gebhart/patrepeval huggingface dataset:
P264 A multi-centre review of the management of pulmonary Non-Tuberculous Mycobacterial (NTM) infection in HIV-negative subjects: Abstract P264 Table 1 (2015)

<h3>Introduction</h3> Non-Tuberculous Mycobacteria (NTM) are ubiquitous in the environment meaning clinical, radiological and microbiological criteria are important in diagnosing NTM lung disease. A multicentre, retrospective review was performed to characterise NTM disease within our region and describe the outcomes of current management. <h3>Methods</h3> All NTM positive sputum samples received by the National Mycobacterium Reference Laboratory (NMRL) from Imperial College NHS Healthcare and North West London Hospitals NHS Trusts between 2010–2014 were extracted. HIV-negative individuals with ≥2 positive sputum samples or ≥1 positive bronchoalveolar lavage were included. Demographic, clinical, radiological, microbiological, management and outcome data was obtained from electronic records. <h3>Results</h3> 1190 NTM sputum samples were identified from 822 individuals. 152 individual patients met inclusion criteria for analysis. Table 1 describes cohort demographics. Within the cohort 48/152 (32%) were treated for NTM disease. All treated subjects and 74/104 (71%) non-treated subjects met international guidelines for diagnosis of NTM infection, which included positive clinical, radiological (cavities or bronchiectasis +/- nodules or infiltrates) and microbiological criteria. <i>Mycobacterium avium complex</i> (MAC) was the most commonly isolated (68/152; 45%) and treated organism (21/48; 44%) followed by <i>Mycobacterium kansasii</i> (11/48; 23%). 19/48 (40%) completed treatment (median duration: 17 months [IQR: 12–24]). 10/48 (21%) remain on treatment (median duration: 18 months [IQR: 11–36]), 11/48 (23%) stopped treatment due to side effects and 13/48 (27%) were either lost to follow up or treated for <i>Mycobacterium tuberculosis</i>. Of those treated, 29/48 (60%) culture converted; 23/29 (79%) remain negative at 12 months post culture conversion. Of 19/48 who completed treatment, 5/19 (26%) had symptomatic or radiological disease progression compared to 11/28 (39%) who did not complete treatment. 11/48 (23%) patients died within the treatment group. Within the untreated subjects who met international guidelines for NTM infection (74/104), mortality was 19/74 (26%) (p = 0.83). <h3>Discussion</h3> NTM is a challenging disease with only 39% of eligible subjects receiving treatment and a high associated mortality. Furthermore, only 40% starting treatment completed it and the 21% who remain on treatment have been treated for a median duration of 18 months to date. Unlike similar HIV-negative UK cohorts, MAC pulmonary disease is the most prevalent.
Peroxiredoxin-controlled G-CSF signalling at the endoplasmic reticulum–early endosome interface (2011)

Reactive oxygen species (ROS) regulate growth factor receptor signalling at least in part by inhibiting oxidation-sensitive phosphatases. An emerging concept is that ROS act locally to affect signal transduction in different subcellular compartments and that ROS levels are regulated by antioxidant proteins at the same local level. Here, we show that the ER-resident antioxidant peroxiredoxin 4 (Prdx4) interacts with the cytoplasmic domain of the granulocyte colony-stimulating factor receptor (G-CSFR). This interaction occurs when the activated G-CSFR resides in early endosomes. Prdx4 inhibits G-CSF-induced signalling and proliferation in myeloid progenitors, depending on its redox-active cysteine core. Protein tyrosine phosphatase 1b (Ptp1b) appears to be a major downstream effector controlling these responses. Conversely, Ptp1b might keep Prdx4 active by reducing its phosphorylation. These findings unveil a new signal transduction regulatory circuitry involving redox-controlled processes in the ER and activated cytokine receptors in endosomes.
Peripheral Blood Neutrophil Activation Patterns Are Associated with Pulmonary Inflammatory Responses to Lipopolysaccharide in Humans (2006)

