gebhart/patrepeval huggingface dataset:
On Optimal Beam Steering Directions in Millimeter Wave Systems (2019)

In order to increase system capacity and transmission rates, fifth-generation (5G) cellular and 802.11ad/ay wireless systems will use millimeter wave frequencies (24GHz-70GHz), which require large antenna arrays and narrow beamforming to mitigate the impact of substantial path-loss. While narrow beamforming maximizes array gain it also entails a significant increase in the number of beams needed to maintain the desired cell coverage. Consequently, there is a considerable increase in the complexity of beam management for initial user access and then tracking. This paper proposes a novel beam steering algorithm to maximize coverage given a prescribed size for the codebook of beam directions. The proposed approach leverages the observation that the problem of finding the optimal set of beam pointing angles can be mapped to the classical quantizer design problem in source coding, albeit with a somewhat unusual distortion measure. A variant of the Generalized Lloyd Algorithm is derived and employed to find the optimal codebook of beam placement angular directions. Numerical results show up to 2 dB gains in average power array factor, in comparison with the conventional uniformly spaced beam steering approach. These performance gains can be traded for codebook size reduction and a corresponding reduction in beam management complexity.
Stimulation and suppression of the oxygenation activity of porcine pulmonary alveolar macrophages by Actinobacillus pleuropneumoniae and its metabolites (1992)

The effects of Actinobacillus (Haemophilus) pleuropneumoniae and its metabolites on the oxygenation activity of porcine pulmonary alveolar macrophages (PAM) were studied, using a chemiluminescence technique. Actinobacillus pleuropneumoniae strains of serotypes 2, 3, and 9 in a dose of 1, 10, and 100 colony-forming units/macrophage first stimulated the oxygen radical production of PAM. After having reached a peak value, oxygenation activity decreased, finally resulting in total suppression of PAM. All these effects were neutralized by homologous convalescent pig sera that had been adsorbed onto inactivated A pleuropneumoniae strains. Moreover, cross-neutralization was shown between serotypes 2 and 3. Inactivated A pleuropneumoniae strains did not influence the oxidative activity of PAM. Undiluted and lower dilutions of sterile A pleuropneumoniae culture supernatants were toxic for PAM, whereas higher dilutions of the supernatants stimulated oxygen radical production of the macrophages. These effects were heat-sensitive and were neutralized by homologous convalescent pig sera. Cross-neutralization was shown between serotypes 2 and 3. These findings indicated that stimulation and inhibition of the oxygenation activity of PAM are attributable to heat-sensitive metabolites produced by A pleuropneumoniae.
The Relationship between T Cell Proliferative Responses and Plasma Viremia during Treatment of Human Immunodeficiency Virus Type 1 Infection with Combination Antiretroviral Therapy (2000)

The relationship between human immunodeficiency virus (HIV) type 1 replication and CD4+ T cell function was examined. T lymphocyte proliferation in response to both HIV-1 antigens and recall antigens was measured in HIV-1-infected individuals before and after they received highly active antiretroviral therapy (HAART). No correlation was observed between baseline viral load or CD4+ T cell count and the T cell proliferative response to HIV-1 Gag. Suppression of viremia was not associated with an increase in T cell proliferative responses. Emergence of viral replication during short periods of intermittent therapy promoted generalized activation of T helper lymphocytes, manifested by increased T cell proliferative responses to HIV-1 Gag and recall antigens. Recovery of CD4+ T cell responses occurred in some individuals who initiated HAART years after infection and who were intermittently adherent to drug treatment. Thus, CD4+ T cell responses can sometimes be regenerated if viral load is suppressed to allow some immune recovery and if antigenic stimulation is later provided.
Affinity Selection of DNA-Binding Proteins Displayed on Bacteriophage (2000)

