gebhart/patrepeval huggingface dataset:
Explainable AI in Industry (2019)

Artificial Intelligence is increasingly playing an integral role in determining our day-to-day experiences. Moreover, with proliferation of AI based solutions in areas such as hiring, lending, criminal justice, healthcare, and education, the resulting personal and professional implications of AI are far-reaching. The dominant role played by AI models in these domains has led to a growing concern regarding potential bias in these models, and a demand for model transparency and interpretability. In addition, model explainability is a prerequisite for building trust and adoption of AI systems in high stakes domains requiring reliability and safety such as healthcare and automated transportation, and critical industrial applications with significant economic implications such as predictive maintenance, exploration of natural resources, and climate change modeling.
Unpacking the Complexity of Epithelial Plasticity: From Master Regulator Transcription Factors to Non-Coding RNAs (2023)

Cellular plasticity in cancer enables adaptation to selective pressures and stress imposed by the tumor microenvironment. This plasticity facilitates the remodeling of cancer cell phenotype and function (such as tumor stemness, metastasis, chemo/radio resistance), and the reprogramming of the surrounding tumor microenvironment to enable immune evasion. Epithelial plasticity is one form of cellular plasticity, which is intrinsically linked with epithelial-mesenchymal transition (EMT). Traditionally, EMT has been regarded as a binary state. Yet, increasing evidence suggests that EMT involves a spectrum of quasi-epithelial and quasi-mesenchymal phenotypes governed by complex interactions between cellular metabolism, transcriptome regulation, and epigenetic mechanisms. Herein, we review the complex cross-talk between the different layers of epithelial plasticity in cancer, encompassing the core layer of transcription factors, their interacting epigenetic modifiers and non-coding RNAs, and the manipulation of cancer immunogenicity in transitioning between epithelial and mesenchymal states. In examining these factors, we provide insights into promising therapeutic avenues and potential anti-cancer targets.
Surface Characterization of Xerographic Developers by Inverse Gas Chromatography: Influence of Surface Acid and Base Properties on Work Functions and Triboelectric Charging (2004)

Inverse Gas Chromatography (IGC) has been applied to study the surface properties of developer materials, measuring acid, base and dispersion interactions. Model carrier and toner particles were prepared, where the toner was blended with various nano-particulate metal oxide surface additives: silica, titania and alumina. Toner charging was determined with these surface additive formulations. IGC was used to characterize carrier and additive surface chemistry. Results from IGC were evaluated with respect to toner charge and to metal oxide work functions. A correlation was found between IGC-determined surface acidbase interaction parameters of the developer materials, and their work functions and triboelectric charge. Together, the IGC, work function and charging results strongly support a work function model for developer charging, where the work function is determined by the acid and base properties of the developer components. Thus, as the ratio of the acid to base interaction parameters of the metal oxide surface additive increased, toner charge became more negative. A charging model incorporating all these results has been proposed and integrated with the current understanding of triboelectric charging in xerographic developers.
Profile of Weak Shock Waves in a Shock Tube (1969)

It is commonly assumed that pressure will undergo a discontinuity at a shock front, and then remain steady or slowly decrease with time. In his work with finite-amplitude tone bursts in an air-filled tube, however, McKittrick [J. Acoust. Soc. Amer. 42, 1153(A) (1967)] observed a rounded top for each shock front, rather than the expected perfect sawtooth shape. Shock amplitudes 10 to 100 times as great have been obtained for the present work with a 2-in.-i.d. shock tube, which uses a compressed-air driver and Cellophane diaphragm. The pressure profile is observed at normal incidence with a wide-band capacitor microphone (0.3 μsec rise time), which was constructed as an integral part of the tube termination. For 0.1–0.4-atm shock waves, the initial pressure jump is followed by a further exponential rise of perhaps one-tenth the shock amplitude, with a rise time of about 0.5 msec. Preliminary results with a 1.25-in. tube indicate a similar profile but shorter rise time. [Work supported in part by ONR and NSF.]
Distinct regulation of dopamine D2S and D2L autoreceptor signaling by calcium (2015)

