gebhart/patrepeval huggingface dataset:
A mathematical model to derive N-glycan structures and cellular enzyme activities from mass spectrometric data (2009)

Effective representation and characterization of biosynthetic pathways of glycosylation can be facilitated by mathematical modeling. This paper describes the expansion of a previously developed detailed model for N-linked glycosylation with the further application of the model to analyze MALDI-TOF mass spectra of human N-glycans in terms of underlying cellular enzyme activities. The glycosylation reaction network is automatically generated by the model, based on the reaction specificities of the glycosylation enzymes. The use of a molecular mass cutoff and a network pruning method typically limits the model size to about 10,000 glycan structures. This allows prediction of the complete glycan profile and its abundances for any set of assumed enzyme concentrations and reaction rate parameters. A synthetic mass spectrum from model-calculated glycan profiles is obtained and enzyme concentrations are adjusted to bring the theoretically calculated mass spectrum into agreement with experiment. The result of this process is a complete characterization of a measured glycan mass spectrum containing hundreds of masses in terms of the activities of 19 enzymes. In addition, a complete annotation of the mass spectrum in terms of glycan structure is produced, including the proportions of isomers within each peak. The method was applied to mass spectrometric data of normal human monocytes and monocytic leukemia (THP1) cells to derive glycosyltransferase activity changes underlying the differences in glycan structure between the normal and diseased cells. Model predictions could lead to a better understanding of the changes associated with disease states, identification of disease-associated biomarkers, and bioengineered glycan modifications.
Duplication of the terminal ileum with intussusception in an adult. (1980)

A case of ileal duplication with an impacted fecalith and intussusception is reported. The inclusion of enteric duplication in the differential diagnosis of abdominal syndromes is suggested. Certain events, often sudden and severe, lead to surgical intervention.
The impact of technology scaling on ESD robustness of aluminum and copper interconnects in advanced semiconductor technologies (1998)

Electrostatic discharge (ESD) testing results of aluminum (Al) and copper (Cu) interconnect wires and vias for advanced semiconductor technologies demonstrate that interconnects will be a limiting failure mechanism in the future for ESD robustness of semiconductor chips. Comparison of Cu and Al interconnect and vias ESD robustness and failure mechanisms will be shown. Results demonstrate an improvement in the ESD robustness of a Cu-based interconnect system, compared to Albased interconnects, with an improvement in the critical current density, Jcrit, in the human body and machine model time regimes.
Origin of Anisotropic Molecular Packing in Vapor-Deposited Alq3 Glasses (2018)

Anisotropic molecular packing is a key feature that makes glasses prepared by physical vapor deposition (PVD) unique materials, warranting a mechanistic understanding of how a PVD glass attains its structure. To this end, we use X-ray scattering and ellipsometry to characterize the structure of PVD glasses of tris(8-hydroxyquinoline) aluminum (Alq3), a molecule used in organic electronics, and compare our results to simulations of its supercooled liquid. X-ray scattering reveals a tendency for molecular layering in Alq3 glasses that depends upon the substrate temperature during deposition and the deposition rate. Simulations reveal that the Alq3 supercooled liquid, like liquid metals, exhibits surface layering. We propose that the layering in Alq3 glasses observed here as well as the previously reported bulk dipole orientation are inherited from the surface structure of the supercooled liquid. This work significantly advances our understanding of the mechanism governing the formation of anisotropic structure in PVD glasses.
<title>Electro-optic properties for liquid crystal phase gratings</title> (1992)

A new type of liquid crystal device was developed by applying a concept of liquid crystal phase gratings (LCPGs). LCPGs are composed of square-wave phase gratings constructed with poly(methyl methacrylate) and liquid crystals which fill the grating grooves. The typical sizes of the phase grating are 10 micrometers in width and 2 micrometers in depth. The transmitted light wavelength can be easily controlled by changing applied voltage. The transmittance varied from less than 1 for monochromatic polarized light, when applied voltage varied from 0 V to 5 V. Rise times for the light varied from 0.2 ms to 7 ms with applied voltage, and were inversely proportional to the square of the applied voltage. Decay times, which depend slightly on the applied voltage, were about 4 ms. A transmitted light, i.e., an observed color (e.g., R,G,B and white), was dependent on not only applied voltage but also grating depth. When two of the LCPGs were combined in such a way that their grating lines were oriented perpendicular to each other, these LCPGs were applicable to nonpolarized light.
Refractive error and glaucoma (2001)

