gebhart/patrepeval huggingface dataset:
Highly Sensitive and Multiplexed Protein Measurements (2018)

Proteins are involved in many biological processes. Misfolded, truncated, or mutated proteins as well as over- or underexpressed proteins have been implicated in many diseases. Therefore, detection and quantification of proteins is extremely important. Conventional techniques such as the enzyme-linked immunosorbent assay, Western Blot, and mass spectrometry have enabled discovery and study of proteins in biological samples. However, many important proteins are present at low concentrations, rendering them undetectable using conventional techniques. Furthermore, limited ability to simultaneously measure multiple proteins in a sample has constrained our ability to fully study the proteome. In this review, we comprehensively discuss approaches for protein detection. We first discuss the fundamentals of proteins and protein assays, including affinity reagents, surface functionalization, assay formats, signal detection, and multiplexing. We then discuss the challenges with these methods and review existing methods for highly sensitive and multiplexed protein detection. Finally, we review recent advances in protein detection from the literature and discuss challenges and future directions.
Character-Level Language Modeling with Hierarchical Recurrent Neural Networks (2016)

Recurrent neural network (RNN) based character-level language models (CLMs) are extremely useful for modeling out-of-vocabulary words by nature. However, their performance is generally much worse than the word-level language models (WLMs), since CLMs need to consider longer history of tokens to properly predict the next one. We address this problem by proposing hierarchical RNN architectures, which consist of multiple modules with different timescales. Despite the multi-timescale structures, the input and output layers operate with the character-level clock, which allows the existing RNN CLM training approaches to be directly applicable without any modifications. Our CLM models show better perplexity than Kneser-Ney (KN) 5-gram WLMs on the One Billion Word Benchmark with only 2% of parameters. Also, we present real-time character-level end-to-end speech recognition examples on the Wall Street Journal (WSJ) corpus, where replacing traditional mono-clock RNN CLMs with the proposed models results in better recognition accuracies even though the number of parameters are reduced to 30%.
HOME AND WANDERLUST: PATRIOTIC WAYFARERS ON THE PATH OF“UNIVERSAL LIFE” IN RABINDRANATH TAGORE (2018)

Scholars have observed that the clash between patriotism and cosmopolitanism constitutes a central theme of Rabindranath Tagore’s novel The Home and the World. What remains to be fully addressed, however, is Tagore’s profound depiction of affective and spiritual sources of sympathy larger than loyalty to one’s country. Tagore’s multi-personal delineation of consciousness illuminates the complicated relations between notions of the constitution of self and allegiances to vital sites of belonging—home, nation, the world, and the infinite. Through a close examination of spatial tropes in the novel, the article illustrates how Tagore draws on Buddhist traditions in presenting his vision of svadeśsamāj, a form of social collectivity that amalgamates inner life with traditional Indian ways of communal existence. Paying special attention to the protagonists’ introspections, this essay argues that the novel suggests how moral judgments can be nurtured by aesthetic sentiments that are tied to such communal existence.
Calibration for a Multichannel Magnetic Sensor Array of a Magnetospinography System (2014)

A method for calibrating a multichannel superconducting quantum interference device (SQUID) magnetic sensor array of a magnetospinography (MSG) system is proposed. The MSG system detects weak magnetic fields generated by the neural activity of the spinal cord using the array of SQUID sensors. To calibrate 120 SQUID magnetic sensors, we employed an array of precisely machined circular coils to generate fundamental magnetic fields instead of employing Helmholtz coils, which are generally used for the calibration of magnetic sensors. The effective position, orientation, and sensitivity of each SQUID sensor were determined simultaneously by a parametric numerical optimization algorithm. These sensor parameters are essential for improving the accuracy of the magnetic source analysis. Using this method, we could calibrate the magnetic sensors even though they were installed in a non-transparent cryostat. In addition, the shifts from the designed position and orientation of the sensors as well as their variability were evaluated.
A screen for short-range paracrine interactions (2014)

