gebhart/patrepeval huggingface dataset:
Importance of diffuse scattering phenomena in moth-eye arrays for broadband infrared applications (2013)

Moth-eye (ME) arrays with varying aspect ratios and profile heights were fabricated in Si using a general colloidal lithography and reactive ion etching technique. Antireflective (AR) properties of the arrays were rigorously assessed from the near to far infrared (λ=2-50 μm) using transmission and reflection measurements via dispersive and Fourier transform infrared spectroscopy and modeled using an effective medium approximation (EMA). Infrared transmission of low aspect ratio structures (~2) matched the EMA model, indicating that the most important factor for AR at higher wavelengths is structure height. High aspect ratio structures (>6) were highly transmissive (>90% of theoretical maximum) over a large bandwidth in the mid-infrared (20-50 μm). Specular reflectance, total transmission, and diffuse reflectance (DR) measurements indicate that ME structures do not reach the theoretical maximum at near-infrared wavelengths due to DR and forward scattering phenomena. Ultimately, correlating optical performance with feature geometry (pitch, profile, height, etc.) over multiple length scales allows intelligent design of ME structures for broadband applications.
INACTIVATION OF LAMBDA PHAGE WITH 658 nm LIGHT USING A DNA BINDING PORPHYRIN SENSITIZER (1992)

Exposure of lambda phage to 658 nm light in the presence of 5,10,15,20-tetrakis-(1-methyl-4-pyridyl)-21H,23H-porphine, tetra-p-tosylate leads to complete (greater than 7 logs) inactivation as measured by the plaque assay. The sensitizer without light and 658 nm photolysis of lambda phage in the absence of sensitizer do not lead to a measurable decrease in viral inactivity. Viral inactivation is not dependent upon the presence of oxygen.
Cumulants of Hawkes Processes are Robust to Observation Noise (2021)

Multivariate Hawkes processes (MHPs) are widely used in a variety of fields to model the occurrence of causally related discrete events in continuous time. Most state-of-the-art approaches address the problem of learning MHPs from perfect traces without noise. In practice, the process through which events are collected might introduce noise in the timestamps. In this work, we address the problem of learning the causal structure of MHPs when the observed timestamps of events are subject to random and unknown shifts, also known as random translations. We prove that the cumulants of MHPs are invariant to random translations, and therefore can be used to learn their underlying causal structure. Furthermore, we empirically characterize the effect of random translations on state-of-the-art learning methods. We show that maximum likelihood-based estimators are brittle, while cumulant-based estimators remain stable even in the presence of significant time shifts.
PD42-07 IMPACT OF LYMPH NODE METASTASES ON PROGNOSIS AFTER RADICAL PROSTATECTOMY FOR PATIENTS WITH OLIGOMETASTATIC PROSTATE CANCER (2018)

INTRODUCTION AND OBJECTIVES: To evaluate the oncological and functional results of SRP in 2 large patient series treated in 2 referal centres between 2000 and 2016.
Beyond CPO: A Motivation and Approach for Bringing Optics Onto the Silicon Interposer (2022)

Co-packaged optics (CPO) technology is well positioned to break through the bottlenecks that impede efficient bandwidth scaling in key near-term commercial integrated circuits. We begin by providing some historical context for this important sea change in the optical communications industry. Then, motivated by GPU-based accelerated computing requirements, we investigate the next pain points that are poised to constrain bandwidth and efficiency in future CPO-based systems. We identify 2.5D integrated optics (i.e., bringing optics onto the interposer) as a promising solution that can enable continued scaling for these systems due to the dense wiring available which facilitates more efficient slow-and-wide electrical interfaces. We explore the benefits, challenges, and requirements associated with such tight coupling of the processors and optical engines by considering high-level photonic link design, technology, and packaging. We demonstrate the viability of a control loop which can adequately regulate temperature within the aggressive thermal environment. Then, we introduce a custom simulation framework that allows quantified comparisons of detailed design decisions; the simulations validate the feasibility of the general approach while also providing key guidance to designers on best directions to pursue for efficient optimization.
Orthogonal solid‐phase synthesis of human gastrin‐I under mild conditions* (1990)

