gebhart/patrepeval huggingface dataset:
Synthesis and Characterization of Aryl Ethynyl Terminated Liquid Crystalline Oligomers and Their Cured Polymers (2006)

In this paper the synthesis and characterization of two series wholly aromatic, main-chain, reactive liquid crystalline oligomers is reported. Phenylethynyl end-capped oligomers, based on 4-hydroxybenzoic acid (HBA) and 6-hydroxy-2-naphthoic acid (HNA), were successfully synthesized using standard high-temperature melt-condensation techniques. Melt processable oligomers, with Mn = 1000, 5000, 9000, and 13 000 g mol-1, and oligomers with HBA or HNA concentrations as high as 95 mol % were prepared. All oligomers showed well-defined, homogeneous, nematic melt behavior over a broad temperature range. The phenylethynyl end-capped oligomers could be cured at 370 °C and formed films with excellent mechanical and thermal properties, and without losing the nematic order. Low molecular weight oligomers, i.e. Mn < 5000 g mol-1, tend to form nematic thermosets, while oligomers with Mn > 5000 g mol-1, polymerize predominantly via chain extension chemistry. The fully cured nematic polymers exhibit glass-transition temperatures (Tg) up to 203 °C, as determined by DMTA measurements, and thermal stabilities (5 wt % loss) up to 500 °C in both air and nitrogen atmosphere. The cured 1000 and 5000 g mol-1 oligomers, with 95 mol % HBA or HNA compositions, show significant improvements in storage modulus at elevated temperatures as compared to their high-molecular weight counterparts. Rheology experiments showed that these reactive nematic oligomers are melt-stable for at least 30 min at 300 °C and exhibit complex melt viscosities |η*| as low as 1 Pa·s at 100 rad·s-1. In all examples no loss of mesophase could be observed during chain extension or cross-linking, which indicates that phenylethynyl cross-link chemistry is completely compatible with mesophase formation.
Plasmalemmal vesicle‐associated protein (PLVAP) is expressed by tumour endothelium and is upregulated by vascular endothelial growth factor‐A (VEGF) (2005)

Vascular endothelial growth factor-A (VEGF) is an important regulator of vascular permeability. In preclinical studies, VEGF induces endothelial fenestrations in pre-existing and neo-vasculature, while inhibition of VEGF leads to a reduction in endothelial fenestrations. Recently, vascular regression in response to VEGF inhibition has been shown to correlate with the presence of endothelial fenestrations. Plasmalemmal vesicle-associated protein (PLVAP) is believed to be a component of diaphragmed endothelial fenestrations, but a direct relationship with VEGF signalling has not been established. The aim of this study was to characterize the expression pattern of PLVAP and investigate whether PLVAP is a transcriptional target of VEGF signal transduction. The expression pattern of PLVAP was characterized in normal and neoplastic human tissues by in situ hybridization and/or immunohistochemistry. The role of VEGF signal transduction in the regulation of PLVAP expression was investigated in vitro using receptor-selective engineered forms of VEGF, a neutralizing monoclonal antibody against VEGF, and inhibitors of downstream signalling pathways. PLVAP mRNA and protein were widely expressed in the endothelium of normal and neoplastic tissues. In cultured endothelial cells, VEGF signalling through receptor 2 stimulated expression of PLVAP total RNA and protein. This induction could be blocked with an anti-VEGF monoclonal antibody and by inhibitors of phosphatidylinositol 3-kinase (LY294002) or p38 mitogen-activated protein kinase (SB203580), but not by PD98059, a mitogen-activated protein/extracellular signal-regulated kinase 1 inhibitor. These data show that PLVAP is more widely expressed in the vasculature of normal tissues than previously thought and that it is expressed in the vasculature of most human tumours. We suggest that PLVAP is a downstream target of VEGF signalling. This work solidifies the association between VEGF and the appearance and maintenance of fenestrations by providing a potential mechanistic link.
Induction of Unresponsiveness to Tumor Necrosis Factor (TNF) after Autocrine TNF Expression Requires TNF Membrane Retention (1998)

