gebhart/patrepeval huggingface dataset:
Abstract 1416: Pan-cancer mutual vulnerability and viability (2018)

Abstract We used a skew-distribution-based statistical methodology to fit parametric models of cell-viability profiles from genome-wide RNAi-gene knockdowns. We identify the subset of genes with the highest degree of skewness that represent most oncogenes and tumor suppressors. We decomposed those genes using matrix decomposition in order to define mutual vulnerabilities. The resulting matrix decomposition components represent coordinated patterns of gene dependency shared by many genes in many cell lines across cancer types. We identify the most salient mutual vulnerabilities, generate a comprehensive catalog of them, and annotate them based on their association with a variety of genomic features including: gene, protein, and pathway expression, mutational landscape, copy number alterations, promoter methylations, metabolites, miRNAs, and drug sensitivities. We also generate an Onco-GPS (Oncogenic Positioning System) Map that provides a summary and visual representation of the mutual vulnerabilities and their components, and allow us to compare them with their counterparts in Pan-Cancer transcriptional and drug sensitivity spaces. Citation Format: Huwate Yeerna, William Kim, William C. Hahn, Jill Mesirov, Pablo Tamayo. Pan-cancer mutual vulnerability and viability [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 1416.
Hydraulic permeability of (un)bounded fibrous media using the lattice Boltzmann method (2000)

Several articles have been written regarding the hydraulic permeability of ordered and disordered fibrous media. Here, we explore wall effects on hydraulic permeabilities for ordered and disordered media using the lattice Boltzmann (LB) simulation method. Simulation results are found to be in excellent agreement with the semi analytic result of Sangani and Acrivos, and simulation results for disordered media are in good agreement with the results of Jackson and James and Higdon and Ford's fcc lattice. The macroscopic behavior, the hydraulic permeability, shows a distinct connection with the geometry of the system. This connection is explored and elucidated for ordered and disordered media. Finally, hydraulic permeabilities for bounded media at various wall separations are presented for both ordered and disordered media and results are compared with hydraulic permeabilities calculated for the unbounded media, and a phenomenological correlation is presented to facilitate rapid prediction of hydraulic permeabilities for both unbounded and bounded fibrous media.
The Role of NG2 Glial Cells in ALS Pathogenesis (2013)

Abstract : A growing body of evidence suggests that glial cells are critical for the support of normal neuronal function, and in particular astrocyte and oligodendroglial dysfunction may contribute to a number of neurodegenerative diseases, including ALS. One important function of glial cells is to transport nutrients from capillaries to neurons. Much of the nutritional support is in the form of glucose; however our lab and others have provided strong evidence that lactate support from oligodendrocytes via monocarboxylate transporters (MCTs) is a major contributor to neuronal metabolism and survival in vivo. Preliminary data from our laboratory indicates that genetic knockdown or pharmacological inhibition of glial specific monocarboxylate transporter 1 (MCT1) leads to loss of spinal cord motor neurons in vitro and in vivo. In addition, our lab and others recently showed in SOD1 mutant mice NG2+ cells, the progenitor cells for oligodendrocytes, upregulate NG2 and show enhanced proliferation in the ventral horn gray matter where motor neurons die. In addition, NG2+ cells formed large numbers of newly generated immature, non-myelinating oligodendroglia, but no astrocytes or neurons. Finally, when we specifically protected oligodendrocyte injury in the SOD1 animal model by deleting mutant SOD1 in NG2+ cells, we were able to delay disease onset by 126 days- many months longer than any other genetic ablation approach to date. We hypothesize that NG2 glial cells play a significant role in ALS pathogenesis. In particular, we are testing how human NG2 glial cells derived from ALS patient iPS cells will impact human motor neurons, also derived from human iPS cells.
Strong, Tough Glass‐Ceramics for Emerging Markets (2016)

