gebhart/patrepeval huggingface dataset:
Evaluation and calibration of a fluorescence-activated cell sorter for the interpretation of the granulocyte immunofluorescence test (GIFT) (1989)

The increasing availability of fluorescence-activated cell sorters (FACS) and flow cytometers makes it reasonable to consider the routine use of these machines for the evaluation of the granulocyte immunofluorescence test (GIFT). A comparison of microscopic reading and FACS reading of the standard GIFT demonstrated equivalent simplicity, specificity, sensitivity, reproducibility and duration of test procedure. Differentiation of a negative GIFT from a weakly positive GIFT using the FACS reading method was, however, made difficult by considerable variation in background fluorescence for different neutrophil donors. However, we demonstrate that the FACS reading method was superior for the interpretation of immunofluorescence on chloroquine-treated neutrophils used in the differentiation of HLA from neutrophil-specific antibodies. The systematic study highlighted the fact that any laboratory contemplating conversion from microscopic reading of the GIFT should carefully evaluate and standardize their interpretation of FACS results with their manual reference method.
Effect of a Polymer Cushion on the Electrical Properties and Stability of Surface-Supported Lipid Bilayers (2009)

A robust biomimetic cell membrane platform is critical for mechanistic studies of membrane protein channels. While polymer cushions are believed to facilitate the incorporation of membrane proteins in such a platform, a systematic characterization and optimization of such cushions is rarely performed. Here, we examine the influence of a polymer cushion on the electrical properties of supported 1,2-diphytanoyl-sn-glycero-3-phosphocholine (DPhPC) bilayers produced via a Langmuir-Blodgett deposition/vesicle fusion assembly process on single-crystal silicon. We show that the resistance of DPhPC bilayers is maximized at the calculated crossover concentration of the polymer (5.9 mol % PEG-lipids). Additionally, these bilayers are sufficiently stable to allow impedance analyses to be performed for nearly 3 weeks. These studies reveal the optimal PEG concentration that yields electrically robust bilayers and demonstrate the utility of the platform for future studies of membrane protein channels and membrane active peptides.
<i>Salmonella</i> type III secretion‐associated chaperones confer secretion‐pathway specificity (2004)

Type III protein secretion systems (TTSSs) are ancestrally related to the flagellar export system and are essential for the virulence of many bacteria pathogenic for humans, animals and plants. Most proteins destined to travel the TTSS pathway possess at least two domains that specifically target them to the secretion apparatus. One of the domains is located within the amino terminal first approximately 20 amino acids and the second domain, located within the first approximately 140 amino acids, serves as a binding site for specific chaperones. It has been previously proposed that these two secretion signals are capable of operating independently of one another to facilitate secretion into the extracellular environment. We have found that in the absence of their chaperone-binding domains, the Salmonella typhimurium TTSS-secreted proteins SptP and SopE are no longer targeted for secretion through their cognate TTSS and, instead, are secreted through the flagellar export pathway. These results indicate the existence of an 'ancestral' flagellar secretion signal within TTSS-exported proteins that is revealed in the absence of the chaperone-binding domain. Furthermore, we found that secretion into culture supernatants as well as translocation into host cells by the cognate TTSS require both, the amino terminal and chaperone-binding domains. We conclude from these studies that a critical function for the TTSS-associated chaperones is to confer secretion-pathway specificity to their cognate secreted proteins.
Strictly aerobic and anaerobic bacteria associated with sinking particulate matter and zooplankton fecal pellets (1992)

Particulate material collected in sediment traps at 80 m depth in coastal northwestern Mediterranean waters, and fresh fecal pellets of copepods harvested in the surrounding water, were examined for the presence and activity of ammonia-oxidizing and methanogenic bacteria. Results provide the first evidence for the coexistence of living and active cells of methanogenic and nitrifying bac- teria in either fresh zooplankton fecal pellets or large settling particles containing numerous large size fecal pellets. In addition, the presence of these 2 bacterial types in both copepods and the fecal pellets produced by them suggests that the bacteria probably originate from the digestive tract of zooplankton, most likely as ingested species for nitrifiers and enteric species for methanogens.
Nanosized Films Based on Multicharged Small Molecules and Oppositely Charged Polyelectrolytes Obtained by Simultaneous Spray Coating of Interacting Species (2013)

