gebhart/patrepeval huggingface dataset:
EcoBLMcrX, a classical modification-dependent restriction enzyme in Escherichia coli B: Characterization in vivo and in vitro with a new approach to cleavage site determination (2017)

Here we characterize the modification-dependent restriction enzyme (MDE) EcoBLMcrX in vivo, in vitro and in its genomic environment. MDE cleavage of modified DNAs protects prokaryote populations from lethal infection by bacteriophage with highly modified DNA, and also stabilizes lineages by reducing gene import when sparse modification occurs in the wrong context. The function and distribution of MDE families are thus important. Here we describe the properties of EcoBLMcrX, an enzyme of the E. coli B lineage, in vivo and in vitro. Restriction in vivo and the genome location of its gene, ecoBLmcrX, were determined during construction and sequencing of a B/K-12 hybrid, ER2566. In classical restriction literature, this B system was named r6 or rglAB. Like many genome defense functions, ecoBLmcrX is found within a genomic island, where gene content is variable among natural E. coli isolates. In vitro, EcoBLMcrX was compared with two related enzymes, BceYI and NhoI. All three degrade fully cytosine-modified phage DNA, as expected for EcoBLMcrX from classical T4 genetic data. A new method of characterizing MDE specificity was developed to better understand action on fully-modified targets such as the phage that provide major evolutionary pressure for MDE maintenance. These enzymes also cleave plasmids with m5C in particular motifs, consistent with a role in lineage-stabilization. The recognition sites were characterized using a site-ranking approach that allows visualization of preferred cleavage sites when fully-modified substrates are digested. A technical constraint on the method is that ligation of one-nucleotide 5' extensions favors G:C over A:T approximately five-fold. Taking this bias into account, we conclude that EcoBLMcrX can cleave 3' to the modified base in the motif Rm5C|. This is compatible with, but less specific than, the site reported by others. Highly-modified site contexts, such as those found in base-substituted virulent phages, are strongly preferred.
IS THERE A ROLE OF THE PHOSPHODIESTERASE TYPE 5 (PDE5) IN THE CONTROL OF HUMAN DETRUSOR SMOOTH MUSCLE? A FUNCTIONAL AND MOLECULAR BIOLOGY STUDY (2009)

INTRODUCTION AND OBJECTIVE: There are hints indicating a signifance of cyclic GMP (cGMP)-mediated mechanisms in the control of human detrusor smooth muscle function. Thus,the use of PDE5 inhibitors to treat the overactive bladder has been suggested. In order to evaluate further the significance of cGMP-PDE isoenzymes in detrusor smooth muscle relaxation, we investigated the effects of selective PDE inhibitors on the tension induced by carbachol and the production of cyclic nucleotides in isolated human detrusor tissue. In addition, the expression of mRNA encoding for PDE isoenzymes 1A, 1B, 1C (cAMP/ cGMP-PDE), 4B, 4D (cAMP-PDE), 5A, 8A and 9A (cGMP-PDE) was evaluated by means of molecular biology (RT-PCR analysis).
Analysis of the allergenicity of natural and recombinant Der p 3 (2012)

Background: Der p 3 a trypsin-like protease is a Dermatophagoides pteronyssinus allergen which is synthesized in the mite under a zymogen form. The enzymatic activity of this allergen has been shown to enhance the inflammatory process of allergy. To date, there are a few studies that described the allergenicity and the IgE reactivity of the group 3 allergens, the allergenic properties of recombinant Der p 3 was also not characterized. Methods: The autolysis of rDer p 3 and rDer p 3 S196A were analyzed by means of SDS-PAGE and enzymatic activity and their allergenicities by means of assays for IgE binding, IgE binding inhibition and basophiles mediator-release. Results: 100% of the sera from allergic patients showed IgE reactivity to natural Der p 3 and recombinant form. However, the IgE binding to the Der p 3 was less 4 times than rDer p 1. The IgE binding to rDer p 3 S196A was higher than rDer p 3. These variations can be linked with the phenomen of autolysis and instability of Der p 3 during the ELISA test. The mediators release performed with RBL sensitized with sera from allergic patients and stimulated with rDer p3, rDer p 3 S196A and natural Der p 3 were similar and lower than Der p 1 for concentration < 10 ng/ml. Conclusions: recombinant mature Der p 3 retained overall identity to its natural form in terms of structure and allergenicity. The instability and autolysis of Der p 3 drastically influence its IgE binding capacity. These results can be explain the considerable variations with the frequencies reactivity (16-100%) of natural Der p 3. The RBL assays demonstrated that the allergenicity of rDer p 3 is similar to rDer p 1 for the concentrations >10 ng /ml.
Contraction and Expansion of Stimuli-Responsive DNA Bonds in Flexible Colloidal Crystals* (2020)

