gebhart/patrepeval huggingface dataset:
CLIM: A Cross-Level Workload-Aware Timing Error Prediction Model for Functional Units (2017)

Timing errors that are caused by the timing violations of sensitized circuit paths, have emerged as an important threat to the reliability of synchronous digital circuits. To protect circuits from these timing errors, designers typically use a conservative timing margin, which leads to operational inefficiency. Existing adaptive approaches reduce such conservative margins by predicting the timing errors in advance and adjusting the timing margin adaptively. However, these error prediction approaches overlook the impact of input workload (i.e., operands) on path sensitization, thereby resulting in a loss of accuracy. The diversity of input operands leads to complex path sensitization behaviors, making them hard to represent in timing error modeling. In this paper, we propose CLIM, a cross-level workload-aware timing error prediction model for functional units (FUs). CLIM predicts whether there are timing errors in FU at two levels: bit-level and value-level. At the bit level or value level, CLIM predicts each output bit or entire output value as one of two classes: {timing correct, timing erroneous} as a function of input workload and clock period, respectively. We apply supervised learning methods to construct CLIM, by using input operands, computation history and circuit toggling as input features, as well as outputs' timing classes as labels. These training data are collected from gate-level simulations (GLS) of post place-and-route designs in TSMC 45nm process. We evaluate CLIM prediction accuracy for various FUs and compare it with baseline models. On average, CLIM exhibits 95 percent prediction accuracy at value-level, 97 percent at bit-level, and executes at a rate 173X faster than GLS. We utilize CLIM to analyze the value-level and bit-level reliability of FUs under random and real-world application workloads. At value-level, CLIM-based reliability estimation is within 2.8 percent deviation on average of detailed GLS ground truth. At bit-level, we introduce the concept of bit-level reliability specification of error-tolerant applications and compare this with the CLIM-based bit-level reliability estimation. By comparison, CLIM will classify the application quality into two classes: {acceptable, non-acceptable}. On average, 97 percent application quality classification is consistent with GLS ground truth.
<1-ms highly-repeatable polarization-state generator and analyzer for 40-Gb/s system performance monitoring (2005)

We demonstrate a fast (&lt;1 millisecond), all solid-state, highly repeatable (variation &lt;0.7° polarization state generator and analyzer using magneto-optic polarization switches and demonstrate OSNR performance monitoring in a 14×40-Gb/s WDM system. (2 pages)
Abstract 5689: Anti-E2F-1 PEGylated liposomal encapsulated peptide regresses human small cell lung cancer & lymphoma xenografts (2012)

Abstract The E2F family of transcription factors is critical to large number of key cellular processes, including replication, DNA repair, and differentiation. E2F-1 is unique among the E2F family of transcription factors in that it can act as a tumor suppressor or as an oncogene, depending on the cellular context. Given the critical functions of E2F target genes in replication, and differentiation, it is perhaps not surprising that dysregulation of E2Fs has been associated with the cancer phenotype. E2F-1,2 and-3, “activating” E2Fs, function as heterodimers with DP proteins and are regulated by the retinoblastoma protein. E2F-1 and 3 are over expressed in many human tumors and overexpression (suggesting oncogene addiction) is associated with a poor prognosis. We have used phage display to obtain peptides that bind tightly to the E2F consensus promoter recognition sequence. When one of these peptides was coupled to a modified penetration sequence to enhance uptake, the penetratin- peptide (PEP) potently inhibited some but not all malignant cell lines. Modeling studies and ChIP studies showed that part of the pentratin sequence was involved in the binding of the PEP to the E2 F1 promoter. The PEP down-regulated E2F-2 and 4, as well as E2F-1, and-down stream targets of E2F-1. The small cell lung carcinoma (SCLC) cell line and the Ramos cell line (Burkitt lymphoma) were sensitive to low micromolar concentrations of the PEP, and apoptosis was seen within 6 h. These cell lines have mutant p53, and over express E2F-1 and cMyc and BCL2, and are “oncogene addicted”. Normal cells (human bone marrow CD34+ hematopoeitic stem cells, human marrow mesenchymal cells and MEFs), were insensitive to high concentrations of the PEP. When encapsulated in PEGylated liposomes, the PEP caused marked regression of advanced SCLC xenografts in mice without appreciable toxicity. These results prompt us to explore further preclinical development of the PEP for tumor 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 5689. doi:1538-7445.AM2012-5689
Arsenic in stream sediments of northern Alabama (2001)

