gebhart/patrepeval huggingface dataset:
Natural Helper Cells and TH2-Type Innate Immunity (2012)

Natural helper (NH) cells are a newly identified innate lymphocyte population, which respond to a combination of interleukin (IL)-2 and IL-25 or IL-33 to produce large amounts of TH2 cytokines, most notably, IL-5 and IL-13. We identified NH cells in lymphoid clusters in adipose tissues, which we termed fat-associated lymphoid clusters. IL-5 and IL-13 produced by activated NH cells induce eosinophilia and goblet cell hyperplasia, respectively, and play an important role in anti-helminth immunity and allergic diseases, such as asthma. In addition, NH cells produce TH2 cytokines constitutively in the absence of stimulation and support the self-renewal of B1 cells and IgA production by B cells. After our identification of NH cells, other groups have also reported novel TH2 cytokine-producing cells, such as nuocytes, and innate helper type 2 cells. There are similarities and differences between these newly identified cell populations and NH cells. Multipotent progenitor cell type 2 (MPP) cells can differentiate to other myeloid cells, making this a distinct cell type from the others. MPP cells, nuocytes, and innate helper type 2 cells respond to IL-25 alone in vivo, whereas NH cells do not respond to IL-25 without IL-2, although they respond strongly to IL-33. Localization of NH cells in fat-associated lymphoid clusters is an intriguing difference compared with the other cell types, which are found in the lymph node and/or spleen. This article summarizes current information regarding the emerging field of TH2-type innate lymphocytes.
Real-Time Ray-Traced Ambient Occlusion of Complex Scenes using Spatial Hashing (2020)

Ambient occlusion is often approximated in real-time using screen-space techniques, leading to visible artifacts. Raytracing provides a unique way to increase the rendering fidelity by accurately sampling the distance to the surrounding objects, but it introduces sampling noise. We propose a real-time ray-traced ambient occlusion technique in which noise is filtered in world space. Using extended spatial hashing for efficient storage, multiresolution AO evaluation and ad-hoc filtering, we demonstrate the usability of our technique as a production feature usable in CAD viewports with scenes comprising hundreds of millions of polygons.
Large-Scale Analysis of Email Search and Organizational Strategies (2017)

Email continues to be an important form of communication as well as a way to manage tasks and archive personal information. As the volume of email grows, organizing and finding relevant email remains challenging. In this paper, we present a large-scale log analysis of the activities that people perform on email mes-sages (accessing external information via links or attachments, responding to messages, and organizing messages), their search behavior, and their organizational practices in a popular web email client.
Angiosarcoma of the Adrenal Gland Treated Using a Multimodal Approach (2016)

Angiosarcoma of the adrenal gland is an extremely rare malignancy. We report a case of a 59-year-old female who presented with abdominal pain and profound anemia. A 7 cm enhancing, lipid-poor adrenal mass with calcifications that extended posterior to the vena cava was identified on imaging. Patient underwent right adrenalectomy with retroperitoneal lymph node dissection. Pathology demonstrated angiosarcoma of the adrenal gland. Consolidative treatment included adjuvant radiation and chemotherapy. Patient remains disease free 1.5 years following treatment. Prior reported literature on the diagnosis and management of adrenal angiosarcoma is reviewed.
Homologues of the Cf-9 Disease Resistance Gene (Hcr9s) Are Present at Multiple Loci on the Short Arm of Tomato Chromosome 1 (1999)

The tomato Cf-4 and Cf-9 genes map at a genetically complex locus on the short arm of chromosome 1 and confer resistance against Cladosporium fulvum through recognition of different pathogen-encoded avirulence determinants. Cf-4 and Cf-9 are members of a large gene family (Hcr9s, Homologues of Cladosporium fulvum resistance gene Cf-9), some of which encode additional distinct recognition specificities. A genetic analysis of the majority of Hcr9s suggests that their distribution is spatially restricted to the short arm of chromosome 1. Two loci of clustered Hcr9 genes have been analyzed physically that mapped distal (Northern Lights) and proximal (Southern Cross) to the Cf-4/9 locus (Milky Way). Sequence homologies between intergenic regions at Southern Cross and Milky Way indicate local Hcr9 duplication preceded cluster multiplication. The multiplication of clusters involved DNA flanking Hcr9 sequences as indicated by conserved lipoxygenase sequences at Southern Cross and Milky Way. The similar spatial distribution of Hcr9 clusters in different Lycopersicon spp. suggests Hcr9 cluster multiplication preceded speciation.
Limitations to compacting a parallel-plate Blumlein pulse-forming line (2008)