Increased nuclear accumulation of NF-kappaB in LPS-stimulated peripheral blood neutrophils has been shown to be associated with more severe clinical course in patients with infection associated acute lung injury. Such observations suggest that differences in neutrophil response may contribute to the pulmonary inflammation induced by bacterial infection. To examine this question, we sequentially measured LPS-induced DNA binding of NF-kappaB in neutrophils collected from healthy humans on at least three occasions, each separated by at least 2 wk, and then determined pulmonary inflammatory responses after instillation of LPS into the lungs. Consistent patterns of peripheral blood neutrophil responses, as determined by LPS-induced NF-kappaB DNA binding, were present in volunteers, with a >80-fold difference between individuals in the mean area under the curve for NF-kappaB activation. The number of neutrophils recovered from bronchoalveolar lavage after exposure to pulmonary LPS was significantly correlated with NF-kappaB activation in peripheral blood neutrophils obtained over the pre-LPS exposure period (r = 0.65, p = 0.009). DNA binding of NF-kappaB in pulmonary neutrophils also was associated with the mean NF-kappaB area under the curve for LPS-stimulated peripheral blood neutrophils (r = 0.63, p = 0.01). Bronchoalveolar lavage levels of IL-6 and TNFRII were significantly correlated with peripheral blood neutrophil activation patterns (r = 0.75, p = 0.001 for IL-6; and r = 0.48, p = 0.049 for TNFRII. These results demonstrate that stable patterns in the response of peripheral blood neutrophils to LPS exist in the human population and correlate with inflammatory response following direct exposure to LPS in the lung.
System aspects of the next-generation data-center networks based on 200G per lambda IMDD links (2020)

Following the standardization of 400 Gigabit Ethernet for data center networks (DCN), the industry will need 800 Gigabit or 1.6 Terabit pluggable modules soon after 2020. 200G per lambda directly detected links are very promising solutions to achieve the best trade-off between cost, size, and power. This paper investigates the challenges of 200G per lambda in DCN, due to the component bandwidth and noise limitations, and shows the technical feasibility enabled by advanced modulation formats and digital signal processing.
Spectroscopy and laser operation of Nd:ZBAN glass (1991)

The results of a study of the spectroscopic and laser properties of a Nd/sup 3+/ doped fluoride glass are presented. Threshold energies and slope efficiencies are reported along with the stimulated emission cross section for the laser transition. The effect of excited state absorption of pump photons on the slope efficiency is investigated.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Data from Cellular Mechanisms Underlying Complete Hematological Response of Chronic Myeloid Leukemia to BRAF and MEK1/2 Inhibition in a Patient with Concomitant Metastatic Melanoma (2023)

&lt;div&gt;Abstract&lt;p&gt;&lt;b&gt;Purpose:&lt;/b&gt; Targeted MEK inhibition is an emerging therapy in a number of solid tumors. It holds particular promise in BRAF V600E mutation–positive malignant melanoma, where constitutive activation and cell growth through the MAP kinase (MAPK) pathway is well established. &lt;i&gt;In vitro&lt;/i&gt; and preclinical research indicates that MAPK pathway activation is important in chronic myeloid leukemia (CML) leukemogenesis; however, the potential of MEK inhibition has not yet been investigated clinically in the setting of such hematologic malignancies.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Experimental Design:&lt;/b&gt; We report a case of complete hematologic response of CML to MEK inhibition in a patient with synchronous metastatic melanoma, who received treatment with combination BRAF and MEK1/2 inhibitors. We studied the effects of these agents on proliferation and outgrowth of myeloid precursors, and longitudinal shifts in peripheral blood phenotyping during the course of treatment. A model cell line system was used to examine the effects of dabrafenib and trametinib on MAPK and BCR–ABL1 signaling.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Results:&lt;/b&gt; After 35 weeks on treatment with BRAF and MEK inhibitors, complete hematologic response was observed without recourse to BCR–ABL1–targeted therapy. MEK inhibition was principally responsible for impaired proliferation of both mature and primitive myeloid precursors, as well as growth and hemoglobinization of erythroid precursors. Paradoxical activation of the MAPK pathway was seen in response to BRAF inhibitor therapy but this was easily overcome by clinically relevant doses of concurrent MEK inhibitor.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Conclusions:&lt;/b&gt; These studies suggest that further evaluation of the optimal MAPK targeting approach is warranted to extend therapeutic options in CML. &lt;i&gt;Clin Cancer Res; 21(23); 5222–34. ©2015 AACR&lt;/i&gt;.&lt;/p&gt;&lt;/div&gt;
Therapeutic Hypothermia in Brain Injuries and Related Diseases (2011)