Two transcription factors, human ATF1, its DNA-binding domain (ATF1BD), and the DNA-binding domain (GAL4BD) of the yeast GAL4 protein, were displayed on the surface of bacteriophage lambda vectors and efficiently selected by DNA fragments immobilized in microtiter wells. The DNA-binding proteins are fused to the carboxy terminus of the tail protein gpV and head protein gpD of the vectors, lambdafoo and lambdafooDc, respectively. After a single round of affinity selection, the fusion phages were successfully enriched 60- to 4,000-fold over the vector phages. Further, the GAL4BD fusion phages were enriched 5- and 15-fold by affinity selection using specific DNA as probes over nonspecific DNA when expressed on lambdafooDc and lambdafoo, respectively. The ATF1BD fusion phages were also sequence-specifically enriched greater than 4-fold when displayed on lambdafoo. These results suggest that the lambdafoo display system is useful for in vitro studying of protein-DNA interactions and may be applied to screening of DNA-binding protein from complex cDNA libraries through DNA-binding affinity.
Production and specificity of monoclonal antibodies against calmodulin from dictyostelium discoideum (1991)

Monoclonal antibodies were raised against calmodulin purified from Dictyostelium discoideum. To increase its antigenicity, the calmodulin was conjugated to keyhole limpet hemocyanin; mice were immunized with the conjugate. Hybridomas producing antibodies against calmodulin were identified by screening culture supernatants with calmodulin coupled to bovine serum albumin. The specificity of antibodies from hybridoma culture supernatants was tested by Western blot of Dictyostelium cell lysates. For the purpose, methods were developed that permitted sensitive detection of calmodulin bound to membranes. The key elements of the blotting protocol were used of PVDF membrane, transfer conducted in phosphate buffer, and glutaraldehyde fixation after transfer. These methods permitted detection of as little as 0.1 ng of calmodulin spotted directly onto the membrane, or 10 ng transferred from an SDS polyacrylamide gel. Ten calmodulin-specific antibodies were identified; most of these reacted preferentially with the calcium-containing form of Dictyostelium calmodulin. Several of the monoclonal antibodies cross-reacted with calmodulin from bovine brain.
Optimizing Reservoir Performance through Utilization of Autonomous Inflow Control Valve – Lessons Learnt from the World’s First Installation (2016)

Abstract One of the major challenges in mature oil fields is to improve recovery from existing fields by developing and implementing new technologies that make operations efficient and cost effective. For a reservoir with a water or gas drive mechanism, the mobility ratio between oil and water or gas becomes more critical due to the lower viscosity of water or gas. Observably, breakthroughs can occur within relatively short periods of production time. Once breakthrough occurs, gas or water production can rapidly dominate production prompting well intervention or the shutting-in of production, leaving unrecovered oil behind. Inflow control device (ICD) and autonomous inflow control device (AICD) have shown oil production and recovery can be increased significantly with better inflow control/pressure regulation along the lateral, which to some degree has resulted in breakthrough delays. However, neither ICD nor AICD are able to shut off unwanted gas and water production completely. The autonomous inflow control valve (ICV) offers the functionality of conventional ICD and can actively shut off unwanted fluid completely. The paper describes the development of Autonomous ICV, experimental test results, and preparations prior to the completion installation. The main challenges and conclusion from the field tests are presented and discussed based on the initial flowback data where the functionality of Autonomous ICV was verified, i.e., by shut-off of low viscosity fluid, such as water, and opening for oil with higher viscosity.
Experimental observation of the effect of laser standing wave pattern on the Catastrophic Optical Mirror Damage threshold for high-power single mode laser diodes. (2008)

Increases in the catastrophic optical mirror damage (COMD) threshold in high power coated semiconductor laser diodes have been theoretically attributed to reducing the optical intensity at the semiconductor/dielectric coating interface. Traditionally, this work has focused on the anti- reflection (AR) facet as this is assumed to have to withstand the highest optical intensity.We have carried out a study of the effect of the optical standing wave intensity at the semiconductor/dielectric interface on COMD at the HR facet. This has been done by means of an elegant experiment in which lasers were made with HR dielectric coatings on both facets. This type of laser has a very high optical intensity trapped in the optical cavity, and hence a high optical stress can be created in the facet regions.
Pharmacological actions of a novel NO‐independent guanylyl cyclase stimulator, BAY 41‐8543: in vitro studies (2002)

