gebhart/patrepeval huggingface dataset:
Hepatitis B Virus Capsid-like Particles Can Display the Complete, Dimeric Outer Surface Protein C and Stimulate Production of Protective Antibody Responses against Borrelia burgdorferi Infection (2006)

Hepatitis B virus capsid-like particles (CLPs), icosahedral assemblies formed by 90 or 120 core protein dimers, hold promise as immune-enhancing vaccine carriers for heterologous antigens. Insertions into the immunodominant c/e1 B cell epitope, a surface-exposed loop, are especially immunogenic. However, display of whole proteins, desirable to induce multispecific and possibly neutralizing antibody responses, can be restrained by an unsuitable structure of the foreign protein and by its propensity to undergo homomeric interactions. Here we analyzed CLP formation by core fusions with two distinct variants of the dimeric outer surface lipoprotein C (OspC) of the Lyme disease agent Borrelia burgdorferi. Although the topology of the termini in the OspC dimer does not match that of the insertion sites in the carrier dimer, both fusions, coreOspCa and coreOspCb, efficiently formed stable CLPs. Electron cryomicroscopy clearly revealed the surface disposition of the OspC domains, possibly with OspC dimerization occurring across different core protein dimers. In mice, both CLP preparations induced high-titered antibody responses against the homologous OspC variant, but with substantial cross-reactivity against the other variant. Importantly, both conferred protection to mice challenged with B. burgdorferi. These data show the principal applicability of hepatitis B virus CLPs for the display of dimeric proteins, demonstrate the presence in OspC of hitherto uncharacterized epitopes, and suggest that OspC, despite its genetic variability, may be a valid vaccine candidate.
Prevention of experimental endotoxin shock by a monocyte activator (1995)

In patients with polytrauma or major surgery, severe bacterial infections leading to septic shock and multiorgan failure are still a major cause of death. Prevention of septic shock in patients at risk would be an alternative to treatment of patients with overt septic shock. We therefore conducted a trial with the monocyte activator muramyl tripeptide phosphatidylethanolamine (MTP-PE) in an experimental pig model. Liposome encapsulated MTP-PE (50 micrograms/kg of body weight) or liposomes alone were given intravenously at 72 or 24 h before endotoxemia was induced by lipopolysaccharide (LPS), simultaneously with the induction of endotoxin shock, or 1 h thereafter. Pretreatment with MTP-PE at 72 and 24 h before endotoxemia was induced resulted in a reduction of endotoxin shock-induced mortality from 81.8% (9 of 11 animals) in the control group to 8.3% (1 of 12 animals) of the MTP-PE-pretreated animals (P < 0.001). The administration of MTP-PE 24 h before the induction of endotoxin shock was more effective (P < 0.01) than administration of MTP-PE 72 h before endotoxemia was induced (P = 0.05). The pretreated animals did not develop fever or cardiovascular complications, and pulmonary function was significantly improved. Furthermore, the alpha-form of the soluble CD14 LPS receptor in pig serum showed a marked decrease in LPS-treated animals, and this decrease was reduced by MTP-PE pretreatment at 24 h before endotoxemia was induced. When MTP-PE was given simultaneously with the induction of septic shock or 1 h thereafter, it did not influence either mortality or morbidity. In conclusion, pretreatment of pigs with MTP-PE improves several parameters of endotoxin shock and it reduces mortality. Patients with high risk of developing septic complications might benefit from a pretreatment with this monocyte-activating substance.
FOMTrace: Interactive Video Segmentation By Image Graphs and Fuzzy Object Models (2016)

Common users have changed from mere consumers to active producers of multimedia data content. Video editing plays an important role in this scenario, calling for simple segmentation tools that can handle fast-moving and deformable video objects with possible occlusions, color similarities with the background, among other challenges. We present an interactive video segmentation method, named FOMTrace, which addresses the problem in an effective and efficient way. From a user-provided object mask in a first frame, the method performs semi-automatic video segmentation on a spatiotemporal superpixel-graph, and then estimates a Fuzzy Object Model (FOM), which refines segmentation of the second frame by constraining delineation on a pixel-graph within a region where the object's boundary is expected to be. The user can correct/accept the refined object mask in the second frame, which is then similarly used to improve the spatiotemporal video segmentation of the remaining frames. Both steps are repeated alternately, within interactive response times, until the segmentation refinement of the final frame is accepted by the user. Extensive experiments demonstrate FOMTrace's ability for tracing objects in comparison with state-of-the-art approaches for interactive video segmentation, supervised, and unsupervised object tracking.
The Structure of Foreign News (1965)

