gebhart/patrepeval huggingface dataset:
Characterization of the extracellular lipase, LipA, of Acinetobacter calcoaceticus BD413 and sequence analysis of the cloned structural gene (1995)

The extracellular lipase from Acinetobacter calcoaceticus BD413 was purified to homogeneity, via hydrophobic-interaction fast performance liquid chromatography (FPLC), from cultures grown in mineral medium with hexadecane as the sole carbon source. The enzyme has an apparent molecular mass of 32 kDa on SDS-polyacrylamide gels and hydrolyses long acyl chain p-nitrophenol (pNP) esters, like pNP palmitate (pNPP), with optimal activity between pH 7.8 and 8.8. Additionally, the enzyme shows activity towards triglycerides such as olive oil and tributyrin and towards egg-yolk emulsions. The N-terminal amino acid sequence of the mature protein was determined, and via reverse genetics the structural lipase gene was cloned from a gene library of A. calcoaceticus DNA in Escherichia coli phage M13. Sequence analysis of a 2.1 kb chromosomal DNA fragment revealed one complete open reading frame, lipA, encoding a mature protein with a predicted molecular mass of 32.1 kDa. This protein shows high similarity to known lipases, especially Pseudomonas lipases, that are exported in a two-step secretion mechanism and require a lipase-specific chaperone. The identification of an export signal sequence at the N-terminus of the mature lipase suggests that the lipase of Acinetobacter is also exported via a two-step translocation mechanism. However, no chaperone-encoding gene was found downstream of lipA, unlike the situation in Pseudomonas. Analysis of an A. calcoaceticus mutant showing reduced lipase production revealed that a periplasmic disulphide oxidoreductase is involved in processing of the lipase. Via sequence alignments, based upon the crystal structure of the closely related Pseudomonas glumae lipase, a model has been made of the secondary-structure elements in AcLipA. The active site serine of AcLipA was changed to an alanine, via site-directed mutagenesis, resulting in production of an inactive extracellular lipase.
Valor Prognóstico da Monitorização em Ambulatório da Pressão Arterial na Gravidez (2006)

Introdução: Na grávida hipertensa, a importância prognóstica da MAPA é defendida em alguns trabalhos. Objectivo: Analisar o valor prognóstico da MAPA. Material e Métodos: Estudo prospectivo a 114 grávidas com PA elevada, vigiadas na consulta de HTA da MAC. Foram divididas em dois grupos: GRUPO 1, grávidas com HTA crónica (n=88) e GRUPO 2, grávidas com HTA diagnosticada na gravidez (n=26). Todas fizeram a MAPA uma vez na gravidez. Resultados: A MAPA diagnosticou 31% de grávidas com HTA, 80% no grupo das hipertensas crónicas. Observaram-se 46.5% de complicações, 36.8% foram no grupo 1 e 9.7% no grupo 2. Da comparação das complicações observadas com a presença de HTA e/ou VR na MAPA nunca se obteve significância estatística. Conclusão: A MAPA não tem um valor prognóstico sendo, no entanto, importante na monitorização da grávida hipertensa. Deverá fazer parte da vigilância de grávidas com HTA não controlada ou suspeita de HBB.
Presynaptic enhancement of excitatory synaptic transmission by beta-adrenergic receptor activation (1994)

1. Previous studies have shown that beta-adrenergic receptor activation has many effects on neuronal function in hippocampal area CA1. However, all of the physiological effects of beta-adrenergic receptor activation in this region reported to date have been attributed to postsynaptic mechanisms. A series of studies was performed to test the hypothesis that beta-adrenergic receptor activation also acts presynaptically to enhance excitatory synaptic transmission. 2. Application of the selective beta-adrenergic agonist isoproterenol to hippocampal slices induced an increase in the amplitude of evoked excitatory postsynaptic currents (EPSCs) in CA1 pyramidal cells. This response was potentiated in the presence of a cyclic nucleotide phosphodiesterase inhibitor. Isoproterenol also resulted in the appearance of a late inward synaptic current that likely represents polysynaptically evoked EPSCs. Both the increased amplitude of the monosynaptic EPSC and the appearance of polysynaptic EPSCs in response to isoproterenol were blocked by H89, an inhibitor of adenosine 3',5'-cyclic monophosphate (cAMP)-dependent protein kinase. 3. Isoproterenol induced an increase in the frequency of spontaneous miniature EPSCs but did not affect the amplitude of these currents. In addition, isoproterenol had no effect on currents elicited by direct application of the ionotropic glutamate receptor agonist, (R,S)-alpha-amino-3-hydroxy-5-methylisoxazole-4-propionic acid (AMPA). 4. These results suggest that activation of presynaptic beta-adrenergic receptors enhances synaptic transmission in area CA1 via activation of cAMP-dependent protein kinase.
Cox Models With Smooth Functional Effect of Covariates Measured With Error (2009)