For the applications of compact pulsed-power systems, we propose a model for optimizing the pulse-forming line (PFL) with respect to the optimum pulse generation. There are multiple parameters that play important and conflicting roles in the design of a PFL. The original notion that a pulse, of a desired duration, can be created and the length of the line shortened by using a dielectric with sufficiently high permittivity, is shown here to be overly simplified, and that it can lead to a deformed pulse instead. In this work, new criteria for successful pulse formation are proposed and their validity demonstrated. © 2008 Wiley Periodicals, Inc. Int J RF and Microwave CAE, 2008.
Data from Somatic Mosaic Chromosomal Alterations and Death of Cardiovascular Disease Causes among Cancer Survivors (2023)

&lt;div&gt;AbstractBackground:&lt;p&gt;Cancer survivors are at an increased risk of cardiovascular disease (CVD) compared with the general population. We sought to evaluate the impact of mosaic chromosomal alterations (mCA) on death of CVD causes, coronary artery disease (CAD) causes, and of any cause in patients with a cancer diagnosis.&lt;/p&gt;Methods:&lt;p&gt;The study was a prospective cohort analysis of 48,919 UK Biobank participants with a cancer diagnosis. mCAs were characterized using DNA genotyping array intensity data and long-range chromosomal phase inference. Multivariable Cox regression models were used to ascertain the associations of mCAs. Exploratory endpoints included various incident cardiovascular phenotypes.&lt;/p&gt;Results:&lt;p&gt;Overall, 10,070 individuals (20.6%) carried ≥ 1 mCA clone. In adjusted analyses, mCA was associated with an increased risk of death of CAD causes [HR, 1.37; 95% confidence interval (CI), 1.09–1.71; &lt;i&gt;P&lt;/i&gt; = 0.006]. In sub-analyses, we found that carriers of mCAs diagnosed with kidney cancer had an increased risk of death of CVD causes (HR, 2.03; 95% CI, 1.11–3.72; &lt;i&gt;P&lt;/i&gt; = 0.022) and CAD causes (HR, 3.57; 95% CI, 1.44–8.84; &lt;i&gt;P&lt;/i&gt; = 0.006). Women diagnosed with breast cancer who carried a mCA also had a higher risk of death of CAD causes (HR, 2.46; 95% CI, 1.23–4.92; &lt;i&gt;P&lt;/i&gt; = 0.011).&lt;/p&gt;Conclusions:&lt;p&gt;Among cancer survivors, carriers of any mCA are at an increased risk of CAD death compared with noncarriers. Mechanistic studies should be considered to better ascertain the biological mechanisms underneath the observed associations between mCAs and cardiovascular events for specific cancer types.&lt;/p&gt;Impact:&lt;p&gt;There may be clinical relevance in considering mCAs in patients diagnosed with cancer and undergoing treatment.&lt;/p&gt;&lt;/div&gt;
Validation of geometric measurements of the left atrium and pulmonary veins for analysis of reverse structural remodeling following ablation therapy (2012)

Geometric analysis of the left atrium and pulmonary veins is important for studying reverse structural remodeling following cardiac ablation therapy. It has been shown that the left atrium decreases in volume and the pulmonary vein ostia decrease in diameter following ablation therapy. Most analysis techniques, however, require laborious manual tracing of image cross-sections. Pulmonary vein diameters are typically measured at the junction between the left atrium and pulmonary veins, called the pulmonary vein ostia, with manually drawn lines on volume renderings or on image cross-sections. In this work, we describe a technique for making semi-automatic measurements of the left atrium and pulmonary vein ostial diameters from high resolution CT scans and multi-phase datasets. The left atrium and pulmonary veins are segmented from a CT volume using a 3D volume approach and cut planes are interactively positioned to separate the pulmonary veins from the body of the left atrium. The cut plane is also used to compute the pulmonary vein ostial diameter. Validation experiments are presented which demonstrate the ability to repeatedly measure left atrial volume and pulmonary vein diameters from high resolution CT scans, as well as the feasibility of this approach for analyzing dynamic, multi-phase datasets. In the high resolution CT scans the left atrial volume measurements show high repeatability with approximately 4% intra-rater repeatability and 8% inter-rater repeatability. Intra- and inter-rater repeatability for pulmonary vein diameter measurements range from approximately 2 to 4 mm. For the multi-phase CT datasets, differences in left atrial volumes between a standard slice-by-slice approach and the proposed 3D volume approach are small, with percent differences on the order of 3% to 6%.
Real Time Active Noise Control of Engine Booming in Passenger Vehicles (2007)