Abstract Using a simplified psychology of perception and some additional assumptions, a system of twelve factors describing events is presented that together are used as a definition of 'newsworthiness'. Three basic hypotheses are presented: the additivity hypothesis that the more factors an event satisfies, the higher the probability that it becomes news; the complementarity hypothesis that the factors will tend to exclude each other since if one factor is present it is less necessary for the other factors to be present for the event to become news; and the exclusion hypothesis that events that satisfy none or very few factors will not become news. This theory is then tested on the news presented in four different Norwegian newspapers from the Congo and Cuba crises of July 1960 and the Cyprus crisis of March-April 1964, and the data are in the majority of cases found to be consistent with the theory. A dozen additional hypotheses are then deduced from the theory and their social implications are discussed. Finally, some tentative policy impli cations are formulated.
The Effect of Alloantisera on Antigen-Induced T Cell Proliferation (1975)

Abstract In the guinea pig, alloantisera raised by cross-immunization of strain 2 and strain 13 animals are capable of specifically inhibiting the in vitro proliferative response of (2 × 13)F1 T lymphocytes to those antigens the response to which is controlled by Ir genes linked to the genes controlling the alloantigens against which the serum is directed. However, in similar studies performed in the two parental strains, the responses to antigens not known to be under unigenic control were also markedly inhibited by the appropriate alloantisera. We have extended our studies of this “nonspecific” inhibitory effect of alloantisera on T cell proliferation and have demonstrated that the proliferative response of strain 2 and strain 13 T cells to a large number of antigens is markedly inhibited by anti-2 and anti-13 sera, respectively. Antisera to the B alloantigen, the product of a linked but distinct histocompatibility locus, which is present in both strain 2 and strain 13 animals, also produced a marked inhibition of T-lymphocyte proliferation. A number of possible explanations for the generalized inhibitory effect of alloantisera on T cell proliferation are discussed.
Electrical Properties of β-Ag2Te and β-Ag2Se from 4.2° to 300°K (1967)

The study of electrical properties of β-Ag2Te and β-Ag2Se has been extended to 4.2°K. The former compound was zone refined without decomposition. Both n- and p-type samples of β-Ag2Te were studied; all samples of β-Ag2Se prepared were n type to 4.2°K. Neither semiconductor showed any indication of extrinsic carrier freeze-out or of impurity banding. Study of oxygen as a possible acceptor in β-Ag2Te showed no significant effect; a selenium-doped sample of β-Ag2Se was n-type to 4.2°K.
A sparsity-based atlas selection technique for multiple-atlas segmentation: Application to neonatal brain labeling (2016)

Quantitative brain tissue volumes from neonatal magnetic resonance imaging (MRI) offer the possibility of improved clinical decision making and diagnosis. However, the neonatal brain presents specific challenges to automated segmentation algorithms. We developed a new method for automatic labeling of neonatal brain MR images. The method uses a new sparsity-based atlas selection strategy that requires a very limited number of atlases 'uniformly' distributed in the low-dimensional data space, combined with a machine learning based label fusion technique. The performance of the method for brain labeling from data of 66 newborns is evaluated and compared with results obtained using majority vote. The proposed method provides accurate brain labeling results with a mean Dice coefficient of 91%. As the proposed method can learn from partially labeled datasets, it can be used to segment large-scale datasets efficiently.
Proposal generation for object detection using cascaded ranking SVMs (2011)