DNA surface ligands can be used as programmable “bonds” to control the arrangement of nanoparticles into crystalline superlattices. Here, 1070we study the intrinsic responsiveness of these DNA bonds to changes in local dielectric constant (εr) as a new approach to dynamically modulate superlattice structure. Remarkably, ethanol (EtOH) addition can be used to controllably tune DNA bond length from 16 to 3 nm and to increase bond stability by &gt;40°C, while retaining long-range order and crystal habit. Interestingly, we find that these structural changes, which involve the expansion and contraction of crystals by up to 75% in volume, occur in a cooperative fashion once a critical percentage of EtOH is reached. These results provide a facile and robust approach to create stimuli-responsive lattices, to access high volume fractions, and to improve thermal stability.
Realizing Colloidal Artificial Ice on Arrays of Optical Traps (2006)

We demonstrate how a colloidal version of artificial ice can be realized on optical trap lattices. Using numerical simulations, we show that this system obeys the ice rules and that for strong colloid-colloid interactions, an ordered ground state appears. We show that the ice-rule ordering can occur for systems with as few as 24 traps and that the ordering transition can be observed at constant temperature by varying the barrier strength of the traps.
Behaviour of RC beams strengthened with FRP laminates and tested under cyclic loading at low temperatures (2003)

Fiber reinforced polymeric (FRP) laminates, which have been used in the aerospace industry for several decades, are becoming increasingly popular in the construction industry for strengthening purposes. Although the use of this strengthening technique is increasing rapidly, more data are needed in the area of bond and long-term durability before it can be fully accepted. The study described in this paper is part of a larger investigation on the use of carbon fiber reinforced polymeric (CFRP) sheets for repair and retrofit of reinforced concrete (RC) beams. The experimental program included tests in flexure and shear of strengthened beams under low temperature (–29°C) and high amplitude cyclic loading which are described in this paper. Four RC beams strengthened with FRP laminates were tested under low temperature conditions. Out of four, two beams were tested monotonically to failure and the other two were tested under high amplitude cyclic load (fatigue load). The amplitude of the cyclic fatigue load was taken as 10–80% of the failure load from the monotonic test. Test results suggest that the presence of the low temperature did not affect the behavior of the CFRP strengthening system itself, or the interface on the laminate side.
Computational Characterization of Exogenous MicroRNAs that Can Be Transferred into Human Circulation (2015)

MicroRNAs have been long considered synthesized endogenously until very recent discoveries showing that human can absorb dietary microRNAs from animal and plant origins while the mechanism remains unknown. Compelling evidences of microRNAs from rice, milk, and honeysuckle transported to human blood and tissues have created a high volume of interests in the fundamental questions that which and how exogenous microRNAs can be transferred into human circulation and possibly exert functions in humans. Here we present an integrated genomics and computational analysis to study the potential deciding features of transportable microRNAs. Specifically, we analyzed all publicly available microRNAs, a total of 34,612 from 194 species, with 1,102 features derived from the microRNA sequence and structure. Through in-depth bioinformatics analysis, 8 groups of discriminative features have been used to characterize human circulating microRNAs and infer the likelihood that a microRNA will get transferred into human circulation. For example, 345 dietary microRNAs have been predicted as highly transportable candidates where 117 of them have identical sequences with their homologs in human and 73 are known to be associated with exosomes. Through a milk feeding experiment, we have validated 9 cow-milk microRNAs in human plasma using microRNA-sequencing analysis, including the top ranked microRNAs such as bta-miR-487b, miR-181b, and miR-421. The implications in health-related processes have been illustrated in the functional analysis. This work demonstrates the data-driven computational analysis is highly promising to study novel molecular characteristics of transportable microRNAs while bypassing the complex mechanistic details.
Optimization of a Constrained-Feed Rotman Lens Beamformer (2005)

