gebhart/patrepeval huggingface dataset:
A novel bacteriochlorin-gold nanoparticle construct for photoacoustic imaging (2016)

Herein we report the synthesis of new gold nanoparticle-bacteriochlorin conjugate (Au-NP-PS) as a highly efficient photoacoustic (PA) imaging agent. The conjugate was obtained by reacting a water soluble thio-bacteriochlorin (derived from bacteriochlorophyll-[Formula: see text] with Au-NP. The resulting NPs were characterized by UV-vis, TEM (transmission electron microscopy)/HRTEM (high resolution TEM) and diffraction pattern. The results obtained from in vitro studies suggest that due to conjugation between the PS and Au-NPs, the photoacoustic (PA) signals from the Au-NP-PS were greatly enhanced by a factor of 2.4 compared to that from PS alone.
Oncolytic Measles Virus Retargeting by Ligand Display (2011)

Despite significant advances in recent years, treatment of metastatic malignancies remains a significant challenge. There is an urgent need for development of novel therapeutic approaches. Virotherapy approaches have considerable potential, and among them measles virus (MV) vaccine strains have emerged as a promising oncolytic platform. Retargeted MV strains deriving from the Edmonston vaccine lineage (MV-Edm) have shown comparable antitumor efficacy to unmodified strains against receptor expressing tumor cells with improved therapeutic index. Here, we describe the construction, rescue, amplification, and titration of fully retargeted MV-Edm derivatives displaying tumor specific receptor binding ligands on the viral surface in combination with H protein CD46 and SLAM entry ablating mutations.
Supplementary Figure S1 from A Four-Gene Promoter Methylation Marker Panel Consisting of <i>GREM1, NEURL, LAD1,</i> and <i>NEFH</i> Predicts Survival of Clear Cell Renal Cell Cancer Patients (2023)

&lt;p&gt;Supplementary Figure S1. Methylation analysis of GREM1, LAD1, NEFH and NEURL by methylation-specific PCR (MSP) in the hospital- and population-based series and in the TCGA series. A. Schematic representation of the CpG island promoter region of the four genes with the location of the primers used for MSP (indicated by horizontal arrows) relative to the probes used in the TCGA analyses (indicated by a vertical arrow) in this study. Vertical lines represent the location of CpG dinucleotides, the black box indicates the first exon, and the grey horizontal line represents the promoter CpG island. TSS: transcription start site. B. Histograms of the beta-values of the selected probes for GREM1, LAD1, NEFH and NEURL. The vertical grey line indicates the beta-value cut-off for each probe that was used in the TCGA analyses.&lt;/p&gt;
Development of Lymphoproliferative Disorder of Granular Lymphocytes in Association with Hairy Cell Leukemia (2000)

Lymphoproliferative disorder of granular lymphocytes (LDGL) is a low grade T-cell disease characterized by clonal expansion of large granular lymphocytes of either T cell or natural killer (NK) cell lineage that express the cytotoxic T-cell/NK cell antigens CD16, CD56 and/or CD57. LDGL has been described in association with other malignancies, leading to theories of a common abnormal stem cell as well as development of the LDGL as an immune response to a primary tumor. We have studied 32 patients with hairy cell leukemia (HCL). In 15 patients (47%) we detected an increase in cells expressing cytotoxic T-cell/NK cell antigens. In 10(31%) patients these cells were of T cell lineage, while 5 patients (16%) had increased NK-cells. T cell clonality was detected by PCR in all cases with increased cytotoxic T-cells in which adequate DNA was obtained from peripheral blood. Since in 2 patients the LDGL was not present at diagnosis but developed during follow up, our data suggests that clonal LDGL may develop in response to the HCL. The significance of LDGL in the setting of HCL and flow cytometric evaluation of HCL versus LDGL will be discussed.
Iron acquisition: a novel perspective on mucormycosis pathogenesis and treatment (2008)

Further investigation and development of iron chelators as adjunctive therapy for mucormycosis is warranted.
Structural and functional stability of the sulfur-free surfactant protein B peptide mimic B-YL in synthetic surfactant lipids (2021)

