gebhart/patrepeval huggingface dataset:
Auxin production and detection of the gene coding for the Auxin Efflux Carrier (AEC) protein in Paenibacillus polymyxa (2008)

Different species of Paenibacillus are considered to be plant growth-promoting rhizobacteria (PGPR) due to their ability to repress soil borne pathogens, fix atmospheric nitrogen, induce plant resistance to diseases and/or produce plant growth-regulating substances such as auxins. Although it is known that indole-3-acetic acid (IAA) is the primary naturally occurring auxin excreted by Paenibacillus species, its transport mechanisms (auxin efflux carriers) have not yet been characterized. In this study, the auxin production of P. polymyxa and P. graminis, which are prevalent in the rhizospheres of maize and sorghum sown in Brazil, was evaluated. In addition, the gene encoding the Auxin Efflux Carrier (AEC) protein from P. polymyxa DSM36(T) was sequenced and used to determine if various strains of P. polymyxa and P. graminis possessed this gene. Each of the 68 P. polymyxa strains evaluated in this study was able to produce IAA, which was produced at concentrations varying from 1 to 17 microg/ml. However, auxin production was not detected in any of the 13 P. graminis strains tested in this study. Different primers were designed for the PCR amplification of the gene coding for the AEC in P. polymyxa, and the predicted protein of 319 aa was homologous to AEC from Bacillus amyloliquefaciens, B. licheniformis, and B. subtilis. However, no product was observed when these primers were used to amplify the genomic DNA of seven strains of P. graminis, which suggests that this gene is not present in this species. Moreover, none of the P. graminis genomes tested were homologous to the gene coding for AEC, whereas all of the P. polymyxa genomes evaluated were. This is the first study to demonstrate that the AEC protein is present in P. polymyxa genome.
Protecting groups (2000)

Covering: the literature published in 1999. Previous review: J. Chem. Soc., Perkin Trans. 1, 1999, 1589.
Synthetic peptides as probes for G protein function. Carboxyl-terminal G alpha s peptides mimic Gs and evoke high affinity agonist binding to beta-adrenergic receptors. (1994)

The molecular interfaces between Gs and the beta-adrenergic receptor were investigated using synthetic peptides corresponding to various regions of its alpha subunit, alpha s. These experiments were carried out on saponin-permeable C6 glioma cells in which the beta-adrenergic receptor appears tightly coupled to Gs. Synthetic site-specific peptides from alpha s (corresponding to amino acids 15-29, 354-372, and 384-394) and alpha i (8-22, 315-324, and 345-455) were tested for their ability to interfere with coupling between the beta-adrenergic receptor and Gs. The two carboxyl-terminal peptides from alpha s blocked beta-adrenergic stimulation of adenylyl cyclase in permeable cells. However, only alpha s-354-372 had this effect in C6 membranes. It is suggested that the partial uncoupling of Gs, which occurs subsequent to cell disruption, may be related to a change in the interaction of the alpha s carboxyl terminus with the beta-adrenoreceptor. Two carboxyl-terminal peptides, 354-372 and 384-394, could also mimic the effect of Gs to increase agonist affinity for the beta-adrenergic receptor. In combination, alpha s-354-372 and alpha s-384-394 increased the ability of isoproterenol to compete with 125I-pindolol binding in a partially additive manner. Synthetic peptides from alpha i and amino-terminal peptides from alpha s had no effect on beta-agonist binding, suggesting a high specificity of peptide effects. Two findings suggest that these peptides bind directly to the beta-adrenergic receptor and stabilize its high agonist affinity conformation. First, GTP and hydrolysis-resistant GTP analogs did not alter the high affinity binding in the presence of high concentrations of the peptides. Second, in S49 lymphoma cyc- cells, which lack Gs, these peptides evoked the high affinity agonist binding state of the beta-receptor. Neither peptide had an effect on antagonist binding affinity, as measured by propranolol displacement of 125I-pindolol. These data suggest that at least two regions on the alpha subunit of Gs participate in high affinity Gs binding to the beta-adrenergic receptor. The fact that these small peptides could mimic the holo-Gs effect on the receptor is rather surprising, and the specificity of the effect suggests that the primary and secondary structure of small regions of alpha s contain much of the information for specific interaction with beta-adrenergic receptors.
Orthogonal Thiol Functionalization at a Single Atomic Center for Profiling Transthiolation Activity of E1 Activating Enzymes (2015)