The discovery of glass‐ceramics, that is, the controlled crystallization of glass, by S. Donald Stookey was a mixture of serendipitous events involving both chance and exploratory research related to a practical concept. However, a combination of awareness of related literature, good observation skills, deductive reasoning, and a strong curiosity for exploratory work, was crucial for this chance event to bear fruit. As was the present case, a review of this story always stimulates new approaches for understanding of the fundamentals of crystallization and the design of glass‐ceramics with improved properties. Two experiments of particular interest are presented in this paper. The first focuses on the change of viscosity of a specimen as a function of crystallization, while the second addresses the improvement of crack resistance by manipulating thermal history during crystallization. Our work reveals that glass‐ceramic viscosity, that is, bulk viscosity during crystallization, is influenced by both temperature and phase assemblage. Further, as observed by Stookey, more than 60 years ago, high viscosity is important in controlling the shape of the final product. Finally, thermal history is shown to have a marked influence on the crack resistance of glass‐ceramics.
Fast Radix-32 Approximate DFTs for 1024-Beam Digital RF Beamforming (2020)

The discrete Fourier transform (DFT) is widely employed for multi-beam digital beamforming. The DFT can be efficiently implemented through the use of fast Fourier transform (FFT) algorithms, thus reducing chip area, power consumption, processing time, and consumption of other hardware resources. This paper proposes three new hybrid DFT 1024-point DFT approximations and their respective fast algorithms. These approximate DFT (ADFT) algorithms have significantly reduced circuit complexity and power consumption compared to traditional FFT approaches while trading off a subtle loss in computational precision which is acceptable for digital beamforming applications in RF antenna implementations. ADFT algorithms have not been introduced for beamforming beyond N = 32, but this paper anticipates the need for massively large adaptive arrays for future 5G and 6G systems. Digital CMOS circuit designs for the ADFTs show the resulting improvements in both circuit complexity and power consumption metrics. Simulation results show similar or lower critical path delay with up to 48.5% lower chip area compared to a standard Cooley-Tukey FFT. The time-area and dynamic power metrics are reduced up to 66.0%. The 1024-point ADFT beamformers produce signal-to-noise ratio (SNR) gains between 29.2-30.1 dB, which is a loss of ≤ 0.9 dB SNR gain compared to exact 1024-point DFT beamformers (worst case) realizable at using an FFT.
Faculty Opinions recommendation of Mapping cortical integration of sensory and affective pain pathways. (2020)

Pain is an integrated sensory and affective experience. Cortical mechanisms of sensory and affective integration, however, remain poorly defined. Here, we investigate the projection from the primary somatosensory cortex (S1), which encodes the sensory pain information, to the anterior cingulate cortex (ACC), a key area for processing pain affect, in freely behaving rats. By using a combination of optogenetics, in vivo electrophysiology, and machine learning analysis, we find that a subset of neurons in the ACC receives S1 inputs, and activation of the S1 axon terminals increases the response to noxious stimuli in ACC neurons. Chronic pain enhances this cortico-cortical connection, as manifested by an increased number of ACC neurons that respond to S1 inputs and the magnified contribution of these neurons to the nociceptive response in the ACC. Furthermore, modulation of this S1→ACC projection regulates aversive responses to pain. Our results thus define a cortical circuit that plays a potentially important role in integrating sensory and affective pain signals.Copyright © 2020 Elsevier Inc. All rights reserved. PMID: 32220320 Funding information This work was supported by: NINDS NIH HHS, United States Grant ID: R01 NS100065 NIGMS NIH HHS, United States Grant ID: R01 GM115384
Prototype e-cigarette and the capillary aerosol generator (CAG) comparison and qualification for use in subchronic inhalation exposure testing (2016)

