gebhart/patrepeval huggingface dataset:
Pharmacokinetics of Agelastatin A in the central nervous system (2011)

Agelastatin A (AA) is an anti-neoplastic agent with anti-osteopontin (OPN) activity. Brain tumors often express OPN significantly. A comprehensive chemoinformatic analysis followed by in vivo pharmacokinetic evaluations in mice is performed. CNS penetration of AA is about 10%. AA should be further tested for activity against brain tumors.
Overview of microbial biofilms (1995)

As the success of this two-issue special section of the Journal of Industrial Microbiology attests, the study of microbial biofilms is truly burgeoning as the uniqueness and the importance of this mode of growth is increasingly recognized. Because of its universality the biofilm concept impacts virtually all of the subdivisions of Microbiology (including Medical, Dental, Agricultural, Industrial and Environmental) and these two issues incorporate contributions from authors in all of these disciplines. Some time ago we reasoned that bacteria cannot possibly be aware (sic) of their precise location, in terms of this spectrum of anthrocentric subspecialties, and that their behavior must be dictated by a standard set of phenotypic responses to environmental conditions in what must seem to them (sic) to be a continuum of very similar aquatic ecosystems. In this overview I will, therefore, stress the common features of microbial biofilms that we should bear in mind as we use this simple universal concept to seek to understand bacterial behavior in literally hundreds of aquatic ecosystems traditionally studied by dozens of subspecies of microbiologists reared in sharply different scientific and academic conventions.
Rigid and flexible thin-film multielectrode arrays for transmural cardiac recording (1992)

Thin-film transmural cardiac multielectric arrays were fabricated using integrated-circuit processing techniques. Several substantial improvements were achieved over conventional handmade arrays such as a smaller cross-sectional area, a larger number of recording sites per needle, more accurately controlled size and spacing of the recording sites, smaller bipolar spacings, and higher throughout yield. These advantages allow for a higher density of closely spaced bipolar electrodes capable of monitoring complex voltage and gradient fields present during ventricular fibrillation and defibrillation. Both rigid and flexible arrays were fabricated and used in the acquisition of transmural electrical signals. The rigid multielectrode arrays were made of gold electrodes on a molybdenum substate, and the flexible arrays of silver and gold electrodes on a polyimide substrate. In vitro and in vivo testing of the thin-film transmural cardiac multielectrode arrays indicates that there are no adhesion or delamination problems observed during acute studies, no implantation difficulties, and that unipolar and bipolar recordings during normal sinus rhythm and injury potentials in unipolar recordings are similar to those obtained using the handmade electrodes.
A Shuffle Image-Encryption Algorithm (2008)

Problem statement: Image encryption needs to be secure by resisting statistical attacks and other types of attacks. Approach: The new algorithm, call it the Shuffle Encryption Algorithm (SEA), applies nonlinear s-box byte substitution. Then, it performed a shuffling operation partially dependent on the input data and uses the given key. Results: SEA was implemented and tested with different data, mainly consisting of images. Results confirmed its security, shown through statistical analysis using histograms, correlation and covariance. Conclusion: New algorithm was suited for encrypting images and other types of data.
Interaction of the RecA Protein of Escherichia coli with Single-stranded Oligodeoxyribonucleotides (1996)

The RecA protein of Escherichia coli performs a number of ATP-dependent, in vitro reactions and is a DNA-dependent ATPase. Small oligodeoxyribonucleotides were used as DNA cofactors in a kinetic analysis of the ATPase reaction. Polymers of deoxythymidilic acid as well as oligonucleotides of mixed base composition stimulated the RecA ATPase activity in a length-dependent fashion. Both the initial rate and the extent of the reaction were affected by chain length. Full activity was seen with chain lengths > or = 30 nt. Partial activity was seen with chain lengths of 15-30 nt. The lower activity of shorter oligonucleotides was not simply due to a reduced affinity for DNA, since effects of chain length on KmATP and the Hill coefficient for ATP hydrolysis were also observed. The results also suggested that single-stranded DNA secondary structure frequently affects the ATPase activity of RecA protein with oligodeoxyribonucleotides.
Bone forming capacity of cell‐ and growth factor‐based constructs at different ectopic implantation sites (2014)

