gebhart/patrepeval huggingface dataset:
Fabrication of channel and wedge plasmon polarition devices by combined UV and nanoimprint lithography (2008)

We present a large-scale compatible fabrication method for channel and wedge plasmon polariton waveguides. Optical characterization of fabricated devices using SNOM shows sub-wavelength confinement and propagation lengths in the hundreds of microns.
STING agonism overcomes STAT3-mediated immunosuppression and adaptive resistance to PARP inhibition in ovarian cancer (2023)

We elucidate an adaptive immunosuppression mechanism rendering resistance to PARPi in BRCA1-mutant ovarian tumors. This is mediated by enrichment of protumor TAMs propelled by PARPi-induced STAT3 activation in tumor cells. We also provide a new strategy to reshape the immunosuppressive TME with STING agonists and overcome PARPi resistance in ovarian cancer.
Electron Microscopy Study of Localized Gate Forward Breakdown in AlGaN/AlN/GaN High Electron Mobility Transistors (2008)

Extended abstract of a paper presented at Microscopy and Microanalysis 2008 in Albuquerque, New Mexico, USA, August 3 – August 7, 2008
Zymodemes ofEntamoeba histolyticain Dhaka, Bangladesh (1990)

Stool samples containing Entamoeba histolytica were obtained from two sources: an urban hospital and an urban slum. Using the enzyme patterns of three enzymes (E.C.2.7.1.1 hexokinase, E.C.5.3.1.9 glucose phosphate isomerase and E.C.2.7.5.1 phosphoglucomutase) stained after cellulose acetate electrophoresis, four zymodemes (I, II, XIV and XVI) were identified in 71 isolates. Zymodemes considered to be pathogenic (II and XIV) were identified from 31 of 34 isolates from the urban hospital, and these zymodemes were strongly associated with dysentery and trophozoites containing ingested red blood corpuscles. Blood visible to the naked eye was more commonly seen in stools from which zymodeme XIV was isolated than in those containing zymodeme II (P less than 0.001). Zymodemes considered to be non-pathogenic (I and XVI) were identified in 34 of 37 isolates from slum dwellers and were not associated with blood in the stools.
Bacterial Antibody Titers in Ligature‐Induced Periodontitis in Beagle Dogs (1983)

Serum antibodies to indigenous bacteria in ten beagle dogs were examined over a 7-month period during the development of ligature-induced periodontitis. Gram-negative strains comprised approximately 75% of the cultivable periodontitis microflora with a predominance of black-pigmented Bacteroides species. A total of 44 bacterial strains representing the predominant cultivable subgingival beagle dog microflora was selected for antibody determination. The IgG and, in some cases, IgM serum antibody titers to these organisms were determined by indirect immunofluorescence. The antibody titers to most test strains remained unchanged during the experimental period. Gram-negative bacteria generally exhibited lower titers than the Gram-positive bacteria. Especially low titers were found for the black-pigmented Bacteroides. Four dogs that developed the most severe periodontitis showed about 2-fold higher IgG titers to some Gram-negative anaerobic rods in the pre-ligation period than dogs that developed a more moderate periodontitis. These data suggested a possible diagnostic value of such antibody determinations. However, the overall finding of the present study was that serum antibody titers to key periodontopathic organisms remained low throughout the experiment. This result may suggest that the rapid periodontal destruction in ligature-induced periodontitis is due in part to an inadequate antibody response against the infecting microorganisms and their pathogenic products.
Strain Construction and Screening Methods for a Yeast Histone H3/H4 Mutant Library (2011)

A mutant library consisting of hundreds of designed point and deletion mutants in the genes encoding Saccharomyces cerevisiae histones H3 and H4 is described. Incorporation of this library into a suitably engineered yeast strain (e.g., bearing a reporter of interest), and the validation of individual library members is described in detail.
Cycloruthenated compounds as efficient catalyst for asymmetric hydride transfer reaction (2006)

