gebhart/patrepeval huggingface dataset:
Viterbi Detector for Non-Markov Recording Channels (2007)

Channel noise in modern perpendicular channels is well approximated by a linear jitter model. In this paper, we propose a new type of Viterbi detector matched to such a channel model. The differentiating feature of this detector is recursive evaluation of whitened noise strengths for survivor paths using the on-the-fly Cholesky factorization of path-dependent correlation matrices. We study the performance of the detector using the simplest example of low-density channels with intersymbol interference length equal to three. We find that at BER = 10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">-4</sup> , the new detector outperforms the data-dependent AR-detector of the comparable complexity by about 0.9 dB.
EDURange: meeting the pedagogical challenges of student participation in cybertraining environments (2014)

This paper reflects on the challenges that arose and the lessons learned when we used hands-on cyberoperations exercises in our courses. After exploring a range of exercises and platforms (and having discovered their limitations), we designed and built an environment for hosting such exercises called EDURange.

These limitations fall into two categories: technical and pedagogical. One of the main pedagogical issues was that most existing exercises were not aimed at teaching analysis skills, (i.e. a set of practices that support the ability to achieve understanding of complex systems). On the other hand, one of the main practical issues with existing cyber-training environments involves scalability limitations imposed by the inherent resource constraints of existing testbeds. A third techno-pedagogical issue was that scenarios were not dynamic. An exercise that is always the same has limited utility in that there is little incentive for students to repeat it, and with time, the solutions can be found on the Internet. EDURange allows instructors to configure aspects of the scenarios to repeatedly create new variations of the exercises. EDURange is designed especially for the needs of teaching faculty. The scenarios we have implemented each are designed specifically to nurture the development of analysis skills in students as a complement to both theoretical security concepts and specific software tools.
T cell-derived migration-inhibitory factor and colony-stimulating factor share common structural elements (1986)

Migration-inhibitory factor (MIF) is a lymphokine that acts to localize mononuclear phagocytes (monocytes and macrophages) and perhaps to activate them. Mo cells are a human T cell leukemia virus II-infected T cell line previously shown to secrete large quantities of MIF upon stimulation with phytohemagglutinin and phorbol myristate acetate. MIF was purified from Mo cell-conditioned medium by gel filtration, phenyl-Sepharose affinity chromatography, isoelectrofocusing, and reverse-phase high-performance liquid chromatography (RP-HPLC). Overall purification was 6,000-fold. The purified MIF fraction was found to display potent colony-stimulating factor (CSF) activity when assayed on human bone marrow cells. The double peak of MIF activity as shown by C 18-RP-HPLC coincided with the double peak of CSF activity. A monoclonal antibody selected for its anti-MIF activity absorbed both the CSF and the MIF activity. These findings indicate that MIF and CSF are either identical molecules or closely related molecules with common structural elements.
Abstract 5131: Identification of the genes that chemosensitize hepatocellular carcinoma cells to interferon-α and 5-fluorouracil therapy (2012)