A previous mathematical analysis has demonstrated the utility of a partially overlapped, constrained-feed network for time-delay control of large linear arrays (R.J. Mailloux, IEEE Trans. 49, February 2001, pp.280-291). In particular, this novel method allows for approximately -30 dB sidelobe suppression over a 20% bandwidth. An array with time-delayed contiguous subarrays with the same separation would have quantization lobes at the -10 dB level; thus, this technique appears to offer significant advantages. We recently developed an experiment to demonstrate this concept. We collected data for the broadside case (array phase shifters set to zero) from -45 degrees to 45 degrees in 0.25 degrees increments and from 9.0 to 11.0 GHz in 0.05 GHz increments (center frequency of 10 GHz). We allowed weighting of both the Rotman lens outputs (constituent beams) and the Butler matrix outputs (subarray patterns). We used a genetic algorithm to optimize these complex weightings. We realized that our data set didn't represent the best measure of system performance, since there is no beam squinting at broadside; therefore, we performed a limited field of view (LFOV) test. Using this LFOV test, we were able to demonstrate at least -28 dB sidelobes over an angular field of view corresponding to a 20% bandwidth.
Towards Mapping the Resting-State Connectome of the Limbic System in Real-Time with Connectome-based Neurofeedback (2023)

In the present study we develop a real-time seed-based correlation analysis (SBC) pipeline with online regression to compute a connectome fingerprint matrix and characterize the performance of this methodology for quantifying intra- and inter-network connectivity dynamics across major resting state networks (RSNs) in healthy subjects. We assess the association between connectivity in the limbic system and intensity of self-induced mood states with neurofeedback based on the connectome matrix.
Magnetic resonance imaging patterns of the development of the sphenoid sinus: a review of 800 patients. (2001)

Accurate knowledge of age-related development and pneumatisation of the paranasal sinuses has become an important issue in diagnosing paranasal sinus diseases in infants and young adults. Magnetic resonance imaging (MRI) has the potential to assess bone marrow conversion and pneumatisation of the paranasal sinuses. We retrospectively reviewed 800 children aged 0-14 years undergoing brain MRI for various indications. T1-weighted sagittal and T2-weighted axial scans were evaluated for bone marrow conversion and development of pneumatisation of the sphenoid sinus. The sphenoid sinus had a uniformly low signal intensity on T1-weighted images in all children less than four months old. Signal intensity began to change to hyperintense marrow at the age of four months. Onset of pneumatisation was observed in 19% at the age of 12-15 months. Pneumatisation was complete in all patients older than 10 years. In conclusion, these data can be used as baseline standards of normal age-related development of the sphenoid sinus and can be of great value for the diagnostic and therapeutic management of pathologic conditions of the child's sphenoid sinus and its surrounds.
Pipemidic Acid, a New Antibacterial Agent Active Against Pseudomonas aeruginosa : In Vitro Properties (1975)

Pipemidic acid, 8-ethyl-5,8-dihydro-5-oxo-2-(1-piperazinyl)-pyrido [2,3-d]pyrimidine-6-carboxylic acid, is a new derivative of piromidic acid. It is active against gram-negative bacteria including Pseudomonas aeruginosa as well as some gram-positive bacteria. Its potency is generally greater than that of piromidic acid and nalidixic acid. Cross-resistance is not observed between pipemidic acid and various antibiotics, and most of bacteria resistant to piromidic acid and nalidixic acid are moderately susceptible to pipemidic acid. The activity of pipemidic acid is scarcely affected by the addition of serum, sodium cholate, or change of medium pH, but is subject to the influence of inoculum size. Its action is bactericidal above minimal inhibitory concentrations.
ChemInform Abstract: DAS VERHALTEN VON WOLFRAMHEXACHLORID UND AETHYLALUMINIUMDICHLORID ALS COKATALYSATOR BEI ALKYLIERUNGS‐ UND METATHESE‐RK. (1972)