Transthiolation is a fundamental biological reaction and is utilized by many enzymes involved in the conjugation of ubiquitin and ubiquitin-like proteins. However, tools that enable selective profiling of this activity are lacking. Transthiolation requires cysteine-cysteine juxtaposition; therefore a method that enables irreversible "stapling" of proximal thiols would facilitate the development of novel probes that could be used to profile this activity. Herein, we characterize biocompatible chemistry that enables sequential functionalization of cysteines within proteins at a single atomic center. We use our method to develop a new class of activity-based probe that profiles transthiolation activity of human E1 activating enzymes. We demonstrate use in vitro and in situ and compatibility with competitive activity-based protein profiling. We also use the probe to gain insight into the determinants of transthiolation between E2 and a RING-in-between-RING (RBR) E3 ligase. Furthermore, we anticipate that this method of thiol functionalization will have broad utility by enabling simple redox-stable cross-linking of proximal cysteines in general.
Modular protein switches derived from antibody mimetic proteins (2015)

Protein switches have potential applications as biosensors and selective protein therapeutics. Protein switches built by fusion of proteins with the prerequisite input and output functions are currently developed using an ad hoc process. A modular switch platform in which existing switches could be readily adapted to respond to any ligand would be advantageous. We investigated the feasibility of a modular protein switch platform based on fusions of the enzyme TEM-1 β-lactamase (BLA) with two different antibody mimetic proteins: designed ankyrin repeat proteins (DARPins) and monobodies. We created libraries of random insertions of the gene encoding BLA into genes encoding a DARPin or a monobody designed to bind maltose-binding protein (MBP). From these libraries, we used a genetic selection system for β-lactamase activity to identify genes that conferred MBP-dependent ampicillin resistance to Escherichia coli. Some of these selected genes encoded switch proteins whose enzymatic activity increased up to 14-fold in the presence of MBP. We next introduced mutations into the antibody mimetic domain of these switches that were known to cause binding to different ligands. To different degrees, introduction of the mutations resulted in switches with the desired specificity, illustrating the potential modularity of these platforms.
DEGRADATION STUDIES OF CURCUMIN (2013)

Curcumin, a yellow phytochemical constituent obtained from Curcuma longa shows profound biological activities. Literature reveals that curcumin is insoluble in water and susceptible to higher pH conditions. This work is focused firstly to study the susceptibility of curcumin in water, various pH conditions in presence and absence of light by a simple UV absorption method. A series of buffer solutions of pH conditions such as 1, 1.2, 6.8, 7, and 7.4 were selected and the result showed that decomposition was pH dependent and occurs faster at neutral-basic conditions. The stability was more in acidic pH and decrease as the pH increases. It was more stable at pH of 1.2; less than 1% of curcumin decomposed within 6hrs of the total curcumin in the absence of light while it was more than 40% in the presence of light. Solution at pH of 1, 1.2, 6.8, 7.4 were studied for Thin layer chromatography (TLC) and compared with the standard curcumin. Fourier transform infrared spectroscopy (FTIR) study was also conducted.
Treatment of detrusor-sphincter dyssynergia with botulinum A toxin: a double-blind study. (1990)

The ability of botulinum A toxin to denervate and relax a spastic external urethral sphincter was evaluated in a double-blind study involving five men with high spinal cord injuries and detrusor-sphincter dyssynergia. The sphincter was injected with either a low dose of botulinum A toxin or normal saline once per week for three weeks. Electromyography of the external urethral sphincter indicated denervation in the three patients who received toxin injections. The urethral pressure profile decreased an average of 25cm of water, postvoiding residual volume of urine decreased an average of 125cc, and bladder pressure during voiding decreased to an average of 30cm of water. Bulbosphincteric reflexes were more difficult to obtain, and they showed a decreased amplitude with normal latency. In the two patients who received normal saline injections, parameters were unchanged from baseline values until subsequent injection with botulinum A toxin once per week for three weeks when their responses were similar to those of the other three patients. Mild generalized weakness lasting two to three weeks was noted by three patients after initial toxin injections. The duration of the toxin's effect averaged two months. The results suggest that botulinum A toxin, an inhibitor of acetylcholine release at the neuromuscular junction, may be useful in the treatment of detrusor-sphincter dyssynergia.
Thioredoxin reductase as a pathophysiological factor and drug target (2000)