Abstract Cycloruthenated complexes obtained by direct C-H activation of enantiopure aromatic primary and secondary amines are efficient catalysts in asymmetric hydride transfer reaction. Reduction of acetophenone has been achieved rapidly with enantiomeric excesses (ee's) ranging from 38 to 89 %. The importance of Ru-C bond in the catalytic efficiency is highlighted.
Cadazolid, a novel antibiotic with potent activity against Clostridium difficile: safety, tolerability and pharmacokinetics in healthy subjects following single and multiple oral doses (2013)

Cadazolid was well tolerated and its systemic exposure was low. The majority of compound was recovered unchanged in the faeces, thus resulting in high concentrations at the site of action (colon).
Effects of glycerol content and film thickness on the properties of vital wheat gluten films cast at pH 4 and 11 (2010)

Abstract This study deals with the optical properties and plasticizer migration properties of vital wheat gluten (WG) films cast at pH 4 and 11. The films contained initially 8, 16, and 25 wt % glycerol and were aged at 23°C and 50% relative humidity for at least 17 weeks on a paper support to simulate a situation where a paper packaging is laminated with an oxygen barrier film of WG. The films, having target thicknesses of 50 and 250 μm, were characterized visually and with ultraviolet/visible and infrared spectroscopy; the mass loss was measured by gravimetry or by a glycerol‐specific gas chromatography method. The thin films produced at pH 4 were, in general, more heterogeneous than those produced at pH 11. The thin pH 4 films consisted of transparent regions surrounding beige glycerol‐rich regions, the former probably rich in gliadin and the latter rich in glutenin. This, together with less Maillard browning, meant that the thin pH 4 films, in contrast to the more homogeneous (beige) thin pH 11 films, showed good contact clarity. The variations in glycerol content did not significantly change the optical properties of the films. All the films showed a significant loss of glycerol to the paper support but, after almost 9 months, the thick pH 11 film containing initially 25 wt % glycerol was still very flexible and, despite a better contact to the paper, had a higher residual glycerol content than the pH 4 film, which was also more brittle. © 2010 Wiley Periodicals, Inc. J Appl Polym Sci, 2010
CD4+ CD8+ murine intestinal intraepithelial Iymphocytes (1990)

We have studied a population of CD4+ intestinal intraepithelial lymphocytes using two-color flow cytometric analyses, and in highly purified fluorescent-activated cell-sorted preparations. Although CD4+ T cells present within the epithelial immune compartment comprised only approximately 10-20% of the total intestinal epithelial lymphoid cells, an unusually high proportion of those CD4+ lymphocytes expressed a CD4+CD8+ phenotype which is rarely encountered in peripheral T cells. By comparison, CD4+ lymphocytes from spleen or lymph nodes existed exclusively as single-positive T cells. Analyses of CD4 and CD8 expression on lymphocytes from Peyer's patches, the lamina propria, and IEL indicated that CD4+CD8+ lymphocytes were unique to the IEL. Using CD4+CD8+ preparations obtained by fluorescent-activated cell sorting, CD4+CD8+ epithelial T cells were found also to express CD3 and Thy-1 surface markers. This heretofore undescribed extrathymic population of double-positive T cells constitutes a unique peripheral T cell subset which may be involved in intestinal T cell maturation and development, or could represent a highly specialized effector population.
Advanced Packaging of High-Power Slab-Coupled Optical Waveguide Laser and Amplifier Arrays for Coherent Beam Combining* (2010)

Individually addressable GaAs-based 9XX-nm Slab-Coupled Optical Waveguide (SCOW) laser and amplifier arrays have been demonstrated in a modular 2-D stacked architecture. Approximately 20 W of coherently-combined power was obtained from two optically stacked amplifier modules.
Correction to: Gestational hypertensive disorders and retinal microvasculature: the Generation R Study (2017)

The original article contained an error whereby the senior author, M. Kamran Ikram's name was mistakenly interchanged. &#13;\nThis error has now been corrected.
Identification of p53 regulators by genome-wide functional analysis (2004)

