gebhart/patrepeval huggingface dataset:
Reconstitution of Active Mycobacterial Binuclear Iron Monooxygenase Complex in Escherichia coli (2013)

Bacterial binuclear iron monooxygenases play numerous physiological roles in oxidative metabolism. Monooxygenases of this type found in actinomycetes also catalyze various useful reactions and have attracted much attention as oxidation biocatalysts. However, difficulties in expressing these multicomponent monooxygenases in heterologous hosts, particularly in Escherichia coli, have hampered the development of engineered oxidation biocatalysts. Here, we describe a strategy to functionally express the mycobacterial binuclear iron monooxygenase MimABCD in Escherichia coli. Sodium dodecyl sulfate-polyacrylamide gel electrophoretic analysis of the mimABCD gene expression in E. coli revealed that the oxygenase components MimA and MimC were insoluble. Furthermore, although the reductase MimB was expressed at a low level in the soluble fraction of E. coli cells, a band corresponding to the coupling protein MimD was not evident. This situation rendered the transformed E. coli cells inactive. We found that the following factors are important for functional expression of MimABCD in E. coli: coexpression of the specific chaperonin MimG, which caused MimA and MimC to be soluble in E. coli cells, and the optimization of the mimD nucleotide sequence, which led to efficient expression of this gene product. These two remedies enabled this multicomponent monooxygenase to be actively expressed in E. coli. The strategy described here should be generally applicable to the E. coli expression of other actinomycetous binuclear iron monooxygenases and related enzymes and will accelerate the development of engineered oxidation biocatalysts for industrial processes.
Anti-inflammatory and Immune Therapy for Alzheimers Disease: Current Status and Future Directions (2007)

From the initial characterizations of inflammatory responses in Alzheimer's disease (AD) affected brains, namely the demonstration of activated microglia and reactive astrocytes, complement system activation, increased production of proinflammatory cytokines, and evidence for microglial-produced neurotoxins, there was hope that reducing inflammation might be a feasible treatment for this memory-robbing disease. This hope was supported by a number of epidemiology studies demonstrating that patients who took non-steroidal anti-inflammatory drugs had significantly lower risk of developing AD. However, clinical trials of anti-inflammatories have not shown effectiveness, and in recent years, the concept of immune therapy has become a treatment option as animal studies and clinical trials with Abeta vaccines have demonstrated enhanced amyloid removal through stimulation of microglial phagocytosis.This review will examine the current status of whether inhibiting inflammation is a valid therapeutic target for treating AD; what lessons have come from the clinical trials; what new pathways and classes of agents are being considered; and how this field of research can progress towards new therapeutics. We will examine a number of agents that have shown effectiveness in reducing inflammation amongst other demonstrated mechanisms of action. The major focus of much AD drug discovery has been in identifying agents that have anti-amyloid properties; however, a number of these agents were first identified for their anti-inflammatory properties. As drug development and clinical testing is a costly and lengthy endeavor, sound justification of new therapeutic targets is required. Possible future directions for AD anti-inflammatory or immune clearance therapy will be discussed based on recent experimental data.
Overlapping Correlation Clustering (2011)

We introduce a new approach to the problem of overlapping clustering. The main idea is to formulate overlapping clustering as an optimization problem in which each data point is mapped to a small set of labels, representing membership to different clusters. The objective is to find a mapping so that the distances between data points agree as much as possible with distances taken over their label sets. To define distances between label sets, we consider two measures: a set-intersection indicator function and the Jaccard coefficient. To solve the main optimization problem we propose a local-search algorithm. The iterative step of our algorithm requires solving non-trivial optimization sub problems, which, for the measures of set-intersection and Jaccard, we solve using a greedy method and non-negative least squares, respectively. Since our frameworks uses pair wise similarities of objects as the input, it lends itself naturally to the task of clustering structured objects for which feature vectors can be difficult to obtain. As a proof of concept we show how easily our framework can be applied in two different complex application domains. Firstly, we develop overlapping clustering of animal trajectories, obtaining zoologically meaningful results. Secondly, we apply our framework for overlapping clustering of proteins based on pair wise similarities of amino acid sequences, outperforming the of state-of-the-art method in matching a ground truth taxonomy.
Passive blood plasma separation at the microscale: a review of design principles and microdevices (2015)