&lt;div class="htmlview paragraph"&gt;While driving, the low frequency interior noise below 200Hz causes the main component that irritates the auditory acoustic sense. In order to remove this low frequency noise, passive noise control methods were used such as application of sound absorbing material or isolation of noise source. These methods bring out increment in cost and weight of the vehicle and result in poor fuel efficiency. Recently, various Active Noise Control (ANC) methods to suppress the low frequency noise began to launch into application. Nissan developed the Single Input, Single Output (SISO) Active Noise Control system and applied it to their passenger vehicle, Blue Bird and Plymouth Prowler (Dodge) was equipped with Active Exhaust Noise Control System mitigating the back pressure inside the muffler. Also, demand for the Active Silencer System is being increased for the emergency vehicles. Main obstacle for the ANC system is cost effectiveness problem. But as long as the demand for the ride comfort is increased, the demand for the ANC system will grow gradually. In this paper, an ANC system for passenger vehicles to cancel the engine booming noise is implemented using DSP based control unit including four microphones and two actuators (speakers). A feed-forward control method called Multiple Error Filtered X- Least Mean Square (MEFX-LMS) algorithm is used and the space between speakers and microphones is modeled as an FIR filter. This system has been implemented on a passenger car and noise reduction at driver and passenger seats are presented. The results of this study show 10 dB reduction in engine booming noise in 2000-3000 rpm of engine speed, which is the cruise range of most cars.&lt;/div&gt;
Millimeter-Wave and Terahertz Fixed Wireless Link Budget Evaluation for Extreme Weather Conditions (2021)

To develop highly reliable fixed wireless links, such as mobile backhaul and fronthaul systems, it is essential to evaluate the link budget under extreme weather conditions. In this paper, we presented a link budget evaluation for fixed wireless links using radio signals at four different carrier frequencies: 75.375, 85.375, 275, and 400 GHz. As examples of extreme weather conditions, we focused on storms which can be defined as the combination of high temperature, violent rain, and strong winds. A theoretical model was proposed to evaluate the attenuation by the wind effect, which was due to mechanical vibration. Using the proposed model, we evaluated the link attenuation with different weather parameters, such as clear weather condition, different rain rates, and strong wind. In addition, the maximum channel capacities were estimated based on the model. According to the calculation results, it can be confirmed that the attenuation caused by heavy rain is the dominant factor to the whole system. Besides, the attenuation due to antenna gain degradation induced by the wind effect is considerable for the wireless link at high frequencies (275 and 400 GHz). This manuscript includes a comprehensive discussion regarding various weather factors including gas, rain, and wind, which impact the fixed wireless links. The obtained results would be useful for designing a high reliability fixed wireless link to operate under different weather conditions.
Database support for matching (2006)

We define a match join of R and S with predicate θ to be a subset of the θ-join of R and S such that each tuple of R and S contributes to at most one result tuple. Match joins and their generalizations belong to a broad class of matching problems that have attracted a great deal of attention in disciplines including operations research and theoretical computer science. Instances of these problems arise in practice in resource allocation scenarios. To the best of our knowledge no one uses an RDBMS as a tool to help solve these problems; our goal in this paper is to explore whether or not this needs to be the case. We show that the simple approach of computing the full θ-join and then applying standard graph-matching algorithms to the result is ineffective for all but the smallest of problem instances. By contrast, a closer study shows that the DBMS primitives of grouping, sorting, and joining can be exploited to yield efficient match join operations. This suggests that RDBMSs can play a role in matching related problems beyond merely serving as expensive file systems exporting data sets to external user programs.
Direct detection of SARS-CoV-2 using CRISPR-Cas13a and a mobile phone (2020)