The structure of the B-YL peptide and the in vitro and in vivo functions of the B-YL surfactant were each maintained after three years of refrigeration storage.
Advances and Applications in Comprehensive Gearbox Aero-Thermodynamics and Tribology Simulation (2017)

The current status of an ongoing effort to develop a comprehensive gearbox aero-thermodynamics and tribology simulation tool, named PSULOL, applicable to both well-lubricated and loss-of-lubrication operation is presented. PSULOL employs a multi-scale approach, wherein various physical effects including: meshing tribology, convection heat transfer within the system and to the environment, high-frequency thermodynamic effects induced by the gear meshing frequency, and the long-time response of the overall gearbox temperature to a net imbalance of heat generation and transfer to the environment are simulated separately and coupled with one another iteratively through appropriate boundary and initial conditions. As established in 2014, the first-generation version of PSULOL was the first computational fluid dynamics-based (CFD-based) tool coupled with an all-lubrication regime tribology model capable of simulating transient loss-of-lubrication failure of high-speed gearboxes. This first version was built on an in-house research CFD code, NPHASE-PSU, and relied on a number of physical simplifications, particularly with regard to the geometric configuration of the housing, and to the effects of the coupling between multiphase flow within the system (retained lubricant dynamics) and meshing tribology. Here, present efforts underway to increase the physical fidelity and ease-of-use of PSULOL are outlined, and progress toward simulating physically-realistic gearbox configurations is shown. This includes modeling the disperse multiphase flow of lubricant droplets and film within the system, and transitioning from NPHASE-PSU, an in-house research CFD code, to StarCCM+, a commercial code that is more user-friendly and features additional geometry-handling capabilities.
Development of a nondestructive fluorescence-based enzymatic staining of microcolonies for enumerating bacterial contamination in filterable products (2010)

The advantage of this nondestructive procedure is to allow contaminants identification after membrane re-incubation. This method could be easily applied in routine in pharmaceutical, clinical and food and beverage industries to monitor contaminations.
Development of fast photospeed chemically amplified resist in EUV lithography (2004)

In EUV lithography, the requirement of the resist sensitivity is less than 2 mJ/cm*, which gives the large relaxation to the requirement of the EUV light source power. Furthermore, the line width roughness (LWR) of less than 2 nm (3 sigma) and outgassing total fragment pressure of less than 10^-6 Pa during the exposure time are required.
Genetic Dissection of Resistance to Common Rust (Puccinia Sorghi) in Tropical Maize (Zea mays L.) by Combined Genetic Mapping and Genomic Prediction (2020)

Abstract Background: Common rust is one of the major foliar diseases of maize, leading to significant grain yield losses and poor grain quality. The most sustainable strategy for controlling common rust is to develop resistant maize varieties, which requires a further understanding of genetic dissection of common rust resistance. Results: In this study, an association panel and two bi-parental doubled haploid (DH) populations were used to perform genome-wide association study (GWAS), linkage mapping, and genomic prediction analyses. All the populations were phenotyped in multi-environment trials for common rust resistance and genotyped with genotyping-by-sequencing (GBS) single-nucleotide polymorphisms (SNPs). GWAS revealed six SNPs significantly associated with common rust resistance at bins 1.05, 1.10, 3.04, 3.05, 4.08, and 10.04, respectively. The SNP effect of each SNP ranged from 0.13 to 0.17. Linkage mapping identified six quantitative trait loci (QTL) in the first DH population (DH1) and two QTL in the second DH population (DH2), distributed on chromosomes 1, 2, 3, 4, 6, 7, and 9, respectively. The phenotypic variation explained (PVE) of each QTL ranged from 3.55% to 12.45%. A new major QTL was detected in DH1 on chromosome 7 in the region between 144,585,945 and 149,528,489 bp, it had the highest LOD score of 7.82 and the largest PVE value of 12.45%. The genomic regions located at bins 1.05, 1.10, and 4.08 were detected by both GWAS and linkage mapping. GRMZM2G114893 (bin 1.05) and GRMZM2G138949 (bin 4.08) were identified as the putative candidate genes conferring common rust resistance. The genomic prediction accuracies observed in the association panel and two bi-parental DH populations were 0.61, 0.51, and 0.10, respectively. Conclusions: These results provided new insight into the genetic architecture of common rust resistance in maize and a better understanding of the application of genomic prediction for common rust resistance in maize breeding.
Analytical Compact Model for PMUTs Interfaces (2018)

