gebhart/patrepeval huggingface dataset:
Dielectric liquids for enhanced field force in macro scale direct drive electrostatic actuators and rotating machinery (2016)

Recently interest towards electrostatic actuators and machinery has increased for use in MEMS, mechatronics and renewable energy applications. Effective electromechanical power conversion using electrostatics requires dielectric liquids whose permittivity and breakdown field strength can facilitate adequate electric shear stress and pressure beyond the capabilities of media such as air or vacuum. This paper discusses design points for practical electrostatic force production and evaluates available off-the-shelf dielectric liquids in terms of electric pressure capability. Key dielectric properties including pressure, breakdown field strength, relative permittivity, and conductivity are measured. A custom test stand measures the attractive force between two electrodes mounted on load cells inside a tank filled with the liquid under test. Measurements demonstrate liquids capable of reaching several psi of electric pressure while correlating with analytical and finite element (FE) models, ultimately forming a basis for electrostatic actuator/machine design. The best liquid candidate, Vertrel XF, was poured into a proof of concept macro scale electrostatic machine demonstrating 0.9 N-m torque and 0.126 N-m/kg. Torque measurements verify the capability of Vertrel XF and the correlation between the electric pressure and shear stress in a rotating machine.
Regulation of Virulence Factors of Enterohemorrhagic Escherichia coli O157:H7 by Self-Produced Extracellular Factors (2000)

Enterohemorrhagic Escherichia coli (EHEC) O157:H7 causes serious diarrhea and hemolytic uremic syndrome in humans. The expressions of EspD and intimin by O157:H7 have now been shown to be down-regulated by medium conditioned by O157:H7 grown at stationary phase. Preparation of conditioned medium showing the effect on the amount of EspD was not dependent on temperature or growth medium, but was dependent on growth phase. Inhibition of EspD and intimin expression was also induced by medium conditioned by E. coli K-12 strains and homoserine lactone, a signal molecule of the quorum-sensing system in gram-negative bacteria. These results suggest the possibility that the quorum-sensing system mediated by self-produced extracellular factors plays an important role in control of colonization of EHEC O157:H7.
The Role of Polyethylene Wax on the Thermal Conductivity of Transparent Ultradrawn Polyethylene Films (2020)

Transparency and thermal conductivity of ultradrawn, ultrahigh-molecular-weight polyethylene films containing different contents of low-molecular-weight polyethylene wax (PE<sub>wax</sub>) are explored from experimental and theoretical viewpoints. It is shown that the addition of PE<sub>wax</sub> decreases light scattering in all directions, resulting from a reduction of defects while having little effect on crystallinity or chain orientation of ultradrawn films. In general, upon the addition of PE<sub>wax</sub>, the thermal conductivity of ultradrawn films increases with the highest conductivity being 47 (W m<sup>-1</sup> K<sup>-1</sup>) and subsequently decreases at higher concentrations. The thermal conductivity also depends on draw ratio and number-average molecular weight (Mn) of the films. A model is presented which correlates the thermal conductivity of the films with the draw ratio and Mn, enabling explanation of the experimental results. Hence, the thermal conductivity of ultradrawn polyethylene films can be predicted as a function of Mn and draw ratio.
Multi-format Continuously Variable Bitrate DPSK/OOK Demodulating Receiver Design (2006)

In this paper we demonstrate a continuously variable bitrate receiver from 10 to 40 Gbit/s for DPSK balanced demodulation. Unlike previous DPSK demodulators, this receiver is also capable of passing intensity modulated waveforms unaffected.
ChemInform Abstract: THE SEQUENTIAL LITHIATION OF 1‐PHENYL‐1,2,4‐TRIAZOLES (1985)

Abstract Metallierung der im Titel genannten Verbindung (Ia) mit BuLi führt ausschließlich zum 5‐Lithio‐Derivat (Ib), aus dem durch Carboxylierung bzw. Reaktion mit Elektrophilen die 5‐substituierten Triazole (Ic)‐(If) und (IIa)‐(IId) erhalten werden.
Figure S2 from Intratumoral Plasmid IL12 Expands CD8<sup>+</sup> T Cells and Induces a CXCR3 Gene Signature in Triple-negative Breast Tumors that Sensitizes Patients to Anti–PD-1 Therapy (2023)

