gebhart/patrepeval huggingface dataset:
Propofol in Anesthesia. Mechanism of Action, Structure-Activity Relationships, and Drug Delivery (2000)

Propofol (2,6-diisopropylphenol) is becoming the intravenous anesthetic of choice for ambulatory surgery in outpatients. It is extensively metabolized, with most of the administered dose appearing in the urine as glucuronide conjugates. Favorable operating conditions and rapid recovery are claimed as the main advantages in using propofol, whereas disadvantages include a relatively high incidence of apnea, and blood pressure reductions. Besides a literature summary of the pharmacodynamics, pharmacokinetics, toxicology, and clinical use, this review provides a deeper discussion on the current understanding of mechanism of action and structure-activity relationships, and recent findings on drug delivery technologies as applied to the improvement of propofol formulations. The action of propofol involves a positive modulation of the inhibitory function of the neurotransmitter gama-aminobutyric acid (GABA) through GABAA receptors. Recent results from recombinant human GABAA receptor experiments and findings from the work exploring the effects at other receptors (e.g., glycine, nicotinic, and M1 muscarinic receptors) are reviewed. Studies showing its antiepileptic and anxiolytic properties are also discussed. The structure-activity relationships (SAR) of series of alkylphenols and p-X-substituted congeners have been reinvestigated. Interestingly, unlike the other congeners tested sofar, p-iodo-2,6-diisopropylphenol displayed anticonvulsant and anticonflict effects, but not sedative-hypnotic and anesthetic properties. Due to its high lipid-solubility, propofol was initially formulated as a solution with the surfactant Cremophor EL, but the occurrence of pain on injection and anaphylactoid reactions prompted to search for alternative formulations. Results from using cyclodextrins, water-soluble prodrugs, and adopting Bodor's approach to the site-specific chemical delivery system (CDS), as well as the advantages provided by computer-controlled infusion systems, are examined in some detail.
Efficient genome editing in filamentous fungus Trichoderma reesei using the CRISPR/Cas9 system (2015)

Filamentous fungi have wide applications in biotechnology. The CRISPR/Cas9 system is a powerful genome-editing method that facilitates genetic alterations of genomes in a variety of organisms. However, a genome-editing approach has not been reported in filamentous fungi. Here, we demonstrated the establishment of a CRISPR/Cas9 system in the filamentous fungus Trichoderma reesei by specific codon optimization and in vitro RNA transcription. It was shown that the CRISPR/Cas9 system was controllable and conditional through inducible Cas9 expression. This system generated site-specific mutations in target genes through efficient homologous recombination, even using short homology arms. This system also provided an applicable and promising approach to targeting multiple genes simultaneously. Our results illustrate that the CRISPR/Cas9 system is a powerful genome-manipulating tool for T. reesei and most likely for other filamentous fungal species, which may accelerate studies on functional genomics and strain improvement in these filamentous fungi.
Acetone and Butanol Production by Clostridium acetobutylicum in a Synthetic Medium (1982)

The effect of the component concentrations of a synthetic medium on acetone and butanol fermentation by Clostridium acetobutylicum ATCC 824 was investigated. Cell growth was dependent on the presence of Mg, Fe, and K in the medium. Mg and Mn had deleterious effects when in excess. Ammonium acetate in excess caused acid fermentation. The metabolism was composed of two phases: an acid phase and a solvent one. Low concentrations of glucose allowed the first phase only. The theoretical ratio of the conversion of glucose to solvents, which was 28 to 33%, was obtained with the following medium: MgSO(4), 50 to 200 mg/liter; MnSO(4), 0 to 20 mg/liter; KCl, 0.015 to 8 g/liter (an equivalent concentration of K was supplied in the form of KH(2)PO(4) and K(2)HPO(4)); FeSO(4), 1 to 50 mg/liter; ammonium acetate, 1.1 to 2.2 g/liter; para-aminobenzoic acid, 1 mg/liter; biotin, 0.01 mg/liter; glucose, 20 to 60 g/liter.
Altered regulation of the 5‐HT system in the brain of MAO‐A knock‐out mice (2002)