Conventional methods for studying paracrine signaling in vitro may not be sensitive to short-range effects resulting from signal dilution or decay. We employ a microfabricated culture substrate to maintain two cell populations in microscale proximity. Individual populations can be quickly retrieved for cell-specific readouts by standard high-throughput assays. We show that this platform is sensitive to short-range interactions that are not detectable by common methods such as conditioned media transfer or porous cell culture inserts, as revealed by gene expression changes in a tumor-stromal crosstalk model. In addition, we are able to detect population-specific gene expression changes that would have been masked in mixed co-cultures. We thus demonstrate a tool for investigating an important class of intercellular communication that may be overlooked in conventional biological studies.
Enzymatic Analysis of Positional Distribution of Fatty Acids in Solid Fat by 1,3‐Selective Transesterification with <i>Candida antarctica</i> Lipase B (2014)

Abstract A protocol for the analysis of the positional distribution of fatty acids (FA) in solid triacylglycerols (TAG) was developed using sn ‐1(3) selective alcoholysis catalyzed by immobilized Candida antarctica lipase B (CALB). One part by weight of solid fat and ten parts by weight of ethanol (99.5 %) were warmed to liquefy the fat. After adding 0.44 parts by weight of CALB, the mixture was shaken at 50 °C for 10 min then at 30 °C for 2.8 h. The recovery of 2‐MAG after the 3‐h transesterification reaction was ca . 85 % of the maximum theoretical yield (33 mol%), with the loss of 15 % attributable to the acyl migration from sn ‐2 to sn ‐1(3). The recovery was similar to that of the solvent‐free alcoholysis of structured lipids, 1,3‐dipalmitoyl, 2‐oleoyl glycerol and 1,3‐dioleoyl, 2‐palmitoyl glycerol, conducted at 30 °C for 3 h. In contrast, the acyl migration from sn ‐1(3) to sn ‐2 was hardly observed. Because the detected acyl migration was only in the direction of sn ‐2 to sn ‐1(3), and not vice versa, it is proposed to determine the FA composition of the sn ‐2 position of TAG by the gas chromatographic analysis of 2‐MAG fraction recovered from the enzymatic reaction mixture, and the FA composition of sn ‐1(3) position by a mass balance using the FA composition of TAG and of the sn ‐2 position as inputs. The procedure was successfully applied to palm oil and shea butter, and docosahexaenoic acid (DHA)‐rich single cell oil from Aurantiochytrium sp. KH105 for the first time.
Fungal endophytes limit pathogen damage in a tropical tree (2003)

Every plant species examined to date harbors endophytic fungi within its asymptomatic aerial tissues, such that endophytes represent a ubiquitous, yet cryptic, component of terrestrial plant communities. Fungal endophytes associated with leaves of woody angiosperms are especially diverse; yet, fundamental aspects of their interactions with hosts are unknown. In contrast to the relatively species-poor endophytes that are vertically transmitted and act as defensive mutualists of some temperate grasses, the diverse, horizontally transmitted endophytes of woody angiosperms are thought to contribute little to host defense. Here, we document high diversity, spatial structure, and host affinity among foliar endophytes associated with a tropical tree (Theobroma cacao, Malvaceae) across lowland Panama. We then show that inoculation of endophyte-free leaves with endophytes isolated frequently from naturally infected, asymptomatic hosts significantly decreases both leaf necrosis and leaf mortality when T. cacao seedlings are challenged with a major pathogen (Phytophthora sp.). In contrast to reports of fungal inoculation inducing systemic defense, we found that protection was primarily localized to endophyte-infected tissues. Further, endophyte-mediated protection was greater in mature leaves, which bear less intrinsic defense against fungal pathogens than do young leaves. In vitro studies suggest that host affinity is mediated by leaf chemistry, and that protection may be mediated by direct interactions of endophytes with foliar pathogens. Together, these data demonstrate the capacity of diverse, horizontally transmitted endophytes of woody angiosperms to play an important but previously unappreciated role in host defense.
Curve-Skeleton Properties, Applications, and Algorithms (2007)