Object recognition has made great strides recently. However, the best methods, such as those based on kernel-SVMs are highly computationally intensive. The problem of how to accelerate the evaluation process without decreasing accuracy is thus of current interest. In this paper, we deal with this problem by using the idea of ranking. We propose a cascaded architecture which using the ranking SVM generates an ordered set of proposals for windows containing object instances. The top ranking windows may then be fed to a more complex detector. Our experiments demonstrate that our approach is robust, achieving higher overlap-recall values using fewer output proposals than the state-of-the-art. Our use of simple gradient features and linear convolution indicates that our method is also faster than the state-of-the-art.
Size-Controlled Synthesis of ZnSnO3 Cubic Crystallites at Low Temperatures and Their HCHO-Sensing Properties (2010)

Uniform and monodisperse ZnSnO3 cubic crystallites were prepared via a solution process involving the reaction of zinc sulfate and sodium stannate at a reaction temperature as low as 0 °C without any surfactant. The size was readily controlled from 40 to 600 nm by varying the reaction temperature. The possible formation mechanism of cubic crystallites was attributed to a nucleation assembly process. The as-fabricated sensors based on ZnSnO3 cubic crystallites showed high sensitivity, fast response, and short recovery times toward HCHO gas. And as the particle-size of ZnSnO3 cubic crystallites decrease, the sensitivity of gas sensors based on them increases and the recovery time shorten rapidly. The detection limit of ZnSnO3 cubic crystallites sensor can reach as little as lower than one per million for HCHO. The performance of a home-built ZnSnO3 cubic crystallites sensor was even better than the competing SnO2 and In2O3 sensor, making this material interesting for sensor devices.
Influence of absorption-edge properties on subpicosecond intrinsic laser-damage threshold at 1053 nm in hafnia and silica monolayers (2019)

Owing to their relatively high resistance to laser-induced damage, hafnia and silica are commonly used in multilayered optical coatings in high-power laser facilities as high- and low-refractive-index materials, respectively. Here, we quantify the laser-induced-damage threshold (LIDT) at 1053 nm in the short-pulse regime of hafnia and silica monolayers deposited by different fabrication methods, including electron-beam evaporation, plasma ion-assisted deposition and ion-assisted deposition. The results demonstrate that nominally identical coatings fabricated by different deposition techniques and/or vendors can exhibit significantly different damage thresholds. A correlation of the LIDT performance of each material with its corresponding absorption edge is investigated. Our analysis indicates a weak correlation between intrinsic LIDT and the optical gap of each material (Tauc gap) but a much better correlation when considering the spectral characteristics in the Urbach tail spectral range. Spectrophotometry and photothermal absorption were used to provide evidence of the correlation between the strength of the red-shifted absorption tail and reduced LIDT at 1053 nm.
Taxonomy Construction of Unseen Domains via Graph-based Cross-Domain Knowledge Transfer (2020)

Extracting lexico-semantic relations as graphstructured taxonomies, also known as taxonomy construction, has been beneficial in a variety of NLP applications. Recently Graph Neural Network (GNN) has shown to be powerful in successfully tackling many tasks. However, there has been no attempt to exploit GNN to create taxonomies. In this paper, we propose Graph2Taxo, a GNN-based cross-domain transfer framework for the taxonomy construction task. Our main contribution is to learn the latent features of taxonomy construction from existing domains to guide the structure learning of an unseen domain. We also propose a novel method of directed acyclic graph (DAG) generation for taxonomy construction. Specifically, our proposed Graph2Taxo uses a noisy graph constructed from automatically extracted noisy hyponym-hypernym candidate pairs, and a set of taxonomies for some known domains for training. The learned model is then used to generate taxonomy for a new unknown domain given a set of terms for that domain. Experiments on benchmark datasets from science and environment domains show that our approach attains significant improvements correspondingly over the state of the art.
Effects of laser frequency chirp on modal noise in short-range radio over multimode fiber links (2010)

An important effect of the frequency chirp of the optical transmitter in radio over multimode fiber links is put into evidence experimentally and modeled theoretically for the first time, to our knowledge. This effect can have an important impact in short-range connections, where, although intermodal dispersion does not generally cause unacceptable limitations to the transmittable bandwidth, the presence of modal noise must be accurately kept under control, since it determines undesired real-time fluctuations of the link.
Stored Energy Function of Rubberlike Materials Derived from Simple Tensile Data (1972)

