gebhart/patrepeval huggingface dataset:
Algorithms for similarity search and clustering in large data sets (2003)

In this thesis we present algorithms for performing similarity search and clustering in large datasets. Similarity search is necessary in order to locate relevant information in a database, and it can be used for prediction and classification. Clustering, a form of data summarization, can facilitate visualization, understanding, and knowledge extraction. 
The core of our algorithms for similarity search rely on an hashing-based algorithmic technique. The idea is to create signatures for data objects so that similar objects are likely to have identical signatures. Then, similar objects in the database can be located by indexing their signatures. 
We first study the problem of nearest-neighbor search in high-dimensional data. We present an efficient algorithm for the approximate version of the problem. The algorithm is designed for external memory and thus is appropriate for very large datasets. Our experimental evaluation shows that our method improves significantly over previous approaches, and that it scales well with the number of dimensions. 
Then we present a study of indexing techniques that facilitate similarity queries for sets. We first show how to reduce the set-indexing problem to a related problem of indexing binary vectors, and then we introduce data structures to solve the latter problem. We perform experiments on real datasets to test the accuracy and efficiency of our algorithms and to study the trade-offs of our data structures. 
We apply our set-indexing algorithm to the problem of similarity search on the Web. For the latter problem, we also we develop a methodology in order to evaluate different strategies for Web-page representation. Our experiments provide useful intuition for understanding the strategies we evaluate, and our system gives good-quality answers within small response time.
Finally we study the problem of temporal clustering. The goal is to discover clusters of similar objects so that the temporal coherence of data is respected. We show that the problem is NP-hard for dimensions greater than one and we give constant-factor-approximation algorithms. We implement our algorithms, and we evaluate their performance on synthetic and real datasets. Our experiments suggest that the proposed algorithms achieve high-quality solutions in practice.
MiniJudge: Software for minimalist experimental syntax (2006)

MiniJudge is free online open-source software to help theoretical syntacticians collect and analyze native-speaker acceptability judgments in a way that combines the speed and ease of traditional introspective methods with the power and statistical validity afforded by rigorous experimental design. This paper shows why MiniJudge is useful, what it feels like to use it, and how it works. 1.
Targeted delivery to macrophages and dendritic cells by chemically modified mannose ligand-conjugated siRNA (2022)

Extrahepatic delivery of small interfering RNAs (siRNAs) may have applications in the development of novel therapeutic approaches. However, reports on such approaches are limited, and the scarcity of reports concerning the systemically targeted delivery of siRNAs with effective gene silencing activity presents a challenge. We herein report for the first time the targeted delivery of CD206-targetable chemically modified mannose-siRNA (CMM-siRNA) conjugates to macrophages and dendritic cells (DCs). CMM-siRNA exhibited a strong binding ability to CD206 and selectively delivered contents to CD206-expressing macrophages and DCs. Furthermore, the conjugates demonstrated strong gene silencing ability with long-lasting effects and protein downregulation in CD206-expressing cells in vivo. These findings could broaden the use of siRNA technology, provide additional therapeutic opportunities, and establish a basis for further innovative approaches for the targeted delivery of siRNAs to not only macrophages and DCs but also other cell types.
Effect of interactions between poly(vinyl alcohol) and urea on the water solubility of poly(vinyl alcohol) (2009)

Abstract Poly(vinyl alcohol) (PVA) is an important water‐soluble polymer. Its many applications (e.g., textile sizing, dispersants, and adhesives) greatly depend on its water solubility and particularly on its dissolution rate in water. In this study, urea, combined with methanol, was adopted to improve the water solubility of PVA. The structures, properties, and dissolving mechanism of the modified PVA were studied with Fourier transform infrared spectroscopy, NMR, laser light scattering, differential scanning calorimetry, and wide‐angle X‐ray diffraction. The results showed that through specific chemical reactions between PVA and urea in methanol, isocyanate and methyl carbamate groups were generated on the lateral chains of PVA. These large side groups could effectively expand PVA macromolecular chains and hence increase their intermolecular distance, weaken the intramolecular and intermolecular hydrogen bonds of PVA, change the aggregation structure of PVA, and decrease its lattice energy and crystallinity. In addition, the isocyanate groups on the PVA macromolecular chains strongly interacted with water. All these effects benefited the water solubility of PVA. Therefore, the dissolution rate of the modified PVA increased by 50% versus that of the neat PVA, and the quality of the modified PVA aqueous solution was improved quite a bit. © 2009 Wiley Periodicals, Inc. J Appl Polym Sci, 2009
Peritoneal application of chitosan and UV‐cross‐linkable chitosan (2006)

