gebhart/patrepeval huggingface dataset:
Assembly of an Active Group II Intron−Maturase Complex by Protein Dimerization (2004)

Group II intron-encoded proteins promote both splicing and mobility of the intron RNA through formation of a specific RNA-protein complex. The Lactococcus lactis L1.LtrB intron encodes a maturase, LtrA, with reverse transcriptase homology and specific binding affinity for two domains of the intron RNA. The catalytically active ribonucleoprotein (RNP) has splicing, endonuclease, and reverse transcriptase activity, enabling efficient insertion of the intron sequence by a retro-homing mechanism. To determine the composition and assembly mechanism of the RNP complex, purified LtrA protein was analyzed for its ability to recognize a series of intron-derived RNAs. Equilibrium dissociation measurements show that LtrA recognizes two intronic domains, DI and DIV. However, distinct electrostatic requirements for binding imply different modes of molecular recognition in each case. Stoichiometric binding experiments show that the functional RNP complex consists of a dimeric protein species bound to a single intron RNA. Significant differences between the measured equilibrium dissociation constants and kinetically derived values suggest that conformational changes accompany assembly of the intron-maturase complex, and results of limited proteolysis and fluorescence spectroscopy experiments suggest that significant RNA-dependent structural changes within the maturase occur upon association with the intron. These results support a mutually induced fit model in which RNA-dependent conformational changes within LtrA enable stable association of the protein dimer with two independent intron domains to form a functional RNP.
Towards high resolution maps of the mouse and human genomes—a facility for ordering markers to 0.1 cM resolution (1994)

982 progeny produced by a mouse Interspecific backcross between C57BL/6 and Mus spretus have been scored for at least 3 markers on each chromosome, completing an anchor map of 78 loci across the mouse genome. The anchor mapping identifies all the available recomblnants in each interanchor Interval allowing access to panels of mice that can be used for the high resolution mapping of any chromosome region. The large number of progeny recovered and scored from the Interspecific backcross allows us to resolve genetically markers that lie on average 200 kb apart on mouse chromosomes and within the cloning capacity of currently available YAC libraries. EUCIB provides the first genetic mapping resource specifically designed for the high resolution mapping of all regions of the mouse genome and will underpin the global physical mapping of the mouse genome. In addition, with the use of conserved sequences the facility is applicable to the high resolution comparative mapping of the mouse and human genomes. A new database has been implemented to support the computation of high resolution and ordered genetic maps.
Real-time impedance-based monitoring of the growth and inhibition of osteomyelitis pathogen Staphylococcus aureus biofilms treated with novel bisphosphonate-fluoroquinolone antimicrobial conjugates (2020)

Anterior cruciate ligament (ACL) rupture increases the risk for osteoarthritis (OA).This study aims to clarify temporal alterations in subchondral bone (SCB) and articular cartilage in a rabbit model with surgical ACL transection (ACLT).Operated (ACLT) and contralateral (C-L) knees were harvested two (n=8) and eight (n=6) weeks after ACLT, surgery together with collection of age-matched control (CNTRL, n=8) knees.Each knee was divided into lateral and medial condyles and plateaus, groove and patella.Bone morphology was quantified using micro-computed tomography.Thickness and fixed charged density (FCD) of the cartilage were measured with optical coherence tomography and digital densitometry, respectively.Trabeculae in ACLT knees were thinner compared to C-L in the lateral plateau (-6.7%;p=0.007)and groove (-10.9%;p=0.015)two weeks after surgery.At eight weeks, thinner trabeculae compared to C-L were observed at all locations.Trabecular bone volume fraction was decreased in ACLT compared to CNTRL at all locations except for the patella.Subchondral plate was thinner than C-L in the lateral plateau (-26.2%;p=0.022),groove (-19.8%;p=0.005)andpatella (-19.5%;p=0.001).Two weeks after surgery, FCD was reduced at the lateral plateau, the medial condyles, the groove, and the patella in ACLT compared to CNTRL.FCD was lower in the ACLT compared to C-L at all locations except for the lateral plateau.Interestingly, eight weeks after surgery, the FCD was increased in the medial plateau of C-L compared to CNTRL group knees.FCD loss in ACLT was progressive in the condyles, but the initial FCD loss was compensated for in the groove and patella.Also, the cartilage was thicker (50.5%;p=0.007) in the lateral plateau of ACLT knees eight weeks after surgery compared to CNTRL.Summarizing, bone loss and cartilage degeneration occurred in a tissue-and site-specific manner in post-ACLT knees and bone loss spread progressively while some compositional changes of cartilage were recovered.
Role of Nanobiotechnology in the Development of Nanomedicine (2007)