Curve-skeletons are thinned 1D representations of 3D objects useful for many visualization tasks including virtual navigation, reduced-model formulation, visualization improvement, animation, etc. There are many algorithms in the literature describing extraction methodologies for different applications; however, it is unclear how general and robust they are. In this paper, we provide an overview of many curve-skeleton applications and compile a set of desired properties of such representations. We also give a taxonomy of methods and analyze the advantages and drawbacks of each class of algorithms.
Numerical Investigations of Wake Expansion in the Offshore Wind Farm Using a Large Eddy Simulation (2022)

Due to abundant wind resources and land saving, offshore wind farms have been vigorously developed worldwide. The wake of wind turbines is an important topic of offshore wind farms, in which the wake expansion is a key issue for the wake model and the layout optimization of a wind farm. The large eddy simulation (LES) is utilized to investigate various offshore wind farms under different operating conditions. The numerical results indicate that it is more accurate to calculate the wake growth rate using the streamwise turbulence intensity or the total turbulence intensity in the environment. By fitting the results of the LES, two formulae are proposed to calculate the wake growth rate of the upstream wind turbine. The wake expansion of the downstream wind turbine is analyzed, and the method of calculating the wake growth rate is introduced. The simulation indicates that the wake expansion of the further downstream wind turbines is significantly reduced. The smaller lateral distance of wind turbines in the offshore wind farm has the less wake expansion of the wind turbines. The wake expansion under different inflow wind speeds is also analyzed, while the wake expansion of wind turbines under more complex conditions needs to be further studied.
Comparison of high frequency signal injection techniques for rotor position estimation at low speed to standstill of PMSM (2012)

Rotor position information is necessary to control PMSM (Permanent Magnet Synchronous Motors). Extracting rotor position information using physical position sensor presents several disadvantages, including increased size, reduced reliability, and additional cost of the whole system. To overcome these drawbacks, there has been considerable interest in sensor less control techniques. Sensor less control of PMSMs can be broadly classified as, fundamental model based methods and machine saliency based methods. Techniques that rely on the fundamental model have the advantages of simplicity and straightforwardness. However these techniques fail to extract rotor position information from low speed to standstill. In the last two decades, a number of high frequency signal injection techniques have been proposed and developed for PMSM rotor position estimation at standstill and low speed without position sensor. These techniques can be classified into continuous signal injection techniques, transient signal injection techniques and high frequency signal embed on to PWM. This paper gives an overview of various approaches to rotor position estimation from low speed to standstill using HFSI techniques. Finally comparison between different rotor position extraction schemes is presented based on hardware complexity, torque ripple, speed range and cost of current measurement system.
Embryonic Chicken Transplantation is a Promising Model for Studying the Invasive Behavior of Melanoma Cells (2015)

Epithelial-to-mesenchymal transition is a hallmark event in the metastatic cascade conferring invasive ability to tumor cells. There are ongoing efforts to replicate the physiological events occurring during mobilization of tumor cells in model systems. However, few systems are able to capture these complex in vivo events. The embryonic chicken transplantation model has emerged as a useful system to assess melanoma cells including functions that are relevant to the metastatic process, namely invasion and plasticity. The chicken embryo represents an accessible and economical 3-dimensional in vivo model for investigating melanoma cell invasion as it exploits the ancestral relationship between melanoma and its precursor neural crest cells. We describe a methodology that enables the interrogation of melanoma cell motility within the developing avian embryo. This model involves the injection of melanoma cells into the neural tube of chicken embryos. Melanoma cells are labeled using fluorescent tracker dye, Vybrant DiO, then cultured as hanging drops for 24 h to aggregate the cells. Groups of approximately 700 cells are placed into the neural tube of chicken embryos prior to the onset of neural crest migration at the hindbrain level (embryonic day 1.5) or trunk level (embryonic day 2.5). Chick embryos are reincubated and analyzed after 48 h for the location of melanoma cells using fluorescent microscopy on whole mounts and cross-sections of the embryos. Using this system, we compared the in vivo invasive behavior of epithelial-like and mesenchymal-like melanoma cells. We report that the developing embryonic microenvironment confers motile abilities to both types of melanoma cells. Hence, the embryonic chicken transplantation model has the potential to become a valuable tool for in vivo melanoma invasion studies. Importantly, it may provide novel insights into and reveal previously unknown mediators of the metastatic steps of invasion and dissemination in melanoma.
Fast-convergence algorithm for ICA-based blind source separation using array signal processing (2002)

