First AID" for T cell adoptive transfer: TCR affinity maturation by somatic hypermutation. (2013)

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Tracking non-stationary spectral peak structure in EEG data (2013)

We develop a particle filter algorithm to simultaneously estimate and track the instantaneous peak frequency, amplitude, and bandwidth of multiple concurrent non-stationary components of an EEG signal in the time-frequency domain. We use this method to characterize human EEG activity during anesthesia-induced unconsciousness.
Link and code: Fast indexing with graphs and compact regression codes (2018)

Similarity search approaches based on graph walks have recently attained outstanding speed-accuracy trade-offs, taking aside the memory requirements. In this paper, we revisit these approaches by considering, additionally, the memory constraint required to index billions of images on a single server. This leads us to propose a method based both on graph traversal and compact representations. We encode the indexed vectors using quantization and exploit the graph structure to refine the similarity estimation. In essence, our method takes the best of these two worlds: the search strategy is based on nested graphs, thereby providing high precision with a relatively small set of comparisons. At the same time it offers a significant memory compression. As a result, our approach outperforms the state of the art on operating points considering 64-128 bytes per vector, as demonstrated by our results on two billion-scale public benchmarks.
<title>Head-mounted ambient vision display for helicopter pilotage</title> (2000)

The relatively new notion that visual perception is served by two functionally distinct visual systems, the focal and the ambient, is supported by research evidence accumulated over the past thirty years. The focal system provides detailed information about the world, is controlled by attention and receives input from the fovea. Its performance is highly dependent on image focus and luminance level. The ambient visual system contributes continuously and importantly to spatial orientation, stability of the visual world, and locomotion. It responds to large areas of optical flow int he visual field and therefore most of its input comes from the peripheral retina. Ambient functions are carried out largely without conscious awareness and are relatively impervious to image defocus and luminance level. The evidence for the ambient visual system is reviewed and its functional characteristics are described.
Synthesis and Investigation of Mixed μ‐Opioid and δ‐Opioid Agonists as Possible Bivalent Ligands for Treatment of Pain (2016)

Several studies have suggested functional association between μ-opioid and δ-opioid receptors and showed that μ-activity could be modulated by δ-ligands. The general conclusion is that agonists for the δ-receptor can enhance the analgesic potency and efficacy of μ-agonists. Our preliminary investigations demonstrate that new bivalent ligands constructed from the μ-agonist fentanyl and the δ-agonist enkephalin-like peptides are promising entities for creation of new analgesics with reduced side effects for treatment of neuropathic pain. A new superposition of the mentioned pharmacophores led to novel μ-bivalent/δ-bivalent compounds that demonstrate both μ-opioid and δ-opioid receptor agonist activity and high efficacy in anti-inflammatory and neuropathic pain models with the potential of reduced unwanted side effects.
Hiding images in plain sight: deep steganography (2017)

Steganography is the practice of concealing a secret message within another, ordinary, message. Commonly, steganography is used to unobtrusively hide a small message within the noisy regions of a larger image. In this study, we attempt to place a full size color image within another image of the same size. Deep neural networks are simultaneously trained to create the hiding and revealing processes and are designed to specifically work as a pair. The system is trained on images drawn randomly from the ImageNet database, and works well on natural images from a wide variety of sources. Beyond demonstrating the successful application of deep learning to hiding images, we carefully examine how the result is achieved and explore extensions. Unlike many popular steganographic methods that encode the secret message within the least significant bits of the carrier image, our approach compresses and distributes the secret image's representation across all of the available bits.
Identification and Isolation of Multiple Modes in Rayleigh Waves Testing Methods (2000)