This chapter provides an integrated overview of application of nanobiotechnology-based molecular diagnostics, drug discovery, and drug delivery in the development of nanomedicine with the relationships. The postgenomic era is revolutionizing the drug-discovery process. Nanodevices such as nanobiosensors and nanobiochips are being used to improve drug discovery and development. There are particular advantages of drug delivery for the treatment of various diseases by nanoscale devices. A drug-delivery system for intravenous administration of ibuprofen has been developed which exhibits sustained-release properties by either oral or intravenous route and may be useful for the treatment of postoperative pain. Nanobiotechnology can be applied to delivery of gene therapy using geneti-cally modified stem cells and further applied in tracking stem cells introduced into the human body. Applied nanobiotechnology aimed at the regeneration and neuroprotection of the central nervous system will significantly benefit from basic nanotechnology research conducted in parallel with advances in cell biology, neurophysiology, and neuropathology.
Supplementary Figure Legend from EZH2 Modifies Sunitinib Resistance in Renal Cell Carcinoma by Kinome Reprogramming (2023)

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Pulmonary Delivery of Nanoparticle-Bound Toll-like Receptor 9 Agonist for the Treatment of Metastatic Lung Cancer (2020)

CpG oligodeoxynucleotides are potent toll-like receptor (TLR) 9 agonists and have shown promise as anticancer agents in preclinical studies and clinical trials. Binding of CpG to TLR9 initiates a cascade of innate and adaptive immune responses, beginning with activation of dendritic cells and resulting in a range of secondary effects that include the secretion of pro-inflammatory cytokines, activation of natural killer cells, and expansion of T cell populations. Recent literature suggests that local delivery of CpG in tumors results in superior antitumor effects as compared to systemic delivery. In this study, we utilized PRINT (particle replication in nonwetting templates) nanoparticles as a vehicle to deliver CpG into murine lungs through orotracheal instillations. In two murine orthotopic metastasis models of non-small-cell lung cancer-344SQ (lung adenocarcinoma) and KAL-LN2E1 (lung squamous carcinoma), local delivery of PRINT-CpG into the lungs effectively promoted substantial tumor regression and also limited systemic toxicities associated with soluble CpG. Furthermore, cured mice were completely resistant to tumor rechallenge. Additionally, nanodelivery showed extended retention of CpG within the lungs as well as prolonged elevation of antitumor cytokines in the lungs, but no elevated levels of proinflammatory cytokines in the serum. These results demonstrate that PRINT-CpG is a potent nanoplatform for local treatment of lung cancer that has collateral therapeutic effects on systemic disease and an encouraging toxicity profile and may have the potential to treat lung metastasis of other cancer types.
Polarization dependence of coherent phonon generation and detection in highly-aligned single-walled carbon nanotubes (2011)

We have investigated the polarization dependence of the generation and detection of radial breathing mode (RBM) coherent phonons (CPs) in highly-aligned single-walled carbon nanotubes. Using polarization-dependent pump-probe differential-transmission spectroscopy, we measured RBM CPs as a function of angle for two different geometries. In Type I geometry, the pump and probe polarizations were fixed, and the sample orientation was rotated whereas, in Type II geometry, the probe polarization and sample orientation were fixed, and the pump polarization was rotated. In both geometries, we observed an almost complete quenching of the RBM CPs when the pump polarization was perpendicular to the nanotubes. For both Type I and II geometries, we have developed a microscopic theoretical model to simulate CP generation and detection as a function of polarization angle and found that the CP signal decreases as the angle goes from 0${}^{ˆ}$ (parallel to the tube) to 90${}^{ˆ}$ (perpendicular to the tube). We compare theory with experiment in detail for RBM CPs created by pumping at the ${E}_{44}$ optical transition in an ensemble of single-walled carbon nanotubes with a diameter distribution centered around 3 nm, taking into account realistic band structure and imperfect nanotube alignment in the sample. We theoretically determined a $\mathrm{cos}{}^{8}(\ensuremath{\theta})$ dependence for Type I CP spectroscopy experiments and a $\mathrm{cos}{}^{4}(\ensuremath{\phi})$ polarization dependence for Type II CP spectroscopy experiments and, after including misalignment effects to our fitting, we determined the nematic order parameter of our sample to be 0.81.
Global identifiability of nonlinear models of biological systems (2001)