OVERVIEW OF ARSENIC IN STREAM SEDIMENTS The overall range of arsenic in the NURE stream sediments was from 0.3 to 44 mg/kg sediment (ppm) As in the sample data set. The mean value was 4.3 ppm with a standard deviation of 4.1 ppm. For comparison, the crustal abundance of arsenic is 1.8 ppm (Taylor, 1964). Shale is higher, with average values of 15 ppm. Coal samples from the entire USGS National Coal Resource Data System coal database (Finkelman, 1994) average 24 ppm arsenic. A study of stream sediments from throughout the U.S. by the USGS NAWQA program reported that the 75th percentile for arsenic in 541 stream sediments was 9.5 ppm (Rice, 1999). Given the relatively low crustal abundance of arsenic, a number of stream-sediment samples in this study may be considered geochemically anomalous in this element.
Fast time domain physical optics for non linear scattering (2007)

The proposed fast time domain physical optics (TDPO) scheme is based on a domain decomposition of the scattering surface or radiating aperture into smaller patches. The scheme exploits the fact that, asymptotically, the number of samples required to describe the scattered or radiated fields in time and angular domains, is proportional to the size of the patch. Therefore the radiation patterns are computed directly only for the smallest subdomains. Subsequently, the radiation patterns are aggregated through a two- or multi-level process comprising temporal and angular interpolations and time- shifts, and leading to reduced computational complexities. (5 pages)
Cigarette smoke and chewing tobacco alter expression of different sets of miRNAs in oral keratinocytes (2018)

Carcinogenic effect of tobacco in oral cancer is through chewing and/or smoking. Significant differences exist in development of oral cancer between tobacco users and non-users. However, molecular alterations induced by different forms of tobacco are yet to be fully elucidated. We developed cellular models of chronic exposure to chewing tobacco and cigarette smoke using immortalized oral keratinocytes. Chronic exposure to tobacco resulted in increased cell scattering and invasiveness in immortalized oral keratinocytes. miRNA sequencing using Illumina HiSeq 2500 resulted in the identification of 10 significantly dysregulated miRNAs (4 fold; p ≤ 0.05) in chewing tobacco treated cells and 6 in cigarette smoke exposed cells. We integrated this data with global proteomic data and identified 36 protein targets that showed inverse expression pattern in chewing tobacco treated cells and 16 protein targets that showed inverse expression in smoke exposed cells. In addition, we identified 6 novel miRNAs in chewing tobacco treated cells and 18 novel miRNAs in smoke exposed cells. Integrative analysis of dysregulated miRNAs and their targets indicates that signaling mechanisms leading to oncogenic transformation are distinct between both forms of tobacco. Our study demonstrates alterations in miRNA expression in oral cells in response to two frequently used forms of tobacco.
Data from Tumor-Derived Small Extracellular Vesicles Inhibit the Efficacy of CAR T Cells against Solid Tumors (2023)