An approach to the solid-phase segment condensation synthesis of the 17-peptide amide human gastrin-I has been developed. N alpha-amino and side-chain protection were provided by 9-fluorenylmethyloxycarbonyl (Fmoc) and tert.-butyl groups, and a series of anchors cleavable under mild conditions were used. The N-terminal pentapeptide pGlu-Gly-Pro-Trp-Leu-OH was prepared using a p-alkoxybenzyl ester linkage made by a preformed handle strategy. Cleavage, in 65% yield, was with the new Reagent M: CF3COOH-CH2Cl2-beta-mercaptoethanol--anisole (70:30:2:1), which was optimized to preserve the labile tryptophan residue. A new preformed handle procedure expedited solid-phase synthesis of the protected "middle" hexapeptide, Fmoc-(Glu(OtBu]5-Ala-OH, anchored as an o-nitrobenzyl ester. Chains were not lost during this assembly, and final photolytic cleavage (350 nm) in toluene--CF3CH2OH (4:1) occurred in 59% yield. Both protected intermediates were purified by simple gel filtration, whereupon they were shown to be pure by analytical HPLC, and gave satisfactory NMR and FABMS spectra. Last, the C-terminal hexapeptide, Tyr(tBu)-Gly-Trp-Met-Asp(OtBu)-Phe, was assembled on a tris(alkoxy)benzylamide "PAL" support. For the polymer-supported segment condensation, the middle and N-terminal pieces were added respectively in greater than 98% and 89% yields (judged by amino acid analysis and solid-phase sequencing), by overnight couplings in N,N-dimethylformamide (DMF) mediated by benzotriazolyl N-oxytrisdimethylaminophosphonium hexafluorophosphate (BOP) in the presence of 1-hydroxybenzotriazole (HOBt) and N-methylmorpholine (NMM). Racemization was 4% and 11% respectively at Ala and Leu. Cleavage with Reagent M followed by reversed-phase chromatography gave pure gastrin-I in an overall 30% isolated yield. These results compare favorably with those from a stepwise assembly.
Cellular expansion of MSCs: Shifting the regenerative potential (2022)

Mesenchymal-derived stromal or progenitor cells, commonly called "MSCs," have attracted significant clinical interest for their remarkable abilities to promote tissue regeneration and reduce inflammation. Recent studies have shown that MSCs' therapeutic effects, originally attributed to the cells' direct differentiation capacity into the tissue of interest, are largely driven by the biomolecules the cells secrete, including cytokines, chemokines, growth factors, and extracellular vesicles containing miRNA. This secretome coordinates upregulation of endogenous repair and immunomodulation in the local microenvironment through crosstalk of MSCs with host tissue cells. Therapeutic applications for MSCs and their secretome-derived products often involve in vitro monolayer expansion. However, consecutive passaging of MSCs significantly alters their therapeutic potential, inducing a broad shift from a pro-regenerative to a pro-inflammatory phenotype. A consistent by-product of in vitro expansion of MSCs is the onset of replicative senescence, a state of cell arrest characterized by an increased release of proinflammatory cytokines and growth factors. However, little is known about changes in the secretome profile at different stages of in vitro expansion. Some culture conditions and bioprocessing techniques have shown promise in more effectively retaining the pro-regenerative and anti-inflammatory MSC phenotype throughout expansion. Understanding how in vitro expansion conditions influence the nature and function of MSCs, and their associated secretome, may provide key insights into the underlying mechanisms driving these alterations. Elucidating the dynamic and diverse changes in the MSC secretome at each stage of in vitro expansion is a critical next step in the development of standardized, safe, and effective MSC-based therapies.
Magnetic Sensors for Protease Assays (2003)

Superparamagnetische Nanosensoren, die an Avidin (CLIO-A) gebunden sind, können sensitiv und quantitativ die proteolytische Spaltung des zweifach biotinylierten Peptidsubstrats (als Stäbe dargestellt) durch Änderungen der magnetischen Resonanz messen. Dieser Ansatz könnte zukünftig bei der Aktivitätsbestimmung von hydrolysierenden Enzymen eine große Rolle spielen.
Efficient Light Bending with Isotropic Metamaterial Huygens’ Surfaces (2014)