D2 autoreceptors regulate dopamine release throughout the brain. Two isoforms of the D2 receptor, D2S and D2L, are expressed in midbrain dopamine neurons. Differential roles of these isoforms as autoreceptors are poorly understood. By virally expressing the isoforms in dopamine neurons of D2 receptor knockout mice, this study assessed the calcium-dependence and drug-induced plasticity of D2S and D2L receptor-dependent G protein-coupled inwardly rectifying potassium (GIRK) currents. The results reveal that D2S, but not D2L receptors, exhibited calcium-dependent desensitization similar to that exhibited by endogenous autoreceptors. Two pathways of calcium signaling that regulated D2 autoreceptor-dependent GIRK signaling were identified, which distinctly affected desensitization and the magnitude of D2S and D2L receptor-dependent GIRK currents. Previous in vivo cocaine exposure removed calcium-dependent D2 autoreceptor desensitization in wild type, but not D2S-only mice. Thus, expression of D2S as the exclusive autoreceptor was insufficient for cocaine-induced plasticity, implying a functional role for the co-expression of D2S and D2L autoreceptors.
An efficient algorithm for locating soft and hard failures in WDM networks (2000)

Fault identification and location in optical networks is hampered by a multitude of factors: the redundancy and the lack of coordination (internetworking) of the managements at the different layers (WDM, SDH/SONET, ATM, IP); the large number of alarms a single failure can trigger; the difficulty in detecting some failures; and the resulting need to cope with missing or false alarms. Moreover, the problem of multiple fault location is NP-complete, so that the processing time may become an issue for large meshed optical networks. We propose an algorithm for locating multiple failures at the physical layer of a WDM network. They can be either hard failures, that is, unexpected events that suddenly interrupt the established channels; or soft failures, that is, events that progressively degrade the quality of transmission; or both, hard failures are detected at the WDM layer. Soft failures can sometimes be detected at the optical layer if proper testing equipment is deployed, but often require performance monitoring at a higher layer (SDH, ATM, or IP). Both types of failures, and both types of error monitoring, are incorporated in our algorithm, which is based on a classification and abstraction of the components of the optical layer and of the upper layer. Our algorithm does not rely on timestamps nor on failure probabilities, which are difficult to estimate and to use in practice. Moreover, our algorithm also handles missing and false alarms. The nonpolynomial computational complexity of the problem is pushed ahead into a precomputational phase, which is done off-line, when the optical channels are set up or cleared down. This results in fast on-line location of the failing components upon reception of the ringing alarms.
HIV-1 mutants expressing B cell clonogenic matrix protein p17 variants are increasing their prevalence worldwide (2022)

AIDS-defining cancers declined after combined antiretroviral therapy (cART) introduction, but lymphomas are still elevated in HIV type 1 (HIV-1)-infected patients. In particular, non-Hodgkin's lymphomas (NHLs) represent the majority of all AIDS-defining cancers and are the most frequent cause of death in these patients. We have recently demonstrated that amino acid (aa) insertions at the HIV-1 matrix protein p17 COOH-terminal region cause protein destabilization, leading to conformational changes. Misfolded p17 variants (vp17s) strongly impact clonogenic B cell growth properties that may contribute to B cell lymphomagenesis as suggested by the significantly higher frequency of detection of vp17s with COOH-terminal aa insertions in plasma of HIV-1-infected patients with NHL. Here, we expand our previous observations by assessing the prevalence of vp17s in large retrospective cohorts of patients with and without lymphoma. We confirm the significantly higher prevalence of vp17s in lymphoma patients than in HIV-1-infected individuals without lymphoma. Analysis of 3,990 sequences deposited between 1985 and 2017 allowed us to highlight a worldwide increasing prevalence of HIV-1 mutants expressing vp17s over time. Since genomic surveillance uncovered a cluster of HIV-1 expressing a B cell clonogenic vp17 dated from 2011 to 2019, we conclude that aa insertions can be fixed in HIV-1 and that mutant viruses displaying B cell clonogenic vp17s are actively spreading.
Immunotherapy utilizing the combination of natural killer– and antibody dependent cellular cytotoxicity (ADCC)–mediating agents with poly (ADP-ribose) polymerase (PARP) inhibition (2018)

