gebhart/patrepeval huggingface dataset:
Conservation and Accessibility of an Inner Core Lipopolysaccharide Epitope of<i>Neisseria meningitidis</i> (1999)

We investigated the conservation and antibody accessibility of inner core epitopes of Neisseria meningitidis lipopolysaccharide (LPS) because of their potential as vaccine candidates. An immunoglobulin G3 murine monoclonal antibody (MAb), designated MAb B5, was obtained by immunizing mice with a galE mutant of N. meningitidis H44/76 (B. 15.P1.7,16 immunotype L3). We have shown that MAb B5 can bind to the core LPS of wild-type encapsulated MC58 (B.15.P1.7,16 immunotype L3) organisms in vitro and ex vivo. An inner core structure recognized by MAb B5 is conserved and accessible in 26 of 34 (76%) of group B and 78 of 112 (70%) of groups A, C, W, X, Y, and Z strains. N. meningitidis strains which possess this epitope are immunotypes in which phosphoethanolamine (PEtn) is linked to the 3-position of the beta-chain heptose (HepII) of the inner core. In contrast, N. meningitidis strains lacking reactivity with MAb B5 have an alternative core structure in which PEtn is linked to an exocyclic position (i.e., position 6 or 7) of HepII (immunotypes L2, L4, and L6) or is absent (immunotype L5). We conclude that MAb B5 defines one or more of the major inner core glycoforms of N. meningitidis LPS. These findings support the possibility that immunogens capable of eliciting functional antibodies specific to inner core structures could be the basis of a vaccine against invasive infections caused by N. meningitidis.
Spatio-Temporal Graph for Video Captioning with Knowledge Distillation (2020)

Video captioning is a challenging task that requires a deep understanding of visual scenes. State-of-the-art methods generate captions using either scene-level or object-level information but without explicitly modeling object interactions. Thus, they often fail to make visually grounded predictions, and are sensitive to spurious correlations. In this paper, we propose a novel spatio-temporal graph model for video captioning that exploits object interactions in space and time. Our model builds interpretable links and is able to provide explicit visual grounding. To avoid unstable performance caused by the variable number of objects, we further propose an object-aware knowledge distillation mechanism, in which local object information is used to regularize global scene features. We demonstrate the efficacy of our approach through extensive experiments on two benchmarks, showing our approach yields competitive performance with interpretable predictions.
Time and Frequency-Domain Spectroscopy with Dual Frequency Combs (2009)

High-resolution spectroscopic measurements of the amplitude and phase spectra from a gas sample can be acquired by use of dual frequency combs. Here we discuss the corresponding gas signature in the time domain.
Electrochemical Flow Capacitors: A New Concept for High-Power Scalable Energy Storage (2012)

Abstract not Available.
Molecular dynamics simulations of thrombin inhibitors at the S' subsites of thrombin. (1994)

Molecular dynamics were carried out to simulate binding interactions between S' subsites of thrombin and hirudin-based thrombin inhibitors. These inhibitors include three segments: an active-site segment, N alpha-acetyl-(D-Phe)-Pro-Arg-Pro-; a fibrinogen-recognition exo-site segment, hirudin 55-65; and a 13-atom-long linker. These linkers have been reported (Szewczuk et al. (1993) Biochemistry 32, 3396) to influence the binding potency while keeping the same active and exo-site segments. The study found that, by combining different omega-amino acids, the potency could be increased 8-fold or decreased 4-fold compared to the native hirudin linker, -Gln-Ser-His-Asn-Asp-Gly-. Five typical linkers were simulated and compared. Analyzing the trajectory files led to the classification of three different dynamic behaviours for the linkers. The flexible linkers had no influence on the antithrombin activity. Other linkers formed hydrogen bonds with the thrombin S' subsite residues Glu39, leu40, and Gln 151. Formations of some hydrogen bonds enhanced the potency of the inhibitor. In other cases, the hydrogen bonds caused the distortion of the inhibitor conformation while affected the binding potency. Based on these observations, a general binding mode in the S' subsites of thrombin is proposed and potential applications are discussed.
Ultrashort electrical pulses open a new gateway into biological cells (2004)

