gebhart/patrepeval huggingface dataset:
Recognition of heparan sulfate by clinical strains of dengue virus serotype 1 using recombinant subviral particles (2013)

Dengue is the most important arthropod-borne viral disease in humans, with an estimated 3.6 billion people at risk for infection and more than 200 million infections per year. Identification of the cellular receptors for dengue virus (DV), the causative agent of dengue, is important toward understanding the pathogenesis of the disease. Heparan sulfate (HS) has been characterized as a DV receptor in multiple model systems, however the physiological relevance of these findings has been questioned by observations that flaviviruses, including DV, can undergo cell culture adaptation changes resulting in increased binding to HS. It thus remains unclear whether HS is utilized by clinical, non-cell culture-adapted strains of DV. To address this question, herein we describe a set of methodologies using recombinant subviral particles (RSPs) to determine the utilization of HS by clinical strains of DV serotype 1 (DV1). RSPs of clinically isolated strains with low cell culture passage histories were used to study HS interaction. Biochemically characterized RSPs showed dose-dependent binding to immobilized heparin, which could be competed by heparin and HS but not structurally related glycosaminoglycans chondroitin sulfate A and hyaluronic acid. The relevance of heparin and HS biochemical interactions was demonstrated by competition of RSP and DV binding to cells with soluble heparin and HS. Our results demonstrate that clinical strains of DV1 can specifically interact with heparin and HS. Together, these data support the possibility that HS on cell surfaces is utilized in the DV-human infection process.
Operation of a Microwave Pulse Compressor With a Laser-Triggered Plasma Switch at Different Laser Beam Directions (2015)

A resonant microwave pulse compressor with laser triggering of the plasma discharge in its switch was studied for the influence of the unfocused laser beam direction with respect to the RF electric field. The compressor was realized as a rectangular waveguide-based cavity connected to an H-plane waveguide tee with a shorted side arm filled with pressurized helium and pumped by a conventional pulsed S-band magnetron. It was found that neither the direction, nor the intensity of the laser beam significantly affect the compressor output pulse peak power and waveform. Meantime, the delay between the moment of plasma discharge initiation and the appearance of the microwave output is shorter and the time jitter for this delay is smaller if the laser beam is directed along the RF electric field. The same effect was observed when increasing the intensity of the laser beam. Time-resolved optical emission spectroscopy was used to evaluate the plasma density, and numerical simulations of the RF energy release from the system with the appearance of plasma showed a good agreement with the experimentally obtained characteristics of the plasma and microwave output pulse.
Probing Sources of Decoherence at Defects and Interfaces in Superconducting Quantum Materials and Devices (2022)

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Rapid Proton-Detected NMR Assignment for Proteins with Fast Magic Angle Spinning (2014)

Using a set of six (1)H-detected triple-resonance NMR experiments, we establish a method for sequence-specific backbone resonance assignment of magic angle spinning (MAS) nuclear magnetic resonance (NMR) spectra of 5-30 kDa proteins. The approach relies on perdeuteration, amide (2)H/(1)H exchange, high magnetic fields, and high-spinning frequencies (ωr/2π ≥ 60 kHz) and yields high-quality NMR data, enabling the use of automated analysis. The method is validated with five examples of proteins in different condensed states, including two microcrystalline proteins, a sedimented virus capsid, and two membrane-embedded systems. In comparison to contemporary (13)C/(15)N-based methods, this approach facilitates and accelerates the MAS NMR assignment process, shortening the spectral acquisition times and enabling the use of unsupervised state-of-the-art computational data analysis protocols originally developed for solution NMR.
First chelate complexes of 4-mercapto-1-methylpiperidine. Synthesis and characterization of [{M(µ-SC5H9NMe)X}2](M = PdII, X = Cl, Br, or I; M = PtII, X = Br or I). Crystal and molecular structure of [{Pt(µ-SC5H9NMe)Br}2] (1990)

