gebhart/patrepeval huggingface dataset:
Molecular characterization of the pH‐inducible and growth phase‐dependent promoter P170 of <i>Lactococcus lactis</i> (1999)

In a previous study, we described the use of transposon Tn917-LTV1 for identification of environmentally regulated promoters in Lactococcus lactis. Here, we report the molecular analysis of one of these promoters, P170, that is upregulated at low pH during the transition to stationary phase. The minimal DNA region required for both promoter activity and pH regulation was mapped to a 51 bp fragment located 7 bp upstream of the transcriptional start site. This fragment lacked the consensus -35 promoter region, but it contained an 'extended' -10 promoter region. When a 28 bp segment, containing the consensus -35 region and 22 bp upstream of this in a constitutive promoter, was replaced with the corresponding sequence of P170, the hybrid promoter became regulated by pH and growth phase. This demonstrates that the P170 segment contains a cis-acting sequence involved in the control of promoter regulation. Transcriptional analysis showed that P170 is responsible for the transcription of a monocistronic gene orfX encoding a polypeptide homologous to a hypothetical protein from Bacillus subtilis. Analysis of total RNA from L. lactis grown at constant pH confirmed that transcription from P170 was induced between pH 6.5 and pH 6.0, but only when the culture entered stationary phase. Deletion analysis and chemical mutagenesis of P170 defined a specific region within the untranslated mRNA leader that is able to modulate the expression level directed by the P170 promoter. Deletion of a 72 bp HaeIII fragment from this leader region resulted in a 150- to 200-fold increase in the level of gene expression, without affecting the regulation. The functionality was confirmed by introducing this modulating element downstream of other lactococcal promoters.
ErbB4 regulates interferon signaling in classically activated macrophages (2021)

Background Classically activated macrophages drive intestinal inflammation, which is necessary to limit infection. However, over‐aggressive responses from these cells, including elevated cytokine release, may contribute to inflammatory bowel disease. Previous studies have implicated the receptor tyrosine kinase ErbB4 and its ligands (neuregulins/NRGs) in regulating macrophage activity and survival. However, the influence of ErbB4 and its specific ligand NRG4 on cytokine expression and downstream signaling pathways in these cells remains untested. We hypothesized that ErbB4 regulates pathways associated with cytokine production in macrophages. Methods We generated bone‐marrow derived macrophages from mice lacking ErbB4 in cells of myeloid lineage (LysMCre/ErbB4 FF ) or sex‐matched littermate controls (ErbB4 FF ), and stimulated pro‐inflammatory activation with interferon (IFN)‐gamma plus lipopolysaccharide (classical activation). Cells were analyzed by RNA sequencing, and gene‐set enrichment analysis (GSEA) was performed using publicly available Hallmark gene‐sets. To test the role of NRG4, activated cells were treated with recombinant ligand at 100 ng/ml for 24 hours to determine effects on cytokine expression. RNA was collected and analyzed for cytokines by qPCR. Results Classically activated macrophages from LysMCre/ErbB4 FF mice displayed an enhanced pro‐inflammatory cytokine profile by GSEA (p<0.05) compared to ErbB4 FF mice. We confirmed elevated levels of Tnf (32% higher, p<0.05) and Cxcl1 (69% higher, p<0.05) by qPCR. NRG4 treatment limited Tnf (p<0.05) and Cxcl1 (p<0.05) expression in classically activated macrophages from wild‐type mice. GSEA showed a reduced type‐I and type‐II IFN gene expression signature in cells from LysMCre/ErbB4 FF mice versus ErbB4 FF mice. Conclusion Loss of ErbB4 in macrophages leads to dysregulated IFN signaling and enhanced pro‐inflammatory cytokine production in macrophages. NRG/ErbB4 signaling in macrophages drives an anti‐inflammatory feedback loop and may limit aberrant intestinal inflammation.
Novolak resin for ultrafast high-resolution positive i-line photoresist compositions (1998)

An improved process for isolation of novolak resins from phenol-formaldehyde condensation products has been developed. The process results in resins having low polydispersity and higher photospeed while typical phenol/formaldehyde resin syntheses generate a broad distribution of molecular weight fragments with a wide polydispersity. The novolak resins were characterized by NMR and GPC and were formulated to obtain ultra fast high resolution i-line photoresists. The characteristics of the resins and their effect on lithographic properties as i-line photoresist compositions will be discussed in this paper.
Secure Proxy ND Support for SEcure Neighbor Discovery (SEND) (2012)