An explicit formulation to obtain the stored energy function W from simple tension experiments alone, based on the Valanis-Landel separable symmetric stored energy function, W(λ1, λ2, λ3) = w(λ1) + w(λ2) + w(λ3), is developed. For a simple extension stress-strain law of the form λσ=Eε, the analytical formula of W in the limited range 1≤λ≤2.5 is found to be W=E ∑ i=l3 [λi−1−lnλi−16 (lnλi)2+118 (lnλi)3−1216 (lnλi)4],where the limitation originates with the stress-strain law. The expression is used to verify the validity of the Valanis-Landel postulation through prediction of the stress-strain behavior in multiaxial deformations.
FORMATION, IMMOBILIZATION AND LOCAL MANIPULATION OF TUBULAR LIPID MEMBRANE STRUCTURES (2011)

We present a microfluidic approach to form, immobilize and chemically treat tubular lipid structures. The structures are formed by micro-extrusion of a lipid film through micron-sized pores into a microfluidic channel where they remain stable under laminar flow conditions. Micron-sized tip features serving as trapping supports have been integrated in the microchannel design to immobilize and align the tubular lipid structures at a predefined position. A further design modification facilitates the local supply of chemical agents to the trapped structures. We demonstrate the local staining with lipophilic fluorescent dye along a short fragment of the tubular lipid membrane structures.
PMAP: databases for analyzing proteolytic events and pathways (2008)

The Proteolysis MAP (PMAP, http://www.proteolysis.org) is a user-friendly website intended to aid the scientific community in reasoning about proteolytic networks and pathways. PMAP is comprised of five databases, linked together in one environment. The foundation databases, ProteaseDB and SubstrateDB, are driven by an automated annotation pipeline that generates dynamic 'Molecule Pages', rich in molecular information. PMAP also contains two community annotated databases focused on function; CutDB has information on more than 5000 proteolytic events, and ProfileDB is dedicated to information of the substrate recognition specificity of proteases. Together, the content within these four databases will ultimately feed PathwayDB, which will be comprised of known pathways whose function can be dynamically modeled in a rule-based manner, and hypothetical pathways suggested by semi-automated culling of the literature. A Protease Toolkit is also available for the analysis of proteases and proteolysis. Here, we describe how the databases of PMAP can be used to foster understanding of proteolytic pathways, and equally as significant, to reason about proteolysis.
Design, development, and analysis of crossover-free fiber optic gyroscope sensor coils (2007)

We describe experiments of fiber coils using different lengths, coil diameters, and configurations wound on a innovative
winder. Geometric and polarimetric analyses of coils and effects on Sagnac area and bending induced birefringence are
examined.
Enteric nervous system modulation of luminal pH modifies the microbial environment to promote intestinal health (2022)

The enteric nervous system (ENS) controls many aspects of intestinal homeostasis, including parameters that shape the habitat of microbial residents. Previously we showed that zebrafish lacking an ENS, due to deficiency of the sox10 gene, develop intestinal inflammation and bacterial dysbiosis, with an expansion of proinflammatory Vibrio strains. To understand the primary defects resulting in dysbiosis in sox10 mutants, we investigated how the ENS shapes the intestinal environment in the absence of microbiota and associated inflammatory responses. We found that intestinal transit, intestinal permeability, and luminal pH regulation are all aberrant in sox10 mutants, independent of microbially induced inflammation. Treatment with the proton pump inhibitor, omeprazole, corrected the more acidic luminal pH of sox10 mutants to wild type levels. Omeprazole treatment also prevented overabundance of Vibrio and ameliorated inflammation in sox10 mutant intestines. Treatment with the carbonic anhydrase inhibitor, acetazolamide, caused wild type luminal pH to become more acidic, and increased both Vibrio abundance and intestinal inflammation. We conclude that a primary function of the ENS is to regulate luminal pH, which plays a critical role in shaping the resident microbial community and regulating intestinal inflammation.
RGB-D SLAM with Structural Regularities (2020)