Tumor necrosis factor (TNF) has a specific gene-inducing activity on many cell types and exerts a cytotoxic effect on a number of tumor cell lines. However, several tumor cell types are resistant to TNF-induced effects, and some of these produce TNF. We previously demonstrated that introduction of an exogenous TNF gene in the TNF-sensitive cell line L929sA induced autocrine TNF production and unresponsiveness to the cytotoxic activity of TNF. This resistance required biologically active TNF and was correlated with complete down-modulation of the TNF receptors on the cell surface. We have now characterized this process in more detail. The role of expression of the membrane-bound TNF proform and its subsequent proteolytic processing in the induction of TNF unresponsiveness was investigated. Exchange of the TNF presequence for the signal sequence of interleukin-6 resulted in production of secreted TNF, but not in induction of TNF resistance. On the other hand, expression of non-secretable, membrane-bound TNF generated complete TNF unresponsiveness. To explore whether the requirement for anchoring reflected a specific functional role of the TNF presequence, the latter was replaced by the membrane anchor of trimeric chicken hepatic lectin. Expression of this construct induced complete TNF unresponsiveness. Hence, the role of the TNF presequence in the induction of TNF unresponsiveness only involves its function as a membrane anchor, which permits oligomerization of the TNF molecule into a biologically active homotrimer.
Photographing long scenes with multi-viewpoint panoramas (2006)

We present a system for producing multi-viewpoint panoramas of long, roughly planar scenes, such as the facades of buildings along a city street, from a relatively sparse set of photographs captured with a handheld still camera that is moved along the scene. Our work is a significant departure from previous methods for creating multi-viewpoint panoramas, which composite thin vertical strips from a video sequence captured by a translating video camera, in that the resulting panoramas are composed of relatively large regions of ordinary perspective. In our system, the only user input required beyond capturing the photographs themselves is to identify the dominant plane of the photographed scene; our system then computes a panorama automatically using Markov Random Field optimization. Users may exert additional control over the appearance of the result by drawing rough strokes that indicate various high-level goals. We demonstrate the results of our system on several scenes, including urban streets, a river bank, and a grocery store aisle.
Point estimation for jump Markov systems: Various MAP estimators (2009)

In this paper we will provide methods to calculate different types of Maximum A Posteriori (MAP) estimators for jump Markov systems. The MAP estimators that will be provided are calculated on the basis of a running Particle Filter (PF). Furthermore, we will provide convergence results for these approximate, or particle based estimators. We will show that the approximate estimators convergence in distribution to the true MAP values of the stochastic variables. Additionally, we will provide an example based on tracking closely spaced objects in a binary sensor network to illustrate some of the results and show their applicability.
Anticoagulants (2021)

Abstract Although blood circulation is highly regulated, dysfunctional activities resulting from either deficient or excessive coagulation have serious health consequences. Insufficient clotting can lead to prolonged bleeding and hemophilia‐related conditions. Over activation of coagulation can lead to thrombosis‐related disorders, such as deep venous thrombosis, pulmonary embolism, and stroke, which together are a major cause of morbidity and mortality. Studies of the biological pathways leading to coagulation, and the resultant development and refinement of the coagulation cascade, have identified many potential biological targets for therapeutic intervention. The major challenge regarding the treatment and prevention of thromboembolic diseases is the requirement for effective anticoagulant therapy without exposing patients to an increased risk of bleeding. Preclinical and clinical evaluations of anticoagulant agents highlight this efficacy/bleeding dichotomy. This article presents the medicinal chemistry efforts leading to the discovery of inhibitors of the coagulation cascade, resulting in marketed thrombin and Factor Xa inhibitors. Also reported is the progress toward identifying emerging anticoagulants.
Algorithms for fault-tolerant distributed systems. Final technical report, February 1985-February 1988 (1989)

The research described is presented in six parts: (1) Interprocess Communication studies interprocess communication without assuming any lower-level communication primitives. A formalism is developed for reasoning about concurrent systems that does not assume an atomic grain of action; (2) The Intersecting Broadcast Machine is a novel array processor architecture, capable of processing efficiently programs whose arbitrary or complex structure would make them difficult to map onto conventional array processors. The architecture also supports fault-tolerant operation: (3) Broadcast Protocols for Distributed Systems considers how the broadcast character of communications media such as Ethernet and packet radio can be exploited to yield reliable communication with very little overhead; (4) Extending Interval Logic to Real Time Systems presents a technique for the formal expression of the real-time constraints that are critical to the specification of fault-tolerant distributed systems; (5) Consistency of Replicated Information in Multichannel Fault Tolerant Systems considers the possibility of using similar, but not identical, processing in the replicas of a fault-tolerant system. Conventional fault-tolerant systems using replicate processing require the replicas to be identical, so that they can be compared by exact match algorithms. This exact replication increases the risk that a common fault will affect all replicas and causemore » system failure; and (6) Experimental Implementation and Evaluation of the TRANS Broadcast Protocol describes an implementation and evaluation of the broadcast protocol outlined in Part III.« less
Analog Signal Processing with Organic FETs (2006)

