gebhart/patrepeval huggingface dataset:
Evolution of Ribonuclease Inhibitor by Exon Duplication (2002)

The leucine-rich repeat (LRR) is a prevalent structural motif that mediates specific protein-protein interactions (Kobe and Deisenhofer 1995b). The LRR is defined by a region of 20–29 residues that contains the consensus sequence: XLXXLXLXXN, where L, N, and X are leucine, asparagine, and any residue, respectively. Typically, LRRs are displayed in 1–30 tandem copies within a protein. The first crystalline structure of an LRR-containing protein revealed a new protein fold (Kobe and Deisenhofer 1993) (fig. 1A and B). In porcine ribonuclease inhibitor (RI [Hofsteenge 1997]), the LRRs are arranged tandemly in a horseshoe shape with 16 a-helices encasing a parallel b-sheet of 17 strands. Hydrophobic forces between the consensus leucine residues appear to stabilize the b-sheet. RI is able to bind tightly to members of the ribonuclease (RNase) A superfamily, which not only catalyze RNA degradation but also mediate angiogenesis, cytotoxicity, and the host-defense response (D’Alessio and Riordan 1997; Raines 1998; Leland and Raines 2001). The RI fold is conserved in other proteins containing LRRs. Human U2A9 is a small nuclear protein that contains five LRRs and binds to U2B0 to form an active spliceosomal complex. Another protein, Skp2, contains both 10 LRRs that function as a protein-binding domain and an F-box motif that binds to the catalytic core of ubiquitin-protein ligases. The LRRs in U2A9 and Skp2 adopt an RI-like fold (Price, Evans, and Nagai 1998; Schulman et al. 2000). The crystalline structures of U2A9 bound to U2B0 and those of RI bound to RNase A and angiogenin reveal that the parallel b-sheet formed by the LRRs furnishes the surface for interacting with other proteins (Kobe and Deisenhofer 1995a; Papageorgiou, Shapiro, and Acharya 1997; Price, Evans, and Nagai 1998). The modularity of the LRR is consistent with the evolution of RI by gene duplication. To test this hypothesis, we investigated the genomic structure of human RI. Our findings provide a new insight into the evolution of RI as well as the many proteins containing LRRs or other modules. Human RI consists of alternating 28or 29-residue LRR units (Kobe and Deisenhofer 1993; Papageorgiou,
Chemical vapor sensing with CVD-grown monolayer MoSe2 using photoluminescence modulation (2018)

Monolayer two-dimensional transition metal dichalcogenides (TMDs) such as MoSe2 are promising materials for chemical vapor sensing applications due to their unique monolayer structure, ease of fabrication, low cost, selectivity, sensitivity, and speed of response. To date, most chemical vapor and gas sensors that use TMDs are based on chemiresistive device properties. However, recent studies indicate that the optical properties, in particular the photoluminescence (PL), could be used to sense vapors as well. In this study, we examine the PL of MoSe2 while it is exposed to triethylamine, a strong electron donor and chemically relevant to nerve gas and explosive sensing. We observe a fast and significant decrease in the PL by as much as 75% during exposure. The PL begins to recover as soon as the vapor is switched off, indicating fast adsorption/desorption of the analyte. We analyze the data in terms of possible applications to chemical vapor sensing.
Bemessung nachträglich ergänzter Betonbauteile mit längsschubbeanspruchter Fuge. Vergleichende Beurteilung aktueller Konzepte für die Baupraxis (2008)

