gebhart/patrepeval huggingface dataset:
Characterization of alkylguaiacol-degrading cytochromes P450 for the biocatalytic valorization of lignin (2020)

Cytochrome P450 enzymes have tremendous potential as industrial biocatalysts, including in biological lignin valorization. Here, we describe P450s that catalyze the <i>O</i>-demethylation of lignin-derived guaiacols with different ring substitution patterns. Bacterial strains <i>Rhodococcus rhodochrous</i> EP4 and <i>Rhodococcus jostii</i> RHA1 both utilized alkylguaiacols as sole growth substrates. Transcriptomics of EP4 grown on 4-propylguaiacol (4PG) revealed the up-regulation of <i>agcA</i>, encoding a CYP255A1 family P450, and the <i>aph</i> genes, previously shown to encode a <i>meta</i>-cleavage pathway responsible for 4-alkylphenol catabolism. The function of the homologous pathway in RHA1 was confirmed: Deletion mutants of <i>agcA</i> and <i>aphC</i>, encoding the <i>meta</i>-cleavage alkylcatechol dioxygenase, grew on guaiacol but not 4PG. By contrast, deletion mutants of <i>gcoA</i> and <i>pcaL</i>, encoding a CYP255A2 family P450 and an <i>ortho</i>-cleavage pathway enzyme, respectively, grew on 4-propylguaiacol but not guaiacol. CYP255A1 from EP4 catalyzed the <i>O</i>-demethylation of 4-alkylguaiacols to 4-alkylcatechols with the following apparent specificities (<i>k</i><sub>cat</sub>/<i>K</i><sub>M</sub>): propyl > ethyl > methyl > guaiacol. This order largely reflected AgcA's binding affinities for the different guaiacols and was the inverse of GcoA<sub>EP4</sub>'s specificities. The biocatalytic potential of AgcA was demonstrated by the ability of EP4 to grow on lignin-derived products obtained from the reductive catalytic fractionation of corn stover, depleting alkylguaiacols and alkylphenols. By identifying related P450s with complementary specificities for lignin-relevant guaiacols, this study facilitates the design of these enzymes for biocatalytic applications. We further demonstrated that the metabolic fate of the guaiacol depends on its substitution pattern, a finding that has significant implications for engineering biocatalysts to valorize lignin.
Regulation of embryonic lung vascular development by vascular endothelial growth factor receptors, Flk‐1 and Flt‐1 (2007)

The biological effects of vascular endothelial growth factor A (VEGF-A) are mediated by fetal liver kinase-1 (Flk-1) and fms-like tyrosine kinase-1 (Flt-1). In lung tissue, VEGF-A is diffusely expressed throughout the embryonic stages, whereas the development of vascular endothelial cells is not uniform. Noting the signaling properties of the two receptors, we hypothesized that Flk-1 and Flt-1 regulate the embryonic development of lung vasculature. We herein show the spatiotemporal expression and experimental inhibition of Flk-1 and Flt-1 of embryonic mouse lung tissue. When Flk-1 was predominantly expressed (embryonic day [E] 9.5-E13.5), then vascular endothelial cells actively proliferated. When Flt-1 was enhanced (E14.5-E16.5), these cells less actively proliferated, thereby constituting organized networks. The treatment of cultured lung buds (E11.5) with antisense oligonucleotides complementary to Flk-1 inhibited branching of capillaries and proliferation of endothelial cells. In contrast, the inhibition of Flt-1 promoted the branching of capillaries and enhanced proliferation of endothelial cells. Of interest, inhibition of Flt-1 promoted Flk-1 expression. These results suggest that the two VEGF-A receptors regulate pulmonary vascular development by modulating the VEGF-A signaling.
Intramuscular meptazinol and morphine in postoperative pain (1985)

