gebhart/patrepeval huggingface dataset:
Olfactory Horizontal Basal Cells Demonstrate a Conserved Multipotent Progenitor Phenotype (2004)

Stem cells of adult regenerative organs share a common goal but few established conserved mechanisms. Within the neural stem cell niche of the mouse olfactory epithelium, we identified a combination of extracellular matrix (ECM) receptors that regulate adhesion and mitosis in non-neural stem cells [intercellular adhesion molecule-1 (ICAM-1), beta1, beta4, and alpha-1, -3, and -6 integrins] and on horizontal basal cells (HBCs), candidate olfactory neuro-epithelial progenitors. Using ECM receptors as our guide, we recreated a defined microenvironment in vitro that mimics olfactory basal lamina and, when supplemented with epidermal growth factor, transforming growth factor alpha, and leukemia inhibitory factor, allows us to preferentially expand multiple clonal adherent colony phenotypes from individual ICAM-1+ and ICAM-1+/beta1 integrin+-selected HBCs. The most highly mitotic colony-forming HBCs demonstrate multipotency, spontaneously generating more ICAM-positive presumptive HBCs, a combination of olfactory neuroglial progenitors, and neurons of olfactory and potentially nonolfactory phenotypes. HBCs thus possess a conserved adhesion receptor expression profile similar to non-neural stem cells, preferential self-replication in an in vitro environment mimicking their in vivo niche, and contain subpopulations of cells that can produce multiple differentiated neuronal and glial progeny from within and beyond the olfactory system in vitro.
Overlapping and discrete aspects of the pathology and pathogenesis of the emerging human pathogenic coronaviruses SARS‐CoV, MERS‐CoV, and 2019‐nCoV (2020)

First reported from Wuhan, The People's Republic of China, on 31 December 2019, the ongoing outbreak of a novel coronavirus (2019-nCoV) causes great global concerns. Based on the advice of the International Health Regulations Emergency Committee and the fact that to date 24 other countries also reported cases, the WHO Director-General declared that the outbreak of 2019-nCoV constitutes a Public Health Emergency of International Concern on 30 January 2020. Together with the other two highly pathogenic coronaviruses, the severe acute respiratory syndrome coronavirus (SARS-CoV) and Middle East respiratory syndrome coronavirus (MERS-CoV), 2019-nCov and other yet to be identified coronaviruses pose a global threat to public health. In this mini-review, we provide a brief introduction to the pathology and pathogenesis of SARS-CoV and MERS-CoV and extrapolate this knowledge to the newly identified 2019-nCoV.
A novel extracellular cyclic lipopeptide which promotes flagellum-dependent and -independent spreading growth of Serratia marcescens (1992)

Serrawettin W2, a surface-active exolipid produced by nonpigmented Serratia marcescens NS 25, was examined for its chemical structure and physiological functions. The chemical structure was determined by degradation analyses, infrared spectroscopy, mass spectrometry, and proton magnetic resonance spectroscopy. Serrawettin W2 was shown to be a novel cyclodepsipeptide containing a fatty acid (3-hydroxydecanoic acid) and five amino acids. The peptide was proposed to be D-leucine (N-bonded to the carboxylate of the fatty acid)-L-serine-L-threonine-D-phenylalanine-L-isoleucine (bonded to the 3-hydroxyl group). By examining the effects of isolated serrawettin W2 on serrawettinless mutants, this lipopeptide was shown to be active in the promotion of flagellum-independent spreading growth of the bacteria on a hard agar surface. The parent strain NS 25 formed a giant colony with a self-similar characteristic after incubation for a relatively long time (1 to 2 weeks), similar to other fractal colony-producing strains of S. marcescens (producers of the different serrawettins W1 and W3). On a semisolid medium that permitted flagellum-dependent spreading growth, an external supply of serrawettin W2 accelerated surface translocation of a serrawettinless mutant during a short period (12 h) of observation. In contrast, bacterial translocation in the subsurface space of the semisolid agar was not enhanced by serrawettins. Thus, the extracellular lipids seem to contribute specifically to the surface translocation of the bacteria by exhibiting surfactant activity.
Histology of Retrieved Immediately and Early Loaded Oxidized Implants: Light Microscopic Observations after 5 to 9 Months of Loading in the Posterior Mandible (2003)

The present study demonstrated that oxidized implants subjected to immediate or early loading do integrate with soft and bone tissues in the posterior mandible.
Characterization of antigens from mycoplasmas of animal origin (1983)

Alcholeplasma laidlawii, Mycoplasma gallisepticum, M mycoides subsp mycoides, M agalactiae, M bovirhinis, mycoplasmal strain ST-6, and culture medium were compared with M bovis by sodium dodecyl sulfate-polyacrylamide gel electrophoresis, enzyme-linked immunosorbent assay (ELISA), and gel electrophoresis-derived ELISA. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis indicated there were areas of homology and areas of heterology among the species tested. Sera from rabbits hyperimmunized with the mycoplasma organisms and noninoculated culture medium demonstrated ELISA reactivity with M bovis antigens immobilized on polystyrene. Absorption of the serum from a rabbit hyperimmunized with M bovis reduced 65.9% of its reactivity with culture medium, 29.7% to 32.7% of its reactivity with the heterologous species, and 21.1% of its reactivity with the homologous species. Gel electrophoresis-derived ELISA performed on immobilized M bovis antigens separated by molecular weight, using sera from rabbits hyperimmunized with the mycoplasmal species under study and noninoculated culture medium revealed antigenic components which are shared among species or with the culture medium and several components which may be unique to M bovis.
Windows and EnvironmentalSatisfaction: A Survey Study ofan Office Building (1993)