The aim of this study was to compare the effect of implantation site (i.e., subcutaneous, SQ vs. intramuscular, IM) on bone forming capacity of cell-based and growth factor-based scaffolds in athymic nude rats after an implantation period of 8 weeks. Cell-based scaffolds consisted of porous hydroxyapatite/tricalcium phosphate (HA/TCP) scaffolds seeded with either human adipose tissue-derived mesenchymal stem cells (AT-MSCs) only or both AT-MSCs and human umbilical vein endothelial cells (HUVECs), which were precultured in osteogenic medium for 7 days. Growth factor-based scaffolds consisted of porous HA/TCP scaffolds with 20 µg preadsorbed bone morphogenetic protein-2 (BMP-2). Histological and histomorphometrical analysis were used to assess bone formation. A differentiation experiment was performed in parallel to compare the in vitro osteogenic capacity of cell-based scaffolds. The results showed that cell-based scaffolds showed evident osteogenic differentiation in vitro, with only marginal differences between AT-MSCs only and AT-MSCs/HUVECs. In vivo, none of the cell-based scaffolds showed bone formation, irrespective of the site of implantation. In contrast, all growth factor-based scaffolds showed bone formation at both implantation sites without differences in the amount of formed bone. In conclusion, the results of this study demonstrated that the bone forming capacity of HA/TCP scaffolds with pre-adsorbed BMP-2 was equal at different ectopic implantation sites. Further, despite obvious in vitro osteogenic differentiation of AT-MSCs and AT-MSCS/HUVECs on HA/TCP scaffolds, no bone formation of these cell-based scaffolds was observed in vivo. This indicates further investigation on bone formation mechanisms of AT-MSCs is needed before AT-MSCs can be used as a cytotherapeutic treatment in clinics.
Potent and Selective Indolomorphinan Antagonists of the Kappa-Opioid Receptor (2000)

The indole moiety in the delta-opioid antagonist, naltrindole (2, NTI), was employed as a scaffold to hold an “address” for interaction with the kappa-opioid receptor. The attachment of the address to the 5‘-position of the indole moiety was based on superposition of NTI upon the kappa antagonist, norbinaltorphimine (1, norBNI). A variety of cationic groups were employed as a kappa address in an effort to investigate its interaction with the anionic address subsite, Glu297, on the kappa receptor. Some of the groups that were employed for this purpose were amines, amidines, guanidines, and quaternary ammonium. Members of the series were found to have a varying degree of kappa antagonist potency and kappa selectivity when tested in smooth muscle preparations. The 5‘-guanidine derivative 12a (GNTI) was the most potent member of the series and had the highest kappa selectivity ratio. GNTI was 2 times more potent and 6−10-fold more selective than norBNI (1). In general, the order of potency in the series was: guanidines > amidines ∼ quaternary ammonium > amines. The kappa antagonist potency appeared to be a function of a combination of the pKa and distance constraint of the cationic substituent of the ligand. Receptor binding studies were qualitatively in agreement with the pharmacological data. Molecular modeling studies on 12a suggested that the protonated N-17 and guanidinium groups of GNTI are associated with Asp138 (TM3) and Glu297 (TM6), respectively, while the phenolic hydroxyl may be involved in donor−acceptor interactions with the imidazole ring of His291. It was concluded that the basis for the high kappa selectivity of GNTI is related both to association with the nonconserved Glu297 residue and to unfavorable interactions with an equivalent position in mu- and delta-opioid receptors.
Targeting HIV reverse transcriptase for anti-AIDS drug design: structural and biological considerations for chemotherapeutic strategies. (1996)