The suitability of chitosan and UV-cross-linkable chitosan for intraperitoneal use, for example as a barrier device for preventing peritoneal adhesions or for drug delivery, was examined. In vitro experiments using two major cell types present in the peritoneal cavity (mesothelial cells and peritoneal macrophages) revealed neither attractive interactions between cross-linked chitosan gels and the cells nor a proliferative effect. However, the same UV-cross-linked chitosan applied in the peritoneal cavity of rabbits caused a granulomatous reaction with adhesion formation within two weeks in all animals, which persisted up to 4 weeks after exposure. Unmodified chitosan also caused adhesions, while UV irradiation did not. UV-cross-linkable chitosan induced significant elevations in MIP-2 and TNF-alpha from peritoneal macrophages, suggesting that soluble mediators could play a role in inducing adhesion formation. These results reinforce the view that the predictive value of in vitro cytotoxicity assays in matters of biocompatibility may not be sufficient, and suggest that other assays such as cytokine levels may be of value in predicting outcomes in situations involving multiple cell types (i.e. in vivo).
Shedding Light on the Dock–Lock Mechanism in Amyloid Fibril Growth Using Markov State Models (2015)

We investigate how the molecular mechanism of monomer addition to a growing amyloid fibril of the transthyretin TTR105-115 peptide is affected by pH. Using Markov state models to extract equilibrium and dynamical information from extensive all atom simulations allowed us to characterize both productive pathways in monomer addition as well as several off-pathway trapped states. We found that multiple pathways result in successful addition. All productive pathways are driven by the central hydrophobic residues in the peptide. Furthermore, we show that the slowest transitions in the system involve trapped configurations, that is, long-lived metastable states. These traps dominate the rate of fibril growth. Changing the pH essentially reweights the system, leading to clear differences in the relative importance of both productive paths and traps, yet retains the core mechanism.
CAP’NN: Class-Aware Personalized Neural Network Inference (2020)

We propose CAP’NN, a framework for Class-Aware Personalized Neural Network Inference. CAP’NN prunes an already-trained neural network model based on the preferences of individual users. Specifically, by adapting to the subset of output classes that each user is expected to encounter, CAP’NN is able to prune not only ineffectual neurons but also miseffectual neurons that confuse classification, without the need to retrain the network. CAP’NN achieves up to 50% model size reduction while actually improving the top-l(5) classification accuracy by up to 2.3%(3.2%) when the user only encounters a subset of VGG-16 classes.
Real-ray-based method for locating individual surface aberration field centers in imaging optical systems without rotational symmetry (2009)

It has been found that the field dependence of the aberrations of misaligned optical systems made of otherwise rotationally symmetric optical surfaces are often multinodal, including low-order astigmatism and distortion and higher-order coma, astigmatism, oblique spherical, elliptical coma (trifoil), and distortion. The exact location of the nodes in the image is a weighted sum of individual surface contributions. The location of the center of rotational symmetry for the field dependence for all aberrations contributed by a particular rotationally symmetric surface is along the line that connects the center of curvature of the surface with the center of the pupil. Previously, a paraxial ray-trace method was developed to locate the aberration field center for a series of rotationally symmetric surfaces with small tilt and decenter perturbations. The method is based on rotating the coordinate system into the local coordinate system of the surface and then advancing using the conventional paraxial ray-trace equations. This method, developed by Buchroeder [Ph.D. dissertation (University of Arizona, 1976)], heavily constrains how tilts and decenters were implemented in the optical system model, which prevented integration of these equations into an optical design environment. In this paper, a method for locating the aberration field centers using real-ray-trace data that is entirely model independent and, significantly, that is not restricted to small tilts and decenters, is presented. With this new insight, it is now possible to extend any optical design and analysis environment to include multinodal aberration analysis.
Utility-driven workload management using nested control design (2006)