Mild or moderate hypothermia is a useful therapeutic method for improving the outcome for patients who have suffered brain injuries including traumatic brain injury and strokes, as well as secondary damages such as neuroinflammation and edema. The feasibility and safety of therapeutic hypothermia have been evaluated in experimental settings and clinical trials. Because the efficacy of therapeutic hypothermia, however, is dependent on the cooling method, application time, duration, and strategies, a continuous effort for obtaining optimal standard protocols of controlling temperature and the documentation of hypothermic devices and drugs are required. Here, we discuss the most recent hypothermia applications in brain injury and related diseases, and review the latest patents in hypothermic devices and cannabinoid-based hypothermia-inducing drugs. Ultimately, we conclude that a localized hypothermia may overcome the limitations, risks, and side effects of systemic hypothermia, and the combination of local hypothermia and drug treatment may improve clinical benefits.
Waterborne Polymer/Silica Hybrid Nanoparticles and Their Structure in Coatings (2015)

The structure control during the formation of films from nanoparticles is investigated. The particles are synthesized by miniemulsion polymerization with different ratios of methyl methacrylate and butyl methacrylate in the presence of silica nanoparticles. The structure of the hybrid particles is controlled by changing the surface properties of the silica through functionalization with 3‐methacryloxypropyltrimethoxysilane (MPS) and octadecyltrimethoxysilane (ODTMS). Fixation of the MPS‐silica due to polymerizable groups leads to a homogeneous distribution inside the polymer, while the inert alkyl chains of ODTMS result in segregation of the silica and the polymer. This difference in the structure is preserved during film formation and aggregation in films can be prevented effectively.
Deep-learning-based vision for earth-moving automation (2021)

Earth-moving machines are heavy-duty vehicles designed for construction operations involving earthworks. The tasks performed by such machines typically involve navigation and interaction with materials such as soil, gravel, and blasted rock. Skilled operators use a combination of visual, sound, tactile and possibly motion feedback to perform tasks efficiently. We survey the literature in this research area and analyse the relative importance of different sensor system modalities focusing on deep-learning-based vision and automation for the short-cycle loading task. This is a common and repetitive task that is attractive to automate. The analysis indicates that computer vision, in combination with onboard sensors, is more critical than coordinate-based positioning. Furthermore, we find that data-driven approaches, in general, have high potential in terms of productivity, adaptability, versatility and wear and tear with respect to automation system solutions. The main knowledge gaps identified relate to loading non-fine heterogeneous material and navigation during loading and unloading.
Abstract 18759: Vascular Smooth Muscle Cells Derived From Inbred Swine Induced Pluripotent Stem Cells for Vascular Tissue Engineering (2016)

Introduction: Development of autologous tissue-engineered vascular constructs using vascular smooth muscle cells (VSMCs) derived from human induced pluripotent stem cells (hiPSCs) holds great poten...
Quantitative Flow Cytometric Analysis in Erythrodermic Cutaneous T-Cell Lymphoma: Implications for Prognosis and Staging (2013)

Erythrodermic cutaneous T-cell lymphoma (eCTCL) is currently considered as stage III disease and indicative of an unfavorable outcome. Further risk stratification depends on convened criteria for stage IV, based on tumor burden assessment on peripheral blood, lymph nodes, and noncutaneous tissues. Although flow cytometry (FC) is routinely used to assess peripheral blood involvement in eCTCL, gating strategies are not standardized and …
A Meso-mechanical Model of the Tensile Behavior of Concrete - Part II: Modeling of Post-Peak Tension Softening Behavior (1989)

Peer Reviewed
A Context-Dependent Gated Module for Incorporating Symbolic Semantics into Event Coreference Resolution (2021)