Blood plasma separation is vital in the field of diagnostics and health care. Due to the inherent advantages obtained in the transition to microscale, the recent trend in these fields is a rapid shift towards the miniaturization of complex macro processes. Plasma separation in microdevices is one such process which has received extensive attention from researchers globally. Blood plasma separation techniques based on microfluidic platforms can be broadly classified into two categories. While active techniques utilize external force fields for separation, the passive techniques are dependent on biophysical effects, cell behavior, hydrodynamic forces and channel geometry for blood plasma separation. In general, passive separation methods are favored in comparison to active methods because they tend to avoid design complexities and are relatively easy to integrate with biosensors; additionally they are cost effective. Here we review passive separation techniques demonstrating separation and blood behavior at microscale. We present an extensive review of relevant biophysical laws, along with experimental details of various passive separation techniques and devices exploiting these physical effects. The relative performances, and the advantages and disadvantages of microdevices discussed in the literature, are compared and future challenges are brought about.
Effects of P‐Aminophenyl Dichloroarsine on Reduced High‐affinity [3H]Nicotine Binding Sites from Chick Brain: A Covalent, Yet Reversible, Agent for Neuronal Nicotinic Receptors (1992)

Neuronal nicotinic acetylcholine receptor (nAChR) alpha-subunits contain a conserved disulphide that is essential for function. Here, we have examined the effects of sulphydryl redox reagents on [3H]nicotine binding to chick brain nAChR immunoisolated with the monoclonal antibody mAb35. The disulphide reducing agent, dithiothreitol (DTT), inhibited [3H]nicotine binding [50% inhibitory concentration (IC50)=146 microM] but this effect was reversed (93 +/- 1.5%) by subsequent reoxidation with 1 mM dithio-bis(nitrobenzoic acid) (DTNB). The trivalent arsenical, p-aminophenyl dichloroarsine (APA), which reacts with pairs of spatially close sulphydryls, was a potent inhibitor of reoxidation by DTNB (IC50=35 nM). However, application of the 'anti-arsenical', 2,3-dimercaptopropane sulphonic acid (DMPS), restored agonist binding after APA treatment (50% effective concentration=120 microM). Paradoxically, DMPS was also found to be a potent oxidizing agent of these receptors. Affinity alkylation of reduced nAChRs with bromoacetylcholine (BAC; 100 microM) irreversibly blocked nicotine binding (>90%). We propose (but have not proven) that APA interacts with the cysteines homologous to Cys192 - 193 in Torpedo AChRs, since APA pretreatment of reduced neuronal receptors protected against irreversible BAC alkylation, as shown by subsequent reversal of DMPS (2 mM; 20 min). This study illustrates the potent and reversible nature of the arsenical's covalent interaction with an isolated nAChR and suggests that modified arsenicals could be useful nAChR probes.
T65 antigen modulation in a phase I monoclonal antibody trial with chronic lymphocytic leukemia patients. (1984)

Antigenic modulation of the T65 cell surface antigen was assessed in chronic lymphocytic leukemia patients (CLL) receiving therapy with the murine monoclonal antibody T101 in a phase I clinical trial. A total of 12 patients received 1, 10, or 40 mg doses administered over 2 hr, or 50 or 100 mg doses administered over 50 hr. Decreases in T65 antigen expression (up to 90%) coincided with decreases in the circulating leukemic cell count in those patients who received T101 over a 2-hr period, indicating that clearance of circulating T65 antigen-positive cells could account for most of the observed decreases in T65 antigen expression. In contrast, analysis of bone marrow specimens from these patients indicated that decreases in T65 antigen density in this relatively stationary population resulted not from a cell decrement but rather from antigenic modulation. Pulmonary toxicity prevented administration of doses greater than 40 mg over a 2-hr period; therefore, higher doses (50 and 100 mg) were administered over a 50-hr period. This treatment schedule resulted in greater than 90% reduction in T65 antigen density of both circulating and bone marrow leukemic cells without dramatic drops in circulating leukemic cell counts, indicating that antigenic modulation accounted for most of the observed decreases in T65 antigen density under these conditions. Reexpression of T65 antigen by modulated cells was observed both in vitro and in vivo within 2 to 4 days. Immunoperoxidase staining of in vivo-modulated specimens and in vitro modulation studies with 125I-T101 suggested that T65 antigen-T101 antibody complexes were internalized during modulation. Although antigenic modulation inhibits the potential therapeutic effectiveness of unconjugated T101 antibody in CLL patients, treatment of CLL with T101 drug or toxin immunoconjugates under conditions that bring about rapid and extensive internalization of the T65 antigen may provide an effective means of therapy.
High level synthesis of immunoglobulins in Chinese hamster ovary cells. (1990)