&lt;div&gt;Abstract&lt;p&gt;Chimeric antigen receptor (CAR) T-cell therapy has shown remarkable success in the treatment of hematologic malignancies. Unfortunately, it has limited efficacy against solid tumors, even when the targeted antigens are well expressed. A better understanding of the underlying mechanisms of CAR T-cell therapy resistance in solid tumors is necessary to develop strategies to improve efficacy. Here we report that solid tumors release small extracellular vesicles (sEV) that carry both targeted tumor antigens and the immune checkpoint protein PD-L1. These sEVs acted as cell-free functional units to preferentially interact with cognate CAR T cells and efficiently inhibited their proliferation, migration, and function. In syngeneic mouse tumor models, blocking tumor sEV secretion not only boosted the infiltration and antitumor activity of CAR T cells but also improved endogenous antitumor immunity. These results suggest that solid tumors use sEVs as an active defense mechanism to resist CAR T cells and implicate tumor sEVs as a potential therapeutic target to optimize CAR T-cell therapy against solid tumors.&lt;/p&gt;Significance:&lt;p&gt;Small extracellular vesicles secreted by solid tumors inhibit CAR T cells, which provide a molecular explanation for CAR T-cell resistance and suggests that strategies targeting exosome secretion may enhance CAR T-cell efficacy.&lt;/p&gt;&lt;p&gt;&lt;i&gt;&lt;a href="https://aacrjournals.org/cancerres/article/doi/10.1158/0008-5472.CAN-23-1484" target="_blank"&gt;See related commentary by Ortiz-Espinosa and Srivastava, p. 2637&lt;/a&gt;&lt;/i&gt;&lt;/p&gt;&lt;/div&gt;
Modeling the Elongation of Nanowires Grown by Chemical Bath Deposition Using a Predictive Approach (2019)

The chemical bath deposition of nanowires is of high interest for a wide variety of optoelectronic, piezoelectric, and sensing devices, but a theoretical description of the elongation process is still missing despite its critical importance. By solving Fick’s diffusion equations in combination with thermodynamic computations, we determine the expression of the axial growth rate of nanowires and its temporal dependence under dynamic conditions, namely, in a sealed reactor, where the depletion of chemical reactants occurs. The theoretical model is found to be in very good agreement with a large set of experimental data specifically collected in the case of the chemical bath deposition of ZnO nanowires. In particular, an activation energy of 198 ± 24 kJ/mol is deduced for the elongation process of ZnO nanowires, involving the energy barriers for both the dehydration process of Zn(II) species (i.e., [Zn(H₂O)₆]²⁺ ions) and their subsequent direct incorporation onto the c-plane top faces. This shows its high potential to enable in-depth investigation of the physicochemical processes at work in the chemical bath. By using the theoretical model as a predictive approach, a complete growth diagram reporting the evolution of the length of ZnO nanowires vs effective growth time and temperature is also obtained over a broad range of conditions, revealing its additional high potential for applied research and industrial purposes. The present general approach is further compatible with a broad range of chemicals in solution and of semiconducting materials grown by chemical bath deposition.
Laser-Induced Choroidal Neovascularization in Mice Attenuated by Deficiency in the Apelin-APJ System (2013)

The results suggested that the apelin-APJ system contributes to CNV development partially independent of the VEGF pathway.
Optimum design of inserted segment (IS) in multi-segment dielectric resonator antenna (MSDRA) (2005)

This paper introduces a simple method for optimum design of IS in MSDRAs. It is assumed that IS acts like an impedance transformer between the feedline and the main segment. The method avoids former time-consuming trial and error for achievement of optimum dielectric constant and thickness of IS, and directly gives these parameters in which best possible bandwidth and feedline-MSDRA coupling is attained. To show the efficiency of the proposed method, many examples are examined and numerical and experimental results are presented.
Monocrystalline Si membranes for pressure sensors fabricated by a novel surface micromachining process using porous silicon (2003)

We developed a novel surface micromachining process to fabricate monocrystalline silicon membranes covering a vacuum cavity without any additional sealing steps. Heart of the process is anodic etching of porous silicon, annealing and epitaxial growth. The porous silicon layer consists of two parts, a starting mesoporous silicon layer with low surface porosity and a nanoporous silicon layer with a high porosity. The following annealing step removes native oxide within the later cavity, and the surface is sealed for the subsequent epitaxial layer deposition. The observed stacking fault density in the epitaxial layer about 1E5 cm-2. The temperature budget of the following ASIC-process leads to a complete transformation of the nanoporous silicon layer into a large cavity. The whole structure can be used as a pressure sensor. The estimated pressure in the cavity is smaller than 1 mbar. First integrated pressure sensors have been fabricated using this process. The sensors show a good linearity over the whole pressure range of 200 mbar to 1000 mbar. This novel process has several advantages compared to already published processes. It is a “MEMS first” process, which means that after the epitaxial growth the surface of the wafer is close to a standard wafer surface. Due to full IC compatibility, standard ASIC processes are possible after the fabrication of the membrane. The use of porous silicon enables a high degree of geometrical freedom in the design of membranes compared to standard bulk micromachining (KOH, TMAH). The monocrystalline membranes can be fabricated with surface micromachining without any additional sealing or backside processing steps.
Efficient feedback methods for MIMO channels based on parameterization (2007)