Secure Neighbor Discovery (SEND) specifies a method for securing
Neighbor Discovery (ND) signaling against specific threats. As defined
today, SEND assumes that the node sending a ND message is the owner of
the address from which the message is sent, so that it is in
possession of the private key used to generate the digital signature
on the message. This means that the Proxy ND signaling performed by
nodes that do not possess knowledge of the address owner's private
key cannot be secured using SEND. This document extends the current
SEND specification in order to secure Proxy ND operation.
Experimental evaluation of leaky least-mean-square algorithms for active noise reduction in communication headsets (2002)

An adaptive leaky normalized least-mean-square (NLMS) algorithm has been developed to optimize stability and performance of active noise cancellation systems. The research addresses LMS filter performance issues related to insufficient excitation, nonstationary noise fields, and time-varying signal-to-noise ratio. The adaptive leaky NLMS algorithm is based on a Lyapunov tuning approach in which three candidate algorithms, each of which is a function of the instantaneous measured reference input, measurement noise variance, and filter length, are shown to provide varying degrees of tradeoff between stability and noise reduction performance. Each algorithm is evaluated experimentally for reduction of low frequency noise in communication headsets, and stability and noise reduction performance are compared with that of traditional NLMS and fixed-leakage NLMS algorithms. Acoustic measurements are made in a specially designed acoustic test cell which is based on the original work of Ryan et al. ["Enclosure for low frequency assessment of active noise reducing circumaural headsets and hearing protection," Can. Acoust. 21, 19-20 (1993)] and which provides a highly controlled and uniform acoustic environment. The stability and performance of the active noise reduction system, including a prototype communication headset, are investigated for a variety of noise sources ranging from stationary tonal noise to highly nonstationary measured F-16 aircraft noise over a 20 dB dynamic range. Results demonstrate significant improvements in stability of Lyapunov-tuned LMS algorithms over traditional leaky or nonleaky normalized algorithms, while providing noise reduction performance equivalent to that of the NLMS algorithm for idealized noise fields.
Recurring Hypocalcemia of Bovine Parturient Paresis Is Associated with Failure to Produce 1,25-Dihydroxyvitamin D (1989)

Parturient paresis (milk fever) is a hypocalcemic disorder caused by the onset of lactation in the dairy cow. In most cows a complete recovery follows a single iv calcium treatment to correct the acute hypocalcemia. However, about 20% of cows treated for parturient paresis experience recurring episodes of hypocalcemia (relapses) requiring further treatment. Analysis of plasma from 8 nonrelapsing parturient paretic and 11 relapsing parturient paretic cows revealed differences in plasma 1,25-dihydroxyvitamin D [1,25-(OH)2D] concentrations before and during the development of hypocalcemia. In nonrelapsing cows, plasma 1,25-(OH)2D increased to 4- to 5-fold as plasma calcium concentrations declined during the first stage of parturient paresis. In relapsing cows, decreases in plasma calcium concentrations during the first stage of parturient paresis were accompanied by just a 2- to 2.5-fold increase in plasma 1,25-(OH)2D. Plasma 1,25-(OH)2D eventually increased 4- to 5-fold in the relapsing cows, but this response was delayed 24-48 h compared with the response in the nonrelapsing cows. Plasma PTH concentration profiles were similar in relapsing and nonrelapsing cows, suggesting that renal 25-hydroxyvitamin D 1 alpha-hydroxylase was temporarily refractory to stimulation by PTH in the relapsing cows. In both groups of cows recovery from parturient paresis began about 12-24 h after plasma 1,25-(OH)2D concentrations had increased 4- to 5-fold. These data imply that lack of production of 1,25-(OH)2D is an important factor in predisposing the cow to relapses of parturient paresis and is critical for recovery from the hypocalcemia associated with the onset of lactation.
The Spider DMA: A miniature radial differential mobility analyzer (2019)

