gebhart/patrepeval huggingface dataset:
Isolation of a human plasmin-derived, functionally active, light (B) chain capable of forming with streptokinase an equimolar light (B) chain-streptokinase complex with plasminogen activator activity. (1976)

A functionally active human plasmin light (B) chain derivative, stabilized by the streptomyces plasmin inhibitor leupeptin, was isolated from a partially reduced and alkylated enzyme preparation by an affinity chromatography method with a L-lysine-substituted Sepharose column. This light (B) chain derivative was found to be relatively homogeneous by electrophoretic analysis in both an acrylamide gel/dodecyl sulfate system and on cellulose acetate. It possessed approximately 3% of the proteolytic activity (casein substrate) of the original enzyme, and it incorporated 0.09 mol of [3H]diisopropyl phosphorofluoridate per mol of protein. It contained 3.1 +/- 0.3 carboxymethylated cysteines per mol of protein and can be designated as a CmCys5-light (B) chain (CmCys)3. When this isolated light (B) chain derivative was mixed in equal molar amounts with streptokinase, the mixture developed both human and bovine plasminogen activator activities; the bovine activator activity was approximately 66% of the bovine activator activity of the equimolar human plasmin-streptokinase complex. Although this complex now incorporated 0.50 mol of [3H]diisopropyl phosphorofluoridate per mol of protein, its proteolytic activity, on a molar basis, was the same as the proteolytic activity of the isolated light (B) chain derivative. It was shown by electrophoretic analysis in both an acrylamide gel/epsilon-aminocaproic acid system and on cellulose acetate that the light (B) chain derivative and streptokinase forms an equimolar light (B) chain-streptokinase complex, indicating that the binding site for streptokinase is located on the light (B) chain of the enzyme. A functionally active equimolar light (B) chain-streptokinase complex was also isolated from a partially reduced and alkylated equimolar human plasmin-streptokinase complex by the affinity chromatography method. The plasminogen activator activities (human and bovine) of this light (B) chain-streptokinase complex were similar to those of the plasmin-streptokinase complex from which it was derived. Although this complex incorporated 0.70 mol of [3H]diisopropyl phosphorofluoridate per mol of protein, its proteolytic activity, on a molar basis, was only 14% of proteolytic activity of the plasmin-streptokinase complex.
Sox‐9 facilitates differentiation of adipose tissue‐derived stem cells into a chondrocyte‐like phenotype in vitro (2011)

The purpose of this study is to test whether ectopic expression of Sox-9 can induce adipose tissue-derived stem cells (ASCs) to function as real nucleus pulposus (NP) cells in vitro. Adenoviral vectors expressing Sox-9 were reported to infect the chondroblastic and human disc cells, which resulted in increased Sox-9 and type II collagen production. ASCs were isolated from rat inguinal adipose pad, characterized, and transduced in vitro with a retroviral vector encoding the Sox-9 gene. Sox-9-engineered ASCs (ASCs/Sox-9) were induced for the chondrocyte-like cell differentiation by 3D cultured in alginate beads and TGF-β3 for 2 weeks. Expression of exogenous Sox-9 protein was detected. Type II collagen and Aggrecan gene expressions of induced ASCs/Sox-9 were measured using real-time PCR; proteoglycans expressions were measured by checking the glycosaminoglycan content and type II collagen production by enzyme-linked immunosorbent assay. Isolated ASCs were CD 29(+) /CD44(+) /C-Kit(-) /Lin(-) /CD34(-) /CD45(-) . ASCs/Sox-9 expressed marked increase in exogenous Sox-9 protein. After induction, type II collagen gene expression was sevenfold higher in mRNA levels, with an approximately twofold increase in protein levels of ASCs/Sox-9 compared to ASCs. Type II collagen and proteoglycan productions were significantly increased in the ASCs/Sox-9 compared to the ASCs. In addition, co-culture of induced ASCs/Sox-9 with matured NP cells resulted in enhanced increase in proteoglycan and type II collagen production. Constitutive retroviral expression of Sox-9 could efficiently induce ASCs differentiation into chondrocyte-like cells. This novel approach may provide a practicable system for a simple and rapid differentiation of ASCs into chondrocyte-like cells which may be potentially used as a stem cell-based therapeutic tool for the treatment of degenerative disc diseases.
LOCAL CACHING ARCHITECTURE FOR RFID TAG RESOLUTION (2007)

