gebhart/patrepeval huggingface dataset:
Plasma-assisted molecular beam epitaxy of high quality In2O3(001) thin films on Y-stabilized ZrO2(001) using In as an auto surfactant (2009)

The surface roughness of In2O3(001) films is a roadblock to potential semiconductor applications of this material. Using plasma-assisted molecular beam epitaxy we found that In2O3(001) films grow rough by the formation of {111} facets and In2O3(111) films grow smooth without facetting due to the conventionally used (oxygen-rich) conditions. This behavior indicates that the (111) surface is thermodynamically prefered over the (001) surface. We demonstrate that under indium-rich growth conditions these thermodynamics are changed allowing In2O3(001) films to grow smoothly without facetting. Surface indium plays a key role by acting as an auto surfactant that lowers the surface free energy difference between the (001) and the (111) surface.
IL-17 in Sera from Patients with Aggressive Periodontitis (2010)

Interleukin-17 (IL-17), the prototype cytokine produced by the Th17 subset of T-helper cells, plays a role in inflammatory responses, autoimmunity, and antimicrobial responses in a variety of infectious and inflammatory diseases. In view of the inflammatory nature and severity of aggressive periodontitis, we hypothesized that IL-17 might be detected in sera from patients with aggressive periodontitis. We used ELISA to measure IL-17 serum concentrations from 67 periodontally healthy (NP) individuals and from 53 patients with localized (LAgP) and 49 patients with generalized (GAgP) aggressive periodontitis. IL-17 was barely detectable in sera from periodontally healthy individuals (1.9 +/- 2.0 pg/mL), but was present at significantly higher concentrations in sera from those with LAgP (7.6 +/- 2.2 pg/mL) and GAgP (17.1 +/- 2.3 pg/mL). Multivariate analyses demonstrated associations of IL-17 concentrations with periodontal attachment loss, but not with current smoking. Therefore, Th17 responses may be characteristic of AgP, and IL-17 may play a role in the pathogenesis of aggressive periodontitis.
Enhanced radiosensitivity by inhibition of the anti-apoptotic gene clusterin using antisense oligodeoxynucleotide in a human bladder cancer model (2005)

Clusterin has been shown to be implicated in the acquisition of resistant phenotype to various kinds of apoptotic stimuli, including radiation. In bladder cancer, our previous study demonstrated that overexpression of clusterin is closely associated with disease progression and recurrence. The objective of this study was to investigate whether radiation sensitivity was enhanced by suppressing clusterin gene expression with antisense (AS) oligodeoxynucleotide (ODN) in the human bladder cancer KoTCC-1 model. Clusterin mRNA in KoTCC-1 cells after radiation was up-regulated in a dose-dependent manner; however, AS clusterin ODN treatment resulted in a marked inhibition of clusterin mRNA even after irradiation. Combined treatment of KoTCC-1 cells with radiation and AS clusterin ODN synergistically decreased plating efficacy and induced apoptotic cell death compared with either radiation or AS clusterin ODN treatment alone. In vivo systemic administration of AS clusterin ODN enhanced radiation sensitivity, significantly reducing subcutaneous KoTCC-1 tumor volume in nude mice, compared with that of mismatch control ODN. Moreover, additional administration of cisplatin to this combined regimen further achieved potential antitumor effects on subcutaneous KoTCC-1 tumor growth in nude mice. Collectively, these findings suggest that clusterin acts as a cell survival protein mediating radioresistance through the inhibition of apoptosis, and that inactivation of clusterin using AS technology might offer a novel strategy to improve the outcome of radiation therapy for patients with bladder cancer.
Microtome Shaving Radiography: Demonstration of Loss of Mammographic Microcalcifications During Histologic Sectioning (2004)