Abstract Nachträglich ergänzte Betonbauteile kommen in der Baupraxis häufig vor, sowohl im Fertigteilbau als auch im Zuge der Verstärkung von bestehenden Konstruktionen durch Aufbringen einer neuen Betonschicht. Im Rahmen dieses Beitrags werden die Annahmen und Modellvorstellungen, die verschiedenen aktuellen Ansätzen zur Bemessung der Schubfugen zugrunde liegen, genauer betrachtet. Vor allem der Traganteil, der sich durch den Verbund zwischen Alt‐ und Neubeton ergeben kann, wird unterschiedlich gewichtet. Geht man davon aus, dass z. B. Verunreinigungen auf der Fugenoberfläche zu einem geschwächten Beton‐Beton‐Verbund führen, so ist zur Sicherstellung der Tragsicherheit eine erhöhte Bewehrungsmenge erforderlich. Umgekehrt kann bei einer sorgfältig vorbereiteten Altbetonoberfläche die Bewehrungsmenge reduziert werden. Die Bemessungsansätze in der europäischen Norm EN 1992‐1‐1 (12.2004 + Berichtigung 2008), in den deutschen Normen (DIN 1045‐1 (07.2001 + Berichtigungen 1 + 2); DIN 1045‐1 (Neufassung 2008)) und in den US‐amerikanischen Richtlinien (ACI 318‐02; AASHTO LRFD Specifications) liefern nur in Kombination mit sorgfältig vorbereiteten Fugenoberflächen ausreichend sichere Ergebnisse. Der Ansatz in ÖNORM B 4700 (06.2001) berücksichtigt den Fall eines durch ungünstige Baustellenbedingungen geschwächten Beton‐Beton‐Verbunds (dies gilt teilweise auch für die Regelungen in ACI 318‐02). Die Auswirkungen dieser Annahmen auf die Bemessungsergebnisse werden durch Bemessungsbeispiele veranschaulicht. In abschließenden Bemerkungen wird auf Stärken und Schwächen der Bemessungskonzepte hingewiesen.
Inhibitors of cyclic nucleotide phosphodiesterases inhibit protein carboxyl methylation in intact blood platelets. (1984)

The cycle of protein-carboxyl methylation and demethylation was studied in intact blood platelets. Platelets rapidly incorporated L-[methyl-3H]methionine and after a delay of about 20 min, they evolved [3H]methanol. This evolution, and the amount of [3H] methanol liberated by treatment with base, was inhibited in a dose-dependent fashion by the cyclic nucleotide phosphodiesterase inhibitors 3-isobutyl-1-methylxanthine, papaverine, dipyridamole, and RA233 (2,6-bis(diethanolamino)-4-piperidinopyrimido[5,4-d] pyrimidine). Each of these compounds increased the incorporation of [3H]methionine into platelets. The effects of RA233 were studied in more detail. Inhibition of [3H]methanol production was not potentiated by stimulators of the adenylate cyclase or the guanylate cyclase. The majority of the base-labile radioactivity was trichloroacetic acid precipitable. Thin layer chromatography of extracts of platelets incubated with L-[35S]methionine showed that RA233 did not induce a cellular accumulation of [35S]S-adenosylhomocysteine, and that it actually increased the amount of cellular [35S]S-adenosylmethionine. Discontinuous polyacrylamide gel electrophoresis at acid pH using the cationic detergent benzyldimethyl-n-hexadecylammonium chloride of platelets incubated with [3H]methionine showed incorporation of radioactivity into more than 30 protein bands, including one which co-migrates with calmodulin. The incorporation into the majority of these bands was inhibited by RA233 in a dose-dependent fashion. It is suggested that caution should be used in ascribing the pharmacological effects of known phosphodiesterase inhibitors to increases in cyclic nucleotides, because some of these effects could be due to inhibition of protein carboxyl methylation.
Quantifying the mechanical properties of polymeric tubing and scaffold using atomic force microscopy and nanoindentation (2019)

Measurement of mechanical parameters of polymeric scaffolds presents a significant challenge due to their intricate shape and small characteristics dimensions of their elements—around 100 μm. In this study, mechanical properties of polymeric tubing and scaffold, made of biodegradable poly( l ‐lactic) acid (PLLA), were characterized using atomic force microscopy (AFM) and nanoindentation, complemented with tensile testing. AFM was employed to assess the properties of the tube and scaffold locally, while nanoindentation produced results with a dependency on the depth of indentation. As a result, the AFM‐measured elastic modulus differs from the nanoindentation data due to a substantial difference in indentation depth between the two methods. With AFM, a modulus between 2 and 2.5 GPa was measured, while a wide range was obtained from nanoindentation on both the tube and scaffold, depending on the indentation scale. Changes in the elastic modulus with in‐vitro degradation and aging were observed over the 1‐year period. To complement the indentation measurements, tensile testing was used to study the structural behavior of the tube, demonstrating the yielding, hardening and fracture properties of the material. POLYM. ENG. SCI., 59:1084–1091, 2019. © 2019 Society of Plastics Engineers
Effect of genetic modifiers on cerebral lesions in Fabry disease (2005)

Fabry disease is associated with increased risk of premature stroke and presumptive ischemic cerebral lesions. In 57 consecutive patients, 35% of whom had lesions on brain MRI, the authors found that genotypes of polymorphisms G-174C of interleukin-6, G894T of endothelial nitric oxide synthase, factor V G1691A mutation, and the A-13G and G79A of protein Z were all significantly associated with cerebral lesions. These findings suggest that these proteins modulate Fabry cerebral vasculopathy.
Coalescence lifetimes of oil and water drops at the planar oil-water interface and their relation to emulsion phase inversion (2007)