We propose, develop, and implement a fully Bayesian inferential approach for the Cox model when the log hazard function contains unknown smooth functions of the variables measured with error. Our approach is to model nonparametrically both the log-baseline hazard and the smooth components of the log-hazard functions using low-rank penalized splines. Careful implementation of the Bayesian inferential machinery is shown to produce remarkably better results than the naive approach. Our methodology was motivated by and applied to the study of progression time to chronic kidney disease as a function of baseline kidney function and applied to the Atherosclerosis Risk in Communities study, a large epidemiological cohort study. This article has supplementary material online.
Self-Assembly of an Optically Active Conjugated Oligoelectrolyte (2011)

Conjugated oligoelectrolytes are of emerging technological interest due to their recent function in the fabrication of optoelectronic devices, application in biosensors, and as species that facilitate transmembrane charge migration. Solubility in aqueous, or highly polar, solvents is important for many of these applications; however, there are few studies on how the self-assembly of conjugated oligoelectrolytes into multichromophore species influences linear and nonlinear optical properties. Here, we examine 1,4-bis(4'-(N,N-bis(6''-(N,N,N-trimethylammonium)hexyl)amino)-styryl)benzene tetraiodide (DSBNI) in water, a conjugated oligoelectrolyte based on the distyrylbenzene framework. We find that DSBNI aggregation leads to increased fluorescence lifetimes, coupled with hypsochromic shifts, and larger two-photon absorption cross sections. Liquid atomic force microscopy (AFM) and cryogenic transmission electron microscopy (cryo-TEM) were used to image DSBNI aggregates and to confirm that the planar molecules stack to form nanocylinders above a critical aggregation concentration. Finally, small-angle neutron scattering (SANS) was used to quantify the aggregate dimensions in situ. Comparison of the results highlights that the hydrophilic mica surface used to image via liquid AFM and the high concentrations required for cryo-TEM facilitate the propagation of the cylinders into long fibers. SANS experiments are consistent with equivalent molecular packing geometry but lower aspect ratios. It is therefore possible to understand the evolution of optical properties as a function of concentration and aggregation and the general geometric features of the resulting supramolecular structures.
Molecular basis of immune evasion by the delta and kappa SARS-CoV-2 variants (2021)

Worldwide SARS-CoV-2 transmission leads to the recurrent emergence of variants, such as the recently described B.1.617.1 (kappa), B.1.617.2 (delta) and B.1.617.2+ (delta+). The B.1.617.2 (delta) variant of concern is causing a new wave of infections in many countries, mostly affecting unvaccinated individuals, and has become globally dominant. We show that these variants dampen the in vitro potency of vaccine-elicited serum neutralizing antibodies and provide a structural framework for describing the impact of individual mutations on immune evasion. Mutations in the B.1.617.1 (kappa) and B.1.617.2 (delta) spike glycoproteins abrogate recognition by several monoclonal antibodies via alteration of key antigenic sites, including an unexpected remodeling of the B.1.617.2 (delta) N-terminal domain. The binding affinity of the B.1.617.1 (kappa) and B.1.617.2 (delta) receptor-binding domain for ACE2 is comparable to the ancestral virus whereas B.1.617.2+ (delta+) exhibits markedly reduced affinity. We describe a previously uncharacterized class of N-terminal domain-directed human neutralizing monoclonal antibodies cross-reacting with several variants of concern, revealing a possible target for vaccine development.
Pushing the limits of CMOS optical parametric amplifiers with USRN:Si7N3 above the two-photon absorption edge (2017)