A prerequisite for well-posedness of parameter estimation of biological and physiological systems is a priori global identifiability, a property which concerns uniqueness of the solution for the unknown model parameters. Assessing a priori global identifiability is particularly difficult for nonlinear dynamic models. Various approaches have been proposed in the literature but no solution exists in the general case. In this paper, we present a new algorithm for testing global identifiability of nonlinear dynamic models, based on differential algebra. The characteristic set associated to the dynamic equations is calculated in an efficient way and computer algebra techniques are used to solve the resulting set of nonlinear algebraic equations. The algorithm is capable of handling many features arising in biological system models, including zero initial conditions and time-varying parameters. Examples of usage of the algorithm for analyzing a priori global identifiability of nonlinear models of biological and physiological systems are presented.
Iterative Learning Pressure and Flow Control of a Bioreactor for Tissue Engineered Heart Valves (2021)

During the in vitro maturation process of tissue engineered heart valves in a bioreactor, the pressures ahead of and behind the heart valve as well as the transvalvular flow rate strongly influence the tissue development. In this paper, a norm-optimal iterative learning control scheme for the control of these three process input variables within a new bioreactor setup is introduced and evaluated using physiological references of an aortic heart valve. A Model-in-the-Loop (MiL) setup is established for this evaluation. The results indicate that the proposed scheme yields good tracking performance for all three controlled variables: The stationary root-mean-square errors (RMSEs) of the aortic and left ventricular pressures are, respectively, 0.9 mmHg and 4.8 mmHg (pressure range: 0 - 120 mmHg). The RMSE of the transvalvular flow rate equals to 12.3 ml s <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">-1</sup> (flow rate range: 0 - 500 ml s <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">-1</sup> ). Consequently, the proposed scheme is suitable for the introduced task and can therefore be investigated further.
Outcome of Noncardiac Operations in Patients with Severe Coronary Artery Disease Successfully Treated Preoperatively with Coronary Angioplasty (1992)

HUBER, K. C.; EVANS, M. A.; BRESNAHAN, J. F.; GIBBONS, R. J.; HOLMES, D. R. JR. Author Information
The Provision of Intelligent Agent-Based Enhanced Multimedia Network Services (1995)

This paper describes some of the latest work in developing infrastructures that will provide customers with multimedia information. The paper discusses the concept of providing enhanced multimedia network services based upon intelligent agents (IAs), and the attributes of a user interface. Examples of emerging and future intelligent agent technologies are discussed, and delivery options for future enhanced multimedia services are examined. By evaluating trends in computer, networking, and multimedia processing technology, an approach is derived for creating and deploying enhanced multimedia network services. The paper concludes with examples of key components of the proposed infrastructure.
Plausible Mechanism for the Formation of 2-Methoxy-2H-azepine Derivatives from 3H-Azepines Using Bromine and NBS (2003)

