gebhart/patrepeval huggingface dataset:
Validation of Multiplex Serology detecting human herpesviruses 1-5 (2018)

Human herpesviruses (HHV) cause a variety of clinically relevant conditions upon primary infection of typically young and immunocompetent hosts. Both primary infection and reactivation after latency can lead to more severe disease, such as encephalitis, congenital defects and cancer. Infections with HHV are also associated with cardiovascular and neurodegenerative disease. However, most of the associations are based on retrospective case-control analyses and well-powered prospective cohort studies are needed for assessing temporality and causality. To enable comprehensive investigations of HHV-related disease etiology in large prospective population-based cohort studies, we developed HHV Multiplex Serology. This methodology represents a low-cost, high-throughput technology that allows simultaneous measurement of specific antibodies against five HHV species: Herpes simplex viruses 1 and 2, Varicella zoster virus, Epstein-Barr virus, and Cytomegalovirus. The newly developed HHV species-specific ('Monoplex') assays were validated against established gold-standard reference assays. The specificity and sensitivity of the HHV species-specific Monoplex Serology assays ranged from 92.3% to 100.0% (median 97.4%) and 91.8% to 98.7% (median 96.6%), respectively. Concordance with reference assays was very high with kappa values ranging from 0.86 to 0.96 (median kappa 0.93). Multiplexing the Monoplex Serology assays resulted in no loss of performance and allows simultaneous detection of antibodies against the 5 HHV species in a high-throughput manner.
Performance evaluation of a real long term evolution (LTE) network (2012)

This paper analyzes the performance of a real LTE network through the real LTE network drive tests. Test cases were performed under stationary and mobile conditions. Paper presents the results under high user mobility conditions and compares these results with the ones collected under stationary conditions. User mobility affects average received user throughput, block error rates (BLER), Reference Signal Received Power (RSRP), Reference Signal Received Quality (RSRQ) and Reference Signal Strength Indicator (RSSI) values significantly. All of the test cases were performed using real LTE device in a real LTE network. Video traffic was used in drive tests under stationary and mobile conditions. The main key performance indicators used in this paper are average sector throughput, the number of codewords (CW) used, channel quality indicator (CQI), block error rate (BLER), signal-to-noise-plus-interference ratio (SNIR), RSSI, RSRQ, and RSRP values. Average throughput values are very important to show the promised throughput performance of the LTE network. User mobility affects average delivered user throughput, BLER, and CQI values significantly.
Large π-Conjugated Condensed Perylene-Based Aromatic Polyimide as Organic Cathode for Lithium-Ion Batteries (2020)

Organic redox-active compounds are promising alternatives to traditional inorganic analogs in organic batteries owing to their high energy density and tunable redox potentials. However, their poor cycling stability due to undesired dissolution in electrolytes and low electronic conductivity limit their applications. Herein, we report the large π-conjugated condensed aromatic structures/extended π-conjugation of perylene-based aromatic polyimide (namely, 5,12-bis(pyren-1-ylamino)perylenediimide– hydrazine, BA-PI) as cathode for use in lithium-ion batteries. This cathode is synthesized by one-step polymerization reaction between the aminopyrene-substituted at the 1,7-bay area of perylene-3,4:9,10-tetracarboxylic dianhydride (PTCDA) unit and hydrazine hydrate. The half-cell battery employing BA-PI exhibits an initial discharge capacity of ∼51 mAh g–1 in the potential range of 1.5–3.5 V vs Li+/Li, which is ∼78% of its theoretical value (∼65.46 mAh g–1). Further, a different BA-PI-based cell delivers initial discharge capacity of ∼85 mAh g–1. When the deep-discharging to 0.01 V vs Li+/Li (at the very low voltage of <1.5 V), about 34 Li+ ions can be incorporated into a BA-PI electrode on copper foil as a current collector, exhibiting an extremely high specific capacity of ∼1096 mAh g–1. Moreover, the non-bay-substituted perylene-based aromatic polyimide, as control cathode, has delivered a discharge capacity of ∼129 mAh g–1 and shows good cyclic stability, indicating that such perylene-based aromatic polyimides are promising organic cathode materials for high-capacity lithium–polyimide batteries.
Effect of Y Content in (TaC)1-xYxGate Electrodes on Flatband Voltage Control for Hf-Based High-kGate Stacks (2011)