Piezoelectric Micromachined ultrasound transducers (PMUT) have been studied extensively in the last few years, with a focus on the transducer fabrication or application driven front-end interface. This paper presents an analytical approach that addresses PMUTs along with their front-end interfaces. It provides an analytical compact model which aids with defining the different signal levels within each of the PMUT's three physical domains: mechanical, electrical and acoustic. The model input parameters are the transducer physical dimensions and its layers stack configuration. The model extends to include the transducer's analog front-end (AFE) interface. Transfer functions of the PMUT along with its frontend are derived showing good agreement when compared with measurements from literature.
<title>Absolute calibration of interpolation errors in interferometers</title> (1996)

Two novel self-calibration methods are proposed for calibrating fringe-interpolation errors of interferometers with nanometer resolution, and the basic characteristics of the methods are discussed. The one method owes its accuracy to the repeatability of the displacement of PZT actuator which gives input displacement to the calibrated interferometer. This method needs only one interferometer. The other method uses two interferometers, which has been proposed for the calibration of linearity error of general displacement sensors. The calibration accuracy of this method theoretically approaches the resolution limit of the interferometer, which is determined by the signal-to-noise ratio and the stability of the measurement system. A compact differential interferometer that uses a laser diode as the light source has been developed in order to demonstrate the viability of the proposed former calibration method. As the specimens for the other method interferometers using optical fiber have been developed. The reflected beam from the one end of the optical fiber and that from the target mirror make interference fringes in this interferometer. The conventional fringe-counting and phase modulation methods are combined in order to extend the measurement range and improve the resolution of these error which causes interpolation error in the interferometer. The calibration results have shown that both methods can attain nanometric accuracy judging from the repeatability. Therefore it was confirmed that the absolute nanometric calibration is realized with each method when the wave length of the interferometer is known.
Controllable Magnetic Metamaterial Using Digitally Addressable Split-Ring Resonators (2009)

An ideal metamaterial is composed of identical elements in a uniformly structured array so that the material response is a single magnetic or electric resonance. Variations in the metamaterial particle characteristics or array assembly result in undesirable broadening of the effective material response. When lumped circuit elements are used in metamaterial particles, this effect can be significant due to element variability. To mitigate this effect, we designed, fabricated, and characterized a magnetic metamaterial in which the response of each particle can be individually tuned. Such a material can be reconfigured into a variety of states for use in different applications.
Randomized comparative long-term survival study of endoscopic and thoracoscopic esophageal wall repair after NOTES mediastinoscopy in healthy and compromised animals (2010)

Transesophageal mediastinoscopy could be performed equally well as the transthoracic procedure, both in healthy and compromised animals. However, on follow-up, the compromised animals had worse outcomes, with more complications and two deaths (17 %), one in each arm.
RHash: Robust Hashing via L_infinity-norm Distortion (2017)

Hashing is an important tool in large-scale machine learning. Unfortunately, current data-dependent hashing algorithms are not robust to small perturbations of the data points, which degrades the performance of nearest neighbor (NN) search. The culprit is the minimization of the L_2-norm, average distortion among pairs of points to find the hash function. Inspired by recent progress in robust optimization, we develop a novel hashing algorithm, dubbed RHash, that instead minimizes the L_1-norm, worst-case distortion among pairs of points. We develop practical and efficient implementations of RHash that couple the alternating direction method of multipliers (ADMM) framework with column generation to scale well to large datasets. A range of experimental evaluations demonstrate the superiority of RHash over ten state-of-the-art binary hashing schemes. In particular, we show that RHash achieves the same retrieval performance as the state-of-the-art algorithms in terms of average precision while using up to 60% fewer bits.
High power performance of ultrahigh bandwidth MSM TWPDs (2002)

