gebhart/patrepeval huggingface dataset:
Fiber Bragg gratings (1997)

Since the discovery of photosensitivity in optical fibers there has been great interest in the fabrication of Bragg gratings within the core of a fiber. The ability to inscribe intracore Bragg gratings in these photosensitive fibers has revolutionized the field of telecommunications and optical fiber based sensor technology. Over the last few years, the number of researchers investigating fundamental, as well as application aspects of these gratings has increased dramatically. This article reviews the technology of Bragg gratings in optical fibers. It introduces the phenomenon of photosensitivity in optical fibers, examines the properties of Bragg gratings, and presents some of the important developments in devices and applications. The most common fabrication techniques (interferometric, phase mask, and point by point) are examined in detail with reference to the advantages and the disadvantages in utilizing them for inscribing Bragg gratings. Reflectivity, bandwidth, temperature, and strain sensitivity of the Bragg reflectors are examined and novel and special Bragg grating structures such as chirped gratings, blazed gratings, phase-shifted gratings, and superimposed multiple gratings are discussed. A formalism for calculating the spectral response of Bragg grating structures is described. Finally, devices and applications for telecommunication and fiber-optic sensors are described, and the impact of this technology on the future of the above areas is discussed.
Simple Strategies to Improve Bioprocess Pure Culture Processing (2010)

Bioreaction and fermentation processes of all scales – from 100,000 liter vessels to small development reactors – require pure culture for their successful, productive operation. In this article the term “pure culture” and “pure culture capability” will be used instead of “sterile” or “sterility assurance” to acknowledge that bioreactions are, by nature, the process of growing large populations of helpful microorganisms or cells as opposed to the more unwanted varieties. Contamination by adventitious agents costs time, money, and lost productivity; moreover, contaminants and their sources can be very difficult to locate and eliminate. Many elements of pure culture bioprocess design and operation are straightforward, often even a matter of common sense. Most modern facilities have pure culture capability built into
Role of Transcriptional cis -Elements, Angiotensinogen Gene–Activating Elements, of Angiotensinogen Gene in Blood Pressure Regulation (1996)

Results of recent genetic studies suggest that the angiotensinogen gene is a possible determinant of hypertension. Using antisense technology, we demonstrated that generation of circulating angiotensinogen is a rate-limiting step in blood pressure regulation. In the present study, we examined how the angiotensinogen gene is regulated in vivo. The transcriptional cis-elements, angiotensinogen gene-activating elements (AGE) 2 and 3, have been reported to regulate angiotensinogen production in human hepatocytes in vitro. To determine the critical transcriptional regulator of angiotensinogen production in vivo, we used synthetic double-stranded oligodeoxynucleotides (ODN) as "decoy" cis-elements to block the binding of nuclear factors to promoter regions of the targeted gene, resulting in the inhibition of gene transactivation. Here we examined whether AGE 2 and AGE 3 in the promoter region of the angiotensinogen gene have a pivotal role in hepatic angiotensinogen production in vivo. Hepatic angiotensinogen mRNA was decreased by the transfection of AGE 2 but not mismatched decoy ODN. Transfection of decoy but not mismatched ODN against AGE 2 resulted in a transient decrease in blood pressure of spontaneously hypertensive rats (SHR), accompanied by a reduction in plasma angiotensinogen and angiotensin II levels. In contrast, transfection of AGE 3 decoy ODN had little effect on blood pressure. Overall, our results demonstrate that transfection of decoy ODN against AGE 2, but not against AGE 3, of the angiotensinogen gene resulted in a transient decrease in high blood pressure of SHR, suggesting that the transcriptional cis-element AGE 2, rather than AGE 3, has an important role in blood pressure regulation through the control of circulating angiotensinogen.
Neutrophils do not contribute to local tissue damage, but play a key role in skeletal muscle regeneration, in mice injected with Bothrops asper snake venom (2003)