The p53 tumor-suppressor protein is a critical mediator of cellular growth arrest and the induction of apoptosis. To identify proteins involved in the modulation of p53 transcriptional activity, a gain-of-function cellular screen was carried out with an arrayed matrix of approximately 20,000 cDNAs. Nine genes previously unknown to be involved in regulating p53 activity were identified. Overexpression of seven of these genes (Hey1, Hes1, TFAP4, Osr1, NR2F2, SFRS10, and FLJ11339) resulted in up-regulation of p53 activity; overexpression of two genes (M17S2 and cathepsin B) resulted in down-regulation of p53 activity in mammalian cells. HES1, HEY1, and TFAP4, which are members of the basic helix-loop-helix transcription family, and OSR1 were shown to activate p53 through repression of HDM2 transcription. Ectopic expression of these basic helix-loop-helix transcription factors in both zebrafish and avian developmental systems activated p53 and induced apoptosis in vivo, resulting in a phenotype similar to that of p53 overexpression. Furthermore, ras- and myc-mediated transformation of mouse embryonic fibroblasts was abrogated by expression of HEY1 in a p53-dependent manner. These results suggest that these transcription factors are members of an evolutionarily conserved network that governs p53 function.
Time-Based Exploration of News Archives (2010)

In this paper, we present NEAT, a prototype system that provides an exploration interface to news archive search. Our prototype visualizes search results making use of two kinds of temporal information, namely, news articles ’ publication dates but also their contained temporal expressions. The displayed timelines are annotated with major events, harvested using crowdsourcing, to make it easier for users to put the shown search results into context. The prototype has been fully implemented and deployed on the New York
Threshold Photodetachment Spectroscopy of the Positronium Negative Ion (2020)

Threshold photodetachment spectroscopy of the positronium negative ion has been accomplished for the first time employing an efficient source of the ions and photodetachment techniques combined with a tunable optical parametric oscillator and amplifier laser. The photodetachment threshold, corresponding to the electron affinity of positronium (1^{3}S_{1}), was determined to be 326.88±0.09(stat)±0.10(syst) meV by laser photodetachment threshold measurements. This result is consistent with a variational calculation corrected for leading relativistic and quantum electrodynamical effects.
Supplementary Figures 11-14 from FTY720 (Fingolimod) Sensitizes Prostate Cancer Cells to Radiotherapy by Inhibition of Sphingosine Kinase-1 (2023)

Supplementary Figures 11-14 from FTY720 (Fingolimod) Sensitizes Prostate Cancer Cells to Radiotherapy by Inhibition of Sphingosine Kinase-1
Bubble Trouble: Conquering Microbubble Limitations in Contrast Enhanced Ultrasound Imaging by Nature-Inspired Ultrastable Echogenic Nanobubbles (2019)

Abstract Advancement of ultrasound molecular imaging applications requires not only a reduction in size of the ultrasound contrast agents (UCAs) but also a significant improvement in the in vivo stability of the shell-stabilized gas bubble. The transition from first generation to second generation UCAs was marked by an advancement in stability as air was replaced by a hydrophobic gas, such as perfluoropropane and sulfur hexafluoride. Further improvement can be realized by focusing on how well the UCAs shell can retain the encapsulated gas under extreme mechanical deformations. Here we report the next generation of UCAs for which we engineered the shell structure to impart much better stability under repeated prolonged oscillation due to ultrasound, and large changes in shear and turbulence as it circulates within the body. By adapting an architecture with two layers of contrasting elastic properties similar to bacterial cell envelopes, our ultrastable nanobubbles (NBs) withstand continuous in vitro exposure to ultrasound with minimal signal decay and have a significant delay on the onset of in vivo signal decay in kidney, liver, and tumor. Development of ultrastable NBs can potentially expand the role of ultrasound in molecular imaging, theranostics, and drug delivery.
Lowering Error Floors in Stochastic Decoding of LDPC Codes Based on Wire-Delay Dependent Asynchronous Updating (2013)

Stochastic decoding provides ultra-low-complexity hardware for high-throughput parallel low-density parity-check (LDPC) decoders. Asynchronous stochastic decoding was pro- posed to demonstrate the possibility of low power dissipation and high throughput in stochastic decoders, but decoding might stop before convergence due to "lock-up", causing error floors. In this paper, we introduce wire-delay dependent asynchronous stochastic decoding to reduce the error floors. Instead of assigning the same delay to all computation nodes in the previous work, different computation delay is assigned to each computation node depending on its wire length. The variation of update timing increases switching activities to decrease the possibility of the "lock-up", lowering the error floors. BER performance using a regular (1024, 512) (3, 6) LDPC code is simulated based on our timing model that has computation and wire delays estimated under ASPLA 90nm CMOS technology. It is demonstrated that the proposed asynchronous decoder achieves an up to 0.25-dB gain compared with that of the synchronous and the conventional asynchronous decoders.
On the Ambiguity of Registration Uncertainty. (2018)