Abstract The increasing numbers of patients with hepatocellular carcinoma (HCC), which is characterized by an extremely poor prognosis, are causing serious problems worldwide. To improve their prognosis, the development of a more effective therapy is required. Combination therapy with interferon-α (IFN-α) and 5-fluorouracil (5-FU) was reported to provide benefits to patients with advanced HCC, although its efficacy is still unsatisfactory. In this study, taking advantage of functional screening, three chemosensitizing genes for this therapy against HCC cells were identified. Identification of chemosensitizing genes was performed using ribozyme-based functional screening. We constructed a plasmid DNA library expressing random ribozyme genes with ∼6.0 × 106 target recognition sequences. We performed a positive-selection strategy based on the ability of 5-FU to eliminate cells expressing a ribozyme that targets chemosensitivity-unrelated genes. The ribozyme library was transfected into HepG2 cells, which were subsequently treated with the IC50 dose of 5-FU. This cycle was repeated 10 times to fully concentrate the ribozymes targeting those genes involved in the sensitivity of 5-FU. Consequently, 100 target ribozyme recognition sequences that were recovered before screening and after 10 cycles of screening were subjected to a BLAST search to retrieve genes with homologous sequences. This analysis indicated 3 genes (PRKAG2, TGFBR2, and EXT1) as candidate genes. The chemosensitizing effects of these genes on IFN-α/5-FU as well as 5-FU treatment were confirmed by adenovirus-mediated gene transfer. In addition, the mechanisms of effects of these genes on enhancing effects on combination therapy with IFN-α/5-FU were also evaluated. Furthermore, to evaluate the relationship between their expression levels in tumor tissues and the clinical outcome of IFN-α/5-FU combination therapy in advanced HCC patients, mRNA expression was measured using real-time reverse transcription-polymerase chain reaction. As a result, PRKAG2, TGFBR2, and EXT1 were identified as novel chemosensitizing genes for the combination therapy against HCC. TGFBR2 and EXT1 induced transforming growth factor-β signal activation and endoplasmic reticulum stress, respectively. Moreover, PRKAG2 and TGFBR2 were suggested to be promising predictive markers for the clinical outcome of this therapy. In conclusion, the identified genes are promising candidates as targets to enhance the therapeutic effect of IFN-α/5-FU combination therapy in advanced HCC and could be used as predictive markers for response to this therapy. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 5131. doi:1538-7445.AM2012-5131
An automated fast neutron computed tomography instrument with on-line focusing for non-destructive evaluation (2022)

A fast neutron tomography imaging instrument has been designed, built, and tested at The Ohio State University 500 kW Research Reactor on a fast neutron beamline with a peak neutron flux ≈5.4 × 10<sup>7</sup> n·cm<sup>-2</sup>·s<sup>-1</sup> at 1.6 MeV median neutron energy. The instrument and beamline are also configurable for thermal neutron imaging. The imaging apparatus is composed of a lens coupled, water-cooled Electron Multiplying Charge Coupled Device camera, a front-surface mirror, and a high light yield plastic Polyvinyl toluene scintillator. The instrument sits on a mobile cart. A total of 5 motion-control stages are built into the system for XYZ and rotational degrees of freedom for sample positioning; the fifth stage fine tunes the focal distance between the camera and the scintillator to achieve on-line focusing. A Python code with a user-friendly graphical user interface controls the fully automated image acquisition, not requiring user interaction, yet facilitating tracking of the image acquisition. A complete fast neutron computed tomography dataset with 360 projections requires less than 3 h, with 30 s per projection. On-line focusing is accomplished with a commercial, off-the-shelf, dielectrically actuated liquid lens. Finally, tomographic reconstructions are visualized using the Livermore Tomography Tools software package. The effective pixel size (width and height) is ≈0.1058 mm, yielding a minimum voxel size of 0.1058 × 0.1058 × 0.1058 mm<sup>3</sup>, and produces a spatial resolution of 231 μm when calculated from knife-edge measurements.
Applicationi of Measurement Models for Interpretation of Impedance Spectra for Corrosion (1998)

Experimental identification of errors has allowed enhanced interpretation of a wide variety of spectroscopy techniques, including measurements for electrochemical systems for which detailed process models are available. The physicochemical models available for corrosion systems, however, are typically not sufficiently detailed to represent adequately impedance data to within the experimentally determined noise level of the measurement. Even in the absence of detailed physicochemical models, enhanced interpretation of corrosion processes is possible through the use of measurement models which can account quantitatively for differences in surface reactivities. In this paper, the necessary steps for the quantification of corrosion processes using the measurement model approach of Agarwal et al. are described. The stationary stochastic error contribution to impedance spectra is identified from replicated measurements. Presence of a bias error contribution, caused, for example, by instrumental artifacts and non-stationary behavior, is identified from application of the Kramers-Kronig transforms. The zero and high frequency limits obtained through the measurement model are used to determine the polarization resistance in a way that accounts for the experimentally determined error structure. The results of this procedure, weighted by an appropriate statistical analysis, can be used to monitor electrochemical systems as functions of time or process conditions. The approach described herein is validated for model systems, such as the reduction of ferricyanide on platinum for which accurate process models are available. The corrosion examples presented here involve the transient growth of corrosion-product films on copper in synthetic seawater and on cast iron in Evian water.
Occurrence and a possible mechanism of penetration of natural killer cells into k562 target cells during the cytotoxic interaction (1995)