Abstract Eine Lösung von Wolframhexachlorid und Äthylaluminiumdichlorid (I) in Toluol (II) reagiert mit 2‐Penten (III) ausschließlich unter Alkylierung des Aromaten, während mit Benzol (V) aufgrund der langsameren Reaktion eine Metathese des Olefins eintritt und nach anschließender Alkylierung von (V) ein Gemisch der Alkylbenzole (VI)‐(IX) isoliert wird.
Chapter 7. Instanton Theory to Calculate Tunnelling Rates and Tunnelling Splittings (2020)

Instanton theory is a rigorous semiclassical theory to calculate tunnelling rate constants and tunnelling splittings of vibrational levels, taking movements of all atoms of a molecular system into account. Rate constants are obtained from the imaginary part of the free energy of a metastable quantum state. The free energy, in turn, is derived from partition functions calculated via Feynman's path integral formulation of quantum mechanics. Its usage has tremendously increased over the last decade in chemistry and surface science. This chapter discusses its basic foundations, its derivation, advantages and limits in applications.
On the multi-threaded computation of integral polynomial greatest common divisors (1991)

We present a parallelization of the Brown-Collins algorithm in the PARSAC-2 Computer Algebra system, and we describe the design of our S- threads parallelization environment. PARSAC-2 is a parallel extension of SAC-2 built upon multiple threads of control provided by S-threads. The Brown-Collins algorithm computes the g.c.d. and its co-factors of two polynomials in Zp[x1,..., xr], r ≥ 2, by first reducing the problem to multiple g.c.d. calculations of modular homomorphic images (MHI) in Zp[x2,..., x r ], and then recovering the result by interpolation. After studying timings of the SAC-2 implementation, we first parallelize the interpolation algorithm, and then we parallelize the main MHI loop by executing the modular g.c.d. computations concurrently. We determine speed-up's and speed-up efficiencies over a wide range of polynomials.
Studies on Diazabenzobicyclo [3.3.1] nonane System. IV. Synthesis of 1, 2, 3, 4, 5, 6-Hexahydro-1, 5-methanobenzo [e] [1, 3] diazocine Derivatives (1966)

In order to test the pharmacological activities, some derivatives of 1, 2, 3, 4, 5, 6-hexahydro-1, 5-methanobenzo [e] [1, 3] diazocine were synthesized.cis-1, 2, 3, 4-tetrahydro-1, 3-naphthalenediamine (V) was prepared by Schmidt reaction of cis-4-amino-1, 2, 3, 4-tetrahydro-2-naphthoic acid (IV) which was obtained by catalytic reduction of methyl 4-hydroximino-1, 2, 3, 4-tetrahydro-2-naphthoate (I), followed by cyclization and hydrolysis. Reduction of N, N′-diacetyl-(VIa) and N, N′-diformyl-(VIb) derivatives of V with lithium aluminum hydride afforded N, N′-diethyl-(VIIa) and N, N′-dimethyl-(VIIb) derivatives, respectively. Condensation of VIIa with formaldehyde and benzaldehyde gave 2, 4-diethyl-(VIIIa) and 2, 4-dimethyl-3-phenyl-1, 2, 3, 4, 5, 6-hexahydro-1, 5-methanobenzo [e] [1, 3]-diazocine (VIIIc). Similarly, 2, 4-dimethyl derivatives (VIIIb) and (VIIId) were prepared.
Surface charge theorem and topological constraints for edge states: Analytical study of one-dimensional nearest-neighbor tight-binding models (2020)

