gebhart/patrepeval huggingface dataset:
Thrombospondin-platelet interactions. Role of divalent cations, wall shear rate, and platelet membrane glycoproteins. (1993)

The role of thrombospondin, a multifunctional matrix glycoprotein, in platelet adhesion is controversial: both adhesive and antiadhesive properties have been attributed to this molecule. Because shear flow has a significant influence on platelet adhesion, we have assessed thrombospondin-platelet interactions both under static and flow conditions. The capacity of thrombospondin to support platelet adhesion depended upon its conformation. In a Ca(2+)-depleted conformation, such as in citrated plasma, thrombospondin was nonadhesive or antiadhesive as it inhibited platelet adhesion to fibrinogen, fibronectin, laminin, and von Willebrand factor by 30-70%. In a Ca(2+)-replete conformation, however, thrombospondin effectively supported platelet adhesion. Shear rate influenced this adhesion; percent surface coverage on thrombospondin increased from 5.4 +/- 0.3 at 0 s-1 to 41.5 +/- 6.7 at 1,600 s-1. In contrast to the extensive platelet spreading observed on fibronectin at all shear rates, platelet spreading on thrombospondin occurred only sporadically and at high shear rates. GPIa-IIa, GPIIb-IIIa, GPIV, and the vitronectin receptor, which are all proposed platelet receptors for thrombospondin, were not solely responsible for platelet adhesion to thrombospondin. These results suggest that thrombospondin may play a dual role in adhesive processes in vivo: (a) it may function in conjunction with other adhesive proteins to maintain optimal platelet adhesion at various shear rates; and (b) it may serve as a modulator of cellular adhesive functions under specific microenvironmental conditions.
Allosteric Control of Self‐Assembly: Modulating the Formation of Guanine Quadruplexes through Orthogonal Aromatic Interactions (2007)

All four one: The covalent attachment (A) of a porphyrin head group onto a guanine-rich oligonucleotide strand can enhance the self-assembly of DNA quadruplexes through porphyrin-based π–π interactions (B). Modulation of these allosteric interactions, by addition of a porphyrin-complexing cyclodextrin derivative, allows for a high degree of control over the formation and disassembly of the guanine quadruplexes (C and D).
Parkin mutations and susceptibility alleles in late‐onset Parkinson's disease (2003)

Parkin, an E2-dependent ubiquitin protein ligase, carries pathogenic mutations in patients with autosomal recessive juvenile parkinsonism, but its role in the late-onset form of Parkinson's disease (PD) is not firmly established. Previously, we detected linkage of idiopathic PD to the region on chromosome 6 containing the Parkin gene (D6S305, logarithm of odds score, 5.47) in families with at least one subject with age at onset (AAO) younger than 40 years. Mutation analysis of the Parkin gene in the 174 multiplex families from the genomic screen and 133 additional PD families identified mutations in 18% of early-onset and 2% of late-onset families (5% of total families screened). The AAO of patients with Parkin mutations ranged from 12 to 71 years. Excluding exon 7 mutations, the mean AAO of patients with Parkin mutations was 31.5 years. However, mutations in exon 7, the first RING finger (Cys253Trp, Arg256Cys, Arg275Trp, and Asp280Asn) were observed primarily in heterozygous PD patients with a much later AAO (mean AAO, 49.2 years) but were not found in controls in this study or several previous reports (920 chromosomes). These findings suggest that mutations in Parkin contribute to the common form of PD and that heterozygous mutations, especially those lying in exon 7, act as susceptibility alleles for late-onset form of Parkinson disease.
Synthesis and biological evaluation of selective CXCR4 antagonists containing alkene dipeptide isosteres (2009)

