gebhart/patrepeval huggingface dataset:
The exploitation of spatial information in narrative discourse (2011)

We present the results of several machine learning tasks that exploit explicit spatial language to classify rhetorical relations and the spatial information of narrative events. Three corpora are annotated with figure and ground (granularity) relationships, mereotopologically classified verbs and prepositions, and frames of reference. For rhetorical relations, Naïve Bayesian models achieve 84.90 % and 57.87 % accuracy in classifying NARRATION and BACKGROUND / ELABORATION relations respectively (16 % and 23 % above baseline). For the spatial information of narrative events, K * models achieve 55.68 % average accuracy (12 % above baseline) for all spatial information types. This result is boosted to 71.85 % (28 % above baseline) when inertial spatial reference and text sequence information are considered. Overall, spatial information is shown to be central to narrative discourse structure and prediction tasks. 1
Atom-Economical Cross-Coupling of Internal and Terminal Alkynes to Access 1,3-Enynes (2021)

Selective carbon-carbon (C-C) bond formation in chemical synthesis generally requires prefunctionalized building blocks. However, the requisite prefunctionalization steps undermine the overall efficiency of synthetic sequences that rely on such reactions, which is particularly problematic in large-scale applications, such as in the commercial production of pharmaceuticals. Herein, we describe a selective and catalytic method for synthesizing 1,3-enynes without prefunctionalized building blocks. In this transformation several classes of unactivated internal acceptor alkynes can be coupled with terminal donor alkynes to deliver 1,3-enynes in a highly regio- and stereoselective manner. The scope of compatible acceptor alkynes includes propargyl alcohols, (homo)propargyl amine derivatives, and (homo)propargyl carboxamides. This method is facilitated by a tailored P,N-ligand that enables regioselective addition and suppresses secondary <i>E</i>/<i>Z</i>-isomerization of the product. The reaction is scalable and can operate effectively with as low as 0.5 mol % catalyst loading. The products are versatile intermediates that can participate in various downstream transformations. We also present preliminary mechanistic experiments that are consistent with a redox-neutral Pd(II) catalytic cycle.
Supplemental Figures 1-7 from Erlotinib Pretreatment Improves Photodynamic Therapy of Non–Small Cell Lung Carcinoma Xenografts via Multiple Mechanisms (2023)

&lt;p&gt;Supplemental Figures 1-7. Supplemental Figure 1. Erlotinib does not alter oxygenation of tumors Supplemental Figure 2. Erlotinib increases in vivo tumor cell death at delayed timepoints. Supplemental Figure 3. In vivo imaging of tumor perfusion is well correlated with ex vivo imaging of the excised tumor. Supplemental Figure 4. VEGF levels decrease in A549 tumors with pre-PDT administration of erlotinib Supplemental Figure 5. Western blot analysis Supplemental Figure 6. BPD levels increase Supplemental Figure 7. A single-dose of erlotinib augments PDT-induced cytotoxicity.&lt;/p&gt;
Investigating influence of data storage organization on structured code search performance (2011)

Code search in an industrial environment is driven by the programmers wish to scan huge source code repositories with high precision in a very short time. Given a challenging scenario of a huge software repository, the question for an efficient code search backend is relevant. This paper discusses the question of an appropriate data storage model for a structured code search engine applied in an industrial development scenario, where a search on large software repositories is common. To investigate this, a search engine approach with integrated Abstract Syntax Trees is adapted. Using the capabilities of a hybrid in-memory database, we stored a big amount of structured data obtained from the source code repository into column-, row-, and a hybrid store layout and performed a set of typical queries using an SQL interface on them. The results have shown the superiority of the column-oriented approach for the investigated scenario.
Completely Miscible Polyethylene Nanocomposites (2012)

A route to fully miscible polyethylene (PE) nanocomposites has been established based on polymer-brush-coated nanoparticles. These nanoparticles can be mixed with PE at any ratio, with homogeneous dispersion, and without aggregation. This allowed a first systematic study of the thermomechanical properties of PE nanocomposites without interference from aggregation effects. We observe that the storage modulus in the semicrystalline state and the softening temperature increase significantly with increasing nanoparticle content, whereas the melt viscosity is unaltered by the presence of nanoparticles. We show that the complete miscibility with the semicrystalline polymer matrix and the improvement of thermomechanical properties in the solid state is caused by the PE-coated nanoparticles being nucleating agents for the crystallization of PE. This provides a general route to fully miscibility nanocomposites with semicrystalline polymers.
Vaccine Targets Expanding from Infectious Diseases to Non-infectious Diseases (2019)

