gebhart/patrepeval huggingface dataset:
The Signature Molecular Descriptor. 2. Enumerating Molecules from Their Extended Valence Sequences (2003)

We present a new algorithm that enumerates molecular structures matching a predefined extended valence sequence or signature. The algorithm can construct molecular structures composed of about 50 non-hydrogen atoms in CPU seconds time scale. The algorithm is run to produce all molecular structures matching the binding affinities (IC(50)) of some HIV-1 protease inhibitors. The algorithm is also used to compute the degeneracy, or the number of molecular structures, corresponding to a given signature. Signature degeneracy is systematically studied for varying signature heights on four molecular series, alkanes, alcohols, fullerene-type structures, and peptides. Signature degeneracy is compared with similar results obtained with popular topological indices (TIs). As a general rule, we find that signature degeneracy decreases as the signature height increases. We also find that alkanes, alcohols, and fullerene-type structures comprising n non-hydrogen atoms are uniquely characterized by signatures of height n/4, while peptides up to 4000 amino acids can be singled out with signatures of heights as small as 2 and 3.
Molecular Beams of Macroions. II (1970)

Using the electrospray technique and nozzle–skimmer system previously described, the influence of polystyrene concentration in the sprayed solution on the magnitude and substructure of the macroion current in the molecular beam has been investigated. Other variables studied include polarity of the beam, needle–nozzle and nozzle–skimmer distances, shape of spray, etc. Attempts to produce isolated macroions in the beam by carrier gas atomization were not successful; operation at reduced pressures and elevated temperatures was not found to be advantageous. In the case of positive macroions the current–repeller-voltage curves had less substructure than in the case of negative beams, and the first stopping potential was more dependent upon the solution concentration, especially when using a relatively large nozzle–skimmer distance. For molecular weights of the polystyrene from 600 to 97 200 the relative macroion positive charge was roughly proportional to the surface area of the macroions, assuming the latter to be spheres and as calculated from the first measured stopping potential. In the case of negative beams the current at zero repeller voltage and at a solution concentration of 2.2 × 10−6 Mw was proportional to the third power of the molecular weight at the lower solute molecular weights, as is predicted for a diffusional charging process.
Synthesis, characterization, biodegradation, and drug delivery application of biodegradable lactic/ glycolic acid oligomers: I. Synthesis and characterization (1997)

A series of oligomers or low molecular weight polymers of lactic and/or glycolic acid has been synthesized with different molar ratios of lactic to glycolic acid. These oligomers have been characterized with respect to oligomer composition, molecular weight, intrinsic viscosity, crystallinity, melting temperature, and glass transition temperature. The polymerization conditions for the lactic/glycolic acid oligomer syntheses were as follows: 180-220°C, 5 mm Hg, 5 h, and 0.1 wt% of catalyst (antimony oxide) concentration. The polymeric compositions correlated to the feed ratios of lactic to glycolic acid. The molecular weight of the oligomers ranged from 895.8 ±48.7 to 1368.0 ± 0 D with the intrinsic viscosity ranging from 0.0513 to 0.0814 dl g-1. The lactic/glycolic acid oligomers were found to be amorphous. The glass transition temperatures of the lactic/glycolic acid oligomers were lower than physiological temperature.
Cellular targets of infection and route of viral dissemination after an intravaginal inoculation of simian immunodeficiency virus into rhesus macaques. (1996)

We used the simian immunodeficiency virus (SIV)/rhesus macaque model to study events that underlie sexual transmission of human immunodeficiency virus type 1 (HIV-1). Four female rhesus macaques were inoculated intravaginally with SIVmac251, and then killed 2, 5, 7, and 9 d later. A technique that detected polymerase chain reaction-amplified SIV in situ showed that the first cellular targets for SIV were in the lamina propria of the cervicovaginal mucosa, immediately subjacent to the epithelium. Phenotypic and localization studies demonstrated that many of the infected cells were likely to be dendritic cells. Within 2 d of inoculation, infected cells were identified in the paracortex and subcapsular sinus of the draining internal iliac lymph nodes. Subsequently, systemic dissemination of SIV was rapid, since culturable virus was detectable in the blood by day 5. From these results, we present a model for mucosal transmission of SIV and HIV-1.
Occurrence of p53 gene deletions and human papilloma virus infection in human head and neck cancer. (1992)