Regular and differential amplifiers as well as differential-to-single-ended circuits based on organic FETs (OFETs) are demonstrated. A numerical OFET model suitable for analog design is developed. Unity-gain bandwidths in excess of 1.4kHz and DC-gains of 10dB are achieved
Intra-operative brain tumor detection with deep learning-optimized hyperspectral imaging (2023)

Surgery for gliomas (intrinsic brain tumors), especially when low-grade, is challenging due to the infiltrative nature of the lesion. Currently, no real-time, intra-operative, label-free and wide-field tool is available to assist and guide the surgeon to find the relevant demarcations for these tumors. While marker-based methods exist for the high-grade glioma case, there is no convenient solution available for the low-grade case; thus, marker-free optical techniques represent an attractive option. Although RGB imaging is a standard tool in surgical microscopes, it does not contain sufficient information for tissue differentiation. We leverage the richer information from hyperspectral imaging (HSI), acquired with a snapscan camera in the 468 − 787 nm range, coupled to a surgical microscope, to build a deep-learning-based diagnostic tool for cancer resection with potential for intra-operative guidance. However, the main limitation of the HSI snapscan camera is the image acquisition time, limiting its widespread deployment in the operation theater. Here, we investigate the effect of HSI channel reduction and pre-selection to scope the design space for the development of cheaper and faster sensors. Neural networks are used to identify the most important spectral channels for tumor tissue differentiation, optimizing the trade-off between the number of channels and precision to enable real-time intra-surgical application. We evaluate the performance of our method on a clinical dataset that was acquired during surgery on five patients. By demonstrating the possibility to efficiently detect low-grade glioma, these results can lead to better cancer resection demarcations, potentially improving treatment effectiveness and patient outcome.
Brain and Spinal Cord Distribution of Biphalin: Correlation with Opioid Receptor Density and Mechanism of CNS Entry (1997)

Biphalin [(Tyr-D-Ala-Gly-Phe-NH)2] is a bivalent, opioid peptide containing two pharmacophores linked by a hydrazine bridge. When administered intracerebroventricularly, it has been shown to be more potent than morphine and etorphine at eliciting antinociception. Biphalin has also been shown to cross both the blood-brain and blood-cerebrospinal fluid barriers. To understand the basis of biphalin's potency, regional brain and spinal cord distribution studies with [125I-Tyr1]biphalin were performed 5, 20, and 40 min after intravenous bolus injections. A statistically greater amount of [125I-Tyr1]biphalin was detected in the nucleus accumbens compared with other brain regions (p < 0.05). This correlates with the high density of delta- and mu-opioid receptor mRNA and binding sites shown to be expressed in the nucleus accumbens. Also, a statistically greater amount of [125I-Tyr1] biphalin was detected in two other circumventricular organs, the choroid plexus and pituitary, when compared with other brain regions. These studies provide evidence that biphalin can reach not only brain sites, but also spinal sites to elicit antinociception. The overall CNS distribution of [125I-Tyr1]biphalin was decreased with naloxone, D-Phe-Cys-Tyr-D-Trp-Arg-Thr-Pen-Thr-NH2, or naltrindole pretreatment, showing that biphalin detected in the brain and spinal cord is binding to delta- and mu-opioid receptors. Additional in situ brain perfusion experiments identified a saturable component contributing to CNS entry of [125I-Tyr1]biphalin, which could be described by Michaelis-Menten kinetics with a Km of 2.6 +/- 4.8 microM, Vmax of 14.6 +/- 2.89 pmol(-1) x min(-1) x g(-1), and Kd of 0.568 +/- 0.157 microl x min(-1) x g(-1). Brain entry of [125I-Tyr1]biphalin was sensitive to 2-aminobicyclo[2.2.1]heptane-2-carboxylic acid and L-phenylalanine, suggesting use of the large neutral amino acid carrier. This work provides evidence that biphalin is a promising, potent analgesic that has a unique mechanism for reaching both spinal and supraspinal opioid receptor sites.
ALRED Blues: New Attacks on AES-Based MAC's. (2011)