<em>Many infections have been overcome by the spread of vaccines. Vaccines are the most cost-effective way of preventing infectious diseases. The main targets of vaccines are infectious diseases. For example, influenza and pertussis are familiar infectious diseases. Although conventional vaccines against influenza and pertussis have achieved some success in controlling these diseases, these infectious diseases have not yet been completely controlled. More effective vaccines against these infectious diseases are required to be developed. On the other hand, the possibility of the vaccines against non-infectious diseases such as Alzheimer's disease, high blood pressure, diabetes and Parkinson's disease have been shown. Patients with Alzheimer's disease have increased with the aging of the population. Overcoming the Alzheimer's disease is important for us to send better old age. Since the possibility of the vaccine for Alzheimer's disease has been shown, so many studies on vaccines for Alzheimer's disease have been carried out. The development of the Alzheimer's disease vaccine will accelerate the development of vaccines for other non-infectious diseases like high blood pressure, diabetes and Parkinson's disease</em>.
The cortical actin network regulates avidity-dependent binding of hyaluronan by the lymphatic vessel endothelial receptor LYVE-1 (2020)

Lymphatic vessel endothelial hyaluronan receptor 1 (LYVE-1) mediates the docking and entry of dendritic cells to lymphatic vessels through selective adhesion to its ligand hyaluronan in the leukocyte surface glycocalyx. To bind hyaluronan efficiently, LYVE-1 must undergo surface clustering, a process that is induced efficiently by the large cross-linked assemblages of glycosaminoglycan present within leukocyte pericellular matrices but is induced poorly by the shorter polymer alone. These properties suggested that LYVE-1 may have limited mobility in the endothelial plasma membrane, but no biophysical investigation of these parameters has been carried out to date. Here, using super-resolution fluorescence microscopy and spectroscopy combined with biochemical analyses of the receptor in primary lymphatic endothelial cells, we provide the first evidence that LYVE-1 dynamics are indeed restricted by the submembranous actin network. We show that actin disruption not only increases LYVE-1 lateral diffusion but also enhances hyaluronan-binding activity. However, unlike the related leukocyte HA receptor CD44, which uses ERM and ankyrin motifs within its cytoplasmic tail to bind actin, LYVE-1 displays little if any direct interaction with actin, as determined by co-immunoprecipitation. Instead, as shown by super-resolution stimulated emission depletion microscopy in combination with fluorescence correlation spectroscopy, LYVE-1 diffusion is restricted by transient entrapment within submembranous actin corrals. These results point to an actin-mediated constraint on LYVE-1 clustering in lymphatic endothelium that tunes the receptor for selective engagement with hyaluronan assemblages in the glycocalyx that are large enough to cross-bridge the corral-bound LYVE-1 molecules and thereby facilitate leukocyte adhesion and transmigration.
Lanthanide-Binding Tags for 3D X-ray Imaging of Proteins in Cells at Nanoscale Resolution (2020)

We report the application of lanthanide-binding tags (LBTs) for two- and three-dimensional X-ray imaging of individual proteins in cells with a sub-15 nm beam. The method combines encoded LBTs, which are tags of minimal size (ca. 15-20 amino acids) affording high-affinity lanthanide ion binding, and X-ray fluorescence microscopy (XFM). This approach enables visualization of LBT-tagged proteins while simultaneously measuring the elemental distribution in cells at a spatial resolution necessary for visualizing cell membranes and eukaryotic subcellular organelles.
Inhibiting the oncogenic translation program is an effective therapeutic strategy in multiple myeloma (2017)