Virtualization and consolidation of IT resources have created a need for more effective workload management tools, one that dynamically controls resource allocation to a hosted application to achieve quality of service (QoS) goals. These goals can in turn be driven by the utility of the service, typically based on the application's service level agreement (SLA) as well as the cost of resources allocated. In this paper, we build on our earlier work on dynamic CPU allocation to applications on shared servers, and present a feedback control system consisting of two nested integral control loops for managing the QoS metric of the application along with the utilization of the allocated CPU resource. The control system was implemented on a lab testbed running an Apache Web server and using the 90th percentile of the response times as the QoS metric. Experiments using a synthetic workload based on an industry benchmark validated two important features of the nested control design. First, compared to a single loop for controlling response time only, the nested design is less sensitive to the bimodal behavior of the system resulting in more robust performance. Second, compared to a single loop for controlling CPU utilization only, the new design provides a framework for dealing with the tradeoff between better QoS and lower cost of resources, therefore resulting in better overall utility of the service.
Unifying Model-Based and Neural Network Feedforward: Physics-Guided Neural Networks with Linear Autoregressive Dynamics (2022)

Unknown nonlinear dynamics often limit the tracking performance of feedforward control. The aim of this paper is to develop a feedforward control framework that can compensate these unknown nonlinear dynamics using universal function approximators. The feedforward controller is parametrized as a parallel combination of a physics-based model and a neural network, where both share the same linear autoregressive (AR) dynamics. This parametrization allows for efficient output-error optimization through Sanathanan-Koerner (SK) iterations. Within each SK-iteration, the output of the neural network is penalized in the subspace of the physics-based model through orthogonal projection-based regularization, such that the neural network captures only the unmodelled dynamics, resulting in interpretable models.
Simulation Study of Light-induced, Current-induced Degradation and Recovery on PERC Solar Cells (2016)

The way to permanently recover the well-known Light-Induced Degradation (LID) which affects the p-type Cz-Si PERC solar cells represents one of the main challenges of photovoltaic research. In this work we have set up a numerical simulations flow which allows us to reproduce the experimental measured values of figures of merit (FOMs) of four different Cz-PERC solar cells lots subjected to a degradation and two regeneration processes. The recombination centres in bulk and the Boron-Oxygen complexes (B-O) are modeled by means of two trap levels tuned on the basis of experimental data. From simulations we confirm that the FOM degradation levels off after 16hours and the regeneration process characterized by relatively long time process is preferred in terms of performance recovery. In addition, further cells with different passivation films are analyzed by adopting the same methodology.
Edge modified vector quantization for image compression (2003)

A new adaptive source coding technique called edge modified vector quantization (EMVQ) is introduced. By using EMVQ, an image is encoded in two stages: coarse image coding and edge modification. The redundancies in the smooth area are further reduced by applying large block segmentation, hierarchical VQ and finite state prediction. Sharp edges are well preserved by compensation of their encoding quantization error. A high compression ratio was achieved and the reconstructed images still had satisfactory perceptual quality. The EMVQ coding results are demonstrated.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Structure and Soft Magnetic Properties of Bulk Fe-Based Glassy Alloy Prepared by Pulse Current Sintering (1999)

Structure and soft magnetic properties for the bulk Fe70Al5Ga2P9.65C5.75B4.6Si3 glassy alloy prepared by pulse current sintering with uniaxial pressure were investigated. The sample consolidated in the temperature range of the supercooled liquid region consisted only of amorphous phase and had a very high relative density of 99%. The flux density at the applied magnetic field of 800 A/m, maximum permeability, coercive force and relative permeability at 1 kHz for the sample sintered at 703 K in as-made state are 1.1 T, 7600, 12 A/m and 1700 respectively. The soft magnetic properties of the sintered bulk Fe-based glassy alloy were much superior to the other magnetic materials of consolidated amorphous powders. It is concluded that the high relative density and good soft magnetic properties for the bulk Fe-based glassy alloy should depend upon its high structural homogeneity originated from its high deformability, that is based on the viscous flow arisen from the appearance of supercooled liquid region.
Genetic Markers (2004)