Formation of 2-bromo-4-t-butyl-7-methoxy-2H-azepine and 4-tbutyl-7-methoxy-2-succinimidyl-2H-azepine by the respective reactions of 5-tbutyl-2-methoxy-3H-azepine with bromine and NBS suggests a plausible mechanism for the conversion of 3H-azepine to 2H-azepine as 1,4-addition of an electrophile and a consequent 1,2-dehydrobromination.Different from the case of cycloheptatriene, reaction of 3H-azepine with bromine did not give any delocalized ionic species.In the 1950's, 1,3,5-cycloheptatriene (CHT) was observed to react with an equivalent of bromine to give a stable delocalized aromatic tropylium bromide (eq.1). 1 Tropylium bromide has been found to react with various nucleophiles to form the corresponding substituted CHT derivatives. 2Recently, we reported the specific formation of 3,6-and 4,7-di-t-butyl-2-methoxy-2H-azepines (2a and 2b) by adding excess methanol to the reaction mixture of 3,6-and 2,5-di-t-butyl-3H-azepines (1a and 1b) 3,4 and bromine followed by work up with aqueous alkaline. 5As the initial conditions of the reactions are similar to those of CHT and bromine, the formation of 2-methoxy-2H-azepine has been presumed to be a nucleophilic Br 2 + + Br -+ HBr (eq. 1)addition of methanol to an azatropylium ion.In order to confirm the reaction mechanism, attempts were made to determine the structure of any reaction products without adding methanol to the reaction mixture.An analogous reaction sequence was applied to 5-t-butyl-and 5-methyl-2-methoxy-3H-azepine (1c and 1d), 6 from which formation of 4-t-butyl-and 4-methyl-2,7-dimethoxy-2H-azepines (2c and 2d) was observed in 52 and 30% yields, respectively (Scheme 1).The structure of 2c and 2d was confirmed by a similar coupling pattern to that of previously obtained 2b in the 1 H-NMR spectrum. 7,8At this point our interest was focused on the reaction mechanism for the formation of 2H-azepine from 3H-azepine.The intermediate formation of delocalized azepinium ion, as in the case of CHT, is a reasonable consideration to explain the specific formation of the products but no attributable peaks to an azepinium ion were detected by careful 1 H-NMR spectral observation of a mixture of 3H-azepine and bromine.We next investigated the reaction of 1c with bromine under similar conditions except no methanol was introduced before treatment with aqueous alkaline.A half equivalent of bromine was used for the reaction because only decomposition products were obtained when a full equivalent of bromine reacted.The compounds formed were separated by chromatography (hexane : ethyl acetate = 3 : 2 v/v) on silica gel at 0˚C and structures assigned to labile 2-bromo-4-t-butyl-7-methoxy-2H-azepine (3) in 12% yield and 5-t-butyl-3H-
Clinical outcomes of transcatheter mitral valve replacement: two-year results of the CHOICE-MI Registry (2023)

In this real-world registry of patients with symptomatic MR undergoing TMVR, treatment with TMVR was associated with a durable resolution of MR and significant functional improvement at 2 years. Two-year mortality was 38.1%. Optimised patient selection and improved access site management are mandatory to improve outcomes.
Adaptive blind channel identification of FIR channels for Viterbi decoding (2002)

Relying upon the diversity introduced by fractional-sampling or by multiple sensors, two different approaches for blind adaptive channel identification are proposed based on existing batch algorithms. We show that the adaptive approach allows tracking of time-variations in the channel and provides robustness to nearly common channel roots. Existing second-order adaptive procedures typically employ suboptimal linear equalizers whereas the adaptive channel estimators we propose can be used in an optimal maximum likelihood sequence estimator. Simulations are provided that demonstrate the performance of the proposed channel estimators when used in the Viterbi algorithm for symbol detection.
Zinc Piracy as a Mechanism of Neisseria meningitidis for Evasion of Nutritional Immunity (2013)

The outer membrane of Gram-negative bacteria functions as a permeability barrier that protects these bacteria against harmful compounds in the environment. Most nutrients pass the outer membrane by passive diffusion via pore-forming proteins known as porins. However, diffusion can only satisfy the growth requirements if the extracellular concentration of the nutrients is high. In the vertebrate host, the sequestration of essential nutrient metals is an important defense mechanism that limits the growth of invading pathogens, a process known as "nutritional immunity." The acquisition of scarce nutrients from the environment is mediated by receptors in the outer membrane in an energy-requiring process. Most characterized receptors are involved in the acquisition of iron. In this study, we characterized a hitherto unknown receptor from Neisseria meningitidis, a causative agent of sepsis and meningitis. Expression of this receptor, designated CbpA, is induced when the bacteria are grown under zinc limitation. We demonstrate that CbpA functions as a receptor for calprotectin, a protein that is massively produced by neutrophils and other cells and that has been shown to limit bacterial growth by chelating Zn²⁺ and Mn²⁺ ions. Expression of CbpA enables N. meningitidis to survive and propagate in the presence of calprotectin and to use calprotectin as a zinc source. Besides CbpA, also the TonB protein, which couples energy of the proton gradient across the inner membrane to receptor-mediated transport across the outer membrane, is required for the process. CbpA was found to be expressed in all N. meningitidis strains examined, consistent with a vital role for the protein when the bacteria reside in the host. Together, our results demonstrate that N. meningitidis is able to subvert an important defense mechanism of the human host and to utilize calprotectin to promote its growth.
Long term enhancement of cerebral vascular resistance in spontaneously hypertensive rats produces short term pressor responses and long term re‐modelling of cerebral circulation (2012)

