gebhart/patrepeval huggingface dataset:
An update on the therapeutic potential of vitamin D analogues (2003)

The review provides an evaluation of the therapeutic potential of vitamin D analogues in the context of the current understanding of vitamin D biochemistry, molecular biology and physiology. Vitamin D activity results from several circulating and intracellular physiological metabolites acting simultaneously through at least three receptors. Common analogues are reviewed. Although most vitamin D analogues have traditionally been analogues of 1,25-dihydroxyvitamin D, it may be better to deliver high doses of base vitamin or (analogues) of 25-hydroxyvitamin D. This would permit physiological endocrine, paracrine and autocrine vitamin D metabolism. Agonists or antagonists of tissue-specific vitamin D metabolic pathways could be coadministered. The importance of measuring endogenous vitamin D metabolites during in vivo studies and the pitfalls of extending data across species and time are emphasised. Human vitamin D analogue trials should include direct comparison against the related endogenous metabolite.
Bcl-2 inhibition sensitizes triple-negative human breast cancer cells to doxorubicin (2018)

Breast cancers can be divided into several types. Because triple-negative breast cancer (TNBC) is the most refractory to current anti-cancer therapies, efficient treatment has been urgently required. Members of the Bcl-2 family play pro- and anti-apoptotic roles in mitochondria-mediated apoptosis. Some Bcl-2 family members are expressed in breast cancer and influence the response to anti-cancer therapies. In this study, we investigated whether Bcl-2 inhibition could sensitize TNBC cells to the genotoxic drug doxorubicin (DR). Treatment with a combination of the Bcl-2 inhibitor ABT-199 and DR synergistically decreased the viability of the TNBC cell lines MDA-MB-231 and BT-549. In an apoptosis assay, the combination treatment resulted in only a marginal effect in BT-549 cells, whereas drastic apoptosis was induced in MDA-MB-231 cells treated with both ABT-199 and DR. Both caspase-8 and -9 were involved in the combination treatment-induced apoptosis. Short interfering RNA-mediated knockdown of Bcl-2 increased the sensitivity of both cell lines to DR. The combination treatment also significantly decreased the colony-forming ability of the TNBC cell lines. In a xenograft mouse model, oral administration of ABT-199 augmented the DR-induced antitumor effect on subcutaneously established MDA-MB-231 cells. These results indicate that the combination of DR with Bcl-2 inhibitors, including ABT-199, may be a promising treatment modality for TNBC patients.
Double-emulsion drops with ultra-thin shells for capsule templates (2011)

We introduce an emulsification technique that creates monodisperse double-emulsion drops with a core-shell geometry having an ultra-thin wall as a middle layer. We create a biphasic flow in a microfluidic capillary device by forming a sheath flow consisting of a thin layer of a fluid with high affinity to the capillary wall flowing along the inner wall of the capillary, surrounding the innermost fluid. This creates double-emulsion drops, using a single-step emulsification, having a very thin fluid shell. If the shell is solidified, its thickness can be small as a hundred nanometres or even less. Despite the small thickness of this shell, these structures are nevertheless very stable, giving them great potential for encapsulation. We demonstrate this by creating biodegradable microcapsules of poly(lactic acid) with a shell thickness of a few tens of nanometres, which are potentially useful for encapsulation and delivery of drugs, cosmetics, and nutrients.
β-Galactosidase α complementation: properties of the complemented enzyme and mechanism of the complementation reaction (1976)