Meptazinol is an agonist-antagonist opioid analgesic believed to be unique in its selectivity for mu1 (high affinity) receptors and its cholinergic activity. Our objectives were to determine the relative analgesic potency of intramuscular meptazinol and morphine and to compare mood and side effects in 102 patients with cancer who have postoperative pain. Meptazinol (50, 100, and 200 mg) and morphine (4, 8, and 16 mg) were given for moderate to severe pain in a double-blind, randomized but balanced, incomplete block design. Serial multiple assessments of pain, relief, mood, and side effects were made. The most precise estimates of relative analgesic potency indicate that meptazinol is equivalent to 10 mg morphine at 120 mg (95% confidence interval 80 to 170 mg) for peak effect and at 175 mg (95% confidence interval 125 to 270 mg) for total effect. Mean (+/- SE) times to peak effect and to remedication were 0.9 +/- 0.1 and 3.6 +/- 0.2 hours for meptazinol and 1.4 +/- 0.1 and 4.8 +/- 0.4 hours for morphine at equianalgesic peak effects. The percentages of subjects with one or more side effects were 18, 49, and 73 for graded meptazinol doses and 32, 49, and 65 for graded morphine doses. Mean numbers of side effects per subject were 0.3, 1.5, and 3.5 for meptazinol and 0.5, 0.7, and 1.7 for morphine. Profiles of side effects differed. Mood improvement and overall satisfaction were dose related and greater for morphine than for meptazinol. Side effects may limit the use of meptazinol in doses that relieve severe postoperative pain.
Remarkable Rate Enhancement Effect of the o-Methoxy Group in the Nucleophilic Substitution Reactions at the Phosphorus of Phosphine–Boranes (1996)

Abstract A remarkable rate enhancement effect of the o-methoxy group is observed in the nucleophilic substitution reactions at the phosphorus of phosphine–boranes.
Splendors and miseries of expired CO2 measurement in the suspicion of pulmonary embolism (2010)

Capnography has been studied for decades as a potential diagnostic tool for suspected pulmonary embolism. Despite technological refinements and its combination with other non-invasive instruments, no evidence to date allows recommending the use of expired carbon dioxide measurement as a rule-out test for pulmonary embolism without additional radiological testing. Further investigations are, however, still warranted.
Searches for scalar leptoquarks and differential cross-section measurements in dilepton–dijet events in proton–proton collisions at a centre-of-mass energy of $$\varvec{\sqrt{s}}$$ = 13 TeV with the ATLAS experiment (2019)

Searches for scalar leptoquarks pair-produced in proton-proton collisions at s = 13 TeV at the Large Hadron Collider are performed by the ATLAS experiment. A data set corresponding to an integrated luminosity of 36.1 fb -1 is used. Final states containing two electrons or two muons and two or more jets are studied, as are states with one electron or muon, missing transverse momentum and two or more jets. No statistically significant excess above the Standard Model expectation is observed. The observed and expected lower limits on the leptoquark mass at 95% confidence level extend up to 1.29 TeV and 1.23 TeV for first-and second-generation leptoquarks, respectively, as postulated in the minimal Buchmller-Rckl-Wyler model, assuming a branching ratio into a charged lepton and a quark of 50%. In addition, measurements of particle-level fiducial and differential cross sections are presented for the Z ee, Z and t t processes in several regions related to the search control regions. Predictions from a range of generators are compared with the measurements, and good agreement is seen for many of the observables. However,
AES and SNOW 3G are Feasible Choices for a 5G Phone from Energy Perspective (2017)

The aspirations for a 5th generation (5G) mobile network are high. It has a vision of unprecedented data-rate and extremely pervasive connectivity. To cater such aspirations in a mobile phone, many existing efficiency aspects of a mobile phone need to be reviewed. We look into the matter of required energy to encrypt and decrypt the huge amount of traffic that will leave from and enter into a 5G enabled mobile phone. In this paper, we present an account of the power consumption details of the efficient hardware implementations of AES and SNOW 3G. We also present an account of the power consumption details of LTE protocol stack on some cutting edge hardware platforms. Based on the aforementioned two accounts, we argue that the energy requirement for the current encryption systems AES and SNOW 3G will not impact the battery-life of a 5G enabled mobile phone by any significant proportion.
MECHANICAL RELIABILITY OF THE AMS 700CXM INFLATABLE PENILE PROSTHESIS FOR THE TREATMENT OF MALE ERECTILE DYSFUNCTION (2001)