Abstract Local tissue damage induced by crotaline snake venoms includes edema, myonecrosis, hemorrhage, and an inflammatory response associated with a prominent cellular infiltrate. The role of neutrophils in the local tissue damage induced by Bothrops asper snake venom and by myotoxin I, a phospholipase A 2 isolated from this venom, was investigated. Male Swiss mice were pretreated with either an antimouse granulocyte rat monoclonal immunoglobulin G (IgG) antibody or with isotype‐matched control antibody. No significant differences in these local effects were observed between mice pretreated with antigranulocyte antibodies and those receiving control IgG. Moreover, myotoxicity induced by B. asper myotoxin I was similar in neutrophil‐depleted and control mice. The role of neutrophils in the process of skeletal muscle regeneration was also assessed. Muscle regeneration was assessed by quantifying the muscle levels of creatine kinase and by morphometric histological analysis of the area comprised by regenerating cells in damaged regions of skeletal muscle. Mice depleted of neutrophils and then injected with B. asper venom showed a more deficient regenerative response than mice pretreated with control IgG. Moreover, a drastic difference in the regenerative response was observed in mice injected with myotoxin I, because animals pretreated with control IgG showed a successful regeneration, whereas those depleted of neutrophils had abundant areas of necrotic tissue that had not been removed 7 days after injection, associated with reduced contents of creatine kinase. It is concluded that (1) neutrophils do not play a significant role in the acute local pathological alterations induced by the venom of B. asper , and (2) neutrophils play a prominent role in the process of skeletal muscle regeneration after injection of B. asper venom and myotoxin I, probably related to the phagocytosis of necrotic material and the recruitment of other inflammatory cells, two events directly associated with a successful muscle regenerative response. Muscle Nerve 28: 449–459, 2003
Inhibition of xanthine oxidase by allopurinol: a therapeutic option for ischaemia induced pathological processes? (1989)

Description des proprietes de l'allopurinol. Ce medicament etait autrefois utilise pour limiter la degradation des mercaptopurines. L'utilisation actuelle, dans la goutte, repose sur l'inhibition de la xanthine oxydase. Interet de ses proprietes anti-ischemiques, decouvertes recemment. Role du raptage des radicaux libres par le medicament
Formation and Behavior of Fluorescent Lewis Acid−Base Exciplexes and Triplexes between 3-Aminostilbenes and Aliphatic Amines (2004)

The excited singlet states of trans-3-aminostilbene and its N-methyl derivatives are strongly fluorescent in cyclohexane solution and have large singlet state dipole moments. Addition of low concentrations of alkylamines results in a continuous red shift of the emission maximum and decreasing fluorescence intensity. Analysis of the fluorescence behavior using a combination of singular value decomposition with self-modeling and kinetic analysis provides evidence for the sequential formation of a 1:1 complex (exciplex) and 1:2 complex (triplex) between the excited stilbene and ground state alkylamine, both of which are strongly fluorescent. Both the formation and decay of the exciplex and triplex are dependent upon the extent of amine N-alkylation, primary amines forming the most stable exciplex and triplex. Similarly, N-aminoalkyl derivatives of the aminostilbenes form intramolecular exciplexes that in turn form 1:1 complexes with added amines. Addition of diaminoalkanes to the aminostilbenes results in sequential formation of 1:1 and 1:2 complexes rather than the formation of a triplex with a single molecule of the diaminoalkanes. Excited state complex formation is attributed to a Lewis acid−base interaction between the excited stilbene (lone pair acceptor) and ground state amine (lone pair donor). An alternative explanation for the red-shifted emission based on Suppan's theory of solvent dielectric enrichment is found to be incompatible with the experimental results.
Intelligent Completion Systems -- The Reservoir Rationale (1998)

Intelligent completion systems (ICS's) integrate reservoir sensors and remotely controllable inflow/outflow devices deployed permanently in the wellbore.
A review of early anterior cruciate ligament surgical repair or reconstruction. Results and caveats. (1993)

Earlier diagnosis and knowledge of the natural history of anterior cruciate ligament (ACL) injuries has made consideration of early operative treatment more important in the active patient at risk for further instability episodes. In a review of early operative treatment options, ACL repair alone has been disappointing for many patients, with long-term follow-up suggesting that the reinjury rate is high. Early repair with augmentation or reconstruction with hamstring or central third bone-tendon-bone graft yielded better results, but long-term follow-up is still needed, especially in the early reconstruction groups. Early ACL reconstruction, especially in patients with medial collateral ligament injury and/or extra-articular surgery, is associated with an increased incidence of arthrofibrosis. The methods of reporting data in these studies have also presented problems in interpreting and comparing data from one study with those of another. Further standardization will be needed if literature regarding ACL surgery can be easily compared from series to series.
Factor Va Is Inactivated by Activated Protein C in the Absence of Cleavage Sites at Arg-306, Arg-506, and Arg-679 (2004)