In this paper, we propose two efficient low-complexity quantization methods for multiple-input multiple-output (MIMO) systems with finite-rate feedback based on proper parameterization of the information to be fed back followed by quantization in the new parameter domain. For a MIMO channel which has multiple orthonormal vectors as channel spatial information, we exploit the geometrical structure of orthonormality while quantizing the spatial information matrix. The parameterization is of two types: one is in terms of a set of unit-norm vectors with different lengths, and the other is in terms of a minimal number of scalar parameters. These parameters are shown to be independent for the i.i.d. flat-fading Rayleigh channel, facilitating efficient quantization. In the first scheme, each of the unit-norm vectors is independently quantized with a finite number of bits using an optimal vector quantization (VQ) technique. Bit allocation is needed between the vectors, and the optimum bit allocation depends on the operating SNR of the system. In the second scheme, the scalar parameters are quantized. In slowly time-varying channels, the scalar parameters are also found to be smoothly changing over time, leading to the development of a simple quantization and feedback method using adaptive delta modulation. The results show that the proposed feedback scheme has a channel tracking feature and achieves a capacity very close to perfect feedback with a reasonable feedback rate
Parameterization of a synchronous generator to represent a doubly fed induction generator with chopper protection for fault studies (2010)

Abstract This paper addresses the representation of the wound rotor asynchronous generators by an equivalent synchronous generator, valid for short circuit current calculations. Modern wind power plants are required and designed to ride through faults in the network, subjected to fault clearing. Accurate knowledge of the wind turbine short circuit current contribution is needed for component sizing and protection relay settings during faults within the wind power plant collector system or in the external networks. When studying fault currents and protection settings for wind power installations, the industry standard is to employ software packages where generators are represented by their equivalent synchronous generator operational impedances. Hence, it is of importance to represent non‐synchronous wind generators by an equivalent synchronous generator. Copyright © 2010 John Wiley &amp; Sons, Ltd.
Interrelating of ventricular pressure and intracellular calcium in intact hearts (1997)

Although the mechanistic link between variations in intracellular calcium and its effects on myofilament regulatory proteins and subsequent impact on cardiac muscle force production have been known for some time, characterization of cardiac contractile properties are predominantly confined to phenomenological descriptions of the relationship between either muscle length and force or ventricular pressure and volume. However, as recognition of the limitations of these theories grow, investigators have begun to look toward more fundamental theories of cardiac contraction to explain whole heart function. The goal of the present study was first to explore, on a theoretical level, the degree of complexity required in a biochemical model necessary to adequately explain both equilibrium and twitch contraction behavior of cardiac muscle. Central to this analysis was a critical examination of the evidence for and against the importance of a calcium-free, force-generating state. Next, we determined whether such theories can actually account for the interrelationships between the experimentally measured time courses of pressure generation and the calcium transient measured from intact ventricles during both normal twitches as well as during complex contraction sequences. The results of this analysis provide strong support for a four-state model, including the calcium-free, force-generating state. These results will help guide the continuing quest for a mechanistic theory of ventricular function.
Extended lithium ion pair indicator scale in tetrahydrofuran (1998)

The lithium pK scale has been extended to 25 indicators with a pK range of 9.7-24.4. The resulting scale is compared with the cesium ion pair acidities and to ionic pK's in DMSO and aqueous DMSO.Key words: ion pair acidity, organolithium compounds, indicator, acidity scale.
The Association of Mid-Regional Pro-Adrenomedullin and Mid-Regional Pro-Atrial Natriuretic Peptide with Mortality in an Incident Dialysis Cohort (2011)

