gebhart/patrepeval huggingface dataset:
Site-specific integration of the Haemophilus influenzae bacteriophage HP1. Identification of the points of recombinational strand exchange and the limits of the host attachment site. (1992)

Isotopic transfer experiments and boundary replacement studies were used to define the size and cleavage points of the Haemophilus influenzae attB site for phage HP1 integration. The points of strand cleavage and transfer were separated by 5' extensions with a spacing or overlap region most probably 7 residues long. The complete HP1 attB site is included within an 18-base pair (bp) sequence surrounding the cleavage sites. The sequence of HP1 attB is remarkably symmetric. Two 8-bp inverted repeats surround the central residue of the 7-bp overlap sequence; this central residue is the second residue of the anticodon sequence of the H. influenzae tRNA(leu)(UUR) gene which contains attB, and this symmetric segment encodes the anticodon stem and loop.
Guselkumab for the Treatment of Crohn’s Disease: Induction Results From the Phase 2 GALAXI-1 Study (2022)

gov, Number: NCT03466411.
Gradient flows and geometric active contour models (2002)

In this paper, we analyze the geometric active contour models discussed previously from a curve evolution point of view and propose some modifications based on gradient flows relative to certain new feature-based Riemannian metrics. This leads to a novel snake paradigm in which the feature of interest may be considered to lie at the bottom of a potential well. Thus the snake is attracted very naturally and efficiently to the desired feature. Moreover, we consider some 3-D active surface models based on these ideas.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
COMPARISON OF THE REACTIVITY OF NANOSIZED ZERO-VALENT IRON (nZVI) PARTICLES PRODUCED BY BOROHYDRIDE AND DITHIONITE REDUCTION OF IRON SALTS (2008)

Dithionite can be used to reduce Fe (II) and produce nanoscale zero-valent iron (nZVI) under conditions of high pH and in the absence of oxygen. The nZVI is coprecipitated with a sulfite hydrate in a thin platelet. The nanoparticles formed are not pure iron but this feature does not appear to affect their degradation performance under air or N 2 gas conditions. The efficiency of trichloroethylene (TCE) degradation, when one is employing nanoparticles manufactured using dithionite ( nZVI S 2 O 4 ), is similar to if not slightly better than that of the more conventional borohydride procedure ( nZVI BH 4 ). The other advantages of the dithionite method are that (i) it uses a less expensive and widely available reducing agent, and (ii) there is no production of potentially explosive hydrogen gas. Oxidation of benzoic acid using the nZVI S 2 O 4 particles results in different byproducts than those produced when nZVI BH 4 particles are used. The low oxidant yield based on hydroxybenzoic acid generation is offset by the production of higher concentrations of phenol. The high concentration of phenol compared to hydroxybenzoic acids suggests that OH • addition is not the primary oxidation pathway when one is using the nZVI S 2 O 4 particles. It is proposed that sulfate radicals ([Formula: see text]) are produced as a result of hydroxyl radical attack on the sulfite matrix surrounding the nZVI S 2 O 4 particles, with these radicals oxidizing benzoic acid via electron transfer reactions rather than addition reactions.
Analysis of the DNA Sequence of a 34 038 bp Region on the Left Arm of Yeast Chromosome XV (1997)

We report the DNA sequence of a 34,038 bp segment of Saccharomyces cerevisiae chromosome XV. Subsequent analysis revealed 20 open reading frames (ORFs) longer than 300 bp and two tRNA genes. Five ORFs correspond to genes previously identified in S. cerevisiae, including RPLA2, PRE6, MSE1, IFM1 and SCM2 (TAT2, TAP2, LTG3). Two putative proteins share considerable homology with other proteins in the current data libraries. ORF O2145 shows 41.2% identity with the glycophospholipid-anchored surface glycoprotein Gas1p of S. cerevisiae and ORF O2197 has 53.2% identity to chromosome segregation protein Dis3p of Schizosaccharomyces pombe.
Recommendations on adapting crowdsourcing to problem types (2015)