A set of cyclic peptide analogues of a selective CXCR4 antagonist FC131 [cyclo(-d-Tyr-Arg-Arg-Nal-Gly-)] were synthesized and bioevaluated. Using (E)-alkene and (Z)-fluoroalkene dipeptide isosteres for Arg-Arg and Arg-Nal substructures, indispensable or the partial contribution of the two peptide bonds to the CXCR4 antagonism and anti-HIV activity was demonstrated. FC131 and the analogues were shown to selectively inhibit SDF-1 binding to CXCR4, whereas no inhibition of binding of SDF-1 to CXCR7 was observed.
Immunotherapy with biochemically dissociated fractions of Propionibacterium acnes in a murine ovarian cancer model. (1984)

The antitumor effect of two strains of Propionibacterium acnes (PAI and PAII) and chemically derived fractions from the whole bacterial cell were studied using a murine ovarian teratocarcinoma (MOT) model. When injected i.p. in high doses (700 to 1400 micrograms/mouse), both strains produce survival of a significant proportion of tumor-bearing mice (30 to 90%). On a weight to weight basis, however, PAI was significantly more effective than PAII. PAI and PAII were extracted using pyridine, which yielded four fractions, i.e., pyridine-extracted strains PAI and PAII (PA-PEI and PA-PEII, respectively) which are composed of the cell wall material extracted by pyridine, and the residues of PA-PEI and PA-PEII (PA-RI and PA-RII, respectively) which are composed of the residue material following the chemical extraction. The chemical composition of PA-PEI was different from that of PA-PEII (the latter had proportionately three times as many carbohydrates and one-third of the protein content of the former) and so were their antitumor properties in the MOT model. PA-PEI had markedly reduced antitumor effect when compared to the untreated cell on a per weight basis. Furthermore, curability was only seen when using a high dose (1400 micrograms/mouse). By contrast, the cell wall components extracted by pyridine from PAII (PA-PEII) had powerful antitumor effects, i.e., greater than 50% of mice given 1400-micrograms injections survived. The material contained in PA-PEII was further fractionated on the basis of its organic solubility in chloroform:methanol solvent. The water-soluble and solvent-insoluble fractions retained most of the antitumor effects of PA-PEII, while the water-insoluble and solvent-soluble fractions were only moderately effective, suggesting that the active moiety(ies) was associated with the nonlipid components of this fraction. Both residue fractions (PA-RI and PA-RII) were as effective on a per weight basis in controlling the growth of 10(5) tumor inoculum as were whole untreated cells. However, periodate oxidation of PA-RI resulted in complete loss of its antitumor effects. When surviving mice that had no evidence of tumor persistence following a tumor challenge (10(5) MOT cells) and i.p. treatment with PA were subsequently rechallenged with 10(4) tumor cells, survival was significantly prolonged, as compared to tumor-challenged (10(4) MOT) naive mice. In addition, 10 to 20% of these rechallenged mice had complete eradication of the tumor inoculum (no evidence of disease for greater than 120 days).(ABSTRACT TRUNCATED AT 400 WORDS)
Synergistic antimicrobial effect of ethanol, sodium chloride, acetic acid and essential oil components. (1983)

Ethanol, NaCl, acetic acid and essential oil components were examined for their synergistic antimicrobial effects, using air-borne microorganisms and pure cultures of fungi. Antimicrobial assays were carried out at 27°C, using 2% glucose Sabouraud agar. In order to completely suppress the growth of all the contaminating air microorganisms for over 20 days, more than 8% (by volume) ethanol, 25% (wt/vol) NaCl, or 0.2% (by volume) acetic acid was required in the medium. All essential oil components examined, at a concentration of 1 or 2mM, were only moderate or very weak in antimicrobial effect. However, when these substances were applied in pairs, in threes and in fours, they exhibited a potent antimicrobial effect at relatively or considerably lower concentrations. The combination of 3% ethanol, 0.05% acetic acid and 1mM perillaldehyde, and thecombination of as low as 0.5% ethanol, 2% NaCl, 0.05% acetic acid and 0.5mM perillaldehyde were sufficient to suppress completely the growth of all contaminating air microorganisms for over 20 days. The combination of 3% ethanol, 3% NaCl and 0.5mM perillaldehyde or 0.05% acetic acid was also fairly potent in this respect. Other essential oil components, such as citral, citronellol, geraniol, cuminaldehyde and eugenol, were as effective as perillaldehyde ; L-menthol, linalool and D-carvone were somewhat less effective ; and hydrocarbons (D-limonene, α-pinene, β-pinene, camphene, β-myrcene and p-cymene), citronellal, 1, 8-cineole, anethole and vanillin were very weak or almost completely ineffective in this respect. Similar synergistic antimicrobial effects of these substances were also observed when using pure cultures of fungi as inocula. Our results strongly suggest that combinations of ethanol, NaCl, acetic acid and certain essential oil components, each at a considerably lower concentration, are applicable for effective preservation of foods without applying synthetic preservatives or other antimicrobial substances uncommon in usual foods.
The repeated GC-rich motifs upstream from the TATA box are important elements of the SV40 early promoter (1983)