Cushing (1901, Bull Johns Hopk Hosp 12, 290‐) discovered that acute increases in cerebral vascular resistance produced hypertension. Based on the Cushing response we propose that hypertension may result from elevated cerebral vascular resistance. We sought to determine the effect of occluding both vertebral and the right common carotid artery (3‐vessel occlusion or 3‐VO) on arterial pressure in spontaneously hypertensive rats (SHR). Given that this strain already has narrowed vertebro‐basilar arteries (Cates et al. 2011; J. Appl. Physiol . 111, 149‐), we hypothesised that the pressor response in the SHR would be larger than that in the Wistar rat. 3‐VO in SHR (n=7) produced a pressor response of 23±3mmHg, which compared with 15±2mmHg in normotensive rats (n=5). Arterial pressure returned to control levels by 8–11 days after 3‐VO. In the SHR there was marked cerebral vessel re‐modelling including dilatation of the right posterior communicating artery (+63%) and ventral spinal artery (+54%) seen from day 11 post 3‐VO. The degree of re‐modelling was associated with the magnitude of the pressure response. 3‐VO in the SHR produces a significant pressor effect and arteriogenesis of cerebral vessels that is associated with a subsequent near normalisation of arterial pressure. Cerebral vascular resistance plays a major role in determining arterial pressure set‐point in the SHR. MRC and BHF funded research.
A BiCMOS 50 MHz cache controller for a superscalar microprocessor (2003)

A description is given of a BiCMOS 50-MHz, 2.2 M-transistor cache controller (CC) chip which supports up to 2 MB of direct-mapped secondary cache for a superscalar microprocessor chip (PU) and interfaces with two multiprocessor (MP) buses. One is the MBus, a circuit-switched MP system bus operating at TTL (transistor-transistor logic) levels. The other is the XBus, a local packet-switched bus operating at either TTL or Gunning-transceiver logic (GTL) levels. In XBus mode, the CC connects to MP buses through buswatcher chips, up to four of which can be connected to the CC to support 4 MP buses. With XBus interface, the CC can support customized MP buses.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
On the mechanism of ion formation from the aqueous solutions irradiated with 3 µm IR laser pulses under atmospheric pressure (2006)

The mechanism of atmospheric pressure (AP) laser ionization of water and water/glycerol liquid samples at a 3-microm wavelength is studied experimentally. For the ion desorption, an in-house built Yb : YAG-pumped optical parametric oscillator (OPO) infrared (IR) laser has been coupled with AP MALDI ion source interfaced to an ion trap mass spectrometer (MS). It has been shown that water is primarily responsible for ion generation in water/glycerol samples, while glycerol increases the solution viscosity and decreases the water evaporation rate and sample losses. In contrast to AP UV-MALDI, the electric field in the case of AP IR-MALDI does not assist in ion production. It was found that the absence of the electrical field provides the optimum ionization condition both for water and water/glycerol liquid samples at the 3-microm laser irradiation. A two-stage ion formation mechanism, which includes the initial emission of microdroplets and release of molecular ions at the second stage, can explain the experimentally observed ion signal dependencies upon the voltage applied between MS inlet and the MALDI sample plate. Postionization using additional corona discharge APCI increases the observed signal by approximately 50%, which indicates that some portion of the analyte is desorbed in the form of neutral molecules.
Ethnic variations in facial skin neurosensitivity assessed by capsaicin detection thresholds (2009)

The capsaicin skin neurosensitivity test is painless and the changes across individuals of different ethnic backgrounds appear minimal.