Crowdsourcing is a paradigm which enables and harnesses the power and wisdom of a usually large, diverse crowd in innovation, problem solving and knowledge acquisition. The scale, benefits and application areas of this traditional model are amplified by the advances of information and communication technology such as the advent of Web 2.0, which, at the same time, has increased the complexity and, hence, the need for systematic development approaches. While crowdsourcing has been successfully applied in several projects and de-facto platforms already exist for them, the research on engineering principles, methods and tools for developing a crowdsourcing project is still in the early stages. In this paper, we study the adaptation of crowdsourcing settings to fit the nature of the problem being crowdsourced. As a method, we review the literature and complement that with an online expert survey involving practitioners and researchers active in the field of crowdsourcing. We then interpret the obtained results and identify a set of recommendations on how to set up crowdsourcing to fit each of the five common categories of problems. Our results inform future crowdsourcing developers with best practice experiences on planning and configuring their projects.
Assessment of rat sciatic nerve function following acute implantation of high density utah slanted electrode array (25 electrodes/mm<sup>2</sup>) based on neural recordings and evoked muscle activity (2014)

These studies demonstrate that HD-USEAs provide a useful neural interface without causing a nerve crush injury that would otherwise negate their use in acute preparations (<12 h).
Spatial Interference Cancellation in Heterogeneous Networks with Biased Cell Association (2015)

Biased cell association has been widely applied in heterogeneous networks (HetNets) to offload users to small cells, which, however, results in degraded signal to interference plus noise (SINR) of these offloaded users. In this paper, we propose a spatial interference cancellation (SIC) scheme in HetNets with biased cell association, by which the interference from high-power base stations (BSs) to users located at the expanded region of lower-power cells is mitigated in the spatial domain. Using stochastic geometric tools, the analytical results are developed in terms of success probability for both the zero-forcing beamforming (ZFBF) scheme with full multiplexing and the proposed SIC scheme. Numerical results evaluate the impact of transmit antenna number and demonstrate the trade-offs between spatial multiplexing and interference mitigation. It is revealed that remarkable improvement of success probability is provided by the SIC scheme in fully loaded scenarios, while it is preferable to employ the SIC scheme to achieve higher network throughput in under loaded scenarios.
Effects of Sintering Aids on the Transparency and Conversion Efficiency of Cr <sup>4+</sup> Ions in Cr: YAG Transparent Ceramics (2015)

Tetravalent chromium‐doped Y 3 Al 5 O 12 ceramics were fabricated by solid‐state reactive sintering method using high‐purity Y 2 O 3 , α‐ Al 2 O 3 , and Cr 2 O 3 powders as the starting materials. CaO and MgO were co‐doped as the sintering aids. The effects of TEOS and divalent dopants (CaO and MgO) on the optical qualities, the conversion efficiency of Cr 4+ ions, and the microstructure evolutions of 0.1 at.% Cr 4+ : YAG ceramics were investigated. Fully dense, dark brown colored Cr 4+ : YAG ceramics with an average grain size of 3.1 μm were achieved. The in‐line transmittance of the as‐prepared ceramic at 2000 nm was 85.3% (4 mm thick), and the absorption coefficient at 1030 nm (the characteristic absorption peak of Cr 4+ ions) was as high as 3.7 cm −1 , which was higher than that of corresponding single crystals fabricated by Czochralski method.
Hierarchical Porous Core−Shell Carbon Nanoparticles (2009)

The excellent physical and chemical properties of porous carbon materials allow them to be widely used in many fields. Their performance in a specific application is usually determined by structural features such as pore diameter, channel length, and architecture. In recent years, great efforts have been made to develop suitable carbon-based materials with short pores and/or hierarchical porous architectures, for use in transport or diffusion of guest objects by reducing pathways and resistance. In the present paper, we report on a novel carbon nanostructure constructed with a mesoporous core and a microporous shell. The mesopore walls are constructed of only a few graphene layers and can be controllably removed by a wetting oxidation reaction, which leaves behind hollow nanoparticles. These short-pore structures could facilitate the diffusion of molecules; they also show a very high and stable catalytic performance during the dehydrogenation of cyclohexane that is far superior to currently available long-pore materials, such as active carbon and carbon nanotubes.
Activation of RIG-I-like receptor signal transduction (2011)

