gebhart/patrepeval huggingface dataset:
Measurements of colliding shock wave and supersonic gas flow (2010)

The collision between a laser generated shock wave and a supersonic flow from a gas jet was studied using pump-probe Schlieren shadowgraphy. The velocity of a gas escaping into vacuum from a high pressure gas jet nozzle was measured and verified in simulation. Time resolved tracking of the shock wave provided critical information about the gas jet vertical velocity and horizontal gas density profile. The measured velocity of the diatomic gas jet was found to be close to the theoretical maximum escape velocity of the gas released into vacuum. Modification of the hemispherical shock wave structure by the supersonic flow was minimal. However, the propagation of the shock wave was observed to be substantially effected by the gas flow.
Electro-optic effect in an optically active nematic chiral liquid-crystal structure (1994)

A new electro-optic effect in an optically active nematic chiral structure beyond Mauguin's region has been studied. The effect is revealed in the absence of oscillations of the transmission-voltage curve, low requirements for orienting surfaces, and the ability to function at any direction of polarization of incident light. The limit relationships among wavelength, helical path, and optical anisotropy of the nematic matrix are determined. The dispersion properties of the effect are studied, and the possibility of its application for white-light modulation is shown as well. The control voltage is 6 V, and the time of switching is 50 µs.
Li4B4M3O12Cl (M = Al, Ga): An Electrochemically Stable, Lithium-Ion-Conducting Cubic Boracite with Substituted Boron Sites (2017)

Abstract A cubic boracite with substituted boron sites, Li4B4M3O12Cl (M = Al, Ga), derived by fully replacing the tetrahedral BO4 units in the parent lithium chloroboracite, Li4B7O12Cl, with AlO4 or GaO4 units, has been discovered. These substituted compounds have the largest unit cell dimensions of known boracites and are formed as the stable primary phase in highly crystalline glass-ceramics derived from the Li2O–B2O3–M2O3–LiCl quarternary system. The conductivity of Li4B4M3O12Cl glass-ceramics at room temperature was ∼10−5 S cm−1, an order of magnitude larger than the highest conductivity recorded for Li4B7O12Cl glass-ceramics. The Li4B4Al3O12Cl glass-ceramic is stable in contact with Li metal and exhibits a wide electrochemical window between 0 and 6 V vs. Li/Li+ and a Li+ ion transport number of ∼1.
Cross-seeding of prions by aggregated α-synuclein leads to transmissible spongiform encephalopathy (2017)

Aggregation of misfolded proteins or peptides is a common feature of neurodegenerative diseases including Alzheimer's, Parkinson's, Huntington's, prion and other diseases. Recent years have witnessed a growing number of reports of overlap in neuropathological features that were once thought to be unique to only one neurodegenerative disorder. However, the origin for the overlap remains unclear. One possibility is that diseases with mixed brain pathologies might arise from cross-seeding of one amyloidogenic protein by aggregated states of unrelated proteins. In the current study we examined whether prion replication can be induced by cross-seeding by α-synuclein or Aβ peptide. We found that α-synuclein aggregates formed in cultured cells or in vitro display cross-seeding activity and trigger misfolding of the prion protein (PrPC) in serial Protein Misfolding Cyclic Amplification reactions, producing self-replicating PrP states characterized by a short C-terminal proteinase K (PK)-resistant region referred to as PrPres. Non-fibrillar α-synuclein or fibrillar Aβ failed to cross-seed misfolding of PrPC. Remarkably, PrPres triggered by aggregated α-synuclein in vitro propagated in animals and, upon serial transmission, produced PrPSc and clinical prion disease characterized by spongiosis and astrocytic gliosis. The current study demonstrates that aggregated α-synuclein is potent in cross-seeding of prion protein misfolding and aggregation in vitro, producing self-replicating states that can lead to transmissible prion diseases upon serial passaging in wild type animals. In summary, the current work documents direct cross-seeding between unrelated amyloidogenic proteins associated with different neurodegenerative diseases. This study suggests that early interaction between unrelated amyloidogenic proteins might underlie the etiology of mixed neurodegenerative proteinopathies.
A hybrid artificial-noise and secret-key scheme for securing OFDM transmissions in V2G networks (2018)