&lt;p&gt;Figure S2&lt;/p&gt;
Genome-wide structural variant analysis identifies risk loci for non-Alzheimer’s dementias (2023)

We characterized the role of structural variants, a largely unexplored type of genetic variation, in two non-Alzheimer's dementias, namely Lewy body dementia (LBD) and frontotemporal dementia (FTD)/amyotrophic lateral sclerosis (ALS). To do this, we applied an advanced structural variant calling pipeline (GATK-SV) to short-read whole-genome sequence data from 5,213 European-ancestry cases and 4,132 controls. We discovered, replicated, and validated a deletion in <i>TPCN1</i> as a novel risk locus for LBD and detected the known structural variants at the <i>C9orf72</i> and <i>MAPT</i> loci as associated with FTD/ALS. We also identified rare pathogenic structural variants in both LBD and FTD/ALS. Finally, we assembled a catalog of structural variants that can be mined for new insights into the pathogenesis of these understudied forms of dementia.
RNase III and RNase E Influence Posttranscriptional Regulatory Networks Involved in Virulence Factor Production, Metabolism, and Regulatory RNA Processing in Bordetella pertussis (2021)

Bordetella pertussis has been shown to encode regulatory RNAs, yet the posttranscriptional regulatory circuits on which they act remain to be fully elucidated. We generated mutants lacking the endonucleases RNase III and RNase E and assessed their individual impact on the B. pertussis transcriptome. Transcriptome sequencing (RNA-Seq) analysis showed differential expression of ∼25% of the B. pertussis transcriptome in each mutant, with only 28% overlap between data sets. Both endonucleases exhibited substantial impact on genes involved in amino acid uptake (e.g., ABC transporters) and in virulence (e.g., the type III secretion system and the autotransporters <i>vag8</i>, <i>tcfA</i>, and <i>brkA</i>). Interestingly, mutations in RNase III and RNase E drove the stability of many transcripts, including those involved in virulence, in opposite directions, a result that was validated by qPCR and immunoblotting for <i>tcfA</i> and <i>brkA</i>. Of note, whereas similar mutations to RNase E in Escherichia coli have subtle effects on transcript stability, a striking >20-fold reduction in four gene transcripts, including <i>tcfA</i> and <i>vag8</i>, was observed in B. pertussis. We further compared our data set to the regulon controlled by the RNA chaperone Hfq to identify B. pertussis loci influenced by regulatory RNAs. This analysis identified ∼120 genes and 19 operons potentially regulated at the posttranscriptional level. Thus, our findings revealed how changes in RNase III- and RNase E-mediated RNA turnover influence pathways associated with virulence and cellular homeostasis. Moreover, we highlighted loci potentially influenced by regulatory RNAs, providing insights into the posttranscriptional regulatory networks involved in fine-tuning B. pertussis gene expression. <b>IMPORTANCE</b> Noncoding, regulatory RNAs in bacterial pathogens are critical components required for rapid changes in gene expression profiles. However, little is known about the role of regulatory RNAs in the growth and pathogenesis of Bordetella pertussis. To address this, mutants separately lacking ribonucleases central to regulatory RNA processing, RNase III and RNase E, were analyzed by RNA-Seq. Here, we detail the first transcriptomic analysis of the impact of altered RNA degradation in B. pertussis. Each mutant showed approximately 1,000 differentially expressed genes, with significant changes in the expression of pathways associated with metabolism, bacterial secretion, and virulence factor production. Our analysis suggests an important role for these ribonucleases during host colonization and provides insights into the breadth of posttranscriptional regulation in B. pertussis, further informing our understanding of B. pertussis pathogenesis.
Two-Step Synthesis of α-Aryl-α-diazoamides as Modular Bioreversible Labels (2021)

α-Aryl-α-diazoamides were synthesized in two steps under mild conditions. This expeditious route employs Pd-catalyzed C-H arylation of <i>N</i>-succinimidyl 2-diazoacetate to obtain <i>N</i>-succinimidyl 2-aryl-2-diazoacetates, followed by aminolysis. The ensuing diazo compounds can esterify carboxyl groups in aqueous solution, and the ester products are substrates for an esterase. The broad scope of the synthetic route enables the continued development of diazo compounds in chemical biology.
3‐(2‐Carboxyethyl)‐4,6‐dichloro‐1H‐indole‐2‐carboxylic Acid: An Allosteric Inhibitor of Fructose‐1,6‐bisphosphatase at the AMP Site. (2003)

