gebhart/patrepeval huggingface dataset:
Frequency domain reflectometry for remaining useful life estimation of instrumentation and control cables (2014)

As the existing fleets of nuclear power plants age, a greater emphasis has been placed on technologies to quantify the remaining useful life of safety-critical components and to ensure that these systems will operate as intended when called upon, especially in emergency situations. Some of the most important, yet often overlooked components, are the cables that provide the signal paths for instrumentation and control systems used to ensure safe and efficient operation of nuclear power plants. Instrumentation and control cable aging, in particular, is primarily concerned with degradation of the polymer material by thermal oxidation while exposed to heat, humidity, radiation, and other environmental stressors. Consequently, as the polymer becomes embrittled, it cracks and becomes susceptible to moisture intrusion that can cause shorts and shunts in the cable circuits. This article describes the development of two prognostic models to estimate the remaining useful life of nuclear power plant cables. The first model uses data compiled in an existing polymer aging database as background for introducing the remaining useful life model development methodology. The second model uses data generated from accelerated cable aging experiments performed by the authors and explores the use of in situ electrical measurements such as frequency domain reflectometry for predicting the remaining useful life of instrumentation and control cables typically found in nuclear power plants.
Single-nucleus resolution mapping of the adult C. elegans and its application to elucidate inter- and trans-generational response to alcohol (2022)

ABSTRACT Single-cell RNA transcriptomic platforms have significantly contributed to our understanding of tissue heterogeneity as well as of developmental and cellular differentiation trajectories. They also provide an opportunity to map an organism’s response to environmental cues with high resolution and unbiasedly identify the cell types that are the most transcriptionally sensitive to exposures. Here, we applied single nucleus RNA-seq experimental and computational approaches to C. elegans to establish the transcriptome of the adult nematode and comprehensively characterize the transcriptional impact of ethanol as a model environmental exposure on the entire organism at cell type-resolution over several generations. Clustering, tissue and phenotype enrichment, and gene ontology analyses identified 31 clusters representing a diverse number of adult cell types, including those from syncytial and multi-nucleated tissues which are difficult to assess by single cell RNA-seq, such as the mitotic and meiotic germline, hypodermal cells, and the intestine. We applied this method to identify the impact of inter- and trans-generational exposure to two human-relevant doses of alcohol. Cell type proportions were not significantly altered by ethanol. However, Euclidean distance analysis identified several germline, striated muscle, and neuronal clusters as being major transcriptional targets of ethanol at both the F1 and F3 generations although the relative order of clusters changed between generations. The impact on germline clusters was further confirmed by phenotypic enrichment analysis as well as functional validation, namely a remarkable inter- and trans-generational increase in germline apoptosis, aneuploidy, and embryonic lethality. Together, snRNA-seq of the adult C. elegans represents a powerful approach for the detailed examination of an adult organism’s response to environmental cues.
Holistic Characterization of a Salmonella Typhimurium Infection Model Using Integrated Molecular Imaging (2021)

A more complete and holistic view on host-microbe interactions is needed to understand the physiological and cellular barriers that affect the efficacy of drug treatments and allow the discovery and development of new therapeutics. Here, we developed a multimodal imaging approach combining histopathology with mass spectrometry imaging (MSI) and same section imaging mass cytometry (IMC) to study the effects of <i>Salmonella</i> Typhimurium infection in the liver of a mouse model using the <i>S.</i> Typhimurium strains SL3261 and SL1344. This approach enables correlation of tissue morphology and specific cell phenotypes with molecular images of tissue metabolism. IMC revealed a marked increase in immune cell markers and localization in immune aggregates in infected tissues. A correlative computational method (network analysis) was deployed to find metabolic features associated with infection and revealed metabolic clusters of acetyl carnitines, as well as phosphatidylcholine and phosphatidylethanolamine plasmalogen species, which could be associated with pro-inflammatory immune cell types. By developing an IMC marker for the detection of <i>Salmonella</i> LPS, we were further able to identify and characterize those cell types which contained <i>S.</i> Typhimurium.
Robust Blood Flow Velocity Estimation from 3D Rotational Angiography (2018)