We propose a new scheme to enhance the physical-layer security of wireless single-input single-output orthogonal-frequency division-multiplexing (OFDM) transmissions from an electric vehicle, Alice, to the aggregator, Bob, in the presence of an eavesdropper, Eve. To prevent information leakage to Eve, Alice exploits the wireless channel randomness to extract secret key symbols that are used to encrypt some data symbols which are then multiplexed in the frequency domain with the remaining unencrypted data symbols. To secure the unencrypted data symbols, Alice transmits an artificial-noise (AN) signal superimposed over her data signal. We propose a three-level optimization procedure to increase the average secrecy rate of this wiretap channel by optimizing the transmit power allocation between the encrypted data symbols, unencrypted data symbols and the AN symbols. Our numerical results show that the proposed scheme achieves considerable secrecy rate gains compared to the benchmark cases.
3-D mesh compensated wavelet lifting for 3-D&#x002B;t medical CT data (2014)

For scalable coding, a high quality of the lowpass band of a wavelet transform is crucial when it is used as a downscaled version of the original signal. However, blur and motion can lead to disturbing artifacts. By incorporating feasible compensation methods directly into the wavelet transform, the quality of the lowpass band can be improved. The displacement in dynamic medical 3-D+t volumes from Computed Tomography is mainly given by expansion and compression of tissue over time and can be modeled well by mesh-based methods. We extend a 2-D mesh-based compensation method to three dimensions to obtain a volume compensation method that can additionally compensate deforming displacements in the third dimension. We show that a 3-D mesh can obtain a higher quality of the lowpass band by 0.28 dB with less than 40% of the model parameters of a comparable 2-D mesh. Results from lossless coding with JPEG 2000 3D and SPECK3D show that the compensated subbands using a 3-D mesh need about 6% less data compared to using a 2-D mesh.
Combined presentation and immunogenicity analysis reveals a recurrent RAS.Q61K neoantigen in melanoma (2021)

Neoantigens are now recognized drivers of the antitumor immune response. Recurrent neoantigens, shared among groups of patients, have thus become increasingly coveted therapeutic targets. Here, we report on the data-driven identification of a robustly presented, immunogenic neoantigen that is derived from the combination of HLA-A*01:01 and RAS.Q61K. Analysis of large patient cohorts indicated that this combination applies to 3% of patients with melanoma. Using HLA peptidomics, we were able to demonstrate robust endogenous presentation of the neoantigen in 10 tumor samples. We detected specific reactivity to the mutated peptide within tumor-infiltrating lymphocytes (TILs) from 2 unrelated patients, thus confirming its natural immunogenicity. We further investigated the neoantigen-specific clones and their T cell receptors (TCRs) via a combination of TCR sequencing, TCR overexpression, functional assays, and single-cell transcriptomics. Our analysis revealed a diverse repertoire of neoantigen-specific clones with both intra- and interpatient TCR similarities. Moreover, 1 dominant clone proved to cross-react with the highly prevalent RAS.Q61R variant. Transcriptome analysis revealed a high association of TCR clones with specific T cell phenotypes in response to cognate melanoma, with neoantigen-specific cells showing an activated and dysfunctional phenotype. Identification of recurrent neoantigens and their reactive TCRs can promote "off-the-shelf" precision immunotherapies, alleviating limitations of personalized treatments.
Structural and Conformational Requirements for Ir-Gene-Controlled Myoglobin Epitope Recognition by Ia-Restricted T Cells and Clones (1986)