Mammographic-pathologic correlation of suspicious microcalcifications is essential for optimal diagnosis and local staging of early breast carcinoma. Loss of microcalcifications during histologic sectioning has been suggested as one reason for the occasional lack of microscopic visualization of microcalcifications in routinely processed breast biopsy specimens obtained for suspicious mammographic microcalcifications. Two case reports utilizing radiography of histologic shavings of stereotactic core biopsies and surgical excisional biopsies of mammographic microcalcifications provide concrete evidence of the loss of large calcific particles during the microtome process.
Improving Simulated Annealing-Based FPGA Placement With Directed Moves (2009)

Simulated annealing remains a widely used heuristic for field-programmable gate array placement due, in part, to its ability to produce high-quality placements while accommodating complex objective functions. This paper discusses enhancements to annealing-based placement which improve upon both quality and run-time. Specifically, intelligent strategies for selecting and placing cells are interspersed with traditional random moves during an anneal, allowing the annealer to converge more quickly and to attain better quality with less statistical variability. For the <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">same</i> <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">amount</i> <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">of</i> <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">computational</i> <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">effort</i> , the contributions discussed in this paper consistently improve both critical path delay and wire length compared to traditional annealing perturbations.
Development of an Exhaled Breath Monitoring System with Semiconductive Gas Sensors, a Gas Condenser Unit, and Gas Chromatograph Columns (2016)

Various volatile organic compounds (VOCs) in breath exhaled by patients with lung cancer, healthy controls, and patients with lung cancer who underwent surgery for resection of cancer were analyzed by gas condenser-equipped gas chromatography-mass spectrometry (GC/MS) for development of an exhaled breath monitoring prototype system involving metal oxide gas sensors, a gas condenser, and gas chromatography columns. The gas condenser-GC/MS analysis identified concentrations of 56 VOCs in the breath exhaled by the test population of 136 volunteers (107 patients with lung cancer and 29 controls), and selected four target VOCs, nonanal, acetoin, acetic acid, and propanoic acid, for use with the condenser, GC, and sensor-type prototype system. The prototype system analyzed exhaled breath samples from 101 volunteers (74 patients with lung cancer and 27 controls). The prototype system exhibited a level of performance similar to that of the gas condenser-GC/MS system for breath analysis.
How Does the Proliferating Cell Nuclear Antigen Modulate Binding Specificity to Multiple Partner Proteins? (2017)

Proliferating cell nuclear antigen (PCNA) is a member of the family of sliding clamp proteins that serves as a clamp during DNA repair, DNA replication, cell cycle control, and multiple forms of chromatin modification. PCNA functions as a homotrimer and complexes with multiple proteins in order to carry out each of these varied functions. PCNA binds to different partner proteins in the same region of its structure, called the " interdomain connecting loop", but with different affinities. This interdomain connecting loop is an intrinsically disordered region that takes different conformations when binding to different partner proteins. In this work, we performed all-atom molecular dynamics simulations on PCNA trimer unbound to any partner protein, PCNA bound to peptides from different partner proteins, and PCNA bound to the full Fen 1 protein in two different conformations. Using this massive amount of simulation results, we analyzed whether PCNA in its free trimeric form samples conformations that are similar to those when it is bound to different partner proteins. We observed that PCNA samples many of these peptide-bound conformations even when not bound to the peptides and selects specific conformations when binding to partner proteins. We also identified PCNA-peptide interactions formed in the peptide bound simulation that play a crucial role in complex formation. The calculated binding energies correlate well with the measured binding affinities of various peptides to PCNA. Lastly, we studied the internal dynamics of PCNA and propose a mechanism through which PCNA recruits binding partners. This work highlights the functional role of intrinsically disordered regions in multifunctional proteins such as PCNA.
Impact of Laser-Processed X'tal Cube Detectors on PET Imaging in a One-Pair Prototype System (2013)