Blood flow velocity estimation techniques from 2D fluoroscopy and more recently rotational angiography images represent a topic of wide interest in various clinical research areas. In particular, they can be an important step towards patient-specific flow simulations. Additionally, it can be of diagnostic interest to evaluate volumetric blood flow in stenotic vessel segments; e.g. in a patient's brain. In this work, we present a robust optimization-based approach to estimate mean blood flow velocities from rotational digital subtraction angiography (DSA) images. Our method was extensively evaluated on 70 simulated datasets and 6 clinical datasets with MR phase contrast ground truth data. Our evaluation explores the limitations of image-based velocity estimation; i.e., measurements over short or small vessel segments. Overall, we were able to estimate the mean velocity with average errors as little as 4% for simulation studies, if the vessel segment is sufficiently long, and achieved results within the confines of the MR phase contrast ground truth data for our clinical data, with an average relative error to the centerline measurement of 9.5%±10.5%. The achieved accuracy enables patient-specific hemodynamic simulations and may also be of immediate diagnostic interest.
Cell-free, methylated DNA in blood samples reveals tissue-specific, cellular damage from radiation treatment (2022)

Abstract Radiation therapy is an effective cancer treatment although damage to healthy tissues is common. Here we characterize the methylomes of healthy human and mouse tissues to establish sequencing-based, cell-type specific reference DNA methylation atlases. Identified cell-type specific DNA blocks were mostly hypomethylated and located within genes intrinsic to cellular identity. Cell-free DNA fragments released from dying cells into the circulation were captured from serum samples by hybridization to CpG-rich DNA panels. The origins of the circulating DNA fragments were inferred from mapping to the established DNA methylation atlases. Thoracic radiation-induced tissue damages in a mouse model were reflected by dose-dependent increases in lung endothelial, cardiomyocyte and hepatocyte methylated DNA in serum. The analysis of serum samples from breast cancer patients undergoing radiation treatment revealed distinct tissue-specific epithelial and endothelial responses to radiation across multiple organs. Strikingly, patients treated for right-sided breast cancers also showed increased hepatocyte and liver endothelial DNA in the circulation indicating the impact on liver tissues. Thus, changes in cell-free methylated DNA can uncover cell-type specific effects of radiation and provide a quantitative measure of the biologically effective radiation dose received by healthy tissues. Graphical Abstract
Baseline serum TARC levels predict therapy outcome in patients with Hodgkin lymphoma (2012)

Hodgkin lymphoma (HL) has become one of the best curable cancers. However, better biomarkers are needed for outcome prediction that would allow protecting patients from over- or under-dosing of treatment. Thymus and activation-regulated chemokine/CCL17 (TARC) is highly and specifically elevated in this disease and has been proposed as possible biomarker in HL patients. In this study, we show that pretreatment TARC levels were associated with established clinical risk factors and predictive for response to treatment in a large cohort of HL patients treated in clinical trials by the German Hodgkin Study Group. Moreover, TARC levels also significantly contributed to a novel multivariate model predicting treatment response. These data clearly suggest an important role for this chemokine as biomarker in HL.
Tumor-Targeting, MicroRNA-Silencing Porous Silicon Nanoparticles for Ovarian Cancer Therapy (2019)

Silencing of aberrantly expressed microRNAs (miRNAs or miRs) has emerged as one of the strategies for molecular targeted cancer therapeutics. In particular, miR-21 is an oncogenic miRNA overexpressed in many tumors, including ovarian cancer. To achieve efficient administration of anti-miR therapeutics, delivery systems are needed that can ensure local accumulation in the tumor environment, low systemic toxicity, and reduced adverse side effects. In order to develop an improved anti-miR therapeutic agent for the treatment of ovarian cancer, a nanoformulation is engineered that leverages biodegradable porous silicon nanoparticles (pSiNPs) encapsulating an anti-miR-21 locked nucleic acid payload and displaying a tumor-homing peptide for targeted distribution. Targeting efficacy, miR-21 silencing, and anticancer activity are optimized in vitro on a panel of ovarian cancer cell lines, and a formulation of anti-miR-21 in a pSiNP displaying the targeting peptide CGKRK is identified for in vivo evaluation. When this nanoparticulate agent is delivered to mice bearing tumor xenografts, a substantial inhibition of tumor growth is achieved through silencing of miR-21. This study presents the first successful application of tumor-targeted anti-miR porous silicon nanoparticles for the treatment of ovarian cancer in a mouse xenograft model.
Impact of birth parameters and early life growth patterns on retinal microvascular structure in children (2015)