In previous studies we have found that at least two distinct (Ir genes, mapping in different subregions of the mouse H-2I region, control both antibody and T-cell responses to distinct regions or epitopes of the myoglobin molecule1,2. This control is mediated in some way through the associative recognition of different epitopes with different la molecules, as shown by the use of genetic recombinant antigen presenting cells bearing one, the other, both, or neither Ir gene, to present myoglobin or its fragments to the same population of myoglobin-immune F3 hybrid T cells1. To understand the molecular mechanism of this control, therefore, it was necessary to understand the biochemistry of T-cell recognition of antigen in association with Ia.
Ru(III)‐Catalyzed Cyclization of Arene‐Alkene Substrates via Intramolecular Electrophilic Hydroarylation. (2004)

Abstract For Abstract see ChemInform Abstract in Full Text.
Contrasting SnTe–NaSbTe2 and SnTe–NaBiTe2 Thermoelectric Alloys: High Performance Facilitated by Increased Cation Vacancies and Lattice Softening (2020)

Defect chemistry is critical to designing high performance thermoelectric materials. In SnTe, the naturally large density of cation vacancies results in excessive hole doping and frustrates the ability to control the thermoelectric properties. Yet, recent work also associates the vacancies with suppressed sound velocities and low lattice thermal conductivity, underscoring the need to understand the interplay between alloying, vacancies, and the transport properties of SnTe. Here, we report solid solutions of SnTe with NaSbTe<sub>2</sub> and NaBiTe<sub>2</sub> (NaSn<sub><i>m</i></sub>SbTe<sub><i>m</i>+2</sub> and NaSn<sub><i>m</i></sub>BiTe<sub><i>m</i>+2</sub>, respectively) and focus on the impact of the ternary alloys on the cation vacancies and thermoelectric properties. We find introduction of NaSbTe<sub>2</sub>, but not NaBiTe<sub>2</sub>, into SnTe nearly doubles the natural concentration of Sn vacancies. Furthermore, DFT calculations suggest that both NaSbTe<sub>2</sub> and NaBiTe<sub>2</sub> facilitate valence band convergence and simultaneously narrow the band gap. These effects improve the power factors but also make the alloys more prone to detrimental bipolar diffusion. Indeed, the performance of NaSn<sub><i>m</i></sub>BiTe<sub><i>m</i>+2</sub> is limited by strong bipolar transport and only exhibits modest maximum ZTs ≈ 0.85 at 900 K. In NaSn<sub><i>m</i></sub>SbTe<sub><i>m</i>+2</sub> however, the doubled vacancy concentration raises the charge carrier density and suppresses bipolar diffusion, resulting in superior power factors than those of the Bi-containing analogues. Lastly, NaSbTe<sub>2</sub> incorporation lowers the sound velocity of SnTe to give glasslike lattice thermal conductivities. Facilitated by the favorable impacts of band convergence, vacancy-augmented hole concentration, and lattice softening, NaSn<sub><i>m</i></sub>SbTe<sub><i>m</i>+2</sub> reaches high ZT ≈ 1.2 at 800-900 K and a competitive average ZT<sub>avg</sub> of 0.7 over 300-873 K. The difference in ZT between two chemically similar compounds underscores the importance of intrinsic defects in engineering high-performance thermoelectrics.
Directed aging, memory, and nature’s greed (2019)

Disordered materials are often out of equilibrium and evolve very slowly in a rugged and tortuous energy landscape. This slow evolution, referred to as aging, is deemed undesirable as it often leads to material degradation. However, we show that aging also encodes a memory of the stresses imposed during preparation. Because of inhomogeneous local stresses, the material itself decides how to evolve by modifying stressed regions differently from those under less stress. Because material evolution occurs in response to stresses, aging can be "directed" to produce sought-after responses and unusual functionalities that do not inherently exist. Aging obeys a natural "greedy algorithm" as, at each instant, the material simply follows the path of most rapid and accessible relaxation. Our experiments and simulations illustrate directed aging in examples in which the material's elasticity transforms as desired because of an imposed deformation.
Abstract 2859: Chloroquine and vitamin D3 modulate proliferation in early stage breast cancer models (2016)