Our objective was to evaluate the suitability of using a capillary aerosol generator (CAG) instead of using e-cigarette devices in 90-day or longer inhalation studies. Aerosol characteristics for both the CAG (which uses heat to produce a condensation aerosol) and e-cigarette generators have been previously reported, but a side-by-side comparison with the identical formulation has not been reported. Aerosols from both devices were analyzed immediately after generation for chemicals in the formulation (propylene glycol [PG], glycerin, water, and nicotine), selected carbonyls (acetaldehyde, acrolein, and formaldehyde) by ultra-performance liquid chromatography with ultraviolet detection (UPLC-UV), and a chemical fingerprint analysis using gas chromatography-mass spectroscopy (GC-MS). Aerosol capture methods for chemical analysis included Cambridge filter pads or two impingers in series each containing solution to trap and stabilize selected carbonyl compounds. Particle size distribution (cascade impactor) and exposure port uniformity (gravimetric) was measured in four rodent inhalation exposure chambers under inhalation study conditions. The aerosol of both generators contained the same known and unknown chemicals. Similar levels of compounds in the formula except for PG were detected in the aerosol of both generators. CAG produced more consistent particulate aerosol than e-cigarette generator and had lower levels of carbonyls primarily due to lower levels of formaldehyde. Exposure port concentrations were consistent and closer to target values with the CAG compared to the e-cigarette aerosol generator. CAG was easier to operate on a daily basis although more difficult to maintain because it required daily cleaning compared to single-use e-cigarettes. CAG was determined to be suitable for use in 90-day or longer inhalation studies.Copyright © 2016 American Association for Aerosol Research
Clinical Evaluation of Burn Injuries Using an Optical Reflectance Technique (1987)

In a multiyear clinical study, the authors tested the reliability of an optical technique for diagnosing tissue damage on burn wounds. Optical reflectivity was measured using a convenient, bedside, noninvasive instrument (the Burn Depth Indicator), which was designed and built by one of the authors. The results show that this optical technique is more accurate than conventional methods for predicting the healing time of burn wounds which are otherwise difficult to assess. The optical properties of burn wounds were modeled using a three layer Kubelka-Munk model. We found that eschar thickness and the volume fraction and oxygen saturation of blood in the dermis determine the optical properties of the burn. These factors, in turn, are known to correlate with the burn depth and healing potential.
Control of modular multilevel converters based on time-scale analysis and orthogonal functions (2014)

Modular multilevel converter (MMC) is a promising multilevel topology for high-voltage applications that has been developed in recent years. The control of MMCs has been analyzed in detail in many papers, showing that the converter capacitors can be kept charged and balanced by controlling the circulating current of each leg. The set-point signal of the circulating current is probably the most difficult variable to choose. Typically, it is chosen in such a way to control the total energy and the energy unbalance of each leg. Although several theories are available, the control of the circulating current is still a complex task and cannot be fully tackled with traditional linear control techniques. In this paper a multiple time-scale analysis is proposed to determine an approximated model of the MMC that can be used to solve the control problem of the capacitor voltages. In addition, it is shown that the reference signal of the circulating current can be built by combining orthogonal functions of the measured voltages and currents. Numerical simulations are used to test the feasibility of the developed approach.
Effect of organic moieties on the scintillation properties of organic–inorganic layered perovskite-type compounds (2016)

Abstract The effects of organic moieties on the scintillation properties of organic–inorganic layered perovskite-type compounds have been investigated. Three kinds of single crystals were fabricated, namely, (C 4 H 9 NH 3 ) 2 PbBr 4 (C4), (C 6 H 5 CH 2 NH 3 ) 2 PbBr 4 (Ben), and (C 6 H 5 C 2 H 4 NH 3 ) 2 PbBr 4 (Phe). Among the single crystals, the light output of Phe was found to have the greatest value when exposed to X-ray radiation (67.4 keV). The light output of Phe was 0.62 times that of YAP:Ce. The relative values of the light outputs among the fabricated single crystals under X-ray radiation correlated well with those of the quantum efficiencies and the luminescence intensity under ultraviolet radiation.
Photochemical control of helical pitch of glass-forming dimeric cholesteric liquid crystals by isomerization of embedded di-mesogenic compounds with both cholesterol and azobenzene groups (2002)

