gebhart/patrepeval huggingface dataset:
Polymer-Coated Magnetic Microspheres Conjugated with Growth Factor Receptor Binding Peptides Enable Cell Sorting (2021)

The separation and sorting of human cells is an important step in the bioprocessing of cell-based therapeutics. Heterogeneous mixtures of cells must be sorted to isolate the desired cell type and purify the final product. This process is often achieved by antibody-based sorting techniques. In this work, we demonstrate that magnetic microspheres may be functionalized with peptides that selectively bind to cells on the basis of their relative concentration of specific surface proteins. Five-micrometer-magnetic microspheres were coated with the synthetic copolymer PVG (poly(poly(ethylene glycol)methyl ether methacrylate-<i>ran</i>-vinyl dimethyl azlactone-<i>ran</i>-glycidyl methacrylate) and functionalized with the vascular endothelial growth factor receptor binding peptide (VRBP), which binds to the vascular endothelial growth factor receptor (VEGFR). These microspheres exhibited low cytotoxicity and bind to cells depending on their relative surface protein expression. Finally, coated, magnetic microspheres were used to separate heterogeneous populations of cells dependent on their VEGFR expression through magnetic-assisted cell sorting (MACS), demonstrating that peptide-based cell sorting mechanisms may be useful in the bioprocessing of human-cell-based products.
Transition metamaterials for local-field enhancement (2017)

We achieve strong local-field enhancement within a novel inhomogeneous metamaterial whose graded refractive index is realized using Dirac-cone metamaterials. This transition metamaterial provides a powerful tool for sensing, nonlinear optics, and quantum optics.
Mapping of a surface-exposed, conformational epitope of the P6 protein of Haemophilus influenzae (1995)

P6 is an outer membrane protein of Haemophilus influenzae that is antigenically conserved and considered a candidate component of future H. influenzae vaccines. P6 contains a surface-exposed epitope recognized by monoclonal antibody (MAb) 3B9. This epitope has been shown to be distinct from that recognized by the P6-specific MAbs 7F3 and 4G4 in a competitive inhibition enzyme-linked immunosorbent assay (ELISA). MAb 3B9 did not bind to synthetic P6-specific sequential and overlapping hexameric peptides. Five peptides made to correspond to P6 sequences with high probabilities of surface exposure did not inhibit binding of MAb 3B9 to P6. An antiserum to one of the peptides, designated SP66, inhibited binding of MAb 3B9 to P6. A rabbit antiserum to P6 bound to sequential hexameric peptides, Gly-87AsnThrAspGluArgGlyThr-94, which were in the SP66 region of P6. This antiserum inhibited the binding of P6 to MAb 3B9 in a competitive inhibition ELISA. P6 mutations with His and Ala substitutions at residues Thr-88 and Asn-89 still bound MAb 3B9. MAb 3B9 reacted with Escherichia coli OmpA and Salmonella typhimurium OmpA. Sequence comparisons of P6 with these proteins indicated that the residue in the SP66 region responsible for binding is either Gly-87, Asp-90, or Gly-93. Mercaptoethanol reduction abolished MAb 3B9 binding to E. coli OmpA and S. typhimurium OmpA. In these proteins, immediately downstream of the second cysteine, there is an ArgArg dipeptide which is identical to and aligns with Arg-147Arg-148 in P6. This dipeptide has a high probability of surface exposure in P6. Mutagenesis of the Arg-147Arg-148 to an AlaAla dipeptide in P6 abolished binding of MAb 3B9, demonstrating that it was either a portion of the epitope or important in the protein folding necessary for expression of this epitope. This study demonstrates that MAb 3B9 recognizes a conserved conformational determinant on the surface of H. influenzae that is composed of two discontinuous regions of P6.
Efficient hole injection in organic light-emitting diodes using C60 as a buffer layer for Al reflective anodes (2006)

The hole injection of the organic light-emitting diodes with Al as a reflective anode for top-emitting devices was improved by using C60 as a thin buffer layer between Al and a hole transport layer. The driving voltage of the devices with C60 buffer layer was 5.5V compared with 11V for the devices without C60 buffer layer. The decrease of interfacial energy barrier by interface dipole formation between Al and C60 contributed to the low driving voltage of the devices.
Structure and absolute configuration of ginkgolide B characterized by IR‐ and VCD spectroscopy (2009)

