gebhart/patrepeval huggingface dataset:
Engineering of the Pyruvate Dehydrogenase Bypass inSaccharomyces cerevisiae: Role of the Cytosolic Mg2+and Mitochondrial K+Acetaldehyde Dehydrogenases Ald6p and Ald4p in Acetate Formation during Alcoholic Fermentation (2000)

Acetic acid plays a crucial role in the organoleptic balance of many fermented products. We have investigated the factors controlling the production of acetate by Saccharomyces cerevisiae during alcoholic fermentation by metabolic engineering of the enzymatic steps involved in its formation and its utilization. The impact of reduced pyruvate decarboxylase (PDC), limited acetaldehyde dehydrogenase (ACDH), or increased acetoacetyl coenzyme A synthetase (ACS) levels in a strain derived from a wine yeast strain was studied during alcoholic fermentation. In the strain with the PDC1 gene deleted exhibiting 25% of the PDC activity of the wild type, no significant differences were observed in the acetate yield or in the amounts of secondary metabolites formed. A strain overexpressing ACS2 and displaying a four- to sevenfold increase in ACS activity did not produce reduced acetate levels. In contrast, strains with one or two disrupted copies of ALD6, encoding the cytosolic Mg(2+)-activated NADP-dependent ACDH and exhibiting 60 and 30% of wild-type ACDH activity, showed a substantial decrease in acetate yield (the acetate production was 75 and 40% of wild-type production, respectively). This decrease was associated with a rerouting of carbon flux towards the formation of glycerol, succinate, and butanediol. The deletion of ALD4, encoding the mitochondrial K(+)-activated NAD(P)-linked ACDH, had no effect on the amount of acetate formed. In contrast, a strain lacking both Ald6p and Ald4p exhibited a long delay in growth and acetate production, suggesting that Ald4p can partially replace the Ald6p isoform. Moreover, the ald6 ald4 double mutant was still able to ferment large amounts of sugar and to produce acetate, suggesting the contribution of another member(s) of the ALD family.
PORTABLE WATER MlST FIRE EXTINGUISHERS AS AN ALTERNATIVE FOR HALON 1211 (2001)

The National Research Council of Canada, with Fountain Fire Protection, Inc., has carried out a series of full-scale fire tests to investigate the capability and limitation of portable water mist extinguishers as an alternative for Halon 121 1 in suppressing various types of fires. The types of fires used in the tests included cooking oils, n-heptanes, diesel fuels, and wood cribs. The impact of key water mist characteristics, such as flow rate, spray angle and droplet size, discharge pressures, nozzle discharge angles, as well as the types of nozzles on fire suppression, was studied. Based on this study, a prototype water mist fire extinguisher for multi-purpose fire protection was developed for use on fires associated with cooking oils, woods, papers, flammable fuels, and electrical equipment.
Classification of Citrobacteria by DNA Hybridization: Designation of Citrobacter farmeri sp. nov., Citrobacter youngae sp. nov., Citrobacter braakii sp. nov., Citrobacter werkmanii sp. nov., Citrobacter sedlakii sp. nov., and Three Unnamed Citrobacter Genomospecies (1993)

DNA relatedness studies (hydroxyapatite method) were done on 112 strains of citrobacteria. By using the recommended definition of a genomospecies 11 genomospecies were identified in the genus Citrobacter. These genomospecies were separable by their biochemical profiles. Citrobacter koseri (Citrobacter diversus) and Citrobacter amalonaticus proved to be homogeneous species, as previously described. C. amalonaticus biogroup 1, as described by Farmer et al. (J. Clin. Microbiol. 21:46-76, 1985), was shown to be a separate homogeneous species, which was named Citrobacter farmeri sp. nov. The Citrobacter freundii complex was quite heterogeneous. C. freundii sensu stricto, as represented by the type strain, contained only 9 of 66 strains in this complex. The remaining 57 strains were members of seven genomospecies. Genomospecies 5, containing 21 strains, was named Citrobacter youngae sp. nov. Genomospecies 6, containing 15 strains, was named Citrobacter braakii sp. nov. Genomospecies 7 and 8, each containing six strains, were named Citrobacter werkmanii sp. nov. and Citrobacter sedlakii sp. nov., respectively. Genomospecies 9, 10, and 11, each containing three strains, were not named.
Concise Synthesis and Structure−Activity Relationships of Combretastatin A-4 Analogues, 1-Aroylindoles and 3-Aroylindoles, as Novel Classes of Potent Antitubulin Agents (2004)