Following publication of the original article [1], an error was noted in the GAPDH in the western blot depicted in Figure 4b.
FPGA-Based Channel Coding Architectures for 5G Wireless Using High-Level Synthesis (2017)

We propose strategies to achieve a high-throughput FPGA architecture for quasi-cyclic low-density parity-check codes based on circulant-1 identity matrix construction. By splitting the node processing operation in the min-sum approximation algorithm, we achieve pipelining in the layered decoding schedule without utilizing additional hardware resources. High-level synthesis compilation is used to design and develop the architecture on the FPGA hardware platform. To validate this architecture, an IEEE 802.11n compliant 608 Mb/s decoder is implemented on the Xilinx Kintex-7 FPGA using the LabVIEW FPGA Compiler in the LabVIEW Communication System Design Suite . Architecture scalability was leveraged to accomplish a 2.48 Gb/s decoder on a single Xilinx Kintex-7 FPGA. Further, we present rapidly prototyped experimentation of an IEEE 802.16 compliant hybrid automatic repeat request system based on the efficient decoder architecture developed. In spite of the mixed nature of data processing—digital signal processing and finite-state machines— LabVIEW FPGA Compiler significantly reduced time to explore the system parameter space and to optimize in terms of error performance and resource utilization. A 4x improvement in the system throughput, relative to a CPU-based implementation, was achieved to measure the error-rate performance of the system over large, realistic data sets using accelerated, in-hardware simulation.
Processing and Properties of Thin-Film Ceria Based SOFC (2003)

A series of doped ceria-based electrolytes were synthesized by the glycine-nitrate method; producing powders of 2-3 µm in particle size. Sintering profiles were determined for all doped ceria compositions. Conductivity measurements were determined in air and open-circuit potential measurements in H2-H2O/air for doped ceria pellets from 400 to 800°C. Preliminary results show that calcium, bismuth and lithium doping lowers the sintering temperature of ceria. At 700°C, a maximum open-circuit-potential of 0.84 V was observed for the composition Ce0.8Y0.18Ca0.02O1.9; this composition also exhibits the lowest grain boundary resistance for the doped samples. The highest total conductivity of 1.7×10−2 Scm−1 was observed for the composition Ce0.8Y0.178Cs0.02Li0.002O1.8.
Coupled plasmonic waveguides: Near field transducers for HAMR (2010)

This paper presents a design for a near field transducer for heat assisted magnetic recording that utilizes evanescent coupling between a dielectric waveguide and a metallic “needle” of uniform triagular cross-section. This design allows for complete coupling of power from an illuminating single mode dielectric waveguide into the plasmonic mode of the metallic needle. Coupling from the plasmonic waveguide into the medium is computed to be localized (40 nm FWHM) with 2.5% efficiency inside the FWHM (8% overall). A single mode dielectric waveguide illumination structure like that needed for the needle's functioning is demonstrated using a curved focusing grating and a thin film waveguide. Illumination efficiencies of better than 5% are shown with room for the required increases.
Antimicrobial Resistance in Commensal Escherichia coli Isolated from Pigs and Pork Derived from Farms Either Routinely Using or Not Using In-Feed Antimicrobials (2018)

The aims of this study were (i) to evaluate whether routine in-feed antimicrobial use in pigs or not resulted in differences in antimicrobial resistance (AMR) E. coli at different pig producing stages, and (ii) to determine whether resistant strains were presented in pig meat postslaughter. A total of 300 commensal E. coli isolates were obtained and examined for antibiograms, AMR genes, plasmid replicons, and molecular types. The isolates were from two farms either using (A) or not using in-feed antimicrobials (NA), sampled four times during the production cycle and once postslaughter. E. coli resistant to aminoglycosides containing aadA1, aadA2, and aadB and extended-spectrum beta-lactamase-producing (ESBLP) E. coli containing bla<sub>CTX-M-1</sub> were significantly increased in the nursery and growing periods in farm A compared to farm NA. IncI1-Iγ and IncHI2 were common in the nursery period and were shown to transfer bla<sub>CTX-M</sub> genes by conjugation. ST10 was the most common type only found in live pigs. ST604, ST877, ST1209, and ST2798 ESBLP were found only in live pigs, whereas ST72, ST302, and ST402 ESBLP were found in pig meat.
Spatiotemporal monitoring of intracellular metabolic dynamics by resonance Raman microscopy with isotope labeling (2020)