Human cytosolic thioredoxin reductase (TrxR), a homodimeric protein containing 1 selenocysteine and 1 FAD per subunit of 55 kDa, catalyses the NADPH-dependent reduction of thioredoxin disulfide and of numerous other oxidized cell constituents. As a general reducing enzyme with little substrate specificity, it also contributes to redox homeostasis and is involved in prevention, intervention and repair of damage caused by H2O2-based oxidative stress. Being a selenite-reducing enzyme as well as a selenol-containing enzyme, human TrxR plays a central role in selenium (patho)physiology. Both dietary selenium deficiency and selenium oversupplementation, a lifestyle phenomenon of our time, appear to interfere with the activity of TrxR. Selenocysteine 496 of human TrxR is a major target of the anti-rheumatic gold-containing drug auranofin, the formal Ki for the stoichiometric inhibition being 4 nM. The hypothesis that TrxR and extracellular thioredoxin play a pathophysiologic role in chronic diseases such as rheumatoid arthritis, Sjögren's syndrom, AIDS, and certain malignancies, is substantiated by biochemical, virological, and clinical evidence. Reduced thioredoxin acts as an autocrine growth factor in various tumour diseases, as a chemoattractant, and it synergises with interleukins 1 and 2. The effects of anti-tumour drugs such as carmustine and cisplatin can be explained in part by the inhibition of TrxR. Consistently, high levels of the enzyme can support drug resistance. TrxRs from different organisms such as Escherichia coli, Mycobacterium leprae, Plasmodium falciparum, Drosophila melanogaster, and man show a surprising diversity in their chemical mechanism of thioredoxin reduction. This is the basis for attempts to develop specific TrxR inhibitors as drugs against bacterial infections like leprosy and parasitic diseases like amebiasis and malaria.
A Novel Use of a Novel Drug: Preoperative Nasal Preparation with Dexmedetomidine for Transnasal Transsphenoidal Neurosurgery Approach in Skull Base Neurosurgery (2017)

Introduction Transnasal transsphenoidal (TNTS) approach is preferred for surgical excision of the pituitary gland. Despite its numerous merits, the TNTS approach creates wide fluctuations in hemodynamic parameters that are attributed to the routine application of adrenaline-soaked nasal packing and the intense noxious stimulus during the surgery. Aims To evaluate the effect of dexmedetomidine for preoperative nasal passage preparation on the surgical field visualization and hemodynamic profile of patients during TNTS surgery. Material and Methods Cotton strips soaked in dexmedetomidine were used for nasal preparation. The primary outcomes studied were the quality of surgical field visualization through the endoscope and the amount of bleeding that occurred while raising the nasal mucosal flap. The secondary outcomes assessed were the intraoperative anesthetic and analgesic requirement and the hemodynamic profile. Statistical Analysis Data from the study were summarized as mean and SD. Associations were tested using chi-square test for nonparametric data and for continuous variables ANOVA for repeated measures. A p-value &lt; 0.05 was considered as statistically significant and &lt; 0.01 as highly significant. SPSS 17.0 was used for analysis. Results Seventeen (85%) patients had a Formmer's score of 1, which was an excellent surgical field quality. Two (10%) patients had a Formmer's score of 2, and one (5%) had a Formmer's score of 3. There were no statistically significant variations in heart rate and blood pressure with reduced anesthetic requirement. Conclusion Intranasal dexmedetomidine provides good surgical field conditions with the added advantage of lesser hemodynamic fluctuations.
Noise reduction for low-dose single-slice helical CT sinograms (2006)

