gebhart/patrepeval huggingface dataset:
Extension of replica analysis to MAP estimation with applications to compressed sensing (2010)

The replica method is a non-rigorous but widely-accepted technique from statistical physics used in the asymptotic analysis of large, random, nonlinear problems. This paper applies the replica method to analyze non-Gaussian maximum a posteriori (MAP) estimation. The main result is a counterpart to Guo and Verdú's replica analysis of minimum mean-squared error estimation. The replica MAP analysis can be readily applied to many estimators used in compressed sensing, including basis pursuit, lasso, linear estimation with thresholding, and zero norm-regularized estimation. Among other benefits, the replica method provides a computationally-tractable method for exactly computing various performance metrics including mean-squared error and sparsity pattern recovery probability.
L-plastin enhances NLRP3 inflammasome assembly and bleomycin-induced lung fibrosis (2022)

Macrophage adhesion and stretching have been shown to induce interleukin (IL)-1β production, but the mechanism of this mechanotransduction remains unclear. Here we specify the molecular link between mechanical tension on tissue-resident macrophages and activation of the NLRP3 inflammasome, which governs IL-1β production. NLRP3 activation enhances antimicrobial defense, but excessive NLRP3 activity causes inflammatory tissue damage in conditions such as pulmonary fibrosis and acute respiratory distress syndrome. We find that the actin-bundling protein L-plastin (LPL) significantly enhances NLRP3 assembly. Specifically, LPL enables apoptosis-associated speck-like protein containing a caspase activation and recruitment domain (ASC) oligomerization during NLRP3 assembly by stabilizing ASC interactions with the kinase Pyk2, a component of cell-surface adhesive structures called podosomes. Upon treatment with exogenous NLRP3 activators, lung-resident alveolar macrophages (AMs) lacking LPL exhibit reduced caspase-1 activity, IL-1β cleavage, and gasdermin-D processing. LPL<sup>-/-</sup> mice display resistance to bleomycin-induced lung injury and fibrosis. These findings identify the LPL-Pyk2-ASC pathway as a target for modulation in NLRP3-mediated inflammatory conditions.
A frequency and sensitivity tunable microresonator array for high-speed quantum processor readout (2016)

Superconducting microresonators have been successfully utilized as detection elements for a wide variety of applications. With multiplexing factors exceeding 1000 detectors per transmission line, they are the most scalable low-temperature detector technology demonstrated to date. For high-throughput applications, fewer detectors can be coupled to a single wire but utilize a larger per-detector bandwidth. For all existing designs, fluctuations in fabrication tolerances result in a non-uniform shift in resonance frequency and sensitivity, which ultimately limits the efficiency of bandwidth utilization. Here, we present the design, implementation, and initial characterization of a superconducting microresonator readout integrating two tunable inductances per detector. We demonstrate that these tuning elements provide independent control of both the detector frequency and sensitivity, allowing us to maximize the transmission line bandwidth utilization. Finally, we discuss the integration of these detectors in a multilayer fabrication stack for high-speed readout of the D-Wave quantum processor, highlighting the use of control and routing circuitry composed of single-flux-quantum loops to minimize the number of control wires at the lowest temperature stage.
Supplementary Figure 2 from <i>TMPRSS2:ERG</i> Fusion-Associated Deletions Provide Insight into the Heterogeneity of Prostate Cancer (2023)

Supplementary Figure 2 from &lt;i&gt;TMPRSS2:ERG&lt;/i&gt; Fusion-Associated Deletions Provide Insight into the Heterogeneity of Prostate Cancer
Well Clean-Up Using a Combined Thermochemical/Chelating Agent Fluids (2019)