The effects of varying the yttrium (Y) level in a (TaC)1-xYx gate electrode on the structural and electrical properties of a hafnium (Hf)-based high-k metal–oxide–semiconductor (MOS) capacitor, including flatband voltage (Vfb), were evaluated. The composition of (TaC)1-xYx was controlled by the power of pure TaC and Y targets in magnetron sputtering. The structure of the formed (TaC)1-xYx film was that of either a face-center cubic (fcc) at all compositions of x≤0.4 or amorphous at x≥0.5 after annealing at temperatures below 600 °C. X-ray photoelectron spectroscopy (XPS) analysis revealed that the TaC and (TaC)1-xYx films all contained about 10% oxygen. The resistivity of the (TaC)1-xYx films was invariant for all compositions of x≤0.5, but it increased with increasing annealing temperature up to 600 °C for compositions of x≥0.68. In the as-deposited case, the effective work function, which was estimated from the relationship between Vfb and the equivalent oxide thickness of the HfO2 film, clearly changed from 4.8 to 4.3 eV as x increased. The Vfb of HfO2 and HfSiOx dielectrics could be controlled within 0.5 V after annealing at 500 °C by changing the composition of the (TaC)1-xYx film (in terms of x). Based on the experimental data, it is clear that (TaC)1-xYx composites are candidate materials for n-metal gate electrodes in the gate-last process.
Bandgap engineering of α-(AlxGa1-x)2O3 by a mist chemical vapor deposition two-chamber system and verification of Vegard's Law (2018)

This work reports growth of α-(AlxGa1-x)2O3 single crystals with high incorporation of Al by a Mist Chemical Vapor Deposition two-chamber system, which was rationally designed to avoid side-reactions between different precursors during solution preparation for multi-component thin film growth. Multiple acceleration voltages were used in Energy Dispersive X-ray measurements to reliably obtain the Al composition x of the films. As a result, Vegard's law for lattice constants was verified and found to be valid in the α-(AlxGa1-x)2O3 system. However, Vegard's law for optical bandgaps, derived from different models, required an additional term to account for the bowing effect. At x = 0.71, the gaps were 7.74, 7.03, 7.26, and 7.34 eV as derived from the Tauc plots for the direct bandgap, indirect bandgap, Tauc-Lorentz model, and O'Leary-Johnson-Lim model, respectively. The two-chamber system provides reliable and effective control of the Al content in α-(AlxGa1-x)2O3 alloys and heterostructures.
Supplementary Data from Safety, Pharmacokinetics, and Efficacy of CPX-1 Liposome Injection in Patients with Advanced Solid Tumors (2023)

Supplementary Data from Safety, Pharmacokinetics, and Efficacy of CPX-1 Liposome Injection in Patients with Advanced Solid Tumors
Graphene: An IR for Optimized Tensor Computations on GPUs (2023)

Modern GPUs accelerate computations and data movements of multi-dimensional tensors in hardware. However, expressing optimized tensor computations in software is extremely challenging even for experts. Languages like CUDA C++ are centered around flat buffers in one-dimensional memory and lack reasonable abstractions for multi-dimensional data and threads. Existing tensor IRs are not expressive enough to represent the complex data-to-thread mappings required by the GPU tensor instructions.
Phosphoproteomic analysis of metastatic colorectal cancer: A new horizon in targeted therapy development (2006)