For a wide class of noninteracting tight-binding models in one dimension, we present an analytical solution for all scattering and edge states on a half-infinite system. Without assuming any symmetry constraints, we consider models with nearest-neighbor hoppings and one orbital per site but the arbitrary size of the unit cell and generic modulations of on-site potentials and hoppings. The solutions are parametrized by determinants that can be straightforwardly calculated from recursion relations. We show that this representation allows for an elegant analytic continuation to complex quasimomentum consistent with previous treatments for continuum models. Two important analytical results are obtained based on the explicit knowledge of all eigenstates. (1) An explicit proof of the surface charge theorem is presented including a unique relationship between the boundary charge ${Q}_{B}^{(\ensuremath{\alpha})}$ of a single band $\ensuremath{\alpha}$ and the bulk polarization in terms of the Zak-Berry phase. In particular, the Zak-Berry phase is determined within a special gauge of the Bloch states such that no unknown integer is left. This establishes a precise form of a bulk-boundary correspondence relating the boundary charge of a single band to bulk properties. (2) We derive a topological constraint for the phase dependence of the edge state energies, where the phase variable describes a continuous shift of the lattice towards the boundary. The topological constraint is shown to be equivalent to the quantization of a topological index $I=\mathrm{\ensuremath{\Delta}}{Q}_{B}\ensuremath{-}\overline{\ensuremath{\rho}}\ensuremath{\in}{\ensuremath{-}1,0}$ introduced in an accompanying paper [M. Pletyukhov et al., Phys. Rev. B 101, 161106 (2020)]. Here, $\mathrm{\ensuremath{\Delta}}{Q}_{B}$ is the change of the boundary charge ${Q}_{B}$ for a given chemical potential in the insulating regime when the lattice is shifted by one site towards the boundary, and $\overline{\ensuremath{\rho}}$ is the average charge per site (both in units of the elementary charge $e=1$). This establishes an interesting link between universal properties of the boundary charge and edge state physics discussed within the field of topological insulators. In accordance with previous results for continuum systems, we also establish the localization of the boundary charge and determine the explicit form of the density given by an exponential decay and a pre-exponential function following a power law with generic exponent $\ensuremath{-}1/2$ at large distances.
Systems biology of mucosal injury in cancer patients (2008)

9634 Background: Mucosal injury (mucositis) caused by high-dose or targeted cancer therapy can result in significant morbidity and financial cost. Understanding the causative complex molecular pathways of this toxicity will enhance design of new therapies. Computational reaction kinetic biological models represent an important strategic advance in this regard. These simulations are cost- and time- efficient and can identify new hypotheses and projected experimental outcomes. The technology also permits integration of complex models based on animal and human data. Methods: A mucositis reaction network structure was developed using COX-2 pathway data derived from literature-based animal and human studies as well as pre- and post-transplant oral mucosal biopsies from three hematopoietic cell transplant patients. Virtual Cell software was used to simulate network dynamics. Results: The nonlinear network mucositis model incorporated feedback loops and accounted for dynamic response of COX-1, COX-2, TNF-α, PGE-2, IL-1β, IL-6, PGI-2, TXA-2 and NF-κB with nonlinear correlation coefficients of −0.73, −4.27, −89.1, −7.85, 0.02, −2.79, 0.63, 0.86 and −0.02 respectively. For 7 of 8 molecular species, the model was able to predict final steady-state value within experimental error with exception of TNF-α. The ninth species, TXA-2, did not achieve steady-state within the timeframe monitored. Conclusions: Using the COX-2 pathway as a prototype, this model successfully incorporated experimental and computational approaches to elucidate mucositis network pathways. The results identify research areas requiring further study such as TNF-α dynamics, thus highlighting benefit of the model. This technology could also facilitate design of new mucositis research protocols including (i) mechanisms of neuropeptide-mediated pain, (ii) identification of tissue-based risk factors and (iii) integration of genetic, cytomorphologic and functional expression of oral and gastrointestinal mucosal injury. Supported by U.S. Public Health Service grants from National Center for Research Resources (P41 RR013186) and NIH Roadmap National Technology Centers for Networks and Pathways (U54 RR022232). Author Disclosure Employment or Leadership Consultant or Advisory Role Stock Ownership Honoraria Research Expert Testimony Other Remuneration The GI Co. ActoGeniX NV, Alizyme Ther. Ltd., Endo Pharm Inc., Genzyme Corp., MGI Pharma Inc., Nuvelo, The GI Co. The GI Co.
Novel Vaginal Microflora Colonization Model Providing New Insight into Microbicide Mechanism of Action (2011)

This report provides experimental evidence supporting the concept that the vaginal microflora regulates the epithelial innate immunity in a species- and strain-specific manner and that topically applied microbicides may alter both the bacterial and epithelial components of this homeostatic interaction. Our data also highlight the importance of differentiating the effects of biomedical interventions on epithelium-associated versus conventional planktonic bacterial growth when assessing vaginal mucosal health and immunity.