gebhart/patrepeval huggingface dataset:
<i>In vivo</i> evaluation of a porous hydroxyapatite/poly‐<scp>DL</scp>‐lactide composite for bone tissue engineering (2007)

As reported previously, a porous composite of uncalcined hydroxyapatite (u-HA) and poly-DL-lactide (PDLLA) showed excellent osteoconductivity and biodegradability as a bone substitute in rabbit model. In this study, to investigate the usefulness of this composite as a scaffold loaded with cells, we estimated whether this material showed osteogenesis on implantation to extraosseous site. On loading with syngeneic bone marrow cells and implantation into rat dorsal subcutaneous tissue, osteogenesis with enchondral ossification was seen both on and in the material at 3 weeks after implantation. The osteogenesis in the u-HA/PDLLA had progressed, and newly formed bone tissue was found in the material by 6 weeks. To investigate the osteoinductive properties of the material, we implanted this porous composite material into extraosseous canine dorsal muscle. At 8 weeks, osteogenesis was seen in the pores of the material. Newly formed bone could be observed adjacent to the material. In addition, cuboidal osteoblasts adjacent to the newly formed bone were evident. Neither cartilage nor chondrocytes were found. These results might indicate that the material induced osteogenesis by intramembranous ossification. Conversely, similar porous PDLLA did not induce osteogenesis during the observation period. Therefore, porous HA/PDLLA, which has osteoconductive and osteoinductive properties, might be a useful material for use as a bone substitute and cellular scaffold.
Analytical performance study of solar blind non-line-of-sight ultraviolet short-range communication links (2008)

Motivated by recent advances in solid-state incoherent ultraviolet sources and solar blind detectors, we study communication link performance over a range of less than 1 km with a bit error rate (BER) below 10(-3) in solar blind non-line-of-sight situation. The widely adopted yet complex single scattering channel model is significantly simplified by means of a closed-form expression for tractable analysis. Path loss is given as a function of transceiver geometry as well as atmospheric scattering and attenuation and is compared with experimental data for model validation. The BER performance of a shot-noise-limited receiver under this channel model is demonstrated.
Probabilistic models for focused web crawling (2004)

A Focused crawler must use information gleaned from previously crawled page sequences to estimate the relevance of a newly seen URL. Therefore, good performance depends on powerful modelling of context as well as the current observations. Probabilistic models, such as Hidden Markov Models(HMMs) and Conditional Random Fields(CRFs), can potentially capture both formatting and context. In this paper, we present the use of HMM for focused web crawling, and compare it with Best-First strategy. Furthermore, we discuss the concept of using CRFs to overcome the difficulties with HMMs and support the use of many, arbitrary and overlapping features. Finally, we describe a design of a system applying CRFs for focused web crawling, that is currently being implemented.
Analysis of skin lesions with pigmented networks (2002)

This paper deals with image processing for automatic analysis of pigmented skin lesions. Special emphasis is put on pigmented networks in epiluminescence microscopy (ELM) images. The purpose of processing images of pigmented skin lesions is the visualisation for education and training as well as for diagnosis support. We use a colour based segmentation applied to the Karhunen-Loeve transform of the RGB colour vectors to separate pigmented lesions from the skin and proceed with histogram equalisation and greyscale morphology to enhance and filter the pigmented networks. We demonstrate that we can enhance pigmented networks in skin lesions visually, and make them accessible to further analysis and classification.
Spontaneous loss of heterozygosity leading to homozygous R132H in a patient-derived IDH1 mutant cell line (2013)

Spontaneous loss of heterozygosity leading to homozygous R132H in a patient-derived IDH1 mutant cell line Dear Editor,
Susceptibility of lodgepole pine stands to the mountain pine beetle: testing of a rating system (2000)

A system for rating the susceptibility of lodgepole pine (Pinus contorta Dougl. var. latifolia Engelm.) stands to the mountain pine beetle (Dendroctonus ponderosae Hopkins) was field tested in 38 stands in the Cariboo forest region of British Columbia in a retrospective study. A linear relationship was defined between the percentage of basal area killed by the mountain pine beetle and the susceptibility indices for the sample stands. The system was further tested using an independent data set of 41 stands from across southern British Columbia. Forty of the 41 stands fell within the 95% prediction interval of the original model data for stand susceptibility. This study provides validation for a susceptibility rating model described in 1992. The regression model and associated confidence interval also provide a useful tool for landscape level loss predictions due to the mountain pine beetle.
Influence of the windlass mechanism on arch-spring mechanics during dynamic foot arch deformation (2018)