The expression of lambda L and microH chain cDNA was examined in Chinese hamster ovary cells. Each cDNA was linked to a different, amplifiable, selectable drug marker gene, and expression was monitored in the presence of increasing concentrations of the selective drugs. Cells were obtained that produced greater than 60 micrograms/10(6) cells/48 h of assembled antibody. This Chinese hamster ovary cell-synthesized IgM was polymeric, and exhibited specific hapten binding and C fixation. The expression strategy employed here may prove useful for the future production of genetically engineered antibodies and other multi-subunit proteins.
Inhibition of proliferation, but not of Ca2+ mobilization, by cyclic AMP and GMP in rabbit aortic smooth-muscle cells (1992)

The effects on cellular proliferation and Ca2+ mobilization of analogues of cyclic AMP (cAMP) and cyclic GMP (cGMP) and of agents that elevate the intracellular concentrations of cyclic nucleotides were compared in closely similar preparations of first-passage rabbit aortic vascular smooth-muscle cells. Proliferation induced by foetal-bovine serum was inhibited by 78% by 1 mM-8-bromo cAMP and by 42% by 1 mM-8-bromo cGMP. In the presence of 100 microM-isobutylmethylxanthine, 100 microM-forskolin increased intracellular cAMP concentration 5-fold and inhibited proliferation by 87%, but did not affect cGMP concentration or cell viability (ATP concentration). Similarly in the presence of 100 microM-isobutylmethylxanthine, 1 mM-SIN-1 (3-morpholinosydnonimine) elevated cGMP concentration 4-fold and inhibited proliferation by 48%, but did not affect cAMP or ATP concentration. Isobutylmethylxanthine (1 mM) elevated cAMP concentration by 3-fold and cGMP concentration by 20-fold and inhibited proliferation by 81%. Concentrations of 8-bromo cAMP, 8-bromo cGMP, forskolin or SIN-1 that inhibited proliferation did not affect the elevation of intracellular free Ca2+ concentration caused by 2% (v/v) foetal-bovine serum, 100 nM-5-hydroxytryptamine or 10 nM-angiotensin II. The results demonstrate that elevation of intracellular cAMP and cGMP concentrations both independently inhibit vascular smooth-muscle cell proliferation, but these effects on proliferation are not mediated by inhibition of Ca2+ mobilization.
A Double-Blind, Placebo-Controlled Study of Memantine in the Treatment of Major Depression (2006)

In an 8-week trial, the low-to-moderate-affinity NMDA antagonist memantine in doses of 5-20 mg/day was not effective in the treatment of major depressive disorder.
Reaction of beta-lapachone and related naphthoquinones with 2-mercaptoethanol: a biomimetic model of topoisomerase II poisoning by quinones. (1998)

1,2-Naphthoquinones, such as beta-lapachone, 4-alkoxy-1,2-naphthoquinones, and tetrahydrofuran-1,2-naphthoquinones, react rapidly with 2-mercaptoethanol in benzene to give 1,4-, 1,2-, 1,3- and 1,6-Michael-type adducts that are formed by the addition of the thiol group to the quinone ring. Menadione (2-methyl-1,4-naphthoquinone) reacts with the thiol reagent very slowly under the same reaction conditions. Although the formation of the adducts can be followed by 1H-NMR, attempts to isolate the adducts failed due to their retroconversion to the starting products. On addition of a Lewis acid, however, the adducts undergo cyclization reactions that give stable derivatives that can be isolated and characterized. Determination of the structures of the derivatives allowed for the identification of the adducts from which they originated. Thus, beta-lapachone and 2,3-dinordunnione underwent 1,4- and 1,2-Michael type additions to the quinone ring, while 4-pentyloxy-1,2-naphthoquinone underwent two simultaneous Michael additions to the quinone ring of the naphthoquinone. Menadione underwent a single 1,3-addition. The alkylation rates of the thiol group of 2-mercaptoethanol by the naphthoquinones parallel the naphthoquinones efficiencies in inducing DNA cleavage through DNA-bound topoisomerase II. These results support our hypothesis that the cytotoxic effect of the naphthoquinones derive, at least in part, from their alkylation of exposed thiol residues on the topoisomerase II-DNA complex.
5-Fluorouracil prodrug: role of anabolic and catabolic pathway modulation in therapy of colorectal cancer. (1995)