The AMS 700CXM inflatable penile prosthesis with medium controlled expansion cylinders was introduced in 1990 to provide a device with controlled expansion in girth and fitness for Asian men. We reviewed our experience with the AMS 700CXM prosthesis with particular regard to postoperative complications and reliability.From January 1991 to April 1999, 273 men with erectile dysfunction underwent primary penile prosthesis implantation with the AMS 700CXM. Functional status of the prosthesis was assessed retrospectively by reviewing the medical records and a telephone interview.Patient age was 24 to 78 years and mean followup was 49 months. Of the 28 complications (10.3%) 8 (3%) were nonmechanical and 20 (7.3%) were mechanical. Nonmechanical complications included infection in 2 cases, erosion in 3, surgical complications in 2 and tube kinking in 1. Mechanical complications involved a cylinder tear in 11 cases (4%), pump failure in 4 (1.5%) and a reservoir tear in 2 (0.7%). Mechanical reliability of the device was 98.2% after 2, 95.7% after 3 and 90.4% after 5 years.The AMS 700CXM is suitable for Asian men and its mechanical reliability is excellent. However, more device modifications are needed to guarantee good reliability during long-term followup.
Glucocorticoids Inhibit the Cerebral Microvascular Dysfunction Associated with Sepsis in Obese Mice (2006)

Low-dose glucocorticoid therapy is beneficial in experimental sepsis in obese animals compared to lean animals.
Effect of Heat Treatment on Pore Architecture and Associated Property Changes in Plasma Sprayed TBCs (2007)

Abstract Plasma sprayed Thermal Barrier Coatings (TBCs) exhibit many interlamellar pores, voids and microcracks. These microstructural features are primarily responsible for the low global stiffnesses and the low thermal conductivities commonly exhibited by such coatings. The pore architecture thus has an important influence on such thermophysical properties. In the present work, the effect of heat treatment (at temperatures up to 1400°C, for times of up to 10 hours) on the pore architecture in detached YSZ top coats has been characterised by Mercury Intrusion Porosimetry (MIP) and gas-sorption techniques. While the overall porosity level remained relatively unaffected (at around 10-12%) after the heat treatments concerned, there were substantial changes in the pore size distribution and the (inter-connected) specific surface area. Fine pores (&amp;lt;~50 nm) rapidly disappeared, while the specific surface area dropped dramatically, particularly at high treatment temperatures (~1400°C). These changes are thought to be associated with intra-splat microcrack healing, improved inter-splat bonding and increased contact area, leading to disappearance of much of the fine porosity. These microstructural changes are reflected in sharply increased stiffness and thermal conductivity. Measured thermal conductivity data are compared with predictions from a recently-developed analytical model, using the deduced inter-splat contact area results as input parameters. Good agreement is obtained, suggesting that the model captures the main geometrical effects and the pore size distribution measurements reflect the most significant microstructural changes.
Mechanical Tuning of 2D Photonic Crystal with MEMS-based Electrostatic Actuator (2006)

In this study, a mechanically tunable PC device with an electrostatic actuator fabricated by MEMS technique is proposed. The device consists of two parts: a flexible PC slab waveguide; and double-layered rods which consist of silicon (upper layer) and silicon dioxide (lower layer). The rods are fixed to the wafer, while the slab is released from the wafer. In the initial state the holes are mostly filled with the silicon part of the rods. When a voltage is applied between the slab and the wafer, the slab is deflected by electrostatic force. Therefore, the holes are mostly filled with the silicon dioxide part of the rods. The deflection (i.e. the insertion depth of the rods) depends on the applied voltage. Since the rods are self-aligned to the holes, this device does not need other alignment apparatus, like an AFM
Buried Linear Extrinsic Defects in Colloidal Photonic Crystals (2005)

Linear extrinsic defects can be embedded inside the lattice of a silica colloidal photonic-crystal film via a directed self-assembly strategy involving a combination of top–down photolithography and bottom–up colloidal assembly. High-spatial-resolution scanning micro-optical spectroscopy proves to be an effective means of characterizing the photonic crystal properties of the buried defects (see Figure) within the film.
REDD‐1 aggravates endotoxin‐induced inflammation VIA atypical NF‐κB activation (2018)