Abstract The cytotoxic interaction between cloned human Natural Killer (NK) cells and K562 target cells was studied using confocal laser scanning microscopy (CLSM) and conventional fluorescence microscopy. We observed, using fixed as well as living cells, the occurrence of (pseudo)emperipolesis during the interaction. About 30% of conjugated NK cells penetrated, partly or completely, into the target cells ( in ‐ conjugation ). Virtually all in‐conjugated target cells exhibited polymerized actin. Killer cells of in‐conjugates were frequently seen approaching the target cell nucleus or aligning along it. If the cytotoxic process was inhibited by the absence of calcium neither actin polymerization nor in‐conjugation were observed. A kinetic study showed that in‐conjugation starts somewhat later than actin polymerization but still within a few minutes after addition of calcium to conjugates previously formed in the absence of calcium. The presence of cytochalasin D (an inhibitor of actin polymerization) completely inhibited in‐conjugation and partly reduced the cytotoxic activity. Zinc ions (endonuclease inhibition) inhibited in‐conjugation and decreased the total number of target cells with polymerized actin in a concentration dependent manner. Cytotoxic activity was also reduced but not as efficiently as in‐conjugation. Our study demonstrates that in‐conjugation represents a significant fraction of the cytotoxic interaction. The results indicate that it may be a consequence of an actin polymerization and endonuclease activity dependent part of a cytotoxic mechanism. © 1995 Wiley‐Liss, Inc.
Model-free estimation of the effective correlation time for C–H bond reorientation in amphiphilic bilayers: 1H–13C solid-state NMR and MD simulations (2015)

Molecular dynamics (MD) simulations give atomically detailed information on structure and dynamics in amphiphilic bilayer systems on timescales up to about 1 μs. The reorientational dynamics of the C-H bonds is conventionally verified by measurements of (13)C or (2)H nuclear magnetic resonance (NMR) longitudinal relaxation rates R1, which are more sensitive to motional processes with correlation times close to the inverse Larmor frequency, typically around 1-10 ns on standard NMR instrumentation, and are thus less sensitive to the 10-1000 ns timescale motion that can be observed in the MD simulations. We propose an experimental procedure for atomically resolved model-free estimation of the C-H bond effective reorientational correlation time τe, which includes contributions from the entire range of all-atom MD timescales and that can be calculated directly from the MD trajectories. The approach is based on measurements of (13)C R1 and R1ρ relaxation rates, as well as (1)H-(13)C dipolar couplings, and is applicable to anisotropic liquid crystalline lipid or surfactant systems using a conventional solid-state NMR spectrometer and samples with natural isotopic composition. The procedure is demonstrated on a fully hydrated lamellar phase of 1-palmitoyl-2-oleoyl-phosphatidylcholine, yielding values of τe from 0.1 ns for the methyl groups in the choline moiety and at the end of the acyl chains to 3 ns for the g1 methylene group of the glycerol backbone. MD simulations performed with a widely used united-atom force-field reproduce the τe-profile of the major part of the acyl chains but underestimate the dynamics of the glycerol backbone and adjacent molecular segments. The measurement of experimental τe-profiles can be used to study subtle effects on C-H bond reorientational motions in anisotropic liquid crystals, as well as to validate the C-H bond reorientation dynamics predicted in MD simulations of amphiphilic bilayers such as lipid membranes.
Photon-correlation Fourier spectroscopy (2006)

We describe a method to probe the spectral fluctuations of a transition over broad ranges of frequencies and timescales with the high spectral resolution of Fourier spectroscopy, and a temporal resolution as high as the excited state lifetime, even in the limit of very low photocounting rates. The method derives from a simple relation between the fluorescence spectral dynamics of a single radi-ating dipole and its fluorescence intensity correlations at the outputs of a continuously scanning Michelson interferometer. These findings define an approach to investigate the fast fluorescence spectral dynamics of single molecules and other faint light sources beyond the time-resolution capabilities of standard spectroscopy experiments.
Accountability for Information Flow via Explicit Formal Proof (2009)