The well clean-up process involves the removal of impermeable filter cake from the formation face. This process is essential to allow the formation fluids to flow from the reservoir to the wellbore. Different types of drilling fluids such as oil- and water-based drilling fluids are used to drill oil and gas wells. These drilling fluids are weighted with different weighting materials such as bentonite, calcium carbonate, and barite. The filter cake that forms on the formation face consists mainly of the drilling fluid weighting materials (around 90%), and the rest is other additives such as polymers or oil in the case of oil-base drilling fluids. The process of filter cake removal is very complicated because it involves more than one stage due to the compatibility issues of the fluids used to remove the filter cake. Different formulations were used to remove different types of filter cake, but the problem with these methods is the removal efficiency or the compatibility. In this paper, a new method was developed to remove different types of filter cakes and to clean-up oil and gas wells after drilling operations. Thermochemical fluids that consist of two inert salts when mixed together will generate very high pressure and high temperature in addition to hot water and hot nitrogen. These fluids are sodium nitrate and ammonium chloride. The filter cake was formed using barite and calcite water- and oil-based drilling fluids at high pressure and high temperature. The removal process started by injecting 500 ml of the two salts and left for different time periods from 6 to 24 h. The results of this study showed that the newly developed method of thermochemical removed the filter cake after 6 h with a removal efficiency of 89 wt% for the barite filter cake in the water-based drilling fluid. The mechanisms of removal using the combined solution of thermochemical fluid and ethylenediamine tetra-acetic acid (EDTA) chelating agent were explained by the generation of a strong pressure pulse that disturbed the filter cake and the generation of the high temperature that enhanced the barite dissolution and polymer degradation. This solution for filter cake removal works for reservoir temperatures greater than 100 °C.
Synthesis and characterization of metal complexes of nickel, cobalt, and iron having monomeric 15-membered lacunar cyclidene ligands, with a representative crystal structure. Dioxygen binding by the cobalt complexes (1988)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTSynthesis and characterization of metal complexes of nickel, cobalt, and iron having monomeric 15-membered lacunar cyclidene ligands, with a representative crystal structure. Dioxygen binding by the cobalt complexesRudolf Thomas, Carol M. Fendrick, Wang Kan Lin, Mark W. Glogowski, Madhav Y. Chavan, Nathaniel W. Alcock, and Daryle H. BuschCite this: Inorg. Chem. 1988, 27, 14, 2534–2540Publication Date (Print):July 1, 1988Publication History Published online1 May 2002Published inissue 1 July 1988https://pubs.acs.org/doi/10.1021/ic00287a032https://doi.org/10.1021/ic00287a032research-articleACS PublicationsRequest reuse permissionsArticle Views124Altmetric-Citations11LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-AlertscloseSupporting Info (1)»Supporting Information Supporting Information Get e-Alerts
Hardware-software architecture for priority queue management in real-time and embedded systems (2014)

The use of hardware-based data structures for accelerating real-time and embedded system applications is limited by the scarceness of hardware resources. Being limited by the silicon area available, hardware data structures cannot scale in size as easily as their software counterparts. We assert a hardware-software co-design approach is required to elegantly overcome these limitations. In this paper, we present a hybrid priority queue architecture that includes a hardware accelerated binary heap that can also be managed in software when the queue size exceeds hardware limits. A memory mapped interface provides software with access to priority-queue structured on-chip memory, which enables quick and low overhead transitions between hardware and software management. As an application of this hybrid architecture, we present a scalable task scheduler for real-time systems that reduces scheduler processing overhead and improves timing determinism of the scheduler.
Disambiguating visual relations using loop constraints (2010)

Repetitive and ambiguous visual structures in general pose a severe problem in many computer vision applications. Identification of incorrect geometric relations between images solely based on low level features is not always possible, and a more global reasoning approach about the consistency of the estimated relations is required. We propose to utilize the typically observed redundancy in the hypothesized relations for such reasoning, and focus on the graph structure induced by those relations. Chaining the (reversible) transformations over cycles in this graph allows to build suitable statistics for identifying inconsistent loops in the graph. This data provides indirect evidence for conflicting visual relations. Inferring the set of likely false positive geometric relations from these non-local observations is formulated in a Bayesian framework. We demonstrate the utility of the proposed method in several applications, most prominently the computation of structure and motion from images.
SWOG0919: a Phase 2 study of idarubicin and cytarabine in combination with pravastatin for relapsed acute myeloid leukaemia (2014)