Thesis (M.S)--Wichita State University, College of Engineering, Dept. of Electrical and Computer Engineering
The Thermal Conversion of Poly[(silylene)‐diacetylene] Metal Oxide Composites: A New Approach to β‐SiCMC Ceramics (1992)

Cross‐linking of 1, formation of a SiC network, and reduction of the encapsulated TiO 2 particles are the three steps in the reaction of poly[(dimethylsilylene)diacetylene] ( 1 ) and TiO 2 which produces SiCTiC ceramics [Eq. (a)]. The reduction of the metal oxide in this case is possible at much lower temperatures than with carbon alone. This method can be applied to a number of metal oxides, and also B 2 O 3 . The ceramic's composition can be modulated by variation of the polymer. equation image
Renal Capsule Xenografting and Subcutaneous Pellet Implantation for the Evaluation of Prostate Carcinogenesis and Benign Prostatic Hyperplasia (2013)

New therapies for two common prostate diseases, prostate cancer (PrCa) and benign prostatic hyperplasia (BPH), depend critically on experiments evaluating their hormonal regulation. Sex steroid hormones (notably androgens and estrogens) are important in PrCa and BPH; we probe their respective roles in inducing prostate growth and carcinogenesis in mice with experiments using compressed hormone pellets. Hormone and/or drug pellets are easily manufactured with a pellet press, and surgically implanted into the subcutaneous tissue of the male mouse host. We also describe a protocol for the evaluation of hormonal carcinogenesis by combining subcutaneous hormone pellet implantation with xenografting of prostate cell recombinants under the renal capsule of immunocompromised mice. Moreover, subcutaneous hormone pellet implantation, in combination with renal capsule xenografting of BPH tissue, is useful to better understand hormonal regulation of benign prostate growth, and to test new therapies targeting sex steroid hormone pathways.
The Structural Basis for Optimal Performance of Oligothiophene‐Based Fluorescent Amyloid Ligands: Conformational Flexibility is Essential for Spectral Assignment of a Diversity of Protein Aggregates (2013)

Protein misfolding diseases are characterized by deposition of protein aggregates, and optical ligands for molecular characterization of these disease-associated structures are important for understanding their potential role in the pathogenesis of the disease. Luminescent conjugated oligothiophenes (LCOs) have proven useful for optical identification of a broader subset of disease-associated protein aggregates than conventional ligands, such as thioflavin T and Congo red. Herein, the molecular requirements for achieving LCOs able to detect nonthioflavinophilic Aβ aggregates or non-congophilic prion aggregates, as well as spectrally discriminate Aβ and tau aggregates, were investigated. An anionic pentameric LCO was subjected to chemical engineering by: 1) replacing thiophene units with selenophene or phenylene moieties, or 2) alternating the anionic substituents along the thiophene backbone. In addition, two asymmetric tetrameric ligands were generated. Overall, the results from this study identified conformational freedom and extended conjugation of the conjugated backbone as crucial determinants for obtaining superior thiophene-based optical ligands for sensitive detection and spectral assignment of disease-associated protein aggregates.
Optimization and comparison of hybrid-resonant switched capacitor DC-DC converter topologies (2017)

This paper explores methods to optimize and compare a variety of switched-capacitor (SC) DC-DC topologies that can be operated in a resonant mode. A figure of merit is developed that is a proxy for minimum achievable power loss, based on conduction and frequency-dependent losses in the active semiconductor components. Similar to past work on pure SC converters, the method leverages a charge-multiplier approach and is used to show the impact of energy or area constraints on capacitors, and tradeoffs between power loss and volumetric overhead of inductors. An analysis and detailed breakdown is provided for several common and emerging topologies.
Emergent structures in supply chains - a study integrating agent-based and system dynamics modeling (2003)