Event coreference resolution is an important research problem with many applications. Despite the recent remarkable success of pretrained language models, we argue that it is still highly beneficial to utilize symbolic features for the task. However, as the input for coreference resolution typically comes from upstream components in the information extraction pipeline, the automatically extracted symbolic features can be noisy and contain errors. Also, depending on the specific context, some features can be more informative than others. Motivated by these observations, we propose a novel context-dependent gated module to adaptively control the information flows from the input symbolic features. Combined with a simple noisy training method, our best models achieve state-of-the-art results on two datasets: ACE 2005 and KBP 2016.
Structured light based 3D reconstruction flexible endoscopic device (2016)

info:eu-repo/semantics/published
Proteotranscriptomic Analysis Reveals Stage Specific Changes in the Molecular Landscape of Clear-Cell Renal Cell Carcinoma (2016)

Renal cell carcinoma comprises 2 to 3% of malignancies in adults with the most prevalent subtype being clear-cell RCC (ccRCC). This type of cancer is well characterized at the genomic and transcriptomic level and is associated with a loss of VHL that results in stabilization of HIF1. The current study focused on evaluating ccRCC stage dependent changes at the proteome level to provide insight into the molecular pathogenesis of ccRCC progression. To accomplish this, label-free proteomics was used to characterize matched tumor and normal-adjacent tissues from 84 patients with stage I to IV ccRCC. Using pooled samples 1551 proteins were identified, of which 290 were differentially abundant, while 783 proteins were identified using individual samples, with 344 being differentially abundant. These 344 differentially abundant proteins were enriched in metabolic pathways and further examination revealed metabolic dysfunction consistent with the Warburg effect. Additionally, the protein data indicated activation of ESRRA and ESRRG, and HIF1A, as well as inhibition of FOXA1, MAPK1 and WISP2. A subset analysis of complementary gene expression array data on 47 pairs of these same tissues indicated similar upstream changes, such as increased HIF1A activation with stage, though ESRRA and ESRRG activation and FOXA1 inhibition were not predicted from the transcriptomic data. The activation of ESRRA and ESRRG implied that HIF2A may also be activated during later stages of ccRCC, which was confirmed in the transcriptional analysis. This combined analysis highlights the importance of HIF1A and HIF2A in developing the ccRCC molecular phenotype as well as the potential involvement of ESRRA and ESRRG in driving these changes. In addition, cofilin-1, profilin-1, nicotinamide N-methyltransferase, and fructose-bisphosphate aldolase A were identified as candidate markers of late stage ccRCC. Utilization of data collected from heterogeneous biological domains strengthened the findings from each domain, demonstrating the complementary nature of such an analysis. Together these results highlight the importance of the VHL/HIF1A/HIF2A axis and provide a foundation and therapeutic targets for future studies. (Data are available via ProteomeXchange with identifier PXD003271 and MassIVE with identifier MSV000079511.).
Evaluation of the reactivity of ultra-lean PRF/air mixtures by weak flames in a micro flow reactor with a controlled temperature profile (2018)

The reactivity of ultra-lean primary reference fuel (PRF)/air mixtures was investigated by weak flames in a vertical-type micro flow reactor (MFR) with a controlled temperature profile. In experiments, steady-separated weak flames were obtained at equivalence ratios between 0.5 and 1.0 for PRF80, 90, and 100. At leaner conditions, all the fuels showed hot flames at lower temperature regions, indicating higher reactivity. In one-dimensional steady simulations of the present micro flow reactor by modified Chemkin-Pro PREMIX, the LLNL PRF mechanism was able to reproduce the experimental tendency, while the KUCRS PRF mechanism showed the opposite trend. By analyzing major reactions leading to the hot flame, seven H–O reactions were identified that primarily control the hot flame response to a change of equivalence ratio. By exchanging the rate parameters of these seven reactions for more recent ones, the reactivity trend was brought to very good agreement with experimental results. This improvement was credited to a better spatial separation of intermediate- and high-temperature reactions in the MFR and emphasizes the strength of this investigation method.
Determination of the Average Aromatic Cluster Size of Fossil Fuels by Solid-State NMR at High Magnetic Field (2013)