The reaction of 4-mercapto-1-methylpiperidine in the presence of NEt3 with palladium(II) and platinum(II) halides or treatment of complexes [M(SC5H9NHMe)2][MX4](M = Pd or Pt; X = Cl, Br, or I) with the same base has led to complexes [{M(µ-SC5H9NMe)X}2](M = Pd, X = Cl, Br, or I; M = Pt, X = Br or I). When M = Pt and X = Br, crystals are monoclinic, space group P21/a, with a= 13.236(8), b= 9.280(8), c= 14.823(5)Å, and β= 92.00(4)°. The crystal structure consists of chemically independent dinuclear molecules, where each ligand is terdentate and simultaneously S,N-chelating and µ-S bridging. One bromine atom completes the co-ordination around each platinum. The metal environment is approximately square planar, both S2PtNBr planes generating a dihedral angle of 125.24°. There is no metal–metal bonding. Based on the i.r. and 1H n.m.r. spectra, the same structure is proposed for the remaining complexes.
Supplementary Figure 8 from Cancer-Associated Fibroblasts Expressing CXCL14 Rely upon NOS1-Derived Nitric Oxide Signaling for Their Tumor-Supporting Properties (2023)

&lt;p&gt;PDF file - 135KB, Recruitment of blood vessels into fibroblast-stimulated prostate and breast tumors.&lt;/p&gt;
Nucleation and Crystal Growth of Zn0.3In1.4Sn0.3O3 (ZITO-30) Thin Films Studied by in-situ TEM (2016)

Journal Article Nucleation and Crystal Growth of Zn0.3In1.4Sn0.3O3 (ZITO-30) Thin Films Studied by in-situ TEM Get access Ran Li, Ran Li Department of Materials Science and Engineering, Northwestern University, Evanston, Illinois, USA Search for other works by this author on: Oxford Academic Google Scholar Mahyar Mohebi Moghadam, Mahyar Mohebi Moghadam Department of Materials Science and Engineering, Northwestern University, Evanston, Illinois, USA Search for other works by this author on: Oxford Academic Google Scholar D Bruce Buchholz, D Bruce Buchholz Department of Materials Science and Engineering, Northwestern University, Evanston, Illinois, USA Search for other works by this author on: Oxford Academic Google Scholar Peter W Voorhees, Peter W Voorhees Department of Materials Science and Engineering, Northwestern University, Evanston, Illinois, USA Search for other works by this author on: Oxford Academic Google Scholar Vinayak P Dravid Vinayak P Dravid Department of Materials Science and Engineering, Northwestern University, Evanston, Illinois, USA Search for other works by this author on: Oxford Academic Google Scholar Microscopy and Microanalysis, Volume 22, Issue S3, 1 July 2016, Pages 840–841, https://doi.org/10.1017/S1431927616005043 Published: 25 July 2016
Molecular and supramolecular dynamics of hybrid organic–inorganic interfaces for the rational construction of advanced hybrid nanomaterials (2010)

Today the capability to rationally design and construct hybrid materials utilizing a performance-property driven methodology is strongly dependent on our ability to control the structure and the dynamics of hybrid interfaces. This control needs a deep knowledge of their molecular and supramolecular dynamics that must be evaluated in situ, in the soft matter or colloidal states. For this purpose the use of modern methodologies of characterization such as time resolved synchrotron experiments and advanced pulsed field gradient NMR methods (DOSY) is particularly relevant. In this critical review, two important examples are discussed. They concern, first, the study of surface capping organic components’ affinity towards nanoparticle surfaces by DOSY NMR. The knowledge and therefore the tuning of this affinity is paramount because it controls solubility, transferability and stability of colloidal dispersions of nanoparticles (NPs). In the second part, the mechanism of micellar templated formation of hybrid mesophases will be discussed in the frame of the main results obtained via in situSAXS (107 references).
Supplementary Figure 1 from Detection of Early Prostate Cancer Using a Hepsin-Targeted Imaging Agent (2023)

Supplementary Figure 1 from Detection of Early Prostate Cancer Using a Hepsin-Targeted Imaging Agent
Foveal contrast thresholds exhibit spatial-frequency- and polarity-specific contour interactions (2003)

