gebhart/patrepeval huggingface dataset:
Genome-Wide Analysis of leafbladeless1-Regulated and Phased Small RNAs Underscores the Importance of the TAS3 ta-siRNA Pathway to Maize Development (2014)

Maize leafbladeless1 (lbl1) encodes a key component in the trans-acting short-interfering RNA (ta-siRNA) biogenesis pathway. Correlated with a great diversity in ta-siRNAs and the targets they regulate, the phenotypes conditioned by mutants perturbing this small RNA pathway vary extensively across species. Mutations in lbl1 result in severe developmental defects, giving rise to plants with radial, abaxialized leaves. To investigate the basis for this phenotype, we compared the small RNA content between wild-type and lbl1 seedling apices. We show that LBL1 affects the accumulation of small RNAs in all major classes, and reveal unexpected crosstalk between ta-siRNA biogenesis and other small RNA pathways regulating transposons. Interestingly, in contrast to data from other plant species, we found no evidence for the existence of phased siRNAs generated via the one-hit model. Our analysis identified nine TAS loci, all belonging to the conserved TAS3 family. Information from RNA deep sequencing and PARE analyses identified the tasiR-ARFs as the major functional ta-siRNAs in the maize vegetative apex where they regulate expression of AUXIN RESPONSE FACTOR3 (ARF3) homologs. Plants expressing a tasiR-ARF insensitive arf3a transgene recapitulate the phenotype of lbl1, providing direct evidence that deregulation of ARF3 transcription factors underlies the developmental defects of maize ta-siRNA biogenesis mutants. The phenotypes of Arabidopsis and Medicago ta-siRNA mutants, while strikingly different, likewise result from misexpression of the tasiR-ARF target ARF3. Our data indicate that diversity in TAS pathways and their targets cannot fully account for the phenotypic differences conditioned by ta-siRNA biogenesis mutants across plant species. Instead, we propose that divergence in the gene networks downstream of the ARF3 transcription factors or the spatiotemporal pattern during leaf development in which these proteins act constitute key factors underlying the distinct contributions of the ta-siRNA pathway to development in maize, Arabidopsis, and possibly other plant species as well.
Voltages before and after current in HBM testers and real HBM (2005)

Voltage is a static parameter in present ESD testers and standards with only current specified in time (dI/dt) parameters. Measurements of real and tester HBM discharges identify the previously unknown voltage rate of change (dV/dt) and how this new threat parameter can affect failure levels in some protection circuits.
OCTAVE-S (Registered) Implementation Guide, Version 1.0. Volume 5: Critical Asset Worksheets for Information (2005)

Abstract : The Operationally Critical Threat, Asset, and Vulnerability EvaluationSM (OCTAVE) approach defines a risk-based strategic assessment and planning technique for security. OCTAVE is a self-directed approach, meaning that people from an organization assume responsibility for setting the organization's security strategy. OCTAVE-S is a variation of the approach tailored to the limited means and unique constraints typically found in small organizations (less than 100 people). OCTAVE-S is led by a small, interdisciplinary team (three to five people) of an organization . personnel who gather and analyze information, producing a protection strategy and mitigation plans based on the organization's unique operational security risks. To conduct OCTAVE-S effectively, the team must have broad knowledge of the organization's business and security processes, so it will be able to conduct all activities by itself.
Thyroglobulin Point of Care Assay for Rapid Detection of Metastatic Differentiated Thyroid Carcinoma- A Pilot Study (2023)

Searchable abstracts of presentations at key conferences in endocrinology ISSN 1470-3947 (print) | ISSN 1479-6848 (online)
Energy Minimization in the Electrochemical Disinfection of Human Liquid Waste Using Boron-Doped Diamond Electrodes (2013)

Abstract not Available.
Nano‐Bio‐Chemical Braille for Cells: The Regulation of Stem Cell Responses using Bi‐Functional Surfaces (2014)