Following p.o. administration to rats bearing advanced colorectal carcinoma, Ftorafur (FT) is converted to 5-fluorouracil (FUra) by microsomal P450 in the liver. To optimize the therapeutic selectivity of the FUra generated from FT, three approaches were utilized: (a) inhibition of FUra degradation to dihydrofluorouracil by uracil as an alternative substrate for uracil reductase in the molar ratio of 4 uracil:1 FT (UFT); (b) modulation of drug inhibition of thymidylate synthase by leucovorin (LV); and (c) by increasing the level of FUra incorporation into cellular RNA by N-(phosphonacetyl)-L-aspartate (PALA), an inhibitor of aspartate transcarbomylase. The maximum tolerated dose (MTD) of FT and UFT, administered 3 times a day for 28 days, was 150 mg/kg/day and 60 mg/kg/day, respectively. The MTDs were not significantly modified by LV (150 or 600 mg/kg/day), administered by the p.o. route with the drugs, or by PALA (100 mg/kg) administered weekly by the i.v. route. The dose-limiting toxicity of FT alone and in combination with the modulators was stomatitis. The severe alopecia observed with FT alone was reduced significantly by uracil. At the MTD, the antitumor activity of UFT was superior to those of FT and FUra alone and in combination with LV and/or PALA. The 3-month sustained complete tumor regression for UFT, FT, and FUra was 38%, 0%, and 13% (for the weekly schedule), respectively. Although uracil, LV, and PALA individually increased the antitumor activity of FT at its MTD, the combination of the three modulators produced the highest therapeutic efficacy in rats bearing advanced colorectal carcinoma, in which 100% of the treated animals achieved complete and sustained tumor regression. The therapeutic efficacy observed with FT modulation could not be achieved with FUra administered by different schedules, each at its MTD alone or in combination with either LV or PALA. In brief, modulation of FT produced greater therapeutic efficacy and selectivity than FUra. Furthermore, the combined use of modulators capable of inhibiting the degradation pathway of FUra and potentiating the effects of the anabolic metabolites action appears to offer the greatest therapeutic potential.
Cloning and characterization of mammalian homologs of the Drosophila dunce+ gene. (1989)

A probe representing the Drosophila dunce+ (dnc+) gene, the structural gene for a cAMP phosphodiesterase (PDEase), detects homologous sequences in many different organisms, including mouse, rat, and human. Genomic and cDNA clones representing a homolog of the Drosophila dnc+ gene were isolated from rat libraries and characterized. This gene has been named ratdnc-1. One cDNA clone defines a large open reading frame of approximately 1.8 kilobases (kb), predicting a protein sequence of 610 amino acids with significant homology to a conserved domain of approximately 275 residues found in most other PDEases. The amino acid identity value to the Drosophila cAMP PDEase within this domain is a striking 75%. Other cDNA clones show blocks of sequence divergence from this cDNA clone close to the predicted N terminus, indicating the potential existence of a family of related enzymes encoded by alternatively spliced messenger RNAs from ratdnc-1. Genomic blotting experiments suggest the existence of at least one other rat gene with homology to ratdnc-1. RNAs homologous to ratdnc-1 are heterogeneous in size between tissues, with heart containing a major transcript of 4.4 kb and brain one of 4.0 kb. The potential identity of the product of the ratdnc-1 gene with known PDEases is discussed.
Optical proximity correction of alternating phase-shift masks for 0.18-um KrF lithography (1997)