We have constructed deletion and point mutations within the Simian virus 40 (SV40) early promoter region which contains two tandemly repeated 21 bp sequences and a related 22 bp sequence (the "upstream" 21 bp repeat region). After transfection into permissive CV-1 cells and non-permissive mouse 3T3-4E cells, the effect of the mutations on early gene expression was studied by measuring T-antigen production, using indirect immunofluoresence. Our results demonstrate that the 21 bp repeat region, and in particular the six GC-rich motifs 5'-CCGCCC-3' which are repeated in this region constitute an important element of the SV40 early promoter. Surprisingly, we found that the requirement for the 21 bp repeat region for early gene expression was partially fulfilled even when it was in the inverted orientation.
Heat transfer enhancement in metal hydride systems (1979)

The Brookhaven National Laboratory, Department of Energy and Environment has been engaged in finding solutions to the engineering problems associated with the storage of hydrogen as metal hydrides - principally iron-titanium hydride. The thermal conductivity in beds of fine particles, whatever their composition, is inherently poor. This paper reports on attempts to enhance the heat transfer by the addition of small fractions of high conductivity materials in various configurations. The results indicate that the form of the enhancement material rather than its composition is the more critical factor.
Improved Biocontrol Efficacy of Trichoderma harzianum 1295-22 for Foliar Phases of Turf Diseases by Use of Spray Applications (1997)

Trichoderma harzianum strain 1295-22 is an effective biocontrol agent for several fungal diseases. The efficacy of granule and spray applications of strain 1295-22 for control of Pythium root rot, brown patch, and dollar spot of creeping bentgrass was investigated. Spray applications of conidial suspensions (SA) of strain 1295-22 significantly reduced all three diseases of creeping bentgrass turf in both greenhouse and field experiments. Control was greatest when Triton X-100 at 0.1% was added to aqueous spray suspensions. When SA were applied weekly, the biocontrol treatments were equivalent to standard fungicides. Broadcast granule applications (GA) also significantly reduced foliar symptoms of Pythium root rot, dollar spot, and brown patch; turf quality also was enhanced. The populations of Trichoderma spp. in the root zone of a bentgrass putting green treated with SA or GA of strain 1295-22 increased 10- to 100-fold after treatment compared with untreated plots. However, strain 1295-22 was present at high levels on bentgrass leaves only following SA. Collectively, the results suggest that strain 1295-22 possesses both rhizosphere and phylloplane competence. The combination of broadcast applications of granules followed by spray applications of conidia reduced damage from both root and foliar diseases.
ECG to Individual Identification (2008)

This paper presents an individual identification system using single lead electrocardiogram (ECG). The proposed techniques for P and T wave delineation are based on time derivative and adaptive thresholding. The performance of proposed delineators is evaluated on manually annotated Physionet QT database. The accuracy of delineators are quantified on mean error and standard deviation of differences between manually annotations and automated results. Especially, lower values of error in standard deviation for onset and offset of P wave fiducials are obtained as 8.1 and 6.29 while for T wave fiducials are 9.4 and 11.2 (where units are in ms). It shows the performance of P and T wave delineators is optimum and also stable in comparison to other published results. Found fiducials are processed for the extraction of heartbeat features. From each heartbeat, 19 stable features related to interval, amplitude and angle are computed. The feasibility of ECG as a new biometric is tested on proposed identification system designed on template matching and adaptive thresholding. The accuracy of identification system is achieved to 99% on the datasize of 125 recordings prepared from 25 individual ECG of Physionet.
A New Method for Production of Chiral 2-Aryl-2-fluoropropanoic Acids Using an Effective Kinetic Resolution of Racemic 2-Aryl-2-fluoropropanoic Acids (2012)