An electrical model for biological cells predicts that for pulses with durations shorter than the charging time of the outer membrane, there is an increasing probability of electric field interactions with intracellular structures. Experimental studies in which human cells were exposed to pulsed electric fields of up to 300-kV/cm amplitude, with durations as short as 10 ns, have confirmed this hypothesis. The observed effects include the breaching of intracellular granule membranes without permanent damage to the cell membrane, abrupt rises in intracellular free calcium levels, and enhanced expression of genes. At increased electric fields, the application of submicrosecond pulses induces apoptosis (programmed cell death) in biological cells, an effect that has been shown to reduce the growth of tumors. Possible applications of the intracellular electroeffect are enhancing gene delivery to the nucleus, controlling cell functions that depend on calcium release (causing cell immobilization), and treating tumors.
3D pulsed laser-triggered high-speed microfluidic fluorescence-activated cell sorter (2013)

We report a 3D microfluidic pulsed laser-triggered fluorescence-activated cell sorter capable of sorting at a throughput of 23 000 cells per s with 90% purity in high-purity mode and at a throughput of 45 000 cells per s with 45% purity in enrichment mode in one stage and in a single channel. This performance is realized by exciting laser-induced cavitation bubbles in a 3D PDMS microfluidic channel to generate high-speed liquid jets that deflect detected fluorescent cells and particles focused by 3D sheath flows. The ultrafast switching mechanism (20 μs complete on-off cycle), small liquid jet perturbation volume, and three-dimensional sheath flow focusing for accurate timing control of fast (1.5 m s(-1)) passing cells and particles are three critical factors enabling high-purity sorting at high-throughput in this sorter.
SiMPLE: Survivability in multi-path link embedding (2015)

Internet applications are deployed on the same network infrastructure, yet they have diverse performance and functional requirements. The Internet was not originally designed to support the diversity of current applications. Network Virtualization can enable heterogeneous applications and network architectures to coexist without interference on the same infrastructure. Embedding a Virtual Network (VN) into a physical network is a fundamental problem in Network Virtualization. A VN Embedding that aims to survive physical (e.g., link) failures is known as the Survivable Virtual Network Embedding (SVNE). A key challenge in the SVNE problem is to ensure VN survivability with minimal resource redundancy. To address this challenge, we propose SiMPLE. By exploiting path diversity in the physical network, SiMPLE provides guaranteed VN survivability against single link failure. In addition, SiMPLE produces highly surviv-able VN embeddings in presence of multiple link failures while incurring very low resource redundancy. We provide an ILP formulation for this problem and implement it using GLPK. We also propose a greedy algorithm to solve larger instances of the problem. Simulation results show that our solution outperforms full backup and shared backup schemes for SVNE, and produces near-optimal results.
HEAT FLOW MODELING OF HVAC SYSTEMS FOR FAULT DETECTION AND DIAGNOSIS (2010)

We present a new graph-based modeling methodology called Heat Flow Modeling (HFM) for HVAC system fault detection and diagnosis. It aims at using the mod- ularity of graphs to achieve a direct automated mapping of HVAC structures and components into HFM graphs and to use node behavior model and software libraries to translate HFM graphs into software systems that can be directly integrated in HVAC control systems. The function of the graph is on one hand a simplified per- formance simulation, on the other hand a failure rule evaluation. The graph structure allows for central or distributed implementations. Prototype implementations in Simulink and in a software specification language have been performed.
Employing fusion of learned and handcrafted features for unconstrained ear recognition (2018)

The authors present an unconstrained ear recognition framework that outperforms state‐of‐the‐art systems in different publicly available image databases. To this end, they developed convolutional neural network (CNN)‐based solutions for ear normalisation and description, they used well‐known handcrafted descriptors, and they fused learned and handcrafted features to improve recognition. They designed a two‐stage landmark detector that successfully worked under untrained scenarios. They used the results generated to perform a geometric image normalisation that boosted the performance of all evaluated descriptors. The proposed CNN descriptor outperformed other CNN‐based works in the literature, especially in more challenging scenarios. The fusion of learned and handcrafted matchers appears to be complementary and achieved the best performance in all experiments. The obtained results outperformed all other reported results for the Unconstrained Ear Recognition Challenge, which contains the most difficult database nowadays.
Extending fault periodicity table for testing faults in memories under 20nm (2014)