Abstract : Logical techniques have been developed that capture both authorization and information flow requirements in security applications. These logical techniques achieve a significantly higher degree of end-to-end accountability in distributed systems than is currently possible. Furthermore, a case study has shown that these techniques are applicable to security policies that are relevant to the needs of the intelligence community while providing much greater flexibility in security policy specification. A prototype implementation has demonstrated the practicality of the proposed file system architecture. Symantec, the industrial partner in the project, is presently pursuing a significant related business opportunity.
Penetration of CD4 T cells by HIV-1. The CD4 receptor does not internalize with HIV, and CD4-related signal transduction events are not required for entry (1991)

Receptor binding of HIV to the CD4 molecule is required for efficient infection of T cells, but the post-binding steps that result in penetration of HIV are not well understood. CD4 is induced to internalize upon T cell activation, and mAb to CD4 modify signal transduction and T cell activation as does HIV in some systems. It is not known whether HIV binding triggers CD4 endocytosis or whether signal transduction events are required for penetration. Selected inhibitors of signal transduction were evaluated for their effects on penetration using two assays that are dependent on penetration. After short term exposure to inhibitor and HIV, cells were analyzed for reverse-transcribed HIV DNA (DNA amplification assay), or productive infection is monitored (infectivity assay). Viral penetration was tested in the presence of H7 (protein kinase C inhibition), EGTA (extracellular Ca2+ chelation), cyclosporine A (inhibition of Ca2+/calmodulin-dependent activation), or pertussis toxin (inhibition of G protein function). All agents were used at concentrations that were inhibitory for their respective signal transduction pathways. None of the inhibitors affected viral penetration. We tracked the CD4 molecule with fluorescent probes that do not interfere with HIV binding in a system where CD4 T cells were saturated with HIV and the penetration event was relatively synchronized. Under conditions where detection of CD4 was more sensitive than the detection of HIV, HIV internalization was readily detected but CD4 internalization was not.
23.3: High Efficiency Green Phosphorescent OLEDs (2009)

Abstract We demonstrate commercial deposition stable green PHOLED emitter data and incorporate this emitter into two top emission microcavity PHOLEDs that show 110cd/A (NTSC green), and a record high efficiency 160cd/A green, at 3,000cd/m 2 . A new unsaturated green is also presented with a record lifetime of 20,000hrs to LT90 from 2000cd/m 2 .
Abstract 613: Copy number variations distinguish lung adenocarcinomas from squamous cell carcinomas (2015)

Abstract Purpose To develop a molecular based classification of non-small cell lung carcinomas based on genome wide copy number variations (CNVs). Background For a number of clinical and biologic reasons, the accurate classification of non small cell lung carcinoma (NSCLC) into adenocarcinoma (ADC) and squamous cell carcinoma (SCC) is essential. DNA based tests, which are not currently used, are more robust when applied to formalin fixed paraffin embedded tissues. Materials and Methods TCGA Dataset: The Cancer Genome Atlas project (TCGA) level 3 CNVs data (Affymetrix Genome-Wide Human SNP Array 6.0) of resected ADC (n = 241) and SCC (n = 210) patients were utilized as a Training set along with 1091 non malignant lung samples. SPORE Patient Dataset: The UT Lung SPORE cohort consists of 248 resected lung cancers (168 ADC and 74 SCC samples) run with the Agilent 244K Human Genome CGH Microarray. Molecular signature identification based on the morphologic subclassification of NSCLC: We used statistical algorithms to identify potential CNV biomarkers and combined them with known amplified oncogenes to identify 28 CNV signature genes that were highly correlated with histological classification. Identification of CNV classifier genes. The CNV signature genes were identified through the following four sequential steps: 1) Paired t-test. 2) Elastic Net. 3) Partial lease squares algorithm. 4) Naive Bayes classifier. Results: The 28 gene CNV signature accurately separated squamous cell carcinomas from adenocarcinomas in the Training and Validation sets as well as distinguished tumors from non-malignant tissues (Table 1). Table 1. The classification results between ADC and SCC DataSensitivitySpecificityAccuracyADC vs SCCTraining set (TCGA)0.940.870.91Validation set (SPORE)0.870.840.86Tumor vs Non-malignantADC0.910.960.94SCC0.970.980.98 Conclusions: A 28 gene CNV signature distinguished lung adenocarcinomas from squamous cell carcinomas with great accuracy (86-91%) and the lung tumor samples can be distinguished from the non-malignant lung samples with an accuracy of 94-98%. Citation Format: Kai Song, Guangqiang Zheng, Luc Girard, Ignacio I. Wistuba, Jack A. Roth, Carmen Behrens, Milind B. Suraokar, John D. Minna, Adi F. Gazdar. Copy number variations distinguish lung adenocarcinomas from squamous cell carcinomas. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 613. doi:10.1158/1538-7445.AM2015-613
TGF-β-dependent lymphoid tissue residency of stem-like T cells limits response to tumor vaccine (2022)