Little is known regarding the molecular genetic events in head and neck carcinoma. Epidemiological evidence suggests that both alcohol and tobacco use are related to the development of these neoplasms, and viral infections have also been postulated to play a role in some tumors. Loss of p53 tumor suppressor gene function has been found in many malignancies and can occur through either gene mutation or by interaction with the E6 protein of oncogenic human papilloma viruses (HPV). Because the mucosal surfaces of the head and neck are exposed to mutagens and HPVs, we studied DNA derived from 30 stage I-IV squamous cell carcinomas of the head and neck (9 primary tumors and 21 early passage cell lines) for p53 gene mutations as well as for the presence of oncogenic HPV DNA. Exons 2 through 11 of the p53 gene were examined using single strand conformation polymorphism analysis followed by direct genomic sequencing of all variants. HPV detection was done using polymerase chain reaction amplification with HPV E6 region type specific primers as well as L1 region degenerate ("consensus") primers; HPV type was determined by restriction fragment length polymorphism analysis of the amplified fragment as well as by Southern blotting of genomic DNA. Sixteen of 30 tumors (53%) had p53 mutations and oncogenic HPV DNA was detected in 3 of 30 (10%) tumors, none of which had p53 mutations. The p53 mutational spectrum observed was characterized by equal frequencies of transversions (6 of 16), transitions (5 of 16), and deletions (5 of 16). This distribution of mutations differs from the spectrum of p53 mutation reported in esophageal (P = 0.05) and lung (P = 0.02) cancers, two other tobacco associated neoplasms. A previously undescribed clustering of 3 mutations at codon 205 was also observed. A trend toward a shorter time to tumor recurrence after treatment was noted for those patients with tumors exhibiting p53 gene mutations, and no relationship between p53 mutations and tumor stage or node status was noted. Alteration in p53 gene function appears common in head and neck cancer, and the mutational spectrum observed may reflect the role of different mutagens or mutagenic processes than those responsible for the p53 mutations in lung and esophageal neoplasms.
Anthrax Toxin as a Molecular Tool for Stimulation of Cytotoxic T Lymphocytes: Disulfide-Linked Epitopes, Multiple Injections, and Role of CD4+Cells (1998)

We have previously demonstrated that anthrax toxin-derived proteins, protective antigen (PA) and the amino-terminal portion of lethal factor (LFn), can be used in combination to deliver heterologous molecules to the cytosol of mammalian cells. In this study we examined the ability of an LFn-peptide disulfide-linked heterodimer to prime cytotoxic T lymphocytes (CTL) in the presence of PA. A mutant of LFn that contains a carboxy-terminal reactive cysteine was generated. This form of LFn could be oxidized with a synthetic cysteine containing peptide to form a heterodimer of the protein and peptide. Mice injected with the heterodimer plus PA mounted a peptide-specific CTL response, indicating that this molecule functioned similarly to the genetically fused forms used previously. We also report the results of an analysis of two aspects of this system important for the development of experimental vaccines. First, CD4 knockout mice were unable to generate a CTL response when treated with PA plus an LFn-epitope fusion protein, suggesting that CD4(+) helper responses are essential for stimulating specific CTL with the PA-LFn system. Second, we now show that primary injection with this system does not generate any detectable antibody response to the vaccine components and that prior immunization has no effect on priming a CTL response to an unrelated epitope upon subsequent injection.
Effects of Exenatide (Exendin-4) on Glycemic Control and Weight Over 30 Weeks in Metformin-Treated Patients With Type 2 Diabetes (2005)

Exenatide was generally well tolerated and reduced HbA(1c) with no weight gain and no increased incidence of hypoglycemia in patients with type 2 diabetes failing to achieve glycemic control with metformin.
Renillafoulins, antifouling diterpenes from the sea pansy Renilla reniformis (Octocorallia) (1986)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTRenillafoulins, antifouling diterpenes from the sea pansy Renilla reniformis (Octocorallia)Paul A. Keifer, Kenneth L. Rinehart Jr., and Irving R. HooperCite this: J. Org. Chem. 1986, 51, 23, 4450–4454Publication Date (Print):November 1, 1986Publication History Published online1 May 2002Published inissue 1 November 1986https://pubs.acs.org/doi/10.1021/jo00373a020https://doi.org/10.1021/jo00373a020research-articleACS PublicationsRequest reuse permissionsArticle Views190Altmetric-Citations80LEARN 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-AlertscloseSupporting Info (1)»Supporting Information Supporting Information Get e-Alerts
Gene Therapy in Lung Disease (2002)

Gene therapy - historical overview and public oversight. Vectorology: adenoviruses as vectors for human gene therapy adeno-associated virus cationic lipids for lung gene therapy. Use of gene therapy to study lung diseases: use of gene transfer tostudy lung cytokine biology use of gene therapy to study lung infection and immunity use of in vivo gene transfer to study pulmonary fibrosis. Use of Gene theraphy to treat lung diseases: gene therapy for lung cancer gene therapy for malignantmesothelioma strategies for gene therapy of cystic fibrosis.
The Heart-Pump Interaction: Effects of a Microaxial Blood Pump (2002)

The heart-pump interaction based on the pump flow-differential pressure relationship can be useful in predicting the possibility to wean the patient from the device.
Voltage-gated potassium channels are required for human T lymphocyte activation. (1984)