Low-temperature-grown GaAs (LTG-GaAs) based photodetectors (PDs) merit a lot of attention due to their ultrahigh electrical bandwidth performance. By utilizing photomixing technique, these high speed PDs can radiate power in the THz frequency regime. In such application, these PDs usually need to experience high optical power illumination and operate in high bias voltage. In this paper, we studied the behavior of a novel MSM traveling wave photodetector (MSM TWPD) under high optical power illumination and high bias level by electrical-optical sampling technique based on a femtosecond Ti:sapphire laser. This novel device has been demonstrated with ultrahigh bandwidth (570 GHz) and reasonable quantum efficiency (8%). With a large photoabsorption volume and better capability of undertaking high bias voltage, improved high power performance can also be obtained in this device compared with previous LTG-GaAs based p-i-n TWPD.
SH2-B Is Required for Both Male and Female Reproduction (2002)

Many growth factors and hormones modulate the reproductive status in mammals. Among these, insulin and insulin-like growth factor I (IGF-I) regulate the development of gonadal tissues. SH2-B has been shown to interact with insulin and IGF-I receptors, although the role of SH2-B in these signals has not been clarified. To investigate the role of SH2-B, we generated mice with a targeted disruption of the SH2-B gene. Both male and female SH2-B(-/-) mice showed slight retardation in growth and impaired fertility. Female knockout mice possess small, anovulatory ovaries with reduced numbers of follicles and male SH2-B(-/-) mice have small testes with a reduced number of sperm. SH2-B(-/-) cumulus cells do not respond to either follicle-stimulating hormone or IGF-I. These data suggest that SH2-B plays a critical role in the IGF-I-mediated reproductive pathway in mice.
Laser Doping and Texturing of Silicon for Advanced Optoelectronic Devices (2016)

Irradiating a semiconductor with intense laser pulses in the presence of dopants changes the sample's optical, material, and electronic properties. The resulting material has applications in detection and energy harvesting.
Williams-Beuren Syndrome (2007)

Williams-Beuren syndrome (WBS; also called Williams syndrome) is a multisystem developmental disorder that is almost always associated with an approx 1.5-Mb deletion of chromosome 7q11.23 (OMIM no. 194050). The deletion was identified in 1993 based on the observation of phenotypic overlap with supravalvular aortic stenosis (SVAS), a distinct autosomal dominant disorder affecting the cardiovascular system (1). It has since been shown that SVAS arises because of the disruption of one copy of the elastin gene, through either deletion, translocation or point mutation (2–4), but the genes contributing to the remaining aspects of WBS have not yet been definitively determined.
Performance Attribution Through a Factor Lens (2018)

We propose an adjustment of standard regression-based factor attribution to address a common issue: implementation constraints often mean that investors cannot realize the full potential of a factor strategy, but standard attribution analysis assumes that they can – leaving part of the portfolio return unexplained. Our alternative classifies stocks based on their factor exposures and identifies the segments most responsible for the unexplained portfolio return. The resulting nonlinear factor attribution better reconciles realized performance with the investment process, mitigating both the long-term average and short-term volatility of any residual. While our focus is on equity investing, the proposed methodology for factor attribution also applies to other asset classes.
380-nm Ultraviolet Light-Emitting Diodes with InGaN/AlGaN MQW Structure (2013)

In this paper, we demonstrate the capabilities of 380-nm ultraviolet (UV) light-emitting diodes (LEDs) using metal organic chemical vapor deposition. The epi-structure of these LEDs consists of InGaN/AlGaN multiple quantum wells on a patterned sapphire substrate, and the devices are fabricated using a conventional LED process. The LEDs are packaged with a type of surface mount device with Al-metal. A UV LED can emit light at 383.3 nm, and its maximum output power is 118.4 mW at 350 mA.
A Hybrid CPV/T System Featuring Transmissive, Spectrum-Splitting Concentrator Photovoltaics (2018)