Genetic deficiency of monoamine oxidase-A (MAO-A) induces major alterations of mood and behaviour in human. Because serotonin (5-HT) is involved in mood regulation, and MAO-A is responsible for the catabolism of 5-HT, we investigated 5-HT mechanisms in knock-out mice (2-month-old) lacking MAO-A, using microdialysis, electrophysiological, autoradiographic and molecular biology approaches. Compared to paired wild-type mice, basal extracellular 5-HT levels were increased in ventral hippocampus (+202%), frontal cortex (+96%) and dorsal raphe nucleus (DRN, +147%) of MAO-A mutant mice. Conversely, spontaneous firing rate of 5-HT neurons in the DRN (recorded under chloral hydrate anaesthesia) was approximately 40% lower in mutants. Acute 5-HT reuptake blockade by citalopram (0.2 and 0.8 mg/kg i.v.) produced a much larger increase in extracellular 5-HT levels (by approximately 4 fold) and decrease in DRN neuronal firing (with a approximately 4.5 fold decrease in the drug's ED50) in MAO-A knock-out mice, which expressed lower levels of the 5-HT transporter throughout the brain (-13 to -34% compared to wild-type levels). The potency of the 5-HT1A agonist 8-OH-DPAT to produce hypothermia and to reduce the firing of DRN serotoninergic neurons was significantly less in the mutants, indicating a desensitization of 5-HT1A autoreceptors. This was associated with a decreased autoradiographic labelling of these receptors (-27%) in the DRN. Altogether, these data indicate that, in MAO-A knock-out mice, the enhancement of extracellular 5-HT levels induces a down-regulation of the 5-HT transporter, and a desensitization of 5-HT1A autoreceptors which allows the maintenance of tonic activity of 5-HT neurons in the DRN.
An architecture for a secure service discovery service (1999)

The widespread deployment of inexpensive communications technology, computational resources in the networking infrastructure, and network-enabled end devices poses an interesting problem for end users: how to locate a particular network service or device out of hundreds of thousands of accessible services and devices. This paper presents the architecture and implementation of a secure Service Discovery Service (SDS). Service providers use the SDS to advertise complex descriptions of available or already running services, while clients use the SDS to compose complex queries for locating these services. Service descriptions and queries use the extensible Markup Language (XML) to encode such factors as cost, performance, location, and device-or service-specific capabilities. The SDS provides a highlyavailable, fault-tolerant, incrementally scalable service for locating services in the wide-area. Security is a core component of the SDS and, where necessary, communications are both encrypted and authenticated.
1/ f noise reduction of metal-oxide-semiconductor transistors by cycling from inversion to accumulation (1991)

A new experimental setup for the study of 1/ f noise of metal-oxide-semiconductor transistor under nonsteady state conditions is presented. The noise measurements demonstrate for the first time that, by interposing periods of negative bias corresponding to accumulation between the monitored periods of positive bias corresponding to inversion, the low-frequency noise sampled in the positive bias intervals is reduced.
Thematic Review Series: Skin Lipids. Peroxisome proliferator-activated receptors and liver X receptors in epidermal biology (2008)

The epidermis is a very active site of lipid metabolism, and all peroxisome proliferator-activated receptor (PPAR) and liver X receptor (LXR) isoforms are expressed in the epidermis. Activation of PPARalpha, -beta/delta, or -gamma or LXRs stimulates keratinocyte differentiation. Additionally, activation of these receptors also improves permeability barrier homeostasis by a number of mechanisms, including stimulating epidermal lipid synthesis, increasing lamellar body formation and secretion, and increasing the activity of enzymes required for the extracellular processing of lipids in the stratum corneum, leading to the formation of lamellar membranes that mediate permeability barrier function. The stimulation of keratinocyte differentiation and permeability barrier formation also occurs during fetal development, resulting in accelerated epidermal development. PPAR and LXR activation regulates keratinocyte proliferation and apoptosis, and studies have shown that these receptors play a role in cutaneous carcinogenesis. Lastly, PPAR and LXR activation is anti-inflammatory, reducing inflammation in animal models of allergic and irritant contact dermatitis. Because of their broad profile of beneficial effects on skin homeostasis, PPAR and LXR have great potential to serve as drug targets for common skin diseases such as psoriasis, atopic dermatitis, and skin cancer.
Nucleotide sequence of a glucosyltransferase gene from Streptococcus sobrinus MFe28 (1987)