SUMMARY The December 2019 outbreak of a novel respiratory virus, SARS-CoV-2, has become an ongoing global pandemic due in part to the challenge of identifying symptomatic, asymptomatic and pre-symptomatic carriers of the virus. CRISPR-based diagnostics that utilize RNA and DNA-targeting enzymes can augment gold-standard PCR-based testing if they can be made rapid, portable and accurate. Here we report the development of an amplification-free CRISPR-Cas13a-based mobile phone assay for direct detection of SARS-CoV-2 from nasal swab RNA extracts. The assay achieved ∼100 copies/μL sensitivity in under 30 minutes and accurately detected a set of positive clinical samples in under 5 minutes. We combined crRNAs targeting SARS-CoV-2 RNA to improve sensitivity and specificity, and we directly quantified viral load using enzyme kinetics. Combined with mobile phone-based quantification, this assay can provide rapid, low-cost, point-of-care screening to aid in the control of SARS-CoV-2.
Discovery and mechanism of action of a novel series of apoptosis inducers with potential vascular targeting activity (2004)

A novel series of 2-amino-4-(3-bromo-4,5-dimethoxy-phenyl)-3-cyano-4H-chromenes was identified as apoptosis-inducing agents through our cell-based apoptosis screening assay. Several analogues from this series, MX-58151, MX-58276, MX-76747, MX-116214, MX-126303, and MX-116407, were synthesized and further characterized. MX-116407, a lead compound from this series, induced apoptosis with an EC50 of 50 nmol/L and inhibited cell growth with a GI50 of 37 nmol/L in T47D breast cancer cells. Treatment of cells with these analogues led to G2-M arrest, cleavage of essential proapoptotic caspase substrates, and induction of nuclear fragmentation. We identified these compounds as tubulin destabilizers with binding site at or close to the colchicine binding site. Compounds in this series were also active in drug-resistant cancer cell lines with a GI50 value for one of the analogues (MX-58151) of 2.5 nmol/L in paclitaxel-resistant, multidrug-resistant MES-SA/DX5 tumor cells. This series of compounds displayed high selectivity against proliferating versus resting cells. Interestingly, these compounds were shown to disrupt preformed endothelial cell capillary tubules in vitro and affect functional vasculature to induce tumor necrosis in vivo and are thus likely to work as tumor vasculature targeting agents. Among these compounds, MX-116407 showed capillary tubule disruption activity in vitro at concentrations well below the cytotoxic dose. In a separate study, we further characterized the antitumor efficacy and pharmacokinetic profile of this series of compounds and identified MX-116407 as a potent apoptosis-inducing agent with apparent activity as tumor vasculature targeting agent.
A Novel Inducible Mouse Model of MLL‐ENL‐driven Mixed‐lineage Acute Leukemia (2018)

Previous retroviral and knock-in approaches to model human t(11;19)<sup>+</sup> acute mixed-lineage leukemia in mice resulted in myeloproliferation and acute myeloid leukemia not fully recapitulating the human disease. The authors established a doxycycline (DOX)-inducible transgenic mouse model "<i>iMLL-ENL</i>" in which induction in long-term hematopoietic stem cells, lymphoid primed multipotent progenitor cells, multipotent progenitors (MPP4) but not in more committed myeloid granulocyte-macrophage progenitors led to a fully reversible acute leukemia expressing myeloid and B-cell markers. <i>iMLL-ENL</i> leukemic cells generally expressed lower <i>MLL-ENL</i> mRNA than those obtained after retroviral transduction. Disease induction was associated with <i>iMLL-ENL</i> levels exceeding the endogenous <i>Mll1</i> at mRNA and protein levels. In leukemic cells from t(11;19)<sup>+</sup> leukemia patients, <i>MLL-ENL</i> mRNA also exceeded the endogenous <i>MLL1</i> levels suggesting a critical threshold for transformation. Expression profiling of <i>iMLL-ENL</i> acute leukemia revealed gene signatures that segregated t(11;19)<sup>+</sup> leukemia patients from those without an MLL translocation. Importantly, B220<sup>+</sup> <i>iMLL-ENL</i> leukemic cells showed a higher in vivo leukemia initiation potential than coexisting B220<sup>-</sup> cells. Collectively, characterization of a novel transgenic mouse model indicates that the cell-of-origin and the fusion gene expression levels are both critical determinants for <i>MLL-ENL</i>-driven acute leukemia.
An exclusion map for facioscapulohumeral (Landouzy-Déjérine) disease. (1989)