A113 Background: CRC is the second leading cause of cancer related death in the western world and the survival of the patients with CRC is significantly related to the presence of metastases rather than the primary tumor. Subsequently, understanding and discovery of new specific targets that could better explain the metastatic process and that could be used as new classes of targeted inhibitors is required. We performed laser capture microdissection followed by reverse phase protein microarrays to establish a phosphoproteomic fingerprint of colorectal cancer cells, to compare the protein kinases signal pathway derangements in the metastatic and non-metastatic CRC primary tumor and in the metastases it can cause.Methods: 20 frozen cases of colorectal cancer, 68 cases of patient-matched colorectal cancer and hepatic metastasis (all taken at the same time at surgery), and 15 cases of pulmonary metastasis, were laser capture microdissected to obtain pure cancer cell populations. The cells were lysed and subjected to reverse phase protein microarray analysis. Using this technique, we were able to measure the phosphorylation state of 70 kinase substrates. Molecular network analysis was performed using commercially available software.Results: Our results, based on the analysis of several endpoints, indicate that the molecular networks of activated kinase substrates appear different between non-metastatic primary colorectal cancer, metastatic colorectal cancer and its metastases.Conclusions: To establish a personalized targeted therapy in these groups of patients, a fundamental prerequisite is to understand which are the functional activations of cell signaling pathways that could be used as targets of the new generations of drug. Selection of the appropriate new therapeutic targets for patients with metastatic colorectal cancer should be based on the analysis of the metastatic tissue and cannot be predicted solely through the molecular analysis of the primary tumor.
2D NMR investigation of the binding of the anticancer drug actinomycin D to duplexed dATGCGCAT: conformational features of the unique 2:1 adduct (1988)

One- and two-dimensional NMR studies on the oligomer dA1T2G3C4G5C6A7T8, with and without actinomycin D (ActD), were conducted. Analysis of the NMR data, particularly 2D NOE intensities, revealed that the free oligonucleotide is a duplex in a standard right-handed B form. At the ratio of 1 ActD/duplex (R = 1), 1D NMR studies indicate that two 1:1 unsymmetric complexes form in unequal proportions with the phenoxazone ring intercalated at a GpC site, in agreement with previous studies [Scott, E.V., Jones, R.L., Banville, D.L., Zon, G., Marzilli, L.G., & Wilson, W.D. (1988) Biochemistry 27, 915-923]. The 2D COSY data also confirm this interpretation since eight cytosine H6 to H5 and two ActD H8 to H7 cross-peaks are observed. At R = 2, both COSY and NOESY spectra confirm the formation of a unique 2:1 species with C2 symmetry. The oligomer remains in a right-handed duplex but undergoes extreme conformational changes both at and adjacent to the binding site. The deoxyribose conformation of T2, C4, and C6 shifts from primarily C2'-endo in the free duplex to an increased amount of C3'-endo in the 2:1 complex as revealed by the greater intensity of the base H6 to 3' NOE cross-peak relative to the intensity of the H6 to H2' NOE cross-peak. This conformational change widens the minor groove and should help alleviate the steric crowding of the ActD peptides. The orientation of the ActD molecules at R = 2 has the quinoid portion of the phenoxazone ring at the G3pC4 site and the benzenoid portion of the phenoxazone ring at the G5pC6 site on the basis of NOE cross-peaks from ActD H7 and H8 to G5H8 and C6H6. All base pairs retain Watson-Crick type H-bonding, unlike echinomycin complexes [e.g., Gao, X., & Patel, D.J. (1988) Biochemistry 27, 1744-1751] where Hoogsteen base pairs have been observed. In contrast to previous studies on ActD, we were able to distinguish the two peptide chains.(ABSTRACT TRUNCATED AT 400 WORDS)
Guided by voices: An audio augmented reality system (2000)

Presented of the 6th International Conference on Auditory Display (ICAD), Atlanta, GA, April 2-5, 2000
Mutant p53 (G199V) Gains Antiapoptotic Function through Signal Transducer and Activator of Transcription 3 in Anaplastic Thyroid Cancer Cells (2009)