Traditionally, contour interaction has been investigated at the visual acuity limit using a Landolt C and flanking bars, performance being quantified in terms of a percent correct measure. More recently, it has been shown that the properties of the contour interaction are different when larger stimuli are used: Contour interaction is not polarity specific, and spatial frequency tuning for an unflanked C is broader. Here we quantify contour interaction for stimuli 5x larger than the resolution limit in terms of contrast thresholds. We show that polarity of bars has little effect on unfiltered stimuli but does show very different effects on the spatial-frequency-tuning curves for discrimination of the Landolt C. This explains the polarity dependence of crowding at the visual acuity limit and its independence for larger unfiltered targets. Thus the underlying filtering function is composed of more than one mechanism, affected differently depending on the relative polarity of the test and flank contours.
Enhancing the nucleation of palladium atomic layer deposition on Al2O3 using trimethylaluminum to prevent surface poisoning by reaction products (2009)

Metal atomic layer deposition (ALD) on oxides can display long nucleation periods and high growth temperatures that may be caused by surface poisoning by reaction products. Exposures of trimethylaluminum (TMA) during Pd ALD using Pd(hfac)2 and formalin on Al2O3 surfaces can shorten the nucleation period and reduce the growth temperatures. Fourier transform infrared spectroscopy studies indicate that TMA removes Al(hfac)∗ species that block surface sites. Pd ALD nucleates more readily and grows at lower temperatures because higher temperatures are not needed to desorb Al(hfac)∗ species. Transmission electron microscopy analysis shows the differences between Pd ALD films deposited with and without TMA.
Feasibility testing of a pre-clinical coded aperture phase contrast imaging configuration using a simple fast Monte Carlo simulator (2013)

A simple method of simulating possible coded aperture phase contrast X-ray imaging apparatus is presented. The method is based on ray tracing, with the rays treated ballistically within a voxelized sample and with the phase-shift-induced angular deviations and absorptions applied at a plane in the middle of the sample. For the particular case of a coded aperture phase contrast configuration suitable for small animal pre-clinical imaging we present results obtained using a high resolution voxel array representation of a mathematically-defined 'digital' mouse. At the end of the article a link to the software is supplied.
13.3: Efficient Direct Light‐Field Rendering for Autostereoscopic 3D Displays (2015)

The rapid advancement of 3D display technologies enables consumers to enjoy the 3D world visually through various display systems such as stereoscopic, multiview, and light field displays. Unfortunately, to achieve a sufficient level of reality, the complexity of the conventional multiview rendering process increases. This may hinder mass deployment of 3D display products. This paper proposes a novel method, called direct light field rendering, which can compose the display light ray image without reconstructing all the multiview images beforehand. By interpreting 3D display as sampling in the light field domain, we attempt to directly compute only the necessary samples, and not the entire light fields or multiview images. Our proposed algorithm consists of solving linear systems of two variables, requiring remarkably low complexities.
High-throughput characterization of MHC I-associated peptides presented by B lymphoblastoid cells (100.11) (2011)

Abstract Sensing of the MHC I-peptide (MHC I-p) repertoire allows elimination of infected or transformed cells. High-throughput strategies used to study MHC I-p include i) the use of secreted forms of MHC I transfected into model cell lines, or ii) chemical or metabolic labeling of MHC I, which is limited to certain MHCs and to cell culture model systems. Here, we used a quantitative proteomics approach to characterize and compare for the first time the MHC I-p repertoire associated to unlabeled HLA-A,B molecules of untransfected B lymphoblastoid cells (B-LCLs). Peptides were obtained from B-LCLs from 3 subjects by mild acid elution, fractionated by liquid chromatography and analyzed by nanoLC-MS/MS on a LTQ-Orbitrap mass spectrometer. We have identified more than 1000 unique 8-11mers associated to 10 HLA-A,B alleles: HLA-A*0101,0201,0205,0301,2902; B*0801,1501,4403,5001,5701. We found MHC-dependent differences in the predicted binding affinity of identified peptides. We used bioinformatic tools to identify the genes source of peptides and to characterize and compare the proteins encoding the MHC I-p repertoire. Peptides were encoded by genes located in all chromosomes and the mitochondria, and were significantly enriched for genes located in chromosomes 17 and 6. Our analysis revealed an enrichment of genes implicated in cell cycle, transcription and protein synthesis, as well as in immune and viral infection-related pathways, reflecting a B cell-specific signature.
Impact of Die Attach Material and Substrate Design on RF GaAs Power Amplifier Devices Thermal Performance (2001)