The synthesis and study of the structure-activity relationships of two new classes of synthetic antitubulin compounds based on 1-aroylindole and 3-aroylindole skeletons are described. Lead compounds 3, 10, and 14 displayed potent cytotoxicities with IC50 = 0.9-26 nM against human NUGC3 stomach, MKN45 stomach, MESSA uterine, A549 lung, and MCF-7 breast carcinoma cell lines. The inhibition of proliferation correlated with in vitro polymerization inhibitory activities. Structure-activity relationships revealed that 6-methoxy substitution of 3-aroylindoles and 5-methoxy substitution of 1-aroylindoles contribute to a significant extent for maximal activity by mimicking the para substitution of the methoxy group to the carbonyl group in the case of aminobenzophenones. Addition of a methyl group at the C-2 position on the indole ring exerts an increased potency. The 3,4,5-trimethoxybenzoyl moiety was necessary for better activity but not essential and can be replaced by 3,5-dimethoxybenzoyl and 3,4,5-trimethoxybenzyl moieties. We conclude that 1- and 3-aroylindoles constitute an interesting new class of antitubulin agents with the potential to be clinically developed for cancer treatment.
A new algorithm for non-rigid point matching (2002)

We present a new robust point matching algorithm (RPM) that can jointly estimate the correspondence and non-rigid transformations between two point-sets that may be of different sizes. The algorithm utilizes the soft assign for the correspondence and the thin-plate spline for the non-rigid mapping. Embedded within a deterministic annealing framework, the algorithm can automatically reject a fraction of the points as outliers. Experiments on both 2D synthetic point-sets with varying degrees of deformation, noise and outliers, and on real 3D sulcal point-sets (extracted from brain MRI) demonstrate the robustness of the algorithm.
Testosterone for Low Libido in Postmenopausal Women Not Taking Estrogen (2008)

In postmenopausal women not receiving estrogen therapy, treatment with a patch delivering 300 microg of testosterone per day resulted in a modest but meaningful improvement in sexual function. The long-term effects of testosterone, including effects on the breast, remain uncertain. (ClinicalTrials.gov number, NCT00131495.)
Differential susceptibility of a rat glioma cell line and its clones to herpes simplex virus types 1 and 2. (1991)

A rat glioma cell line, C6-BU-1, showed differential susceptibility to herpes simplex virus type 1 (HSV-1) and type 2 (HSV-2), namely, all the HSV-1 strains tested so far persisted in this cell line but the HSV-2 strains did not. Two clones were derived from C6-BU-1 cells and designated C-17 and C-72. The C-72 as well as the parental C6-BU-1 cells supported the replication of HSV-1, but not that of HSV-2. In contrast, C-17 was highly resistant to both HSV-1 and HSV-2. Hydrocortisone treatment converted C-17 to being susceptible to HSV-1, but not to HSV-2. Therefore, C6-BU-1 cells consist of subpopulations heterogeneous in susceptibility to HSV-1 which may be possibly interchangeable.
Chronic Obstructive Pulmonary Disease (2011)

Abstract Chronic obstructive pulmonary disease is a group of conditions characterised by the presence of persistent airflow obstruction during expiration, primarily owing to narrowing of the smaller airways. Its prevalence is increasing and soon it will be the third most common cause of illness and death worldwide. The condition is a slowly progressive one punctuated by acute episodes of deterioration (exacerbations) and there is currently no specific therapy confirmed to slow the progression. The underlying pathophysiology is believed to be uncontrolled inflammation owing to a combination of genetic and environmental factors. Although classically associated with smoking, increasing pollution in the industrialised world and the burning of biomass fuels indoors in the third world also influences its prevalence. Key Concepts: COPD is a group of conditions in which airflow obstruction cannot be fully reversed. The pathophysiology is owing to uncontrolled inflammation in the lung. COPD is associated with an increased risk of co‐morbidities such as arteriosclerosis, type II diabetes and osteoporosis probably as a result of common inflammatory processes. Thoracic imaging is being increasingly used to identify different pathological processes that contribute to COPD. Large clinical trials of inhaled therapy have demonstrated a reduction in the number of acute episodes of deterioration and possibly mortality.
Context-aware middleware for mobile multimedia applications (2004)