Inhibition of cholesterol synthesis and uptake sensitizes acute myeloid leukaemia (AML) blasts to chemotherapy. A Phase 1 study demonstrated the safety of high dose pravastatin given with idarubicin and cytarabine in patients with AML and also demonstrated an encouraging response rate. The Southwestern Oncology Group (SWOG) trial, SWOG S0919, was a Phase 2 trial evaluating the complete remission (CR) rate in a larger number of patients with relapsed AML treated with idarubicin, cytarabine and pravastatin. This study closed to accrual after meeting the defined criterion for a positive study. Thirty-six patients with a median age of 59 years (range 23-78) were enrolled. The median time from diagnosis to registration was 18 months. Relapse status was first relapse, 17 patients (47%); second relapse, 15 patients (42%); third relapse, two patients (5·5%) and fourth relapse, two patients (5·5%). The response rate was 75% [95% confidence interval: 58-88%; 20 CRs, 7 CR with incomplete count recovery (CRi)], and the median overall survival was 12 months. The P-value comparing 75-30% (the null response rate based on prior SWOG experience) was 3·356 × 10(-4) . Given the encouraging CR/CRi rate, this regimen should be considered for testing in a prospective randomized trial against best conventional therapy.
Hydrometeorological analysis of the December 2008 flood in Rome (2011)

Abstract Rome has been plagued by flooding since its foundation, and, in December 2008, the largest flood event over the past 20 years caused a fatality and more than €150 million in economic damage. Meteorological conditions associated with the December 2008 flooding are shown to be typical of flooding in the Tiber. The long record of discharge measurements of the Tiber River at the Ripetta station in downtown Rome was used to examine flood frequency for the Tiber, including assessment of the return interval of the December 2008 flood. Particular attention is given to examination of the stationarity assumption for flood peaks through change-point and trend analyses, quantile regression, and statistical modelling of the flood-peak distribution. Once anthropogenic changes linked to reservoir regulation of the Tiber River have been accounted for, the stationarity assumption holds and can be used for flood frequency analysis. We highlight the difficulties in detecting departures from the stationarity assumption due to climate change. In the current regime, the December 2008 flood event has a return period of the order of 10–20 years. Citation Villarini, G., Smith, J.A., Napolitano, F. & Baeck, M.L. (2011) Hydrometeorological analyses of the December 2008 flood in Rome. Hydrol. Sci. J. 56(7), 1150–1165.
Evidence for non‐adaptive immune response in HIV infection (1997)

Increased levels of soluble forms of adhesion molecules such as intercellular adhesion molecule 1 (ICAM-1) and E-selectin have been found in the sera of HIV-infected patients and have been associated with disease progression. The aim of the present study was to investigate whether this phenomenon reflects activation of the non-adaptive immune response in HIV infection. Fifty-one patients with HIV infection (42 men, nine women) were classified into two subgroups: those with HIV infection but without evidence of AIDS indicator conditions (HIV infected non-AIDS cases, n = 27) and those with AIDS (AIDS cases, n = 24). The activation of non-adaptive immune response was evaluated as the production of reactive oxygen species that cause lipid peroxidation, which was assessed by measuring thiobarbituric reactive substances (TBARS) using the thiobarbituric acid assay (TBA). Plasma levels of von Willebrand factor (vWF), measured by rocket immunoelectrophoresis, were used to show activation of endothelial cells even in the absence of any other causative agent, in these patients. TBARS levels in non-AIDS cases were significantly higher than in control subjects (n = 17) or AIDS cases (P < 0.001). The mean vWF levels were higher in AIDS cases than in non-AIDS cases or normal subjects (P < 0.05). TBARS levels remained significantly higher in non-AIDS cases after adjusting for age, CD4 T-cell and neutrophil counts, antiretroviral therapy and vWF plasma levels. The above findings indicate that in HIV infection, the virus per se is responsible for the increased oxidative stress that in turn activates various transduction pathways, may be leading to endothelial cell activation and shedding of adhesion molecules from the cell surface.
Cryogen-free operation of a voltage-biased superconducting bolometer (2010)