Activated protein C (APC) exerts its anticoagulant activity via proteolytic degradation of the heavy chains of activated factor VIII (FVIIIa) and activated factor V (FVa). So far, three APC cleavage sites have been identified in the heavy chain of FVa: Arg-306, Arg-506, and Arg-679. To obtain more insight in the structural and functional implications of each individual cleavage, recombinant factor V (rFV) mutants were constructed in which two or three of the APC cleavage sites were mutated. After expression in COS-1 cells, rFV mutants were purified, activated with thrombin, and inactivated by APC. During this study we observed that activated rFV-GQA (rFVa-GQA), in which the arginines at positions 306, 506, and 679 were replaced by glycine, glutamine, and alanine, respectively, was still inactivated by APC. Further analysis showed that the inactivation of rFVa-GQA by APC was phospholipid-dependent and sensitive to an inhibitory monoclonal antibody against protein C. Inactivation proceeded via a rapid phase (kx1=5.4 x 10(4) M(-1) s(-1)) and a slow phase (kx2=3.2 x 10(3) M(-1) s(-1)). Analysis of the inactivation curves showed that the rapid phase yielded a reaction intermediate that retained approximately 80% of the original FVa activity, whereas the slow cleavage resulted in formation of a completely inactive reaction product. Inactivation of rFVa-GQA was accelerated by protein S, most likely via stimulation of the slow phase. Immunoblot analysis using a monoclonal antibody recognizing an epitope between Arg-306 and Arg-506 indicated that during the rapid phase of inactivation a fragment of 80 kDa was generated that resulted from cleavage at a residue very close to Arg-506. The slow phase was associated with the formation of fragments resulting from cleavage at a residue 1.5-2 kDa carboxyl-terminal to Arg-306. Our observations may explain the unexpectedly mild APC resistance associated with mutations at Arg-306 (FV HongKong and FV Cambridge) in the heavy chain of FV.
Numerical investigation of the effects of shear waves in transcranial photoacoustic tomography with a planar geometry (2012)

Using a recently developed reconstruction method for photoacoustic tomography (PAT) valid for a planar measurement geometry parallel to a layered medium, we investigate the effects of shear wave propagation in the solid layer upon the ability to estimate Fourier components of the object. We examine this ability as a function of the thickness of the layer supporting shear waves as well as of the incidence angle of the field in the planewave representation. Examples are used to demonstrate the importance of accounting for shear waves in transcranial PAT. Error measures are introduced to quantify the error found when omitting shear waves from the forward model in PAT.
Single shot electroporation of premature ventricular contractions from the right ventricular outflow tract (2021)

The first approved ablation device for pulsed field ablation (PFA, FARAWAVE) consists of a 12-Fr catheter with five splines carrying four electrodes each that is navigated over-the-wire via a steerable sheath. Its shape can be changed from a basket-like pose to a flower-like pose depending on the underlying anatomy. In this case, a 48-year-old female with symptomatic premature ventricular contractions (PVCs) was referred for ablation. PVC morphology was compatible with an origin in the right ventricular outflow tract (RVOT). Conventional mapping with a diagnostic catheter confirmed RVOT site of origin. A steerable sheath (FARADRIVE) was advanced to the right atrium. Using a 6F pigtail catheter a guidewire was deployed in the left pulmonary artery. The 31-mm FARAWAVE ablation catheter was deployed in the RVOT in a basket like pose. Pulsed field ablation was carried out using pulses of 2.5 s duration with a voltage of 1.8 kV. After the first...
Acoustic force distribution in resonators for ultrasonic particle separation (1998)