Experimental and calculated (B3LYP/6-31G(d)) vibrational circular dichroism (VCD) and IR spectra are compared, illustrating that the structure and absolute configuration of ginkgolide B (GB) may be characterized directly in solution. A conformational search for GB using MacroModel and subsequent DFT optimizations (B3LYP/6-31G(d)) provides a structure for the lowest energy conformer which agrees well with the structure determined by X-ray diffraction. In addition, a conformer at an energy of 7 kJ mol(-1) (B3LYP/6-311+G(2d,2p)) with respect to the lowest energy conformer is predicted, displaying different intramolecular hydrogen bonding. Differences between measured and calculated IR and VCD spectra for GB at certain wavenumbers are rationalized in terms of interactions with solvent, intermolecular GB-GB interactions, and the potential presence of more than one conformer. This is the first detailed investigation of the spectroscopic fingerprint region (850-1300 cm(-1)) of the natural product GB employing infrared absorption and VCD spectroscopy.
pH dependence of the urea and guanidine hydrochloride denaturation of ribonuclease A and ribonuclease T1 (1990)

To investigate the pH dependence of the conformational stability of ribonucleases A and T1, urea and guanidine hydrochloride denaturation curves have been determined over the pH range 2-10. The maximum conformational stability of both proteins is about 9 kcal/mol and occurs near pH 4.5 for ribonuclease T1 and between pH 7 and 9 for ribonuclease A. The pH dependence suggests that electrostatic interactions among the charged groups make a relatively small contribution to the conformational stability of these proteins. The dependence of delta G on urea concentration increases from about 1200 cal mol-1 M-1 at high pH to about 2400 cal mol-1 M-1 at low pH for ribonuclease A. This suggests that the unfolded conformations of RNase A become more accessible to urea as the net charge on the molecule increases. For RNase T1, the dependence of delta G on urea concentration is minimal near pH 6 and increases at both higher and lower pH. An analysis of information of this type for several proteins in terms of a model developed by Tanford [Tanford, C. (1964) J. Am. Chem. Soc. 86, 2050-2059] suggests that the unfolded states of proteins in urea and GdnHCl solutions may differ significantly in the extent of their interaction with denaturants. Thus, the conformations assumed by unfolded proteins may depend to at least some extent on the amino acid sequence of the protein.
Multi-Source Acquisition Based on the Principles of Signal Apparition (2019)

Summary Signal apparition is a recent signal processing advance that has numerous applications in seismic data acquisition and processing. In this paper we review the basic principles of signal apparition and discuss applications related to simultaneous source acquisition. We discuss the generalization of the technique to large number of sources and the application in a full 3D configuration enabling large productivity gains and the acquisition of broad band seismic data.
A high I/O reconfigurable crossbar switch (2003)

A crossbar switch with 928 inputs and 928 outputs is presented. Switching elements are constructed using logic in the routing fabric. This approach yields a 16/spl times/ improvement in logic density compared with using conventional logic. Normally, the routing is fixed. However, in FPGAs (field programmable gate arrays), the interconnection is defined by the state of SRAM configuration cells, which are dynamically modifiable. Therefore, the switch is implemented on an FPGA using partial configuration to modify routing resources during operation. All paths are synchronously clocked at 155.5 MHz, creating a total throughput of 144.3 Gbits/s. to maintain constant clock latency across all paths, partially configurable delay registers are used. Finally, the partial reconfiguration controller is implemented in hardware to enable fast switch updates.
Preparation of Heteroaryloxetanes and Heteroarylazetidines by Use of a Minisci Reaction (2009)

Introduction of oxetan-3-yl and azetidin-3-yl groups into heteroaromatic bases was achieved by using a radical addition method (Minisci reaction). To demonstrate utility, the process was used to introduce an oxetane or azetidine into heteroaromatic systems that have found important uses in the drug discovery industry, such as the marketed EGFR inhibitor gefitinib, a quinolinecarbonitrile Src tyrosine kinase inhibitor, and the antimalarial hydroquinine.
TLR2 Activation by Porphyromonas gingivalis Requires Both PPAD Activity and Fimbriae (2022)

