gebhart/patrepeval huggingface dataset:
Dielectric studies of proton transport in proteins (1988)

Abstract Various studies of the electrical and dielectric properties of proteins of low hydration content are reviewed to indicate that proton transport processes provide a major contribution to the effects that have been observed. New experimental data is described to show that the pH dependence of the low frequency dispersion in lysozyme is mainly associated with the transfer of protons between ionisable basic side groups in the protein structure. Such dielectric studies may usefully be extended to investigations of proton transfer processes in energy-transducing membranes, as well as forming the basis for the development of new biosensors.
Shape recovery algorithms using level sets in 2-D/3-D medical imagery: a state-of-the-art review (2002)

The class of geometric deformable models, also known as level sets, has brought tremendous impact to medical imagery due to its capability of topology preservation and fast shape recovery. In an effort to facilitate a clear and full understanding of these powerful state-of-the-art applied mathematical tools, this paper is an attempt to explore these geometric methods, their implementations and integration of regularizers to improve the robustness of these topologically independent propagating curves/surfaces. This paper first presents the origination of level sets, followed by the taxonomy of level sets. We then derive the fundamental equation of curve/surface evolution and zero-level curves/surfaces. The paper then focuses on the first core class of level sets, known as "level sets without regularizers." This class presents five prototypes: gradient, edge, area-minimization, curvature-dependent and application driven. The next section is devoted to second core class of level sets, known as "level sets with regularizers." In this class, we present four kinds: clustering-based, Bayesian bidirectional classifier-based, shape-based and coupled constrained-based. An entire section is dedicated to optimization and quantification techniques for shape recovery when used in the level set framework. Finally, the paper concludes with 22 general merits and four demerits on level sets and the future of level sets in medical image segmentation. We present applications of level sets to complex shapes like the human cortex acquired via MRI for neurological image analysis.
Prolonged Activation of the Baroreflex Produces Sustained Hypotension (2004)

The role of baroreflexes in long-term control of arterial pressure is unresolved. To determine whether chronic activation of the baroreflex produces sustained hypotension, we developed a method for prolonged activation of the carotid baroreflex in conscious dogs. This was achieved by chronically implanting electrodes around both carotid sinuses and using an externally adjustable pulse generator to electrically activate the carotid baroreflex. Control values for mean arterial pressure (MAP) and heart rate were 93+/-3 mm Hg and 64+/-4 bpm, respectively. After control measurements, the carotid baroreflex was activated bilaterally for 7 days at a level that produced a prompt and substantial reduction in MAP, and for day 1 MAP was reduced to 75+/-4 mm Hg. Moreover, this hypotensive response was sustained throughout the entire 7 days of baroreflex activation (day 7, MAP=72+/-5 mm Hg). During prolonged baroreflex activation, heart rate decreased in parallel with MAP, although the changes were not as pronounced (day 7, heart rate=51+/-3 bpm). Prolonged baroreflex activation was also associated with approximately 35% reduction in plasma norepinephrine concentration (control=87+/-15 pg/mL). After baroreflex activation, hemodynamic measures and plasma levels of norepinephrine returned to control levels. Interestingly, despite the pronounced fall in MAP, plasma renin activity did not increase during prolonged baroreflex activation. These data indicate that prolonged baroreflex activation can lead to substantial reductions in MAP by suppressing the sympathetic nervous system. Furthermore, sustained sympathoinhibitory effects on renin secretion may play an important role in mediating the long-term hypotensive response.
Membrane Surface Dynamics of DNA-Threaded Nanopores Revealed by Simultaneous Single-Molecule Optical and Ensemble Electrical Recording (2003)