The spectral-analyses-of-surface-waves (SASW), developed in the early eighties, has constituted an important step, in the use of surface waves for definition of shear wave velocity profiles without intrusion. The SASW testing procedure was designed to minimize the contribution of higher Rayleigh modes and thus assumes that the average dispersion curve is representative of the fundamental Rayleigh mode. A number of numerical studies have however demonstrated that this basic assumption is valid only when the shear wave velocity varies regularly with depth. This study demonstrates, based in numerical simulations and an experimental case, that the multi-Rayleigh mode problem can occur in various situations even if the shear wave velocity increases regularly with depth. Techniques are proposed in order to identify and separate the energy of higher modes. The applicability of those techniques is demonstrated with simulated and experimental cases.
Sphingosine 1-phosphate receptor agonists: a patent review (2010 – 2012) (2013)

Limited progress has been made on agonists at S1P(4,5)-R subtypes, with some families of S1P5-R agonists showing promising results in animal models of age-related cognitive disorders. A discrete number of reviewed molecules are S1P1-R agonists with a promising clinical outlook in transplantation, inflammation, cancer and autoimmune settings. Further preclinical and clinical studies will determine whether the new developed S1P1-R agonists do indeed improve the safety profile of FTY720.
Immunologic findings precede rapid lupus flare after transient steroid therapy (2019)

Systemic lupus erythematosus (SLE) flares elicit progressive organ damage, leading to disability and early mortality. This study evaluated clinical and immunologic factors associated with impending flare in the Biomarkers of Lupus Disease study. Autoantibodies and 32 soluble mediators were measured by multiplex assays, immune pathway activation by gene expression module scores, and immune cell subset frequencies and activation states by flow cytometry. After providing baseline samples, participants received transient steroids to suppress disease and were followed until flare. Flare occurred early (within 60 days of baseline) in 21 participants and late (90-165 days) in 13. At baseline, compared to the late flare group, the early flare group had differential gene expression in monocyte, T cell, interferon, and inflammation modules, as well as significantly higher frequencies of activated (aCD11b<sup>+</sup>) neutrophils and monocytes, and activated (CD86<sup>hi</sup>) naïve B cells. Random forest models showed three subgroups of early flare patients, distinguished by greater baseline frequencies of aCD11b<sup>+</sup> monocytes, or CD86<sup>hi</sup> naïve B cells, or both. Increases in these cell populations were the most accurate biomarkers for early flare in this study. These results suggest that SLE flares may arise from an overlapping spectrum of lymphoid and myeloid mechanisms in different patients.
Considering Genomic and Immunological Correlates of Protection for a Dengue Intervention (2019)

Over three billion are at risk of dengue infection with more than 100 million a year presenting with symptoms that can lead to deadly haemorrhagic disease. There are however no treatments available and the only licensed vaccine shows limited efficacy and is able to enhance the disease in some cases. These failures have mainly been due to the complex pathology and lack of understanding of the correlates of protection for dengue virus (DENV) infection. With increasing data suggesting both a protective and detrimental effect for antibodies and CD8 T-cells whilst having complex environmental dynamics. This review discusses the roles of genomic and immunological aspects of DENV infection, providing both a historical interpretation and fresh discussion on how this information can be used for the next generation of dengue interventions.
Porphyrins Fused with Unactivated Polycyclic Aromatic Hydrocarbons (2011)

A systematic study of the preparation of porphyrins with extended conjugation by meso,β-fusion with polycyclic aromatic hydrocarbons (PAHs) is reported. The meso-positions of 5,15-unsubstituted porphyrins were readily functionalized with PAHs. Ring fusion using standard Scholl reaction conditions (FeCl(3), dichloromethane) occurs for perylene-substituted porphyrins to give a porphyrin β,meso annulated with perylene rings (0.7:1 ratio of syn and anti isomers). The naphthalene, pyrene, and coronene derivatives do not react under Scholl conditions but are fused using thermal cyclodehydrogenation at high temperatures, giving mixtures of syn and anti isomers of the meso,β-fused porphyrins. For pyrenyl-substituted porphyrins, a thermal method gives synthetically acceptable yields (>30%). Absorption spectra of the fused porphyrins undergo a progressive bathochromic shift in a series of naphthyl (λ(max) = 730 nm), coronenyl (λ(max) = 780 nm), pyrenyl (λ(max) = 815 nm), and perylenyl (λ(max) = 900 nm) annulated porphyrins. Despite being conjugated with unsubstituted fused PAHs, the β,meso-fused porphyrins are more soluble and processable than the parent nonfused precursors. Pyrenyl-fused porphyrins exhibit strong fluorescence in the near-infrared (NIR) spectral region, with a progressive improvement in luminescent efficiency (up to 13% with λ(max) = 829 nm) with increasing degree of fusion. Fused pyrenyl-porphyrins have been used as broadband absorption donor materials in photovoltaic cells, leading to devices that show comparatively high photovoltaic efficiencies.
PURIFICATION AND CHARACTERIZATION OF A PROTEIN C ACTIVATOR FROM THE VENOM OF AGKISTRODON CONTORTRIX CONTORTRIX (1987)