<i>Porphyromonas gingivalis</i>, a keystone oral pathogen implicated in development and progression of periodontitis, may also contribute to the pathogenicity of diseases such as arthritis, atherosclerosis, and Alzheimer's. <i>P. gingivalis</i> is a master manipulator of host immune responses due to production of a large variety of virulence factors. Among these, <i>P. gingivalis</i> peptidilarginine deiminase (PPAD), an enzyme unique to <i>P. gingivalis</i>, converts C-terminal Arg residues in bacterium- and host-derived proteins and peptides into citrulline. PPAD contributes to stimulation of proinflammatory responses in host cells and is essential for activation of the prostaglandin E2 (PGE2) synthesis pathway in gingival fibroblasts. Since <i>P. gingivalis</i> is recognized mainly by Toll-like receptor-2 (TLR2), we investigated the effects of PPAD activity on TLR2-dependent host cell responses to <i>P. gingivalis</i>, as well as to outer membrane vesicles (OMVs) and fimbriae produced by this organism. Using reporter cell lines, we found that PPAD activity was required for TLR2 activation by <i>P. gingivalis</i> cells and OMVs. We also found that fimbriae, an established TLR2 ligand, from wild-type ATCC 33277 (but not from its isogenic PPAD mutant) enhanced the proinflammatory responses of host cells. Furthermore, only fimbriae from wild-type ATCC 33277, but not from the PPAD-deficient strains, induced cytokine production and stimulated expression of genes within the PGE2 synthesis pathway in human gingival fibroblasts <i>via</i> activation of the NF-ĸB and MAP kinase-dependent signaling pathways. Analysis of ten clinical isolates revealed that type I FimA is preferable for TLR2 signaling enhancement. In conclusion, the data strongly suggest that both PPAD activity and fimbriae are important for TLR2-dependent cell responses to <i>P. gingivalis</i> infection.
Modulation-transfer-function-enhanced readout for SPRITE detectors (1996)

A new readout structure is investigated for signal-processing-in-the-element detectors that yields a modulation transfer function that is 3.5 dB better than those currently used. Experimental verification is performed in Si rather than HgCdTe, with similarity relations derived for the two semiconductors.
Hypoxia induces differential expression of the integrin receptors ?v?3 and ?v?5 in cultured human endothelial cells (2000)

The integrins alpha(vbeta3) and alpha(vbeta5) have been implicated in playing a key role in the process of angiogenesis. In this study, we examined the effects of hypoxia, an important stimulus of angiogenesis, on the differential expression of the integrin subunits beta(3) and beta(5). beta(3) and beta(5) messenger RNA (mRNA), protein levels, and alpha(v)beta(3) function were measured in human umbilical vein endothelial cells (HUVECs) cultured under normoxic and hypoxic (1% O(2)) conditions. Cells exposed to hypoxic conditions for up to 72 h showed gradually increased mRNA levels of alpha(V) and beta(3), peaking at 24 h, in comparison with cells cultured under normoxic conditions. However, beta(5) mRNA levels, under the same hypoxic conditions, remained at a constant level. Results from Western blot analysis of HUVECs, cultured under hypoxic conditions, paralleled those of the Northern analysis with an increased expression in alpha(v)beta(3) protein levels, measured by blotting with LM609, evident by 24 h. alpha(v)beta(5) protein levels, measured by blotting with P1F6, did not change for up to 72 h. HUVECs cultured under hypoxic conditions for 72 h showed increased attachment to fibrinogen, an alpha(v)beta(3) mediated process. These results indicate that hypoxia can increase expression of alpha(v)beta(3) in HUVECs, and that hypoxic regulation of alpha(v)beta(3) may be an important regulator of angiogenesis.
SU‐FF‐I‐63: Temporal Constrained Registration of Arbitrary Surface Contours for Use in 4D Radiation Therapy (2007)