Mammalian cells have the ability to recognize virus infection and mount a powerful antiviral response. Pattern recognition receptor proteins detect molecular signatures of virus infection and activate antiviral signaling cascades. The RIG-I-like receptors are cytoplasmic DExD/H box proteins that can specifically recognize virus-derived RNA species as a molecular feature discriminating the pathogen from the host. The RIG-I-like receptor family is composed of three homologous proteins, RIG-I, MDA5, and LGP2. All of these proteins can bind double-stranded RNA species with varying affinities via their conserved DExD/H box RNA helicase domains and C-terminal regulatory domains. The recognition of foreign RNA by the RLRs activates enzymatic functions and initiates signal transduction pathways resulting in the production of antiviral cytokines and the establishment of a broadly effective cellular antiviral state that protects neighboring cells from infection and triggers innate and adaptive immune systems. The propagation of this signal via the interferon antiviral system has been studied extensively, while the precise roles for enzymatic activities of the RNA helicase domain in antiviral responses are only beginning to be elucidated. Here, current models for RLR ligand recognition and signaling are reviewed.
Phospholipids Chiral at Phosphorus. 13. Stereochemical Comparison of Phospholipase A<sub>2</sub>, Lecithin-Cholesterol Acyl Transferase, and Platelet-Activating Factor (1987)

Abstract Thiophospholipids and thiophosphate analogs of platelet activating factor were synthesized and used to compare the stereochemical properties in three different biological systems. Phospholipase A2 shows high stereo-specificity, and this has been substantiated by computer graphics. Lecithin-cholesterol acyl transferase shows no stereospecificity. Platelet aggregation shows, preliminarily, a small degree of stereospecificity.
Membrane-bound Dictyostelium myosin heavy chain kinase: a developmentally regulated substrate-specific member of the protein kinase C family. (1992)

A cDNA clone corresponding to the Dictyostelium myosin heavy chain kinase (MHCK) gene was isolated using antibodies specific to the purified enzyme. Sequence analysis of the cDNA revealed that the Dictyostelium MHCK possesses all of the domains characteristic of members of the protein kinase C family. The amino-terminal region of the MHCK contains the cysteine-rich motif with an internal duplication that is present in all known protein kinase C species. This domain precedes sequences that are highly homologous to protein kinase catalytic domains. The carboxyl-terminal region contains a cluster of 23 serine and threonine residues that may represent the autophosphorylation domain of the Dictyostelium MHCK. These results, along with previous studies that indicate that this enzyme has very restrictive substrate specificity, incorporates approximately 20 mol of phosphate per mol of kinase through an autophosphorylation reaction, and is expressed only during development, suggest that the Dictyostelium MHCK is a distinct member of the protein kinase C family and imply that this kinase family, which may include members with very specific cellular functions, may be even more heterogeneous than previously thought.
Effects of frequency separation in periodic active noise control systems (2006)

In many practical active noise control (ANC) applications, the primary noise contains multiple closely-spaced harmonics. A narrow-band feedforward ANC system consists of an adaptive filter excited by a composite reference signal, which is the sum of multiple sinusoids corresponding to the harmonic frequencies of the primary noise. This paper analyzes and shows that the convergence of this direct-form controller is dependent on the frequency separation between two adjacent sinusoids in the reference signal. The analysis also proves that the length of the adaptive filter required for achieving the same convergence speed decreases with an increase in frequency separation. This paper also performs mathematical analysis of the direct/parallel-form controller, which significantly improves the convergence speed and reduces filter length by increasing the frequency separation in the individual reference signal for each adaptive filter. Computer simulations are conducted to verify the analysis presented in the paper
Fabrication and calibration of three temperature probes for monitoring the effects of thermal cancer ablation (2017)