Simultaneous spraying of polyelectrolytes and small multicharged molecules of opposite charges onto a vertical substrate leads to continuous buildups of organic films. Here, we investigate the rules governing the buildup of two such systems: poly(allylamine hydrochloride)/sodium citrate (PAH/citrate) and PAH/sulfated α-cyclodextrin (PAH/CD-S). Special attention is paid to the film growth rate as a function of the spraying rate ratio of the two constituents. This parameter was varied by increasing the spraying rate of one of the constituents while maintaining constant that of the other. For PAH/CD-S systems, whatever the constituent (PAH or CD-S) whose spraying rate was kept fixed, the film growth rate first increases and passes through a maximum before decreasing when the spraying rate of the other constituent is increased. For PAH/citrate, the film growth rate reaches a plateau value when the spraying rate of citrate is increased while that of PAH is maintained constant, whereas when the spraying rate of citrate is maintained constant and that of PAH is increased, a behavior similar to that of PAH/CD-S is observed. The composition of PAH/CD-S sprayed films determined by X-ray photoelectron spectroscopy is independent of the spraying rate ratio of the two constituents and corresponds to one allylamine for one sulfate group. For PAH/citrate, by increasing the PAH/citrate spraying rate ratio, the carboxylic/nitrogen ratio in the film increases and tends to 1. There is thus always a deficit of carboxylic groups (COO(-) + COOH) with respect to amines (NH2 + NH3(+)). Yet, the ratio (COO(-)/NH3(+)) is always close to 1, ensuring exact charge compensation. The film morphology determined by atomic force microscopy is granular for PAH/CD-S and is smooth and liquid-like for PAH/citrate. A model based on strong (respectively weak) interactions between PAH and CD-S (respectively citrate) is proposed to explain these features.
Evaluating the Genetic Component of Ischemic Stroke Subtypes (2003)

A family history of vascular disease is an independent risk factor for both large-vessel atherosclerosis and small-vessel disease, especially in cases presenting before age 65 years. The estimated sample sizes for case-control studies illustrate how candidate gene studies for ischemic stroke might be made more effective by focusing on these specific phenotypes, in which the genetic component of the disease appears to be strongest.
Mast cells: A possible link between psychological stress, enteric infection, food allergy and gut hypersensitivity in the Irritable Bowel syndrome (1998)

Intestinal mast cell activation (degranulation), which results from previous enteric infection and/or intestinal allergy, may play a central role in the gut hypersensitivity in both motor response and visceral perception in the Irritable Bowel syndrome. This occurs through various mediators acting on enteric neurons and smooth muscle cells. Psychological stress may trigger this sensitive alarm system via the brain-gut axis.
Plasmid-mediated transformation of Streptococcus mutans (1982)

Streptococcus mutans GS-5 was transformed to erythromycin resistance with streptococcal plasmid pVA736. Transformation frequencies were higher with plasmids reisolated from transformed GS-5 cells relative to plasmid originally derived from S. sanguis Challis.
Treatment of epilepsy by stimulation of the vagus nerve (1993)

We treated 14 patients with medically refractory partial seizures by stimulation of the vagus nerve in two single-blind pilot studies. Patients received stimulation through an implantable, programmable NeuroCybernetic Prosthesis, consisting of a pulse generator and a lead-electrode assembly. The mean reduction in seizure frequency after 14 to 35 months of vagal stimulation was 46.6%. Of the 14 patients, five (35.7%) had a 50% or greater reduction in seizure frequency. Two patients, one of whom had had 10 to 100 seizures per day before stimulation, have been seizure-free for over 1 year. Adverse events were primarily limited to initial hoarseness and a tingling sensation at the electrode site in the neck when the device was activated. Most patients tolerated the device and stimulation well. There were no permanent adverse events. Some cases of medically refractory partial seizures are improved by vagal stimulation.
Scheduling of near-future workload in distributed computing systems (2002)