There are two recent reports on the purification and properties of a protein C activator (PCA) from the venom of the Southern copperhead snalce. The purification of a 37,000 Mr nonenzymatic PCA (Martinoli and Stocker, Thrcmb. Res. 43, 253, 1976) as well as of a 20,000 Mr thrombin-like enzyme (Klein and Walker, Biochem. ,25, 4175, 1986) have been described. The purpose of this investigation was to purify and further characterize the PCA(s) from this vencm. A PCA has been isolated by sulphopropyl-Sephadex followed by gel filtration chromatography resulting in approximately a 100-fold purification with a 50% yield. PCA appeared as a single band on SDS-PAGE with an estimated Mr of 32,000 or 37,000 in the absence or presence of β-mercaptoethanol, respectively. High pressure gel permeation cinematography of PCA in Tris-buffered saline, pH 7.5 resulted in a single protein peak with a Mr of 39,000 which was coincident with activity. PCA was a potent activator of human protein C (PC) with a Km for PC of 0.6uM and a Vm of 0.02 sec-1. In addition, PCA catalyzed the arnidolysis of Tosyl-gly-pro-arg-p-nitroanilide (TGPRpNA) with a Km of 1.1 irM and a Vim of 66 sec-1. The rate of arnidolysis of five other pept idyl-arginyl-pNA substrates each tested at 1.0 mM was < 10% that of TGPRpNA. PCA was inhibited by nitrophenylguanidi-nobenzoate (NPGB), phenylmethylsulphonylflouride, D-phe-pro-arg-chloromethyi_ketone (PPACK) and soybean trypsin inhibitor indicating that PCA is a serine protease. The active site concentration of PCA as measured by NPGB titration was 90% that of the protein concentration. Measurement of the rate of PCA inhibition at varying levels of PPACK indicated that it had a Ki of 34uM .and an aUcylation rate constant of 0.09 min-1. PCA activation of PC was completely inhibited by CaC12 with an apparent Ki of 99uM. Since neither PCA arnidolysis of TGPRpNA nor inhibition by PPACK was affected by Ca2+, the effect of this metal was likely on the substrate PC. In summary, a PCA has been purified to homogeneity and has properties which are distinct from those reported. PCA premises to be a useful enzyme in studies of PC and its activation.
Preliminary results of a novel approach for glucose regulation using an actor-critic learning based controller (2010)

In this paper, a novel approach for glucose regulation in individuals with type 1 diabetes mellitus is considered using the principles of adaptive reinforcement learning techniques. More specifically a controller based on Actor-Critic (AC) learning algorithm is used for the estimation of insulin infusion rate in adult patients using continuous glucose monitoring devices and insulin infusion pumps. Generally, AC algorithms are able to solve control problems of nonlinear, dynamic systems. Aim of the paper is to investigate the applicability of the AC learning method to the problem of glucose regulation and the feasibility to be used for an artificial pancreas. The implemented controller has been tested in an in silico environment. Preliminary results have shown that although the algorithm prevents hypoglycemic events, further research is needed in order to reduce the percentage of glucose concentration values over the acceptable normoglycaemia bound. Furthermore, open issues with the proposed algorithm have been identified, while the next research steps have been defined.
Obstruction-free synchronization: double-ended queues as an example (2004)