Postoccupancy evaluations of office buildings often are conducted without taking into consideration certain characteristics which cause the survey sample units to be different. This study examines the differences in the responses of two groups of workers within the same building by examining differences characterized by the presence or absence of windows at workers’ stations. This parameter is important to study as its existence is inevitable especially in large office buildings, where a proportion of the workstations is located along the peripheral window walls and the other in the core area of the floor. This study indicates that the proximity to windows can affect workers’ perception of the importance of some workspace attributes, their satisfaction with them, as well as their overall satisfaction with the workplace.
Analysis of a continuous-culture technique for the selection of mutants tolerant to extreme environmental stress (1999)

An analysis is presented of a continuous-culture technique named "Brown and Oliver Interactive-Continuous Selection" (BOICS; Brown and Oliver, 1982), that was devised for the selection of microbial mutants tolerant to extreme environmental stress. The case in which the stress is due to a growth inhibitor is considered. The possible steady outcomes of competition between mutants in BOICS are analyzed under the assumption that the specific growth rates of the competing mutants depend only on the inhibitor concentration. The analysis indicates that BOICS selects mutants that sustain a given specific growth rate (equal to the dilution rate in the selection experiment) at an increased concentration of the inhibitor. Simulation results support the steady-state analysis. Further simulation results show that BOICS may fail if the specific growth rate of a mutant has to be considered to depend on a factor beside the inhibitor concentration. The choice of experimental conditions that promote the success of BOICS is discussed. An interpretation of BOICS emerges from the analysis. Namely, that BOICS implements (at least approximately) a strategy for the selection of tolerant mutants in which (1) all factors in the growth environment, beside the stress of interest (inhibitor concentration) are maintained constant, and (2) the stress is adjusted as the culture evolves so that it is always maximized subject to a specified minimum value of the mean specific-growth rate being maintained. This interpretation suggests new (possibly improved) ways of implementing essentially the same selection technique. It is noted that a chemostat implements the same strategy in the case that the stress is due to the lack of a growth-rate-limiting nutrient. The outcome of selection for inhibitor tolerant mutants in chemostats, turbidostats, and in BOICS is compared. Only BOICS selects specifically for mutants tolerant to extreme concentrations of the inhibitor.
Phase I trial of intratumoral liposome E1A gene therapy in patients with recurrent breast and head and neck cancer. (2001)

Gene therapy with an E1A gene:lipid complex appears to be safe and warrants further testing.
Theory of the differential capacity of the oxide/aqueous electrolyte interface (1971)

The conditions under which an oxide surface in aqueous solution will obey the Nernst equation with respect to H+/OH– as potential-determining ions are investigated and a modified form of the Nernst equation is derived. This is combined with a model of the inner part of the double layer involving adsorption of both anions and cations of a supporting uni-univalent electrolyte and a discreteness-of-charge correction in their adsorption isotherms. Theoretical total differential capacities at the interface are compared with experimental data for TiO2 and SiO2.
Starch branching enzymes belonging to distinct enzyme families are differentially expressed during pea embryo development (1995)

cDNA clones for two isoforms of starch branching enzyme (SBEI and SBEII) have been isolated from pea embryos and sequenced. The deduced amino acid sequences of pea SBEI and SBEII are closely related to starch branching enzymes of maize, rice, potato and cassava and a number of glycogen branching enzymes from yeast, mammals and several prokaryotic species. In comparison with SBEI, the deduced amino acid sequence of SBEII lacks a flexible domain at the N‐terminus of the mature protein. This domain is also present in maize SBEII and rice SBEIII and resembles one previously reported for pea granule‐bound starch synthase II (GBSSII). However, in each case it is missing from the other isoform of SBE from the same species. On the basis of this structural feature (which exists in some isoforms from both monocots and dicots) and other differences in sequence, SBEs from plants may be divided into two distinct enzyme families. There is strong evidence from our own and other work that the amylopectin products of the enzymes from these two families are qualitatively different. Pea SBEI and SBEII are differentially expressed during embryo development. SBEI is relatively highly expressed in young embryos whilst maximum expression of SBEII occurs in older embryos. The differential expression of isoforms which have distinct catalytic properties means that the contribution of each SBE isoform to starch biosynthesis changes during embryo development. Qualitative measurement of amylopectin from developing and maturing embryos confirms that the nature of amylopectin changes during pea embryo development and that this correlates with the differential expression of SBE isoforms.
Stable Incorporation of Gold Nanorods into N-Isopropylacrylamide Hydrogels and Their Rapid Shrinkage Induced by Near-Infrared Laser Irradiation (2007)