We present a context-aware middleware for mobile multimedia applications. The middleware offers functionality for service discovery, asynchronous messaging, publish/subscribe event management, storing and management of context information, building the user interface, and handling the local and network resources. It supports a wide range of context information including location, time, and user's preferences. Further, it allows controlling the connectivity of the device; the middleware is capable of switching traffic from one network connection to another. It can locate the services and software components as well. It facilitates development of multimedia applications by handling such functions as capture and rendering, storing, retrieving and adapting of media content to various mobile devices. The middleware offers facilities for media alerts, which are multimedia messages that are generated when predefined context is recognized. With these capabilities, it enables development of complex context-aware multimedia applications for mobile devices.
Technetium-99m radiolabeling using a phage-derived single-chain Fv with a C-terminal cysteine. (1996)

Our study demonstrates an effective method to enable scFvs radiolabeling with 99mTc and also shows the potential of using a 99mTc-labeled scFv for clinical imaging studies.
Tropical Canine Pancytopenia: in Vitro Cultivation of the Causative Agent—Ehrlichia canis (1971)

SUMMARY Ehrlichia canis , causative agent of tropical canine pancytopenia ( tcp ), has been propagated in monocyte cell cultures derived from the blood of dogs acutely infected with this agent. Tissue culture medium consisted of Eagle's minimum essential medium supplemented with 20% canine serum. Results of microscopic examination of monolayers stained by Giemsa and fluorescent antibody ( fa ) methods indicated that the intracytoplasmic ehrlichia underwent a specific cycle of development. Principal developmental forms were elementary bodies (individual ehrlichia organisms), initial bodies (immature organismal inclusions), and morulae (mature organismal inclusions). Five dogs each inoculated with 2- to 8-ml. volumes of cell culture suspensions harvested on days 5, 7, 20, 23, and 28 of incubation developed signs of tcp . The organism was reisolated from these dogs. Because developmental cycle of ehrlichia demonstrated in the present study closely resembled that of the agents belonging to psittacosis-lymphogranuloma venereum ( plv ) group of agents, and because the latter agents have also been found in ticks, reclassification of the agent from family Rickettsiaceae to family Chlamydiaceae has been suggested. This work is considered a significant prerequisite for assays of fundamental properties of the organism, and it has all the essentials which would allow development of immunizing and diagnostic reagents for tcp .
Microbial symbionts: a resource for the management of insect‐related problems (2011)

Microorganisms establish with their animal hosts close interactions. They are involved in many aspects of the host life, physiology and evolution, including nutrition, reproduction, immune homeostasis, defence and speciation. Thus, the manipulation and the exploitation the microbiota could result in important practical applications for the development of strategies for the management of insect-related problems. This approach, defined as 'Microbial Resource Management' (MRM), has been applied successfully in various environments and ecosystems, as wastewater treatments, prebiotics in humans, anaerobic digestion and so on. MRM foresees the proper management of the microbial resource present in a given ecosystem in order to solve practical problems through the use of microorganisms. In this review we present an interesting field for application for MRM concept, i.e. the microbial communities associated with arthropods and nematodes. Several examples related to this field of applications are presented. Insect microbiota can be manipulated: (i) to control insect pests for agriculture; (ii) to control pathogens transmitted by insects to humans, animals and plants; (iii) to protect beneficial insects from diseases and stresses. Besides, we prospect further studies aimed to verify, improve and apply MRM by using the insect-symbiont ecosystem as a model.
Genetic and Cytogenetic Variation in Plants Regenerated from Organogenic and Friable, Embryogenic Tissue Cultures of Maize (1988)

Recent advances in maize( Zea mays L.) tissue culture methods permit reproducible establishment of rapid‐growing, friable, embryogenic (Type‐II) cultures from some genotypes. Although Type‐II cultures have replaced the more common Type‐I (relatively compact, organogenic) cultures for many applications, little information is available concerning somaclonal variation in plants regenerated from Type‐II cultures. This study was conducted to determine the relative frequency of genetic and cytogenetic variants in plants regenerated from Type‐I compared to Type‐II maize tissue cultures. Type‐I and Type‐II cultures were initiated from immature embryos of the inbred line A188, A188‐BC6 lines containing various genetic markers, and segregating progenies of an A188/B73 genetic background. Plants were regenerated 16 and 36 wk after culture initiation and were analyzed for pollen sterility, cytological abnormalities, and phenotypic variants in progeny generations. After 16 wk in culture, 33.3 and 20.8% of the regenerants from Type‐II and Type‐I cultures, respectively, possessed at least one abnormality. These values increased to 37.2 (Type‐II) and 24.2% (Type‐I) after 36 wk in culture. As expected, the frequency of chimeric plants was lower from Type‐II than from Type‐I cultures: however, culture age had a larger effect on the frequency of chimeric plants than culture type. Although reduced compared to Type‐I cultures, the frequency of chimerism in regenerants from Type‐II cultures was still quite high, ranging from 9.4 to 50.0% of the variant regenerants. The results demonstrate that genetic and cytogenetic abnormalities are frequently recovered in plants regenerated from both organogenic and friable, embryogenic maize tissue cultures.
Inverse Dynamics of Flexible Robot Arms: Modeling and Computation for Trajectory Control (1990)