A major issue in distributed computing systems is the choice of an adequate load balancing policy. 'Traditional' load balancing policies assign independent tasks to servers, while scheduling policies assume complete knowledge of task dependencies and treat the assignment problem as a large search problem. However, both approaches are based on assumptions that do not hold in distributed computing systems: the job context of tasks exists and thus dependencies between tasks, but they cannot be predicted a long time in advance. In this paper, a dynamic decentralized load balancing policy is introduced that utilizes neat-future workload predictions based on knowledge about the job context. A performance evaluation by simulation and a comparison to widely used load balancing policies is presented.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Biotransformation of Unsaturated Long-Chain Fatty Acids by <i>Eubacterium lentum</i> (1986)

Eubacterium lentum (33 strains) isomerized the 12-cis double bond of C(18) fatty acids with cis double bonds at C-9 and C-12 into an 11-trans double bond before reduction of the 9-cis double bond. The 14-cis double bond of homo-gamma-linolenic acid was isomerized by 29 strains into a 13-trans double bond. The same strains isomerized the 14-cis double bond of arachidonic acid into a 13-trans double bond and then isomerized the 8-cis double bond into a 7-trans double bond; the 13-cis double bond of 10-cis, 13-cis-nonadecadienoic acid was isomerized into a 12-trans double bond. None of these isomerization products was further reduced. Studies with resting cells showed optimal isomerization velocity at a linoleic acid concentration of 37.5 muM; higher concentrations were inhibitory. The pH optimum for isomerization was 7.5 to 8.5. The isomerase was inhibited by the sulfhydryl reagents iodoacetamide, bromoacetate, and N-ethylmaleimide and by the chelators EDTA and 1,10-phenanthroline.
Adenovirus-mediated gene transfer in the ovine pituitary gland is associated with hypophysitis (2002)

Gene therapy for pituitary disease requires evaluation for safety as well as efficacy. We have reported results of adenovirus-mediated gene transfer using the sheep as a large animal model that allows longitudinal evaluation of hormone secretion and have confirmed high levels of transgene expression up to 7 days after direct stereotaxic injection into the pituitary gland. Here we report the results of detailed histological examination of the pituitary glands from animals injected with two recombinant adenoviruses expressing the beta-galactosidase marker gene, or with saline vehicle to control for the potential tissue-disruptive effect of the injection volume itself. Pituitaries injected with saline showed no evidence of inflammatory response apart from occasional minor foci of apoptosis. In all other respects they were indistinguishable from normal uninjected control pituitary glands. Glands injected with recombinant adenoviruses containing either the hCMV-beta-gal or the hPRL-beta-gal transgene, on the other hand, displayed variable degrees of inflammatory response, with periglandular fibrosis, lymphocytic infiltrate and venulitis in almost all cases. Focal necrosis and/or apoptosis was noted in six of nine cases. In summary, we have found evidence of severe inflammatory reaction within the first seven days of adenovirus injection, amounting to significant hypophysitis. The histological extent of this reaction has not previously been recognised by studies of the efficacy of gene transfer in rodents, and was underestimated by immunocytochemical studies of hormone and transgene expression. The findings emphasise the need for careful evaluation of the safety of endocrine gene therapy, and for caution with the dose of vector used.
Phencyclidine: behavioral and biochemical evidence supporting a role for dopamine. (1983)