We describe a method for simultaneous single-molecule optical and electrical characterization of membrane-based sensors that contain ion-channel nanopores. The technique is used to study the specific and nonspecific interactions of streptavidin-capped DNA polymers with lipid bilayers composed of diphytanoyl phosphatidylcholine and diphytanoyl phosphatidylglycerol. Biotinylated DNA that is bound to fluorescently labeled streptavidin is electrophoretically driven into, or away from, the lumen of alpha hemolysin (αHL) ion channels by an external electric field. Confocal microscopy simultaneously captures single-molecule fluorescence dynamics from the membrane interface at different applied potentials. Fluorescence correlation analysis is used to determine the surface number density and diffusion constant of membrane-associated complexes. The dual optical and electrical approach can detect membrane-associated species at a surface coverage below 10-5 monolayers of streptavidin, a sensitivity that surpasses most other in vitro surface analysis techniques. By comparing the change in transmembrane current to the number of fluorescent molecules leaving the bilayer when the electrical potential is reversed, we demonstrate the general utility of the approach within the context of nanopore-based sensing and discuss a mechanism by which DNA−streptavidin complexes can be nonspecifically retained at the membrane interface.
Optical characterization of lateral epitaxial overgrown GaN layers (1998)

The optical properties of homoepitaxial GaN layers deposited by organometallic vapor phase epitaxy on stripe-patterned GaN films on 6H-SiC substrates have been investigated. Analysis of the spatially-resolved Raman scattering spectra indicate an improvement in material quality of the overgrown region. Room-temperature color cathodoluminescence imaging and low-temperature photoluminescence measurements indicate that a donor and an acceptor, different from those detected in the underlying GaN/AlN/SiC substrate, have been incorporated in the epitaxial layer. Detailed photoluminescence studies of the near-band-edge emission strongly suggest that Si is the additional donor detected in the homoepitaxial GaN layer. Its occurrence, along with that of an acceptor-related defect which is primarily found in the laterally overgrown region, is discussed.
Evolution of the Isoprene Biosynthetic Pathway in Kudzu (2005)

Isoprene synthase converts dimethylallyl diphosphate, derived from the methylerythritol 4-phosphate (MEP) pathway, to isoprene. Isoprene is made by some plants in substantial amounts, which affects atmospheric chemistry, while other plants make no isoprene. As part of our long-term study of isoprene synthesis, the genetics of the isoprene biosynthetic pathway of the isoprene emitter, kudzu (Pueraria montana), was compared with similar genes in Arabidopsis (Arabidopsis thaliana), which does not make isoprene. The MEP pathway genes in kudzu were similar to the corresponding Arabidopsis genes. Isoprene synthase genes of kudzu and aspen (Populus tremuloides) were cloned to compare their divergence with the divergence seen in MEP pathway genes. Phylogenetic analysis of the terpene synthase gene family indicated that isoprene synthases are either within the monoterpene synthase clade or sister to it. In Arabidopsis, the gene most similar to isoprene synthase is a myrcene/ocimene (acyclic monoterpenes) synthase. Two phenylalanine residues found exclusively in isoprene synthases make the active site smaller than other terpene synthase enzymes, possibly conferring specificity for the five-carbon substrate rather than precursors of the larger isoprenoids. Expression of the kudzu isoprene synthase gene in Arabidopsis caused Arabidopsis to emit isoprene, indicating that whether or not a plant emits isoprene depends on whether or not it has a terpene synthase capable of using dimethylallyl diphosphate.
71. A new method for the preparation of p-dialkylaminobenzaldehydes (1945)

J. C. Duff, J. Chem. Soc., 1945, 276 DOI: 10.1039/JR9450000276
Mechanism of inhibition of duck hepatitis B virus polymerase by (-)-beta-L-2',3'-dideoxy-3'-thiacytidine (1995)