Abstract For Abstract see ChemInform Abstract in Full Text.
Shwachman-Bodian Diamond syndrome is a multi-functional protein implicated in cellular stress responses (2009)

Shwachman-Diamond syndrome (SDS; OMIM 260400) results from loss-of-function mutations in the Shwachman-Bodian Diamond syndrome (SBDS) gene. It is a multi-system disorder with clinical features of exocrine pancreatic dysfunction, skeletal abnormalities, bone marrow failure and predisposition to leukemic transformation. Although the cellular functions of SBDS are still unclear, its yeast ortholog has been implicated in ribosome biogenesis. Using affinity capture and mass spectrometry, we have developed an SBDS-interactome and report SBDS binding partners with diverse molecular functions, notably components of the large ribosomal subunit and proteins involved in DNA metabolism. Reciprocal co-immunoprecipitation confirmed the interaction of SBDS with the large ribosomal subunit protein RPL4 and with DNA-PK and RPA70, two proteins with critical roles in DNA repair. Function for SBDS in response to cellular stresses was implicated by demonstrating that SBDS-depleted HEK293 cells are hypersensitive to multiple types of DNA damage as well as chemically induced endoplasmic reticulum stress. Furthermore, using multiple routes to impair translation and mimic the effect of SBDS-depletion, we show that SBDS-dependent hypersensitivity of HEK293 cells to UV irradiation can be distinguished from a role of SBDS in translation. These results indicate functions of SBDS beyond ribosome biogenesis and may provide insight into the poorly understood cancer predisposition of SDS patients.
Nucleation Kinetics in Materials with a Time-independent Driving Force during Phase Transformation (2000)

The dynamics of clusters during phase transformation can be described by the Fokker-Planck equation. In this paper asympototic behaviours of the Fokker-Planck equation were investigated. The driving force for nucleation in an infinite system is time dependent and the nucleation rate approaches a constant value, steady state nucleation rate. However, if the drivig force is constant during the phase transformation, the number of clusters having the critical size increases with time. Therefore, the number of the stable clusters increases with time in the case that an external driving force is applied to compensate the decrease in the chemical driving force. This result may be helpful to develop a new method of thermomechanical control process.
Exponential Decay of Reconstruction Error From Binary Measurements of Sparse Signals (2017)

Binary measurements arise naturally in a variety of statistics and engineering applications. They may be inherent to the problem-for example, in determining the relationship between genetics and the presence or absence of a disease-or they may be a result of extreme quantization. A recent influx of literature has suggested that using prior signal information can greatly improve the ability to reconstruct a signal from binary measurements. This is exemplified by one-bit compressed sensing, which takes the compressed sensing model but assumes that only the sign of each measurement is retained. It has recently been shown that the number of one-bit measurements required for signal estimation mirrors that of unquantized compressed sensing. Indeed, s-sparse signals in Rn can be estimated (up to normalization) from Ω(slog (n/s)) one-bit measurements. Nevertheless, controlling the precise accuracy of the error estimate remains an open challenge. In this paper, we focus on optimizing the decay of the error as a function of the oversampling factor λ := m/(s log(n/s)), where m is the number of measurements. It is known that the error in reconstructing sparse signals from standard one-bit measurements is bounded below by Ω(λ-1). Without adjusting the measurement procedure, reducing this polynomial error decay rate is impossible. However, we show that an adaptive choice of the thresholds used for quantization can lower the error rate to e-Ω(λ). This improves upon guarantees for other methods of adaptive thresholding, such as sigma- delta quantization. We develop a general recursive strategy to achieve this exponential decay and two specific polynomial-time algorithms, which fall into this framework, one based on convex programming and one on hard thresholding. Our work bridges the one-bit compressed sensing model, in which the engineer controls the measurement procedure, to sigma-delta and successive approximation quantization. Moreover, the principle is extendable to signal reconstruction problems in a variety of binary statistical models as well as statistical estimation problems like logistic regression.
Expression of Type V Adenylyl Cyclase Is Required for Epidermal Growth Factor-mediated Stimulation of cAMP Accumulation (1995)