Multiple myeloma (MM) is a frequently incurable hematological cancer in which overactivity of MYC plays a central role, notably through up-regulation of ribosome biogenesis and translation. To better understand the oncogenic program driven by MYC and investigate its potential as a therapeutic target, we screened a chemically diverse small-molecule library for anti-MM activity. The most potent hits identified were rocaglate scaffold inhibitors of translation initiation. Expression profiling of MM cells revealed reversion of the oncogenic MYC-driven transcriptional program by CMLD010509, the most promising rocaglate. Proteome-wide reversion correlated with selective depletion of short-lived proteins that are key to MM growth and survival, most notably MYC, MDM2, CCND1, MAF, and MCL-1. The efficacy of CMLD010509 in mouse models of MM confirmed the therapeutic relevance of these findings in vivo and supports the feasibility of targeting the oncogenic MYC-driven translation program in MM with rocaglates.
Combinatorial Approach to Polymer Design for Nanomedicines (2020)

Polymers have been the most widely studied materials for drug delivery because of their rich history of applications in biomedical field, including implants, sutures, and medical devices and recently as drug carrier micro and nanoparticles. The traditional approach to polymeric drug delivery system included use of biocompatible and biodegradable polymers that were used as drug-conjugates or carriers housing the active pharmaceutical ingredient and ferrying them to the disease sites. Combinatorial design of polymeric material for nanoparticle drug delivery has gained tremendous popularity due to the inherent flexibility with the approach. It offers potential to change the way material design is perceived and allows a very systematic but rigorous and stringent material selection criteria for biomedical application. Combinatorial design of material is still in its early stages of inception but as the technology matures, many of these challenges will be overcome and this approach will become more streamlined and accepted in commercial development of nanomedicines.
Roadblock-qPCR: a simple and inexpensive strategy for targeted measurements of mRNA stability (2020)

The stability of mRNAs is fundamental to determining expression level and dynamics. Nonetheless, current approaches for measuring transcript half-lives (e.g., transcription shutoff) are generally toxic or technically complex. Here we describe an alternative strategy for targeted measurements of endogenous mRNA stability that is simple, inexpensive, and nontoxic. Cells are first metabolically labeled with the nucleoside analog 4-thiouridine (4sU). Extracted mRNA can then be treated with the thiol-reactive compound N-ethylmaleimide. This compound modifies 4sU nucleotides and sterically interferes with reverse transcription of 4sU-containing transcripts, disrupting their conversion into cDNA. The decay rate of non-4sU-containing preexisting mRNA can then be monitored by quantitative PCR (qPCR). Importantly, this approach avoids the biochemical isolation of 4sU-labeled transcripts and/or RNA-seq analysis required for other metabolic-labeling strategies. In summary, our method combines the simplicity of "transcription shutoff" strategies with the accuracy of metabolic-labeling strategies for measurements of mRNA stability across a wide range of half-lives.
Discussion: The Role of Peripheral Nerve Surgery in Diabetic Limb Salvage (2011)

Norfolk, Va. From the Neuroendocrine Unit, Strelitz Diabetes Center, Eastern Virginia Medical School. Received for publication October 8, 2010; accepted October 11, 2010. Disclosure:The author has no financial interest to declare in relation to the content of this Discussion or of the associated article. Aaron Vinik, M.D., Ph.D.; Neuroendocrine Unit; Strelitz Diabetes Center; Eastern Virginia Medical School; 855 W. Brambleton Avenue; Norfolk, Va. 23510; [email protected]
Sensitivity enhanced and polarization independent evanescent field planar ridge waveguide Bragg grating refractometer (2005)

Optical Bragg grating sensors based on side polished or etched waveguides have been demonstrated for the measurement of refractive index [1, 2, 3, 4]. However, these devices typically exhibit polarization dependent behavior for index values around 1.3. In this report, a ridge waveguide Bragg grating (WBG) sensor with high sensitivity, for refractive index measurement in liquids is presented. The device is based on a small core size silica open top cladding ridge waveguide and polarization independent Bragg gratings (PIBG) written and optimized using UV light [5,6,7]. The WBG is surrounded by a liquid analyte and is accessed via evanescent field interaction of the guided waveguide mode with the liquid layer. In the theoretical analysis, enhancement of sensitivity by optimizing waveguide structures is proposed. In the experiment, Bragg grating is induced in the open top cladding ridge waveguide using a phase mask and excimer laser radiation at 193 nm. A series of refractive index matching liquids are used to test the device. Results indicate the sensitivity is as high as 50 pm of wavelength shift for a change of the index 3×10<sup>-4</sup>. This technology can offer many advantages over previously proposed waveguide sensors, including enhanced sensitivity, and dynamic measurement range, better polarization stability, and a simpler fabrication processes.
GENERATING AND PRINTING OF HIGH QUALITY DOCUMENTS IN A DISTRIBUTED OFFICE AUTOMATION NETWORK ENVIRONMENT (1982)