A new solution for building memory BIST infrastructure, based on rules of fault periodicity and regularity in test algorithms was introduced recently. These rules are represented in a form of a Fault Periodicity Table (FPT) considering both known and unknown memory faults in one table. Each column of FPT corresponds to a fault nature which can be associated with a variety of different test mechanisms while each row of FPT corresponds to a fault family determined by the complexity of fault sensitization. In this paper, application of the proposed methodology for description of memory faults in technologies below 20nm, including 16/14nm FinFET-based memories, is shown. Specifically, it is shown that all recently discovered FinFET-specific faults successfully fit into FPT.
Cold Sintering: Progress, Challenges, and Future Opportunities (2019)

Cold sintering is an unusually low-temperature process that uses a transient transport phase, which is most often liquid, and an applied uniaxial force to assist in densification of a powder compact. By using this approach, many ceramic powders can be transformed to high-density monoliths at temperatures far below the melting point. In this article, we present a summary of cold sintering accomplishments and the current working models that describe the operative mechanisms in the context of other strategies for low-temperature ceramic densification. Current observations in several systems suggest a multiple-stage densification process that bears similarity to models that describe liquid phase sintering. We find that grain growth trends are consistent with classical behavior, but with activation energy values that are lower than observed for thermally driven processes. Densification behavior in these low-temperature systems is rich, and there is much to be investigated regarding mass transport within and across the liquid-solid interfaces that populate these ceramics during densification. Irrespective of mechanisms, these low temperatures create a new opportunity spectrum to design grain boundaries and create new types of nanocomposites among material combinations that previously had incompatible processing windows. Future directions are discussed in terms of both the fundamental science and engineering of cold sintering.
Differentially Private Oblivious RAM (2018)

Abstract In this work, we investigate if statistical privacy can enhance the performance of ORAM mechanisms while providing rigorous privacy guarantees. We propose a formal and rigorous framework for developing ORAM protocols with statistical security viz., a differentially private ORAM (DP-ORAM). We present Root ORAM, a family of DP-ORAMs that provide a tunable, multi-dimensional trade-off between the desired bandwidth overhead, local storage and system security. We theoretically analyze Root ORAM to quantify both its security and performance. We experimentally demonstrate the benefits of Root ORAM and find that (1) Root ORAM can reduce local storage overhead by about 2× for a reasonable values of privacy budget, significantly enhancing performance in memory limited platforms such as trusted execution environments, and (2) Root ORAM allows tunable trade-offs between bandwidth, storage, and privacy, reducing bandwidth overheads by up to 2×-10× (at the cost of increased storage/statistical privacy), enabling significant reductions in ORAM access latencies for cloud environments. We also analyze the privacy guarantees of DP-ORAMs through the lens of information theoretic metrics of Shannon entropy and Min-entropy [16]. Finally, Root ORAM is ideally suited for applications which have a similar access pattern, and we showcase its utility via the application of Private Information Retrieval.
Advanced Techniques for Signal and Image Compression/Reconstruction with Wavelets. (1995)

Abstract : This document presents wavelet based techniques and its application in the undersea environment for data compression. Performance comparisons with other traditional data compression/reconstruction techniques are made. The energy based method for wavelet coefficient selection is introduced. Performance comparison between global threshold and energy based methods are presented. (MM)
New Surface Capacitive Touchscreen Technology To Detect DNA (2016)