We have used the endogenous reverse transcriptase reaction of viral core particles from duck liver to elucidate the mechanism of inhibition of duck hepatitis B virus (DHBV) replication by the nucleoside analog (-)-beta-L-2',3'-dideoxy-3'-thiacytidine (3TC). As is the case in human immunodeficiency virus replication, 3TC-5'-triphosphate (3TC-TP) acts as a chain terminator for the DNA polymerase activities. The results of several different experiments support this conclusion, which explains the potent activity of 3TC against the hepadnaviruses. In isolated DHBV core particles, 3TC-TP inhibited the reverse transcriptase in a manner that resembled competitive inhibition with respect to dCTP. However, the kinetics of inhibition was not linear on a double-reciprocal plot for the highest concentrations of 3TC-TP and the lowest concentration of dCTP. This anomaly would be expected if binding to the nucleotide site was followed by DNA chain termination. Calculations that used only the linear part of the curve yielded a Ki of 0.78 +/- 0.10 microM 3TC-TP. The inhibition of core particles incubated in vitro with 3TC-TP was not reversed by removal of the free inhibitor. 3TC-TP inactivated the reverse transcriptase activity in a concentration-dependent manner. The Km of the chain termination reaction was calculated at 0.71 +/- 0.05 microM. Similar competitive kinetics and irreversible inhibition were also obtained on the endogenous DNA polymerase from viral particles from serum, suggesting that 3TC-TP also acts as a chain terminator of the DNA-directed DNA polymerase of DHBV replication.(ABSTRACT TRUNCATED AT 250 WORDS)
A lightweight security protocol for ultra-low power ASIC implementation for wireless Implantable Medical Devices (2011)

The newest generation of Implantable Medical Devices (IMDs) employs wireless communication with a nearby base station in order to provide better treatment and monitoring of the patients. However, a wireless connection opens a host of potential security threats to the privacy and safety of patients. This paper proposes a lightweight security protocol providing authentication and confidentiality to wireless energy-limited IMDs that operate on small energy sources such as a battery for many years. Adding security features to these devices can impose an unacceptable overhead. The protocol presented here employs lightweight encryption and is suitable for implementation on ultra-low power ASIC chips.
Non-Radioactive Labelling: A Practical Introduction (1997)

Introduction to Non-Radioactive Signals and Labels. Proteins and Peptides: Chemistry Background. Conjugation of Proteins with Enzymes and Other Proteins. Fluorescent Labelling of Proteins and Peptides. Use of Tags in the Labelling and Detection of Biomolecules. Labelling of Oligonucleotides. Labelling of Long Nucleic Acid Probes. Labelling of Small Biomolecules. Appendices.
Constrained-storage vector quantization with a universal codebook (1998)

Many image compression techniques require the quantization of multiple vector sources with significantly different distributions. With vector quantization (VQ), these sources are optimally quantized using separate codebooks, which may collectively require an enormous memory space. Since storage is limited in most applications, a convenient way to gracefully trade between performance and storage is needed. Earlier work addressed this problem by clustering the multiple sources into a small number of source groups, where each group shares a codebook. We propose a new solution based on a size-limited universal codebook that can be viewed as the union of overlapping source codebooks. This framework allows each source codebook to consist of any desired subset of the universal code vectors and provides greater design flexibility which improves the storage-constrained performance. A key feature of this approach is that no two sources need be encoded at the same rate. An additional advantage of the proposed method is its close relation to universal, adaptive, finite-state and classified quantization. Necessary conditions for optimality of the universal codebook and the extracted source codebooks are derived. An iterative design algorithm is introduced to obtain a solution satisfying these conditions. Possible applications of the proposed technique are enumerated, and its effectiveness is illustrated for coding of images using finite-state vector quantization, multistage vector quantization, and tree-structured vector quantization.
Effect of a music intervention on noise annoyance, heart rate, and blood pressure in cardiac surgery patients (1997)

Results of this study support the idea that noise annoyance is a highly individual phenomenon, influenced by a transaction of personal and environmental factors. Use of a music intervention with cardiac surgery patients during the first postoperative day decreased noise annoyance, heart rate, and systolic blood pressure, regardless of the subject's noise sensitivity.
Performance characteristics of scintigraphic transit measurements for studies of experimental therapies (2002)

These data demonstrate the reproducibility and performance to be expected of transit measurements and are essential for designing studies in experimental therapeutics.
Use of Irradiated Blood Components:Practice Parameter (1996)