In this large population, the prevalence of glaucoma increased with increasing myopia. The association between myopia and glaucoma was strong at lower IOP levels, and weakened gradually with increasing IOP. Our findings indicate that myopia is an important risk factor for glaucoma and particularly for normal tension glaucoma.
619 HIGH DISCOVERY RATE OF GASTRODUODENAL EOSINOPHILIA BUT NOT EOSINOPHILIC ESOPHAGITIS IN PATIENTS WITH CHRONIC GASTROINTESTINAL SYMPTOMS (2021)

Abstract Although the prevalence of eosinophilic gastrointestinal disorders (EGIDs) is increasing, there is evidence that eosinophilic gastritis and/or duodenitis (EG/EoD) are underdiagnosed. Patients with EG/EoD often present with chronic, non-specific gastrointestinal (GI) symptoms, similar to patients with functional GI disorders. We hypothesized that systematic evaluation, including multiple esophageal, gastric and duodenal biopsies, of patients with chronic GI symptoms might reveal a high rate of gastroduodenal eosinophila, with or without eosinophilic esophagitis (EoE). Methods We performed a prospective multi-center study of patients with non-specific GI symptoms for ≥6 months, from 20 sites. Patients completed a questionnaire assessing abdominal pain, abdominal cramping, early satiety, bloating, nausea, vomiting, diarrhea, and loss of appetite. Those with daily average symptom severity scores ≥3/10 for any single symptom underwent esophagogastroduodenoscopy (EGD) with collection of 4 esophageal (EoE), 8 gastric, and 4 duodenal biopsies, analyzed by central pathologists. Histologic criteria for EoE was ≥15eos/hpf in ≥1 esophageal site and for EG/EoD was peak eosinophil counts ≥30/hpf in ≥5 gastric hpfs and/or 3 duodenal hpfs—criteria used in randomized trials. Results Of 556 patients screened, 405 (73%) met symptom criteria and underwent EGD; 181 patients (45%, mean age 45, 73% female) who underwent EGD met the histologic criteria for EG/EoD, and of these, 7% also had EoE diagnosed. Overall 2% met histologic criteria for EoE alone. Of patients who met the histologic criteria for EG/EoD, 93% were previously diagnosed with gastroesophageal reflux disease (GERD), irritable bowel syndrome (IBS), or functional dyspepsia (FD) (Figure 1). The average duration of GI symptoms in the screened population as well as those that met histologic criteria for EG/EoD was 11 years. Conclusion Forty-five percent of patients with moderate-to-severe GI symptoms who underwent EGD met histologic criteria for EG/EoD. Over 90% of these patients had previously been diagnosed with GERD, IBS, and/or FD, and had minimal overlap with EoE. EGD with systematic gastroduodenal biopsies, and intentional evaluation for tissue eosinophilia, should be performed in patients with chronic GI symptoms. Accurate diagnosis of EG/EoD is required for appropriate, targeted treatment and improved outcomes of patients with moderate-to-severe GI symptoms.
Determination of Physical Properties of Reaction-Injection-Molded Polyurethanes by NIR-FT-Raman Spectroscopy (1990)

Near-infrared-FT-Raman spectroscopy can be used to nondestructively analyze reaction-injection-molded (RIM) Polyurethane elastomers. Unlike conventional 514.5-nm excitation, the 1064.1-nm excitation of NIR-FT-Raman spectroscopy does not produce significant sample fluorescence. In this work, the ability of NIR-FT-Raman spectroscopy to determine flex moduli of Polyurethane elastomers is evaluated. Comparisons are made between NIR-FT-Raman, dispersive Raman with 514.5-nm and 752-nm excitation, and NIR diffuse reflectance spectroscopy for Polyurethane analysis.
Metadynamics-Biased ab Initio Molecular Dynamics Study of Heterogeneous CO2 Reduction via Surface Frustrated Lewis Pairs (2016)