Previously, this laboratory has demonstrated that epidermal growth factor (EGF) increases adenylyl cyclase activity in cardiac membranes and elevates cAMP accumulation in hearts and cardiac myocytes. Since EGF does not increase cAMP accumulation in all tissues, we investigated the possibility that the expression of a specific isoform of adenylyl cyclase (AC) was necessary to observe EGF-elicited stimulation of cAMP accumulation. HEK 293 cells were transfected with different isoforms of AC, and the ability of EGF to increase AC activity as well as elevate cAMP accumulation was determined. In cells transfected with AC I, II, V, and VI cDNAs, neither the expression nor the amount of the two isoforms of Gs alpha (45 and 52 kDa) were altered. Similarly, EGF-elicited phosphorylation of cellular proteins on tyrosine residues in various transfectants was unaltered. However, EGF increased AC activity and elevated cAMP accumulation only in cells expressing the rat and canine ACV. EGF did not alter either AC activity or cAMP accumulation in cells overexpressing types I, II, and VI isozymes. As assessed by the ability of an anti-Gs alpha antibody to obliterate the effect, stimulation of AC activity in AC V transfectants involved the participation of Gs alpha, a finding consistent with previous data concerning EGF effects on cardiac AC (Nair, B. G., Parikh, B., Milligan, G., and Patel, T. B. (1990) J. Biol. Chem. 265, 21317-21322). Thus we conclude that the expression of AC V isoform confers specificity to the ability of EGF to stimulate AC activity.
Regulation of Mycobacterium tuberculosis-Dependent HIV-1 Transcription Reveals a New Role for NFAT5 in the Toll-Like Receptor Pathway (2012)

Tuberculosis (TB) disease in HIV co-infected patients contributes to increased mortality by activating innate and adaptive immune signaling cascades that stimulate HIV-1 replication, leading to an increase in viral load. Here, we demonstrate that silencing of the expression of the transcription factor nuclear factor of activated T cells 5 (NFAT5) by RNA interference (RNAi) inhibits Mycobacterium tuberculosis (MTb)-stimulated HIV-1 replication in co-infected macrophages. We show that NFAT5 gene and protein expression are strongly induced by MTb, which is a Toll-like receptor (TLR) ligand, and that an intact NFAT5 binding site in the viral promoter of R5-tropic HIV-1 subtype B and subtype C molecular clones is required for efficent induction of HIV-1 replication by MTb. Furthermore, silencing by RNAi of key components of the TLR pathway in human monocytes, including the downstream signaling molecules MyD88, IRAK1, and TRAF6, significantly inhibits MTb-induced NFAT5 gene expression. Thus, the innate immune response to MTb infection induces NFAT5 gene and protein expression, and NFAT5 plays a crucial role in MTb regulation of HIV-1 replication via a direct interaction with the viral promoter. These findings also demonstrate a general role for NFAT5 in TLR- and MTb-mediated control of gene expression.
Cerebral Autoregulation in the Microvasculature Measured with Near-Infrared Spectroscopy (2015)

Cerebral autoregulation (CA) is the mechanism that allows the brain to maintain a stable blood flow despite changes in blood pressure. Dynamic CA can be quantified based on continuous measurements of systemic mean arterial pressure (MAP) and global cerebral blood flow. Here, we show that dynamic CA can be quantified also from local measurements that are sensitive to the microvasculature. We used near-infrared spectroscopy (NIRS) to measure temporal changes in oxy- and deoxy-hemoglobin concentrations in the prefrontal cortex of 11 human subjects. A novel hemodynamic model translates those changes into changes of cerebral blood volume and blood flow. The interplay between them is described by transfer function analysis, specifically by a high-pass filter whose cutoff frequency describes the autoregulation efficiency. We have used pneumatic thigh cuffs to induce MAP perturbation by a fast release during rest and during hyperventilation, which is known to enhance autoregulation. Based on our model, we found that the autoregulation cutoff frequency increased during hyperventilation in comparison to normal breathing in 10 out of 11 subjects, indicating a greater autoregulation efficiency. We have shown that autoregulation can reliably be measured noninvasively in the microvasculature, opening up the possibility of localized CA monitoring with NIRS.
Image-guided Percutaneous Sclerotherapy of Vascular Malformations of the Male Genitalia - A Retrospective Study (2019)