The complete nucleotide sequence was determined for the Streptococcus sobrinus MFe28 gtfI gene, which encodes a glucosyltransferase that produces an insoluble glucan product. A single open reading frame encodes a mature glucosyltransferase protein of 1,559 amino acids (Mr, 172,983) and a signal peptide of 38 amino acids. In the C-terminal one-third of the protein there are six repeating units containing 35 amino acids of partial homology and two repeating units containing 48 amino acids of complete homology. The functional role of these repeating units remains to be determined, although truncated forms of glucosyltransferase containing only the first two repeating units of partial homology maintained glucosyltransferase activity and the ability to bind glucan. Regions of homology with alpha-amylase and glycogen phosphorylase were identified in the glucosyltransferase protein and may represent regions involved in functionally similar domains.
<title>Video fingerprinting: features for duplicate and similar video detection and query-based video retrieval</title> (2007)

A video "fingerprint" is a feature extracted from the video that should represent the video compactly, allowing faster search without compromising the retrieval accuracy. Here, we use a keyframe set to represent a video, motivated by the video summarization approach. We experiment with different features to represent each keyframe with the goal of identifying duplicate and similar videos. Various image processing operations like blurring, gamma correction, JPEG compression, and Gaussian noise addition are applied on the individual video frames to generate duplicate videos. Random and bursty frame drop errors of 20%, 40% and 60% (over the entire video) are also applied to create more noisy "duplicate" videos. The similar videos consist of videos with similar content but with varying camera angles, cuts, and idiosyncrasies that occur during successive retakes of a video. Among the feature sets used for comparison, for duplicate video detection, Compact Fourier-Mellin Transform (CFMT) performs the best while for similar video retrieval, Scale Invariant Feature Transform (SIFT) features are found to be better than comparable-dimension features. We also address the problem of retrieval of full-length videos with shorter-length clip queries. For identical feature size, CFMT performs the best for video retrieval.
Unravelling the Mystery of Stem/Progenitor Cells in Human Breast Milk (2010)

The identification of primitive cell types within human breast milk may provide a non-invasive source of relevant mammary cells for a wide-range of applications; even the possibility of banking one's own stem cell for every breastfeeding woman.
Biochemistry and cell biology of bacterial endotoxins (1996)

Endotoxin was first described by Richard Pfeiffer as a heat-stable, cell-associated material isolated from Vibrio cholerue [l] which induced toxic reactions in guinea-pigs. He recognized this material to be clearly distinguishable from the heat-labile exotoxins which are secreted by bacteria. Endotoxin consists of polysaccharides and a lipid part and, therefore, was termed lipopolysaccharide (LPS). Both terms endotoxin and LPS are used for the same molecule and thus represent synonyms. Lipopolysaccharides (LPS; endotoxin) are cellwall constituents of most Gram-negative bacteria [2-41. Despite being essential for bacterial survival, as they shield the bacterium from cellular host defense strategies, bile acids and hydrophobic antibiotics, LPS play a prominent role in the infected host during severe infections, trauma, and shock. The presence of LPS in the bloodstream, as observed during severe Gram-negative, bacterial infections (notably after application of antibiotics) or possibly caused by translocation of enterobacteria from the gut, leads to various pathophysiological reactions such as fever, leukopenia, tachycardia, tachypnoea, hypotension, disseminated intravascular coagulation
Treatment of Passive Experimental Autoimmune Encephalomyelitis in SJL Mice with a Recombinant TCR Ligand Induces IL-13 and Prevents Axonal Injury (2005)