A new surface capacitive touchscreen technology to detect DNA has been developed. In this approach, advantage is taken of the fact that a signal location is determined by the relative conductivities of touching materials at two points that are simultaneously touched. In the system, buffer and target-specific probe solutions are first applied to two separate positions on the touch panel. The target DNA sample is then applied to both positions. Based on the fact that the electrical conductivity of ssDNA is different from that of dsDNA, a hybridization taking place between the probe and target DNA can be identified by determining the location of the resulting touching signal. A mathematical treatment was employed to model the new detecting principle. By using equations derived from this treatment, the experimental results were correctly estimated. Because the new technology utilizes a simple touchscreen, it should be applicable to the development of POCT or personalized medical devices.
Highly Luminescent Bulk Quantum Materials Based on Zero-Dimensional Organic Tin Halide Perovskites (2017)

Bulk quantum materials based on zero-dimensional (0D) lead-free organic tin halide perovskites have been developed for the first time, which give broadband Gaussian-shaped and strongly Stokes shifted emissions with quantum efficiencies of up to near-unity at room temperature due to excited state structural reorganization.
Liquid Crystal Active Glasses for 3D Cinema (2010)

Liquid crystals have been extensively studied and are massively used in display technology. Their recent use to provide optical shutters in active glasses for 3D cinema has focused the attention on new specific requirements. Recent improvements in the quality of 3D movies production and projection (e.g., involving triple flash projectors) resulted in the need for high quality glasses with no ghosting, no color banding, large viewing angle and good residual light. We present here the main relevant parameters to assess the quality required today by the studios and we compare the main liquid crystal options which can be used with their respective advantages.
Diastereoselective 14β-Hydroxylation of Baccatin III Derivatives (2003)

14beta-Hydroxybaccatin III, a compound with limited availability by natural sources, is the starting material for the synthesis of the second-generation anticancer taxoid ortataxel. The 7-tert-butoxycarbonyl (1a) and 7-triethylsilyl (1b) derivatives of 14beta-hydroxybaccatin III 1,14-carbonate were synthesized from 10-deacetylbaccatin III (3). The crucial steps were (a) the C(14)beta hydroxylation of the corresponding 13-oxobaccatin III derivatives by oxaziridine-mediated electrophilic oxidation and (b) the reduction of the C(13) carbonyl group with sodium or alkylammonium borohydrides. This protocol provides a practical way for the semisynthesis of ortataxel from 10-deacetylbaccatin III, a compound readily available from various yews.
Abstract 5487: Targeting glycolysis for the treatment of cancer (2018)

Abstract Tumors exhibit markedly increased glucose uptake and glycolysis and this metabolic phenotype serves to satisfy their increased requirement for energy and biosynthetic intermediates. Tumor glucose metabolism is stimulated in part by fructose-2,6-bisphosphate (F26BP), which is the product of a family of 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatases (PFKFB1-4) and allosterically activates a key glycolytic enzyme, 6-phosphofructo-1-kinase (PFK-1). Previous studies have found the PFKFB3 family member to be a dominant source of F26BP in cancer cells due to a high kinase activity, expression in multiple tumor types and the inhibition of tumor growth by specific PFKFB3 inhibitors including a compound, PFK158, that is currently under evaluation in a phase I trial. Recent data, however, indicate that the PFKFB4 enzyme plays a significant role in regulating glucose metabolism in neoplastic cells. We have found that PFKFB4 is highly expressed in multiple cancers, strongly induced by HIF-1α, and that its suppression markedly reduced F26BP and glycolytic flux, increased apoptosis and inhibited growth of xenograft tumors in vivo, thus providing strong rationale for the development of antineoplastic agents selectively targeting PFKFB4. Using virtual screening, we have discovered a first-in-class small molecule inhibitor of PFKFB4, termed 5MPN, that selectively inhibits recombinant PFKFB4 activity with a resultant decrease in F26BP, glycolytic flux and cancer cell growth in vitro and markedly reduces the growth of established tumors without systemic toxicity. During our studies, we unexpectedly observed that PFKFB4 expression is increased by PFKFB3 inhibition, suggesting that PFKFB4 may compensate for decreased PFKFB3 expression and activity. We examined the effects of simultaneous silencing of PFKFB4 and PFKFB3 on cancer cell lines and found that co-knockdown led to a significant decrease in cell viability and glycolysis and to a near-complete abrogation of anchorage-independent growth in vitro. We additionally examined the effect of simultaneous inhibition of PFKFB4 and PFKFB3 using 5MPN and several PFKFB3 inhibitors in vitro and found a synergistic increase in cell death. Taken together, our data indicate that targeting PFKFB4 may be a viable therapeutic option against cancer and strongly support the further development of PFKFB4 small-molecule inhibitors as well as the co-targeting of PFKFB4 and PFKFB3 as potential strategies for the treatment of cancer. Citation Format: Jason Chesney, Aubrey Mojesky, Yoannis Imbert-Fernandez, John Trent, Sucheta Telang. Targeting glycolysis for the treatment of cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 5487.
Convex hull based neuro-retinal optic cup ellipse optimization in glaucoma diagnosis (2009)