The X'tal cube is our original PET detector, which is being developed to achieve isotropic 3D positioning detectability. The X'tal cube is based on a 3D segmented crystal block for which all surfaces are covered with photo-detectors. Previously, instead of our initial approach of gluing segmented pieces of crystals, we successfully constructed a crystal block segmented by laser processing, and we developed the X'tal cube with the laser-processed 3D square grids of 2 mm length. In this paper, we extend the laser processing to 3D square grids of 1 mm length. The volume of a 1-mm crystal segment is 1/8 of that of a 2-mm crystal segment. We also evaluate imaging resolution performance with a newly developed one-pair prototype system to simulate a ring-type scanner, while our previous reports were limited to development and evaluation of a single detector. In particular, we compare 1-mm X'tal cube detectors to 2-mm X'tal cube detectors. The one-pair prototype system consisted of two X'tal cubes, two rotating stages, and a 192-channel data acquisition system. Each X'tal cube consisted of the LYSO cubic crystal block of 18 × 18 × 18 mm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sup> in which the 3D grids of 1 mm pitch were fabricated by internal laser processing. The 4 × 4 arrays of multi pixel photon counters were optically coupled to each surface of the crystal block. The detector positions were automatically controlled to simulate a ring-type PET with a 14.6 cm diameter. Data were collected for all assumed detector positions and then a sinogram was obtained. The data were reconstructed using filtered backprojection. The average spatial resolution of the 2-mm X'tal cube was 1.9 mm full width at half maximum (FWHM) over the field-of-view (FOV). On the other hand, the average spatial resolution of the 1-mm X'tal cube was 1.3 mm FWHM over the FOV. By applying deconvolution with the assumption that the point source was a Gaussian function of 1.0 mm FWHM, we estimated the average spatial resolution of the 2-mm X'tal cube and the 1-mm X'tal cube as 1.6 mm FWHM and 0.83 mm FWHM, respectively. The average spatial resolution of the 1-mm X'tal cube was improved approximately 48% compared to the 2-mm X'tal cube. In conclusion, we confirmed the potential of the X'tal cube for uniform and high resolution imaging.
Ligand binding to the cell surface receptor for reovirus type 3 stimulates galactocerebroside expression by developing oligodendrocytes. (1990)

Viruses utilize normal cell surface structures as attachment sites. Interaction of viral components with these structures may alter target cell growth. In the present study, the expression and function of the cell surface receptor for reovirus type 3 (Reo3R) was studied in neonatal rat optic nerve glial cultures. The Reo3R is expressed by mature oligodendrocytes and astrocytes but not by O-2A progenitor cells. It appears at an early stage of oligodendrocyte development, coincident with the O4 marker but prior to galactocerebroside or myelin basic protein. Anti-Reo3R antibodies stimulate the expression of galactocerebroside by developing oligodendrocytes. Divalent Reo3R-binding peptides are similarly active. Maximal stimulation of galactocerebroside expression occurs with treatment as short as 4 hr, consistent with a receptor-mediated process. Cell surface structures used as an attachment site by reovirus type 3 may also play a role in the regulation of oligodendrocyte differentiation.
Completion of the swine genome will simplify the production of swine as a large animal biomedical model (2012)

The completion of the swine genome will enhance the continued use and development of swine as models of human health, syndromes and conditions.
End expiratory oxygen concentrations to predict central venous oxygen saturation: an observational pilot study (2006)

We found no significant correlation between EtO2 and ScVO2. A linear equation incorporating EtCO2 and EtO2 had at best modest predictive accuracy for ScVO2.
Three-dimensional micropatterning of semiconducting polymers via capillary force-assisted evaporative self-assembly (2019)

Controlled evaporative self-assembly of semiconducting polymers has mostly been studied on 2-dimensional flat substrates. In this study, we reported capillary-assisted evaporative self-assembly of poly(3-hexylthiophene 2,5-diyl) (P3HT) into 3-D micro-ring patterns through the stick-slip phenomenon within a 3-dimensional cylinder. We deconvoluted the well-known two-step stick-slip phenomenon into three regimes through in situ monitoring of the P3HT self-assembly process using a high-speed camera: pinning and deposition; depinning and slip; and retraction regimes. Furthermore, we investigated the effects of various parameters associated with the self-assembly, including polymer concentration, tilt angle, magnetic field, and evaporation temperature, thus achieving self-assembled microarchitectures with diverse dimensions ranging from dots to lines and networks. The self-assembled microstructures were analyzed qualitatively and quantitatively by evaluating the fast Fourier transform image, surface coverage, fractal dimension and lacunarity of the micropatterns.
Molecular Events Implicated in Brain Tumor Angiogenesis and Invasion (2000)