Minimally invasive thermal techniques are gaining acceptance in cancer removal. These approaches aim at destroying the tumour while minimizing the damage of surrounding healthy structures. Several solutions have already proved their effectiveness in improving treatment outcomes and in minimizing adverse events. However, it is still challenging to selectively remove the cancer. To help tackle this challenge, several groups of research are focusing on the use of thermometry for monitoring the effects on biological tissue of hyperthermal treatments, since the irreversible damage of tissue depends on temperature and time of application. Given the rising complexity of treatment settings, a temperature feedback may be useful to improve the clinical outcome by minimizing the thermal damage of surrounding healthy tissue. Fiber Bragg grating (FBG) sensors are used in this scenario thanks to several advantages, such as the small size, Magnetic Resonance (MR) compatibility and the possibility to perform spatially distributed measurements; moreover, with the use of specific coating their thermal sensitivity may be increased. However, they are fragile and their insertion within the organ can be challenging and time consuming. In this paper we describe the fabrication of three thermal probes embedding FBG sensors. Each probe consists of a MR-compatible needle which embeds a FBG sensor glued with epoxy adhesive. The three probes showed a sensitivity of about 24 pm/°C, which his higher than the one showed by non-encapsulated FBG (about 10 pm/°C). Moreover, the output of the three probes showed a negligible output drift and a negligible sensitivity drift after 4 thermal cycles in a wide range of temperature (i.e., from environmental temperature up to about 80 °C). The investigated solution shows some advantages considering the specific field of application: it allows an easy insertion within the organ being embedded within a needle; the probes' sensitivity is better than non-encapsulated FBGs; it can be used also during MR-guided procedures since both the needle and the FBG are MR-compatible. Future testing will assess the feasibility for temperature monitoring during thermal ablation treatment of the probes in ex vivo and in vivo animal model.
Human β-Defensin 3 Inhibits Cell Wall Biosynthesis in Staphylococci (2010)

Human beta-defensin 3 (hBD3) is a highly charged (+11) cationic host defense peptide, produced by epithelial cells and neutrophils. hBD3 retains antimicrobial activity against a broad range of pathogens, including multiresistant Staphylococcus aureus, even under high-salt conditions. Whereas antimicrobial host defense peptides are assumed to act by permeabilizing cell membranes, the transcriptional response pattern of hBD3-treated staphylococcal cells resembled that of vancomycin-treated cells (V. Sass, U. Pag, A. Tossi, G. Bierbaum, and H. G. Sahl, Int. J. Med. Microbiol. 298:619-633, 2008) and suggested that inhibition of cell wall biosynthesis is a major component of the killing process. hBD3-treated cells, inspected by transmission electron microscopy, showed localized protrusions of cytoplasmic contents, and analysis of the intracellular pool of nucleotide-activated cell wall precursors demonstrated accumulation of the final soluble precursor, UDP-MurNAc-pentapeptide. Accumulation is typically induced by antibiotics that inhibit membrane-bound steps of cell wall biosynthesis and also demonstrates that hBD3 does not impair the biosynthetic capacity of cells and does not cause gross leakage of small cytoplasmic compounds. In in vitro assays of individual membrane-associated cell wall biosynthesis reactions (MraY, MurG, FemX, and penicillin-binding protein 2 [PBP2]), hBD3 inhibited those enzymes which use the bactoprenol-bound cell wall building block lipid II as a substrate; quantitative analysis suggested that hBD3 may stoichiometrically bind to lipid II. We report that binding of hBD3 to defined, lipid II-rich sites of cell wall biosynthesis may lead to perturbation of the biosynthesis machinery, resulting in localized lesions in the cell wall as demonstrated by electron microscopy. The lesions may then allow for osmotic rupture of cells when defensins are tested under low-salt conditions.
Basics, types and applications of molecular docking: A review (2022)

From hit discovery through lead optimization and beyond, computational methods have become an essential part of many drugs development processes. There are typically several steps in the docking process, and each one provides a new level of complexity. Docking methods are used to place small molecules in the active region of the enzyme. In addition to these methods, scoring functions are used to estimate a compound's biological activity by looking at how it interacts with prospective targets. Molecular docking is considered to be the most widely utilized computational phenomenon in the field of computer-aided drug design (CADD). It is being utilized at the academic level as well as in pharmaceutical companies for the lead discovery process. Molecular docking is mainly associated with two terms: ligand and protein. Protein is the target site where ligand may bind to give specific activity. Molecular docking provides information on the ability of the ligand to bind with protein which is known as binding affinity. Applications of molecular docking in drug development have evolved significantly since it was first created to aid in the study of molecular recognition processes between small and large compounds. This review emphasizes the basic features of molecular docking along with the types, approaches and applications.
Evidence for Two Separate One-Electron Transfer Events in Excited Fulleropyrrolidine Dyads Containing Tetrathiafulvalene (TTF) (2000)