The calcium channel blockers, verapamil and diltiazem, inhibit phytohemagglutinin (PHA)-induced mitogenesis at concentrations that block the T lymphocyte K channel currents. K channel blockers also inhibit the allogeneic mixed lymphocyte response in a dose-dependent manner with the same potency sequence as for block of K currents. K channel blockers inhibit PHA-stimulated mitogenesis only if added during the first 20-30 h after PHA addition, but not later, indicating a requirement for functional K channels during this period. We investigated the effect of K channel blockers on various aspects of protein synthesis for two reasons: first, protein synthesis appears to be necessary for the events leading to DNA synthesis, and second, the increase in the protein synthetic rate commences during the first 24-48 h after PHA addition. PHA-induced total protein synthesis was reduced to the level in unstimulated T lymphocytes by K channel blockers in a dose-dependent manner with the same potency sequence as for the block of K currents and inhibition of [3H]thymidine incorporation. Two-dimensional gel electrophoresis demonstrated that although the synthesis of the majority of proteins was reduced by K channel blockers to the level in unstimulated T cells, some proteins continued to be synthesized at an enhanced rate compared with resting cells. Two proteins, S and T, detected by two-dimensional gel electrophoresis in unstimulated T lymphocytes, appeared to be reduced in intensity in gels of PHA-treated T lymphocytes, in contrast to the increased synthesis of the remaining proteins. 4-Aminopyridine (4-AP), at concentrations that inhibit protein synthesis, prevented the apparent PHA-induced reduction of proteins S and T. These proteins may play a role in maintaining the T lymphocyte in a resting state and may be related to the translation inhibitory factors reported to be present at a higher specific activity in quiescent T lymphocytes than in PHA-activated T cells. The expression of the IL-2 receptor (Tac) during T lymphocyte activation was not altered by K channel blockers, whereas the production of interleukin 2 (IL-2) was reduced to the level in unstimulated T lymphocytes. Exogenous IL-2 partially relieved the inhibition of mitogenesis by low, but not by high, concentrations of 4-AP. These experiments clarify the role of K channels in T lymphocyte activation and suggest that functional K channels are required either for protein synthesis or for events leading to protein synthesis.
Absence of BRAF and NRAS mutations in uveal melanoma. (2003)

Uveal melanoma (UM) and cutaneous melanoma (CM) differ significantly in their epidemiological, clinical, immunophenotypical, and cytogenetic features, but the molecular basis for these differences has not been delineated. CMs frequently harbor an activating mutation in either NRAS or the RAS-regulated kinase BRAF, suggesting that either of these oncogenes may increase signaling through the mitogen-activated protein (MAP) kinase pathway and promote melanoma development. The aim of this study was to examine BRAF and NRAS gene mutations in UM. Genomic DNA from CM and UM was screened for mutations in BRAF exons 11 and 15 and NRAS exons 1 and 2 using a combination of denaturing high-performance liquid chromatography and direct sequencing. Mutations in BRAF exon 15 were detected in 16 (36.4%) of 44 CMs and 0 (0%) of 62 UMs. The most common mutation in CM was V599E, but a novel point mutation (L596Q) was identified in two cases and an in-frame deletion/insertion (VKSRWK599-604D) was discovered in one case. No BRAF exon 11 mutations were observed among seven CMs and nine UMs that were wild-type for exon 15. Mutation of NRAS exon 2 was rare in CM [1 (3.7%) of 27] and absent in UM [0 (0%) of 47]. No NRAS exon 1 mutations were detected in either type of melanoma. We conclude that UMs arise independent of oncogenic BRAF and NRAS mutations, an observation that may have implications for therapies targeted to the NRAS-BRAF pathway.
Mesoporous perovskite solar cells: material composition, charge-carrier dynamics, and device characteristics (2014)

We report on our investigations on charge transport and recombination in TiO(2)-based mesoporous solar cells using PbI(2) and various perovskite compositions, including CH(3)NH(3)PbI(3), CH(3)NH(3)PbI(2)Br, CH(3)NH(3)PbIBr(2), and CH(3)NH(3)PbBr(3). The mesoporous TiO(2) film is about 650 nm thick. Electron microscopy measurements show that no perovskite capping layer is formed on the top surface of the TiO(2) film. Intensity-modulated photocurrent/photovoltage spectroscopies show that the electron diffusion coefficient and recombination lifetime are governed by the underlying mesoporous TiO(2) film and thus do not depend on the perovskite composition. However, replacing the perovskite absorber with PbI(2) leads to a diffusion coefficient that is about a factor of 5 slower than that in perovskite-based devices. We also find that TiCl(4) treatment of the mesoporous TiO(2) film prior to device fabrication substantially reduces the charge recombination kinetics in mesoporous perovskite solar cells.
PRECLINICAL STUDIES OF ALLOGRAFT TOLERANCE IN RHESUS MONKEYS (1997)