CMOS platforms operating at the telecommunications wavelength either reside within the highly dissipative two-photon regime in silicon-based optical devices, or possess small nonlinearities. Bandgap engineering of non-stoichiometric silicon nitride using state-of-the-art fabrication techniques has led to our development of USRN (ultra-silicon-rich nitride) in the form of Si<sub>7</sub>N<sub>3</sub>, that possesses a high Kerr nonlinearity (2.8 × 10<sup>-13</sup> cm<sup>2</sup> W<sup>-1</sup>), an order of magnitude larger than that in stoichiometric silicon nitride. Here we experimentally demonstrate high-gain optical parametric amplification using USRN, which is compositionally tailored such that the 1,550 nm wavelength resides above the two-photon absorption edge, while still possessing large nonlinearities. Optical parametric gain of 42.5 dB, as well as cascaded four-wave mixing with gain down to the third idler is observed and attributed to the high photon efficiency achieved through operating above the two-photon absorption edge, representing one of the largest optical parametric gains to date on a CMOS platform.
Figure S4 from A KDM5 Inhibitor Increases Global H3K4 Trimethylation Occupancy and Enhances the Biological Efficacy of 5-Aza-2′-Deoxycytidine (2023)

&lt;p&gt;Differential H3K4me3 enrichment profiling after KDM5i, DAC, or both&lt;/p&gt;
Control of human achaete‐scute homologue‐1 (hASH1) mRNA translation by fragile X‐mental retardation protein (FMRP) (2009)

The basic helix‐loop‐helix transcription factor human achaete‐scute homologue‐1 (hASH1; ASCL1) is required for normal development of the nervous system and has been implicated in the formation of neuroendocrine tumors. Here we show that the mRNA of hASH1 is a new target of the fragile X‐mental retardation protein (FMRP). We provide several lines of evidence that hASH1 and FMRP are co‐expressed in distinct areas of the nervous system, e.g. by double‐immunofluorescent staining of both proteins in newborn mice brain. Forced expression of FMRP significantly increased hASH1 protein, but not its mRNA, in cultured HEK293 cells. Sucrose density gradient centrifugation revealed that hASH1 transcripts were translocated into a translationally active polysomal fraction in response to increased FMRP level. Luciferase reporter gene assays indicated that the influence of FMRP is mediated by interaction with the 5′‐untranslated region (UTR) of hASH1 mRNA. The responsible cis‐element was mapped by UV‐cross‐linking experiments and reporter mutagenesis assays to a (U)10‐sequence. In conclusion, hASH1 is a novel downstream target of FMRP. Improved translation efficiency of hASH1 mRNA by FMRP may represent an important switch in neuronal differentiation.
Supplementary Figure 7 from c-Src Modulates Estrogen-Induced Stress and Apoptosis in Estrogen-Deprived Breast Cancer Cells (2023)

&lt;p&gt;PDF file - 53K, 7A, Inhibitors of Akt could not block growth inhibition induced by E2 in MCF-7:5C cells. MCF-7:5C cells were treated with vehicle (0.1% EtOH), E2 (10-9 mol/L), LY294002 (10-6mol/L), and E2 (10-9 mol/L) plus LY294002 (10-6mol/L) respectively. Cells were harvested after 7 days treatment and total DNA was determined using a DNA fluorescence quantitation kit. 7B, Inhibitor of MAPK could not block growth inhibition induced by E2 in MCF-7:5C cells. MCF-7:5C cells were treated with vehicle (0.1% EtOH), E2 (10-9 mol/L), U0126 (5x10-6 mol/L), and E2 (10-9 mol/L) plus U0126 (5x10-6 mol/L) respectively. Cells were harvested after 7 days treatment and total DNA was determined using a DNA fluorescence quantitation kit. All data shown were representative of at least three separate experiments with similar results.&lt;/p&gt;
Polyoxometalates in Polyelectrolyte Multilayer Films: Direct Loading of [H7P8W48O184]33– vs. Diffusion into the Film (2009)

Abstract The immobilization of polyoxometalates (POMs) into thin organized films is of major importance for the development of functional devices like electrochromic films and catalysts. We investigate herein two methods to incorporate the wheel‐shaped tungstophosphate [H 7 P 8 W 48 O 184 ] 33– (P 8 W 48 ) polyoxometalates (POM) into polyelectrolyte multilayer (PEM) films, which offer the advantage of controlled thickness and ease of processability. The first method, whose feasibility has been widely demonstrated, consists in the alternate deposition of a polycation and the negatively charged POM. The second method has never been used to load POMs into thin films: an exponentially grown polyelectrolyte multilayer film, made from sodium hyaluronate (HA) and poly‐ L ‐lysine (PLL), is brought in contact with the POM solution to allow its passive diffusion into the PEM film. Both methods of incorporation are compared in terms of effective POM concentration in the film. In addition it is shown that the second method leads to a maximum in the amount of incorporated POM as a function of its concentration in solution.(© Wiley‐VCH Verlag GmbH &amp; Co. KGaA, 69451 Weinheim, Germany, 2009)
An embedded flexible content-addressable memory core for inclusion in a Field-Programmable Gate Array (2004)