Abstract. The ALRED family of Message Authentication Codes (MACs) is based on three principles: Using a keyless block cipher in CBC mode to process the message, choosing AES-128 as this cipher, and reducing the effective number of rounds to 4 in order to speed up the processing. In this paper we show that each one of these principles creates significant weaknesses. More specifically, we show that any ALRED-typeMAC which uses a keyless block cipher is vulnerable to new time/memory tradeoff attacks which are faster than generic tradeoff attacks on one-way functions. We then use the special properties of keyless AES to attack any number of rounds (4, 10, or a million) by forging the MAC of essentially any desired message in negligible time and space after a one-time preprocessing stage requiring 2 96 time and negligible space. For the recommended 4-round version we show how to do the same using an improved preprocessing stage with a semi-practical time complexity of 2 65, which is the best one can hope for in such MAC constructions. Finally, we show that even if we replace the 4-round keyless AES by a 5-round or a 6-round version with additional secret round keys we can still compute such MACs much faster than via exhaustive search. 1
An architecture for stable, analyzable Internet routing (1999)

In today's Internet, individuals, campuses, and organizations obtain IP connectivity from transit providers. Internet interprovider routing is governed by bilateral traffic exchange agreements between providers. Such independently established policies can adversely impact the stability and analyzability of Internet routing. We describe an architecture for coordinating Internet routing policies. This architecture allows providers to publish high-level specifications of their policies, and to analyze the effects of their policies on Internet routing. Several pieces of the architecture have been implemented and are in production use; we also discuss the experiences gleaned from these deployments.
Experimental Characterization of Low-Latency Multiple and Tunable Delays of Wideband Analog LFM Signal Using Concatenated Linearly Chirped and Sampled FBGs (2019)

Concatenated chirped and sampled fiber Bragg gratings are used to simultaneously generate multiple wavelength-tunable delayed versions of a wide bandwidth (10GHz) analog linear-frequency-modulated (LFM) pulse. We measured peak sidelobe level (PSL) &gt; 31 dB.
DAIS-ITA scenario (2019)

Ongoing research with The International Technology Alliance in Distributed Analytics and Information Sciences (DAIS-ITA) aims to enable secure, dynamic, semantically-aware, distributed analytics for deriving situational understanding in future coalitions. This paper sets out an example military scenario and operations in a future time frame, to capture the expected battlespace context and key future challenges. Key considerations involve complex multi-actor situations, high complexity information, high tempo processing, all within human-machine hybrid-teams. The coalition composition of these teams is critical and all resources will be constrained. A phased operation is proposed across rural and urban operation involving a range of ISR sensors and autonomous devices. All these are subject to enemy action and perturbation and must be used across a highly contested and congested electromagnetic spectrum. Agile command and control is required across the coalition with information arriving from multiple sources and partners that may also be utilised for learning.
Unspecific CTL Killing Is Enhanced by High Glucose via TNF-Related Apoptosis-Inducing Ligand (2022)

TNF-related apoptosis inducing ligand (TRAIL) is expressed on cytotoxic T lymphocytes (CTLs) and TRAIL is linked to progression of diabetes. However, the impact of high glucose on TRAIL expression and its related killing function in CTLs still remains largely elusive. Here, we report that TRAIL is substantially up-regulated in CTLs in environments with high glucose (HG) both <i>in vitro</i> and <i>in vivo</i>. Non-mitochondrial reactive oxygen species, NFκB and PI3K/Akt are essential in HG-induced TRAIL upregulation in CTLs. TRAIL<sup>high</sup> CTLs induce apoptosis of pancreatic beta cell line 1.4E7. Treatment with metformin and vitamin D reduces HG-enhanced expression of TRAIL in CTLs and coherently protects 1.4E7 cells from TRAIL-mediated apoptosis. Our work suggests that HG-induced TRAIL<sup>high</sup> CTLs might contribute to the destruction of pancreatic beta cells in a hyperglycemia condition.
Altered promoter usage characterizes monoallelic transcription arising with ERBB2 amplification in human breast cancers (2006)