The function of the human foot is described dichotomously as a compliant structure during mid-stance and a stiff lever during push-off. The arch-spring and the windlass mechanisms, respectively, describe each of these behaviours; however, their interaction has not been quantified to date. We hypothesized that by engaging the windlass mechanism with metatarsophalangeal joint (MTPJ) dorsiflexion, we would observe stiffening of the arch and reduced energy absorption and dissipation during dynamic compressions of the foot. Using a custom apparatus, the MTPJ angle was fixed at 30 degrees of plantarflexion, neutral or 30 degrees of dorsiflexion for nine participants, with the shank positioned similarly to the end of mid-stance. The arch was compressed at two speeds, with the faster speed comparable to walking around 1.5 m s<sup>-1</sup> Six cameras captured the compression and elongation of the arch, along with other kinematic variables, synchronously with the ground reaction force. Combining these measures, we computed the energy absorbed, returned and dissipated in the arch. Contrary to our hypothesis, when the windlass mechanism was engaged, the arch elongated more, and absorbed and dissipated more energy than when it was not engaged. This engagement of the windlass altered the rotational axis of the mid-foot, which probably oriented the arch-spanning structures closer to their resting length, increasing their compliance. This study provides novel evidence for an interplay between the windlass and arch-spring mechanisms that aids in regulation of energy storage within the foot.
Design Simulation of a Rotating Dual-Headed PET/CT Scanner for Breast Imaging (2006)

A PET system based on a pair of opposing LSO detectors for breast imaging has previously been described by Doshi et al (IEEE Trans. Nucl. Sci. 48: 811-815, 2001). This system has undergone some modifications in geometry and electronics and is being integrated into a dedicated breast CT system. In this work we perform a design simulation of the new system with a view to determining areas for future improvements. Simulations were performed using the public domain GATE software, based on the GEANT 4 particle simulation engine. The NURBS-based NCAT phantom was used to create an anthropomorphic activity and attenuation distribution. We show that activity outside of the field of view has a major impact on singles-to-trues ratios and is an important design constraint. The coincidence time window width and system dead-time both have a significant effect on noise equivalent count-rates, and efforts to reduce them on a future prototype are likely to be worthwhile.
Association of Tumor Microenvironment T-Cell Repertoire and Mutational Load With Clinical Outcome After Sequential Checkpoint Blockade in Melanoma (2019)

To understand prognostic factors for outcome between differentially sequenced nivolumab and ipilimumab in a randomized phase II trial, we measured T-cell infiltration and PD-L1 by immunohistochemistry, T-cell repertoire metrics, and mutational load within the tumor. We used next-generation sequencing (NGS) and assessed the association of those parameters with response and overall survival. Immunosequencing of the T-cell receptor -chain locus (TCR) from DNA of 91 pretreatment tumor samples and an additional 22 pairs of matched pre- and post treatment samples from patients who received nivolumab followed by ipilimumab (nivo/ipi), or the reverse (ipi/nivo), was performed to measure T cell clonality and fraction. Mutational and neoantigen load were also assessed by NGS in 82 of the 91 patients. Tumors were stained using immunohistochemistry for PD-L1&#43; and CD8&#43; T cells. Pretreatment tumor TCR clonality and neoantigen load were marginally associated with best response with nivo/ipi (P &#61; 0.04 and 0.05, respectively), but not with ipi/nivo. Amalgamated pretreatment mutational load and tumor T cell fraction were significantly associated with best response with nivo/ipi (P &#61; .002). Pretreatment PD-L1 staining intensity and CD8&#43; T-cell counts were correlated with T-cell fraction and clonality, but not mutational or neoantigen load. Patients with increased T-cell fraction post-treatment at week 13 had a 30-fold increased likelihood of survival (P &#61; .002). Mutational and neoantigen load, and T-cell infiltrate within the tumor, were associated with outcome of sequential checkpoint inhibition using nivolumab then ipilimumab, but not when ipilimumab was administered before nivolumab.
New Edition of HITRAN Database (2001)