High levels of the plasma peptides mid-regional pro-adrenomedullin (MR-proADM) and mid-regional pro-atrial natriuretic peptide (MR-proANP) are associated with clinical outcomes in the general population. Data in patients with chronic kidney disease are sparse. We therefore investigated the association of MR-proANP and MR-proADM levels with all-cause and cardiovascular (CV) mortality, CV events and peripheral arterial disease in 201 incident dialysis patients of the INVOR-Study prospectively followed for a period of up to more than 7 years. The overall mortality rate was 43%, thereof 43% due to CV events. Both baseline MR-proANP and MR-proADM were associated with higher risk of all-cause (HR = 1.44, p = 0.001 and HR = 1.32, p = 0.002, respectively) and CV mortality (HR = 1.75, p<0.001 and HR = 1.41, p = 0.007, respectively) after adjustment for age, sex, previous CV events, diabetes mellitus and time-dependent type of renal replacement therapy. We then stratified patients in high risk (both peptides in the upper tertile), intermediate risk (only one of the two peptides in the upper tertile) and low risk (none in the upper tertile). Although demographic, clinical and laboratory variables were similar among the intermediate and high risk group, to be with both parameters in the upper tertile was associated with a 3-fold higher risk for all-cause (HR = 2.87, p<0.001) and CV mortality (HR = 3.58, p = 0.001). In summary, among incident dialysis patients MR-proANP and MR-proADM were shown to be associated with all-cause and CV mortality, with the highest risk when both parameters were in the upper tertiles.
Characterizing mechanical system integrity using structural surface intensity (2000)

Many structural intensity measurements have been made on simple beam and plate-like structures to determine source strengths and transmission paths. When analyzing more complex structures it is often difficult to compute the intensity throughout the depth of an element. Using a method developed by Pavic [G. Pavic, J. Sound Vib. 115, 405–422 (1987)], the structural surface intensity (SSI) is computed on a gearbox housing using an array of accelerometers and strain gauges. The focus of this research is to use SSI as a machinery fault indicator, with the objective of developing a method that is more sensitive than other conventional diagnostic methods. Experimental data were taken on a gearbox from the Mechanical Diagnostic Test Bed (MDTB) at the Penn State Applied Research Laboratory as the gearbox was run to failure. The changes in energy flow are analyzed and characterized to provide criteria for fault detection. Analysis of the data indicates that significant changes in structural surface intensity occur as geartooth faults develop and that SSI can be more sensitive than other traditional indicators. [This research was supported by the Multidisciplinary University Research Initiative for Integrated Predictive Diagnostics (Grant No. N00014-95-1-0461) sponsored by the Office of Naval Research.]
Blueberry Opposes β -Amyloid Peptide-Induced Microglial Activation Via Inhibition of p44/42 Mitogen-Activation Protein Kinase (2008)

Alzheimer's Disease (AD) is the most common age-related dementia, with a current prevalence in excess of five million individuals in the United States. The aggregation of amyloid-beta (A beta) into fibrillar amyloid plaques is a key pathological event in the development of the disease. Microglial proinflammatory activation is widely known to cause neuronal and synaptic damage that correlates with cognitive impairment in AD. However, current pharmacological attempts at reducing neuroinflammation mediated via microglial activation have been largely negative in terms of slowing AD progression. Previously, we have shown that microglia express proinflammatory cytokines and a reduced capacity to phagocytose A beta in the context of CD40, A beta peptides and/or lipopolysaccharide (LPS) stimulation, a phenomenon that can be opposed by attenuation of p44/42 mitogen-activated protein kinase (MAPK) signaling. Other groups have found that blueberry (BB) extract both inhibits phosphorylation of this MAPK module and also improves cognitive deficits in AD model mice. Given these considerations and the lack of reduced A beta quantities in behaviorally improved BB-fed mice, we wished to determine whether BB supplementation would alter the microglial proinflammatory activation state in response to A beta. We found that BB significantly enhances microglial clearance of A beta, inhibits aggregation of A beta(1-42), and suppresses microglial activation, all via suppression of the p44/42 MAPK module. Thus, these data may explain the previously observed behavioral recovery in PSAPP mice and suggest a means by which dietary supplementation could mitigate an undesirable microglial response toward fibrillar A beta.