This paper describes a novel architecture for a content-addressable memory core which is intended to be included in a Field-Programmable Gate Array or an Embedded Programmable Logic Core. Compared to a standard content-addressable memory, our architecture allows for arbitrary data and tag widths; this flexibility is vital in FPGA applications, since the size of the data and tag fields are not known when the FPGA is manufactured.
Inkjet printer model-based halftoning (2005)

The quality of halftone prints produced by inkjet (IJ) printers can be limited by random dot-placement errors. While a large literature addresses model-based halftoning for electrophotographic printers, little work has been done on model-based halftoning for IJ printers. In this paper, we propose model-based approaches to both iterative least-squares halftoning and tone-dependent error diffusion (TDED). The particular approach to iterative least-squares halftoning that we use is direct binary search (DBS). For DBS, we use a stochastic model for the equivalent gray-scale image, based on measured dot statistics of printed IJ halftone patterns. For TDED, we train the tone-dependent weights and thresholds to mimic the spectrum of halftone textures generated by model-based DBS. We do this under a metric that enforces both the correct radially averaged spectral profile and angular symmetry at each radial frequency. Experimental results generated with simulated printers and a real printer show that both IJ model-based DBS and IJ model-based TDED very effectively suppress IJ printer-induced artifacts.
Matching field effects at tesla-level magnetic fields in critical current density in high-Tcsuperconductors containing self-assembled columnar defects (2012)

We have investigated the superconductive transport properties of Y Ba2Cu3O7 films containing self-assembled columnar arrays of second phase SrZrO3 or BaSnO3 precipitates. A matching condition between columnar pinning sites (aligned at or near the c axis) and external magnetic flux, tilted with respect to them, is identified in the critical current JC(H) data. The results for the material containing SrZrO3-based pins are analyzed within a simple intuitive model. At matching, the critical current is enhanced above the model prediction. In complementary contact-free investigations of BaSnO3-doped material, matching effects are observed over a wide range of temperatures in the field dependence of JC(H). The deduced matching fields agree reasonably well with the densities of columnar pins directly observed by scanning electron microscopy.
CCDC 235453: Experimental Crystal Structure Determination (2006)

An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
Expression of type IV collagen α1(IV)–α6(IV) polypeptides in normal and developing human kidney and in renal cell carcinomas and oncocytomas (1997)

Type IV collagen trimer is a major component of basement membranes (BMs). It is composed of polypeptides named α1(IV)–α6(IV) chains. Chains α1,2(IV) are widely expressed in BMs while α3(IV)–α6(IV) are more restricted in human tissues. We have now studied by immunohistochemical means the distribution of collagen IV chains in fetal and adult human kidney, in oncocytomas, in renal cell carcinomas (RCCs) and their metastases and in experimental xenografts of human tumors. α1,2(IV) chains were found in all BMs of fetal and adult kidney as well as of renal tumors, while α3(IV)–α6(IV) chains were found in BMs of distal segments of developing and mature tubules. α3(IV)–α5(IV) chains were seen also in BMs of developing fetal glomeruli after the capillary loop stage. Most of the RCCs and their metastases showed occasional expression of α3(IV)–α6(IV) with papillary variants showing only expression of α5(IV) chain. There was a distinct expression of α3(IV)–α5(IV) chains in BMs of 3 oncocytomas. In 2 of them a variable expression of the α6(IV) chain was seen. In 3 of 4 xenografts, immunoreactivity for human-specific monoclonal antibody (MAb) for α1,2(IV) was seen in the BM-like structures. No α3–α6(IV) was seen in any of the xenografts, while polyclonal antiserum for type IV collagen presented immunoreactivity in BMs of all xenografts. Our results show that oncocytomas and most of the RCCs express scarce variants of type IV collagen containing α3(IV)–α6(IV) chains. In experimental xenograft tumors, both implanted RCC cells and host stromal cells have a capacity to produce type IV collagen. Int. J. Cancer 72:43–49, 1997. © 1997 Wiley-Liss Inc.
Expectation-Maximization-Based Channel Estimation for Multiuser MIMO Systems (2017)