Glaucoma is the second leading cause of blindness. Glaucoma can be diagnosed through measurement of neuro-retinal optic cup-to-disc ratio (CDR). Automatic calculation of optic cup boundary is challenging due to the interweavement of blood vessels with the surrounding tissues around the cup. A Convex Hull based Neuro-Retinal Optic Cup Ellipse Optimization algorithm improves the accuracy of the boundary estimation. The algorithm's effectiveness is demonstrated on 70 clinical patient's data set collected from Singapore Eye Research Institute. The root mean squared error of the new algorithm is 43% better than the ARGALI system which is the state-of-the-art. This further leads to a large clinical evaluation of the algorithm involving 15 thousand patients from Australia and Singapore.
Phospho-kinase profile of colorectal tumors guides in the selection of multi-kinase inhibitors (2015)

Protein kinases play a central role in the oncogenesis of colorectal tumors and are attractive druggable targets. Detection of activated kinases within a tumor could open avenues for drug selection and optimization of new kinase inhibitors. By using a phosphokinase arrays with human colorectal tumors we identified activated kinases, including the Epidermal Growth Factor Receptor (EGFR), components of the PI3K/mTOR pathway (AKT and S6), and STAT, among others. A pharmacological screening with kinase inhibitors against these proteins helped us to identify a new kinase inhibitor, termed EC-70124 that showed the highest anti-proliferative activity in cell lines. EC-70124 also inhibited cell migration and biochemical experiments demonstrated its effect targeting the PI3K/mTOR pathway. This drug also arrested cells at G2/M and induced apoptosis. Experiments in combination with standard chemotherapy used in the clinical setting indicated a synergistic effect. EC-70124 also reduced tumor growth in vivo and inhibited pS6 in the implanted tumors. In conclusion, by studying the kinase profile of colorectal tumors, we identified relevant activated pathways, and a new multi-kinase compound with significant antitumor properties.
Overview of the Development of Hydrazinium Nitroformate-Based Propellants (2002)

Recent improvements in thequality ofhydrazinium nitroformate (HNF)and binderpolymerdevelopmentshave shown that it is possible to produce HNF-based propellants with hydroxyl-terminated polybutadiene (HTPB), glycidylazidepolymer (GAP),andpoly3‐nitromethoxy ‐3‐methyloxetane[polynimmo (PNM)]asbinders.Especially when considering space applications, HNF-based propellants show results that encourage further research and development. An alternative method to cure GAP has been evaluated. This curing method eliminates the use of isocyanates, which always require special attention when used together with HNF. Combustion studies, experimental and theoretical, led to a good understanding of the steady-state combustion of HNF/GAP sandwiches and HNF/GAP propellants. Burning-rate modie ers have been identie ed, which lower the burning-rate exponent in GAP/HNF propellants by at least 25%. HNF/GAP and HNF/PNM propellants have a low temperature sensitivity. Liquid HNF monopropellants look attractive as a hydrazine replacement. They offer the same or a substantially higher Isp, combined with a 30 ‐40% higher density. The progress made in the manufacture of HNF and the HNF-based propellants (solid and liquid ) was possible through extensive international cooperation.