Helical computed tomography (HCT) has several advantages over conventional step-and-shoot CT for imaging a relatively large object, especially for dynamic studies. However, HCT may increase X-ray exposure significantly. This work aims to reduce the radiation by lowering X-ray tube current (mA) and filtering low-mA (or dose) sinogram noise of HCT. The noise reduction method is based on three observations on HCT: (1) the axial sampling of HCT projections is nearly continuous as detection system rotates; (2) the noise distribution in sinogram space is nearly a Gaussian after system calibration (including logarithmic transform); and (3) the relationship between the calibrated data mean and variance can be expressed as an exponential functional across the field-of-view. Based on the second and third observations, a penalized weighted least-squares (PWLS) solution is an optimal choice, where the weight is given by the mean-variance relationship. The first observation encourages the use of Karhunen-Loève (KL) transform along the axial direction because of the associated correlation. In the KL domain, the eigenvalue of each principal component and the derived data variance provide the signal-to-noise ratio (SNR) information, resulting in a SNR-adaptive noise reduction. The KL-PWLS noise-reduction method was implemented analytically for efficient restoration of large volume HCT sinograms. Simulation studies showed a noticeable improvement, in terms of image quality and defect detectability, of the proposed noise-reduction method over the Ordered-Subsets Expectation-Maximization reconstruction and the conventional low-pass noise filtering with optimal cutoff frequency and/or other filter parameters.
Derivation of Neutralizing Monoclonal Antibodies Against Rotavirus (1983)

Monoclonal antibodies were derived against the SA11 simian, NIC bovine, and Wa human rotavirus strains and characterized by enzyme-linked immunosorbent assay, plaque neutralization, and hemagglutination inhibition. Several strain SA11-specific antibodies were found to have neutralizing and hemagglutination-inhibiting capacity.
Identification of Single Bacterial Cells in Aqueous Solution Using Confocal Laser Tweezers Raman Spectroscopy (2005)

We report on a rapid method for reagentless identification and discrimination of single bacterial cells in aqueous solutions using a combination of laser tweezers and confocal Raman spectroscopy (LTRS). The optical trapping enables capturing of individual bacteria in aqueous solution in the focus of the laser beam and levitating the captured cell well off the cover plate, thus maximizing the excitation and collection of Raman scattering from the cell and minimizing the unwanted background from the cover plate and environment. Raman spectral patterns excited by a near-infrared laser beam provide intrinsic molecular information for reagentless analysis of the optically isolated bacterium. In our experiments, six species of bacteria were used to demonstrate the capability of the confocal LTRS in the identification and discrimination between the diverse bacterial species at various growth conditions. We show that synchronized bacterial cells can be well-discriminated among the six species using principal component analyses (PCA). Unsynchronized bacterial cells that are cultured at stationary phases can also be well-discriminated by the PCA, as well as by a hierarchical cluster analysis (HCA) of their Raman spectra. We also show that unsynchronized bacteria selected from random growth phases can be classified with the help of a generalized discriminant analysis (GDA). These findings demonstrate that the LTRS may find valuable applications in rapid sensing of microbial cells in diverse aqueous media.
Learning surface text patterns for a Question Answering system (2001)

In this paper we explore the power of surface text patterns for open-domain question answering systems. In order to obtain an optimal set of patterns, we have developed a method for learning such patterns automatically. A tagged corpus is built from the Internet in a bootstrapping process by providing a few hand-crafted examples of each question type to Altavista. Patterns are then automatically extracted from the returned documents and standardized. We calculate the precision of each pattern, and the average precision for each question type. These patterns are then applied to find answers to new questions. Using the TREC-10 question set, we report results for two cases: answers determined from the TREC-10 corpus and from the web.
Automating cell segmentation evaluation with annotated examples (2003)

Previously the development of a cell nucleus segmentation algorithm had been evaluated by eye by the author. This is an impractical method when attempting to evaluate and compare many algorithms and parameter sets on very large data sets. For this work, a dataset of 20,000 cell nucleus images was annotated by hand by three non-expert assistants. This paper concentrates on comparing the previous interactive approach to evaluating a segmentation algorithm to automated techniques using this annotated data.
Dendrimers Functionalized with a Single Fluorescent Dansyl Group Attached “Off Center”:  Synthesis and Photophysical Studies (2000)