Regulated in development and DNA damage responses 1 (REDD-1), an inhibitor of mammalian target of rapamycin (mTOR), is induced by various cell stressors, including LPS, a major player in the pathogenesis of endotoxemic shock. However, the pathologic role of REDD-1 in endotoxemia is largely unknown. We found that LPS increased REDD-1 expression, nuclear transcription factor-κB (NF-κB) activation, and inflammation and that these responses were suppressed by REDD-1 knockdown and in REDD-1<sup>+/-</sup> macrophages. REDD-1 overexpression stimulated NF-κB-dependent inflammation without additional LPS stimulation. REDD-1-induced NF-κB activation was independent of 2 classic IKK-dependent NF-κB pathways and the mTOR signaling pathway; however, REDD-1, particularly its C-terminal region (178-229), interacted with and sequestered IκBα, to elicit atypical NF-κB activation during the delayed and persistent phases of inflammation after stimulation. Moreover, REDD-1 knockdown mitigated vascular inflammation and permeability in endotoxemic mice, resulting in decreases in immune cell infiltration, systemic inflammation, caspase-3 activation, apoptosis, and consequent mortality. We further confirmed the inflammatory and cytotoxic effects of REDD-1 in endotoxemic REDD-1<sup>+/-</sup> mice. Our data support the likelihood that REDD-1 exacerbates endotoxemic inflammation via atypical NF-κB activation by sequestering IκBα.-Lee, D.-K., Kim, J.-H., Kim, J., Choi, S., Park, M., Park, W., Kim, S., Lee, K.-S., Kim, T., Jung, J., Choi, Y. K., Ha, K.-S., Won, M.-H., Billiar, T. R., Kwon, Y.-G., Kim, Y.-M. REDD-1 aggravates endotoxin-induced inflammation via atypical NF-κB activation.
ChemInform Abstract: Synthesis and Photochemistry of 2,2‐Di‐tert‐butyl‐6‐(4,4‐di‐tert‐butylbuta‐1,3‐dienyl)‐2H‐pyran. (2001)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Opto/Computer Methods Applied to the Evaluation of a Range of Acetabular Cups (1988)

Non-contact optical measurements have been made for acetabular cups of both the Charnley (worn in vivo) and Stanmore (simulator worn) types.
Improving coverage analysis and test generation for large designs (1999)

State space techniques have proven to be useful for measuring and improving the coverage of test vectors that are used during functional validation via simulation. By comparing the state and edge coverage provided by tests with that which is possible in the design's state graph, the designer can estimate how well tested the design is and identify areas that need better testing. Unfortunately, for many interesting designs, the full state graph may be too large to fully explore, or if it is explorable, the resulting coverage may be so low as to provide limited feedback. Several techniques have been proposed that identify and work with an interesting subset of the design's state machines, but they still require computing the full state graph before projecting it. In this paper we discuss projection directed state exploration, in which a projection from the full graph is found while exploring only the relevant portion of the full graph. Even with this limited exploration, BDD size blowup is still a problem. To deal with this, we have also developed several interactive tools that provide feedback to the designer, and allow them to add hints to help with the exploration.
Predicting early death after cardiovascular surgery by using the Texas Heart Institute Risk Scoring Technique (THIRST). (2013)

Preoperative risk-prediction models are an important tool in contemporary surgical practice. We developed a risk-scoring technique for predicting in-hospital death for cardiovascular surgery patients. From our institutional database, we obtained data on 21,120 patients admitted from 1995 through 2007. The outcome of interest was early death (in-hospital or within 30 days of surgery). To identify mortality predictors, multivariate logistic regression was performed on data from 14,030 patients from 1995 through 2002 and risk scores were computed to stratify patients (low-, medium-, and high-risk). A recalibrated model was then created from the original risk scores and validated on data from 7,090 patients from 2003 through 2007. Significant predictors of death included urgent surgery within 48 hours of admission, advanced age, renal insufficiency, repeat coronary artery bypass grafting, repeat aortic aneurysm repair, concomitant aortic aneurysm or left ventricular aneurysm repair with coronary bypass or valvular surgery, and preoperative intra-aortic balloon pump support. Because the original model overpredicted death for operations performed from 2003 through 2007, this was adjusted for by applying the recalibrated model. Applying the recalibrated model to the validation set revealed predicted mortality rates of 1.7%, 4.2%, and 13.4% and observed rates of 1.1%, 5.1%, and 13%, respectively. Because our model discriminates risk groups by using preoperative clinical criteria alone, it can be a useful bedside tool for identifying patients at greater risk of early death after cardiovascular surgery, thereby facilitating clinical decision-making. The model can be recalibrated for use in other types of patient populations.
Broadly neutralizing antibodies target the coronavirus fusion peptide (2022)