The Spider differential mobility analyzer (DMA) is a novel, miniaturized radial DMA developed to provide size classification in the 10–500 nm range for applications requiring high portability and time resolution. Its external dimensions are ∼12 cm in diameter by 6 cm in height (excluding tubing); it weighs ∼350 g, and is designed to operate at 0.6–1.5 L/min sheath and 0.3 L/min sample flowrates. It features a new sample inlet geometry that is designed to produce a uniform azimuthal particle distribution at the entrance of the classifier, optimized sample/sheath flow streams introduction in the classifier to minimize particle delays, and extension of the electric field interaction volume for ∼30% enhanced dynamic range. Based on three-dimensional finite element simulations of flows, electric fields, and particle trajectories, we demonstrate that the Spider DMA transfer functions can be predicted with high fidelity using a parameterized fit based on the Stolzenburg semi-analytical model. Experimental characterization of the instrument response with size-selected particles confirmed close agreement with model prediction; mobility size response is linear over three orders of magnitude in mobility span. Electrical ground shielding of the external surfaces of the DMA has been found to be necessary to avoid particle losses associated with field effects as the high voltage operating limit is approached. The mean deviation between the reference size of polystyrene latex spheres and the Spider DMA measurement is less than 2%, corroborating its high sizing precision and potential for high quality size distribution measurements. Copyright © 2019 American Association for Aerosol Research
ChemInform Abstract: Synthesis of Levoglucosenone. (1990)

Abstract The title compound (I) is a major product of the acid‐catalyzed pyrolysis of allulose.
Wavelength selection for low-saturation pulse oximetry (1997)

Conventional pulse oximeters are accurate at high oxygen saturation under a variety of physiological conditions but show worsening accuracy at lower saturation (below 70%). Numerical modeling suggests that sensors fabricated with 735 and 890 nm emitters should read more accurately at low saturation under a variety of conditions than sensors made with conventionally used 660 and 900 nm band emitters. Recent animal testing confirms this expectation. It is postulated that the most repeatable and stable accuracy of the pulse oximeter occurs when the fractional change in photon path lengths due to perturbations in the tissue (relative to the conditions present during system calibration) is equivalent at the two wavelengths. Additionally, the penetration depth (and/or breadth) of the probing light needs to be well matched at the two wavelengths in order to minimize the effects of tissue heterogeneity. At high saturation these conditions are optimally met with 660 and 900 nm band emitters, while at low saturation 735 and 890 nm provide better performance.
Silent Mother-to-Child Transmission of Hepatitis C Virus through Two Generations Determined by Comparative Nucleotide Sequence Analysis of the Viral cDNA (1992)

To investigate the routes of transmission of hepatitis C virus (HCV), a family in which HCV was considered to be transmitted from mother to child through two generations was studied. By the polymerase chain reaction method, HCV cDNA was isolated from the serum of a female baby with self-limited hepatitis C. HCV cDNA was also obtained from her mother and grandmother, who are healthy carriers of HCV, as well as from her uncle suffering from chronic persistent hepatitis C. The nucleotide sequence of the HCV cDNA fragment obtained from the baby was identical to that of the mother and was much closer to those of the grandmother and the uncle than to HCV cDNA isolates previously obtained from other Japanese patients or carriers. These results indicate the presence of mother-to-child transmission of HCV and suggest a role of this transmission route in establishing HCV carriers and maintaining a high incidence of HCV infection.
CeO<sub>2</sub>–M<i><sub>x</sub></i>O<i><sub>y</sub></i> (M = Fe, Co, Ni, and Cu)-Based Oxides for Direct NO Decomposition (2019)