In the present study, we identified a missense mutation (G199V) in KAT-18 cell line established from primary cultures of anaplastic thyroid cancer (ATC). Notably, knockdown of this mutant (mt) p53 reduced cell viability and exerted antitumor activity equivalent to high doses of several chemotherapeutic agents. We showed that p53 knockdown had an antitumor effect via the induction of apoptosis. We further examined the underlying mechanism by which mt p53 (G199V) gains antiapoptotic function in KAT-18 cells. Microarray analysis revealed that p53 knockdown modified the expression of numerous apoptosis-related genes. Importantly, p53 knockdown led to downregulation of signal transducer and activator of transcription-3 (STAT3) gene expression. We further observed that p53 knockdown induced the downregulation of STAT3 protein. We also observed that a STAT3 inhibitor augmented the reduction of cell viability induced by p53 knockdown, whereas interleukin-6 treatment alleviated this effect. In addition, overexpression of STAT3 protected ATC cells against cell death induced by p53 knockdown. Taken together, these data show that mt p53 (G199V) gains antiapoptotic function mediated by STAT3 in ATC cells. Inhibition of the function of mt p53 (G199V) could be a novel and useful therapeutic strategy for decreasing the extent and severity of toxicity due to chemotherapeutic agents.
Demo (2014)

We present a demonstration of WalkCompass, a system to appear in the MobiSys 2014 main conference. WalkCompass exploits smartphone sensors to estimate the direction in which a user is walking. We find that several smartphone localization systems in the recent past, including our own, make a simplifying assumption that the user's walking direction is known. In trying to relax this assumption, we were not able to find a generic solution from past work. While intuition suggests that the walking direction should be detectable through the accelerometer, in reality this direction gets blended into various other motion patterns during the act of walking, including up and down bounce, side-to-side sway, swing of arms or legs, etc. WalkCompass analyzes the human walking dynamics to estimate the dominating forces and uses this knowledge to find the heading direction of the pedestrian. In the demonstration we will show the performance of this system when the user holds the smartphone on the palm. A collection of YouTube videos of the demo is posted at http://synrg.csl.illinois.edu/projects/ localization/walkcompass.
Electron-Deficient-Type Electride Ca5Pb3: Extension of Electride Chemical Space (2021)

Electrides have been identified so far by two major routes: one is conversion of elemental metals and stoichiometric compounds by high pressure; the other is to search for electron-rich compounds, and this approach is more general. In contrast, few electron-deficient structures in existing databases have been revealed as potential electride candidates. In this work, we found an electron-deficient compound Ca<sub>5</sub>Pb<sub>3</sub> could be transformed into electrides upon applying external pressure or strain along the <i>c</i>-axis, which induces the electron immigration from Pb to interstitial sites. Furthermore, the electron doping via Hf substitution of Ca atoms for Ca<sub>5</sub>Pb<sub>3</sub> was found to be capable of tuning the interstitial electron density under ambient pressure, resulting in a new stable ternary electride Ca<sub>3</sub>Hf<sub>2</sub>Pb<sub>3</sub>, Hf-substituted Ca<sub>5</sub>Pb<sub>3</sub>. The electron-deficient electride discovered here is of novel type and can largely expand the research scope of electrides. Considering a recently reported neutral electride Na<sub>3</sub>N and the present finding, it is now clarified that electrides can be identified irrespective of stoichiometry (electron-rich, -neutral, or -poor) for compounds.
Robust error correction in infofuses (2011)

An infofuse is a combustible fuse in which information is encoded through the patterning of metallic salts, with transmission in the optical range simply associated with burning. The constraints, advantages and unique error statistics of physical chemistry require us to rethink coding and decoding schemes for these systems. We take advantage of the non-binary nature of our signal with a single bit representing one of N =7 states to produce a code that, using a single or pair of intensity thresholds, allows the recovery of the intended signal with an arbitrarily high recovery probability, given reasonable assumptions about the distribution of errors in the system. An analysis of our experiments with infofuses shows that the code presented is consistent with these schemes, and encouraging for the field of chemical communication and infochemistry given the vast permutations and combinations of allowable non-binary signals.
Diversity of cwp loci in clinical isolates of Clostridium difficile (2013)