Abstract The defining feature of premalignant mammary lesions is proliferation of cells within the intraductal niche. Survival in this stressful duct microenvironment requires sophisticated mechanisms to avoid apoptosis caused by hypoxia, nutrient deprivation, metabolic acidosis, and intracellular calcium overload. Two major survival mechanisms of breast ductal carcinoma cells (DCIS) are 1) the upregulation of autophagy and 2) the enhanced export of calcium via plasma membrane calcium-ATPase isoform 2 (PMCA2) efflux pumps. We hypothesize that calcium efflux, through PMCA2, and activation of autophagic catabolism are critical interdependent mechanisms for the survival of pre-invasive human breast neoplastic cells. To assess the proteomic response to autophagy inhibition and/or elevated intracellular calcium, 41 signal transduction proteins/post-translationally modified proteins related to proliferation, autophagy, and calcium pathways were quantified by reverse phase protein microarrays (RPPA) in time course studies of T-47D metastatic ductal breast cancer cell line, and MCF-10A non-tumorigenic breast cell line, both of which express low basal levels of PMCA2, and in human primary DCIS organoid cultures. Cell lines were treated with chloroquine (50μM), or 1,25 dihydroxyvitamin D3 (Calcitriol) (50nM or 100nM), or chloroquine + Calcitriol, and harvested at periodic intervals over 197 hours. Stoichiometric time course studies (24 hours) were evaluated for Calcitriol as a single agent in both T-47D and MCF-10A cell lines. Cell morphology, adhesion, proliferation and autophagic flux in the DCIS organoids were assessed by Immunohistochemistry and RPPA. Calcitriol alone did not increase proliferation based on PCNA expression within DCIS ducts. Chloroquine markedly increased Cleaved PARP (Chi Sq p = 0.004) and CAMKinase II (p = 0.0068). Chloroquine (50μM) plus Calcitriol (100nM) increased E-Cadherin (p = 0.0379) and phosphoPAK1/2 (p = 0.0163), while PMCA2 levels were not significantly different between treatment groups. Autophagy inhibition and calcium efflux may be exploited therapeutically by co-administration of chloroquine and Calcitrol, to inhibit lysosomal catabolism and increase intracellular calcium levels, respectively, switching them from autophagic survival into apoptotic death. Citation Format: Virginia A. Espina, Solomon Yeon, Joshua N. VanHouten, John Wysolmerski, Lance A. Liotta. Chloroquine and vitamin D3 modulate proliferation in early stage breast cancer models. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 2859.
Several Decades of Fluid Diversion Evolution, Is There a Good Solution? (2021)

Abstract The success of any matrix treatment depends upon the complete coverage of all zones. Consequently, the selection of the diversion technology is critical for treatment success. While various types of diverting agents are commercially available, the proper selection of optimal diverter depends on many factors, including well completion and history, compatibility with reservoir and treatment fluids, treatment objectives, operational constraints, and safety and environment considerations. The study will cover five major types of non-mechanical diversion technologies considered as potential solutions for offshore deepwater oil reservoirs: dynamic diversion, relative permeability modifiers (RPM), viscoelastic surfactants (VES), particulate diversion, and perforation diversion. All of them, but a dynamic diversion, are based on different chemicals or products to be added to the injected treatment fluid, and occasionally some can be complementary to each other. Given the offshore and deepwater settings, mechanical diversion techniques were not covered in the study, aiming to find a solution that would achieve acceptable diversion while minimizing operational effort, which would enable riser-less intervention and the use of light intervention techniques. This study was driven by the need to effectively stimulate a 500ft of a cased and perforated interval with a permeability of 500 md, and injection rate limited to 16 bpm due to completion limitations. The sandstone formation, with static in situ temperature of 270F, was far beyond the applicability of dynamic diversion and, to achieve the desired full coverage for the planned scale inhibition treatment required and combination with another diverter system was needed. The process applied included compatibility tests, regained permeability tests, and test well trials. Depending on the specific diversion product analyzed the testing procedures were adapted to obtain the information to properly guide to the optimal solution.
Large Hexagonal Bi‐ and Trilayer Graphene Single Crystals with Varied Interlayer Rotations (2014)