Abstract The effectiveness of particle–liquid separation by ultrasonic radiation forces depends on the acoustic energy density distribution in the standing‐wavefield. The energy distribution in an ultrasonic particle‐separation device was analyzed to assist continued optimization and design efforts. Measurements of the energy‐density distribution in the liquid using a microscope‐based imaging system were compared to laser interferometer measurements of the velocity‐amplitude distribution on the transducer and reflector surfaces of the ultrasonic separator. The energy density followed the same trend as the surface velocity, being highest near the resonator center and approaching zero near the walls. The energy density gradients and local gridlike reflector‐amplitude variation had characteristic lengths of 1.4 mm. These results suggest that the energy‐density distribution in the liquid is a defined function of the dimensions, imposed boundary conditions and physical properties of the reflector and transducer. This understanding provides a practical basis for developing a mathematical model of cell aggregation and retention, potentially enabling the design of resonators with predetermined energy density distributions for specific particle aggregation, separation, and fractionation applications.
A conserved tripeptide sorts proteins to peroxisomes. (1989)

The firefly luciferase protein contains a peroxisomal targeting signal at its extreme COOH terminus (Gould et al., 1987). Site-directed mutagenesis of the luciferase gene reveals that this peroxisomal targeting signal consists of the COOH-terminal three amino acids of the protein, serine-lysine-leucine. When this tripeptide is appended to the COOH terminus of a cytosolic protein (chloramphenicol acetyltransferase), it is sufficient to direct the fusion protein into peroxisomes. Additional mutagenesis experiments reveal that only a limited number of conservative changes can be made in this tripeptide targeting signal without abolishing its activity. These results indicate that peroxisomal protein import, unlike other types of transmembrane translocation, is dependent upon a conserved amino acid sequence.
Potential novel targets for Alzheimer pharmacotherapy: I. Secretases (2002)

The prevailing major theory of Alzheimer's disease (AD) is that insoluble amyloid beta-peptide (Abeta) found in the cerebral plaques characteristic of the disease is causative or is at least a contributing factor. According to this theory, inhibition of aberrant Abeta production should prevent or at least limit the extent of AD pathophysiology. As three 'secretase' enzymes (alpha, beta and gamma) catalyse the proteolytic cleavage of amyloid precursor protein (APP) (the precursor protein of Abeta), one or more secretases have become targets for potential novel AD pharmacotherapy. Secretase inhibitors have been designed and are in various stages of development. The clinical trials of these compounds will, if positive, result in drugs with dramatically better clinical efficacy or, if negative, will force a reassessment of the theory about the role of Abeta in AD.
Acute In Vitro Effects of Dronedarone, an Iodine-Free Derivative, and Amiodarone, on the Rabbit Sinoatrial Node Automaticity: A Comparative Study (2007)

Amiodarone is a potent antiarrhythmic drug commonly used in the treatment of supraventricular and ventricular arrhythmias. Dronedarone is a recently developed iodine-free compound (Sanofi Recherche), structurally related to amiodarone. Amiodarone and dronedarone have shown similar long-term effects on sinoatrial node automaticity in vivo and in vitro in the rabbit heart. In the present study, we used a microelectrode technique to compare the acute in vitro electrophysiologic effects of amiodarone (100 microM) and dronedarone (100 microM) on the rabbit sinus node. Like amiodarone, dronedarone induces a marked reduction in sinus node automaticity, evidenced by decreases in spontaneous beating rate, action potential amplitude, and slope of phase 4 depolarization. Isoproterenol dose-dependently increases sinus node automaticity in the presence of either amiodarone or dronedarone. The data suggest that dronedarone may be a useful antiarrhythmic alternative to amiodarone in the treatment of supraventricular arrhythmias.
Isolation and Characterization of a cDNA Encoding the SecA Protein from Spinach Chloroplasts (1995)