BAY 41-8543 is a novel, highly specific and so far the most potent NO-independent stimulator of sGC. Here we report the effects of BAY 41-8543 on the isolated enzyme, endothelial cells, platelets, isolated vessels and Langendorff heart preparation. BAY 41-8543 stimulates the recombinant sGC concentration-dependently from 0.0001 microM to 100 microM up to 92-fold. In combination, BAY 41-8543 and NO have synergistic effects over a wide range of concentrations. Similar results are shown in implying that BAY 41-8543 stimulates the sGC directly and furthermore makes the enzyme more sensitive to its endogenous activator NO. In vitro, BAY 41-8543 is a potent relaxing agent of aortas, saphenous arteries, coronary arteries and veins with IC(50)-values in the nM range. In the rat heart Langendorff preparation, BAY 41-8543 potently reduces coronary perfusion pressure from 10(-9) to 10(-6) g ml(-1) without any effect on left ventricular pressure and heart rate. BAY 41-8543 is effective even under nitrate tolerance conditions proved by the same vasorelaxing effect on aortic rings taken either from normal or nitrate-tolerant rats. BAY 41-8543 is a potent inhibitor of collagen-mediated aggregation in washed human platelets (IC(50)=0.09 microM). In plasma, BAY 41-8543 inhibits collagen-mediated aggregation better than ADP-induced aggregation, but has no effect on the thrombin pathway. BAY 41-8543 is also a potent direct stimulator of the cyclic GMP/PKG/VASP pathway in platelets and synergizes with NO over a wide range of concentrations. These results suggest that BAY 41-8543 is on the one hand an invaluable tool for studying sGC signaling in vitro and on the other hand its unique profile may offer a novel approach for treating cardiovascular diseases.
Rhodococcus fascians Impacts Plant Development Through the Dynamic Fas-Mediated Production of a Cytokinin Mix (2010)

The phytopathogenic actinomycete Rhodococcus fascians D188 relies mainly on the linear plasmid-encoded fas operon for its virulence. The bacteria secrete six cytokinin bases that synergistically redirect the developmental program of the plant to stimulate proliferation of young shoot tissue, thus establishing a leafy gall as a niche. A yeast-based cytokinin bioassay combined with cytokinin profiling of bacterial mutants revealed that the fas operon is essential for the enhanced production of isopentenyladenine, trans-zeatin, cis-zeatin, and the 2-methylthio derivatives of the zeatins. Cytokinin metabolite data and the demonstration of the enzymatic activities of FasD (isopentenyltransferase), FasE (cytokinin oxidase/dehydrogenase), and FasF (phosphoribohydrolase) led us to propose a pathway for the production of the cytokinin spectrum. Further evaluation of the pathogenicity of different fas mutants and of fas gene expression and cytokinin signal transduction upon infection implied that the secretion of the cytokinin mix is a highly dynamic process, with the consecutive production of a tom initiation wave followed by a maintenance flow.
Summ^N: A Multi-Stage Summarization Framework for Long Input Dialogues and Documents (2021)

Text summarization helps readers capture salient information from documents, news, interviews, and meetings. However, most state-of-the-art pretrained language models (LM) are unable to efficiently process long text for many summarization tasks. In this paper, we propose Summ$^N$, a simple, flexible, and effective multi-stage framework for input texts that are longer than the maximum context length of typical pretrained LMs. Summ$^N$ first splits the data samples and generates a coarse summary in multiple stages and then produces the final fine-grained summary based on it. Our framework can process input text of arbitrary length by adjusting the number of stages while keeping the LM input size fixed. Moreover, it can deal with both single-source documents and dialogues, and it can be used on top of different backbone abstractive summarization models. To the best of our knowledge, Summ$^N$ is the first multi-stage split-then-summarize framework for long input summarization. Our experiments demonstrate that Summ$^N$ outperforms previous state-of-the-art methods by improving ROUGE scores on three long meeting summarization datasets AMI, ICSI, and QMSum, two long TV series datasets from SummScreen, and a long document summarization dataset GovReport. Our data and code are available at https://github.com/psunlpgroup/Summ-N.
Structure and magnetic properties of L10 FePt film with Ag heat sink layer (2009)

In this work, the L10 FePt films with a Ag heat sink layer for the application of heating assisted magnetic recording (HAMR) were developed. It was found that the crystalline orientation of the FePt layer depended on the texture of the fcc Ag layer, which was strongly affected by the deposition conditions. The (200) textured Ag layer can induce the L10 FePt (001) texture films due to epitaxial growth with the epitaxial growth relationship of FePt (001) [100]//Ag (001) [100]//CrRu (002) [110] and thus can act as the heat sink layer for HAMR application,. The magnetic properties of the L10 FePt films were maintained with the thickness of the Ag heat sink layer from 30 to 100 nm.
A Hybrid Computational and Analytical Model of Irrigation Drip emitters (2017)