The reverse transcriptase of HIV is a key target for the antiviral treatment of AIDS. Numerous potent inhibitors of RT have been described including all of the drugs that have been currently licensed for the treatment of AIDS, but their efficacy has been limited by the emergence of drug-resistant HIV variants. Extensive biochemical, genetic, and clinical data about HIV RT enzymatic mechanisms, inhibition, and drug resistance have been reported. This information, taken together with structural data from crystallographic studies of HIV-1 RT, has set the stage for structure-based design of improved inhibitors of this essential viral enzyme. Comparisons of the different crystal structures of HIV-1 RT shows that the enzyme has great conformational flexibility, providing additional possibilities for drug targeting. Recent clinical and virological data suggest that HIV-1 RT enzymes that carry drug-resistance mutations can be substantially impaired and that combinations of RT inhibitors can produce significant clinical benefit in the treatment of AIDS. An immediate goal is to use the available information to design specific inhibitors or combination therapies that will select for relatively less fit HIV variants.
Spot the differences: the X-ray spectrum of SU Aur compared to TW Hya (2005)

We present high-resolution Chandra HETGS X-ray spectra of the classical T Tauri star SU Aur. The quiescent X-ray emission is dominated by a 20-40 MK plasma, which contrasts strongly with the cool 3 MK plasma dominating the X-ray emission of the CTTS TW Hya. A large flare occurred during the first half of our 100 ks observation, and we have modelled the emitting plasma both during this flare and during the apparently quiescent periods. During the flare, an extremely high temperature plasma component (at least 60 MK) accounts for the bulk of the emission. There is an indication of the presence of Fe XXVI emission at 1.78 Angstrom, which is maximally formed at 130 MK.
5-Substituted Pyrimidines with a 1,5-Anhydro-2,3-dideoxy-d-arabino-hexitol Moiety at N-1:  Synthesis, Antiviral Activity, Conformational Analysis, and Interaction with Viral Thymidine Kinase (1998)

A new series of anhydrohexitol nucleosides are described. These compounds have a pyrimidine base moiety substituted in the 5-position with a chloro (1b), trifluoromethyl (1c), vinyl (1d), 2-thienyl (1e), ethynyl (1f) or propynyl (1g) substituent. The vinyl, propynyl, and, in particular, the 5-trifluoromethyl analogue showed potent activity against herpes simplex virus (HSV), 1c with a selectivity index of >16000 against HSV-1 and >1000 against HSV-2. Conformational analysis of anhydrohexitol nucleosides using computational methods indicates that these nucleosides occur in an equilibrium between the C1 and 1C form with a DeltaE of 5.9 kJ/mol. When the anhydrohexitol nucleoside is cocrystallized with the HSV-1 thymidine kinase it adopts a 1C conformation, which is opposite to the conformation found for the small molecule alone. The enzyme, apparently, induces a conformational change, and conformational flexibility of an anhydrohexitol nucleoside may be advantageous for recognition by viral enzymes.
[Optic biometry in intraocular lense calculation for cataract surgery. Comparison with usual methods]. (2001)

Optic biometry has a number of advantages. This is new method, is non invasive, easy to use, with no contact, and it is reliable. Results with this method are more precise than with ultrasonic biometry. For high myopia, optic biometry is a very valuable method. Its limits are total cataract and intraocular opacities; in these cases ultrasonic biometry is the best method.
Intracoelomic Acoustic Tagging of Juvenile Sockeye Salmon: Swimming Performance, Survival, and Postsurgical Wound Healing in Freshwater and during a Transition to Seawater (2013)

Abstract Juvenile hatchery‐reared Sockeye Salmon Oncorhynchus nerka from Cultus Lake, British Columbia, were implanted during their smolt phase with one of three sizes of dummy acoustic tags to assess how tag burden (tag mass: body mass ratios ranging from 1.3% to 13.6% in air) influenced prolonged swimming performance, survival, and postsurgical wound healing in freshwater for up to 16.5 d and following a transition to seawater for 9 d. Tagged fish were compared with surgical shams and control fish (no tag, no surgery). Fish subjected to sham surgery treatments had mean swim times similar to those of control fish; however, tagged fish had a significantly lower probability of swimming the mean time of nontagged control fish. In addition, we found that the effect of tagging on swimming performance was exacerbated by tag burden and that higher tag burdens decreased the swimming performance of tagged individuals. Fish with tag burdens ≥8% had shorter swimming durations than fish with tag burdens &lt;8%. The incisions of fish implanted with smaller tags healed more quickly than those of fish implanted with the largest tag. Overall, survival was high (≥95%) and in freshwater mortalities only occurred in fish that had tag burdens greater than 6%. These findings have important implications for studies using tagging technologies to examine the behavior and survival of migrating salmon smolts.
Quinolone antibacterial agents substituted at the 7-position with spiroamines. Synthesis and structure-activity relationships (1990)