Intracistronic alpha complementation involving Escherichia coli beta-galactosidase occurs between the cyanogen bromide peptide CB2, derived from residues 3-92 of beta-galactosidase (Langley, K.E., Fowler, A.V., and Zabin, I. (1975), J. Biol. Chem. 250, 2587), and the defective beta-galactosidase from the Z-deletion mutant strain M15. The M15 protein, a dimer, lacks residues 11-41 of beta-galactosidase (Langley, K.E., Villarejo, M.R., Fowler, A.V., Zamenhof, P.J., and Zabin, I. (1975), Proc. Natl. Acad. Sci. U.S.A. 72, 1254). The complemented enzyme formed from purified components has a molecular weight of 533 000+/-25 000, is therefore tetrameric, and has a probable stoichiometry of 1 CB2:1 M15 monomer. The complemented enzyme has the same Km for substrate as wild type enzyme, but is less stable to heat or urea treatment. The overall equilibrium constant for the complementation reaction is approximately 1-2 X 10(9) M-1. Initial velocity studies indicate saturation kinetics when either component is fixed and limiting, with an apparent Kd of about 10(-6) M. A first-order rate constant of 0.05-0.1 min-1 was estimated. The kinetics favor a model of rapid complex formation, followed by slow conformational change, as the mechanism of activation. Ultraviolet difference spectroscopy indicated an increased absorbance in the 290-300 nm region as a result of the complementation reaction. The kinetics of the increase suggest that two processes, one rapid and the other slower, could be responsible. The temperature dependence of complementation (Ea approximately 24 000 cal) is also consistent with the rate-determining step being a conformational change.
Properties of Thiol-Subtilisin (1968)

The conversion of a catalytic residue of an enzyme into a functional group with similar chemical and steric properties has been investigated in order to clarify the role of the catalytic group and its tolerance to change. The active site serine residue of the proteolytic enzyme, subtilisin, was converted into a cysteine residue by a two-step chemical process with no change in other properties of the enzyme, such as sedimentation pattern, starch gel electrophoresis pattern, amino acid composition, fluorescence, ultraviolet absorption, and chemical reactivity of tryptophan residues. A small change in the optical rotatory dispersion pattern was observed. The modified enzyme, thiol-subtilisin, was found to be inactive toward normal substrates, such as other proteins and simple esters, although a slight activity toward the labile nitrophenyl esters was observed. This inactivity of thiol-subtilisin could not be attributed to the binding of substrate, which appeared to be essentially unchanged, or to the deacylation step of the over-all reaction, which was decreased up to 100-fold. Rather, it is due to the diminished rate of the acylation step, which was undetectable. This result is contrary to the rates of model reactions of thiols and alcohols as nucleophiles. It is postulated that in the active site of the enzyme there is a critical alignment of catalytic groups and substrates which is necessary for activity. The polarizability and size of the —SH group, then, may be sufficiently greater than that of the —OH group that it perturbs this critical arrangement and prevents catalytic action.
The molecular basis of CO 2 reception in Drosophila (2007)

CO(2) elicits a response from many insects, including mosquito vectors of diseases such as malaria and yellow fever, but the molecular basis of CO(2) detection is unknown in insects or other higher eukaryotes. Here we show that Gr21a and Gr63a, members of a large family of Drosophila seven-transmembrane-domain chemoreceptor genes, are coexpressed in chemosensory neurons of both the larva and the adult. The two genes confer CO(2) response when coexpressed in an in vivo expression system, the "empty neuron system." The response is highly specific for CO(2) and dependent on CO(2) concentration. The response shows an equivalent dependence on the dose of Gr21a and Gr63a. None of 39 other chemosensory receptors confers a comparable response to CO(2). The identification of these receptors may now allow the identification of agents that block or activate them. Such agents could affect the responses of insect pests to the humans they seek.
Saccharomyces cerevisiae mitochondria can synthesise FMN and FAD from externally added riboflavin and export them to the extramitochondrial phase (1998)

Evidence is given that mitochondria isolated from Saccharomyces cerevisiae can take up externally added riboflavin and synthesise from it both flavin mononucleotide (FMN) and flavin adenine dinucleotide (FAD) probably due to the existence of the mitochondrial riboflavin kinase already reported and the novel mitochondria FAD synthetase. Moreover Saccharomyces cerevisiae mitochondria can export the newly synthesised flavin derivatives to the extramitochondrial phase. This has been proven to take place with 1:1 stoichiometry with riboflavin decrease outside mitochondria, thus showing that flavin traffic occurs across the mitochondrial membranes.
Synthesis and biophysical characterization of engineered topographic immunogenic determinants with .alpha..alpha. topology (1990)