The inverse dynamics of robot manipulators based on flexible arm models are considered. Actuator torques required for a flexible arm to track a given trajectory are formulated and computed by using special moving coordinate systems, called virtual rigid link coordinates. Dynamic deformations of the flexible arm can be represented in a simple and compact form with use of the virtual coordinate systems. This eliminates a number of terms involved in the equations of motion and significantly reduces complexity in the inverse dynamics computation. An efficient algorithm for computing the actuator torques is then presented on the basis of the simplified formulation, and applied to a two-link arm problem.
Signaling Pathways for Tumor Necrosis Factor-α and Interleukin-6 Expression in Human Macrophages Exposed to Titanium-Alloy Particulate Debris in Vitro* (1999)

These data suggest that particle induced macrophage release of TNF-alpha and IL-6 does not require phagocytosis but is dependent on tyrosine and serine/threonine kinase activity culminating in activation of
Paclitaxel and docetaxel in the treatment of breast cancer (2008)

Based on existing evidence, clinicians should choose a taxane-based regimen for their patients, according to clinical activity, toxicity profile, pharmacokinetics, and a dosing schedule that best meets the therapeutic needs and convenience.
Optimization of methods to achieve mRNA-mediated transfection of tumor cells in vitro and in vivo employing cationic liposome vectors. (1994)

Direct in vivo transfection of tumor nodules in situ via liposome-DNA complexes has been employed as a strategy to accomplish antitumor immunization. To circumvent the potential safety hazards associated with systemic localization of delivered DNA, the utility of mRNA transcript-mediated gene delivery was explored. Capped, polyadenylated mRNA transcripts encoding the firefly luciferase and Escherichia coli lacZ reporter genes were derived by in vitro transcription. Transfection of the human breast cancer cell line MDA-MB-435 in vitro was accomplished employing cationic liposome-mRNA complexes. Evaluation of a panel of cationic liposome preparations demonstrated significant differences in the capacity of the various preparations to accomplish mRNA-mediated transfection. Quantitative evaluation of in vitro transfection demonstrated that target cells could be transfected at a high level of efficiency. The mRNA liposome-complexes were evaluated for in vivo transfection of tumor nodules in human xenografts in athymic nude mice. It could be demonstrated the liposome-mRNA complexes were comparable in efficacy to liposome-DNA complexes in accomplishing in situ tumor transfection. Thus, mRNA may be considered as an alternative to plasmid DNA as a gene transfer vector for genetic immunopotentiation applications.
Discovery of Two Bacterial Nitric Oxide-Responsive Proteins and Their Roles in Bacterial Biofilm Regulation (2017)