1,3-Dipolar cycloadditions of TTF-azomethine ylides (TTF = tetrathiafulvalene) to C60 have been used to synthesize a series of novel donor−bridge−acceptor dyads. In these dyads the pyrrolidine[3',4':1,2][60]fullerene is covalently attached to the electron donor TTF either directly (5) or alternatively through one (2a) or two (7) vinyl groups. In the ground state, dyads 2a, 5, and 7 undergo four quasireversible one-electron reductions and two reversible oxidation steps. The former are associated with the reduction of the C60 core, whereas the latter correspond to the formation of the radical cation and dication of the TTF moiety, respectively. Semiempirical PM3 calculations reveal donor−acceptor distances of 4.8 Å (5), 7.6 Å (2a), and 10.5 Å (7), and a deviation from planarity between the TTF fragment and the vinylogous spacer. In relation to an N-methylfulleropyrrolidine, the emission of the fullerene singlet excited state in dyads 2a, 5, and 7 is substantially reduced. Furthermore, the fluorescence quantum yield correlates well with the solvent dielectric constant and also with the spatial separation of the donor and acceptor moieties in the dyads. These correlation suggest that intramolecular electron-transfer processes evolving from the fullerene singlet excited state generate the (C60•-)−(TTF•+) pair. Pico- and nanosecond-resolved transient spectroscopy further substantiate a rapid transformation of the initially formed singlet excited state into the charge-separated radical pair with intramolecular rates ranging between 1.17 × 1010 s-1 and 1.47 × 109 s-1. In all cases, the product of back electron transfer is the triplet excited state, which is generated with markedly high quantum yields (0.61−0.97). The latter is, in addition to the rapid primary intramolecular electron transfer, subject to a slower, secondary intermolecular electron transfer with rate constants of 7 × 108 M-1s-1 (5) in benzonitrile and 1.6 × 109 M-1 s-1 (5) in toluene.
Implementing Restaurant Revenue Management (1999)

Revenue management (or yield management) rests on a measure of the time involved in the guest-service cycle. Such a time-related measure raises complications for restaurants, because they explicitly sell meals, rather than a period of time at the table. Existing measures of restaurant success do not give restaurant managers an effective gauge for revenue management because they do not capture the time element. Instead, would-be restaurant revenue managers must gain control of the timing and duration of restaurants' meals. The timing depends mostly on guest arrival, which can sometimes by altered with price and menu promotions. Managing duration is complex and relies on control of food production and the service cycle. A time-based measure of restaurant operation is revenue per available seat-hour (RevPASH). That calculation is total revenue for a given period (e.g., meal period, day part, or day) divided by the product of the number of available seats and the length of the period in question. Managers must understand their operation's RevPASH patterns to develop strategies for augmenting revenue, whether those strategies involve shifting customer demand to shoulder periods or tightening the service cycle.
Dachaihu decoction ameliorates pancreatic fibrosis by inhibiting macrophage infiltration in chronic pancreatitis (2017)

The dominant role of macrophages in the development of CP was mainly related to IL-6 production. DCHD was effective in ameliorating pancreatic fibrosis by inhibiting macrophage infiltration and inflammatory factor secretion in the pancreas.
Queueing analysis of transport-layer connections in an internet environment (2003)

The performance of transport-layer connections in an internet environment is investigated. The scenario of multiple-sender hosts and a single-receiver host, which are connected through a transport network, is considered. Application-layer processes in the sender hosts generate messages which are transferred to a peer process in the receiver host. Messages are transferred over window flow-controlled end-to-end connections between transport-layer entities. Buffer space in the host machines is assumed to be limited; thus process blocking can occur. The performance model developed considers the system to be comprised of three submodels: sender, receiver, and communications control. The analysis technique develops a queuing model for each submodel. Approximate results are obtained through an iterative solution method, using the results of one submodel as inputs to the others. The accuracy of the approximate analysis is discussed and performance characteristics are presented.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>