Model peptides with predetermined secondary, tertiary, and quaternary conformation have been successfully designed, synthesized, and characterized in an attempt to mimic the three-dimensional structure of an antigenic determinant. This work is a continuing effort to map the antigenic structure of the protein antigen lactate dehydrogenase C4 (LDH-C4) to develop a contraceptive vaccine. A putative topographic determinant with alpha alpha topology which associates into four-helix bundles was designed on the basis of the framework model of protein folding. An idealized amphiphilic 18-residue sequence (alpha 1) and a 40-residue alpha alpha fold (alpha 3) have been shown to form stable 4-helix structures in solution with a free energy of association on the order of -20.8 kcal/mol (tetramerization of alpha 1) and -7.8 kcal/mol (dimerization of alpha 3). Both alpha 1 and alpha 3 form stable monolayers at the air-water interface. The CD spectra of Langmuir-Blodgett monolayers are characteristically alpha-helical. Both CD and FTIR spectroscopic studies reval a high degree of secondary structure. The SAXS data strongly suggest that the helices are arranged in a four-helix bundle since the radius of gyration of 17.2 A and the vector distribution function are indicative of a prolate ellipsoid of axial dimensions and molecular weight appropriate for the four-helix bundle. The major contribution to the formation and stabilization of alpha 1 and alpha 3 is believed to be hydrophobic interaction between the amphiphilic alpha-helices. The displayed heptad repeat, helix dipole, ion pairs, and the loop sequence may have also contributed to the overall stability and antiparallel packing of the helices. A detailed structural analysis of a relevant topographic immunogenic determinant will elucidate the nature of antigen-antibody interactions as well as provide insight into protein folding intermediates.
Controlling the rates of biochemical reactions and signaling networks by shape and volume changes (2008)

In biological systems, chemical activity takes place in micrometer- and nanometer-sized compartments that constantly change in shape and volume. These ever-changing cellular compartments embed chemical reactions, and we demonstrate that the rates of such incorporated reactions are directly affected by the ongoing shape reconfigurations. First, we show that the rate of product formation in an enzymatic reaction can be regulated by simple volume contraction-dilation transitions. The results suggest that mitochondria may regulate the dynamics of interior reaction pathways (e.g., the Krebs cycle) by volume changes. We then show the effect of shape changes on reactions occurring in more complex and structured systems by using biomimetic networks composed of micrometer-sized compartments joined together by nanotubes. Chemical activity was measured by implementing an enzymatic reaction-diffusion system. During ongoing reactions, the network connectivity is changed suddenly (similar to the dynamic tube formations found inside Golgi stacks, for example), and the effect on the reaction is registered. We show that spatiotemporal properties of the reaction-diffusion system are extremely sensitive to sudden changes in network topology and that chemical reactions can be initiated, or boosted, in certain nodes as a function of connectivity.
Oral feeding in premature infants: advantage of a self-paced milk flow (2000)

An earlier study demonstrated that oral feeding of premature infants (<30 wk gestation) was enhanced when milk was delivered through a self-paced flow system. The aims of this study were to identify the principle(s) by which this occurred and to develop a practical method to implement the self-paced system in neonatal nurseries. Feeding performance, measured by overall transfer, duration of oral feedings, efficiency, and percentage of successful feedings, was assessed at three time periods, when infants were taking 1-2, 3-5, and 6-8 oral feedings/day. At each time period, infants were fed, sequentially and in a random order, with a self-paced system, a standard bottle, and a test bottle, the shape of which allowed the elimination of the internal hydrostatic pressure. In a second study, infants were similarly fed with the self-paced system and a vacuum-free bottle which eliminated both hydrostatic pressure and vacuum within the bottle. The duration of oral feedings, efficiency, and percentage of successful feedings were improved with the self-paced system as compared to the standard and test bottles. The results were similar in the comparison between the self-paced system and the vacuum-free bottle. Elimination of the vacuum build-up naturally occurring in bottles enhances the feeding performance of infants born <30 wk gestation as they are transitioned from tube to oral feeding. The vacuum-free bottle is a tool which caretakers can readily use in neonatal nurseries.
RSVP keyboard: An EEG based typing interface (2012)