Insufficient integration with local host tissues is a significant problem that adversely affects the performance of implanted biomedical devices. Poor tissue integration leaves patients susceptible to complications associated with adverse foreign body reactions and infections that typically mandate expensive and elevated‐risk revision surgery. The aging population and growing incidence of medical implants makes the development of bio‐functional implant surfaces a high priority research imperative. Here multifunctional surfaces are reported that are capable of regulating cell adhesion and triggering cell differentiation to facilitate osseointegration of implantable devices. The approach described is universal, cost‐ and time‐effective. It relies on a unique combination of two advances: i) a reactive interface provided by a plasma activated coating (PAC) that covalently immobilises bioactive molecules with significantly higher efficiency than conventional technologies, and ii) multifunctional molecules (bi‐functional fusion‐proteins) that regulate multiple cellular responses. Covalent linking of the molecules, their high density, and desired orientation are demonstrated. The effectiveness of these functional interfaces to regulate mesenchymal stem cell attachment and differentiation is confirmed suggesting the ability to regulate osseointegration. This method is a leap forward in the fabrication of truly biofunctional materials tailored for particular applications.
The Pompe Registry: tracking Pompe disease symptoms in a broad patient population (2008)

These results show significant delay from symptom onset to diagnosis in adult patients, highlighting the need for greater disease awareness. Registry data on prevalence and age at onset of symptoms may allow earlier patient identification, enabling intervention before irreversible muscle damage occurs. Analysis of registry data over time may increase understanding of the evolution of, and interaction between, impairments and function under varying conditions and interventions, allowing improved clinical management.
Magnetostriction and soft magnetic properties of (Co1−xFex)–Al–O granular films with high electrical resistivity (1999)

We have investigated the magnetic properties of (Co1−xFex)–Al–O granular thin films prepared by a reactive sputtering method in an atmosphere of O2+Ar. The coercivity and electrical resistivity of the films are almost independent of x, but with increasing x the anisotropy field decreases linearly and the saturation induction has a broad maximum of 20 kG around x=0.7. The granular films show the same general tendency as bulk Co–Fe alloys in the compositional dependence of magnetostriction (λ). The magnitude of λ varies with increasing annealing temperature. Using a film with x=0.08 as the core of a spiral-wound inductor gave a quality factor Q=25 at a frequency of 300 MHz.
Decreased QTc dispersion after coronary revascularization: relationships with the quantitative degree of improvement in myocardial ischemia (2000)

Object and Methods: : : :Thirty-four patients (mean age:58.1±8.3 years, M:F=21:13 with angina in the absence of previous myocardial infarction, who underwent percutaneous coronary intervention (stenting and/or balloon PTCA, n=25 or coronary arterial bypass grafting (CABG, n=9 were evaluated to assess the relations- hips between the degree of improvement in myocardial dipyridamole Tl-201 SPECT and the degree of decrease in QTc dispersion after coronary revascularization. QTc dispersions were measured manually using digitizer by a single observer from ECGs printed at 25 mm/sec, 1 day before, immediately, 1 day, and 1 month after the revasc- ularization procedure. Myocardial Tl-201 SPECTs were performed before and 1 month after the revascularization and ischemic indices were measured in all cases. Results:Mean QTc dispersion was 51.4±17.0 msec before revascularization, 42.6±15.1 msec immediately after, 45.6±19.3 msec 1 day after and 37.4±11.6 msec 1 month after revascularization. The decrease of QTc dispersion immediate (p=0.001 and 1 month (p<0.001 after revascularization, were statistically significant. Mean Tl-201 SPECT ischemic index measured before the revascularization (7.8±5.9 was significantly higher (p<0.001 than the one measured 1 month after the revascu- larization (1.5±2.8. But, in Δischemic index (ischemic index before revascularization-ischemic index 1 month afer revascularization, there was no significant difference between the patients with decrease in QTc dispersion after revascularization (6.2±6.3, n=27 and the patients without decrease in QTc dispersion (6.6±5.2, n=7). There was no statistically significant correlation between Δ QTc (QTc dispersion before revascularization- QTc dispersion 1 month afer revascularization and Δischemic index in total subjects. Conclusion:QTc dispersions decrease after successful coronary revascularizations in patients with angina, but considering the relationships between the changes of QTc dispersions and ischemic indices in myocardial dipyridamole Tl-201 SPECT, the degree of decrease in QTc dispersion after coronary revascularization does not have the relationships with the quantitative degree of improvement in myocardial ischemia. (Korean Circulation J 2000;30(8 :998-1003
Investigating the hepatitis B virus life cycle using engineered reporter hepatitis B viruses (2017)