We have measured the coalescence lifetimes of AOT-stabilised oil and water drops with the AOT monolayer present at the planar oil-water interface. Measurements were made as a function of aqueous phase NaCl concentration over the range over which phase inversion of the emulsions occurs and for heptane, dodecane and tetradecane as oil. The drop lifetimes decrease sharply with increasing [NaCl]. Below a crossover [NaCl], the oil drop lifetimes are longer than the water drops, whereas this behaviour is reversed at higher [NaCl]. The [NaCl] at the crossover points for the three oils increases with alkane chain length. This behaviour is compared with that of the corresponding emulsion systems which are water continuous at low [NaCl] but phase invert to give oil-continuous emulsions at high [NaCl]. The NaCl concentrations required for emulsion phase inversion increase with increasing oil chain length but are not identical to the [NaCl] values at the drop coalescence crossover points.
Aspartame and Human Behavior: Cognitive and Behavioral Observations (1988)

Little is known regarding the possible cognitive and behavioral effects of the artificial sweetener aspartame in humans. Few, if any, studies have addressed the issues raised by the potential elevation of brain phenylalanine levels which may be induced by aspartame ingestion and the concomitant depletion in specific neurotransmitter supplies which may result. In this chapter, the relevant literature addressing this topic is reviewed, the results of a new double-blind, acute study are briefly summarized, and findings from the pilot phase of a new chronic exposure study are reviewed.
Pericyte growth and contractile phenotype: Modulation by endothelial‐synthesized matrix and comparison with aortic smooth muscle (1993)

We compared the effects of endothelial-synthesized matrix and purified matrix molecules on pericyte (PC) and aortic smooth muscle cell (SMC) growth, heparin sensitivity, and contractile phenotype in vitro. When PC are plated on endothelial-synthesized (EC) matrix, cell number is, on average, 3.1-fold higher than identical populations grown on plastic. Under the same conditions, SMC proliferation is stimulated 1.6-fold. Purified matrix molecules, such as collagen type IV (COLL) or fibronectin (FN), both major components of the EC matrix, stimulate PC/SMC growth 1.2-1.7-fold. Heparin (100 micrograms/ml), which inhibits the growth of early passage SMC by 60%, inhibits PC growth approximately 50%, when cells were plated on plastic. However, PC plated on EC matrix in the presence of heparin (100 micrograms/ml) grow as well as parallel cultures grown on plastic (in the absence of heparin). Concomitant with matrix-stimulated proliferation, we observed a marked reduction in PC containing alpha vascular smooth muscle actin (alpha VSMA), as seen by immunofluorescence using affinity-purified antibodies (173/615 positive pericytes on DOC matrix (28%) vs. 221/285 (77%) positive on glass). SMC respond similarly. Whereas alpha VSMA protein is markedly altered when PC and SMC are cultured on EC matrix, similar reductions in mRNA are not observed. However, Northern blotting does reveal that PC contain 17-30 times the steady-state levels of alpha VSMA mRNA compared to SMC. When SMC and PC cultures on plastic are treated with heparin, the steady-state levels of vascular smooth muscle actin mRNA increase 5 and 1.5 fold, respectively. Similarly, heparin treatment of PC grown on plastic induces a 1.8 fold increase in nonmuscle actin mRNA. These heparin-induced alterations in isoactin mRNA levels are not seen when PC are cultured on EC matrix. We also observed reductions in alpha VSMA and beta actin mRNA levels when PC are plated on FN, where they maintain a ratio of 13:1 (alpha:beta). Similar ratios are found in SMC present in rat and bovine aortae in vivo. These steady-state isoactin mRNA ratios are slightly different from those seen in cultured PC (8-10:1; alpha:beta). These results suggest that selective synthesis and remodelling of the endothelial basal lamina may signal alterations in pericyte growth and contractile phenotype during normal vascular morphogenesis, angiogenesis, or during the microvascular remodelling that accompanies hypertensive onset.
Abstract 10793: Alterations of the Ionic Current Profile Underlie the Defective Electromechanical Coupling of Old Myocytes (2012)

Cardiac pathologies are characterized by prolongation of the action potential (AP) in myocytes, but whether a similar adaptation is present in the aging myocardium and impact on electromechanical c...
The Early Classification Problem: Successive LP for Machine Learning (1999)