Abstract Bi‐ and trilayer graphene have attracted intensive interest due to their rich electronic and optical properties, which are dependent on interlayer rotations. However, the synthesis of high‐quality large‐size bi‐ and trilayer graphene single crystals still remains a challenge. Here, the synthesis of 100 μm pyramid‐like hexagonal bi‐ and trilayer graphene single‐crystal domains on Cu foils using chemical vapor deposition is reported. The as‐produced graphene domains show almost exclusively either 0° or 30° interlayer rotations. Raman spectroscopy, transmission electron microscopy, and Fourier‐transformed infrared spectroscopy were used to demonstrate that bilayer graphene domains with 0° interlayer stacking angles were Bernal stacked. Based on first‐principle calculations, it is proposed that rotations originate from the graphene nucleation at the Cu step, which explains the origin of the interlayer rotations and agrees well with the experimental observations.
Expression of cancer/testis (CT) antigens MAGE-A1, MAGE-A3, MAGE-A4, CT-7, and NY-ESO-1 in malignant gammopathies is heterogeneous and correlates with site, stage and risk status of disease. (2003)

Cancer/testis (CT) antigens are expressed in several malignant tumors, but not in normal tissues except for testicular germ cells. The expression of CT antigenic proteins in malignant gammopathies has not been characterized. We examined the expression of a panel of CT antigenic proteins in 29 patients with malignant gammopathies by immunohistochemistry using the following monoclonal antibodies (mAbs): mAb MA454 to MAGE-A1, mAb M3H67 to MAGE-A3, mAb 57B to MAGE-A4, mAb CT7-33 to CT7/MAGE-C1 and mAb ES121 to NY-ESO-1. We could detect at least one CT antigen in tumors from 27 of 29 patients. The expression pattern of MAGE-A1, -A3, -A4 and NY-ESO-1 is heterogeneous in most cases, revealing staining in <25% of the tumor cells. Monoclonal antibodies CT7-33 and M3H67 show the highest incidence of immunoreactivity. Importantly, CT-7 can also be detected on the surface of some myeloma cells by flow cytometry, and in one plasmacytoma case by immunohistochemistry. Expression of CT antigens is greater in patients with stage III extramedullary plasmacytoma or high-risk myeloma relative to other cohorts. These data suggest that CT antigens may have important biological implications in malignant gammopathies and that CT-7 may be a suitable target for T cell-based and possibly antibody-mediated immunotherapy of myeloma.
Rapid identification of disease-causing mutations using copy number analysis within linkage intervals (2007)

SNP and comparative genome hybridization arrays (aCGH) are powerful techniques for identifying genome rearrangements, deletions, and duplications. We hypothesized that current array-based detection of copy number variation (CNV) could complement parametric linkage analysis and allow the rapid identification of functional mutations in families with inherited disorders. Herein, we demonstrate the utility of this technique by rapidly identifying a disease causing microdeletion within the PARK2 gene in a family with autosomal recessive Parkinsonism.
Rapidly Fatal Pulmonary Fibrosis in a Patient with Psoriatic Arthritis Treated with Adalimumab (2011)

To the Editor: Anti-tumor necrosis factor-α (TNF-α) drugs are used with increasing frequency for disorders involving the skin, joints, and gastrointestinal tract. A wide range of adverse effects have been identified among over one million patients treated with this class of drugs1. These include bacterial infections, mycobacterial infections, fungal infections, cutaneous malignancies, exacerbations of congestive heart failure, and autoimmune diseases1,2,3. In addition, anecdotal reports have linked interstitial lung disease (ILD) and pulmonary fibrosis to etanercept4, infliximab5, or adalimumab6,7. Recently, one study reported no clear pattern of causal relationship of treatment with infliximab and hospitalization for ILD in patients with rheumatoid arthritis (RA)8. Another … Address correspondence to Dr. Cohen; E-mail: justine.cohen{at}uphs.upenn.edu