Multiuser multiple-input multiple-output (MU-MIMO) transmission techniques have been popularly used to improve the spectral efficiency and user experience. However, due to the coarse knowledge of channel state information at the transmitter, the quality of transmit precoding to control multiuser interference is degraded, and hence, co-scheduled user equipment may suffer from large residual multiuser interference. In this paper, we propose a new channel estimation technique employing reliable soft symbols to improve the channel estimation and subsequent detection quality of MU-MIMO systems. To this end, we pick reliable data tones from both desired and interfering users and then use them as pilots to re-estimate the channel. In order to jointly estimate the channel and data symbols, we employ the expectation maximization algorithm, where the channel estimation and data decoding are performed iteratively. From numerical experiments in realistic MU-MIMO scenarios, we show that the proposed method achieves substantial performance gain in channel estimation and detection quality over conventional channel estimation approaches.
Figure S4 from Oral IRAK-4 Inhibitor CA-4948 Is Blood-Brain Barrier Penetrant and Has Single-Agent Activity against CNS Lymphoma and Melanoma Brain Metastases (2023)

&lt;p&gt;Supplemental Figure 4. CA-4948 viability assessment in A20 and B16F10 cancer cells.&lt;/p&gt;
EFFECTS OF KETAMINE ON VASCULAR SMOOTH MUSCLE FUNCTION (1980)

1In vitro studies were undertaken on rat aortic strips and portal vein segments to determine whether or not the amine-type anaesthetic, ketamine, can exert direct actions on vascular smooth muscle.2 Ketamine was found to inhibit development of spontaneous mechanical activity and lower basal tension. This action took place with ketamine concentrations found in anaesthetic plasma concentrations, i.e., 1 x 10(-5) to 2 x 10(-4) M.3 Ketamine (10(-5) to 10(-3) M) dose-dependently attenuated contractions induced by adrenaline, noradrenaline, angiotensin II, vasopressin and KCl. These inhibitory actions were observed with ketamine added either before or after the induced contractions.4 Ca(2+)-induced contractions of K(+)-depolarized aortae and portal veins were also attenuated, dose-dependently, by ketamine.5 In contrast to the above inhibitory actions, ketamine (2 x 10(-6) to 1 x 10(-4) M) was found to potentiate specifically 5-hydroxytryptamine(5-HT)-induced contractions of both aortic and venous smooth muscle. However, this was only observed if ketamine was added after 5-HT had initiated a contractile response.6 All of the inhibitory, as well as 5-HT-potentiating, effects were completely, and almost immediately, reversed upon washing out the anaesthetic from the organ baths.7 A variety of pharmacological antagonists failed to mimic or affect the inhibitory effects induced by ketamine.8 These data suggest that rat plasma concentrations of ketamine commonly associated with induction of surgical anaesthesia can induce, directly, relaxation and contractile potentiation of vascular muscle.9 These diverse findings may aid in explaining the well-known biphasic pressor actions of ketamine.
A comparison of four porewater sampling methods for metal mixtures and dissolved organic carbon and the implications for sediment toxicity evaluations (2017)

Evaluations of sediment quality conditions are commonly conducted using whole-sediment chemistry analyses but can be enhanced by evaluating multiple lines of evidence, including measures of the bioavailable forms of contaminants. In particular, porewater chemistry data provide information that is directly relevant for interpreting sediment toxicity data. Various methods for sampling porewater for trace metals and dissolved organic carbon (DOC), which is an important moderator of metal bioavailability, have been employed. The present study compares the peeper, push point, centrifugation, and diffusive gradients in thin films (DGT) methods for the quantification of 6 metals and DOC. The methods were evaluated at low and high concentrations of metals in 3 sediments having different concentrations of total organic carbon and acid volatile sulfide and different particle-size distributions. At low metal concentrations, centrifugation and push point sampling resulted in up to 100 times higher concentrations of metals and DOC in porewater compared with peepers and DGTs. At elevated metal levels, the measured concentrations were in better agreement among the 4 sampling techniques. The results indicate that there can be marked differences among operationally different porewater sampling methods, and it is unclear if there is a definitive best method for sampling metals and DOC in porewater. Environ Toxicol Chem 2017;36:2906-2915. Published 2017 Wiley Periodicals Inc. on behalf of SETAC. This article is a US government work and, as such, is in the public domain in the United States of America.