The goal of this effort is to provide the Atmospheric Radiation Measurement (ARM) community with an archival database of spectroscopic parameters that serve as input to atmospheric radiation modeling codes. The high-resolution transmission (HITRAN) compilation includes molecular spectroscopic parameters for simulating absorption and radiance by gases in the atmosphere, infrared (IR) cross
Highly Specific Plasmonic Biosensors for Ultrasensitive MicroRNA Detection in Plasma from Pancreatic Cancer Patients (2014)

MicroRNAs (miRs) are small noncoding RNAs that regulate mRNA stability and/or translation. Because of their release into the circulation and their remarkable stability, miR levels in plasma and other biological fluids can serve as diagnostic and prognostic disease biomarkers. However, quantifying miRs in the circulation is challenging due to issues with sensitivity and specificity. This Letter describes for the first time the design and characterization of a regenerative, solid-state localized surface plasmon resonance (LSPR) sensor based on highly sensitive nanostructures (gold nanoprisms) that obviates the need for labels or amplification of the miRs. Our direct hybridization approach has enabled the detection of subfemtomolar concentration of miR-X (X = 21 and 10b) in human plasma in pancreatic cancer patients. Our LSPR-based measurements showed that the miR levels measured directly in patient plasma were at least 2-fold higher than following RNA extraction and quantification by reverse transcriptase-polymerase chain reaction. Through LSPR-based measurements we have shown nearly 4-fold higher concentrations of miR-10b than miR-21 in plasma of pancreatic cancer patients. We propose that our highly sensitive and selective detection approach for assaying miRs in plasma can be applied to many cancer types and disease states and should allow a rational approach for testing the utility of miRs as markers for early disease diagnosis and prognosis, which could allow for the design of effective individualized therapeutic approaches.
Wine Polyphenols: Potential Agents in Neuroprotection (2012)

There are numerous studies indicating that a moderate consumption of red wine provides certain health benefits, such as the protection against neurodegenerative diseases. This protective effect is most likely due to the presence of phenolic compounds in wine. Wine polyphenolic compounds are well known for the antioxidant properties. Oxidative stress is involved in many forms of cellular and molecular deterioration. This damage can lead to cell death and various neurodegenerative disorders, such as Parkinson's or Alzheimer's diseases. Extensive investigations have been undertaken to determine the neuroprotective effects of wine-related polyphenols. In this review we present the neuroprotective abilities of the major classes of wine-related polyphenols.
Prevention of model stratum corneum lipid phase transitions in vitro by cosmetic additives : differential scanning calorimetry, optical microscopy, and water evaporation studies (1993)

DSC of the model lipid (32% water content) showed a broad endothermic transition at about 52oC, with an enthalpy of 15 J/g lipid. The enthalpy of the transition and water loss from the model lipid were time-dependent; at 6% RH, the enthalpy increased to 43 J/g lipid, with 29.5% water loss by 24 h. This suggests significant crystallization of the model lipid on dehydration, which was confirmed by microscopy. At 92% RH, both the changes in enthalpy and water loss were significantly reduced by 24 h, indicating maintenance of the liquid crystalline phase of the model lipid with very little crystallization. Incorporation of Glyceridacid (5-15 wt%) into the model lipid produced enthalpies between 17-21 J/g lipid after 24 h at 6% RH, with reduced water loss (20-26%). Therefore, Glyceridacid can function as a skin conditioner at low humidity by maintaining the liquid crystalline phase of the model lipid in addition to preventing water loss. Glycerol (10 wt%), a known skin conditioner in vivo, inhibited the crystallization of the model lipid, despite almost complete dehydration: enthalpy is 30 J/g lipid after 24 h with few solid crystals present. This suggests an alternative mechanism to humectancy for the moisturizing action of glycerol at low humidity, in agreement with our earlier investigation (4) of the model lipid/glycerol system by microscopy. The results clearly show the potential of DSC as a quantitative tool to monitor the phase behavior of the model lipid and its alteration by potential moisturizers, under different humidity conditions.
Future Electrical Power Supply System (1998)