Cholesterol ester transfer protein LPL Lipoprotein lipase ACE Angiotensin I converting enzyme 1 ATIIR1 Angiotensin II receptor type 1 CBS Cystathionine-synthase GPIIIA Glycoprotein IIIa FGA Fibrinogen ELAM Endothelial leukocyte adhesion molecule-1 Atherothrombosis (angina pectoris) TAFI Thrombin activatable fibrinolysis inhibitor Brugada syndrome SCN5A Sodium channel voltage-gated Calcific aortic valve stenosis VDR Vitamin D receptor Cardiac arrhythmia, inherited SCN5A Sodium channel voltage
ChemInform Abstract: Synthesis of Benzylic Ketones and Alcohols by Electroreductive Coupling of Benzylic Compounds Bearing a Leaving Group Other than Halogen with Anhydrides and Carbonyl Compounds. (1996)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Effects of Zn Doped Mesa Sidewall on Gain Enhanced InGaAs/InP Heterobipolar Phototransistor (2010)

The excellent detectability of the gain enhanced InGaAs/InP heterobipolar phototransistor (GE-HPT) is demonstrated and attributed to a reduction in the reverse leakage current at the base-collector junction and the enhancement of current gain at the emitter-base junction achieved by using a current blocking structure with a Zn doped mesa sidewall. The common emitter grounded current gain agrees well with the photo-conversion efficiency of several tens of thousands of A/W at incident optical powers in the hundred nanowatt to sub-picowatt range over several orders of magnitude. The deep mesa structure in the GE-HPT is also effective in ensuring superior isolation of better than 25 dB between adjacent arrays.
Performance of Electro-Chemical (EC) Disinfection in The Treatment Of Septic Tank Effluent under Plug Flow Condition (2020)

This work investigates the performance of electrochemical disinfection system in treating effluent of septic tank. The electrolysis cells employed Ti/IrO2 anodes and stainless steel cathodes. DC-power supply bench-scale were performed under 12V using actual effluent of septic tank without adding chemical reagent. More than 70% removal in TSS, and greater than 50% of TCOD and SCOD reduction, while TKN and NH3-N where achieved within 1-4hours with the removal efficiency ≤10%. Additionally, lowest energy consumption for organic pollutants removal were 4.41 mA/cm2, while highest energy requirement 4.86 mA/cm2. Meanwhile, operating cost per day were in range between 0.88 – 3.86 Bath/day and average energy use per capita per day 1.25 Bath/cap/d. Tracer study was an instrument to measure hydraulic characteristics such as mean residence time, dispersion index, short circuit, hydraulic efficiency (λ), and dead space. The NaCl was used as chemical tracer in this experiment which injected into the electrochemical tank by pulse injection. The effluent concentration of NaCl concentration were analyzed by plotting RTD curves. The mean residence time varied between 1 – 2 hours using electricity current and without electricity current. Tracer experiment using electricity current provide less mean space value (0.072) illustrated high treatment performance. Hydraulic efficiency showed higher performance (0.65 0 0.80) which is known has a good efficiency. Lower dispersion number (0.001) achieved plug flow condition.
VEGF-C inhibition reverses resistance of bladder cancer cells to cisplatin via upregulating maspin (2015)