We introduce obstruction-freedom, a new nonblocking property for shared data structure implementations. This property is strong enough to avoid the problems associated with locks, but it is weaker than previous nonblocking properties-specifically lock-freedom and wait-freedom-allowing greater flexibility in the design of efficient implementations. Obstruction-freedom admits substantially simpler implementations, and we believe that in practice it provides the benefits of wait-free and lock-free implementations. To illustrate the benefits of obstruction-freedom, we present two obstruction-free CAS-based implementations of double-ended queues (deques); the first is implemented on a linear array, the second on a circular array. To our knowledge, all previous nonblocking deque implementations are based on unrealistic assumptions about hardware support for synchronization, have restricted functionality, or have operations that interfere with operations at the opposite end of the deque even when the deque has many elements in it. Our obstruction-free implementations have none of these drawbacks, and thus suggest that it is much easier to design obstruction-free implementations than lock-free and wait-free ones. We also briefly discuss other obstruction-free data structures and operations that we have implemented.
Development of Absorbable, Antibiotic-Eluting Sutures for Ophthalmic Surgery. (2017)

No antibiotic-eluting suture exists for ophthalmic surgery. A biocompatible, high strength suture capable of sustained antibiotic release could prevent ocular infection and preclude compliance issues with topical eye drops.
A<i>trans</i>-AB-Bacteriochlorin Building Block (2011)

Synthetic bacteriochlorins are of interest for fundamental studies in photochemistry because of their strong absorption in the near-infrared spectral region and close similarity with natural bacteriochlorophylls. A de novo route to 5-methoxybacteriochlorins entails self-condensation of a dihydrodipyrrin-acetal, which in turn is prepared from a 2-(2-nitroethyl)pyrrole species and an α,β-unsaturated ketone-acetal (e.g., 1,1-dimethoxy-4-methylpent-3-en-2-one). Here, four new results are reported concerning the synthesis of substituted bacteriochlorins. First, a new, scalable route to 1,1-dimethoxy-4-methylpent-3-en-2-one removes a significant previous impediment to the overall route. Second, the new route was employed to gain access to new α,β-unsaturated ketones and corresponding dihydrodipyrrins bearing alternative substituents in place of the dimethoxy unit. Third, a dihydrodipyrrin bearing a 1,3-dioxolan-2-yl moiety afforded the bacteriochlorin (30% yield) containing a 2-hydroxyethoxy substituent at the 5-position. Fourth, subsequent bromination proceeded regioselectively at the 15-position to give a trans-(5,15)-AB-bacteriochlorin building block. The linear 5,15-substitution pattern is attractive for a number of molecular designs. The results taken together afford deeper understanding of the scope and limitations of the de novo route and also advance the capabilities for tailoring synthetic bacteriochlorins.
Widely tunable picosecond optical parametric generation and amplification in BiB3O6 (2007)

Efficient generation of widely tunable picosecond pulses from the visible to near-infrared is demonstrated by optical parametric generation and amplification in BiB(3)O(6). Pumped by the second harmonic of an amplified mode-locked Nd:YAG laser at 532 nm, also generated in BiB(3)O(6), a signal and idler tuning range of 740-1893 nm has been achieved with angle tuning under type I (o?e+e) phase-matching in the optical yz-plane. With 40-ps pump pulses of 420-muJ energy, single-pass signal pulse energies of up to 48.6 muJ have been obtained at total OPA pump to signal and idler conversion efficiency as high as 30%. Significant temperature tuning under type I (o?e+e) noncritical interaction along the optical z-axis is also demonstrated, extending the signal tuning range from 740 nm down to 676 nm and idler tuning range from 1893 nm up to 2497 nm. Using second harmonic generation of the amplified signal pulses, also in BiB(3)O(6),wavelength extension to 370-500 nm has been achieved at 24% conversion efficiency, providing 10-muJ pulses across the tuning range. Optical parametric generation and amplification in BiB(3)O(6) under strong two-photon absorption pumped by 210-muJ pulses at 355 nm is also reported, providing amplified signal pulse energies of 14.2 muJ at OPA conversion efficiency as high as 21% and a spectral coverage across 450-1674 nm.
Advanced Heterojunction Structure of Polymer Photovoltaic Cell Generating High Photocurrent with Internal Quantum Efficiency Approaching 100% (2013)