An increased incidence of Clostridium difficile infection (CDI) is associated with the emergence of epidemic strains characterized by high genetic diversity. Among the factors that may have a role in CDI is a family of 29 paralogues, the cell-wall proteins (CWPs), which compose the outer layer of the bacterial cell and are likely to be involved in colonization. Previous studies have shown that 12 of the 29 cwp genes are clustered in the same region, named after slpA (cwp1), the slpA locus, whereas the remaining 17 paralogues are distributed throughout the genome. The variability of 14 of these 17 cwp paralogues was determined in 40 C. difficile clinical isolates belonging to six of the currently prevailing PCR ribotypes. Based on sequence conservation, these cwp genes were divided into two groups, one comprising nine cwp loci having highly conserved sequences in all isolates, and the other five loci showing low genetic conservation among isolates of the same PCR ribotype, as well as between different PCR ribotypes. Three conserved CWPs, Cwp16, Cwp18 and Cwp25, and two variable ones, Cwp26 and Cwp27, were characterized further by Western blot analysis of total cell extracts or surface-layer preparations of the C. difficile clinical isolates. Expression of genetically invariable CWPs was well conserved in all isolates, whilst genetically variable CWPs were not always expressed at comparable levels, even in strains containing identical sequences but belonging to different PCR ribotypes. This is the first report on the distribution and variability of a number of genes encoding CWPs in C. difficile.
Application of the singular valve decomposition–Prony method for analyzing deep-level transient spectroscopy capacitance transients (1998)

In this article, a modified covariance method for analyzing deep-level transient spectroscopy (DLTS) capacitance transients using a combined singular value decomposition/Prony (SVD–Prony) method is presented. This combined method is based upon using the SVD method first to accurately estimate the number of exponentials contained in transient capacitance data, then the Prony method is applied to obtain an accurate estimate of the exponential time constants. Results are presented for simulated exponential data with additive white-Gaussian noise and for real DLTS data to demonstrate the applicability of the presented technique. In addition, a statistical analysis is performed to study the behavior of this technique and its effectiveness in extracting the capacitance parameters at different noise levels. Finally, the problem of multiple exponential detection is addressed.
Relaxation Mechanism of the Defect-Free 3C-SiC Epitaxial Films Grown on Step-Free 4H SiC Mesas (2006)

Cross-sectional transmission electron microscopy (TEM) was used to investigate the extended defects in 3C-SiC films deposited on atomically flat 4H-SiC mesas. The nominal layer thickness was 10 μm and was considerably larger than the critical thickness determined by either the Matthews and Blakeslee or People and Bean models. Threading dislocation densities determined by KOH etching are far below densities typical of relaxed heteroepitaxial layers, down to as low as 104cm-2 densities found in 4H-SiC. Misfit dislocations with Burgers vectors of &lt;11 2 0&gt; were observed in planes parallel to the 3C/4H SiC interface. These defects were interpreted as due to nucleation of dislocation half loops at mesa edges and glide along the 3C/4H interface.
Anomalous diamagnetism of electride electrons in transition metal silicides (2021)

Intermetallic silicide compounds, LaScSi and ${\mathrm{Y}}_{5}{\mathrm{Si}}_{3}$, known for being hydrogen (H) storage materials, are drawing attention as candidates for electrides in which anions are substituted by unbound electrons. It is inferred from a muon spin rotation experiment that the local field at the muon site (which is the same site as that for H) in these compounds exhibits a large negative shift under an external magnetic field, which is mostly independent of temperature. Such anomalous diamagnetism signals a unique property of electride electrons associated with transition metals. Moreover, the diamagnetic shift decreases with increasing H content, suggesting that the electride electrons existing coherently in the hollow interstitial positions are adsorbed by H to form hydride ions $({\mathrm{H}}^{\ensuremath{-}})$.