We have conducted studies designed to help elucidate the molecular mechanisms involved in brain tumor invasion and angiogenesis, which are critical in the growth of malignant tumors of the central nervous system. A variety of molecular factors have been implicated in these processes. Here we focus on three that are of particular importance in the progression of brain tumors. Angiopoietins are involved in the regulation of vascular development. Hypoxia inducible factor-1 is a transcription factor that up-regulates genes, including genes encoding vascular endothelial growth factor under hypoxic conditions. Focal adhesion kinase is associated with infiltration of tumor cells and angiogenesis.
Abstract 3825: Targeting activated PI3K/mTOR signaling overcomes resistance to CDK4/6-based therapies in preclinical ER+ breast cancer models (2019)

Abstract Addition of CDK4/6 inhibitors such as palbociclib, ribociclib or abemaciclib to endocrine-based therapies significantly improves progression-free and in some subgroups, overall survival in patients with advanced estrogen receptor-positive (ER+) breast cancer. However, acquired resistance to CDK4/6 inhibitors remains a significant unmet clinical need. It is critical to ascertain the mechanisms by which tumor cells evade CDK4/6 based therapy. In this study we screen multiple in vitro and in vivo models of acquired resistance to CDK4/6 inhibitors to identify potential resistance/escape pathways and targets for pharmaceutical intervention to overcome resistance. ER+ breast cancer cell lines of diverse molecular backgrounds were conditioned to acquire resistance to CDK4/6 inhibitors through either long-term culture in the presence of clinically relevant concentrations of inhibitors or as cell line xenografts treated through progression on a CDK4/6 inhibitor plus fulvestrant. Baseline and pharmacodynamic changes in cell signaling were measured using reverse phase protein array (RPPA) and RNAseq analysis. Acquired resistance to CDK4/6 inhibitors was associated with decreases in phosphorylated-Rb (pRb) and ER-alpha protein and increases in pAKT and pS6 relative to isogenic controls. The p110α-selective PI3K-inhibitor, alpelisib, in combination with fulvestrant or ribociclib/fulvestrant blocked pAKT signaling in xenografts progressing on palbociclib/fulvestrant and induced significant tumor regressions. Apelisib plus fulvestrant also produced robust anti-tumor responses in xenografts progressing on ribociclib/fulvestrant. Triple combination treatment with ribociclib/alpelisib/fulvestrant induced significant regressions in resistant tumors and in treatment naïve models, where complete tumor regressions occurred regardless of PIK3CA mutation status. Regressions were maintained for &amp;gt;9 weeks post withdrawal of treatment, indicating that therapeutic resistance may be prevented by this triple combination approach. RPPA analysis of responding tumors identified sustained inhibition of both PI3K- and CDK4/6:Rb-pathway signaling accompanied by activation of pro-apoptotic proteins. These data support clinical investigation of targeting PI3K with alpelisib in breast cancers progressing on CDK4/6 based therapies and investigation of upfront triple combination therapy prior to acquisition of resistance to CDK4/6. Citation Format: Neil A. O'Brien, Martina SJ McDermott, Dylan F. Conklin, Alex Gaither, Tong Luo, Raul Ayala, Suruchi Salgar, Emmanuelle DiTomaso, Naveen Babbar, Faye Su, Sara A. Hurvitz, Ronald Linnartz, Kristine Rose, Samit Hirawat, Dennis J. Slamon. Targeting activated PI3K/mTOR signaling overcomes resistance to CDK4/6-based therapies in preclinical ER+ breast cancer models [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 3825.
Analysis of the shorting pin effects on an Inverted-F Antenna using a equivalent model for impedance matching (2010)