This paper looks at some of the essential architecture features associated with future demands of the electrical power supply such as increased power requirements, improved efficiency, and increased availability. Fundamental features of a new electrical power supply architecture are defined, and the management of the electrical power supply is discussed. The paper concludes with a discussion of the electrical door look serving as an example of high reliability power supply.
Fooling Neural Network Interpretations via Adversarial Model Manipulation (2019)

We ask whether the neural network interpretation methods can be fooled via adversarial model manipulation, which is defined as a model fine-tuning step that aims to radically alter the explanations without hurting the accuracy of the original models, e.g., VGG19, ResNet50, and DenseNet121. By incorporating the interpretation results directly in the penalty term of the objective function for fine-tuning, we show that the state-of-the-art saliency map based interpreters, e.g., LRP, Grad-CAM, and SimpleGrad, can be easily fooled with our model manipulation. We propose two types of fooling, Passive and Active, and demonstrate such foolings generalize well to the entire validation set as well as transfer to other interpretation methods. Our results are validated by both visually showing the fooled explanations and reporting quantitative metrics that measure the deviations from the original explanations. We claim that the stability of neural network interpretation method with respect to our adversarial model manipulation is an important criterion to check for developing robust and reliable neural network interpretation method.
Shape memory effect of ethylene–vinyl acetate copolymers (1999)

Crosslinked ethylene–vinyl acetate (EVA) copolymers with VA content of 28% by weight were prepared by a two-step method by evenly dispersing the crosslinking agent (dicumyl peroxide) into the EVA matrix and then crosslinking at elevated temperatures. The crosslinking features of the samples were analyzed by Soxhlet extraction with xylene and dynamic mechanical measurements. All the samples were crystalline at room temperature, and the chemical crosslinks seemed to have little effect on the melting behavior of polyethylene segment crystals in the EVA copolymers. The shape recovery results indicated that only those specimens that had a sufficiently high crosslinking degree (gel content higher than about 30%) were able to show the typical shape memory effect, a large recoverable strain, and a high final recovery rate. The degree of crosslinking can be influenced by the amount of the peroxide and the time and temperature of the reaction. The response temperature of the recovery effect (about 61°C) was related to the melting point of the samples. The EVA shape memory polymer was characterized by its low recovery speed that resulted from the wide melting range of the polyethylene segment crystals. © 1999 John Wiley & Sons, Inc. J Appl Polym Sci 71: 1063–1070, 1999
Immune Responses to an Oral Typhoid Vaccine Strain That Is Modified to Constitutively Express Vi Capsular Polysaccharide (2004)

Protection against typhoid fever might be best achieved by a vaccine that stimulates IgG antibody to Vi capsular polysaccharide (Vi) in serum, IgG antibody to O antigen in serum, and cell-mediated immune responses. Live typhoid vaccines have not elicited anti-Vi antibody, presumably because Vi expression is highly regulated. CVD 909 is an oral attenuated typhoid vaccine candidate that is engineered to constitutively express Vi. In the present study, CVD 909, at doses of 10(6-9) cfu, was orally administered to 32 healthy adults, and immune responses were measured. Although many of the volunteers generated antibody-secreting cell responses to Vi, only 2 of the 32 volunteers generated anti-Vi IgG antibody in serum.
Withanolide Derivatives from the Roots of Withania somnifera and Their Neurite Outgrowth Activities. (2002)

Five new withanolide derivatives (1, 9-12) were isolated from the roots of Withania somnifera together with fourteen known compounds (2-8, 13-19). On the basis of spectroscopic and physiochemical evidence, compounds 1 and 9-12 were determined to be (20S,22R)-3 alpha,6 alpha-epoxy-4 beta,5 beta,27-trihydroxy-1-oxowitha-24-enolide (1), 27-O-beta-D-glucopyranosylpubesenolide 3-O-beta-D-glucopyranosyl (1-->6)-beta-D-glucopyranoside (withanoside VIII, 9), 27-O-beta-D-glucopyranosyl (1-->6)-beta-D-glucopyranosylpubesenolide 3-O-beta-D-glucopyranosyl (1-->6)-beta-D-glucopyranoside (withanoside IX, 10), 27-O-beta-D-glucopyranosylpubesenolide 3-O-beta-D-glucopyranoside (withanoside X, 11), and (20R,22R)-1 alpha,3 beta,20,27-tetrahydroxywitha-5,24-dienolide 3-O-beta-D-glucopyranoside (withanoside XI, 12). Of the isolated compounds, 1, withanolide A (2), (20S,22R)-4 beta,5 beta,6 alpha,27-tetrahydroxy-1-oxowitha-2,24-dienolide (6), withanoside IV (14), withanoside VI (15) and coagulin Q (16) showed significant neurite outgrowth activity at a concentration of 1 microM on a human neuroblastoma SH-SY5Y cell line.
3D mesh based wall thickness measurement: Identification of left ventricular hypertrophy phenotypes (2010)