The aim of the current study was to elucidate the association between vascular endothelial growth factor C (VEGF-C) and resistance of bladder cancer cells to cisplatin and the underlying mechanism involving maspin. A total of 32 bladder cancer tissue samples from patients (18 males and 14 females with an average age of 65.9 years) were collected from the Fifth Affiliated Hospital of Zhengzhou University (Zhengzhou, China). All patients had undergone cisplatin-based combination chemotherapy. In addition, the BIU87 human bladder cancer cell line was cultured and a cisplatin-resistant subline (BIU87-CisR) was established by continuous exposure to cisplatin. The mRNA expression levels of VEGF-C and maspin in tissue samples, BIU87 cells and BIU87-CisR cells were analyzed by reverse transcription-quantitative polymerase chain reaction (RT-qPCR). Targeted inhibition of VEGF-C in BIU87-CisR cells was performed using small interfering (si)RNA technology and the alteration in levels of maspin was confirmed by RT-qPCR and western blot analysis. siRNA-treated and -untreated BIU87-CisR cells were divided into the following four groups: Control group (no drug treatment), 3 μM cisplatin treated group, 3 μM cisplatin + siRNA treated group and the siRNA treated group. Cell viability following treatment in each group was evaluated by the cell counting kit 8 assay. The cell cycle and apoptotic rate of BIU87-CisR cells was analyzed by propidium iodide (PI) staining and Annexin V-PI double staining with flow cytometry. Furthermore, pcDNA-maspin transfected BIU78-CisR cells were used to establish the effect of maspin on the sensitivity to cisplatin. VEGF-C expression in chemoresistant patients and BIU87-CisR cells was significantly increased compared with chemosensitive patients and normal BIU87 cells, respectively. By contrast, maspin levels were lower in chemoresistant patients and BIU87-CisR cells. Subsequent to VEGF-C inhibition, maspin expression was markedly increased. Cisplatin (3 μM) resulted in moderate proliferation inhibition of BIU87-CisR cells without siRNA pretreatment; however, significant inhibition was observed in the VEGF-C siRNA treated group. In addition, the cell cycle arrest and apoptosis induced by cisplatin was enhanced by VEGF-C inhibition. Overexpression of maspin was able to improve the sensitivity of BIU87-CisR cells to cisplatin. In conclusion, the resistance of bladder cancer cells to cisplatin may be induced by upregulation of VEGF-C, and inhibition of VEGF-C reverses resistance by elevating maspin expression levels.
Copolymerization of liquid sulfur with certain olefinic systems and structure‐property studies on the polymeric materials (1980)

Abstract Liquid sulfur–olefinic reactions at 140°C forming crosslinked polysulfide polymers have been investigated. A systematic approach to the characterization and some structure–property studies on these new polymeric materials has been presented. The olefinic systems of interest are endo‐and exo‐dicyclopentadiene and an oligomeric alkenyl polysulfide. Equimolar S 8 –olefinic system copolymers are amorphous and they show no tendency for sulfur crystallization. A correlation has been drawn between chemical structure and glass transition temperature of the copolymers and terpolymers. Mechanical properties and, in particular, chemical stress relaxation of the crosslinked polysulfide polymers have been investigated.
Supplementary Table 1 from 17β-Estradiol Mobilizes Bone Marrow–Derived Endothelial Progenitor Cells to Tumors (2023)

Supplementary Table 1 from 17β-Estradiol Mobilizes Bone Marrow–Derived Endothelial Progenitor Cells to Tumors
Bioactive Steroids from the Formosan Soft Coral Umbellulifera petasites (2016)

Three new steroids, petasitosterones A and B (<b>1</b> and <b>2</b>) and a spirosteroid petasitosterone C (<b>3</b>), along with eight known steroids (<b>4</b>-<b>11</b>), were isolated from a Formosan marine soft coral <i>Umbellulifera petasites</i>. The structures of these compounds were elucidated by extensive spectroscopic analysis and comparison of spectroscopic data with those reported. Compound <b>3</b> is a marine steroid with a rarely found A/B spiro[4,5]decane ring system. Compounds <b>1</b>-<b>3</b> and <b>5</b> displayed inhibitory activity against the proliferation of a limited panel of cancer cell lines, whereas <b>2</b> and <b>5</b> exhibited significant anti-inflammatory activity to inhibit nitric oxide (NO) production. The inhibitory activities for superoxide anion generation and elastase release of compounds <b>1</b>-<b>11</b> were also examined to evaluate the anti-inflammatory potential, and <b>2</b>-<b>4</b> were shown to exhibit significant activities.