We report on the performance of a Nb voltage-biased superconducting bolometer cooled by a closed cycle pulse tube cooler. The VSB has a Tc ~ 8.1 K and an operating impedance of R ~ 800 Ω. A preliminary value for the system optical noise equivalent power (NEP) = 1.8 × 10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">-12</sup> WHz-1/2 and τ = 0.6 ms.
1xEV-DO system performance: analysis and simulation (2005)

1/spl times/EV-DO, also known as high rate packet data (HRFD-0), was introduced to provide spectrally efficient high speed forward link packet data services. To enable high speed services, advanced techniques such as adaptive modulation and coding, hybrid ARQ, and fast scheduling were introduced in HRPD-0. In this paper, link and system level performance of the HRPD-0 forward link are presented. In addition, HRPD-0 system performance is compared to that of the baseline cdma2000-1/spl times/ and 1/spl times/EV-DV. The results show that the spectral efficiency of HRPD-0 is similar to 1/spl times/EV-DV, but is much higher than cdma2000-1x. However, analysis indicates that the performance of HRPD-0 is limited by the reliability of the reverse-link data rate control channel.
Effects of Minor Sc and Zr Additions on Commercial Al‐Mg‐Mn Alloys (2000)

This chapter contains sections titled: Introduction Experiment Results and Discussion Summary Acknowledgments
Selection and Characterization of Anti-Dengue NS1 Single Domain Antibodies (2018)

Reliable detection and diagnosis of dengue virus (DENV) is important for both patient care and epidemiological control. Starting with a llama immunized with a mixture of recombinant nonstructural protein 1 (NS1) antigen from the four DENV serotypes, a phage display immune library of single domain antibodies was constructed and binders selected which exhibited specificity and affinity for DENV NS1. Each of these single domain antibodies was evaluated for its binding affinity to NS1 from the four serotypes, and incorporated into a sandwich format for NS1 detection. An optimal pair was chosen that provided the best combination of sensitivity for all four DENV NS1 antigens spiked into 50% human serum while showing no cross reactivity to NS1 from Zika virus, yellow fever virus, tick-borne encephalitis virus, and minimal binding to NS1 from Japanese encephalitis virus and West Nile virus. These rugged and robust recombinant binding molecules offer attractive alternatives to conventional antibodies for implementation into immunoassays destined for resource limited locals.
Free-space modules and fiber array data links for optical interconnect systems (2005)

It is generally agreed that optics is advantageous for interconnect applications requiring high speed signal propagation over distances greater than several centimeters. This is especially true when signals must be transferred between substrates. Evidence of this exists in the development of high speed VCSEL based parallel data links. One approach to increasing the capacity of these systems is to use free-space optics to provide fanout, and fiber optic arrays to transfer signals over long connection distances. In this paper we summarize the transfer and interconnect properties of free-space optical systems used in conjunction with multi-mode parallel fiber arrays, and then discuss two designs for accomplishing fanout and fiber coupling functions.
Fabrication and Characterization of Dual‐Channeled Zirconia Ceramic Scaffold (2006)

A novel porous ceramic with a structure containing two three‐dimensional (3D) pore channels in a tetragonal zirconia polycrystals (TZP) ceramic was fabricated using a combination of a CNC‐machining method and slurry coating process. A graphite scaffold with a single interconnected 3D channel as a template was prepared using CNC machining and lamination. The surfaces of the graphite scaffold were then coated uniformly with the TZP slurry, followed by heat treatment at 900°C for 3 h in air to remove the graphite material completely via thermal oxidation and at 1400°C for 3 h in air to sinter the TZP walls. This process produced a dual‐channeled TZP scaffold with an additional 3D channel, which replicated the 3D graphite structure with the pre‐existing channel. The fabricated scaffold showed ultra‐high porosity (91%), high surface area, and high compressive strength (2.04 MPa), as well as a tightly controlled pore structure.
An acidic oligopeptide displayed on AAV2 improves axial muscle tropism after systemic delivery (2012)

An acidic oligopeptide displayed on AAV2 improves axial muscle tropism and decreases liver tropism after systemic delivery. This modification should be useful in creating AAV vectors that are suitable for gene therapy for diseases involving the proximal muscles.
Optimization of injected dose based on noise equivalent count rates for 2- and 3-dimensional whole-body PET. (2002)