Estimating the uncertainty in image registration is an area of current research that is aimed at providing information that will enable surgeons to assess the operative risk based on registered image data and the estimated registration uncertainty. If they receive inaccurately calculated registration uncertainty and misplace confidence in the alignment solutions, severe consequences may result. For probabilistic image registration (PIR), most research quantifies the registration uncertainty using summary statistics of the transformation distributions. In this paper, we study a rarely examined topic: whether those summary statistics of the transformation distribution truly represent the registration uncertainty. Using concrete examples, we show that there are two types of uncertainties: the transformation uncertainty, Ut, and label uncertainty Ul. Ut indicates the doubt concerning transformation parameters and can be estimated by conventional uncertainty measures, while Ul is strongly linked to the goal of registration. Further, we show that using Ut to quantify Ul is inappropriate and can be misleading. In addition, we present some potentially critical findings regarding PIR.
An Epigenetically Distinct Subset of Children With Autism Spectrum Disorder Resulting From Differences in Blood Cell Composition (2021)

<b>Background:</b> Autism spectrum disorder (ASD) is a complex neurodevelopmental disorder that often involves impaired cognition, communication difficulties and restrictive, repetitive behaviors. ASD is extremely heterogeneous both clinically and etiologically, which represents one of the greatest challenges in studying the molecular underpinnings of ASD. While hundreds of ASD-associated genes have been identified that confer varying degrees of risk, no single gene variant accounts for >1% of ASD cases. Notably, a large number of ASD-risk genes function as epigenetic regulators, indicating potential epigenetic dysregulation in ASD. As such, we compared genome-wide DNA methylation (DNAm) in the blood of children with ASD (<i>n</i> = 265) to samples from age- and sex-matched, neurotypical controls (<i>n</i> = 122) using the Illumina Infinium HumanMethylation450 arrays. <b>Results:</b> While DNAm patterns did not distinctly separate ASD cases from controls, our analysis identified an epigenetically unique subset of ASD cases (<i>n</i> = 32); these individuals exhibited significant differential methylation from both controls than the remaining ASD cases. The CpG sites at which this subset was differentially methylated mapped to known ASD risk genes that encode proteins of the nervous and immune systems. Moreover, the observed DNAm differences were attributable to altered blood cell composition, i.e., lower granulocyte proportion and granulocyte-to-lymphocyte ratio in the ASD subset, as compared to the remaining ASD cases and controls. This ASD subset did not differ from the rest of the ASD cases in the frequency or type of high-risk genomic variants. <b>Conclusion:</b> Within our ASD cohort, we identified a subset of individuals that exhibit differential methylation from both controls and the remaining ASD group tightly associated with shifts in immune cell type proportions. This is an important feature that should be assessed in all epigenetic studies of blood cells in ASD. This finding also builds on past reports of changes in the immune systems of children with ASD, supporting the potential role of altered immunological mechanisms in the complex pathophysiology of ASD. The discovery of significant molecular and immunological features in subgroups of individuals with ASD may allow clinicians to better stratify patients, facilitating personalized interventions and improved outcomes.
Fractal geometry of individual river channels and its computer simulation (1993)

A new method for analyzing the self‐similarity and self‐affinity of single‐thread channels is proposed. It permits the determination of the fractal scaling exponents, of the characteristic scales, and the evaluation of the degree of anisotropy for self‐similar fractal lines. Based upon the application of this method to the Dniester and Pruth rivers we established the self‐similarity of the river pattern on small scales and the self‐affinity on large scales. For these rivers we obtained the fractal scaling exponents, the characteristic scales, and the anisotropy parameters. A computer model has been developed which simulates river patterns whose fractal properties are close to the properties of natural objects. A generalized model of fractal behavior of natural rivers is proposed. On the basis of self‐affinity of natural and simulated rivers on large scales, a hypothesis has been formulated which explains the violation of the dimension principle in the well‐known relation between the river length and the catchment area.
Inverse Design of an Efficient, On-chip Path-entangled Photon-pair Source Based on Single Quantum Dots (2022)