Thylakoid membranes of chloroplasts in higher plants harbor different pathways for the translocation of proteins. One of these routes is related to the prokaryotic Sec pathway, which mediates the secretion of particular proteins into the periplasmic space and involves the SecA protein as an essential component. We have isolated a full size cDNA of 3739 nucleotides encoding the SecA homologue from spinach. It contains an open reading frame of 1036 codons corresponding to a polypeptide with a calculated mass of 117 kDa. The deduced amino acid sequence shows between 43 and 49% identity to SecA proteins from bacteria and lower algae and 62% identity to SecA of the cyanobacterium Synechococcus sp. PCC7942. Compared with the Escherichia coli protein, spinach SecA carries an amino-terminal extension of approximately 80 residues. In organello experiments performed with the protein made in vitro by transcription of the cDNA and cell-free translation of the resulting RNA showed that this extension comprises a transit peptide that mediates the import of the protein into the chloroplast. The processed product of approximately 107 kDa accumulates predominantly in the stroma and to a lower extent associates with the thylakoid membrane. Comparably to E. coli, in which SecA activity can be inhibited by sodium azide, thylakoid translocation of a subset of lumenal proteins is sensitive to sodium azide in pea but not in spinach chloroplasts, suggesting that the latter contain an azide-resistant SecA variant.
Gut-associated microbes of Drosophila melanogaster (2012)

There is growing interest in using Drosophila melanogaster to elucidate mechanisms that underlie the complex relationships between a host and its microbiota. In addition to the many genetic resources and tools Drosophila provides, its associated microbiota is relatively simple (1-30 taxa), in contrast to the complex diversity associated with vertebrates (> 500 taxa). These attributes highlight the potential of this system to dissect the complex cellular and molecular interactions that occur between a host and its microbiota. In this review, we summarize what is known regarding the composition of gut-associated microbes of Drosophila and their impact on host physiology. We also discuss these interactions in the context of their natural history and ecology and describe some recent insights into mechanisms by which Drosophila and its gut microbiota interact.
Advanced Catalytic Enzyme System (ACES) - Dual Use Capabilities (2003)

An enzyme-based decontaminant (Advanced Catalytic Enzyme System - ACES) has been developed at the Edgewood Chemical Biological Center (ECBC) for use by military services and civilian first responders. The ACES will contain enzymes for the detoxification of nerve agents (G and V) and related pesticides, sulfur mustard, bacterial cells, and anthrax spores. Catalytic enzymes are highly efficient, detoxifying many times their own weight of agent in seconds or minutes. The ACES is also noncorrosive, non-flammable, and environmentally safe. The ACES can fulfill a dual-use role as both decontaminant and fire extinguisher through the addition of environmentally safe fire-fighting materials.
The transcription factor DNR from Pseudomonas aeruginosa specifically requires nitric oxide and haem for the activation of a target promoter in Escherichia coli (2009)

Pseudomonas aeruginosa is a well-known pathogen in chronic respiratory diseases such as cystic fibrosis. Infectivity of P. aeruginosa is related to the ability to grow under oxygen-limited conditions using the anaerobic metabolism of denitrification, in which nitrate is reduced to dinitrogen via nitric oxide (NO). Denitrification is activated by a cascade of redox-sensitive transcription factors, among which is the DNR regulator, sensitive to nitrogen oxides. To gain further insight into the mechanism of NO-sensing by DNR, we have developed an Escherichia coli-based reporter system to investigate different aspects of DNR activity. In E. coli DNR responds to NO, as shown by its ability to transactivate the P. aeruginosa norCB promoter. The direct binding of DNR to the target DNA is required, since mutations in the helix-turn-helix domain of DNR and specific nucleotide substitutions in the consensus sequence of the norCB promoter abolish the transcriptional activity. Using an E. coli strain deficient in haem biosynthesis, we have also confirmed that haem is required in vivo for the NO-dependent DNR activity, in agreement with the property of DNR to bind haem in vitro. Finally, we have shown, we believe for the first time, that DNR is able to discriminate in vivo between different diatomic signal molecules, NO and CO, both ligands of the reduced haem iron in vitro, suggesting that DNR responds specifically to NO.
Novel NMDA receptor modulators: an update (2012)

The complex nature of the NMDA receptor structure and function is becoming better understood. As knowledge about this receptor increases, it opens up new opportunities for targeting the receptor for many therapeutic indications. New strategies and advances in older technologies will need to be further developed before clinical success can be achieved. First-in-class potentiators and subunit-selective agents form the basis for most new strategies, complemented by efforts to limit off-target liability and fine-tune on-target properties.