Humans need communication. The desire to communicate remains one of the primary issues for people with locked-in syndrome (LIS). While many assistive and augmentative communication systems that use various physiological signals are available commercially, the need is not satisfactorily met. Brain interfaces, in particular, those that utilize event related potentials (ERP) in electroencephalography (EEG) to detect the intent of a person noninvasively, are emerging as a promising communication interface to meet this need where existing options are insufficient. Existing brain interfaces for typing use many repetitions of the visual stimuli in order to increase accuracy at the cost of speed. However, speed is also crucial and is an integral portion of peer-to-peer communication; a message that is not delivered timely often looses its importance. Consequently, we utilize rapid serial visual presentation (RSVP) in conjunction with language models in order to assist letter selection during the brain-typing process with the final goal of developing a system that achieves high accuracy and speed simultaneously. This paper presents initial results from the RSVP Keyboard system that is under development. These initial results on healthy and locked-in subjects show that single-trial or few-trial accurate letter selection may be possible with the RSVP Keyboard paradigm.
Compartmentalized autocrine signaling to cystic fibrosis transmembrane conductance regulator at the apical membrane of airway epithelial cells (2001)

Physical stimulation of airway surfaces evokes liquid secretion, but the events that mediate this vital protective function are not understood. When cystic fibrosis transmembrane conductance regulator (CFTR) channel activity was used as a functional readout, we found signaling elements compartmentalized at both extracellular and intracellular surfaces of the apical cell membrane that activate apical Cl(-) conductance in Calu-3 cells. At the outer surface, ATP was released by physical stimuli, locally converted to adenosine, and sensed by A(2B) adenosine receptors. These receptors couple to G proteins, adenylyl cyclase, and protein kinase A, at the intracellular face of the apical membrane to activate colocalized CFTR. Thus, airways have evolved highly efficient mechanisms to "flush" noxious stimuli from airway surfaces by selective activation of apical membrane signal transduction and effector systems.
Growth characteristics of the veterinary vaccine candidate ChimeriVax™‐West Nile (WN) virus in Aedes and Culex mosquitoes (2003)

In 1999 West Nile (WN) virus was introduced to North America where this flavivirus has spread rapidly among wildlife (especially birds) transmitted by various species of mosquitoes (Diptera: Culicidae). Increasing numbers of cases and deaths among humans, horses and other domestic animals require development of effective vaccines. 'ChimeriVax-West Nile(vet)' is being developed for use as a veterinary vaccine to protect against WN infection. This chimeric virus contains the pre-membrane (prM) and envelope (E) genes from the wild-type WN NY99 virus (isolated from a flamingo in New York zoo during the 1999 WN epidemic) in the backbone of yellow fever (YF) 17D vaccine virus. Replication kinetics of ChimeriVax-WN(vet) virus were evaluated in mosquito cell culture (Aedes albopictus C6/36), in WN vector mosquitoes [Culex tritaeniorhynchus Giles, Cx. nigripalpus Theobald and Cx. quinquefasciatus Say (Diptera: Culicidae)] and in YF vectors [Aedes aegypti (L) and Ae. albopictus (Skuse)], to determine whether these mosquitoes become infected through feeding on a viraemic vaccine, and their potential infectivity to transmit the virus. Growth of ChimeriVax-WN(vet) virus was found to be restricted in mosquitoes, compared to WN virus in Ae. albopictus C6/36 cells. When inoculated intrathoracically, ChimeriVax-WN(vet) and YF 17D viruses did not replicate in Cx. tritaeniorhynchus or Cx. nigripalpus; replication was very restricted compared to the wild-type WN virus in Cx. quinquefasciatus, Ae. aegypti and Ae. albopictus. When fed on hanging drops with ChimeriVax-WN(vet) virus (7.7 log10 PFU/mL), none of the Culex mosquitoes became infected; one Ae. albopictus and 10% of the Ae. aegypti became infected, but the titre was very low and virus did not disseminate to head tissue. ChimeriVax-WN(vet) virus had a replication profile similar to that of the attenuated vaccine virus YF 17D, which is not transmitted by mosquitoes. These results suggest that the natural mosquito vectors of WN and YF viruses, which may incidentally take a bloodmeal from a vaccinated host, will not become infected with ChimeriVax-WN(vet) virus.
An Improved 32P-Postlabeling Assay for the Sensitive Detection of 8-Oxodeoxyguanosine in Tissue DNA (2001)