Preterm birth and accelerated infant growth are associated with narrower retinal arteriolar caliber in childhood. Whether these microvascular adaptations explain the well known associations of fetal and infant characteristics with cardiovascular disease in later life should be further studied.
Combined Effects of Thrombosis Pathway Gene Variants Predict Cardiovascular Events (2007)

The genetic background of complex diseases is proposed to consist of several low-penetrance risk loci. Addressing this complexity likely requires both large sample size and simultaneous analysis of different predisposing variants. We investigated the role of four thrombosis genes: coagulation factor V (F5), intercellular adhesion molecule 1 (ICAM1), protein C (PROC), and thrombomodulin (THBD) in cardiovascular diseases. Single allelic gene variants and their pair-wise combinations were analyzed in two independently sampled population cohorts from Finland. From among 14,140 FINRISK participants (FINRISK-92, n = 5,999 and FINRISK-97, n = 8,141), we selected for genotyping a sample of 2,222, including 528 incident cardiovascular disease (CVD) cases and random subcohorts totaling 786. To cover all known common haplotypes (>10%), 54 single nucleotide polymorphisms (SNPs) were genotyped. Classification-tree analysis identified 11 SNPs that were further analyzed in Cox's proportional hazard model as single variants and pair-wise combinations. Multiple testing was controlled by use of two independent cohorts and with false-discovery rate. Several CVD risk variants were identified: In women, the combination of F5 rs7542281 x THBD rs1042580, together with three single F5 SNPs, was associated with CVD events. Among men, PROC rs1041296, when combined with either ICAM1 rs5030341 or F5 rs2269648, was associated with total mortality. As a single variant, PROC rs1401296, together with the F5 Leiden mutation, was associated with ischemic stroke events. Our strategy to combine the classification-tree analysis with more traditional genetic models was successful in identifying SNPs-acting either in combination or as single variants--predisposing to CVD, and produced consistent results in two independent cohorts. These results suggest that variants in these four thrombosis genes contribute to arterial cardiovascular events at population level.
High Serum Creatinine Kinase Level: Possible Risk Factor for Neuroleptic Malignant Syndrome (2002)

High creatinine kinase (CK) levels and leukocytosis are known to be associated with neuroleptic malignant syndrome (NMS). The authors sought to determine if their presence during non-NMS psychotic episodes is predictive of the later development of NMS. Sixteen psychotic inpatients who met the criteria for NMS were included. For statistical comparison, two control groups were formed by matching each study patient with two non-NMS patients for age, gender, ethnicity, and year and ward of hospitalization (n = 32). The maximal individual serum levels of CK, lactate dehydrogenase (LDH), serum glutamic oxaloacetic transaminase (SGOT), and white blood cell count (WBC) during all non-NMS psychotic episodes (Brief Psychiatric Rating Scale 40) were averaged. To normalize the distribution, the individual averages were transformed to natural logarithms (Ln). Mean Ln (average [CK]) in the patients with NMS was found to be 6.46 +/- 0.91 IU/L, and in the non-NMS patients, 5.24 +/- 0.90 IU/L (actual serum CK levels, 911 +/- 747 IU/L and 343 +/- 620 IU/L, respectively). This difference was statistically significant (F [2,15] = 10.5, p < 0.0001). In addition, CK levels above the upper limit of normal were noted in 76% of psychotic episodes in the patients with NMS and in only 30% of psychotic episodes in the non-NMS patients (p < 0.0001). There was no significant difference between the NMS and non-NMS groups in Ln(LDH), Ln(SGOT), or Ln(WBC) (F [2,15] = 1.4, 2.1, and 0.9, respectively). The authors concluded that high serum CK level during non-NMS psychotic episodes seems to be a risk factor for future NMS. Therefore, CK measurement may be justified on admission of acutely psychotic patients who have other risk factors and a history of psychosis-associated CKemia.
Adaptive laboratory evolution reveals general and specific chemical tolerance mechanisms and enhances biochemical production (2019)