Direct decomposition of nitrogen oxides (NOx) into N2 and O2 offers the ideal route to catalytic removal of this air pollutant that contributes to photochemical smog and acid rain. Direct decomposition of NOx is simple and economic, because no reductants are required. Despite their extensive use in automotive exhaust catalytic applications, only a few ceria-based oxides are reported in the literature for direct NO decomposition. In the present study, transition-metal-doped (Fe, Co, Ni, and Cu) ceria-based catalysts were synthesized using a co-precipitation method and examined for direct NO decomposition in the temperature region 400–650 °C. Both CeO2–Co3O4 and CeO2–NiO catalysts exhibit higher activity and N2 selectivity compared to CeO2–Fe2O3 and CeO2–CuO catalysts. Remarkably, Ce–Ni catalysts exhibit 100% selectivity toward N2 at 400 °C and more than 95% selectivity at the remaining temperatures (450, 550, and 650 °C). Structural characterization measurements (X-ray diffraction) indicate that the transition metal enters the ceria lattice, and the extent of doping into CeO2 depends on the transition-metal identity. Surface characterization by X-ray photoelectron spectroscopy reveals that both Co and Ni result in the presence of Ce3+/Ce4+ and M2+/M3+ (M = Co, Ni), and the synergy between these dual redox sites is the origin of their higher activity. The effect of this synergy on the direct NOx decomposition is confirmed via NO adsorption/desorption studies, identifying a change in the nature and stability of adsorbed surface NOx species. Conversely, Fe and Cu remain in single oxidation states (Fe3+ and Cu2+) in the Ce–Fe and Ce–Cu catalysts, respectively, thus their impact on the redox properties and NO adsorption species of ceria are less significant, yielding little effect on the direct NO decomposition activity.
Beneficial Effects of Growth Hormone and Insulin-Like Growth Factor-1 in Experimental Heart Failure in Rats Treated with Chronic ACE Inhibition (1995)

The effects of growth hormone (GH) plus insulin-like growth factor-1 (IGF-1) were tested in an experimental model of cardiac failure treated with chronic angiotensin-converting enzyme (ACE) inhibition. Myocardial infarction was induced in rats by left coronary artery ligation. Two weeks after ligation, the animals received either captopril (2 g/L in drinking water) or water for 3 months. The rats were then given either GH (2 mg/kg/day) plus IGF-1 (2 mg/kg/day) or vehicle for 14 days. Captopril treatment decreased mean arterial pressure (MAP), left ventricular end-diastolic pressure (LVEDP) and systemic vascular resistance (SVR) (p < 0.05), and increased cardiac index (CI) and stroke volume index (SVI) (p < 0.05). GH/IGF-1 or captopril+GH/IGF-1 treatment decreased MAP, LVEDP, and SVR (p < 0.05), and increased left ventricular maximum dP/dt, CI, and SVI (p < 0.05). The increases in CI and SVI were significantly greater in the captopril+GH/IGF-1-treated animals than in those treated with captopril alone (p < 0.05). The beneficial effect of captopril in reducing cardiac hypertrophy was preserved in the captopril+GH/IGF-1 group. The results indicate that GH/IGF-1 and captopril can improve cardiac performance in congestive heart failure by independent and complementary mechanisms.
Mining succinct and high-coverage API usage patterns from source code (2013)

During software development, a developer often needs to discover specific usage patterns of Application Programming Interface (API) methods. However, these usage patterns are often not well documented. To help developers to get such usage patterns, there are approaches proposed to mine client code of the API methods. However, they lack metrics to measure the quality of the mined usage patterns, and the API usage patterns mined by the existing approaches tend to be many and redundant, posing significant barriers for being practical adoption. To address these issues, in this paper, we propose two quality metrics (succinctness and coverage) for mined usage patterns, and further propose a novel approach called Usage Pattern Miner (UP-Miner) that mines succinct and high-coverage usage patterns of API methods from source code. We have evaluated our approach on a large-scale Microsoft codebase. The results show that our approach is effective and outperforms an existing representative approach MAPO. The user studies conducted with Microsoft developers confirm the usefulness of the proposed approach in practice.
Mitomycin derivatives having unique condensed-ring structures. Their synthesis and antitumor activity. (1994)

A series of mitomycin derivatives 1-3 having unique condensed-ring structures was synthesized and evaluated for their anticellular and antitumor activity. These compounds were synthesized by the Michael addition of 1.3-dicarbonyl compounds to 6-demethyl-7,7-(ethylenedioxy)-6,7-dihydro-6-methylenemitosanes (4-6, and 14) and the subsequent cyclization. For the preparation of 1. the allyloxycarbonyl (Aloc) group was employable for the protection of the aziridine (1a-N-H), since the deprotection proceeded without decomposition of the substrates under the mild conditions with Pd(0) and HCO2H-NEt3. Among these structurally unique derivatives, compounds 1a, 1b, 1d and 1e were quite potent against HeLa S3 human tumor cells and sarcoma 180 solid tumor in mice.
Selective Oxidation of Lignin Model Compounds (2018)