A major challenge in clinical transplantation today is to design a practical and effective protocol for tolerance induction compatible with cadaver organ transplantation. A preclinical rhesus monkey kidney allograft model using immediate peritransplant anti-CD3 immunotoxin (anti-CD3-IT) and donor bone marrow (DBM) is shown here to induce operational tolerance with prolonged graft survival in the absence of chronic immunosuppressive drugs. Bone marrow harvested from the kidney donor was depleted of mature alloantigen-presenting cells and T cells by removing DR(bright) cells and CD3(bright) cells, respectively. In outbred, major histocompatibility complex-incompatible donor-recipient pairs with high pretransplant mixed lymphocyte response and cytotoxic T lymphocyte precursor activity, four of six allografts survived for periods of 120 days to >1.5 years. Graft acceptance after peritransplant treatment followed robust elimination of both peripheral blood T cells and lymph node T cells. In most recipients given anti-CD3-IT and DBM infusion, anti-donor immunoglobulin G responses were completely inhibited. Microchimerism was observed in all recipients studied, including those not given DBM, but levels of microchimerism did not correlate with graft survival. Anti-CD3-IT induction in combination with modified DBM protocols such as the depletion of mature T cells and DR(bright) antigen-presenting cells may offer new opportunities to improve clinical tolerance protocols beyond those attempted in the clinic to date. Overall, these results with anti-CD3-IT show promise for development of cadaver transplant tolerance induction.
SIGNIFICANCE OF THE PLANNED HIGH STANDARD ROADS IN THE ROAD NETWORK OF BOSNIA AND HERZEGOVINA (1990)

The article discusses integration of Bosnia and Herzegovina into the European road network by the construction of motorways. It presents characteristics of the existing road network in Bosnia and Herzegovina and its integration into the Yugoslav road network. It describes development of the future road network in Bosnia and Herzegovina (motorways, semi-motorways and expressways) up to the year 2020. The future Bosanski Samac-Opuzen motorway as part of the Trans European motorway network has been described as a skeleton of the road network.
Key Agreement in Peer-to-Peer Wireless Networks (2006)

We present a set of simple techniques for key establishment over a radio link in peer-to-peer networks. Our approach is based on the Diffie-Hellmankey agreement protocol, which is known to be vulnerable to the "man-in-the-middle" attack if the two users involved in the protocol do not share any authenticated information about each other (e.g., public keys, certificates, passwords,shared keys, etc.) prior to the protocol execution. In this paper, we solve the problem by leveraging on the natural ability of users to authenticate each other by visual and verbal contact. We propose three techniques. The first is based on visual comparison of short strings, the second on distance bounding, and the third on integrity codes; in each case, the users do not need to enter any password or other data, nor do they need physical or infrared connectivity between their devices. We base our analysis on a well-established methodology that leads us to a rigorous modularization and a thorough robustness proof of our proposal.
The antioxidant effects of a novel iron chelator salicylaldehyde isonicotinoyl hydrazone in the prevention of H2O2 injury in adult cardiomyocytes (2000)

The data indicate that SIH provides a very powerful and very fast protection against the oxidative stress exerted by H(2)O(2) presumably via the iron-mediated Fenton reaction producing hydroxyl radical (OH), whereas the protective effect of DFO is hindred by its very slow and rather limited intracellular entry, and the protection that MIA exerts via the inhibition of Na(+)/H(+) exchange against H(2)O(2) much less effective.
Implantable Sensors for Regenerative Medicine (2016)

The translation of many tissue engineering/regenerative medicine (TE/RM) therapies that demonstrate promise in vitro are delayed or abandoned due to reduced and inconsistent efficacy when implemented in more complex and clinically relevant preclinical in vivo models. Determining mechanistic reasons for impaired treatment efficacy is challenging after a regenerative therapy is implanted due to technical limitations in longitudinally measuring the progression of key environmental cues in vivo. The ability to acquire real-time measurements of environmental parameters of interest including strain, pressure, pH, temperature, oxygen tension, and specific biomarkers within the regenerative niche in situ would significantly enhance the information available to tissue engineers to monitor and evaluate mechanisms of functional healing or lack thereof. Continued advancements in material and fabrication technologies utilized by microelectromechanical systems (MEMSs) and the unique physical characteristics of passive magnetoelastic sensor platforms have created an opportunity to implant small, flexible, low-power sensors into preclinical in vivo models, and quantitatively measure environmental cues throughout healing. In this perspective article, we discuss the need for longitudinal measurements in TE/RM research, technical progress in MEMS and magnetoelastic approaches to implantable sensors, the potential application of implantable sensors to benefit preclinical TE/RM research, and the future directions of collaborative efforts at the intersection of these two important fields.