A series of three new fluorescent dendrimers containing a single, focally located dansyl group and 3 (1), 9 (2), and 27 (3) carboxylic acid groups in their peripheries were synthesized and characterized. The photophysical properties of these dendrimers were investigated in aqueous solution. The host−guest interactions of the dendrimers through their dansyl subunits with β-cyclodextrin and polyclonal anti-dansyl antibodies were also investigated by various methods. Photophysical measurements on the dendrimers demonstrate that the dansyl residue is progressively shielded from the solvent as the dendrimer generation increases, resulting in marked changes in spectral features, fluorescence quantum yields, excited-state fluorescence lifetimes, radiative and nonradiative decay rates, and rotational reorientation times. The excited-state intensity decay kinetics for 1−3 are well described by a single exponential. Contrary to the popularly held belief that lower generation dendrimers are “floppy” species in solution, the molecular motions of 1−3 are described by a single rotational reorientation time. Access to the dansyl moiety is impeded with increasing dendrimer size as the dendrimer mass affords a significant degree of protection from binding by nonselective (β-cyclodextrin (β-CD)) and selective (anti-dansyl antibody) hosts for the dansyl residue. The equilibrium constant for β-CD binding of the dansyl residue in 1 is ∼2.5-fold lower than that for binding to dansylamine (DA). Dendrimers 2 and 3 do not associate with β-CD at all. Anti-dansyl antibodies can bind to the dansyl residue in dendrimers 1−3 with remarkably large binding affinities. The equilibrium constant for the antibody complex decreases systematically from 5.0 × 107 M-1 for DA to 1.5 × 106 M-1 for 3.
Emergence of Community-Associated Methicillin-Resistant Staphylococcus aureus USA300 Genotype as a Major Cause of Health Care--Associated Blood Stream Infections (2006)

MRSA USA300 genotype, the predominant cause of community-associated MRSA infections in our area (Atlanta, GA), has now emerged as a significant cause of health care-associated and nosocomial BSI. MRSA USA300 as a nosocomial pathogen presents new challenges to infection control programs.
CTLA-4 is a second receptor for the B cell activation antigen B7. (1991)

Functional interactions between T and B lymphocytes are necessary for optimal activation of an immune response. Recently, the T lymphocyte receptor CD28 was shown to bind the B7 counter-receptor on activated B lymphocytes, and subsequently to costimulate interleukin 2 production and T cell proliferation. CTLA-4 is a predicted membrane receptor from cytotoxic T cells that is homologous to CD28 and whose gene maps to the same chromosomal band as the gene for CD28. It is not known, however, if CD28 and CTLA-4 also share functional properties. To investigate functional properties of CTLA-4, we have produced a soluble genetic fusion between the extracellular domain of CTLA-4 and an immunoglobulin C gamma chain. Here, we show that the fusion protein encoded by this construct, CTLA4Ig, bound specifically to B7-transfected Chinese hamster ovary cells and to lymphoblastoid cells. CTLA4Ig also immunoprecipitated B7 from cell surface 125I-labeled extracts of these cells. The avidity of 125I-labeled B7Ig fusion protein for immobilized CTLA4Ig was estimated (Kd approximately 12 nM). Finally, we show that CTLA4Ig was a potent inhibitor of in vitro immune responses dependent upon cellular interactions between T and B lymphocytes. These findings provide direct evidence that, like its structural homologue CD28, CTLA-4 is able to bind the B7 counter-receptor on activated B cells. Lymphocyte interactions involving the B7 counter-receptor are functionally important for alloantigen responses in vitro.
The Treatment of Severe Psoriasis (1987)

In 1974, we conducted a randomized survey of dermatologists to determine trends in the use of chemotherapeutic agents for psoriasis. The present survey updates and extends the earlier one to include phototherapy, photochemotherapy, and other modalities being used in the treatment of psoriasis too extensive or severe for topical agents alone. Questionnaires were sent to approximately 20% of dermatologists nationwide and also to all training/research programs. Results of the survey include: (1) approximately 523,000 patients with psoriasis were treated by dermatologists in 1984, and 30% of these were severe enough to require more than topical care; (2) the majority of dermatologists use ultraviolet B (71%) and methotrexate (58%), while 36% use psoralen and ultraviolet A; (3) creatinine clearance rates and liver biopsy specimens are being obtained for approximately half of methotrexate-treated patients; and (4) of those physicians using methotrexate, most (74%) use weekly divided orally administered methotrexate doses.