Cellular metabolites are valuable in a diverse range of applications. For example, the unicellular green alga <i>Haematococcus lacustris</i> produces as a secondary metabolite the carotenoid pigment astaxanthin (AXT), which is widely used in nutraceutical, cosmetic, and food industries due to its strong antioxidant activity. In order to enhance the productivity of <i>H. lacustris</i>, spatial and temporal understanding of its metabolic dynamics is essential. Here we show spatiotemporal monitoring of AXT production in <i>H. lacustris</i> cells by resonance Raman microscopy combined with stable isotope labeling. Specifically, we incorporated carbon dioxide (<sup>13</sup>CO<sub>2</sub>) labeled with a stable isotope (<sup>13</sup>C) into <i>H. lacustris</i> cells through carbon fixation and traced its conversion to <sup>13</sup>C-AXT using our resonance Raman microscope. We incubated <i>H. lacustris</i> cells under various conditions by switching, pulsing, and replacing <sup>13</sup>CO<sub>2</sub> and <sup>12</sup>CO<sub>2</sub>. By measurement of these cells we determined the fixation time of <sup>13</sup>C-carbon, visualized the intracellular localization of <sup>13</sup>C- and <sup>12</sup>C-AXTs, and revealed the dynamic consumption-production equilibrium of the accumulated AXT. This work is a valuable step in the development of effective screening criteria for high AXT-producing <i>H. lacustris</i> cells.
System Level Transient Thermal Performance of High-Power Dynamic Microelectronics (2009)

System-level thermal transient analysis of High-Power Dynamic Microelectronics System is performed using numerical simulations. The SmartMOS-type device is packaged in 20 lead SOIC module with exposed copper slug. The package is attached to 4-layer PCB with embedded thermal vias. The challenge resides in the transient thermal interaction between the dynamic heat sources (high/low side motors), activated simultaneously at different powering profiles. Several operating steps are simulated, and the transient thermal behavior for each source is analyzed then optimized during the process. The low side motor reaches a peak temperature of ∼126.1°C at 2.25s, while the final temperature reached by the motor after one cycle (2.565 s) is ∼75.9°C. The DC current limit study indicates that the current over 1A exceeds the thermal budget. The case with 0.5A current limit reaches 135°C after 4 cycles, satisfying the thermal budget. Additional studies for an equivalent system were performed with only the high side driver actively dissipating 120W for 2.56 ms. The peak temperature reached by the system during the first cycle (2.56 us) is ∼65°C. Analytical study was performed to evaluate the steady state (final) temperature after a large number of dynamic powering cycles, based on heating/cooling behavior and superposition principle. The peak temperature reached by the IC will not exceed 92°C (using the steady state value and the temperature fluctuations per transient cycle). A correlation to predict the peak temperatures reached by the dynamic system after a long number of powering cycles is provided.
Ever-Present Dangers (2000)