Thesis: S.M., Massachusetts Institute of Technology, Department of Mechanical Engineering, 2017.
GLoMo: Unsupervised Learning of Transferable Relational Graphs (2018)

Modern deep transfer learning approaches have mainly focused on learning generic feature vectors from one task that are transferable to other tasks, such as word embeddings in language and pretrained convolutional features in vision. However, these approaches usually transfer unary features and largely ignore more structured graphical representations. This work explores the possibility of learning generic latent relational graphs that capture dependencies between pairs of data units (e.g., words or pixels) from large-scale unlabeled data and transferring the graphs to downstream tasks. Our proposed transfer learning framework improves performance on various tasks including question answering, natural language inference, sentiment analysis, and image classification. We also show that the learned graphs are generic enough to be transferred to different embeddings on which the graphs have not been trained (including GloVe embeddings, ELMo embeddings, and task-specific RNN hidden units), or embedding-free units such as image pixels.
Surface Structure and Chemical Composition of Nanostructured Vanadium Nitride Supercapacitors: An XPS Study (2010)

Abstract not Available.
Is Paradoxical Pain Induced by Sustained Opioid Exposure an Underlying Mechanism of Opioid Antinociceptive Tolerance? (2005)

Opiates are the primary treatment for pain management in cancer patients reporting moderate to severe pain, and are being increasingly used for non-cancer chronic pain. However, prolonged administration of opiates is associated with significant problems including the development of antinociceptive tolerance, wherein higher doses of the drug are required over time to elicit the same amount of analgesia. High doses of opiates result in serious side effects such as constipation, nausea, vomiting, dizziness, somnolence, and impairment of mental alertness. In addition, sustained exposure to morphine has been shown to result in paradoxical pain in regions unaffected by the initial pain complaint, and which may also result in dose escalation, i.e. 'analgesic tolerance'. A concept that has been gaining considerable experimental validation is that prolonged use of opioids elicits paradoxical, abnormal pain. This enhanced pain state requires additional opioids to maintain a constant level of antinociception, and consequently may be interpreted as antinociceptive tolerance. Many substances have been shown to block or reverse antinociceptive tolerance. A non-inclusive list of examples of substances reported to block or reverse opioid antinociceptive tolerance include: substance P receptor (NK-1) antagonists, calcitonin gene-related peptide (CGRP) receptor antagonists, nitric oxide (NO) synthase inhibitors, calcium channel blockers, cyclooxygenase (COX) inhibitors, protein kinase C inhibitors, competitive and non-competitive antagonists of the NMDA (N-methyl-D-aspartate) receptor, AMPA (alpha-amino-3-hydroxy-5-methyl-4 isoxazolepropionic acid) antagonists, anti-dynorphin antiserum, and cholecystokinin (CCK) receptor antagonists. Without exception, these substances are also antagonists of pain-enhancing agents. Prolonged opiate administration indeed induces upregulation of substance P (SP) and calcitonin gene-related peptide (CGRP) within sensory fibers in vivo, and this is accompanied by an enhanced release of excitatory neurotransmitters and neuropeptides from primary afferent fibers upon stimulation. The enhanced evoked release of neuropeptides is correlated with the onset of abnormal pain states and opioid antinociceptive tolerance. Importantly, the descending pain modulatory pathway from the brainstem rostral ventromedial medulla (RVM) via the dorsolateral funiculus (DLF) is critical for maintaining the changes observed in the spinal cord, abnormal pain states and antinociceptive tolerance, because animals with lesion of the DLF did not show enhanced evoked neuropeptide release, or develop abnormal pain or antinociceptive tolerance upon sustained exposure to opiates. Microinjection of either lidocaine or a CCK antagonist into the RVM blocked both thermal and touch hypersensitivity as well as antinociceptive tolerance. Thus, prolonged opioid exposure enhances a descending pain facilitatory pathway from the RVM that is mediated at least in part by CCK activity and is essential for the maintenance of antinociceptive tolerance.
Transcriptomic architecture of nuclei in the marmoset CNS (2022)