Transfusion-associated graft-versus-host disease (TA-GVHD) is a rare but fatal potential complication of transfusions. It is mediated by immunocompetent donor lymphocytes that cannot be eliminated by the recipient. Patients at risk for developing TA-GVHD are those who have a profound deficiency in cell-mediated immunity or those who share histocompatibility antigens with the donor and do not recognize the donor cells as foreign. Irradiation of cellular blood components is currently the only acceptable method for prevention of TA-GVHD. This practice guideline identifies the patient population who should receive irradiated blood components and describes the technical aspects of blood component irradiation that may affect the safety of the final product.
Characterization of terminally differentiated cell state by categorizing cDNA clones derived from chicken lens fibers (1996)

To characterize a terminally differentiated state of cells at the gene expression level, a cDNA library of chicken lens fibers was analyzed. The major population of the library consisted of cDNAs encoding delta-crystallin (about 35% of the recombinants) and other crystallins (alpha A-, alpha B-, beta A3/A1-, beta B1-, beta B2-), as well as cytoskeletal proteins (CP49, CP95), and membrane protein (MP28). These cDNA clones representing lens structural proteins known, accounted for about 60% of the library. When 96 clones were randomly selected from this library, 55 clones corresponded to the above-mentioned major class proteins. Analyses of the remaining clones indicated that many of them were expressed in a lens-specific manner at very low levels. The partial nucleotide sequence analysis of these clones revealed that two cDNAs corresponded to the genes encoding lens-type connexin, three cDNAs to the genes encoding housekeeping proteins, and some cDNAs to the genes encoding regulatory proteins. The mRNA composition in the chicken lens fiber cells indicated rather simple organization of mRNA species of this cell type, and gave scope to the possibility of full description of differentiated lens fiber cells at gene activity level.
Repression of BCL-6 is required for the formation of human memory B cells in vitro (2007)

Memory B cells provide rapid protection to previously encountered antigens; however, how these cells develop from germinal center B cells is not well understood. A previously described in vitro culture system using human tonsillar germinal center B cells was used to study the transcriptional changes that occur during differentiation of human memory B cells. Kinetic studies monitoring the expression levels of several known late B cell transcription factors revealed that BCL-6 is not expressed in memory B cells generated in vitro, and gene expression profiling studies confirmed that BCL-6 is not expressed in these memory B cells. Furthermore, ectopic expression of BCL-6 in human B cell cultures resulted in formation of fewer memory B cells. In addition, the expression profile of in vitro memory B cells showed a unique pattern that includes expression of genes encoding multiple costimulatory molecules and cytokine receptors, antiapoptotic proteins, T cell chemokines, and transcription factors. These studies establish new molecular criteria for defining the memory B cell stage in human B cells.
Recent insights into antioxidant defenses of legume root nodules (2010)

Legume root nodules are sites of intense biochemical activity and consequently are at high risk of damage as a result of the generation of reactive oxygen species (ROS) and reactive nitrogen species (RNS). These molecules can potentially give rise to oxidative and nitrosative damage but, when their concentrations are tightly controlled by antioxidant enzymes and metabolites, they also play positive roles as critical components of signal transduction cascades during nodule development and stress. Thus, recent advances in our understanding of ascorbate and (homo)glutathione biosynthesis in plants have opened up the possibility of enhancing N(2) fixation through an increase of their concentrations in nodules. It is now evident that antioxidant proteins other than the ascorbate-glutathione enzymes, such as some isoforms of glutathione peroxidases, thioredoxins, peroxiredoxins, and glutathione S-transferases, are also critical for nodule activity. To avoid cellular damage, nodules are endowed with several mechanisms for sequestration of Fenton-active metals (nicotianamine, phytochelatins, and metallothioneins) and for controlling ROS/RNS bioactivity (hemoglobins). The use of 'omic' technologies has expanded the list of known antioxidants in plants and nodules that participate in ROS/RNS/antioxidant signaling networks, although aspects of developmental variation and subcellular localization of these networks remain to be elucidated. To this end, a critical point will be to define the transcriptional and post-transcriptional regulation of antioxidant proteins.
Beta-cell lines derived from transgenic mice expressing a hybrid insulin gene-oncogene. (1988)