The major goal of this study was to evaluate the efficacy and mechanism of a rTCR ligand (RTL) construct (I-A(s)/proteolipid protein (PLP)-139-151 peptide = RTL401) for treatment of SJL/J mice developing passive experimental autoimmune encephalomyelitis (EAE) that did not involve coimmunization with the highly inflammatory CFA. Our results demonstrated clearly that RTL401 was highly effective in treating passive EAE, with kinetics of recovery from disease very similar to treatment of actively induced EAE. The potent RTL401 treatment effect was reflected by a partial reduction of infiltrating mononuclear cells into CNS, minimal inflammatory lesions in spinal cord, and preservation of axons injured in vehicle-treated mice during the progression of EAE. Interestingly, in the absence of CFA, RTL401 treatment strongly enhanced production of the Th2 cytokine, IL-13, in spleen, blood, and spinal cord tissue, with variable effects on other Th1 and Th2 cytokines, and no significant effect on the Th3 cytokine, TGF-beta1, or on FoxP3 that is expressed by regulatory T cells. Moreover, pretreatment of PLP-139-151-specific T cells with RTL401 in vitro induced high levels of secreted IL-13, with lesser induction of other pro- and anti-inflammatory cytokines. Given the importance of IL-13 for protection against EAE, these data strongly implicate IL-13 as a dominant regulatory cytokine induced by RTL therapy. Pronounced IL-13 levels coupled with marked reduction in IL-6 levels secreted by PLP-specific T cells from blood after treatment of mice with RTL401 indicate that IL-13 and IL-6 may be useful markers for following effects of RTL therapy in future clinical trials in multiple sclerosis.
Ulotaront: A TAAR1 Agonist for the Treatment of Schizophrenia (2021)

Ulotaront (SEP-363856) is a trace-amine associated receptor 1 (TAAR1) agonist with 5-HT1A receptor agonist activity in Phase 3 clinical development, with FDA Breakthrough Therapy Designation, for the treatment of schizophrenia. TAAR1 is a G-protein-coupled receptor (GPCR) that is expressed in cortical, limbic, and midbrain monoaminergic regions. It is activated by endogenous trace amines, and is believed to play an important role in modulating dopaminergic, serotonergic, and glutamatergic circuitry. TAAR1 agonism data are reported herein for ulotaront and its analogues in comparison to endogenous TAAR1 agonists. In addition, a human TAAR1 homology model was built around ulotaront to identify key interactions and attempt to better understand the scaffold-specific TAAR1 agonism structure-activity relationships.
Soft scissors (2007)

We present Soft Scissors , an interactive tool for extracting alpha mattes of foreground objects in realtime. We recently proposed a novel offline matting algorithm capable of extracting high-quality mattes for complex foreground objects such as furry animals [Wang and Cohen 2007]. In this paper we both improve the quality of our offline algorithm and give it the ability to incrementally update the matte in an online interactive setting. Our realtime system efficiently estimates foreground color thereby allowing both the matte and the final composite to be revealed instantly as the user roughly paints along the edge of the foreground object. In addition, our system can dynamically adjust the width and boundary conditions of the scissoring paint brush to approximately capture the boundary of the foreground object that lies ahead on the scissor's path. These advantages in both speed and accuracy create the first interactive tool for high quality image matting and compositing.
Software architecture for Smart Metering systems with Virtual Power Plant (2010)

This paper presents a novel architecture for Smart Metering systems which enables their seamless, secure and efficient integration in wider SmartGrid software structures. Smart metering solutions represent one of the fastest evolving areas in the field of power distribution systems. There is an extensive interest of leading software vendors in the field, for development of architectures that can efficiently manage transmission, processing and storing of tremendous amount of data produced by such metering devices deployed at the end-end side. The integration of these systems into existing power system software architectures (outage management, workforce management, etc.) represents a major challenge for research community. In such an environment it is of fundamental importance to adopt standardized data exchange mechanisms. The proposed architecture is conceived as modular and scalable structure so that it can support implementation of novel power distribution concepts as Virtual Power Plants (VPPs). The proposed architecture has been successfully tested and verified in real life operation as one of modules of Smart Metering system named Meter Data Management (MDM).
Magnetophoretic mobilities correlate to antibody binding capacities (2000)

The results, in agreement with theory, indicate a linear relationship between magnetophoretic mobility and ABC for microbeads with less than 30,000 ABC. The mathematical relationships and QSC standardization curve obtained allow determination of the number of surface antigens on similarly immunomagnetically labeled cells.
Direct Soil Gypsum Quantification via Portable X-Ray Fluorescence Spectrometry (2013)