Chronic infection with hepatitis B virus (HBV) increases the risk of developing fibrosis, cirrhosis or hepatocellular carcinoma. Current therapies are limited to type-I interferons and/or nucleos(t)ide analogues; however, these are only partially effective. The development of novel anti-HBV agents for new treatment strategies has been hampered by the lack of a suitable system that allows the in vitro replication of HBV. Studies of virus infection/replication at the molecular level using wild-type HBV are labor-intensive and time-consuming. To overcome these problems, we previously constructed a recombinant reporter HBV bearing the NanoLuc gene and showed its usefulness in identifying factors that affect HBV proliferation. Because this system mimics the early stage of the HBV life cycle faithfully, we conducted a quantitative analysis of HBV infectivity to several human hepatocyte cell lines as well as the effect of dimethyl sulfoxide and HBV protein X on the early stage of HBV proliferation using this system. Furthermore, we developed a system to produce a reporter HBV expressing a pol gene. These reporter HBV may provide an opportunity to enhance our understanding of the HBV life cycle and aid strategies for the development of new anti-HBV agents.
Reduced matrix viscosity in DNA sequencing by CE and microchip electrophoresis using a novel thermo‐responsive copolymer (2009)

High viscosity is an inherent problem of sequencing matrices made of hydrophilic polymers. This problem is amplified in separations using microchips where the channels are even smaller. A novel thermal-associating graft copolymer, using linear polyacrylamide (LPA) as the backbone and poly(propylene oxide) (PPO) as the graft side chain was synthesized. The injection problem could be resolved by introducing PPO side chains that can be assembled by using temperature changes but without an obvious detrimental effect on the sieving ability of the LPA. Viscosity measurement showed that these LPA-g-PPO copolymers had a transition temperature of approximately 40 degrees C, above which a significant increase in viscosity was observed. The sequencing performance depended on the thermal association properties of PPO and related parameters. Without optimization, a read length of 1000 bases with a single base resolution of 0.3 was achieved within an hour on an ABI 310 analyzer, using 1.8 wt% LPA-g-PPO (1.8 MDa, PPO, 0.2%). This novel thermal reversible copolymer solution can be a promising candidate as a viable matrix for DNA sequencing in CE, and even more so in microchip electrophoresis.
Towards high-power mid-IR frequency combs via 2-μm-pumped difference frequency generation (2019)

We numerically demonstrate that 2-μm-pumped DFG in a GaSe is able to generate mid-IR pulses with sub-Watt level average power thanks to a reduced group-velocity mismatch compared with conventional 1-μm-pumped DFG.
Simplified Development of Multiplex Real-Time PCR Through Master Mix Augmented by Universal Fluorogenic Reporters (2016)

Mediator probe (MP) PCR is a real-time PCR approach that uses standardized universal fluorogenic reporter oligonucleotides (UR) in conjunction with label-free sequence-specific probes. To enable multiplex real-time MP PCR, we designed a set of five optimized URs with different fluorescent labels. Performance of the optimized URs was verified in multiplex real-time MP PCR for the detection of a pentaplex food panel and a quadruplex methicillin-resistant Staphylococcus aureus (MRSA) panel. Results were comparable to corresponding multiplex hydrolysis probe (HP) PCR, also designated as TaqMan PCR. Analyses of MRSA DNA standards and DNA extracted from patient swab samples showed improved lower limits of detection (LoDs) by a factor of 2-5 when using quadruplex real-time MP PCR instead of HP PCR. The novel set of standardized URs we present here simplifies development of multiplex real-time PCR assays by requiring only the design of label-free probes. In the future, real-time PCR master mixes could be augmented with up to five standardized fluorogenic URs, each emitting light at a different wavelength.
Real-Time Fault Detection and Identification for MMC Using 1-D Convolutional Neural Networks (2018)