We report a new method for the preparation of chiral 2-aryl-2-fluoropropanoic acids, including 2-fluoroibuprofen, a fluorinated analogue of non-steroidal anti-inflammatory drugs (NSAIDs), by the kinetic resolution of racemic 2-aryl-2-fluoropropanoic acids using enantioselective esterification. By applying pivalic anhydride (Piv2O) as a coupling agent, bis(α-naphthyl)methanol [(α-Np)2CHOH] as an achiral alcohol, and (+)-benzotetramisole (BTM) as a chiral acyl-transfer catalyst, a series of racemic 2-aryl-2-fluoropropanoic acids were kinetically separated to afford the optically active carboxylic acids and the corresponding esters with good to high enantiomeric excesses. This technology can provide a convenient approach to furnish the chiral α-fluorinated drugs containing quaternary carbons at the α-positions in the 2-aryl-2-fluoropropanoic acid structure.
The Energetic Conversion Competence of Escherichia coli during Aerobic Respiration Studied by 31P NMR Using a Circulating Fermentation System (2004)

To determine the actual potential of the energetic conversion efficiency of Escherichia coli during aerobic respiration, apparent P/O ratios (P/O(app)) under either limited or standard glucose-feeding conditions were estimated. The previously reported circulating fermentation system (CFS) was used, and (31)P NMR saturation-transfer (ST) techniques were employed. By coupling with on-line NMR observations, CFS allowed us to evaluate cellular energetics directly, with both the dissolved oxygen tension and glucose feeding precisely controlled to prevent the effect of substrate-level phosphorylation based on aerobic or anaerobic acidogenesis in E. coli cells. Phosphate consumption rates under standard and limited glucose-conditions were estimated as 4.62 +/- 0.46 and 1.99 +/- 0.11 micromol/s g of dry cell weight (DCW), respectively. Using simultaneously assessed O(2) consumption rates, the P/O(app) values under these two conditions were estimated as 1.4 +/- 0.3 and 1.5 +/- 0.1, respectively. To correlate the obtained P/O(app) values with the potential efficiency of respiratory enzymes, we determined the activities of two NADH dehydrogenases (NDH 1 and 2) and two ubiquinol oxidases (bo- and bd-type) during the periods when ST was performed. NDH-1 activities in standard or limited glucose cultures were maintained at 57% or 58% of the total NADH oxidizing activity. The percentages of bo-type oxidase activity in relation to the total ubiqinol oxidizing activity under the standard and limited glucose conditions were 32% and 36%, respectively. These percentages of enzymatic activities represent the respiratory competence of E. coli cells, suggesting that, during the NMR observatory period, the enzymatic activity was not at a maximum, which could also explain the estimated P/O(app) values. If this is the case, enhancing the expression of the bo-type oxidase or disrupting of the bd-type oxidase gene could be effective approach to increasing both the P/O ratio and cellular yields.
An analytic model for full spectral sky-dome radiance (2012)

We present a physically-based analytical model of the daytime sky. Based on the results of a first-principles brute force simulation of radiative transfer in the atmosphere, we use the same general approach of fitting basis function coefficients to radiance data as the Perez and Preetham models do. However, we make several modifications to this process, which together significantly improve the rendition of sunsets and high atmospheric turbidity setups -- known weak points of the Preetham model. Additionally, our model accounts for ground albedo, and handles each spectral component independently. The latter property makes it easily extensible to the near ultraviolet range of the spectrum, so that the daylight appearance of surfaces that include optical brighteners can be properly predicted. Due to its similar mathematical properties, the new model can be used as a drop-in replacement of the Preetham model.
Potent Non-Nucleoside Inhibitors of the Measles Virus RNA-Dependent RNA Polymerase Complex (2008)