A series of fluoroquinolone antibacterials having the 7-position (10-position of pyridobenzoxazines) substituted with 2,7-diazaspiro[4.4]nonane (4b), 1,7-diazaspiro[4.4]nonane (5a), or 2,8-diazaspiro[5.5]undecane (6b) was prepared, and their biological activities were compared with piperazine and pyrrolidine substituted analogues. Most exhibited potent Gram-positive and Gram-negative activity, especially when side chain 4b was N-alkylated.
Unlimited microanalytical system (1973)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTUnlimited microanalytical systemOliver H. LowryCite this: Acc. Chem. Res. 1973, 6, 9, 289–293Publication Date (Print):September 1, 1973Publication History Published online1 May 2002Published inissue 1 September 1973https://pubs.acs.org/doi/10.1021/ar50069a001https://doi.org/10.1021/ar50069a001research-articleACS PublicationsRequest reuse permissionsArticle Views58Altmetric-Citations20LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Telomere Length, Aging, and Somatic Cell Turnover (1999)

Telomeres are unique protein–DNA structures that comprise the termini of eukaryotic linear chromosomes (for review see references ([1][1]), ([2][2])). Telomeric DNA does not contain protein-encoding genes but rather consists of G-rich hexanucleotide repeats that in vertebrate cells are (TTAGGG)n
The anticancer effects of chaetocin are independent of programmed cell death and hypoxia, and are associated with inhibition of endothelial cell proliferation (2011)

Chaetocin has intriguing and wide-ranging in vitro and in vivo anticancer effects, and is an attractive candidate for further preclinical and clinical development.
Block Copolymers with Strongly Interacting Groups (2002)

Chapter 18 covers the main experimental findings and theoretical predictions of block copolymers with strongly interacting groups, including the morphology, scattering intensity distributions and viscoelasticity. The effect of added salt on the lamellar spacing and microdomain morphology is also discussed.
Terrorism Within the Community Context (2011)

Terrorism within the community context investigates and discusses the processes of terrorist recruitment within communities and societies. It focuses on the different types of terrorists, their motivations and the social and psychological factors which are correlated with the transformation of an individual from a community member to a community threat. This analysis invokes the perspectives of Durkheim, Sykes and Matza, Snow and others as the role of terrorist is identified, acquired and acted upon. Particular attention is directed to strategies and tactics of role acquisition and social support.
Production and characterization of monoclonal antibodies showing a different spectrum of reactivity to human breast tissue. (1987)

We have generated three hybridoma-producing monoclonal antibodies (MAs) that show a different spectrum of reactivity to human mammary tissues. Two of these antibodies, 1F10B4 and 1F10G2, recognize a cytoplasmic determinant highly expressed in most of the primary and metastatic breast carcinomas studied, and weakly (or not at all) in normal breast and nonbreast tissues. 3C6F9 detected a surface determinant common to both normal and neoplastic mammary epithelium. Five hundred hybridomas were obtained from the fusion of NS-1 myeloma cells with spleen cells of mice hyperimmunized with the well-characterized human breast carcinoma cell line BT-20. After the initial screenings and clonings, three monoclonal antibodies (1F10B4, 1F10G2, and 3C6F9) showing a restricted range of reactivity were selected for further investigation. These three antibodies recognized a panel of neoplastic mammary cell lines; however, the degree of reactivity could not be correlated to any of the various characteristics of these epithelial cell lines. Moreover, immunofluorescence analysis of acetone-fixed cryostat section showed that 1F10B4 and 1F10G2 recognize the vast majority of the 37 primary and metastatic breast cancers tested, binding strongly to 47% and 67% of them respectively. Only one of the primary carcinomas was not recognized by 1F10B4. On the other hand, these two MAs reacted weakly or not at all with normal breast and nonbreast tissues showing only few focal reactivities with the luminal pole of some ducts of the breast; very weak staining in renal tubular epithelial cells, in few keratinocytes and epithelial cells lining some sebaceous glands in the skin; and a moderate staining in biliary ducts of the liver. All mesenchymal structures including smooth and striated muscle tissues, lymph nodes, and connective tissue were negative. On the other hand, 3C6F9 recognized a more limited number of human mammary tumors and reacted with normal ductal epithelium in the breast and with nonbreast tissues. Because of their wide spectrum of reactivity with breast cancer cells and restricted recognition of normal mammary tissues, their cytoplasmic localization, and their heterogeneous distribution within a single neoplasm, 1F10B4 and 1F10G2 are now being used to characterize antigenic phenotypes of tumor-associated antigens in retrospective studies performed on conventional formalin-fixed, paraffin-embedded human mammary carcinomas.
Structure of the Prefusion Form of the Vesicular Stomatitis Virus Glycoprotein G (2007)