Pharmacological studies of phencyclidine (PCP)-induced behaviors such as stereotypy and turning suggest that PCP is an indirectly acting dopamine (DA) agonist with some anticholinergic potential. In vitro studies show that PCP is a potent, competitive inhibitor of monoamine uptake. PCP has also been shown to stimulate synaptosomal striatal tyrosine hydroxylase activity via a release of DA (which normally inhibits this enzyme). The mechanism by which PCP releases DA is unknown, but is similar to that of methylphenidate and distinct from that of amphetamine. In vivo studies also show similarities between PCP and the nonamphetamine class of stimulants. For example, PCP and amfonelic acid, but not amphetamine, potentiate haloperidol-induced DA metabolism. This effect can be blocked by baclofen, which suggests a dependence on nigrostriatal impulse flow. Other studies suggest that PCP releases a pool of DA that is in rapid equilibrium with the vesicular compartment, thereby activating a feedback mechanism (probably transsynaptic) that inhibits the synthesis of DA. Despite the similarities between PCP and nonamphetamine stimulants, there are both behavioral and biochemical anomalies that caution against the strict classification of PCP as a nonamphetamine stimulant.
Self-defined AlAs-oxide–current-aperture buried heterostructure vertical cavity surface-emitting laser (1998)

We demonstrate a promising technique to fabricate self-defined AlAs-oxide–current-apertures for vertical cavity surface-emitting lasers (VCSELs). A self-defined AlAs-oxide–current-aperture buried heterostructure VCSEL was fabricated using a three-step growth sequence. The active region mesa size was 10 μm×10 μm. The lowest threshold current of the lasers was 0.7 mA under continuous-wave operation at room temperature. The differential quantum efficiency was 32%. The lasers operate at temperatures of up to 50 °C.
SecA2 functions in the secretion of superoxide dismutase A and in the virulence of <i>Mycobacterium tuberculosis</i> (2003)

Tuberculosis remains a severe worldwide health threat. A thorough understanding of Mycobacterium tuberculosis pathogenesis will facilitate the development of new treatments for tuberculosis. Numerous bacterial pathogens possess specialized protein secretion systems that are dedicated to the export of virulence factors. Mycobacterium tuberculosis is part of a developing group of pathogenic bacteria that share the uncommon property of possessing two secA genes (secA1 and secA2). In mycobacteria, SecA1 is the essential 'housekeeping' SecA protein whereas SecA2 is an accessory secretion factor. Here we demonstrate that SecA2 contributes to the pathogenesis of M. tuberculosis. A deletion of the secA2 gene in M. tuberculosis attenuates the virulence of the organism in mice. By comparing the profile of proteins secreted by wild-type M. tuberculosis and the DeltasecA2 mutant, we identified superoxide dismutase A (SodA) as a protein dependent on SecA2 for secretion. SodA lacks a classical signal sequence for protein export. Our data suggests that SecA2-dependent export is a new type of secretion pathway that is part of a virulence mechanism of M. tuberculosis to elude the oxidative attack of macrophages.
Listen (on the frequency domain) before you talk (2010)

Conventional WiFi networks perform channel contention in time domain. This is known to be wasteful because the channel is forced to remain idle, while all contending nodes are backing off for multiple time slots. This paper proposes to break away from convention and recreate the backing off operation in the frequency domain. Our basic idea is to pretend that OFDM subcarriers are integer numbers, and thereby, view today's random backoff process as equivalent to transmitting on a randomly chosen subcarrier. By employing a second antenna to listen to all the subcarriers, each node can determine whether its chosen integer (or subcarrier) is the smallest among all others. In fact, each node can even determine the rank of its chosen integer, enabling the feasibility of a TDMA-like schedule from every round of contention. We develop these ideas into a Time to Frequency (T2F) protocol and prototype it on a small testbed of 8 USRPs. Experiments confirm its feasibility, along with promising throughput gains of more than 35% at high bit rates. A fuller design and thorough evaluation of T2F is a topic of ongoing work.
CD11b/CD18 mediates the neutrophil chemotactic activity of fibrin degradation product D domain. (1997)