Supply chain management is a demanding and complicated task due to its broad scope and the strong connectedness of its objects and issues. In order to make theoretical investigations of supply chains feasible and to support decision-making in real world supply chains, simulation models are used. An integration of system dynamics and discrete agent-based modeling is a promising combination of methods for reducing the a priori complexity of the model. The paper discusses the strengths and weaknesses of system dynamics and discrete agent-based modeling. An approach for integration of the two modeling methodologies is presented. Issues concerning the practical coupling of software environments and a simple, prototypical supply chain model are discussed. Experiments for which the integrated simulation solution is applied are described. Insights in emergent structures in supply chains are derived from these simulation analyses.
Clinical and physiological assessments for elucidating falls risk in Parkinson's disease (2009)

The study aims were to devise (1) a fall risk screen for people with PD using routine clinical measures and (2) an explanatory (physiological) fall risk assessment for guiding fall prevention interventions. One hundred thirteen people with PD (age 66 +/- 95% CI 1.6 years) underwent clinical assessments and quantitative tests of sway, gait, strength, reaction time, and lower limb sensation. Participants were then followed up for 12 months to determine fall incidence. In the follow-up year, 51 participants (45%) fell one or more times whereas 62 participants (55%) did not fall. Multivariate analyses of routine clinical measures revealed that a fall in the past year, abnormal axial posture, cognitive impairment, and freezing of gait were independent risk factors for falls and predicted 38/51 fallers (75%) and 45/62 non-fallers (73%). A multivariate model combining clinical and physiological measures that elucidate the pathophysiology of falls identified abnormal posture, freezing of gait, frontal impairment, poor leaning balance, and leg weakness as independent risk factors. This model correctly classified 39/51 fallers (77%) and 51/62 non-fallers (82%). Patients with PD at risk of falls can be identified accurately with routine clinical assessments and quantitative physiological tests. Many of the risk factors identified are amenable to targeted intervention.
Seamless Bare-Hand Interaction in Mixed Reality (2018)

Unrealistic Mixed Reality (MR) experiences can be caused by unprocessed occlusions between real and augmented objects during interactions. Depth knowledge is indeed key to achieve a seamless visualisation when a bare hand interacts with an augmented object. This can be addressed by blending real-time 3D finger tracking information with the visualisation of the hand in MR. We propose an approach that automatically localises the hand in RGB images and associates the respective depth, estimated with an auxiliary infrared stereo camera used for hand tracking, to each RGB hand pixel. Because misalignments between the outline of the hand and its depth may occur due to tracking errors, we use the distance transform algorithm to densely associate depth values to hand pixels. In this way hand and augmented object depths can be compared, and the object can be rendered accordingly. We evaluate our approach by using an MR setup composed of a smartphone and a Leap Motion mounted on it. We analyse several hand configurations and measure the erroneously classified pixels when occlusions occur.
Design and analysis of digital watermarking, information embedding, and data hiding systems (2000)

Heavy drinking during pregnancy may increase the risk of preterm delivery.
Class prediction of closely related plant varieties using gene expression profiling (2007)

In recent years, class prediction experiments have been largely developed in cancer research with the aim of classifying unknown samples by examining their expression signature. In natural populations, a significant component of gene expression variability is also heritable. Citrus species are an ideal model to accomplish the study of these questions in plants, due to the existence of varieties derived from somatic mutations that are likely to differ from each other by one or a few point mutations but are phenotypically indistinguishable at early vegetative stages. The small genetic variability existing among these varieties makes molecular markers ineffective in distinguishing genotypes within a particular species. Gene expression profiles have been used to predict mandarin clementine varieties (Citrus clementina Hort. ex Tan.) by means of two independent supervised learning algorithms: Support Vector Machines and Prediction Analysis of Microarrays. The results show that transcriptional variation is variety-dependent in citrus, and supervised clustering methods may correctly assign blind samples to varieties when both training and test samples are under the same experimental conditions.
An automatic image-gathering system for the World-Wide Web by integration of keywords and image features (2002)