We synthesized di-mesogenic liquid crystals with both cholesterol and azobenzene groups by esterification of 10,12-docosadiynedioic acid or docosanedioic acid with 4-alkyl-4'f-hydroxyazobenzene (or 4-hydroxyazobenzene) and cholesterol. Two compounds without an alkyl chain on the azobenzene unit show cholesteric and smectic phases, while five compounds with an alkyl chain from butyl to hexadecyl show only a smectic phase. When the compounds were doped in 2-10 w% to a dicholesteryl ester forming stable cholesteric glass, the mixture became photo-responsive. Upon irradiation at 366 nm, the cholesteric band of the mixtures shifted toward shorter wavelength caused by the photo-isomerization from trans to cis of the azobenzene unit on the dopant. The extent of the shift depends on irradiation energy, temperature and the length of the alkyl chain on the azobenzene unit. When a thin film of the dicholesteryl compounds containing 5w% of the dopant having a heptyl substituent on the azobenzene unit was irradiated at 90&deg;C, the reflection band shifted from 730 nm (infrared) to 490 nm (blue). The mixture went into the glassy state keeping the shifted cholesteric reflection band after rapid cooling from the liquid crystalline temperature to 0&deg;C. The cholesteric glassy state was stable up to 80&deg;C. Since the molecular arrangement of the dicholesteryl compound and the conformation of the doped azobenzene derivatives completely returned to the initial state upon reheating to isotropic temperature, the photo-responsibility and glass-forming property of the mixture is applicable to full-color rewritable recording materials.
A feasibility and safety study of vaccination with Poly-ICLC and peptide-pulsed dendritic cells in patients with advanced pancreatic adenocarcinoma. (2016)

e14579 Background: Dendritic cells (DCs) shape the quantity and quality of anti-tumor immunity in patients with cancer. We hypothesized that DC-based immunotherapy, in conjunction with a novel long-lasting TLR3 agonist, Poly-ICLC, is a promising approach against metastatic or locally advanced unrespectable pancreatic cancer (PC). Methods: To address our clinical concept, we generated autologous DCs from peripheral blood monocytes from HLA-A2+ patients with pancreatic cancer (PC) and pulsed DCs with three immunogenic A2-restricted epitopes: human telomerase reverse transcriptase (hTERT, TERT572Y), carcinoembryonic antigen (CEA; Cap1-6D) and survivin (SRV.A2). Patients received four intradermal injections of 1 x 107peptide-pulsed DC vaccines every 2 weeks (Day 0, 14, 28 and 42). Concurrently, patients received intramuscular administration of Poly-ICLC at 30 µg/Kg on vaccination days (Day 0, 14, 28, and 42), as well as on Days 3, 17, 21, 31, 37 and 45). Our primary objective was to assess safety and feasibility. The effect of DC vaccination on immune response was measured at each DC injection time point by enumerating the phenotype and function of patient T cells. Results: A total of 12 patients underwent leukapheresis: 9 patients with metastatic disease, and 3 with locally advanced unresectable PC. Manufacturing of vaccines was uniformly successful. Study treatment was well tolerated, with the most common symptoms being fatigue and/or self-limiting flu-like symptoms. Among the 8 patients who underwent imaging on Day 56, 4 had stable disease and 4 had disease progression. Overall, the median survival was 7.7 months from date of leukapheresis. One patient has survived for 28 months. IFN-gamma ELISPOT and MHC class I – tetramer analysis, before and after vaccination, revealed effective generation of antigen-specific T cells in 3 patients with stable disease. Conclusions: Vaccination with Poly-ICLC and peptide-pulsed dendritic cells is safe and induces a measurable tumor specific T cell population in patients with advanced PC. Clinical trial information: NCT01410968.
Assessing Finite-Control-Set Model Predictive Control: A Comparison with a Linear Current Controller in Two-Level Voltage Source Inverters (2014)

Model predictive control (MPC) methods for applications in power converters have received considerable attention in recent years. The idea behind MPC is to use a mathematical model of the system to predict its future behavior within a predefined time. An optimization problem that includes the control objectives, the predicted variables, and possible constraints of the system is solved, yielding the control actions to be applied.
Pore size distributions in nanoporous methyl silsesquioxane films as determined by small angle x-ray scattering (2002)

Small angle x-ray scattering (SAXS) measurements were performed on nanoporous methyl silsesquioxane films that were generated by the incorporation of a sacrificial polymeric component into the matrix and subsequently removed by thermolysis. The average pore radii ranged from 1 to 5 nm over a porosity range of ∼5–50%. The distribution in pore size was relatively broad and increases in breadth with porosity. The values and observations obtained by SAXS are in good agreement with field emission scanning electron microscopy.
DynaMaR: Dynamic Prompt with Mask Token Representation (2022)