Lignin, the planet's most abundant renewable source of aromatic compounds, is difficult to degrade efficiently to welldefined aromatics. We developed a microwave-assisted catalytic Swern oxidation system using an easily prepared catalyst, MoO<sub>2</sub> Cl<sub>2</sub> (DMSO)<sub>2</sub> , and DMSO as the solvent and oxidant. It demonstrated high efficiency in transforming lignin model compounds containing the units and functional groups found in native lignins. The aromatic ring substituents strongly influenced the selectivity of β-ether phenolic dimer cleavage to generate sinapaldehyde and coniferaldehyde, monomers not usually produced by oxidative methods. Time-course studies on two key intermediates provided insight into the reaction pathway. Owing to the broad scope of this oxidation system and the insight gleaned with regard to its mechanism, this strategy could be adapted and applied in a general sense to the production of useful aromatic chemicals from phenolics and lignin.
Magnetic Switching Behavior of Granular Perpendicular Magnetic Media With Different Lateral and Vertical Exchange Coupling (2014)

The magnetic switching behavior was measured for granular oxide media containing an exchange control layer (ECL). Investigations of the switching behavior show that the initial minor loop slope represents the degree of incoherent switching in the film. Multilayered granular oxide media with different inter-granular coupling in both lateral and vertical directions, is prepared by varying the oxide grain isolation and ECL thickness. The switching behavior of well isolated oxide grains strongly depends on the thermal stability of the switching segments through the ECL layer. The oxide grains with higher thermal stability vertically decouple at thinner ECL, resulting in a stronger incoherency of switching. In addition, the increase of lateral exchange coupling between oxide grains reduces the vertical decoupling at given ECL condition. For media with a smaller cluster size, the ECL magnetization and thickness has a more pronounced effect on the switching, indicating that fabrication of well isolated grains is important to optimize the media switching mode.
Preparation of benzyl acetate using polyaniline salts as catalysts ‐ Part II (2004)

Abstract Polyaniline salts were prepared by oxidizing aniline in presence of acid using benzoyl peroxide as an oxidizing agent. Polyaniline salt was used as catalyst for the esterification reaction of phenyl acetic acid with methanol. The process is being reported for the first time. Preparation of catalyst, recovery and reusability of the catalyst were found to be good. Copyright © 2004 John Wiley & Sons, Ltd.
A single-shot imaging magnetometer using cold atoms (2008)

We demonstrate a technique for imaging magnetic fields using velocity-selective two-photon resonances in a cold atom cloud. Freely expanding (85)Rb atoms released from a magneto-optical trap are exposed to a brief (approximately 1 ms), off-resonant, retro-reflected laser pulse in a lin-perp-lin configuration. Two-photon resonance between magnetic sublevels occurs only for atoms in narrow velocity classes dependent on the magnetic field strength. The momentum of resonant atoms is altered by the pulse, and this two-photon momentum change is easily visible after further ballistic expansion. When the momentum pulse is applied to an atom cloud with finite size, magnetic field variations across the sample result in position-dependent features in images of the expanded cloud. We demonstrate the technique by imaging magnetic field variations over approximately 5 mm with approximately 250 microm spatial resolution.
Adaptive Character Segmentation Method Based on Minimum Variance Criterion (1986)

Abstract Character segmentation is a technique which separates individual characters from character line image. It is one of the most important prerequisites for character recognition. In the past, segmentation of individual characters from a general object, such as mailing address and existing document, had strong constraints imposed on the character segmentation. These included contact between adjacent characters and separation of a single character, thereby preventing the segmentation technique from being a systematic approach. This paper discusses character segmentation, an indispensable means of pre‐processing in character recognition which has been considered to cope with the individual cases. A character segmentation method is proposed which is based on the clustering for the character cluster interval histogram by linear square‐error function, and on the dynamic programming using the minimum variance criterion for separation between character sectioning candidate positions in a line image. The first method is applied to the estimation of the character pitch, i.e., estimating the statistically best character pitch. It also extracts the parameters representing the placement properties for a series of characters. The second method is used to determine in a stable way a series of character sectioning positions. In the experiment, the method is applied to English language mail addresses, containing fixed and unspecified character pitches as well as contact between adjacent characters. A 99.2% correct segmentation rate was obtained for characters and 98.0% was obtained for words, indicating the effectiveness of the method.