Soil scientists have long struggled with an effective method for quantifying gypsum content in soils. Several methods exist, but each is fraught with problems. Recent enhancements to portable X-ray fluorescence (PXRF) spectrometers have provided better detection limits especially for lighter elements such as S, a key component of gypsum. Thus, this research aimed to test the effectiveness of PXRF as a means of directly quantifying gypsum in soils. A total of 102 soil samples containing a wide variety of gypsum (∼2–95%) were subjected to both traditional laboratory analysis (thermogravimetry) and elemental analysis via PXRF. Simple linear regression and multiple linear regression were used to establish the relationship between the two datasets. Log transformation of some datasets was necessary to normalize the data. Using simple linear regression for Ca, laboratory data and PXRF Ca data produced an R2 of 0.8794. Similarly, simple linear regression for laboratory-quantified gypsum vs. PXRF S produced an R2 of 0.9120. Multiple linear regression of laboratory quantified gypsum vs. both PXRF S and Ca produced an R2 of 0.9127. No significant differences were observed between model generation and validation datasets. Overall, PXRF shows great promise for the direct quantification of gypsum in soils.
The presence of messenger RNA for HLA class I in human platelets and its capability for protein biosynthesis (1993)

In order to determine whether platelets contain specific messenger RNA encoding for HLA class I molecules, polymerase chain reaction (PCR) was performed with RNA from different platelet donors. Two amplified 300 bp and 279 bp cDNA fragments were obtained which encompassed sequences from 321 to 620 and from 795 to 1073. The 300 bp fragment encodes exon 2 and exon 3, the 279 bp encodes a portion of exon 4, exon 5, exon 6 and a portion of exon 7. A 300 bp nested PCR product from one donor, that encoded for the highly polymorphic region alpha 2, was cloned and sequenced. The resulting nucleotide sequences fitted to the expected sequence for HLA B*3801 of this donor. Sequence analysis of the 279 bp PCR product demonstrated the presence of exon 5 encoding for the 117 bp transmembrane domain. In addition, de novo protein biosynthesis was studied by radioimmunoprecipitation of HLA class I molecules from 35S-methionine metabolically labelled platelet lysates with a monoclonal antibody (mab) w6/32 specific for a monomorphic epitope on the heavy chain of HLA class I antigens. Analysis of the immunoprecipitates on SDS polyacrylamide gel electrophoresis showed a specific band with apparent molecular weight (M(r)) of 44 kD corresponding to integral membrane HLA protein. On the basis of these results, we conclude that platelets contain specific messenger RNA encoding for HLA class I molecules and have the capability to synthesize the integral HLA membrane protein.
Production and functional analysis of rat CD59 and chimeric CD59‐Crry as active soluble proteins in Pichia pastoris (2000)

Crry (CR1-related gene/protein) is a rodent complement regulator that inhibits C3 convertases. CD59 is a conserved protein inhibitor active towards C8 and C9. We have previously produced rat Crry as a recombinant soluble (rs) protein in Pichia pastoris. In this study we produced functionally active rat rsCD59 and a chimeric rsCD59-Crry protein in P. pastoris. The GPI anchor addition site of rat CD59 (Asn-79) was replaced either by a stop codon to produce rsCD59, or with the sequence of the first five short consensus repeats of Crry to produce rsCD59-Crry. Proteins were generated by fermentation and purified by affinity chromatography on an anti-CD59 column. In a standard classical pathway haemolysis assay, all three rs proteins had inhibitory activity, with 50% inhibition at 0.5 microM (rsCrry and rsCD59-Crry) and 4.4 microM (rsCD59). In an assay examining inhibition of C5b-9, in which C5b-7 was first formed, followed by purified C8 and C9, rsCD59 and rsCD59-Crry were active with 50% inhibition at 0.8 microM (rsCD59-Crry) and 1.3 microM (rsCD59). The degree of inhibition was independent of whether the C8 and C9 were of rat or human origin. Therefore, we have produced rsCD59 and rsCD59-Crry in P. pastoris. The rsCD59 retains its inhibitory activity towards C5b-9, while rsCD59-Crry appears to have the combined activities of Crry and CD59. In a haemolytic assay, the inclusion of CD59 to Crry is of no additional benefit to Crry, which may illustrate the overall importance of the C3 convertase step. Yet, inclusion of Crry to CD59 increases the potency of CD59 towards C5b-9.