The recent discovery of frustrated Lewis pairs (FLPs) capable of heterolytically splitting hydrogen gas at the surface of hydroxylated indium oxide (In2O3–x(OH)y) nanoparticles has led to interesting implications for heterogeneous catalytic reduction of CO2. Although the role of surface FLPs in the reverse water-gas shift (RWGS) reaction (CO2 + H2 → CO + H2O) has been experimentally and theoretically demonstrated, the interplay between surface FLPs and temperature and their consequences for the reaction mechanism have yet to be understood. Here we use well-tempered metadynamics-biased ab initio molecular dynamics to obtain the free energy landscape of the multistep RWGS reaction at finite temperatures. The reaction is simulated at 20 and 180 °C, and the minimum energy reaction pathways and energy barriers corresponding to H2 dissociation and CO2 reduction are obtained. The reduction of CO2 at the surface FLP catalytically active site, where H2 is heterolytically dissociated and bound, is found to be the rate-limiting step and is mostly unaffected by increased temperature conditions; however, at 180 °C the energetic barriers associated with the splitting of H2 and the subsequent adsorption of CO2 are reduced by 0.15 and 0.19 eV, respectively. It is suggested that increased thermal conditions may enhance reactivity by enabling the surface FLP to become further spatially separated. Product H2O is found to favor dissociative adsorption over direct desorption from the surface of In2O3–x(OH)y and may therefore impede sustained catalytic activity by blocking surface sites.
Unleashing the Unused Potential of i-Vectors Enabled by GPU Acceleration (2019)

Speaker embeddings are continuous-value vector representations that allow easy comparison between voices of speakers with simple geometric operations. Among others, i-vector and x-vector have emerged as the mainstream methods for speaker embedding. In this paper, we illustrate the use of modern computation platform to harness the benefit of GPU acceleration for i-vector extraction. In particular, we achieve an acceleration of 3000 times in frame posterior computation compared to real time and 25 times in training the i-vector extractor compared to the CPU baseline from Kaldi toolkit. This significant speed-up allows the exploration of ideas that were hitherto impossible. In particular, we show that it is beneficial to update the universal background model (UBM) and re-compute frame alignments while training the i-vector extractor. Additionally, we are able to study different variations of i-vector extractors more rigorously than before. In this process, we reveal some undocumented details of Kaldi's i-vector extractor and show that it outperforms the standard formulation by a margin of 1 to 2% when tested with VoxCeleb speaker verification protocol. All of our findings are asserted by ensemble averaging the results from multiple runs with random start.
Al-2.110 Post-Exposure Delay (Ped) (2021)

As increasingly smaller molecular materials and material structures are devised or developed for technological applications, the demands on the processes of lithography now routinely include feature sizes that are of the order of 10 nm. In reaching such a fine level of resolution, the methods of lithography have increased markedly in sophistication and brought into play 2terminology that is unfamiliar, on the one hand, to scientists tasked with the development of new lithographic materials or, on the other, to the engineers who design and operate the complex equipment that is required in modern-day processing. Publications produced by scientists need to be understood by engineers and vice versa, and these commonly arise from collaborative research that draws heavily on the terminology of two or more of the traditional disciplines. It is developments in polymer science and material science that lead progress in areas that cross traditional boundaries, such as microlithography. This document provides the exact definitions of a selection of unfamiliar terms that researchers and practitioners from different disciplines might encounter.
Supplementary Figure S4 from Induction of Telomere Dysfunction Mediated by the Telomerase Substrate Precursor 6-Thio-2′-Deoxyguanosine (2023)

&lt;p&gt;Ki67 IHC.&lt;/p&gt;
The thyroid gland is a major source of circulating T3 in the rat. (1993)