Optical proximity correction (OPC) was applied to alternating phase shift masks to improve printed resist pattern fidelity. Mask patterns were modified with jog type corrections. DRAM cell patterns were exposed by using a 0.55 NA, 0.36/0.55 (sigma) , KrF excimer laser stepper onto 0.5 micrometers thick chemically amplified negative resist. With 0.55 (sigma) , OPC was effective and printed resist pattern was very close to designed one. However, with 0.36 (sigma) , large pattern deformation was observed due to coma aberration.
Gene Expression of Human DNA Polymerase α during Cell Proliferation and the Cell Cycle (1988)

We studied the expression of the human DNA polymerase alpha gene during cell proliferation, during cell progression through the cell cycle, and in transformed cells compared with normal cells. During the activation of quiescent cells (G0 phase) to proliferate (G1/S phases), the steady-state mRNA levels, rate of synthesis of nascent polymerase protein, and enzymatic activity in vitro exhibited a substantial and concordant increase prior to the peak of in vivo DNA synthesis. In transformed cells, the respective values were amplified greater than 10-fold. In actively growing cells separated into discrete stages of the cell cycle by counterflow elutriation or by mitotic shakeoff, levels of steady-state transcripts, translation rates, and enzymatic activities of polymerase alpha were constitutively and concordantly expressed at all stages of the cell cycle, with only a moderate elevation prior to the S phase and a slight decline in the G2 phase. These findings support the conclusion that the regulation of human DNA polymerase alpha gene expression is at the transcriptional level and strongly suggest that the regulatory mechanisms that are operative during the entrance of a cell into the mitotic cycle are fundamentally different from those that modulate polymerase alpha expression in continuously cycling cells.
Domestic Poultry and SARS Coronavirus, Southern China (2004)

SARS coronavirus injected intratracheally into chickens, turkeys, geese, ducks, and quail, or into the allantoic sac of their embryonating eggs, failed to cause disease or replicate. This finding suggests that domestic poultry were unlikely to have been the reservoir, or associated with dissemination, of SARS coronavirus in the animal markets of southern China.
Unrecognized Misplacement of Endotracheal Tubes in a Mixed Urban to Rural Emergency Medical Services Setting (2003)

The incidence of unrecognized misplacement of endotracheal tubes by EMS personnel may be higher than most previous studies, making regular EMS evaluation and the out-of-hospital use of devices to confirm placement imperative. The authors were unable to show a difference in misplacement rates based on provider experience or level of training.
ChemInform Abstract: Functionalized Poly(ethylene glycol) for Preparation of Biologically Relevant Conjugates (1995)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Increased Risk of Adrenal Insufficiency Following Etomidate Exposure in Critically Injured Patients (2008)

Exposure to etomidate is a modifiable risk factor for the development of AI in this sample of critically injured patients. The use of etomidate for procedural sedation and rapid-sequence intubation in this patient population should be reevaluated.
Recombinant chymotrypsin inhibitor 2: expression, kinetic analysis of inhibition with .alpha.-chymotrypsin and wild-type and mutant subtilisin BPN', and protein engineering to investigate inhibitory specificity and mechanism (1990)

The serine protease inhibitor chymotrypsin inhibitor 2 (CI2 or BSPI2) has been expressed in Escherichia coli with the pINIIIompA3 expression vector to produce 20-40 mg/L of culture. Recombinant CI2 purified from this system has been characterized and found to be identical with CI2 from barley. Slow-binding kinetics were observed for the interaction between CI2 and subtilisin BPN', with Ki = 2.9 x 10(-12) M. Analysis of slow-binding data indicates that binding of the inhibitor follows the simplest model of E + I = EI with no kinetically detectable intermediate steps or proteolytic cleavage of the reactive site bond in CI2 (Met-59-Glu-60). This, in agreement with crystallographic data, indicates that the enzyme-inhibitor adduct is the Michaelis complex, which is not chemically processed by the enzyme. Three mutant CI2 molecules with new P1 residues have also been examined with a range of serine proteases, including a mutant subtilisin. In agreement with earlier studies, we find the P1 amino acid an important determinant of specificity. CI2 Met----Lys-59 was found to be a temporary inhibitor of subtilisin BPN' but an effective inhibitor of subtilisin Carlsberg and subtilisin BPN'(Glu----Ser-156). The structural reasons for this are discussed in relation to mechanisms of inhibition of serine proteases.