Purpose: To quantify the validity of the temporal interpolation provided by a nonlinear uncorrelated contour based path length minimizing deformable registration algorithm in 4D radiation therapy. Method and Materials: The anatomical surfaces are represented as triangulated meshes. The registration algorithm is implemented by defining a norm between the triangulated meshes, based on the algorithms of Glaunès and Vaillant. This algorithm matches two surfaces as opposed to image intensities or specific points. Additionally, it optimizes the path between them allowing for a temporal interpolation. The registration is defined as the flow of an unlabeled 3D point set to an arbitrary target surface that minimizes both the norm between the target and registered surface and the non‐linear path length between the source and registered surface. Ground truth surfaces were generated from 4D lung datasets using the semi‐automatic mesh segmentation routine from a research version of Pinnacle, with expert manual correction. Results: To test this algorithm we compared its ability to interpolate intermediate shapes with a standard linear interpolation technique. We found that this algorithm performs comparably. The similarity metric used was an Euclidean distance error metric between the ground truth surface and a surface interpolated between a previous and subsequent ground truth surface. It was calculated between the interpolated and truth vertexes and their closest points on the truth and interpolated surfaces, respectively. This metric is independent of the interpolation and surface triangulation used, and thus is applicable to other interpolation algorithms. Conclusion: This work shows that this general, path length minimizing deformable registration algorithm based interpolation performs similarly to linear interpolation in approximately correlated, intrafractional datasets. This algorithm has the advantage of utilizing surfaces with arbitrary triangulations without point correspondences. We further discovered that this specific algorithm exhibited numerical instabilities that require further investigation.
Dirac-like cone-based electromagnetic zero-index metamaterials (2021)

Metamaterials with a Dirac-like cone dispersion at the center of the Brillouin zone behave like an isotropic and impedance-matched zero refractive index material at the Dirac-point frequency. Such metamaterials can be realized in the form of either bulk metamaterials with efficient coupling to free-space light or on-chip metamaterials that are efficiently coupled to integrated photonic circuits. These materials enable the interactions of a spatially uniform electromagnetic mode with matter over a large area in arbitrary shapes. This unique optical property paves the way for many applications, including arbitrarily shaped high-transmission waveguides, nonlinear enhancement, and phase mismatch-free nonlinear signal generation, and collective emission of many emitters. This review summarizes the Dirac-like cone-based zero-index metamaterials' fundamental physics, design, experimental realizations, and potential applications.
Use of benthic invertebrate community structure and the sediment quality triad to evaluate metal-contaminated sediment in the upper clark fork river, montana (1994)

Abstract The upper Clark Fork River, above Flathead River, is contaminated with large amounts of As, Cd, Cu, Pb, Mn, and Zn ores from past mining activities. The contaminated area extends from the Butte and Anaconda area to at least 230 km downstream to Milltown Reservoir. Both the upper Clark Fork River and Milltown Reservoir have been designated as U.S. Environmental Protection Agency Superfund sites because of metal-contaminated bottom sediments. We evaluated the impacts of past mining activities on the Clark Fork River ecosystem using benthic invertebrate community assessment, residue chemistry, and toxicity testing. Oligochaeta and Chironomidae generally accounted for over 90% of the benthic invertebrate community in the soft sediment depositional areas. Taxa of Oligochaeta and Chironomidae were predominantly pollution tolerant. Higher numbers of Chironomidae genera were present at stations with higher concentrations of metals in sediment identified as toxic by the amphipod Hyalella azteca in 28-d exposures. Frequency of mouthpart deformities in genera of Chironomidae was low and did not correspond to concentrations of metals in sediment. Total abundance of organisms/m2 did not correspond to concentrations of metals in the sediment samples. Chemical analyses, laboratory toxicity tests, and benthic community evaluations all provide evidence of metal-induced degradation to aquatic communities in both the reservoir and the river. Using a weight-of-evidence approach-the Sediment Quality Triad - provided good concurrence among measures of benthic community structure, sediment chemistry, and laboratory toxicity.
The Histone Deacetylase Inhibitor Vaproic Acid Induces Cell Growth Arrest in Hepatocellular Carcinoma Cells via Suppressing Notch Signaling (2015)

Hepatocellular carcinoma (HCC) is a type of malignant cancer. Notch signaling is aberrantly expressed in HCC tissues with more evidence showing that this signaling plays a critical role in HCCs. In the present study, we investigate the effects of the anti-convulsant drug valproic acid (VPA) in HCC cells and its involvement in modulating Notch signaling. We found that VPA, acting as a histone deacetylase (HDAC) inhibitor, induced a decrease in HDAC4 and an increase in acetylated histone 4 (AcH4) and suppressed HCC cell growth. VPA also induced down-regulation of Notch signaling via suppressing the expression of Notch1 and its target gene HES1, with an increase of tumor suppressor p21 and p63. Furthermore, Notch1 activation via overexpressing Notch1 active form ICN1 induced HCC cell proliferation and anti-apoptosis, indicating Notch signaling played an oncogenic role in HCC cells. Meanwhile, VPA could reverse Notch1-induced increase of cell proliferation. Interestingly, VPA was also observed to stimulate the expression of G protein-coupled somatostatin receptor type 2 (SSTR2) that has been used in receptor-targeting therapies. This discovery supports a combination therapy of VPA with the SSTR2-targeting agents. Our in vitro assay did show that the combination of VPA and the peptide-drug conjugate camptothecin-somatostatin (CPT-SST) displayed more potent anti-proliferative effects on HCC cells than did each alone. VPA may be a potential drug candidate in the development of anti-HCC drugs via targeting Notch signaling, especially in combination with receptor-targeting cytotoxic agents.
Optical Physical Layer SDN: Enabling Physical Layer Programmability through Open Control Systems (2017)