A murderously recurrent theme surfaces as we read the record of technology. It can be decocted into the tidy epigram: “The fastest route to success is through failure. The greatest enemy of success is success.” When my civil engineering colleague Jack Matson recognized the validity of that idea, he began vigorously to promote the concept of intelligent fast failure. He said that we can speed our own creativity if we begin by running through as many wrong or foolish ways of accomplishing our end as we can think of. That process both emboldens us and instructs us in the full range of possibility. Conversely, success that fails to keep the boundaries of error within sight eventually takes itself for granted and leaves us open to failure on a grand scale. We skirted this issue toward the end of Chapter 9; now let us look at it more closely. A story of three bridges helps to expose the complex way in which success and failure work together. Henry Petroski takes us back to the forty-six-mile rail trip from Edinburgh to Dundee, which took half a day in 1870. Passengers had to ride the ferry over two wide fjords, arms of the North Sea slicing into Scotland. They are the Firth of Tay and the Firth of Forth. Then an English engineer, Thomas Bouch, sold backers on the idea of building bridges over those inlets. The first was an immense two-mile bridge over the Firth of Tay. When its eighty-five spans were finished in 1877, they made up the longest bridge in the world, and Queen Victoria knighted Bouch. Disaster followed almost immediately. The Tay Bridge collapsed in 1879, killing seventy-five people. Cost-cutting had yielded a bridge that couldn’t stand up to the wind forces. Bouch died in humiliation four months later. By 1881 the Tay Bridge had been rebuilt with heavy, unbeautiful trusses, and attention turned to the second bridge, the one over the Firth of Forth. The Firth of Forth bridge was to cross where the center of the firth was a mile wide, with only one shallow spot for a central pier.
The Asymptotic Posterior Normality of the Latent Trait in an IRT Model (1993)

It has long been part of the item response theory (IRT) folklore that under the usual empirical Bayes unidimensional IRT modeling approach, the posterior distribution of examinee ability given test response is approximately normal for a long test. Under very general and nonrestrictive nonparametric assumptions, we make this claim rigorous for a broad class of latent models.
Conditional activation of a single‐copy L1 transgene in mice by Cre (2008)

The synthetic L1 retrotransposon, ORFeus, is useful for probing mechanisms of L1 retrotransposition in vivo and for genome-wide mouse mutagenesis because of its high level of activity. To achieve controlled activation of ORFeus in mice, we constructed ORFeus(LSL), in which ORFeus coding sequences were separated from the promoter by a loxP-beta-geo-stop-loxP (LSL) cassette, and derived transgenic mouse lines containing single-copy ORFeus(LSL). We observed tissue-specific ORFeus activation by crossing ORFeus(LSL) to various Cre-expressing lines, specifically in the germ line or the pancreas, providing definite evidence that all host factors and machinery required posttranscriptionally for L1 retrotransposition are available in somatic tissues in living animals. Notably, the single-copy ORFeus transgene is about threefold more active per copy than a previously described multicopy ORFeus transgene in the germ line and even more active somatically. This conditional transgenic ORFeus mouse model should allow further exploration of posttranscriptional cellular requirements for L1 retrotransposition and facilitate the development of ORFeus mouse lines suitable for in vivo mutagenesis.
Structural Characterization of Melanin Pigments from Commercial Preparations of the Edible Mushroom Auricularia auricula (2015)

Many of the most widely consumed edible mushrooms are pigmented, and these have been associated with some beneficial health effects. Nevertheless, the majority of the reported compounds associated with these desirable properties are non-pigmented. We have previously reported that melanin pigment from the edible mushroom Auricularia auricula can protect mice against ionizing radiation, although no physicochemical characterization was reported. Consequently, in this study we have characterized commercial A. auricula mushroom preparations for melanin content and carried out structural characterization of isolated insoluble melanin materials using a panel of sophisticated spectroscopic and physical/imaging techniques. Our results show that approximately 10% of the dry mass of A. auricula is melanin and that the pigment has physicochemical properties consistent with those of eumelanins, including hosting a stable free radical population. Electron microscopy studies show that melanin is associated with the mushroom cell wall in a manner similar to that of melanin from the model fungus C. neoformans. Elemental analysis of melanin indicated C, H, and N ratios consistent with 5,6-dihydroxyindole-2-carboxylic acid/5,6-dihydroxyindole and 1,8-dihydroxynaphthalene eumelanin. Validation of the identity of the isolated product as melanin was achieved by EPR analysis. A. auricula melanin manifested structural differences, relative to the C. neoformans melanin, with regard to the variable proportions of alkyl chains or oxygenated carbons. Given the necessity for new oral and inexpensive radioprotective materials coupled with the commercial availability of A. auricula mushrooms, this product may represent an excellent source of edible melanin.