TGF-β signaling is necessary for CD8<sup>+</sup> T cell differentiation into tissue resident memory T cells (T<sub>RM</sub>). Although higher frequency of CD8<sup>+</sup> T<sub>RM</sub> cells in the tumor microenvironment is associated with better prognosis, TGF-β-blockade typically improves rather than worsens outcomes. Here we show that in a mouse melanoma model, in the tumor-draining lymph nodes (TDLN) rather than in the tumors themselves, stem-like CD8<sup>+</sup> T cells differentiate into T<sub>RM</sub>s in a TGF-β and tumor antigen dependent manner. Following vaccination against a melanoma-specific epitope, most tumour-specific CD8<sup>+</sup> T cells are maintained in a stem-like state, but a proportion of cells lost T<sub>RM</sub> status and differentiate into CX3CR1<sup>+</sup> effector CD8<sup>+</sup> T cells in the TDLN, which are subsequently migrating into the tumours. Disruption of TGF-β signaling changes the dynamics of these developmental processes, with the net result of improving effector CD8<sup>+</sup> T cell migration into the tumours. In summary, TDLN stem-like T cells transiently switch from a TGF-β-dependent T<sub>RM</sub> differentiation program to an anti-tumor migratory effector development upon vaccination, which transition can be facilitated by targeted TGF-β blockade.
Occurrence and removal of four artificial sweeteners in wastewater treatment plants of China (2022)

Artificial sweeteners discharged into aquatic environments have raised concern because of their ubiquitous occurrence and potential biological effect. And some of them, such as sucralose (SUC) and acesulfame (ACE), have been identified as emerging contaminants. Wastewater treatment plants (WWTPs) are considered as important sources and sinks of artificial sweeteners discharged into the environment. In this study, the occurrence and removal of four representative artificial sweeteners in 12 WWTPs located in different provinces of China were investigated. The results showed that artificial sweeteners were detected widely in the investigated WWTPs. The median concentrations of the four target artificial sweeteners were detected in influents at levels of 0.03-3.85 μg L<sup>-1</sup> and decreased in the order of SUC > ACE > aspartame (APM) > neotame (NTM). Additionally, the per capita mass loads of total artificial sweeteners in the WWTPs could be affected by the location of the WWTPs and were higher in southern cities than in northern cities. It was also found that there was a distinct linear correlation between the per capita mass load of ACE in influents and population density. During the treatment of WWTPs, the overall removal efficiency of artificial sweeteners ranged from -116% to 99.1%. Among the target artificial sweeteners, SUC and ACE might have potential risk to aquatic environments based on the calculation of the risk quotient. Thus, advanced treatment processes were carried to further remove SUC and ACE to reduce their long-term cumulative effect. Overall, UV/H<sub>2</sub>O<sub>2</sub> and UV/PDS showed a better effect than granular activated carbon (GAC) adsorption in the removal of artificial sweeteners. The reaction constants of ACE by UV/H<sub>2</sub>O<sub>2</sub> and UV/PDS were higher than those of SUC, which is related to molar extinction coefficients. Meanwhile, the adsorption ability of GAC adsorption for SUC was better than that of ACE, which is in correlation with the octanol-water partition coefficient. By comparison of removal efficiency, UV/PDS was considered as the most suitable advanced treatment process to remove ACE and SUC.