Left ventricular hypertrophy (LVH) is a complex cardiac condition mainly identified by the thickening of the myocardial wall. Although most of the contemporary cardiac imaging modalities provide high resolution 3D images, the wall thickness (WT) is still measured within the acquired planes. This way of measurement may introduce an error as cardiac wall is not necessarily orthogonal to the plane. In this study we analyze how different approaches to measure WT can affect an automatic identification of hypertrophy. The compared approaches are: WT measured along surface normal and the one provided by a medial surface. For both approaches we evaluated their ability to identify LVH phenotypes by testing with two classifiers: Transductive Confidence Machine-k Nearest Neighbor (TCM-kNN) and Linear Discriminant Analysis (LDA). Fifty three subjects were included in this study: 18 patients with hypertrophic cardiomyopathy (HCM), 13 patients with hypertensive heart disease (HDD) and 22 sedentary subjects (CG). Medial surface based approach allowed obtaining higher classification accuracy in HDD patients, while normal based approach allowed for higher classification accuracy in HCM patients.
Shape and Reflectance Recovery using Multiple Images with Known Illumination Conditions (2007)

We develop a variational method to recover both the shape and the reflectance of a scene surface(s) using multiple images, assuming that illumination conditions are fixed and known in advance. Scene and image formation are modeled with known information about cameras and illuminants, and scene recovery is achieved by minimizing a global cost functional with respect to both shape and reflectance. Unlike most previous methods recovering only the shape of Lambertian surfaces, the proposed method considers general dichromatic surfaces. We verify the method using synthetic data sets containing specular reflection.
Shoal: A Lossless Network for High-density and Disaggregated Racks (2017)

Rack-scale computers comprise hundreds of micro-servers connected to internal storage and memory through an internal network. However, their density and disaggregated nature pose a problem for existing packet-switched networks: they are too costly, draw too much power, and the network latency is too high for converged traffic (comprising IP, storage, and memory traffic). We propose Shoal, a rack-scale network that tightly integrates a circuit-switched physical fabric with the nodes? network stack to efficiently support converged traffic. Shoal?s fabric comprises circuit switches with no buffers, no arbitration, and no packet inspection mechanism. Micro-servers transmit according to a static schedule such that there is no in-network contention. Shoal?s congestion control leverages the physical fabric to achieve fairness, losslessness, and both bounded worst-case throughput and queuing. We use an FPGA-based prototype and simulations to illustrate Shoal?s mechanisms are practical and achieve low latency within the rack at low cost and power.
Cytoskeleton mediates inhibition of the fast Na<sup>+</sup> current in respiratory brainstem neurons during hypoxia (1999)

Whole-cell Na+ currents (INa) were recorded in inspiratory neurons in a medullary slice preparation from neonatal mouse that contains the functional respiratory network. Hypoxia and metabolic poisoning with KCN rapidly inhibited INa by reducing the number of Na+ channels available for opening during depolarization. Application of agents specific for G-proteins, protein kinase C and A, intracellular Ca2+ and pH did not prevent the hypoxic inhibition of INa. The effects of hypo-osmolarity and hypoxia were additive, whereas hyperosmolarity partially prevented a subsequent hypoxic inhibition of INa. Cytochalasin B and colchicine decreased, and taxol or phalloidin increased INa and reduced its hypoxic inhibition. We conclude that cytoskeleton rearrangements during hypoxia are responsible for suppression of a fast INa in brainstem respiratory neurons, which could be mediated by the uncoupling of channel inactivation gates from cytoskeletal elements.