This paper analyses the process of creating a printed document, which includes text processing, formatting and printing. Corresponding file formats, soft-copy generation algorithms as well as requirements of high quality graphics displays and printing systems are described. A special architecture for a printer interface system is presented which enables the high-speed generation of a document page on a printer frame-buffer, To limit mass-storage requirements, this architecture supports the generation of characters from an analytical description of their contour. Such a printer interface system has a moderate price, due to the decreasing cost of microprocessor and memory components.
Extensor Mechanism Reconstruction with Use of Marlex Mesh (2019)

The procedure avoids the limitations of allograft with regard to availability, cost, and risk of disease transmission. The technique is reproducible and cost-effective, and it has excellent functional and survivorship outcomes.
Association of Polymorphisms in the CRP Gene With Circulating C-Reactive Protein Levels and Cardiovascular Events (2006)

Genetic variation in the CRP gene is associated with plasma CRP levels and CVD risk in older adults.
Temporal Logic Inference for Hybrid System Observation with Spatial and Temporal Uncertainties (2020)

In this paper, we present a mechanism for building hybrid system observers to differentiate between specific positions of the hybrid system. The mechanism is designed through inferring metric temporal logic (MTL) formulae from simulated trajectories from the hybrid system. We first approximate the system behavior by simulating finitely many trajectories with timerobust tube segments around them. These time-robust tube segments account for both spatial and temporal uncertainties that exist in the hybrid system with initial state variations. The inferred MTL formulae classify different time-robust tube segments and thus can be used for classifying the hybrid system behaviors in a provably correct fashion. We implement our approach on a model of a smart building testbed to distinguish two cases of room occupancy.
A SCANNING TUNNELING MICROSCOPE FOR SURFACE MODIFICATION (1986)

With the recent success for the scanning tunneling microscope (STM) has come question of whether the instrument might be used for material modifications lithography. We embarked on the design of an STM with this application in mind. Its features include a wide x-y piezoelectric scan range of 10 or more microns, plus coarse mechanical motion in the x direction to a new region on the sample while in vacuum. Coarse motion in the z direction is accomplished with a micrometer drive, while fine movement is done with a piezoelectric transducer. Both the sample and the tip can be quickly changed. Finally, the instrument is mounted on the stage of a scanning electron microscope which allows real-time observation while it is operating. Using this instrument we were able to pattern sub-micron gold lines on silicon substrates by sputter etching through a contamination resist pattern laid down by the tunneling electrons polymerizing organic molecules present on the target. We were also able to expose lines using a Langmuir-Blodgett film, which consists of several molecular monolayers of a material known to act as an electron beam resist deposited individually on the surface of the substrate.
Low-Protein Diet Suppresses Serum Insulin-Like Growth Factor-1 and Decelerates the Progression of Growth Hormone-Induced Glomerulosclerosis (2001)

A low-protein (LP) diet has been associated with amelioration of renal function in glomerulosclerosis (GS). However, the mechanisms involved are still unclear. We have used a mouse transgenic for bovine growth hormone (GH), which develops progressive GS and exhibits consistently elevated levels of circulating GH and insulin-like growth factor (IGF)-1, to study the effect of dietary protein restriction. LP (6% protein) and normal-protein (NP, 20% protein) diets were maintained for 30 weeks in mice with established GS of mild/moderate degree. The degree of GS was markedly attenuated in LP compared to NP mice. Quantitative analysis revealed a significantly lower GS index (1.4 +/- 0.9 in LP vs. 2.8 +/- 0.8 in NP) and glomerular volume (0.8 x 10(6) +/- 0.1 x 10(6) microm(3) in LP vs. 1.2 x 10(6) +/- 0.1 x 10(6) microm(3) in NP) in mice with restricted protein intake. These morphologic changes were accompanied by a significant reduction in renal expression of alpha(1) type-IV collagen (2.4-fold) and tenascin (1.4-fold) in LP mice. Serum IGF-1 decreased by 40% and showed a significant correlation with alpha(1) type-IV collagen expression with the LP diet. The present finding supports the use of the LP diet to decelerate the progression of GS and furthermore suggests that one of the mechanisms involved in this process is the GH/IGF-1 regulation by protein intake.
Flexible pseudo-relevance feedback via selective sampling (2005)