Rare monoclonal antibodies from COVID-19 convalescent individuals broadly neutralize coronaviruses by targeting the fusion peptide.
The application of a material parameter extraction algorithm to MRI-based displacement measurements (2000)

A novel algorithm based on the variational formulation is presented for the determination of the material parameters (λ+2μ)/ρ and μ/ρ throughout inhomogeneous media given volumetric displacement information. The performance of the inversion algorithm is subsequently investigated when applied to measured displacement data throughout an inhomogeneous test phantom. The vector displacement components throughout the test phantom subject to monochromatic shear excitation measured in time using MRI (Magnetic Resonance Imaging) were temporally Fourier transformed to extract the components of monochromatic excitation, and the data were delivered to the inversion algorithm. A sequence of studies is presented on the basis of subsequent wavenumber filtering, polarization selection, and variation in the size of the volume elements of resolution. The resulting performance is assessed and recommendations for future efforts are discussed. [Work supported by ONR and NIH.]
Elimination of Near-Wellbore Tortuosities by Means of Hydrojetting (1994)

Abstract Near-wellbore tortuosity is one of many conditions that can cause additional friction pressure loss during the injection or production phase of a well. Production pressure loss reduces the potential production capacity of the well. In addition, difficulties with proppant placement are often attributed to the presence of tortuous fracture paths, which can lead to premature screenouts in the fracturing operation. This paper discusses the importance of proper design and placement of perforations to obtain good fracture initiation. By doing so, optimal well production can be attained. Practical implementations of hydrojetting techniques as a substitute for the shaped-charge perforating process are discussed. The formation of tortuosities and the use of hydrojetting are demonstrated through laboratory tests. Hydrojetting tools that are used to achieve a fracture initiation from deviated or horizontal wells are also discussed.
Automatic Identification of Jacquard Warp-knitted Fabric Patterns Based on the Wavelet Transform (2014)

Engineering Research Center of Warp Knitting Technology, Ministry of Education, Jiangnan University, Wu xi, Jiangsu, 214122, P.R.China E-mail: jiang@526.cn Abstract In view of the fact that the design of jacquard warp knitting patterns is time-consuming, this paper proposes a rapid segmentation method to divide the multi-textural regions of jacquard warp-knitted fabric which could be used for automatic identification of fabric patterns to improve the efficiency of design. After pretreatment, the images scanned were decomposed by a two-layer two-dimensional wavelet transform and the standard deviations of five channels were extracted as the eigen values. Then, after giving the cluster centers, a multi-channel clustering was made combined with a K-means clustering algorithm. Finally the removal of noises caused by classification errors was needed , after which an accurate identification image was obtained. The experiments show that this method can achieve automatic texture segmentation of jacquard warp-knitted fabric with more than three textural regions. The identification results have high regional consistency, and the segmentation accuracy is up to 92%. The method can also adapt to a variety of mesh regions. Besides this, the approach is fast and can simplify craft personnel’s traditional process of pattern tracing classification when it is combined with CAD. Through this method, the efficiency of jacquard warp-knitted product designing can be improved a lot.
A Ring‐Distortion Strategy from Marine Natural Product Ilimaquinone Leads to Quorum Sensing Modulators (2018)

We report herein a ring‐distortion strategy applied to marine natural substances ilimaquinone and 5‐ epi ‐ilimaquinone. A chemically diverse library of molecules was synthesised that included rearrangements of the sesquiterpene moiety and original reorganisations of the quinone ring. Chemoinformatic analyses evaluated the rise of structural diversity and the exploration of chemical space. Some focussed biological activities of this library were also investigated; quorum sensing activity of Vibrio harveyi was envisaged and some of the new compounds were shown to be good quorum sensing inhibitor candidates, whereas others were activators. Toxicities were also evaluated and some products showed micromolar activities against human umbilical vein endothelium, human hepatocellular carcinoma and human lung carcinoma (A549) cells.