The effect of the shorting pin on an Inverted-F Antenna (IFA) was analyzed using a equivalent model to realize the best impedance matching condition. To do this, it was proved that the shorting pin can be modelled with an equivalent circuit at first. Then, the impedance characteristics of an IFA according to the locations of a shorting pin were analyzed by using the parameters in the equivalent model. From the results, it was verified that the input impedance can be controlled without changing the radiating arm, which enables to realize the best impedance matching condition at a desired frequency.
Inverting sampled ADSL traffic (2005)

On the basis of a reference model for ADSL traffic on an IP backbone link, established in an earlier study, we show that it is possible to infer the characteristics of long flows by performing a deterministic 1/N packet sampling. By using the fact that the number of active long flows can be represented by means of the number of customers in an M/G//spl infin/ queue with Weibullian service times, we derive some probabilistic properties of the sampled data. These properties are then used to infer the characteristics of the original flows. The method is illustrated by considering an actual traffic trace captured in the France Telecom IP backbone network. Experimental data show that the method proves quite efficient.
An Effective Distributed Architecture for OPC & RET Applications (2002)

The computational power needed to generate mask layouts for OPC and resolution enhancement techniques increases exponentially with process node. Rapidly growing design complexity is compounded with the more aggressive methods now required for smaller feature sizes. Layers once considered non-critical now routinely receive correction. While some improvement in code efficiency can be expected, algorithms are maturing to the point where improvements will likely not keep pace with the computational need. To maintain required processing cycle times massively parallel processing methods must be employed. In this paper we discuss loosely-coupled distributed computing architectures applied to OPC/RET layout synthesis. The degree to which an application is scalable depends on how well the problem can be divided into independent sets of data. Furthermore, data must also be partitioned into reasonably sized blocks so that memory requirements per processor can be bounded. Communication overhead, I/O overhead and serial processeses all degrade scalability, and may increase overall storage requirements. In this paper we analyze behavior of distributed processing architectures with large numbers of processors, and we present performance data on an existing massively parallel system.
Biomechanics of the Distal Radioulnar Joint (1992)

The distal radioulnar joint (DRUJ) is a complex joint involved in pronosupination and ulnocarpal motion and support. The ulnar head, in a rolling, sliding motion, moves from the dorsal to the volar rim of the sigmoid notch as the joint moves from pronation to supination. The triangular fibrocartilage (TFC) is taut first dorsally and then volarly in the same sequence. The ulnar carpus is supported variably, as a function of ulnar length relative to the radial articular surface, by the pole of the distal ulna through the TFC. The TFC does not resist the pistonlike movement of the DRUJ, which occurs under dynamic loading. The coronal alignment of the DRUJ minimizes shear stress on the articular surfaces because of its alignment with the rotational axis of the forearm. Ulnar variance is a factor in the development of several clinical conditions.
Mass Spectrometry and Antibody-Based Characterization of Blood Vessels from Brachylophosaurus canadensis (2015)

Structures similar to blood vessels in location, morphology, flexibility, and transparency have been recovered after demineralization of multiple dinosaur cortical bone fragments from multiple specimens, some of which are as old as 80 Ma. These structures were hypothesized to be either endogenous to the bone (i.e., of vascular origin) or the result of biofilm colonizing the empty osteonal network after degradation of original organic components. Here, we test the hypothesis that these structures are endogenous and thus retain proteins in common with extant archosaur blood vessels that can be detected with high-resolution mass spectrometry and confirmed by immunofluorescence. Two lines of evidence support this hypothesis. First, peptide sequencing of Brachylophosaurus canadensis blood vessel extracts is consistent with peptides comprising extant archosaurian blood vessels and is not consistent with a bacterial, cellular slime mold, or fungal origin. Second, proteins identified by mass spectrometry can be localized to the tissues using antibodies specific to these proteins, validating their identity. Data are available via ProteomeXchange with identifier PXD001738.