In rats, the respective contribution of the thyroid and peripheral tissues to the pool of T3 remains unclear. Most, if not all, of the circulating T3 produced by extrathyroidal sources is generated by 5'-deiodination of T4, catalyzed by the selenoenzyme, type I iodothyronine 5'-deiodinase (5'D-I). 5'D-I in the liver and kidney is almost completely lost in selenium deficiency, resulting in a marked decrease in T4 deiodination and an increase in circulating T4 levels. Surprisingly, circulating T3 levels are only marginally decreased by selenium deficiency. In this study, we used selenium deficiency and thyroidectomy to determine the relative contribution of thyroidal and extrathyroidal sources to the total body pool of T3. Despite maintaining normal serum T4 concentrations in thyroidectomized rats by T4 replacement, serum T3 concentrations remained 55% lower than those seen in intact rats. In intact rats, restricting selenium intake had no effect on circulating T3 concentrations. Decreasing 5'D-I activity in the liver and kidney by > 90% by restricting selenium intake resulted in a further 20% decrease in serum T3 concentrations in the thyroidectomized, T4 replaced rats, suggesting that peripheral T4 to T3 conversion in these tissues generates approximately 20% of the circulating T3 concentrations. While dietary selenium restriction markedly decreased intrahepatic selenium content (> 95%), intrathyroidal selenium content decreased by only 27%. Further, thyroid 5'D-I activity actually increased 25% in the selenium deficient rats, suggesting the continued synthesis of this selenoenzyme over selenoproteins in other tissues in selenium deficiency. These data demonstrate that the thyroid is the major source of T3 in the rat and suggest that intrathyroidal T4 to T3 conversion may account for most of the T3 released by the thyroid.
Differential ABC transporter expression during hematopoiesis contributes to neutrophil-biased toxicity of Aurora kinase inhibitors (2022)

Drug-induced cytopenias are a prevalent and significant issue that worsens clinical outcomes and hinders the effective treatment of cancer. While reductions in blood cell numbers are classically associated with traditional cytotoxic chemotherapies, they also occur with newer targeted small molecules and the factors that determine the hematotoxicity profiles of oncologic drugs are not fully understood. Here, we explore why some Aurora kinase inhibitors cause preferential neutropenia. By studying drug responses of healthy human hematopoietic cells in vitro and analyzing existing gene expression datasets, we provide evidence that the enhanced vulnerability of neutrophil-lineage cells to Aurora kinase inhibition is caused by early developmental changes in ATP-binding cassette (ABC) transporter expression. These data show that hematopoietic cell-intrinsic expression of ABC transporters may be an important factor that determines how some Aurora kinase inhibitors affect the bone marrow.
Handwheel Force Feedback for Lanekeeping Assistance: Combined Dynamics and Stability (2005)

Lanekeeping assistance could save thousands of lives each year by maintaining lane position in the absence of driver steering commands. In order to work smoothly with the driver, handwheel force feedback must be an integral part of such a system. Here we combine force feedback with a lanekeeping controller based on lateral and heading error. In addition to force feedback replicating the feel in a conventional vehicle, the force can be based on the level of lanekeeping assistance being given. This coupling of the force feedback and assistance systems can destabilize the vehicle if not designed properly. Linear modeling verified by experiments shows the effect of varying the gains on both the force feedback and the lanekeeping assistance itself. In this analysis we show that within a range of values that feel reasonable to the driver, changes to the lanekeeping controller or force feedback can have marked effects on the response of the vehicle. It also shows that stability of the system can be ensured by injecting artificial damping or reproducing the on-center characteristics of a conventional vehicle. The analysis allows the force feedback designer to determine a range of stable force feedback gains, from which a set most acceptable to the driver can be chosen.
Additive Manufacture of Three Dimensional Nanocomposite Based Objects through Multiphoton Fabrication (2016)

Three-dimensional structures prepared from a gold-polymer composite formulation have been fabricated using multiphoton lithography. In this process, gold nanoparticles were simultaneously formed through photoreduction whilst polymerisation of two possible monomers was promoted. The monomers, trimethylopropane triacrylate (TMPTA) and pentaerythritol triacrylate (PETA) were mixed with a gold salt, but it was found that the addition of a ruthenium(II) complex enhanced both the geometrical uniformity and integrity of the polymerised/reduced material, enabling the first production of 3D gold-polymer structures by single step multiphoton lithography.
Characterization of novel breast carcinoma–associated BA46-derived peptides in HLA-A2.1/Db-β2mtransgenic mice (2002)