Automated early detection and identification of switch faults are essential in high-voltage applications. Modular multilevel converter (MMC) is a new and promising topology for such applications. MMC is composed of many identical controlled voltage sources called modules or cells. Each cell may have one or more switches and a switch failure may occur in anyone of these cells. The steady-state normal and fault behavior of a cell voltage will also significantly vary according to the changes in the load current and the fault timing. This makes it a challenging problem to detect and identify such faults as soon as they occur. In this paper, we propose a real-time and highly accurate MMC circuit monitoring system for early fault detection and identification using adaptive one-dimensional convolutional neural networks. The proposed approach is directly applicable to the raw voltage and current data and thus eliminates the need for any feature extraction algorithm, resulting in a highly efficient and reliable system. Simulation results obtained using a four-cell, eight-switch MMC topology demonstrate that the proposed system has a high reliability to avoid any false alarm and achieves a detection probability of 0.989, and average identification probability of 0.997 in less than 100 ms.
Circulating Myeloid Regulatory Cells: Promising Biomarkers in B-Cell Lymphomas (2021)

The monocyte/macrophage lineage has been shown to be involved in the promotion of a protumoral tumor microenvironment and resistance to treatment in B cell lymphomas. However, it is still poorly described at the single cell level, and tissue samples are not easily accessible. Thus, a detailed analysis of the circulating myeloid cell compartment in the different B lymphomas is needed to better understand the mechanisms of resistance to treatment and identify at risk patients. In this Perspective, we review current knowledge on the phenotypic and functional description of the circulating monocytic lineage in B cell lymphomas and provide first insights into the heterogeneity of these cell populations in health and lymphoma, using mass cytometry. Indeed, the monocytic compartment is a continuum more than distinct subpopulations, as demonstrated by our high-resolution approach, explaining the sometimes confusing and contradictory conclusions on the prognostic impact of the different populations, including monocytes and monocytic myeloid derived suppressor cells (M-MDSC). By identifying S100A9<sup>high</sup> monocytic cells as a potential biomarker in diffuse large B cell lymphoma (DLBCL) in this proof-of-concept preliminary study including a limited number of samples, we underline the potential of circulating myeloid regulatory cells as diagnostic and prognostic biomarkers in B-cell lymphomas.
Identification of Proteins Sensitive to Thermal Stress in Human Neuroblastoma and Glioma Cell Lines (2012)

Heat-shock is an acute insult to the mammalian proteome. The sudden elevation in temperature has far-reaching effects on protein metabolism, leads to a rapid inhibition of most protein synthesis, and the induction of protein chaperones. Using heat-shock in cells of neuronal (SH-SY5Y) and glial (CCF-STTG1) lineage, in conjunction with detergent extraction and sedimentation followed by LC-MS/MS proteomic approaches, we sought to identify human proteins that lose solubility upon heat-shock. The two cell lines showed largely overlapping profiles of proteins detected by LC-MS/MS. We identified 58 proteins in detergent insoluble fractions as losing solubility in after heat shock; 10 were common between the 2 cell lines. A subset of the proteins identified by LC-MS/MS was validated by immunoblotting of similarly prepared fractions. Ultimately, we were able to definitively identify 3 proteins as putatively metastable neural proteins; FEN1, CDK1, and TDP-43. We also determined that after heat-shock these cells accumulate insoluble polyubiquitin chains largely linked via lysine 48 (K-48) residues. Collectively, this study identifies human neural proteins that lose solubility upon heat-shock. These proteins may represent components of the human proteome that are vulnerable to misfolding in settings of proteostasis stress.
Psychosis and epilepsy: Seizure-type comparisons and high-risk variables (1981)

Compared 153 patients with temporal lobe epilepsy (TLE) and 79 patients with generalized epilepsy on the Goldberg Index, an MMPI-derived measure of psychosis. Analysis of covariance indicated that seizure type was not related to psychosis. Multiple regression analyses indicated that, in TLE, being female was correlated positively with Goldberg Index scores. In the group with generalized epilepsy, none of the variables was associated significantly with psychosis scores.
Major Nutrient Recycling for Sustainable Algal Culture. (2015)

Abstract not provided.
Novel enzyme preparations with high pectinase and hemicellulase activity based on Penicillium canescens strains (2015)