By using the genetic linkage data between the facioscapulohumeral muscular dystrophy (FSHD) gene and 57 markers on various autosomes, we have constructed an exclusion map for this disorder. The maximum likelihood location of the FSHD gene and the percentage of the excluded areas on each chromosome are presented here. This exclusion map shows that more than 80% of the genome has been excluded as a likely location of any locus responsible for FSHD in the majority of families. Chromosomes 3, 5, 10, 11, 15, and 19 remain largely unexcluded. Concentration on the highlighted areas of the genome should facilitate the identification of the site of the FSHD gene.
Linear Current Sensing for Detecting and Locating Underground Structures (2022)

This paper introduces a new triaxial magnetic field gradiometer to detect, locate, and map underground metallic utilities, such as a thin-wires, railroad tracks, and pipes. The system couples a primary electric field along target’s elongation to maximize excited linear electric (i.e. non-solenoidal) currents and uses magnetic field induction sensing (i.e. Faradays induction law) to measure secondary magnetic fields. First, theoretical, and numerical studies are presented for the broadband electromagnetic response from long thin wires buried in a conducting soil at varying depths. Second, numerical calculations are validated against experimental data. Favorable comparisons between model and measured data are illustrated for wires subjected to both plane wave excitation, originating from a 1.4 MHz AM station as well as local excitation. Third, forward and inverse electromagnetic models are applied to electromagnetic gradiometer field data to extract the wire’s burial depths from different survey track data, showing good agreement for wire depths from 0 to ~6 m. Finally, multi-wire location and orientation are extracted from the triaxial vector gradiometer data set. These results illustrate the applicability of linear current sensing for detecting, locating, and mapping deep underground metallic infrastructures such as wires, railroad tracks, and pipes.
Protection against Influenza A Virus Challenge with M2e-Displaying Filamentous Escherichia coli Phages (2015)

Human influenza viruses are responsible for annual epidemics and occasional pandemics that cause severe illness and mortality in all age groups worldwide. Matrix protein 2 (M2) of influenza A virus is a tetrameric type III membrane protein that functions as a proton-selective channel. The extracellular domain of M2 (M2e) is conserved in human and avian influenza A viruses and is being pursued as a component for a universal influenza A vaccine. To develop a M2e vaccine that is economical and easy to purify, we genetically fused M2e amino acids 2-16 to the N-terminus of pVIII, the major coat protein of filamentous bacteriophage f88. We show that the resulting recombinant f88-M2e2-16 phages are replication competent and display the introduced part of M2e on the phage surface. Immunization of mice with purified f88-M2e2-16 phages in the presence of incomplete Freund's adjuvant, induced robust M2e-specific serum IgG and protected BALB/c mice against challenge with human and avian influenza A viruses. Thus, replication competent filamentous bacteriophages can be used as efficient and economical carriers to display conserved B cell epitopes of influenza A.
Primary structure of alpaca growth hormone (1991)

Reduced and carbamidomethylated alpaca growth hormone was submitted to tryptic digestion. Peptides in the mixture were purified by reverse phase HPLC and N-terminal determination and an amino acid analysis of each was performed. Data obtained and the already known primary structure of the equine growth hormone allowed the assembly-by homology-of a definite sequence of amino acids for the polypeptide chain of the protein. Present data provide further information about the relationship between growth factors.
Mobile systems location privacy: &#x201C;MobiPriv&#x201D; a robust k anonymous system (2010)

With the rapid advancement of positioning and tracking capabilities (mobile phones, on-board navigation systems) location based services are rapidly increasing. Privacy in location based systems is addressed in many papers. Our work is focused on the trusted third party privacy framework that utilizes the concept of k-anonymity with or without l-diversity. In previous anonymization models k may be defined as a personalization parameter of the mobile user or as uniform system parameter for all mobile users . Clearly, k other users may not be available at the time of request in these systems. These requests are discarded because the quality of service (QoS) they require cannot be satisfied. In this paper we introduce a novel suite of algorithms called MobiPriv that guarantees a 100% success rate of processing a mobile request using k-anonymity with diversity considerations. We evaluated our suite of algorithms experimentally against previously proposed anonymization algorithms using real world traffic volume data, real world road network and mobile users generated realistically by a mobile object generator.