The human milk fat globule membrane protein BA46 (lactadherin) is highly overexpressed in human breast tumors, making it a potential target for tumor immunotherapy. We have identified BA46-derived peptides that contain the motif recognized by the MHC class I molecule HLA-A2.1 and that are processed and presented by human breast carcinoma cells. In mice lacking normal class I molecules but expressing an HLA-A2.1/D(b)-beta2 microglobulin single chain (HHD mice), three peptides elicited specific CTL activity. Two of these peptides also stimulated cytotoxic activity in peripheral blood lymphocytes from HLA-A2.1-positive breast carcinoma patients. Adoptive transfer of HHD-derived bulk CTLs to nude mice bearing human breast carcinoma transplants reduced tumor growth. These peptides therefore represent naturally processed BA46-derived CTL epitopes that can be used in peptide-based antitumor vaccines.
Karhunen–Loève treatment to remove noise and facilitate data analysis in sensing, spectroscopy and other applications (2014)

Resolving weak spectral variations in the dynamic response of materials that are either dominated or excited by stochastic processes remains a challenge. Responses that are thermal in origin are particularly relevant examples due to the delocalized nature of heat. Despite its inherent properties in dealing with stochastic processes, the Karhunen-Loève expansion has not been fully exploited in measurement of systems that are driven solely by random forces or can exhibit large thermally driven random fluctuations. Here, we present experimental results and analysis of the archetypes (a) the resonant excitation and transient response of an atomic force microscope probe by the ambient random fluctuations and nanoscale photothermal sample response, and (b) the photothermally scattered photons in pump-probe spectroscopy. In each case, the dynamic process is represented as an infinite series with random coefficients to obtain pertinent frequency shifts and spectral peaks and demonstrate spectral enhancement for a set of compounds including the spectrally complex biomass. The considered cases find important applications in nanoscale material characterization, biosensing, and spectral identification of biological and chemical agents.
Stokes-space analysis of modal dispersion in fibers with multiple mode transmission (2012)

Modal dispersion (MD) in a multimode fiber may be considered as a generalized form of polarization mode dispersion (PMD) in single mode fibers. Using this analogy, we extend the formalism developed for PMD to characterize MD in fibers with multiple spatial modes. We introduce a MD vector defined in a D-dimensional extended Stokes space whose square length is the sum of the square group delays of the generalized principal states. For strong mode coupling, the MD vector undertakes a D-dimensional isotropic random walk, so that the distribution of its length is a chi distribution with D degrees of freedom. We also characterize the largest differential group delay, that is the difference between the delays of the fastest and the slowest principal states, and show that it too is very well approximated by a chi distribution, although in general with a smaller number of degrees of freedom. Finally, we study the spectral properties of MD in terms of the frequency autocorrelation functions of the MD vector, of the square modulus of the MD vector, and of the largest differential group delay. The analytical results are supported by extensive numerical simulations.
Quantifying Ligand Adsorption to Nanoparticles Using Tandem Differential Mobility Mass Analysis (2012)

Although electrospray-differential mobility analyzers (ES-DMA) have been previously employed to characterize ligand binding to nanoparticles, absolute quantification of surface coverage can be inaccurate at times because of ligand conformational effects. In this Letter, we report a quantitative technique by in-flight coupling of a particle mass analyzer (APM) with ES-DMA, thus enabling a direct quantitative analysis of mass independent of particle size, material, morphology and conformation. We demonstrate the utility of ES-DMA-APM by studying two model complex systems (gold nanoparticle-bovine serum albumin and polystyrene bead-antibody) as a function of concentration and pH. Our results obtained with ES-DMA-APM are in excellent agreement with prior work. We anticipate that this will enhance the capabilities of online quantitative characterization of ligand binding to nanoparticles.