Analysis of a collection of human breast cancers (n = 150), enriched in ERBB2-positive cases (n = 57) and involving tumor genotyping relative to population-matched blood genotyping (n = 749) for a common ERBB2 single nucleotide polymorphism Ala(G)1170Pro(C), revealed that ERBB2 amplification in breast cancer is invariably monoallelic. Analysis of paired breast cancer and blood samples from informative (G1170C heterozygotic) ERBB2-positive (n = 12) and ERBB2-negative (n = 17) cases not only confirmed monoallelic amplification and ERBB2 transcriptional overexpression but also revealed that most low ERBB2 expressing breast cancers (12/17) exhibit unbalanced allelic transcription, showing 3-fold to nearly 5,000-fold preferential expression from one of two inherited alleles. To explore cis-acting transcriptional mechanisms potentially selected during ERBB2 amplification, levels of four different ERBB2 transcript variants (5.2, 4.7, 2.1, and 1.4 kb) were correlated with total (4.6 kb) ERBB2 mRNA levels in ERBB2-positive (n = 14) versus ERBB2-negative (n = 43) primary breast cancers. Relative expression of only the 2.1 kb extracellular domain-encoding splice variant and a 4.7 kb mRNA variant that uses an alternative start site were significantly increased in association with ERBB2-positivity, implicating altered promoter usage and selective transcript regulation within the ERBB2 amplicon. Altogether, these findings provide new mechanistic insights into the development of ERBB2-positive breast cancer and strong rationale for delineating candidate cis-acting regulatory elements that may link allele-specific ERBB2 transcription in premalignant breast epithelia with subsequent development of breast cancers bearing monoallelic ERBB2 amplicons.
Development of Integrated Systems for On-Site Infection Detection (2021)

The modern healthcare system faces an unrelenting threat from microorganisms, as evidenced by global outbreaks of new viral diseases, emerging antimicrobial resistance, and the rising incidence of healthcare-associated infections (HAIs). An effective response to these threats requires rapid and accurate diagnostic tests that can identify causative pathogens at the point of care (POC). Such tests could eliminate diagnostic uncertainties, facilitating patient triaging, minimizing the empiric use of antimicrobial drugs, and enabling targeted treatments. Current standard methods, however, often fail to meet the needs of rapid diagnosis in POC settings. Culture-based assays entail long processing times and require specialized laboratory infrastructure; nucleic acid (NA) tests are often limited to centralized hospitals due to assay complexity and high costs. Here we discuss two new POC tests developed in our groups to enable the rapid diagnosis of infection. The first is nanoPCR that takes advantages of core-shell magnetoplasmonic nanoparticles (MPNs): (i) Au shell significantly accelerates thermocycling via volumetric, plasmonic light-to-heat conversion and (ii) a magnetic core enables sensitive <i>in situ</i> fluorescent detection via magnetic clearing. By adopting a Ferris wheel module, the system expedites multisamples in parallel with a minimal setup. When applied to COVID-19 diagnosis, nanoPCR detected SARS-CoV-2 RNA down to 3.2 copy/μL within 17 min. In particular, nanoPCR diagnostics accurately identified COVID-19 cases in clinical samples (<i>n</i> = 150), validating its clinical applicability. The second is a polarization anisotropy diagnostic (PAD) system that exploits the principle of fluorescence polarization (FP) as a detection modality. Fluorescent probes were designed to alter their molecular weight upon recognizing target NAs. This event modulates the probes' tumbling rate (Brownian motion), which leads to changes in FP. The approach is robust against environmental noise and benefits from the ratiometric nature of the signal readout. We applied PAD to detect clinically relevant HAI bacteria (<i>Escherichia coli</i>, <i>Klebsiella pneumoniae</i>, <i>Acinetobacter baumannii</i>, <i>Pseudomonas aeruginosa</i>, and <i>Staphylococcus aureus</i>). The PAD assay demonstrated detection sensitivity down to the single bacterium level and determined both drug resistance and virulence status. In summary, these new tests have the potential to become powerful tools for rapid diagnosis in the infectious disease space. They do not require highly skilled personnel or labor-intensive analyses, and the assays are quick and cost-effective. These attributes will make nanoPCR and PAD well-aligned with a POC workflow to aid physicians to initiate prompt and informed patient treatment.