Xiaodi Sun, Sunny Rajagopalan, Priyanka Nigam, Weiyi Lu, Yi Xu, Iman Keivanloo, Belinda Zeng, Trishul Chilimbi. Proceedings of the 2022 Conference on Empirical Methods in Natural Language Processing: Industry Track. 2022.
Effects of process plasma on nitrogen-vacancy density in ultra-high purity diamond (2011)

We report on optical measurements which assess the impact of processing plasmas on the density of Nitrogen-Vacancy centres in ultra-high purity diamond. In particular we look at the depletion of NV- before and after exposure to a hydrogen plasma using confocal microscopy.
Conjugation Dependent Interaction of Folic Acid with Folate Binding Protein (2017)

Serum proteins play a critical role in the transport, uptake, and efficacy of targeted drug therapies, and here we investigate the interactions between folic acid-polymer conjugates and serum folate binding protein (FBP), the soluble form of the cellular membrane-bound folate receptor. We demonstrate that both choice of polymer and method of ligand conjugation affect the interactions between folic acid-polymer conjugates and serum FBP, resulting in changes in the folic acid-induced protein aggregation process. We have previously demonstrated that individual FBP molecules self-aggregate into nanoparticles at physiological concentrations. When poly(amidoamine) dendrimer-folic acid conjugates bound to FBP, the distribution of nanoparticles was preserved. However, the dendritic conjugates produced larger nanoparticles than those formed in the presence of physiologically normal human levels of folic acid, and the conjugation method affected particle size distribution. In contrast, poly(ethylene glycol)-folic acid conjugates demonstrated substantially reduced binding to FBP, did not cause folic acid-induced aggregation, and fully disrupted FBP self-aggregation. On the basis of these results, we discuss the potential implications for biodistribution, trafficking, and therapeutic efficacy of targeted nanoscale therapeutics, especially considering the widespread clinical use of poly(ethylene glycol) conjugates. We highlight the importance of considering specific serum protein interactions in the rational design of similar nanocarrier systems. Our results suggest that prebinding therapeutic nanocarriers to serum FBP may allow folate-specific metabolic pathways to be exploited for delivery while also affording benefits of utilizing an endogenous protein as a vector.
Deep Learning Coordinated Beamforming for Highly-Mobile Millimeter Wave\n Systems (2018)

Supporting high mobility in millimeter wave (mmWave) systems enables a wide\nrange of important applications such as vehicular communications and wireless\nvirtual/augmented reality. Realizing this in practice, though, requires\novercoming several challenges. First, the use of narrow beams and the\nsensitivity of mmWave signals to blockage greatly impact the coverage and\nreliability of highly-mobile links. Second, highly-mobile users in dense mmWave\ndeployments need to frequently hand-off between base stations (BSs), which is\nassociated with critical control and latency overhead. Further, identifying the\noptimal beamforming vectors in large antenna array mmWave systems requires\nconsiderable training overhead, which significantly affects the efficiency of\nthese mobile systems. In this paper, a novel integrated machine learning and\ncoordinated beamforming solution is developed to overcome these challenges and\nenable highly-mobile mmWave applications. In the proposed solution, a number of\ndistributed yet coordinating BSs simultaneously serve a mobile user. This user\nideally needs to transmit only one uplink training pilot sequence that will be\njointly received at the coordinating BSs using omni or quasi-omni beam\npatterns. These received signals draw a defining signature not only for the\nuser location, but also for its interaction with the surrounding environment.\nThe developed solution then leverages a deep learning model that learns how to\nuse these signatures to predict the beamforming vectors at the BSs. This\nrenders a comprehensive solution that supports highly-mobile mmWave\napplications with reliable coverage, low latency, and negligible training\noverhead. Simulation results show that the proposed deep-learning coordinated\nbeamforming strategy approaches the achievable rate of the genie-aided solution\nthat knows the optimal beamforming vectors with no training overhead.\n