Abstract Tolerance to high product concentrations is a major barrier to achieving economically viable processes for bio-based chemical production. Chemical tolerance mechanisms are often unknown, thus their rational design is not achievable. To reveal unknown tolerance mechanisms we used an automated platform to evolve Escherichia coli to grow in previously toxic concentrations of 11 chemicals that have applications as polymer precursors, chemical intermediates, or biofuels. Re-sequencing of isolates from 88 independently evolved populations, reconstruction of mutations, and cross-compound tolerance profiling was employed to uncover general and specific tolerance mechanisms. We found that: 1) the broad tolerance of strains towards chemicals varied significantly depending on the chemical stress condition under which the strain was evolved; 2) the strains that acquired high levels of NaCl tolerance also became broadly tolerant to most chemicals; 3) genetic tolerance mechanisms included alterations in regulatory, cell wall, transcriptional and translational functions, as well as more chemical-specific mechanisms related to transport and metabolism; 4) using pre-tolerized starting strains can significantly enhance subsequent production of chemicals when a production pathway is inserted; and 5) only a subset of the evolved isolates showed improved production indicating that this approach is especially useful when a large number of independently evolved isolates are screened for production. We provide a comprehensive genotype-phenotype map based on identified mutations and growth phenotypes for 224 chemical tolerant strains.
Metabolic changes following eccentric exercise in trained and untrained men (1986)

The effects of one 45-min bout of high-intensity eccentric exercise (250 W) were studied in four male runners and five untrained men. Plasma creatine kinase (CK) activity in these runners was higher (P less than 0.001) than in the untrained men before exercise and peaked at 207 IU/ml 1 day after exercise, whereas in untrained men the maximum was 2,143 IU/ml 5 days after exercise. Plasma interleukin-1 (IL-1) in the trained men was also higher (P less than 0.001) than in the untrained men before exercise but did not significantly increase after exercise. In the untrained men, IL-1 was significantly elevated 3 h after exercise (P less than 0.001). In the untrained group only, 24-h urines were collected before and after exercise while the men consumed a meat-free diet. Urinary 3-methylhistidine/creatinine in the untrained group rose significantly from 127 mumol/g before exercise to 180 mumol/g 10 days after exercise. The results suggest that in untrained men eccentric exercise leads to a metabolic response indicative of delayed muscle damage. Regularly performed long distance running was associated with chronically elevated plasma IL-1 levels and serum CK activities without acute increases after an eccentric exercise bout.
Total knee arthroplasty after distal femoral osteotomy long-term survivorship and clinical outcomes (2019)

Aims There is little literature about total knee arthroplasty (TKA) after distal femoral osteotomy (DFO). Consequently, the purpose of this study was to analyze the outcomes of TKA after DFO, with particular emphasis on: survivorship free from aseptic loosening, revision, or any re-operation; complications; radiological results; and clinical outcome. Patients and Methods We retrospectively reviewed 29 patients (17 women, 12 men) from our total joint registry who had undergone 31 cemented TKAs after a DFO between 2000 and 2012. Their mean age at TKA was 51 years (22 to 76) and their mean body mass index 32 kg/m 2 (20 to 45). The mean time between DFO and TKA was ten years (2 to 20). The mean follow-up from TKA was ten years (2 to 16). The prostheses were posterior-stabilized in 77%, varus-valgus constraint (VVC) in 13%, and cruciate-retaining in 10%. While no patient had metaphyseal fixation (e.g. cones or sleeves), 16% needed a femoral stem. Results The ten-year survivorship was 95% with aseptic loosening as the endpoint, 88% with revision for any reason as the endpoint, and 81% with re-operation for any reason as the endpoint. Three TKAs were revised for instability (n = 2) and aseptic tibial loosening (n = 1). No femoral component was revised for aseptic loosening. Patients under the age of 50 years were at greater risk of revision for any reason (hazard ratio 7; p = 0.03). There were two additional re-operations (6%) and four complications (13%), including three manipulations under anaesthetic (MUA; 10%). The Knee Society scores improved from a mean of 50 preoperatively (32 to 68) to a mean of 93 postoperatively (76 to 100; p &lt; 0.001). Conclusion A cemented posterior-stabilized TKA has an 88% ten-year survivorship with revision for any reason as the endpoint. No femoral component was revised for aseptic loosening. Patients under the age of 50 years have a greater risk of revision. The clinical outcome was significantly improved but balancing the knee was challenging in 13% of TKAs requiring VVC. Overall, 10% of TKAs needed an MUA, and 6% of TKAs were revised for instability. Cite this article: Bone Joint J 2019;101-B:660–666.
Circulating current suppression strategies for D-STATCOM based on modular multilevel converters (2015)