Three pancreatic beta-cell lines have been established from insulinomas derived from transgenic mice carrying a hybrid insulin-promoted simian virus 40 tumor antigen gene. The beta tumor cell (beta TC) lines maintain the features of differentiated beta cells for about 50 passages in culture. The cells produce both proinsulin I and II and efficiently process each into mature insulin, in a manner comparable to normal beta cells in isolated islets. Electron microscopy reveals typical beta-cell type secretory granules, in which insulin is stored. Insulin secretion is inducible up to 30-fold by glucose, although with a lower threshold for maximal stimulation than that for normal beta cells. beta TC lines can be repeatedly derived from primary beta-cell tumors that heritably arise in the transgenic mice. Thus, targeted expression of an oncogene with a cell-specific regulatory element can be used both to immortalize a rare cell type and to provide a selection for the maintenance of its differentiated phenotype.
[Functional outcomes and quality of life in patients with anterior resection for rectal cancer. Does preoperative manometry predict the feasibility of a J-pouch?]. (2004)

Performing LAR with colon pouch after neoadjuvant chemotherapy in patients with hypotonic sphincter improves quality of life. Preoperative anorectal manometry could select patient who would benefit from pouch construction.
Brimonidine (Alphagan®): A Clinical Profile Four Years after Launch (2001)

The early information on the clinical efficacy, safety, and tolerability of brimonidine 0.2% were obtained from studies that compared brimonidine monotherapy with timolol and betaxolol. These studies showed its intra-ocular pressure lowering efficacy to be comparable with timolol and superior to betaxolol. The data from the timolol studies showed consistent results after four years. These findings have been confirmed by additional studies in the clinical setting. More recently, several clinical trials have been completed investigating the role of brimonidine as adjunctive medication to beta-blockers and as replacement therapy to other intraocular pressure lowering compounds. When added to beta-blockers, brimonidine is superior to dorzolamide, similar in efficacy but better tolerated than pilocarpine, and more predictable than latanoprost. Data from replacement studies have indicated that there may be advantages in replacing rather than adding medications in the treatment of glaucoma.
Characterization of the Enzymatic Activity of the Actin Cross-linking Domain from the Vibrio cholerae MARTX Toxin (2007)

Vibrio cholerae is a Gram-negative bacterial pathogen that exports enterotoxins, which alter host cells through a number of mechanisms resulting in diarrheal disease. Among the secreted toxins is the multifunctional, autoprocessing RTX toxin (MARTX(Vc)), which disrupts actin cytoskeleton by covalently cross-linking actin monomers into oligomers. The region of the toxin responsible for cross-linking activity is the actin cross-linking domain (ACD). In this study, we demonstrate unambiguously that ACD utilizes G- and not F-actin as a substrate for the cross-linking reaction and hydrolyzes one molecule of ATP per cross-linking event. Furthermore, major actin-binding proteins that regulate actin cytoskeleton in vivo do not block the cross-linking reaction in vitro. Cofilin inhibits the cross-linking of G- and F-actin, at a high mole ratio to actin but accelerates F-actin cross-linking at low mole ratios. DNase I completely blocks the cross-linking of actin, likely due to steric hindrance with one of the cross-linking sites on actin. In the context of the holotoxin, the inhibition of Rho by the Rho-inactivating domain of MARTX(Vc) (Sheahan, K. L., and Satchell, K. J. F. (2007) Cell. Microbiol. 9, 1324-1335) would accelerate F-actin depolymerization and provide G-actin, alone or in complex with actin-binding proteins, for cross-linking by ACD, ultimately leading to the observed rapid cell rounding.