Metamaterial Huygens' surfaces manipulate electromagnetic wavefronts without reflection. A broadband Huygens' surface that efficiently refracts normally incident light at the telecommunication wavelength of 1.5 μm is reported. The electric and magnetic responses of the surface are independently controlled by cascading three patterned, metallic sheets with a subwavelength overall thickness of 430 nm. The peak efficiency of the device is significantly enhanced by reducing the polarization and reflection losses that are inherent to earlier single-layer designs.
Stabilization of Phosphatidylserine/Phosphatidylethanolamine Liposomes with Hydrophilic Polymers Having Multiple “Sticky Feet” (2001)

The ability of three novel polymers to protect phosphatidylethanolamine/phosphatidylserine (1:1) vesicles against calcium-induced destabilization (dye leakage) has been investigated. The polymers are a telechelic, hydrophobically terminated poly(ethylene glycol) (PEG), a polymer of the macromonomer PEG8000−lysine-stearylamide, and a hydrophobically modified poly(acrylic acid). These polymers are predominantly hydrophilic but have multiple hydrophobic moieties which serve to anchor them in the lipid bilayers. Like singly anchored PEG, the two PEG-based polymers were able to provide effective stabilization at concentrations sufficient to produce a polymer “brush” on the liposome surface. Interestingly, the poly(acrylic acid) polymer did not provide full stabilization even at concentrations that should have produced brush coverage, possibly owing to a more expanded polymer conformation. The potential advantages of stabilization with polymers having multiple “sticky feet” are discussed.
Peginterferon Lambda-1a for treatment of outpatients with uncomplicated COVID-19: a randomized placebo-controlled trial (2020)

Abstract Type III interferons have been touted as promising therapeutics in outpatients with coronavirus disease 2019 (COVID-19). We conducted a randomized placebo-controlled trial in 120 patients with mild to moderate COVID-19 to determine whether a single, 180 mcg subcutaneous dose of Peginterferon Lambda-1a (Lambda) could shorten the duration of viral shedding (primary endpoint) or symptoms (secondary endpoint, NCT04331899 ). In both the 60 patients receiving Lambda and the 60 receiving placebo, the median time to cessation of viral shedding was 7 days (hazard ratio [HR] = 0.81; 95% confidence interval [CI] 0.56 to 1.19). Symptoms resolved in 8 and 9 days in Lambda and placebo, respectively (HR 0.94; 95% CI 0.64 to 1.39). At enrollment; 41% of subjects were SARS-CoV-2 IgG seropositive; compared to placebo, lambda tended to delay shedding cessation in seronegatives (aHR 0.66, 95% CI 0.39-1.10) and to hasten shedding cessation in seropositives (aHR 1.58, 95% CI 0.88-2.86; p for interaction = 0.03). Liver transaminase elevations were more common in the Lambda vs. placebo arm (15/60 vs 5/60; p = 0.027). In this study, a single dose of subcutaneous Peginterferon Lambda-1a neither shortened the duration of SARS-CoV-2 viral shedding nor improved symptoms in outpatients with uncomplicated COVID-19.
Modeling and circuit simulation of GaN-based light-emitting diodes for optimum efficiency through uniform current spreading (2002)

Uniform current spreading is desirable for both light emitting diodes (LEDs) performance and reliability. It enhances optical efficiency because the joule losses due to current crowding in some parts of the die would be eliminated. The LED design for optimal light extraction and uniform current spreading is therefore a necessity. In this paper we report on preliminary current spreading results obtained from circuit simulation, using Pspice and Aimspice, for LED designs with and without an n-metal ring as well as the epi-up and flip chip LEDs. For the epi-up, both the lateral and vertical resistances of the transparent metals were taken into account. Whereas in the flip chip, the lateral resistance was negligibly small thus only the vertical component contributed to the total p-lump resistance. The n-lateral resistance in the active mesa was critical to uniform current spreading. It was found that the lower the n-lateral resistance, the more uniform the current spreads and flows through the active region. In both the epi-up and flip-chip structures, the contact resistance of the p-metal (including the thin Ni/Au transparent metal) dominated the total p-lump resistance. The larger this value, with fixed n-layer lateral resistance, the more uniform the current spreads in the device. However, high p-contact resistance is not desirable as it reduces the overall efficiency of the device due to excessive heating and increased leakage current. Therefore, for uniform current spreading, the n-lateral resistance should be made small while maintaining an optimum p-lump resistance to achieve a high efficiency.
Boron Compensation of 6H Silicon Carbide (1998)