Due to the recent explosive progress of WWW (World-Wide Web), we can easily access a large number of images from WWW. However, methods to utilize WWW as a large image database have not been established yet. In this paper, we propose an automatic image-gathering system from WWW employing both keywords and image features, which is called Image Collector. By exploiting some existing keyword-based search engines and selecting images by their image features, the system obtains more than one hundred images related to query keywords in about five minutes.
Comparison of CNG and Gasoline Vehicle Exhaust Emissions: Mass and Composition - The Auto/Oil Air Quality Improvement Research Program (1995)

<div class="htmlview paragraph">Exhaust emissions of three vehicles fueled with compressed natural gas (CNG) were compared with emissions of three counterpart gasoline vehicles. The natural gas vehicles were tested on four CNG fuels covering a wide range of pipeline natural gas compositions. The gasoline vehicles were tested on AQIRP Industry Average gasoline and a reformulated gasoline meeting California 1996 regulatory requirements.</div> <div class="htmlview paragraph">Nonmethane hydrocarbon (NMHC) and toxic air pollutant emissions of the CNG vehicles were about one-tenth those of their counterpart gasoline vehicles, while methane emissions were about ten times those of the gasoline vehicles. Carbon monoxide (CO) and nitrogen oxides (NO<sub>x</sub>) emissions were more variable among the three vehicle pairs. CO emissions ranged from 20 to 80% lower with CNG than with gasoline, and NO<sub>x</sub> ranged from 80% lower with CNG to equivalent to gasoline.</div> <div class="htmlview paragraph">Comparing the four CNG fuels, methane increased about 40%, NMHC decreased about 40%, and reactivity-weighted emissions decreased about 15% when CNG fuel methane content increased from 91 to 98% of fuel hydrocarbons (86 to 97% of total gas composition). There were no statistically significant effects on CO, NO<sub>x</sub> or toxic air pollutants.</div> <div class="htmlview paragraph">Fuel economy expressed as miles per million BTUs was about 20% lower for the CNG vehicles than for their gasoline counterparts. Reactivity-weighted emissions (RWE), calculated to estimate differences in potential ozone forming characteristics of emissions, were about 90% lower for the three CNG vehicles than for their gasoline counterparts when the calculation was based on NMHC emissions alone, and about 80% lower when exhaust methane and CO were included. The fuel effects on RWE parallel the effects on NMHC mass.</div> <div class="htmlview paragraph">Reformulated test gasoline C<sub>2</sub> representing California Phase 2 gasoline, tested in the gasoline vehicles, had consistently lower NMHC, CO, and NO<sub>x</sub> and toxics emissions than AQIRP Industry Average gasoline. The average decreases in the three emissions were 24%, 21%, 12% and 36%, respectively. These results are consistent with other AQIRP data for these fuels.</div>
POET: a portable approach to minimizing energy under soft real-time constraints (2015)

Embedded real-time systems must meet timing constraints while minimizing energy consumption. To this end, many energy optimizations are introduced for specific platforms or specific applications. These solutions are not portable, however, and when the application or the platform change, these solutions must be redesigned. Portable techniques are hard to develop due to the varying tradeoffs experienced with different application/platform configurations. This paper addresses the problem of finding and exploiting general tradeoffs, using control theory and mathematical optimization to achieve energy minimization under soft real-time application constraints. The paper presents POET, an open-source C library and runtime system that takes a specification of the platform resources and optimizes the application execution. We test POET's ability to portably deliver predictable timing and energy reduction on two embedded systems with different tradeoff spaces - the first with a mobile Intel Haswell processor, and the second with an ARM big.LITTLE System on Chip. POET achieves the desired latency goals with small error while consuming, on average, only 1.3% more energy than the dynamic optimal oracle on the Haswell and 2.9% more on the ARM. We believe this open-source, library-based approach to resource management will simplify the process of writing portable, energy-efficient code for embedded systems.
Chemotherapy in the elderly – How intense should treatment be? (2015)

Chemotherapy in the elderly -How intense should treatment be?
Mechanisms of Liver Injury. I. TNF-α-induced liver injury: role of IKK, JNK, and ROS pathways (2006)