We show that the average aromatic cluster size in complex carbonaceous materials can be accurately determined using fast magic-angle spinning (MAS) NMR at a high magnetic field. To accurately quantify the nonprotonated aromatic carbon, we edited the 13C spectra using the recently reported MAS-synchronized spin–echo, which alleviated the problem of rotational recoupling of 1H-13C dipolar interactions associated with traditional dipolar dephasing experiments. The dependability of this approach was demonstrated on selected Argonne Premium coal standards, for which full sets of basic structural parameters were determined with high accuracy.
Data Collection by a Mobile Observer in a Single-hop Sensor Network (2005)

In this paper, we demonstrate significant reduction in communication power by using a mobile observer to collect data from a wireless single-hop network of static sensors.The key challenge in using a mobile observer is that it remains within range of any sensor for a limited period, and inability to transfer data in this period causes data loss.This prompts us to choose the fraction of nodes successful in communicating data as our performance constraint as we try to minimize network power.First, we establish that the process of data collection by a mobile observer is analogous to a queue.The queuing-based data collection model is then used as a design tool to identify the combination of system parameters that satisfies the performance metric with minimum power.Second, we derive a sufficient condition on node placement for zero data loss in a mobile observer network.As our third contribution, we demonstrate that in a dense network, the data collection analysis is much simpler, which allows us to obtain closed expressions for the network power.Power comparisons with static observer networks show that power reduction by multiple orders of magnitude is typical.The scenarios chosen for power comparisons also provide guidelines on the choice of path, if such a choice is available.As an example, a disc shaped network is analyzed and among the set of concentric circular paths, the best path is identified.
High-speed IPM Motors with Rotor Sleeve: Structural Design and Performance Evaluation (2023)

This paper deals with the structural design of sleeves for high-speed interior permanent magnet (IPM) synchronous machines. Wrapped IPM (WIPM) motors are a new player in the field of high-speed e-machines for traction, where a retaining sleeve is used to hold the magnetic poles in place against centrifugal forces, replacing the role of conventional iron bridges. The wrapping technique, originating from surface-mounted permanent magnet rotors, is believed to push speed limitations to new heights, as demanded by the increasing requirements of the automotive industry. By developing an equivalent rotor geometry of the WIPM rotor, an analytical model is formulated to evaluate the stress in the rotor and to provide a quick and intuitive tool for the sleeve design. The results are successfully validated by structural finite element analysis. Also, the output figures of a WIPM machine are compared to those of an equivalent IPM machine with iron bridges.
Molecular Recognition of Cyclic Urea HIV-1 Protease Inhibitors (1998)

As long as the threat of human immunodeficiency virus (HIV) protease drug resistance still exists, there will be a need for more potent antiretroviral agents. We have therefore determined the crystal structures of HIV-1 protease in complex with six cyclic urea inhibitors: XK216, XK263, DMP323, DMP450, XV638, and SD146, in an attempt to identify 1) the key interactions responsible for their high potency and 2) new interactions that might improve their therapeutic benefit. The structures reveal that the preorganized, C2 symmetric scaffolds of the inhibitors are anchored in the active site of the protease by six hydrogen bonds and that their P1 and P2 substituents participate in extensive van der Waals interactions and hydrogen bonds. Because all of our inhibitors possess benzyl groups at P1 and P1', their relative binding affinities are modulated by the extent of their P2 interactions, e.g. XK216, the least potent inhibitor (Ki (inhibition constant) = 4.70 nM), possesses the smallest P2 and the lowest number of P2-S2 interactions; whereas SD146, the most potent inhibitor (Ki = 0.02 nM), contains a benzimidazolylbenzamide at P2 and participates in fourteen hydrogen bonds and approximately 200 van der Waals interactions. This analysis identifies the strongest interactions between the protease and the inhibitors, suggests ways to improve potency by building into the S2 subsite, and reveals how conformational changes and unique features of the viral protease increase the binding affinity of HIV protease inhibitors.