We propose a new algorithm for blind source separation (BSS), in which independent component analysis (ICA) and beamforming are combined to resolve the low-convergence problem through optimization in ICA. The proposed method consists of the following two parts: frequency-domain ICA with direction-of-arrival (DOA) estimation, and null beamforming based on the estimated DOA. The alternation of learning between ICA and beamforming can realize fast- and high-convergence optimization. The results of the signal separation experiments reveal that the signal separation performance of the proposed algorithm is superior to that of the conventional ICA-based BSS method.
Monolithic InP Multi-Wavelength Coherent Receiver (2010)

We propose and demonstrate a novel four-channel monolithic polarization-diversity dual-quadrature coherent receiver with balanced detection in InP. It uses an interleave-chirped arrayed waveguide grating that acts simultaneously as a demultiplexer, 90° hybrid, and polarization splitter.
Correlation between Cytotoxicity and DNA Binding of Polypyridyl Ruthenium Complexes (1995)

The cytotoxicity of chloropolypyridyl ruthenium complexes of structural formulas [Ru(terpy)-(bpy)Cl]Cl, cis-[Ru(bpy)2Cl2], and mer-[Ru(terpy)Cl3] (terpy = 2,2':6'2"-terpyridine, bpy = 2,2'-bipyridyl) has been studied in murine and human tumor cell lines. The results show that mer-[Ru(terpy)Cl3] exhibits a remarkably higher cytotoxicity than the other complexes. Moreover, investigations of antitumor activity in a standard tumor screen have revealed the highest efficiency for mer-[Ru(terpy)Cl3]. In a cell-free medium, the ruthenium complexes coordinate to DNA preferentially at guanine residues. The resulting adducts can terminate DNA synthesis by thermostable VentR DNA polymerase. The reactivity of the complexes to DNA, their efficiency to unwind closed, negatively supercoiled DNA, and a sequence preference of their DNA adducts (studied by means of replication mapping) do not show a correlation with biological activity. On the other hand, the cytotoxic mer-[Ru(terpy)Cl3] exhibits a significant DNA interstrand cross-linking, in contrast to the inactive complexes which exhibit no such efficacy. The results point to a potential new class of metal-based antitumor compounds acting by a mechanism involving DNA interstrand cross-linking.
The influence of magnetite nano particles on the behaviour of insulating oils for pulse power applications (2011)

The effects of the addition of magnetite nanoparticles on the breakdown strength of three insulating liquids have been examined. The liquids considered are: a mineral transformer oil; a synthetic ester liquid, Midel 7131, and a specialist high permittivity liquid for pulse power applications THESO. The expected increases in breakdown strength were observed in the mineral oil and synthetic ester liquids. However in the case of the high permittivity liquid no significant changes in the breakdown strength were observed. Possible explanations for the differences in the observed behavior for the THESO insulating liquid are discussed.
Exact Design of the Marchand Balun (1979)

Exact methods for the synthesis of commensurate length distributed networks are used to compute the circuit element values of three implementations of the Marchand balun. One of these is a new implementation which incorporates a quarter-wave line at both the balanced and unbalanced ports. As a result, the practical operating range of the Marchand balun is expanded without compromising on its inherent compact physical realization. Graphs of the element values of the second and third types have been prepared to simplify the design of the balun for a wide range of load resistance and bandwidth combinations.
An unsupervised model for statistically determining coordinate phrase attachment (1999)

This paper examines the use of an unsupervised statistical model for determining the attachment of ambiguous coordinate phrases (CP) of the form nl p n2 cc n3. The model presented here is based on JAR98], an unsupervised model for determining prepositional phrase attachment. After training on unannotated 1988 Wall Street Journal text, the model performs at 72% accuracy on a development set from sections 14 through 19 of the WSJ TreeBank [MSM93].
Surfactant-assisted growth of CdS thin films for photovoltaic applications (2006)