Abstract The latest commercial applications for microelectronics use GaAs material for RF Power Amplifier devices. This leads to the necessity of identifying low cost packaging solutions with high standards for reliability, electrical and thermal performance. A detailed thermal analysis for the wirebonded GaAs devices is performed using numerical simulations. The main interest of the study focuses on the impact of die attach thermal conductivity (1.0 to 7.0 W/mK), substrate’s top metal layer thickness (25 to 50 μm), and via wall thickness (25 to 50 μm) on GaAs IC device overall thermal performance. The study uses a 2-layer organic substrate; the die attach thickness is 15μm. The peak temperatures reached by PA stages range from 102.7°C to 113.5°C, below the prohibitive/critical value of 150°C (based on 85°C ambient temperature). The increase of die attach thermal conductivity (3 times) led to a slight decrease in peak temperatures (up to 5°C) and the decay is much larger between the cases with 1 and 2.4 W/mK. The largest temperature differences were obtained by varying the thermal via thickness, as opposed to only increasing the top metal layer thickness. The peak temperatures and corresponding junction to ambient thermal resistances are documented. It is determined that for the same die attach thickness, for a thermal conductivity larger than 7 W/mK, the impact on the PA’s peak temperature is insignificant.
Immune responses in vitro. IV. A comparison of the protein‐free and mouse serum‐supplemented mouse mixed lymphocyte interaction assays (1973)

Abstract Various parameters that optimize the cellular responses of mouse spleen lymphoid cells against alloantigens in a protein‐free and a mouse serum‐supplemented culture medium are defined. Results indicate: (a) The addition of sulfhydryl agents to either culture system caused an increase in thymidine incorporation, the percent increase being greater in allogeneic cultures than in syngeneic cultures. (b) The optimal ratio of responder cells to stimulator cells in the absence and presence of serum were different. The presence of mouse serum reduced by one‐half the number of stimulator cells necessary to maximize the response, while the optimal number of responder cells was similar in both systems. (c) The maximum incorporation of isotope for strain combinations which involved incompatibility at the major histocompatibility complex (H‐2) was at 66 h of culture in the protein‐free medium and at 98 h of culture in the serum‐supplemented medium.
89-05: Validation of NOGA-derived assessment of left ventricular function against MRI (2016)

Purpose: Measurements of left ventricular (LV) systolic function, in particular strain, are gaining popularity as predictor of CRT effectiveness. Also, spatially accurate strain mapping, may help guiding intramyocardial biological therapy delivery and assessment. We recently developed a method for the simultaneous assessment of the LV electrical and mechanical activity. We sought to compare volume and strain measurements derived from electromechanical anatomical mapping (EMAM) with the gold standard technique, MRI. Methods: In 22 patients, EMAM maps (NOGA XP, BDS) and MRI images (3.0 T Magnetom Skyra, Siemens) were obtained within 1 month. MRI images were analyzed to obtain end-systolic (ESV), end-diastolic volumes (EDV) and ejection fractions (EF) from cine images and circumferential strain (CS) from MRI tagging images. EMAM was analyzed using custom software: volumes were calculated as the volume enclosed by the convex surface fitting the catheter tip positions, while CS was derived from the motion field of the catheter tip at the different locations. Regional peak CS values were averaged over points belonging to the same cardiac sector (6 sectors for the basal, mid and apical levels). Inter-technique agreement was tested through correlation and Bland-Altman analysis. Conclusion: This is the first study demonstrating the feasibility of assessing ventricular systolic function based on EMAM, and validating it against the current reference technique. The proposed approach allows the combined assessment of the electrical and mechanical activities without the need of error-prone separate strain and electrical imaging. EMAM-based strain analysis may be extended to the entire cardiac cycle, overcoming the limitations associated with the fading MRI tags.
An alternative approach to avoid overfitting for surrogate models (2011)