Measles virus (MV) is one of the most infectious pathogens known. In spite of the existence of a vaccine, approximately 350000 deaths/year result from MV or associated complications. Antimeasles compounds could conceivably diminish these statistics and provide a therapy that complements vaccine treatment. We recently described a high-throughput screening hit compound 1 (16677) against MV-infected cells with the capacity to eliminate viral reproduction at 250 nM by inhibiting the action of the virus's RNA-dependent RNA polymerase complex (RdRp). The compound, 1-methyl-3-(trifluoromethyl)- N-[4-sulfonylphenyl]-1 H-pyrazole-5-carboxamide, 1 carries a critical CF 3 moiety on the 1,2-pyrazole ring. Elaborating on the preliminary structure-activity (SAR) study, the present work presents the synthesis and SAR of a much broader range of low nanomolar nonpeptidic MV inhibitors and speculates on the role of the CF 3 functionality.
UPDATE ON IDEC-Y2B8 (ZEVALIN) RADIOIMMUNOTHERAPY OF B-CELL NHL (1999)

Gordon, L. I.; White, C. A.; Witzig, T. E.; Wiseman, G. A.; Grillo-López, A. J. Author Information
Phase Behavior of Thin Film Blends of Block Copolymers and Homopolymers:  Changes in Domain Dimensions (1999)

We used atomic force microscopy to examine the phase behavior of thin film mixtures of a symmetric A−B diblock copolymer of degree of polymerization NA-B = 650 with (i) two homopolymers (NA = 20 and 250) and (ii) a symmetric A−B diblock copolymer (NA-B = 200). Thin film symmetric diblock copolymers are known to undergo a transition from a disordered phase to an ordered lamellar phase in which the lamellae orient parallel to the plane of the substrate. We examined films sufficiently thin in order to determine the effect of the substrate on the phase behavior. Homopolymer volume fractions of up to 50% were studied. The interlamellar spacing increased with the addition of both low- and high-molecular-weight homopolymers, although it was less extensive for the lower molecular weight homopolymer. Both situations could be well-described by theory relying on assumptions about the homopolymer distribution in the domains and the areal densities occupied by the copolymer junctions. In contrast to the homopolymers, the lamellar spacing of blends formed with the second diblock copolymer (NA-B = 200) decreased with increasing volume fraction of this shorter chain copolymer. This behavior could be described by assuming that L ∝ Nw2/3, where Nw is the weight-average degree of polymerization of the mixture. We also show that the degree of swelling of the domains depends on the proximity of the domain to the substrate.
Common Inflammatory Mechanisms in Lewy Body Disease and Alzheimer Disease (2007)

Cortical Lewy body disease as a cause of dementia has been recognized for more than 40 years. Only in the past 15 to 20 years, however, has the true frequency of this entity come to be appreciated, primarily because of the advent of sensitive and specific immunohistochemical diagnostic techniques. We now know that there is frequent and extensive overlap, both clinically and pathologically, between Lewy body and Alzheimer diseases. Although some of this overlap may be attributable to common genetic and environmental risk factors, it is also now apparent that the 2 diseases share common neuroinflammatory mechanisms involving activation of microglia, overexpression of interleukin-1 and other inflammatory mediators, and inflammatory toxicity to neurons. Activated microglia are found in association with alpha-synuclein-containing neurons and glia in Parkinson disease, in dementia with Lewy bodies, and in multiple system atrophy, and these associations are reminiscent of microglial associations with neurofibrillary tangle-containing neurons in Alzheimer disease. In vitro and in vivo experimental work has shown reciprocal induction between alpha-synuclein and injured neurons on one hand and activated microglia and cytokine overexpression on the other. These neuroinflammatory processes may be a common link driving progression in both diseases and explaining the frequent overlap between the 2 diseases.