This work proposes a RGB-D SLAM system specifically designed for structured environments and aimed at improved tracking and mapping accuracy by relying on geometric features that are extracted from the surrounding. Structured environments offer, in addition to points, also an abundance of geometrical features such as lines and planes, which we exploit to design both the tracking and mapping components of our SLAM system. For the tracking part, we explore geometric relationships between these features based on the assumption of a Manhattan World (MW). We propose a decoupling-refinement method based on points, lines, and planes, as well as the use of Manhattan relationships in an additional pose refinement module. For the mapping part, different levels of maps from sparse to dense are reconstructed at a low computational cost. We propose an instance-wise meshing strategy to build a dense map by meshing plane instances independently. The overall performance in terms of pose estimation and reconstruction is evaluated on public benchmarks and shows improved performance compared to state-of-the-art methods. The code is released at \url{https://github.com/yanyan-li/PlanarSLAM}
Phase I trial of SNS-595 in patients with advanced malignancies (2005)

2099 Background: SNS-595 is a novel naphthyridine analog that induces a G2 cell cycle arrest in vitro and shows broad activity in xenograft and drug resistant tumor models. Methods: SNS-595 was administered to patients (pts) with advanced solid cancers every 3 weeks as an IV infusion over 10 minutes without premedications. Cohorts of 3–6 pts were accrued to doses based on a modified Fibonacci sequence. Results: As of 12/04 16 patients were treated in the first five cohorts at doses starting at 3 mg/m2 and advancing to 48 mg/m2. Tumor types included lung (4), adenocarcinoma of unknown primary (4), renal (3), ovarian, melanoma, bladder, sarcoma and cholangiocarcinoma (1 each). The median age was 57 years (range 46 to 74) and median ECOG PS was 1 (range 0–2). No dose limiting toxicity has been seen. Transient Grade 4 hematological toxicity (ANC <500/μL) was seen in 2 of 3 pts in cohort 5 (48 mg/m2). Non-hematologic toxicities were mild and all grade 1/2. PK samples were collected on treatment Day 1 and were assayed using a noncompartmental analysis. Plasma SNS-595 concentrations were determined using a validated LC-MS/MS assay. AUC increased proportionally with dose and mean AUC(0-Inf) were 6329±182, 12655±851 and 25440±9512 ng*hr/ml, respectively, for 12, 24 and 48 mg/m2 dose levels. The terminal half-life is approximately 19 hours. Conclusions: In this phase I study SNS 595 is well tolerated with consistent and predictable PK effects. Dose escalation is continuing. Further data will be presented. Author Disclosure Employment or Leadership Consultant or Advisory Role Stock Ownership Honoraria Research Funding Expert Testimony Other Remuneration Sunesis Sunesis Sunesis
Both exogenous and endogenous interleukin‐10 affects the maturation of bone‐marrow‐derived dendritic cells in vitro and strongly influences T‐cell priming in vivo (2002)

In order to avoid autoimmunity and excessive tissue destruction, the action of certain immunoinhibitory substances are very important for negative regulation of the immune system. Interleukin-10 (IL-10) is an important immunoregulatory cytokine which is thought to negatively affect both T cells and antigen-presenting cells in vivo. Adoptive transfer of IL-10-treated bone-marrow-derived dendritic cells (BMDCs) may be one therapeutic avenue to inhibit autoimmunity. In this study we present a comprehensive analysis of the effects of IL-10 on murine BMDC. We demonstrate that IL-10 can prevent BMDC maturation, as measured by both cytokine production and T-cell priming capacity in vitro. Furthermore, we show that IL-10 can inhibit DC maturation induced by strong stimulatory signals such as lipopolysaccharide or a mixture of cytokines (interferon-gamma, tumour necrosis factor-alpha, IL-4). Interestingly, maturation of both T helper 1- and T helper 2-inducing DCs, characterized by the induction of high levels of interferon-gamma and IL-4-production by responding T cells, respectively, was inhibited by IL-10 in vitro. Finally, our data suggest that both endogenous and exogenous IL-10 affect the T-cell stimulatory capacity of BMDCs after injection of in vitro-treated BMDCs into naïve mice. These data both support existing data as well as point towards a new understanding of the many aspects of IL-10-mediated immunosuppression.