To use oxidative DNA lesions as biomarkers of exposure and disease in the human scenario, the assay should not only be sensitive but also applicable to small quantities of DNA that is obtained from human tissue biopsies. Previously, we reported a nonenrichment (32)P-postlabeling method for measuring the oxidative DNA lesion, 8-oxo-7,8-dihydro-2'-deoxyguanosine (8-oxo-dG) [Devanaboyina, U., and Gupta, R. C. (1996) Carcinogenesis 17, 917-924]. Here we report a substantial improvement of the assay by enriching 8-oxo-dGp by TLC prior to (32)P-labeling. Thus, unmodified nucleotides were removed by 1-directional polyethyleneimine (PEI)-cellulose TLC in 0.2 M formic acid. 8-Oxo-dGp, retained close to the origin, was eluted in 2 M triethylammonium acetate (pH 7.0), lyophilized, (32)P-labeled, resolved by TLC, and quantitated. The 8-oxo-dG signal was found to increase linearly with increasing amount of DNA. Its recovery was found to be 55-70%, as determined by using synthetic 8-oxo-dGp. Since the modified assay allowed using larger quantities of DNA and higher specific activity [gamma-(32)P]ATP than those used in the nonenrichment procedure, the signal-to-noise ratio increased to 30-100:1 from 3-5:1. The assay has a sensitivity of detection of <1 8-oxo-dG/10(7) nucleotides using submicrogram to microgram DNA. The 8-oxo-dG levels (mean +/- SE; n = 5) in the liver, lung, heart, bladder, and trachea DNA of 3 month-old female Sprague-Dawley rats were found to be 1.05 +/- 0.24, 0.97 +/- 0.09, 0.75 +/- 0.15, 0.79 +/- 0.15, and 1.17 +/- 0.28 per 10(6) nucleotides, respectively.
Transbilayer movement of phosphatidylserine in erythrocytes: inhibition of transport and preferential labeling of a 31 000-dalton protein by sulfhydryl reactive reagents (1988)

A series of labeled thiolation reagents were synthesized on the basis of the parent structure pyridyldithioethylamine (PDA). These compounds specifically and reversibly inhibit the active intrabilayer transport of phosphatidylserine (PS) in human red blood cells. The binding of PDA to cells can be quantified since the thiol-disulfide exchange reaction yields a chromophore. In addition, the presence of a primary amine makes it amenable to derivatization with a variety of compounds. An iodinated derivative of PDA preferentially labeled a 31,000-dalton red blood cell peptide. The labeled component, which may represent the PS transporter, comigrated with integral membrane protein band 7.
CLINICAL EVALUATION OF INDUCTION IMMUNOSUPPRESSION WITH A MURINE IgG2b MONOCLONAL ANTIBODY (BMA 031) DIRECTED TOWARD THE HUMAN α/β-T CELL RECEPTOR (1994)

Mouse mAbs directed against the alpha/beta-TCR were tested in clinical phase II and in triple-blind, randomized phase III studies. A clinical phase II trial administered 50 mg of murine anti-human alpha/beta-TCR mAb (BMA 031) intravenously on the day of, as well as 2 and 4 days after, cadaveric donor renal transplantation in combination with a CsA/prednisone regimen. None of 12 patients showed even moderately adverse side effects. A phase III, triple-blind randomized trial enrolled 24 patients in the BMA 031 group and 22 patients in a placebo control group. BMA 031 treatment significantly reduced the incidence of rejection events within the first 10 posttransplant days to 1 patient versus 9 episodes in the placebo group (P < 0.01). By the end of 30 days, 6 rejection episodes had occurred in the BMA 031 group and 11 in the control cohort (P = NS). After a minimum of 30 months follow-up, the actual allograft survival rate was 87% in the BMA-treated group compared with 68% in the control cohort.
Interleukin-6 and risk of cognitive decline (2002)

The results suggest a relationship between elevated baseline plasma IL-6 and risk for subsequent decline in cognitive function. These findings are consistent with the hypothesized relationship between brain inflammation, as measured here by elevated plasma IL-6, and neuropathologic disorders.
Nonsteroidal Anti-inflammatory Drugs and Cyclooxygenase-2 Selective Inhibitors for Prostate Cancer Chemoprevention (2004)

COX-2 inhibitors are promising agents for the chemoprevention of prostate cancer but further research is needed.