A common nonionic surfactant, Triton X-100, was used to modify the chemical bath deposition of CdS “buffer” layers on Cu(In,Ga)Se2 (CIGS) thin films. Addition of the surfactant to the CdS deposition bath allowed increased wetting of Cu(In,Ga)Se2 substrates and an increase in the uniformity of films, especially on model hydrophobic substrates. X-ray photoelectron spectroscopy and ultraviolet photoelectron spectroscopy data demonstrate that films produced with the surfactant have the same chemical and electronic properties as films grown without it. In CdS∕Cu(In,Ga)Se2 devices, it was found that Triton X-100 allowed the use of CdS layers that were three to four times thinner than those used normally in high efficiency CIGS-based devices and eliminated the large drops in open-circuit voltage that usually accompany very thin buffer layers. For these thin CdS layers and relative to devices made without the surfactant, average absolute cell efficiencies were increased from 10.5% to 14.8% or by a relative 41%. Visual inspection of the CdS depositions reveals one possible mechanism of the surfactant’s effects: Bubbles that form and adhere to the CIGS surface during the chemical bath deposition are almost completely eliminated with the addition of the TX-100. Thus, junction nonuniformities, pinholes, and thin areas in the CdS layer caused by poor wetting of the substrate surface are sharply reduced, leading to large increases in the open-circuit voltage in devices produced with the surfactant.
The Danger Within (2004)

A recent study shows that crystalline uric acid acts as an immunologic adjuvant by triggering the maturation of dendritic cells, which can then prime the T-cell response.
<title>Human face recognition method based on the statistical model of small sample size</title> (1992)

Automatic recognition of human faces is a frontier topic in computer vision. In this paper, a novel recognition approach to human faces is proposed, which is based on the statistical model in the optimal discriminant space. Singular value vector has been proposed to represent algebraic features of images. This kind of feature vector has some important properties of algebraic and geometric invariance, and insensitiveness to noise. Because singular value vector is usually of high dimensionality, and recognition model based on these feature vectors belongs to the problem of small sample size, which has not been solved completely, dimensionality compression of singular value vector is very necessary. In our method, an optimal discriminant transformation is constructed to transform an original space of singular value vector into a new space in which its dimensionality is significantly lower than that in the original space. Finally, a recognition model is established in the new space. Experimental results show that our method has very good recognition performance, and recognition accuracies of 100 percent are obtained for all 64 facial images of 8 classes of human faces.
SLM of Net-Shaped High Strength Ceramics: New Opportunities for Producing Dental Restorations (2011)

Oxide ceramics yield excellent mechanical properties along with outstanding thermal and wear resistance. However, little work on additive Manufacturing (AM) of high-strength ceramics has been stated. In the present paper the current state of development in Selective Laser Melting (SLM) of pure ceramic specimens is reviewed. During the present approach the eutectic mixture of pure alumina (Ah0 3) and zirconia (Zr02) powder is completely molten while crack formation is prevented by a high-temperature C02-Iaser preheating. This approach yields net-shaped, fully dense specimens reaching flexural strengths of above 500 MPa without post-processing. One potential application for this technology are fully-ceramic dental restorations frameworks, as the demanded maximum loads of above I 000 N are met. Alternative preheating strategies are presented to allow for manufacturing larger volumetric parts.
High‐sensitivity OAM phase gradient detection based on time‐modulated harmonic characteristic analysis (2017)

A novel phase gradient method for detecting orbital angular momentum modes is proposed. By utilising a two‐element time‐modulated array, the phase gradient of the received signal is estimated through analysing the modulated harmonic component. The bit error rate performances are evaluated using Monte‐Carlo simulation. Results show that the sensitivity strongly depends on the number of sampling modulation pulses. Compared with the conventional phase gradient receiver, the proposed method obviously enhances the performance of detection.