Bacterial biofilms form when bacteria adhere to a surface and produce an exopolysaccharide matrix ( Costerton Science 1999 , 284 , 1318 ; Davies Science 1998 , 280 , 295 ; Flemming Nat. Rev. Microbiol. 2010 , 8 , 623 ). Because biofilms are resistant to antibiotics, they are problematic in many aspects of human health and welfare, causing, for instance, persistent fouling of medical implants such as catheters and artificial joints ( Brunetto Chimia 2008 , 62 , 249 ). They are responsible for chronic infections in the lungs of cystic fibrosis patients and in open wounds, such as those associated with burns and diabetes. They are also a major contributor to hospital-acquired infections ( Sievert Infec. Control Hosp. Epidemiol. 2013 , 34 , 1 ; Tatterson Front. Biosci. 2001 , 6 , D890 ). It has been hypothesized that effective methods of biofilm control will have widespread application ( Landini Appl. Microbiol. Biotechnol. 2010 , 86 , 813 ). A promising strategy is to target the mechanisms that drive biofilm dispersal, because dispersal results in biofilm removal and in the restoration of antibiotic sensitivity. First documented in Nitrosomonas europaea ( Schmidt J. Bacteriol. 2004 , 186 , 2781 ) and the cystic fibrosis-associated pathogen Pseudomonas aeruginosa ( Barraud J. Bacteriol. 2006 , 188 , 7344 ; J. Bacteriol. 2009 , 191 , 7333 ), regulation of biofilm formation by nanomolar levels of the diatomic gas nitric oxide (NO) has now been documented in numerous bacteria ( Barraud Microb. Biotechnol. 2009 , 2 , 370 ; McDougald Nat. Rev. Microbiol. 2012 , 10 , 39 ; Arora Biochemistry 2015 , 54 , 3717 ; Barraud Curr. Pharm. Des. 2015 , 21 , 31 ). NO-mediated pathways are, therefore, promising candidates for biofilm regulation. Characterization of the NO sensors and NO-regulated signaling pathways should allow for rational manipulation of these pathways for therapeutic applications. Several laboratories, including our own, have shown that a class of NO sensors called H-NOX (heme-nitric oxide or oxygen binding domain) affects biofilm formation by regulating intracellular cyclic di-GMP concentrations and quorum sensing ( Arora Biochemistry 2015 , 54 , 3717 ; Plate Trends Biochem. Sci. 2013 , 38 , 566 ; Nisbett Biochemistry 2016 , 55 , 4873 ). Many bacteria that respond to NO do not encode an hnoX gene, however. My laboratory has now discovered an additional family of bacterial NO sensors, called NosP (nitric oxide sensing protein). Importantly, NosP domains are widely conserved in bacteria, especially Gram-negative bacteria, where they are encoded as fusions with or in close chromosomal proximity to histidine kinases or cyclic di-GMP synthesis or phosphodiesterase enzyme, consistent with signaling. In this Account, we briefly review NO and H-NOX signaling in bacterial biofilms, describe our discovery of the NosP family, and provide support for its role in biofilm regulation in Pseudomonas aeruginosa, Vibrio cholerae, Legionella pneumophila, and Shewanella oneidensis.
Systemic Cholinergic Agents Induce Seizures and Brain Damage in Lithium-Treated Rats (1983)

Administration of pilocarpine or physostigmine to rats treated with lithium chloride produced sustained limbic seizures, widespread brain damage, and increased concentrations of D-myo-inositol-1-phosphate (a metabolite of the phosphoinositides, lipids involved in membrane receptor function) in the brain. The syndrome was preventable with atropine. The physostigmine doses and concentrations of blood lithium that caused the syndrome are similar to those considered appropriate for psychiatric chemotherapy.
The Self-Aware Matching Measure for stereo (2009)

We revisit stereo matching functions, a topic that is considered well understood, from a different angle. Our goal is to discover a transformation that operates on the cost or similarity measures between pixels in binocular stereo. This transformation should produce a new matching curve that results in higher matching accuracy. The desired transformation must have no additional parameters over those of the original matching function and must result in a new matching function that can be used by existing local, global and semi-local stereo algorithms without having to modify the algorithms. We propose a transformation that meets these requirements, taking advantage of information derived from matching the input images against themselves. We analyze the behavior of this transformation, which we call Self-Aware Matching Measure (SAMM), on a diverse set of experiments on data with ground truth. Our results show that the SAMM improves the performance of dense and semi-dense stereo. Moreover, as opposed to the current state of the art, it does not require distinctiveness to match pixels reliably.
Microdomains with High Ca 2+ Close to IP 3 -Sensitive Channels that Are Sensed by Neighboring Mitochondria (1993)

Microdomains of high intracellular calcium ion concentration, [Ca2+]i, have been hypothesized to occur in living cells exposed to stimuli that generate inositol 1,4,5-trisphosphate (IP3). Mitochondrially targeted recombinant aequorin was used to show that IP3-induced Ca2+ mobilization from intracellular stores caused increases of mitochondrial Ca2+ concentration, [Ca2+]m, the speed and amplitude of which are not accounted for by the relatively small increases in mean [Ca2+]i. A similar response was obtained by the addition of IP3 to permeabilized cells but not by perfusion of cells with Ca2+ at concentrations similar to those measured in intact cells. It is concluded that in vivo, domains of high [Ca2+]i are transiently generated close to IP3-gated channels and sensed by nearby mitochondria; this may provide an efficient mechanism for optimizing mitochondrial activity upon cell stimulation.