Databased marketing’ Horizontal Marketing and customer value management represent growing applications able to build one-to-one relationships with the customer.
Combined In-Situ X-ray Absorption Spectroscopy and First-Principles Calculation Studies on Local Structural and Electronic Structural Alternations of LiNi<sub>1/3</sub>Co<sub>1/3</sub>Mn<sub>1/3</sub>O<sub>2</sub> (2013)

We report a result of combined in-situ x-ray absorption spectroscopy (XAS) and first-principles calculation study on LiNi 1/3 Co 1/3 Mn 1/3 O 2 cathode material, especially focusing on the roles of individual transition metals and oxygen for the battery reactions The theoretical X-ray Absorption Near Edge Structure (XANES) spectra simulations of Li x Ni 1/3 Co 1/3 Mn 1/3 O 2 have been well reproduced experimental in situ XANS spectra, and behaviors of XANES spectral shapes are reasonably explained with electronic structure considerations. Results of such analysis revealed that Ni mainly contribute to the battery-redox-reaction, while Co contribute only at high potential regions, and Mn does not contribute to the reaction.
New game, new goal posts (2015)

Timing closure is the most critical phase of modern system-on-chip implementation: without timing closure, there is no tapeout. Timing closure is the end result of (i) years of methodology development, script development, signoff recipe development, etc.; (ii) months of block- and top-level final physical implementation; and (iii) a last set of manual noise and DRC fixes, with a final signoff analysis and physical verification. Over the past decade, key aspects of the underlying process and device technologies, modeling standards, EDA tooling, design methodology, and signoff criteria have changed the nature of timing closure. This paper surveys such recent evolutions in timing closure and notes directions for near-term future evolutions.
Neuregulin expression in solid tumors: Prognostic value and predictive role to anti-HER3 therapies (2016)

NRG expression is not associated with either OS or PFS, but is a predictor of benefit from anti-HER3 antibodies.
Structural Thermodynamics: Prediction of Protein Stability and Protein Binding Affinities (1993)

The relationships between the structure of a protein and the thermodynamic parameters that determine its stability constitute the focus of attention of an increasing number of research laboratories. Advances in this area have reached the point in which accurate protein stability predictions and interaction energetics based on crystallographic information appear to be within reach. The purpose of this article is to summarize these developments and discuss future goals and trends.
Shining a Light on the Challenging Behaviors of Adolescents with Comorbid Diagnoses: Use of Pictorial Concurrent Operant Preference Assessment (2021)

Currently, there are no published studies that have used the concurrent operant preference assessment procedure to identify functions of challenging behaviors displayed by individuals with comorbid diagnoses. Four participants (aged 11-16 years) with comorbid diagnoses who displayed multiple challenging behaviors were referred to this study. We modified the standard concurrent operant preference assessment and used the new modified version, the <i>pictorial concurrent operant preference assessment</i>, to identify the functions of the challenging behaviors. Utilizing the triangulation mixed-methods design, we compared the indirect functional behavioral assessment (FBA) and the direct FBA with the pictorial concurrent operant preference assessment. The results obtained successfully demonstrated the concordance among these assessments in identifying the behavioral function for each participant. The results further showed that (1) the preferences served the same functional effects on both the challenging behaviors and the adaptive behaviors and (2) the pictorial concurrent operant preference assessment can be used independently to identify potential behavioral function and to specify the reinforcing potency of each behavioral function. The significance of the study results, limitations of this study, and directions for future research and clinical practice are discussed.
The Association of Polish Surgeons (APS) clinical guidelines for the use of laparoscopy in the management of abdominal emergencies. Part I. (2023)

There are 63 recommendations divided into 12 sections: diagnostic laparoscopy, perforated ulcer, acute pancreatitis, incarcerated hernia, acute cholecystitis, acute appendicitis, acute mesenteric ischemia, abdominal trauma, bowel obstruction, diverticulitis, laparoscopy in pregnancy, and postoperative complications requiring emergency surgery. Each recommendation was supported by scientific evidence and supplemented with expert comments. The guidelines were created on the initiative of the Videosurgery Chapter of the Association of Polish Surgeons and are recommended by the national consultant in the field of general surgery. The first part of the guidelines covers 5 sections and the following challenges for surgical practice: diagnostic laparoscopy, perforated ulcer, acute pancreatitis, incarcerated hernia and acute cholecystitis. Contraindications for laparoscopy and the ERAS program are discussed.
Predictors of multiple seizures in a cohort of children prospectively followed from the time of their first unprovoked seizure (2000)