This work focuses on the circulating current control of a STAtic synchronous COMpensator (STATCOM) based on Modular Multilevel Converter (MMC). Two circulating current estimation strategies are analyzed, with focus on the converter performance improvement The conventional method to estimated the circulating current has been improved using a Second Order Generalized Integrator (SOGI) structure. The proposed strategy eliminates the third harmonic component from the circulating current through a SOGI filter. Simulated and experimental results compare both classical and proposed strategy in terms of reduction in the circulating current, dynamic behavior during reference changes and reduction in the STATCOM losses.
X-ray streak camera with 2 ps response (1990)

We have developed an x-ray streak camera system with a temporal response of 2 ps (full width at half maximum). The response of the camera was measured using soft x rays in the 30 eV to 1 keV energy range which were emitted from a plasma created by a high-intensity, subpicosecond laser pulse. A single shot, resolution-limited, relative timing precision of 0.2 ps was demonstrated for x-ray emission events.
Mid-infrared supercontinuum generation spanning 18 octaves using step-index indium fluoride fiber pumped by a femtosecond fiber laser near 2 µm (2015)

A nearly two-octave wide coherent mid-infrared supercontinuum is demonstrated in a dispersion-engineered step-index indium fluoride fiber pumped near 2 µm. The pump source is an all-fiber femtosecond laser with 100 fs pulse width, 570 mW average power and 50 MHz repetition rate. The supercontinuum spectrum spans from 1.25 µm to 4.6 µm. Numerical modelling of the supercontinuum spectra show good agreement with the measurements. The coherence of the supercontinuum is calculated using a numerical model and shows a high degree of coherence across the generated bandwidth allowing it to be used for frequency comb applications.
Tunable Er3+-doped Fiber Amplifiers Covering S-and C + L-bands (1490 ~ 1610 nm) Using Discrete All-fiber ASE Suppressing Filters (2006)

We have demonstrated thermo-optically tunable EDFAs using a 17.5-m-long silica-based single-cladding C-band EDF with discrete ASE suppressing filters in a simple and cost-effective way. The short-pass filters can provide widely tunable lambda <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">c</sub> with high cutoff efficiency such that the amplification of EDFA can be tuned to cover S- and C+L-bands over 1490~1610 nm
A New Unconventional Magnet Arrangement for Linear Permanent Magnet Motors with Semi-FEA-Based Optimization Approach (2021)

Linear actuators are frequently used in numerous applications where precise linear movement is needed. Permanent magnet linear motors (PMLM) provide high force density and accurate positioning and high-operating drive cycle as to other types of linear motors. The quality of force output for the PMLM mainly depends on detent force component. In this paper, a new approach is presented to minimize the detent force for PMLM. Proposed approach consists of semi-FEA based optimization of the magnet track, which considers minimization of the detent force and maximization of the average force output. Proposed approach generates the magnet layout arbitrarily and tries to find the optimum solutions by 2-dimensioanal (2D) Pareto front. A reference coreless PMLM is used as a benchmark and the results show that proposed approach is an effective method as to conventional methods and it is possible to determine the optimum magnet track arrangement design by the proposed approach.