TNF-alpha activates several intracellular pathways to regulate inflammation, cell death, and proliferation. In the liver, TNF-alpha is not only a mediator of hepatotoxicity but also contributes to the restoration of functional liver mass by driving hepatocyte proliferation and liver regeneration. This review summarizes recent advances in TNF-alpha signaling mechanisms that demonstrate how the IKK, ROS, and JNK pathways interact with each other to regulate hepatocyte apoptosis and proliferation. Activation of these pathways is causatively linked to liver injury induced by concanavalin A, TNF-alpha, and ischemia-reperfusion and to liver regeneration and hepatocarcinogenesis. In light of recent findings, pharmacological inhibitors of JNK and IKK and antioxidants may be promising new tools for the treatment of hepatitis, ischemia-reperfusion injury, and hepatocellular carcinoma.
The Gestalt Photomapping System (1977)

The Gestalt Photo Mapping System is made up of the GPM II and GPM Plotting System. The GPM II is a computer-controlled, auto-correlating, analytical photomapper. It is composed of two scanners, an automatic image correlator, a control computer, an operator's console, and one or two printers. A typical stereomodel is completed automatically in less than an hour and a half after a 10 minute operator-assisted analytical orientation. Principal topographic output consists of a 700,000-point digital terrain model (DTM) on magnetic tape: Planimetric output consists of an orthophoto on 20 X 25 cm stable-base film. The GPM Plotting System is an off-line automatic DTM processing system. It consists of a disk-based minicomputer and plotter. Smoothed contours and slope maps may be plotted at map scale with annotation in less than an hour and a half. A GPM III orthophoto and GPM Plotting System contours may be combined without editing by using conventional photographic techniques to produce a reproduction-quality contoured orthophot map in less than a day. /Author/
The "Is-Ought" Fallacy and Musicology: The Assumptions of Pedagogy (1997)

Many years ago I formulated a presentation that I thought would be an effective way of communicating some of the major issues surrounding Schubert's Heder to my undergraduates.
An Update on Software Updates (2005)

When I raised the idea at the Queue editorial advisory board meeting several months ago, it was because I think the way that software is now being delivered to us is quite interesting. Things have changed. Nowadays you much less often expect to “install” whole systems or indeed even individual applications. Instead you’ve probably become quite used to the idea of accepting ongoing updates to what you already have - a behavior of happily receiving incremental changes to your software systems and/or applications - by what I like to describe as the process of “bit dripping” from vendors over the Web.
New trends and ideas in visual concept detection (2010)

The MIR Flickr collection consists of 25000 high-quality photographic images of thousands of Flickr users, made available under the Creative Commons license. The database includes all the original user tags and EXIF metadata. Additionally, detailed and accurate annotations are provided for topics corresponding to the most prominent visual concepts in the user tag data. The rich metadata allow for a wide variety of image retrieval benchmarking scenarios.
Human eye sensitivity and photometric qualities (2006)

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Predictive QSAR Modeling Workflow, Model Applicability Domains, and Virtual Screening (2007)

Quantitative Structure Activity Relationship (QSAR) modeling has been traditionally applied as an evaluative approach, i.e., with the focus on developing retrospective and explanatory models of existing data. Model extrapolation was considered if only in hypothetical sense in terms of potential modifications of known biologically active chemicals that could improve compounds' activity. This critical review re-examines the strategy and the output of the modern QSAR modeling approaches. We provide examples and arguments suggesting that current methodologies may afford robust and validated models capable of accurate prediction of compound properties for molecules not included in the training sets. We discuss a data-analytical modeling workflow developed in our laboratory that incorporates modules for combinatorial QSAR model development (i.e., using all possible binary combinations of available descriptor sets and statistical data modeling techniques), rigorous model validation, and virtual screening of available chemical databases to identify novel biologically active compounds. Our approach places particular emphasis on model validation as well as the need to define model applicability domains in the chemistry space. We present examples of studies where the application of rigorously validated QSAR models to virtual screening identified computational hits that were confirmed by subsequent experimental investigations. The emerging focus of QSAR modeling on target property forecasting brings it forward as predictive, as opposed to evaluative, modeling approach.