Glycoprotein G of the vesicular stomatitis virus triggers membrane fusion via a low pH-induced structural rearrangement. Despite the equilibrium between the pre- and postfusion states, the structure of the prefusion form, determined to 3.0 angstrom resolution, shows that the fusogenic transition entails an extensive structural reorganization of G. Comparison with the structure of the postfusion form suggests a pathway for the conformational change. In the prefusion form, G has the shape of a tripod with the fusion loops exposed, which point toward the viral membrane, and with the antigenic sites located at the distal end of the molecule. A large number of G glycoproteins, perhaps organized as in the crystals, act cooperatively to induce membrane merging.
Mechanisms of Epithelial Cell–Cell Adhesion and Cell Compaction Revealed by High-resolution Tracking of E-Cadherin– Green Fluorescent Protein (1998)

Cadherin-mediated adhesion initiates cell reorganization into tissues, but the mechanisms and dynamics of such adhesion are poorly understood. Using time-lapse imaging and photobleach recovery analyses of a fully functional E-cadherin/GFP fusion protein, we define three sequential stages in cell-cell adhesion and provide evidence for mechanisms involving E-cadherin and the actin cytoskeleton in transitions between these stages. In the first stage, membrane contacts between two cells initiate coalescence of a highly mobile, diffuse pool of cell surface E-cadherin into immobile punctate aggregates along contacting membranes. These E-cadherin aggregates are spatially coincident with membrane attachment sites for actin filaments branching off from circumferential actin cables that circumscribe each cell. In the second stage, circumferential actin cables near cell-cell contact sites separate, and the resulting two ends of the cable swing outwards to the perimeter of the contact. Concomitantly, subsets of E-cadherin puncta are also swept to the margins of the contact where they coalesce into large E-cadherin plaques. This reorganization results in the formation of a circumferential actin cable that circumscribes both cells, and is embedded into each E-cadherin plaque at the contact margin. At this stage, the two cells achieve maximum contact, a process referred to as compaction. These changes in E-cadherin and actin distributions are repeated when additional single cells adhere to large groups of cells. The third stage of adhesion occurs as additional cells are added to groups of >3 cells; circumferential actin cables linked to E-cadherin plaques on adjacent cells appear to constrict in a purse-string action, resulting in the further coalescence of individual plaques into the vertices of multicell contacts. The reorganization of E-cadherin and actin results in the condensation of cells into colonies. We propose a model to explain how, through strengthening and compaction, E-cadherin and actin cables coordinate to remodel initial cell-cell contacts to the final condensation of cells into colonies.
Production of hybridomas secreting monoclonal antibodies to the human leukocyte interferons. (1981)

Thirteen monoclonal antibodies to human leukocyte interferon have been obtained. They exhibit different patterns of binding to purified leukocyte interferon species that are consistent with the structural multiplicity of the human leukocyte interferons. These antibodies will be useful as probes into the structure of the human leukocyte interferons, for their purification, and for rapid assay of leukocyte interferon.