Surrogate models are data-driven models used to accurately mimic the complex behavior of a system. They are often used to approximate computationally expensive simulation code in order to speed up the exploration of design spaces. A crucial step in the building of surrogate models is finding a good set of hyperparameters, which determine the behavior of the model. This is especially important when dealing with sparse data, as the models are in that case more prone to overfitting. Cross-validation is often used to optimize the hyperparameters of surrogate models, however it is computationally expensive and can still lead to overfitting or other erratic model behavior. This paper introduces a new auxiliary measure for the optimization of the hyperparameters of surrogate models which, when used in conjunction with a cheap accuracy measure, is fast and effective at avoiding unexplained model behavior.
Affinity Maturation Enhances Antibody Specificity but Compromises Conformational Stability (2019)

Monoclonal antibodies (mAbs) have recently emerged as one of the most promising classes of biotherapeutics. A potential advantage of B cell-derived mAbs as therapeutic agents is that they have been subjected to natural filtering mechanisms, which may enrich for B cell receptors (BCRs) with favorable biophysical properties. Here, we evaluated 400 human mAbs for polyreactivity, hydrophobicity, and thermal stability using high-throughput screening assays. Overall, mAbs derived from memory B cells and long-lived plasma cells (LLPCs) display reduced levels of polyreactivity, hydrophobicity, and thermal stability compared with naive B cell-derived mAbs. Somatic hypermutation (SHM) is inversely associated with all three biophysical properties, as well as BCR expression levels. Finally, the developability profiles of the human B cell-derived mAbs are comparable with those observed for clinical mAbs, suggesting their high therapeutic potential. The results provide insight into the biophysical consequences of affinity maturation and have implications for therapeutic antibody engineering and development.
Clinical sequencing using a next‐generation sequencing‐based multiplex gene assay in patients with advanced solid tumors (2017)

Advances in next-generation sequencing (NGS) technologies have enabled physicians to test for genomic alterations in multiple cancer-related genes at once in daily clinical practice. In April 2015, we introduced clinical sequencing using an NGS-based multiplex gene assay (OncoPrime) certified by the Clinical Laboratory Improvement Amendment. This assay covers the entire coding regions of 215 genes and the rearrangement of 17 frequently rearranged genes with clinical relevance in human cancers. The principal indications for the assay were cancers of unknown primary site, rare tumors, and any solid tumors that were refractory to standard chemotherapy. A total of 85 patients underwent testing with multiplex gene assay between April 2015 and July 2016. The most common solid tumor types tested were pancreatic (n = 19; 22.4%), followed by biliary tract (n = 14; 16.5%), and tumors of unknown primary site (n = 13; 15.3%). Samples from 80 patients (94.1%) were successfully sequenced. The median turnaround time was 40 days (range, 18-70 days). Potentially actionable mutations were identified in 69 of 80 patients (86.3%) and were most commonly found in TP53 (46.3%), KRAS (23.8%), APC (18.8%), STK11 (7.5%), and ATR (7.5%). Nine patients (13.0%) received a subsequent therapy based on the NGS assay results. Implementation of clinical sequencing using an NGS-based multiplex gene assay was feasible in the clinical setting and identified potentially actionable mutations in more than 80% of patients. Current challenges are to incorporate this genomic information into better therapeutic decision making.
Integrating diverse research and development approaches to the construction of social cyberspaces (2001)

Researchers take a broad range of approaches in studying social cyberspaces, and each approach has its own theoretical underpinnings, goals, methods, advantages, and disadvantages. We intend to bring researchers from various backgrounds together, document the range of variation in this interdisciplinary area, and build connections among these practitioners. Using a survey instrument, this workshop will create a resource catalog (distributed through the web) that can be used by others in this field to guide them through the range of approaches in current use. Particular attention will be paid to the advantages and disadvantages of the different methodological approaches researchers take to understand, develop and enhance specific research topics.