An advanced heterojunction structure is introduced for polymer photovoltaic cells that can approach almost 100% internal quantum efficiency (IQE) even with over 300 nm thick electron-donor layer for adequate light absorption. These devices show superior charge transport properties as well as non-Langevin type bimolecular recombination. The resultant short circuit current of the device is about 50% higher than that of the thermally annealed BHJ polymer PV cell.
Generation of T-cell-redirecting bispecific antibodies with differentiated profiles of cytokine release and biodistribution by CD3 affinity tuning (2021)

T-cell-redirecting bispecific antibodies have emerged as a new class of therapeutic agents designed to simultaneously bind to T cells via CD3 and to tumor cells via tumor-cell-specific antigens (TSA), inducing T-cell-mediated killing of tumor cells. The promising preclinical and clinical efficacy of TSAxCD3 antibodies is often accompanied by toxicities such as cytokine release syndrome due to T-cell activation. How the efficacy and toxicity profile of the TSAxCD3 bispecific antibodies depends on the binding affinity to CD3 remains unclear. Here, we evaluate bispecific antibodies that were engineered to have a range of CD3 affinities, while retaining the same binding affinity for the selected tumor antigen. These agents were tested for their ability to kill tumor cells in vitro, and their biodistribution, serum half-life, and anti-tumor activity in vivo. Remarkably, by altering the binding affinity for CD3 alone, we can generate bispecific antibodies that maintain potent killing of TSA + tumor cells but display differential patterns of cytokine release, pharmacokinetics, and biodistribution. Therefore, tuning CD3 affinity is a promising method to improve the therapeutic index of T-cell-engaging bispecific antibodies.
Protein recognition by bivalent, ‘turn-on’ fluorescent molecular probes (2015)

We show that the conversion of a known intercalating dye (<i>i.e.</i>, thiazole orange) into a bivalent protein binder could lead to the realization of a novel class of 'turn-on' fluorescent molecular probes that detect proteins with high affinity, selectivity, and a high signal-to-noise (<i>S</i>/<i>N</i>) ratio. The feasibility of the approach is demonstrated with monomolecular probes that light-up in the presence of three different proteins: acetylcholinesterase (AChE), glutathione-<i>s</i>-transferase (GST), or avidin (Av) at low concentrations and with minimal background signal. The way by which such probes can be used to detect individual protein isoforms and be applied in inhibitor screening, cell imaging, and biomarker detection is described.
Low temperature direct growth of graphene patterns on flexible glass substrates catalysed by a sacrificial ultrathin Ni film (2016)

Direct deposition of graphene on substrates would avoid costly, time consuming and defect inducing transfer techniques. In this paper we used ultrathin films of Ni, with thickness ranging from 5 to 50 nm, as a catalytic surface on glass to seed and promote chemical vapor deposition (CVD) of graphene. Different regimes and dynamics were studied for various parameters including temperature and reaction time. When a critical temperature (700 °C) was reached, Ni films retracted and holes formed that are open to the glass surface, where graphene deposited. After CVD, the residual Ni could be etched away and the glass substrate with graphene regained maximum transparency (>90%). The fact that we could achieve low growth temperatures indicates the potential of the technique to widen the range of substrate materials over which graphene can be directly deposited. We demonstrated this by depositing graphene patterns on ultrathin, 100 μm thick, sheet of glass with low strain point (670 °C), particularly suitable for flexible electronic and optoelectronic devices.