Experimental results are reported for boron-doping 6H silicon carbide epitaxial layers from a solid boronnitride source. Boron doping concentrations from more than 10 cm to less than 10 cm are observed. Doping concentrations are correlated with the proximity of the boron-nitride solid source to the heat source controlling the temperature of the boron nitride during CVD growth of the 6H SiC. Donor codoping, most likely from nitrogen, is also observed, in some cases leading to substantial compensation.
The Impact of Stacked Cap Layers on Effective Work Function With HfSiON and SiON Gate Dielectrics (2008)

Cap layers have been used to modulate the effective work function (EWF) for high- /metal-gate CMOS devices. We have investigated the impact of stacking cap layers on the EWF. Stacked cap layers consisting of two sequential cap layers, including, Al <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> O <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sub> , Dy <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> O <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sub> , Sc <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> O <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sub> and La <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> O <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sub> , were formed on HfSiON or SiON as host dielectrics. It is demonstrated that the EWF change due to the stacked cap layers corresponds to the sum of the EWF change from each single cap layer. Furthermore, no host dielectric dependence on the shifts is observed. This behavior is attributed to the complete intermixing of the stacked cap layers with the host dielectrics.
Out-of-sample extrapolation using semi-supervised manifold learning (OSE-SSL): Content-based image retrieval for prostate histology grading (2011)

In this paper, we present an out-of-sample extrapolation (OSE) scheme in the context of semi-supervised manifold learning (OSESSL). Manifold learning (ML) takes samples with high dimensionality and learns a set of low dimensional embeddings. Embeddings generated by ML preserve nonlinear relationships between samples allowing dataset visualization, classification, or evaluation of object similarity. Semi-supervised ML (SSL), a recent ML extension, exploits known class labels to learn embeddings, which may result in greater separation between samples of different classes compared to unsupervised ML schemes. Most ML schemes utilize the eigenvalue decomposition (EVD) to learn embeddings. For instance, Graph Embedding (GE) learns embeddings by EVD on a similarity matrix that models high dimensional feature vector similarity between samples. In datasets where new samples are acquired, such as a content-based image retrieval (CBIR) system, recalculating EVD is infeasible. OSE schemes obtain new embeddings without recalculating EVD. The Nyström method (NM) is an OSE algorithm where new embeddings are estimated as a weighted sum of known embeddings. Known embeddings must describe the embedding space for NM to accurately estimate new embeddings. In this paper, NM and semi-supervised GE (SSGE) are combined to learn embeddings which cluster samples by class and rapidly calculate embeddings for new samples without recalculating EVD. OSE-SSL is compared to (i) NM paired with GE (NM-GE), and (ii) SSGE obtained for the full database, where SSGE results represent ground truth embeddings. OSE-SSL, NM-GE, and SSGE are evaluated in their ability to: (1) cluster samples by label, measured by Silhouette Index (SI); (2) CBIR accuracy, measured by area under the precision-recall curve (AUPRC). In a synthetic Swiss roll dataset of 2000 samples, OSE-SSL requires training on 50% of the dataset to achieve SI and AUPRC similar to SSGE while NM-GE requires 70% of dataset to achieve SI and AUPRC similar to GE. For a prostate histology dataset of 888 glands, a CBIR system was evaluated on its ability to retrieve images according to Gleason Grade. OSE-SSL had AUPRC of 0.6 while NM-GE had AUPRC of 0.3.
ChemInform Abstract: CYANOGEN BROMIDE AS A CLEAVAGE PROCEDURE IN SOLID PHASE PEPTIDE SYNTHESIS (1976)