To understand the cellular composition and region-specific specialization of white matter - a disease-relevant, glia-rich tissue highly expanded in primates relative to rodents - we profiled transcriptomes of ~500,000 nuclei from 19 tissue types of the central nervous system of healthy common marmoset and mapped 87 subclusters spatially onto a 3D MRI atlas. We performed cross-species comparison, explored regulatory pathways, modeled regional intercellular communication, and surveyed cellular determinants of neurological disorders. Here, we analyze this resource and find strong spatial segregation of microglia, oligodendrocyte progenitor cells, and astrocytes. White matter glia are diverse, enriched with genes involved in stimulus-response and biomolecule modification, and predicted to interact with other resident cells more extensively than their gray matter counterparts. Conversely, gray matter glia preserve the expression of neural tube patterning genes into adulthood and share six transcription factors that restrict transcriptome complexity. A companion Callithrix jacchus Primate Cell Atlas (CjPCA) is available through https://cjpca.ninds.nih.gov .
Internal charge-phosphor field characteristics of alternating-current thin-film electroluminescent devices (1993)

The internal charge versus phosphor field (Q–Fp) technique is proposed as a method for characterization of the electrical properties of alternating-current thin-film electroluminescent (ACTFEL) devices. Q–Fp analysis provides direct information about the internal behavior of the ACTFEL device. The steady-state field and internal conduction, polarization, leakage, and relaxation charges may be readily deduced from a Q–Fp plot.
The beneficial role of functional food components in mitigating ultraviolet‐induced skin damage (2019)

Excessive exposure to ultraviolet (UV) radiation can chemically alter biological molecules and is one of the major environmental health risks with potential to damage the structure and function of the skin. Numerous dietary supplements are known to optimize the skin's defenses against radiation exposure. Several studies in which the beneficial roles of functional food components, that can protect against UV-induced skin damage, have been demonstrated. Supplemental dietary sphingomyelin maintains covalently bound ω-hydroxy ceramides to avert skin barrier defects after UVB irradiation. The oral administration of collagen hydrolysates has been shown to limit decreases in skin elasticity via increases in the dermal hyaluronic acid content. Milk fermented with lactic acid bacteria has been shown to augment DNA repair mechanisms and improve skin immunity in the aftermath of UVB damage. Furthermore, long-term ingestion of fermented milk containing lactic acid bacteria, collagen hydrolysates and sphingomyelin increases the minimal erythema dose (MED) in human subjects with moderate sunburn or redness and tanned skin after exposure to UV solar radiation. Thus, products containing these functional food components are one means by which the adverse effects of UV radiation on the skin can be mitigated.
Deep learning-based prediction of response to HER2-targeted neoadjuvant chemotherapy from pre-treatment dynamic breast MRI: A multi-institutional validation study. (2020)

peer reviewed
PrPSc-specific antibodies do not induce prion disease or misfolding of PrPCin highly susceptible Tga20 mice (2013)

Transmissible spongiform encephalopathies (TSEs) are fatal neurodegenerative disorders caused by misfolding of a cellular protein PrP(C) into an infectious conformation PrP(Sc). Previously our group demonstrated induction of PrP(Sc)-specific antibodies with a SN6b vaccine that targets regions of the protein that are exposed upon misfolding. There are concerns that these antibodies could function as templates to promote misfolding and cause disease. To evaluate the consequences of prolonged exposure to PrP(Sc)-specific antibodies in a prion sensitized animal, tga20 mice were vaccinated with the SN6b vaccine. No clinical signs of disease were detected up to 255 d post-vaccination, and postmortem assay of brains and spleens revealed no proteinase-K resistant PrP. These results suggest that vaccinating against TSEs with the SN6b antigen is safe from the standpoint of prion disease induction.
Coupling a nanomechanical resonator to a Cooper-pair-box qubit (2008)

We demonstrate dispersive coupling between a Cooper-pair box (CPB) qubit and a VHF NEMS (nanoelectromechanical systems) resonator. The observed interaction strength is sufficient to pursue more advanced experiments to elicit quantum behavior in NEMS.