Purpose: Regarding genital lesions, the incidence of male external genitalia vascular anomalies is circa 3%, thereof one-tenth tumors and nine-tenth malformations according to the International Society for the Study of Vascular Anomalies classification. Image-guided percutaneous sclerotherapy in male external genitalia vascular malformations has rarely been described. Therefore, a retrospective analysis of sclerotherapy in a series of eight patients was conducted. Materials and Methods: The study was IRB approved. Two radiologists reviewed angiographic reports and analyzed interventionally treated male patients with external genitalia vascular malformations between February 2, 2014, and November 11, 2017, at an interdisciplinary tertiary care Vascular Anomalies Center. Inclusion criteria were a slow-flow malformation of the male external genitalia and no interventional treatment before. Operations longer than 1-year past were no exclusion criteria. Patients suffered from lymphatic and/or venous malformations and received percutaneous sclerotherapy. Malformations were treated with polidocanol, ethanol in gel form or OK-432. Patients answered a questionnaire regarding symptoms with repeat after follow-up. The initial state and post-treatment results were compared. Magnetic resonance imaging pre- and post-intervention was assessed. Complications were reported standardized. Results: Eight patients with a mean age of 21.6 years suffered from genital swelling, bleeding, thrombophlebitis, lymphorrhea, skin changes, pain, and functional genitourinary symptoms and were treated with sclerotherapy. All patients reported clinical improvement of symptoms during the average follow-up period of 30 months. No complications ensued. Conclusion: Sclerotherapy seems to be a safe and effective treatment of slow-flow malformations of the male external genitalia. Due to the low incidence of the disease, multicenter studies are necessary to assess a larger number of cases.
Greenhouse Gas Programs, Energy Efficiency, and the Industrial Sector (2009)

The United States has made significant progress in reducing total energy use through energy efficiency improvements over the past decade, yet the United States still ranks as the highest absolute greenhouse gas (GHG) emitter in the world with 23.6 metric tons of carbon dioxide equivalent per capita in 2006. The industrial sector (agriculture is excluded) is responsible for 28.7 percent of the GHG emissions in the U.S. However, the U.S. industrial sector has numerous economically viable opportunities to reduce energy use and GHG emissions. Energy efficiency, including new clean technologies, plays a significant role in increasing productivity and reducing energy intensity, and thus emissions. Increasing energy efficiency in industrial processes is central to addressing climate change issues in the industrial sector.&#13;\nThis paper describes the energy-efficiency programs, methodologies, and technologies that can economically lead to significant GHG reductions in the industrial sector. The paper also discusses the impacts of climate change policies and programs to the application of advanced low-carbon industrial technologies.
Simple and Knowledge-intensive Generative Model for Named Entity Recognition (2013)

Almost all of the existing work on Named Entity Recognition (NER) consists of the following pipeline stages – part-of-speech tagging, segmentation, and named entity type classification. The requirement of hand-labeled training data on these stages makes it very expensive to extend to different domains and entity classes. Even with a large amount of hand-labeled data, existing techniques for NER on informal text, such as social media, perform poorly due to a lack of reliable capitalization, irregular sentence structure and a wide range of vocabulary. In this paper, we address the lack of hand-labeled training data by taking advantage of weak super vision signals. We present our approach in two parts. First, we propose a novel generative model that combines the ideas from Hidden Markov Model (HMM) and n-gram language models into what we call an N-gram Language Markov Model (NLMM). Second, we utilize large-scale weak supervision signals from sources such as Wikipedia titles and the corresponding click counts to estimate parameters in NLMM. Our model is simple and can be implemented without the use of Expectation Maximization or other expensive iterative training techniques. Even with this simple model, our approach to NER on informal text outperforms existing systems trained on formal English and matches state-of-the-art NER systems trained on hand-labeled Twitter messages. Because our model does not require hand-labeled data, we can adapt our system to other domains and named entity classes very easily. We demonstrate the flexibility of our approach by successfully applying it to the different domain of extracting food dishes from restaurant reviews with very little extra work.