The objective of this study was to assess the risk of multiple recurrences after an initial seizure recurrence in childhood. In a prospective study, 407 children were followed for a mean of 9.6 years from the time of their first unprovoked seizure. Data regarding each seizure recurrence were obtained and analyzed using statistical methods for survival analysis. The cumulative risk of a second seizure was 29%, 37%, 43%, and 46% at 1, 2, 5, and 10 years, respectively. Of the 182 children who experienced a second seizure, 131 (72%) experienced a third seizure, 105 (58%) have had 4 or more seizures, and 52 (29%) have experienced 10 or more seizures. The cumulative risk of a third seizure was 57%, 63%, and 71% at 1, 2, and 5 years, respectively, after the second seizure. After a third seizure, the cumulative risk of another seizure was 69%, 72%, and 81% at 1, 2, and 5 years, respectively. After a second seizure, factors associated with an increased risk of additional recurrences included a remote symptomatic etiology (rate ratio = 1.7) and the occurrence of a second seizure within 6 months of the first seizure (rate ratio = 1.7). After a second seizure, the risk of subsequent seizures was greater than 50% even in the lowest risk group. With the exception of etiology, factors associated with an increased risk of multiple recurrences after the initial seizure were different than those associated with multiple recurrences after a second seizure. Factors associated with multiple recurrent seizures may be different than those associated with an initial recurrence. As most patients who experience a second seizure experience further seizures, these data suggest that two seizures are a sufficient epidemiological criterion for the definition of epilepsy.
3D micro-structures folded by Lorentz force (2002)

We've made a spatial micro-structure by folding at elastic hinges. However, the micro-folding causes the difficulties, e.g. hard access, a time-consuming task, and damage to the structure. In this report, we propose installing micro-actuators on a microstructure to fold it out of a planar structure. The actuator is based on the Lorentz force, which acts on a current in a magnetic field. This actuator can be made simply by using an external magnetic field. The amplitude of the Lorentz force can be controlled by either the current or the magnetic field. Also, the direction of the force can be controlled by the direction of the field.
PACAP Is Lethal to Flavobacterium psychrophilum Through Either Direct Membrane Permeabilization or Indirectly, by Priming the Immune Response in Rainbow Trout Macrophages (2019)

Pituitary adenylate cyclase-activating polypeptide (PACAP) is a multifunctional neuropeptide that is widely distributed in mammals and is capable of performing roles as a neurotransmitter, neuromodulator, and vasodilator. This polypeptide belongs to the glucagon/secretin superfamily, of which some members have been shown to act as antimicrobial peptides in both mammalian and aquatic organisms. In teleosts, PACAP has been demonstrated to have direct antimicrobial activity against several aquatic pathogens, yet this phenomenon has never been studied throughout a live bacterial challenge. The present study focuses on the influence of synthetic <i>Clarias gariepinus</i> 38 amino acid PACAP on the rainbow trout monocyte/macrophage-like cell line, RTS11, when exposed to the coldwater bacterial pathogen <i>Flavobacterium psychrophilum</i>. PACAP was shown to have direct antimicrobial activity on <i>F. psychrophilum</i> when grown in both cytophaga broth and cell culture media (L-15). Further, the ability of teleostean PACAP to permeabilize the membrane of an aquatic pathogen, <i>F. psychrophilum</i>, was demonstrated for the first time. The viability of RTS11 when exposed to PACAP was also observed using a trypan blue exclusion assay to determine optimal experimental doses of the antimicrobial peptide. This displayed that only concentrations higher than 0.1 μM negatively impacted RTS11 survival. Interestingly, when RTS11 was pre-treated with PACAP for 24 h before experiencing infection with live <i>F. psychrophilum</i>, growth of the pathogen was severely inhibited in a dose-dependent manner when compared to cells receiving no pre-treatment with the polypeptide. Relative expression of pro-inflammatory cytokines (IL-1β, TNFα, and IL-6) and PACAP receptors (VPAC1 and PAC1) was also analyzed in RTS11 following PACAP exposure alone and in conjunction with live <i>F. psychrophilum</i> challenge. These qRT-PCR findings revealed that PACAP may have a synergistic effect on RTS11 immune function. The results of this study provide evidence that PACAP has immunostimulatory activity on rainbow trout immune cells as well as antimicrobial activity against aquatic bacterial pathogens such as <i>F. psychrophilum</i>. As there are numerous pathogens that plague the aquaculture industry, PACAP may stimulate the teleost immune system while also providing an efficacious alternative to antibiotic use.