Abstract Eine neue Methode zur Abspaltung eines nach der Festphasenmethode synthetisie Peptids vom polymeren Träger wird entwickelt.
Supplementary Figure Legend from CCL2/CCR2-Dependent Recruitment of Functional Antigen-Presenting Cells into Tumors upon Chemotherapy (2023)

&lt;p&gt;PDF file - 53K&lt;/p&gt;
Echoscopie van de blaas, vagina, uterus en tubae (2016)

Sinds de introductie van de vaginale echotransducer, in de tweede helft van de jaren tachtig van de vorige eeuw, is de transvaginale echoscopie wijdverspreid als onderzoeksmethode in de gynaecologische praktijk. Aanvankelijk werd de techniek vooral gebruikt voor het onderzoek van de ovaria in het kader van een infertiliteitsbehandeling.
Towards flat and distributed mobility management: A 3GPP evolved network design (2012)

The last few years have seen an exponential increase in mobile data use, coming primarily as a result of the “iPhone revolution”. Mobile operators are currently facing traffic demands higher than what their networks can support, which has triggered the need of implementing offloading mechanisms at different levels of the architecture. One of the problems is that existing mobility procedures are highly centralized, requiring all data traffic to traverse the mobile operator's network core. This paper presents an evolved 3GPP architecture that supports full distributed mobility management, while allowing incremental deployment and co-existence with existing solutions.
Systems Biology: Constraint-based Reconstruction and Analysis (2015)

Recent technological advances have enabled comprehensive determination of the molecular composition of living cells. The chemical interactions between many of these molecules are known, giving rise to genome-scale reconstructed biochemical reaction networks underlying cellular functions. Mathematical descriptions of the totality of these chemical interactions lead to genome-scale models that allow the computation of physiological functions. Reflecting these recent developments, this textbook explains how such quantitative and computable genotype-phenotype relationships are built using a genome-wide basis of information about the gene portfolio of a target organism. It describes how biological knowledge is assembled to reconstruct biochemical reaction networks, the formulation of computational models of biological functions, and how these models can be used to address key biological questions and enable predictive biology. Developed through extensive classroom use, the book is designed to provide students with a solid conceptual framework and an invaluable set of modeling tools and computational approaches
Implementation and Evaluation of Reliable Visual Marks Using Digital Watermark for Web Site Authentication (2003)

Recently, World Wide Web plays an essential role in public and business applications such as information publication and electronic commerce, and its reliability is strongly required. Mark-based authentication has therefore started. It evaluates web sites and issues authentication marks to the sites. The marks are displayed on web pages of the sites, and users of the sites can judge their reliability by seeing the marks. This paper describes a web site authentication mark system which realizes generation, presentation and verification of marks. Especially the paper describes : (1) requirements for the system concerning security, usability, response speed, cost, and extensibility, (2) mark verification by digital signatures embedded in marks and by online queries, (3) implementation of verification programs as plug-ins of web browsers, (4) version management by embedded version IDs in marks, (5) life cycle management of marks using databases, (6) examples of the system behavior. The paper also explains reality of the proposed system through evaluations and comparison with previous systems.
Effect of fluoro-substituted proline residues on the conformational stability of triple-helical collagen mimics (2006)

Collagen is the most abundant protein in animals. In connective tissue, is present as chains wound in tight triple helices, which are organized into fibrils great tensile strength and thermal stability [1,2]. 'We have identified a new component of this stability. Collagen consists of XaaYaaGly repeats where Xaa is often L-proline (Pro) and Yaa is often 4(R)-hydroxY-L-proline (Hyp). The Hyp residues in a (ProHypGlY)1l triple helix confer substantial additional thermal stability relative to a (ProProGIY)n triple helix. It has been proposed that the extra stability ensues il'om a network of water bridges in which the 4(R)-hydroxyl group participates [1,3]. \Vater bridges that link a Hyp sidechain of one strand to a main-chain carbonyl of another strand have been seen in a crystalline collagen mimic. We believe that \vater bridges are unllkely to contribute significantly to triple-helical stability [4,5].