Recombinant strains of Penicillium canescens producing homologous pectin lyase A and heterologous endo- 1,5-α-arabinase A and endo- 1,4-α-polygalacturonase, as well as enzymes of the host strain (α-L-arabinofuranosidases, xylanases, and others), were obtained by genetic engineering. The enzyme preparations (EPs) obtained from the cultural medium of recombinant P. canescens strains efficiently hydrolyzed raw plant material with a high content of pectin compounds. It was shown that the yield of reducing sugars and arabinose increased 16 and 22% in comparison with the control EP based on the host strain when one of the obtained EPs was used for beet pulp hydrolysis. It was established that the most active EP consisted of pectin lyase (10%), endo-1,5-arabinase (26%), α-L-arabinofuranosidase and arabinoxylan-arabinofuranohydrolase (12%), and xylanase (10%). The activities of pectin lyase, polygalacturonase, and arabinase of the EP in reactions with various substrates were determined. The specificity, pH and T-optima, and thermal stability of the homogenous recombinant endo- 1,5-α-arabinase were investigated. The kinetic parameters (K(m), K(cat)) of the linear arabinan hydrolysis were determined.
Quantification of gene-specific methylation of DNMT3B and MTHFR using sequenom EpiTYPER® (2015)

Among 272 patients undergoing a screening colonoscopy, DNA methylation of DNMT3B and MTHFR, genes encoding enzymes critical to one-carbon metabolism, was quantified in blood leukocytes using Sequenom EpiTYPER®. DNA methylation was quantified in 66 and 28 CpG sites of DNMT3B and MTHFR respectively, and conceptualized using two approaches. First, measures representing average methylation across all CpG sites were created. Second, unsupervised principal component (PC) analysis was used as a pattern derivation and data-reduction approach, to develop two summary variables (PC1 and PC2). These two summary variables represented methylation around the transcription start site (PC1) and in the gene-coding area (PC2) for both DNMT3B and MTHFR. The data contained in this article presents the variation of methylation levels for individual CpG sites within the DNMT3B and MTHFR genes and possible correlations uncovered using PC analysis. The data are related to the research article “Gene-specific DNA methylation of DNMT3B and MTHFR and colorectal adenoma risk” in Mutation Research – Fundamental and Molecular Mechanisms of Mutagenesis.
Ligation of the OX40 co-stimulatory receptor reverses self-Ag and tumor-induced CD8 T cell anergy in vivo (40.30) (2009)

Abstract Tumor-specific CD8 T cell peripheral tolerance occurs through a variety of mechanisms including clonal deletion, suppression, and the induction of anergy and is an important barrier that limits the generation of anti-tumor immunity. Several groups have demonstrated that prostate cancer can render tumor-specific CD8 T cells anergic, suggesting that strategies to reverse tumor-induced anergy may augment anti-tumor immunity. Recent work has demonstrated that signaling through the OX40 (CD134) co-stimulatory receptor, a member of the TNFR super-family, can augment both CD4 and CD8 T cell expansion, differentiation, and the generation of memory cells. However, whether OX40 ligation can reverse CD8 T cell anergy, and more specifically, tumor-induced CD8 T cell anergy, remains unclear. In the current study, we demonstrate that OX40 ligation can reverse CD8 T cell anergy to a prostate-specific self-antigen in non-tumor bearing hosts. Furthermore, OX40 engagement reversed tumor-specific CD8 T cell anergy and restored the proliferative capacity of tumor-reactive CD8 T cells in vivo, which attenuated the extent of tumor growth and enhanced the survival of tumor-bearing hosts. This is the first demonstration that OX40 ligation can rescue the function of anergic self or tumor-reactive CD8 T cells in vivo and suggests that OX40-mediated therapy may provide a novel means of boosting anti-tumor immunity by restoring the responsiveness of previously anergic tumor-specific CD8 T cells. Supported by an American Cancer Society - Sam E. and Kathleen Henry post-doctoral fellowship, a Prostate Cancer Foundation Young Investigator Award (W.L.R.), and grants from the NIH (A.D.W.).
Antenna analysis using properties of metamaterials (2010)

As part of the Student Internship Programs at Wright-Patterson Air Force Base, including the AFRL Wright Scholar Program for High School Students and the AFRL STEP Program, sample results from preliminary investigation and analysis of integrated antenna structures are reported. Investigation of these novel integrated antenna geometries can be interpreted as a continuation of systems analysis under the general topic area of potential integrated apertures for future software radar/radio solutions [1] [2]. Specifically, the categories of novel integrated aperture geometries investigated in this paper include slotted-fractal structures on microstrip rectangular patch antenna models in tandem with the analysis of exotic substrate materials comprised of a type of synthesized electromagnetic structure known as metamaterials [8] - [10].