A hybrid solar energy conversion system has been developed for converting sunlight into electricity and thermal energy. The system increases efficiency and reduces cost by utilizing a transmissive, spectrum-splitting concentrator photovoltaic module featuring triple junction III-V solar cells. This enables cell temperatures to be maintained below 100°C while thermal temperatures may rise as high as 600°C. The presentation will discuss module and system design, a series of prototype iterations, and multi-day outdoor field testing. Techno-economic analysis will be presented in a variety of locations and industrial process heat contexts.
Label‐Free, Longitudinal Visualization of PDT Response In Vitro with Optical Coherence Tomography (2012)

A major challenge in creating and optimizing therapeutics in the fight against cancer is visualizing and understanding the microscale spatiotemporal treatment response dynamics that occur in patients. This is especially true for photodynamic therapy (PDT), where therapeutic optimization relies on understanding the interplay between factors such as photosensitizer localization and uptake, in addition to light dose and delivery rate. In vitro 3D culture systems that recapitulate many of the biological features of human disease are powerful platforms for carrying out detailed studies on PDT response and resistance. Current techniques for visualizing these models, however, often lack accuracy due to the perturbative nature of the sample preparation, with light attenuation complicating the study of intact models. Optical coherence tomography (OCT) is an ideal method for the long-term, non-perturbative study of in vitro models and their response to PDT. Monitoring the response of 3D models to PDT by time-lapse OCT methods promises to provide new perspectives and open the way to cancer treatment methodologies that can be translated towards the clinic.
Spin-on carbon based on fullerene derivatives as hardmask materials for high-aspect-ratio etching (2013)

The advance of lithographic resolution has made it necessary to adopt extremely thin photoresist films for the fabrication of “2× nm” structures in order to mitigate problems such as resist collapse during development but limiting achievable etch depths at the same time. By using multilayer hardmask stacks, a considerable increase in achievable aspect ratio is possible. We have previously presented a fullerene-based spin-on carbon hardmask material capable of high-aspect-ratio etching. We report our latest findings in material characterization of an original and a modified formulation. By using a higher adduct derivative fullerene, the solubility in industry-friendly solvents and thermal stability could be improved. The etching performance and materials characteristics of the new higher-adduct fullerene hardmask were found to be comparable to those of the original hardmask.
The Genomic Architecture of Sporadic Heart Failure (2011)

Common or sporadic systolic heart failure (heart failure) is the clinical syndrome of insufficient forward cardiac output resulting from myocardial disease. Most heart failure is the consequence of ischemic or idiopathic cardiomyopathy. There is a clear familial predisposition to heart failure, with a genetic component estimated to confer between 20% and 30% of overall risk. The multifactorial etiology of this syndrome has complicated identification of its genetic underpinnings. Until recently, almost all genetic studies of heart failure were designed and deployed according to the common disease-common variant hypothesis, in which individual risk alleles impart a small positive or negative effect and overall genetic risk is the cumulative impact of all functional genetic variations. Early studies used a candidate gene approach focused mainly on factors within adrenergic and renin-angiotensin pathways that affect heart failure progression and are targeted by standard pharmacotherapeutics. Many of these reported allelic associations with heart failure have not been replicated. However, the preponderance of data supports risk-modifier effects for the Arg389Gly polymorphism of β1-adrenergic receptors and the intron 16 in/del polymorphism of angiotensin-converting enzyme. Recent unbiased studies using genome-wide single nucleotide polymorphism microarrays have shown fewer positive results than when these platforms were applied to hypertension, myocardial infarction, or diabetes, possibly reflecting the complex etiology of heart failure. A new cardiovascular gene-centric subgenome single nucleotide polymorphism array identified a common heat failure risk allele at 1p36 in multiple independent cohorts, but the biological mechanism for this association is still uncertain. It is likely that common gene polymorphisms account for only a fraction of individual genetic heart failure risk, and future studies using deep resequencing are likely to identify rare gene variants with larger biological effects.