We use inverse design to develop an optimized nanophotonic geometry for efficient, waveguide-coupled, path-entangled photon pair sources based on single embedded quan-tum dots.
FAIR QUEUEING SYSTEM (2003)

We analyse in this paper the fluid weighted fair queueing system with two classes of customers, who arrive according to Poisson processes and require arbitrarily distributed service times. In a first step, we express the Laplace transform of the joint distribution of the workloads in the two virtual queues of the system by means of unknown Laplace transforms. Such an unknown Laplace transform is related to the distribution of the workload in one queue provided that the other queue is empty. We explicitly compute the unknown Laplace transforms by means of a Wiener-Hopf technique. The determination of the unknown Laplace transforms can be used to compute some performance measures characterizing the system (e.g. the mean waiting time for each class) which we compute in the exponential service case.
Discussion (1995)

Lasa, Carlos Jr. M.D.; Hollinger, Jeffrey D.D.S., Ph.D.; Drohan, William Ph.D.; MacPhee, Martin Ph.D.; Urist, Marshall R. M.D.
Encoded Fiber‐Optic Microsphere Arrays for Probing Protein–Carbohydrate Interactions (2003)

Protein–carbohydrate interactions can be evaluated by using randomly ordered fiber optic microsphere arrays bearing immobilized synthetic oligosaccharides (see scheme). Two systems are examined: the mannose-binding lectin concanavalin A, and cyanovirin N. The latter allows the simultaneous evaluation of five distinct structures against a carbohydrate-binding protein with unambiguous results.
Experimental re-infected cats do not transmit SARS-CoV-2 (2021)

Abstract SARS-CoV-2 is the causative agent of COVID-19 and responsible for the current global pandemic. We and others have previously demonstrated that cats are susceptible to SARS-CoV-2 infection and can efficiently transmit the virus to naïve cats. Here, we address whether cats previously exposed to SARS-CoV-2 can be re-infected with SARS-CoV-2. In two independent studies, SARS-CoV-2-infected cats were re-challenged with SARS-CoV-2 at 21 days post primary challenge (DPC) and necropsies performed at 4, 7 and 14 days post-secondary challenge (DP2C). Sentinels were co-mingled with the re-challenged cats at 1 DP2C. Clinical signs were recorded, and nasal, oropharyngeal, and rectal swabs, blood, and serum were collected and tissues examined for histologic lesions. Viral RNA was transiently shed via the nasal, oropharyngeal and rectal cavities of the re-challenged cats. Viral RNA was detected in various tissues of re-challenged cats euthanized at 4 DP2C, mainly in the upper respiratory tract and lymphoid tissues, but less frequently and at lower levels in the lower respiratory tract when compared to primary SARS-CoV-2 challenged cats at 4 DPC. Histologic lesions that characterized primary SARS-CoV-2 infected cats at 4 DPC were absent in the re-challenged cats. Naïve sentinels co-housed with the re-challenged cats did not shed virus or seroconvert. Together, our results indicate that cats previously infected with SARS-CoV-2 can be experimentally re-infected with SARS-CoV-2; however, the levels of virus shed was insufficient for transmission to co-housed naïve sentinels. We conclude that SARS-CoV-2 infection in cats induces immune responses that provide partial, non-sterilizing immune protection against reinfection.
Barrier height modulation and dipole moments in metal-molecule-silicon diodes (2007)

In this study, Schottky barrier height in a series of gold-molecule-n Si diodes has been determined by reverse-bias capacitance-voltage measurements. Trends in measured barrier height correlate with calculated molecular dipoles. Samples were prepared by electrochemically grafting para-substituted aryl-diazonium salts on n-type silicon substrates. Bromobenzene (B-benz), diethylaminobenzene (D-benz), 2-methyl 4-nitrobenzene (FRS), methoxybenzene (M-benz), and nitrobenzene (N-benz) molecular layers were used.