Coagulation and fibrinolysis universally accompany tissue injury and repair. The accumulation of regionally generated fibrin degradation products (FDP) may modify the local inflammatory response. We have found FDP to be potent neutrophil chemotaxins. We separated plasmin FDP by chromatofocusing and found chemotactic activity limited to fractions containing the fibrinogen D domain (D-D dimer and D monomer). The bioactivity of the D-D dimer did not require an intact cross link site as removal of this sequence with puff adder venom or hypocalcemic plasmic digestion did not decrease chemotaxis. Peptide inhibition studies confirmed that the chemotactic region did not involve terminal gamma chain sequences or alpha chain RGD motifs. The internal gamma chain peptide KYGWTVFQKRLDGSV (P1), known to bind CD11b/CD18, exhibited concentration dependent chemotactic activity. Similarly, monoclonal antibodies directed against CD11b/CD18 blocked PMN migration to FDP without similar inhibition of chemotaxis to IL-8 or LTB4. Thus, neutrophil chemotaxis to FDP is mediated by interactions between the fibrinogen D domain and CD11b/CD18.
Surface gate and contact alignment for buried, atomically precise scanning tunneling microscopy–patterned devices (2007)

The authors have developed a complete electron beam lithography (EBL)-based alignment scheme for making multiterminal Ohmic contacts and gates to buried, planar, phosphorus-doped nanostructures in silicon lithographically patterned by scanning tunneling microscopy (STM). By prepatterning a silicon substrate with EBL-defined, wet-etched registration markers, they are able to align macroscopic contacts to buried, conducting STM-patterned structures with an alignment accuracy of ∼100nm. A key aspect of this alignment process is that, by combining a circular marker pattern with step engineering, they are able to reproducibly create atomically flat, step-free plateaus with a diameter of ∼300nm so that the active region of the device can be patterned on a single atomic Si(100) plane at a precisely known position. To demonstrate the applicability of this registration strategy, they show low temperature magnetoresistance data from a 50nm wide phosphorus-doped silicon nanowire that has been STM-patterned onto a single atomically flat terrace.
Automated Facial Expression Measurement: recent Applications to Basic Research in Human Behavior, Learning, and Education (2011)

Automatic facial expression recognition has now advanced to the point that we are able to apply it to spontaneous expressions. The automated tools enable new research activity in cognitive neuroscience, psychiatry, education, human–machine communication, and human social dynamics. Moreover, automated facial expression analysis enables investigations into facial expression dynamics that were previously intractable by human coding because of the time required to code intensity changes. This article provides an overview on the state of the art in computer vision approaches to facial expression recognition, including methods for characterizing expression dynamics. It then discusses behavioral studies that have employed automatic facial expression recognition to learn new information about the relationships of facial expression to internal state, and reviews the first generation of applications in learning and education that take advantage of the real-time expression signal.
The Nature and Evaluation of Commercial Expert System Building Tools (1987)

This memorandum reviews the factors that constitute an Expert System Building Tool (ESBT) and evaluates current tools in terms of these factors. Evaluation of these tools is based on their structure and their alternative forms of knowledge representation, inference mechanisms and developer/end-user interfaces. Next, functional capabilities, such as diagnosis and design, are related to alternative forms of mechanization. The characteristics and capabilities of existing commercial tools are then reviewed in terms of these criteria.
Architectural-level risk analysis using uml (2003)

Risk assessment is an essential part in managing software development. Performing risk assessment during the early development phases enhances resource allocation decisions. In order to improve the software development process and the quality of software products, we need to be able to build risk analysis models based on data that can be collected early in the development process. These models will help identify the high-risk components and connectors of the product architecture, so that remedial actions may be taken in order to control and optimize the development process and improve the quality of the product. In this paper, we present a risk assessment methodology which can be used in the early phases of the software life cycle. We use the Unified Modeling Language (UML) and commercial modeling environment Rational Rose Real Time (RoseRT) to obtain UML model statistics. First, for each component and connector in software architecture, a dynamic heuristic risk factor is obtained and severity is assessed based on hazard analysis. Then, a Markov model is constructed to obtain scenarios risk factors. The risk factors of use cases and the overall system risk factor are estimated using the scenarios risk factors. Within our methodology, we also identify critical components and connectors that would require careful analysis, design, implementation, and more testing effort. The risk assessment methodology is applied on a pacemaker case study.