Software defined networking in the optical physical layer is complicated by transmission control used to both optimize performance and stabilize optical signals across multiple nodes. Different approaches are emerging to address these problems.
Measurement of CP violation in $B_{s}^{0}→ϕϕ$ decays (2014)

A measurement of the decay time-dependent C P -violating asymmetry in B 0 s → ϕ ϕ decays is presented, along with measurements of the T -odd triple-product asymmetries. In this decay channel, the C P -violating weak phase arises from the interference between B 0 s − ¯ B 0 s mixing and the loop-induced decay amplitude. Using a sample of proton-proton collision data corresponding to an integrated luminosity of 3.0 fb − 1 collected with the LHCb detector, a signal yield of approximately 4000 B 0 s → ϕ ϕ decays is obtained. The C P -violating phase is measured to be ϕ s = − 0.17 ± 0.15 ( stat ) ± 0.03 ( syst ) rad . The triple-product asymmetries are measured to be A U = − 0.003 ± 0.017 ( stat ) ± 0.006 ( syst ) and A V = − 0.017 ± 0.017 ( stat ) ± 0.006 ( syst ) . Results are consistent with the hypothesis of C P conservation.
Extended dynamic range imaging for noise mitigation in fluorescence anisotropy imaging (2020)

The method presented is shown to outperform standard FA imaging microscopy narrowing the spread of the propagated error and yielding higher quality images. The method can be effectively and routinely used on any commercial imaging system and could be also translated to other microscopy ratiometric imaging modalities.
A Multi-User Spatial Domain Link Adaptation Concept for Beyond 3G Systems (2006)

This paper summarizes current work within the IST-Project WINNER (Wireless World Initiative New Radio) towards a spatial processing solution as an integral part of the overall system concept. Major requirements for the WINNER multi-antenna concept include high performance, robustness, and adaptation to a wide range of scenarios and terminal classes, as well as efficient interworking with the basic transmission and network concept. Based on these guidelines, a first proposal for the WINNER multi-antenna concept is elaborated upon and presented in the form of a generic downlink transmitter that will serve as baseline for further investigation and system integration
Supplementary Figure S3 from Direct Detection and Quantification of Neoantigens (2023)

&lt;p&gt;Sanger sequencing to confirm G12D mutation from KRAS G12D-knockin cell line.&lt;/p&gt;
TGF-B Inhibition Rescues Hematopoietic Defects in Fanconi Anemia (2018)

Abstract Four different combinations of double knock-out mouse strains have been created (SMAD3-/- Fancd2-/-) consisting of combinations of the individual knock-out strains on either the C57BL/6 or 129/Sv background. Sets of breeding experiments were carried out and the frequency of detection of double knock-out mice was significantly below the expected frequency of detecting DKO mice by breeding double heterozygotes (1 out of 16 or 6.25%). In fact, DKO mice were detected at a frequency ranging from 3.4% to 0.54%. Mice of all four DKO genotypes showed resistance of bone marrow hematopoietic progenitor cells to canonical TGF-β signaling, consistent with the SMAD3-/- parent. However, the predominant phenotype was that of the Fancd2-/- parent including reduced duration of hematopoiesis in long-term bone marrow cultures, reduced marrow stem cell competitive repopulation capacity, and retained mitomycin C and radiation sensitivity of bone marrow stromal cells. These mice should be a valuable resource for elucidating the bypass pathways involved in the reduced, but successful gestation of SMAD3-/- Fancd2-/- mice, and the interactions of the FA and TGF-β signaling pathways. Supported by the NIAID/NIH U19-A168021 and the Fanconi Anemia Research Fund. Disclosures No relevant conflicts of interest to declare.