Although Pseudo-Relevance Feedback (PRF) is a widely used technique for enhancing average retrieval performance, it may actually hurt performance for around one-third of a given set of topics. To enhance the reliability of PRF, Flexible PRF has been proposed, which adjusts the number of pseudo-relevant documents and/or the number of expansion terms for each topic. This paper explores a new, inexpensive Flexible PRF method, called Selective Sampling, which is unique in that it can skip documents in the initial ranked output to look for more “novel” pseudo-relevant documents. While Selective Sampling is only comparable to Traditional PRF in terms of average performance and reliability, per-topic analyses show that Selective Sampling outperforms Traditional PRF almost as often as Traditional PRF outperforms Selective Sampling. Thus, treating the top P documents as relevant is often not the best strategy. However, predicting when Selective Sampling outperforms Traditional PRF appears to be as difficult as predicting when a PRF method fails. For example, our per-topic analyses show that even the proportion of truly relevant documents in the pseudo-relevant set is not necessarily a good performance predictor.
1P161 Advanced TIRF microscopy to detect single-molecule conformational changes in both azimuth and axial axis using polarization switching(11.Molecular motor,Poster,The 51st Annual Meeting of the Biophysical Society of Japan) (2013)

Mycoplasma mobile has hundreds of legs approximately 100 nm long and glides on the substrate at the speed of 2.5 m/sec. It is hypothesized that a cycle of attachment to and detachment from surface-immobilized sialyllactose (SL) drives the force of the gliding. To reveal the mechanism of directed movement as the sum of the force in each leg, we quantified the interaction between legs and SL by using optical tweezers in the presence of different nucleotides or analogues: AMP-PNP ; ADP; ADP+Vi ; nucleotide-free condition. We found that unbinding force depends on chemical states, and also, loading directions in terms of a bacterium gliding polarity. These nucleotide-dependent asymmetric variations could contribute to decipher the gliding mechanism at the molecular level.
Using microsphere or fluorescein tracers and total oocyst output to measure ingestion of material following live-coccidiosis vaccinations (2023)

One method of prevention of coccidiosis in broiler chickens raised without antibiotics relies on coccidiosis vaccination. Live-coccidiosis vaccines carry the risk for pathogenic effects if the Eimeria species overcycle. However, all chicks must receive an appropriate dose of Eimeria oocysts to induce immunity and reduce the risk of adverse effects. At the hatchery, coccidiosis vaccines are administered topically to boxes of chicks by spray or gel-droplet application. Determining the volume of vaccine ingested by individual chicks could provide a means of evaluating the success of different application methods. For each of 2 mass application methods (spray, gel-droplet), we used 3 quantification methodologies to determine the amount of vaccine material ingested by chicks: total oocyst counts from feces collected 5- to 8-days postvaccination; and counts of either microsphere or fluorescein tracers recovered from the gastrointestinal tract 30-min postvaccination. For each quantification methodology, chicks vaccinated via spray or gel-droplet application were compared to chicks vaccinated via oral gavage using the same concentration of oocysts per mL for all groups. Chicks vaccinated via gel-droplet application shed 10-fold more oocysts than those vaccinated by spray application. Individual chick consumption of vaccine material using tracers also revealed that chicks ingested more material following gel-droplet application than spray application, although the magnitude of the difference varied based on quantification methodology. The results of this study suggest that all 3 quantification methodologies can be used to help validate and improve mass vaccine application methods to ensure optimal ingestion, and therefore, coccidiosis vaccination success.
The Regenerative Horizon: Opportunities for Nursing Research and Practice (2019)

The regenerative care model imposes on the nursing community the imperative to (a) increase research awareness; (a) educate, develop, and deploy a skilled nursing workforce; (c) integrate regenerative technologies into nursing practice; and (d) embrace the regenerative technologies horizon as a future in health care.