The injected dose was adapted to patient morphology for 2D and 3D whole-body acquisitions using the NEC rate as a figure of merit of the statistical quality of the sinogram data. This study is a first step toward a more comprehensive comparison of the image quality obtained using both acquisition modes.
Supplementary Figure 6 from Pacritinib Combined with Sirolimus and Low-Dose Tacrolimus for GVHD Prevention after Allogeneic Hematopoietic Cell Transplantation: Preclinical and Phase I Trial Results (2023)

&lt;p&gt;CD4+ T cell Aurora kinase A activation as a GVHD resistance mechanism. A) Graph shows frequency of CD4+, pHistone 3 serine 10+ (pH3ser10) (downstream of CD28, and parallel to mTOR) T cells (mean{plus minus} SEM) at day +21 among patients treated on dose level 1 or dose level 2 of the phase I trial compared to baseline control values. B) Graph depicts the frequency (mean {plus minus} SEM) of CD4+, pH3ser10+ T cells recovered from NSG spleens at day +14, following transplantation with human PBMCs and then treated with vehicle, pacritinib, 531-201, sirolimus, pacritinib plus sirolimus, or 531-201 plus sirolimus for 2 weeks.&lt;/p&gt;
Visual Computing for Computer Assisted Interventions (2010)

Continuous improvement in medical imaging technology provides an ever increasing amount
of peri-operative and multi-modal image data. However, the sheer amount of image data, its objective fusion for diagnosis and therapy postulates the request for efficient image processing, real-time visualization and data presentation techniques. This thesis focuses on developing visual computing solutions for improving computer assisted medical interventions. Advanced simulation, registration and visualization algorithms have been developed and implemented on Graphic Processing Units (GPU), merging computation of the result and real-time visualization of the data. The methods are investigated in detail for three medical applications: Advanced in-situ medical AR visualization, simulation of US data from patient CT data and multi-modal registration of US and CT data, and evaluated on phantom real patient data.
Supplementary Figure Legend from Impaired IFN-α Production by Plasmacytoid Dendritic Cells Favors Regulatory T-cell Expansion That May Contribute to Breast Cancer Progression (2023)

&lt;p&gt;PDF file, 108K.&lt;/p&gt;
20 × 960-Gb/s Space-division-multiplexed 32QAM transmission over 60 km few-mode fiber (2014)

We show transmission of 20 wavelength-division-multiplexed (WDM) × 960-Gb/s space-division-multiplexed 32QAM modulated channels (spectral efficiency (SE) of 15 bits/s/Hz) over 60 km of few-mode fiber (FMF) with inline few-mode EDFA (FM-EDFA). Soft-decision FEC was implemented and used to achieve error-free transmission.
Physical and in silico immunopeptidomic profiling of a cancer antigen prostatic acid phosphatase reveals targets enabling TCR isolation (2022)

Tissue-specific antigens can serve as targets for adoptive T cell transfer-based cancer immunotherapy. Recognition of tumor by T cells is mediated by interaction between peptide-major histocompatibility complexes (pMHCs) and T cell receptors (TCRs). Revealing the identity of peptides bound to MHC is critical in discovering cognate TCRs and predicting potential toxicity. We performed multimodal immunopeptidomic analyses for human prostatic acid phosphatase (PAP), a well-recognized tissue antigen. Three physical methods, including mild acid elution, coimmunoprecipitation, and secreted MHC precipitation, were used to capture a thorough signature of PAP on HLA-A*02:01. Eleven PAP peptides that are potentially A*02:01-restricted were identified, including five predicted strong binders by NetMHCpan 4.0. Peripheral blood mononuclear cells (PBMCs) from more than 20 healthy donors were screened with the PAP peptides. Seven cognate TCRs were isolated which can recognize three distinct epitopes when expressed in PBMCs. One TCR shows reactivity toward cell lines expressing both full-length PAP and HLA-A*02:01. Our results show that a combined multimodal immunopeptidomic approach is productive in revealing target peptides and defining the cloned TCR sequences reactive with prostatic acid phosphatase epitopes.