In this study, we prepared gold nanorod (NR)-embedded N-isopropylacrylamide (NIPAM) hydrogels and studied their volume phase transition behavior induced by near-infrared (near-IR) laser irradiation utilizing the photothermal conversion characteristics of the NRs. When poly(ethylene glycol)-modified NRs were used for the preparation of composite gels, the NRs showed marked dispersion stability in the gel. Near-IR laser irradiation of the gel (cylindrical shape, diameter = 140 microm) under the following conditions, NR concentrations in the gel > or =100 microM and laser irradiation power > or =490 mW, resulted in shrinkage of the gel in the following manner: (1) waist formation around the irradiation spot and (2) growth of the waist along the axial directions of the gel. The gel shrinking induced by near-IR irradiation occurred much more rapidly than that afforded by a temperature jump, because the former was not accompanied by the skin layer formation, which disturbs the rapid shrinking of the gels. When a composite gel containing the model drug (rhodamine-labeled dextran) was irradiated with a near-IR laser, the rapid release of the drug was observed. Taking advantage of the high spatial resolution of the irradiation point, we further achieved the irradiation-point-specific release of the drug from one such gel.
Mechanisms of atrial natriuretic peptide secretion from the atrium (2005)

Since the discovery of atrial natriuretic peptide (ANP) more than 20 years ago, numerous studies have focused on the mechanisms regulating ANP secretion. From a physiological standpoint, the most important factor governing ANP secretion is mechanical stretching of the atria, which normally occurs when extracellular fluid volume or blood volume is elevated. In addition, the ability of several vasoconstrictors to increase ANP secretion can be traced to their indirect effects on atrial stretch via increases in cardiac preload or afterload. Whether vasoconstrictors such as angiotensin II and vasopressin have a direct positive or negative effect on ANP secretion has not been determined with certainty. Two paracrine factors derived from endothelial cells play important roles in modulating ANP secretion. Endothelin, a potent vasoconstrictor, stimulates ANP secretion and augments stretch induced ANP secretion. The dramatic increase in ANP release produced by cardiac ischemia appears to be mediated in part by endothelin. Nitric oxide (NO), an important vasodilator, is also produced by endothelial cells and inhibits ANP secretion acting through cyclic GMP as an intracellular messenger. Several recent studies have helped to define the cellular mechanism contributing to regulation of ANP secretion including stretch-activated ion channels, prostaglandins, cytochrome P450, G proteins and cell calcium. A number of steps in the cellular transduction of the ANP signal remain to be resolved. The release of ANP in disease states such as myocardial infarction and heart failure appears to be related to both mechanical and cellular events.
Selective Mitochondrial Damage by a Ruby Laser Microbeam: An Electron Microscopic Study (1965)

A pulsed ruby laser microbeam produces changes in single living cells stained with a low concentration of Janus green B. Electron micrographs show that such alterations are the result of morphological damage sustained by and restricted to the mitochondria in the irradiated area.
Laser‐Assisted Fabrication Techniques (2011)

This chapter contains sections titled: Introduction Pulsed Laser Techniques Continuous Laser Heating Summary
Phase 1 study of the antimesothelin immunotoxin SS1P in combination with pemetrexed and cisplatin for front‐line therapy of pleural mesothelioma and correlation of tumor response with serum mesothelin, megakaryocyte potentiating factor, and cancer antigen 125 (2014)

SS1P given with pemetrexed and cisplatin is safe and well tolerated and exhibits significant antitumor activity in patients with unresectable, advanced pleural mesothelioma. Serum mesothelin, megakaryocyte potentiating factor, and cancer antigen 125 levels correlated with objective tumor responses.
Synthesis and Properties of New Antisense Oligodeoxynucleotides Containing Benzylphosphonate Linkages (1996)

Synthetic antisense oligonucleotides are widely used as inhibitors of gene expression in cultured cells and have been proposed as potential therapeutic agents. In recent years, a great deal of effort has been directed toward the synthesis of analogs with an altered phosphodiester linkage to improve the stability of duplex formation, to improve the cellular uptake, and to decrease the rate of degradation of oligonucleotides by nucleases that cleave the phosphodiester linkage. We report here on the synthesis of oligonucleotides containing benzylphosphonate linkages. For this purpose, we prepared four fully protected benzylamidites and incorporated them into oligonucleotides using an automated DNA synthesizer. Compared with unmodified oligonucleotides and methylphosphonates, the benzylphosphonates are more stable against nucleases and exhibit a higher lipophilicity. Incorporation of benzylphosphonate linkages only slightly weakens the thermal stability of the duplex. The 18-mer oligonucleotide 5' A*T*GTT*GCCC*CATC*ATA*AA 3' with seven benzylphosphonate linkages (*) directed against the start of the pre-S-region of duck hepatitis B virus resulted in a 40% inhibition of viral replication at a concentration of 1.5 mumol.
Enzymatic Discovery of a HER-2/neu Epitope That Generates Cross-Reactive T Cells (2012)

Patients with HER-2/neu-expressing breast cancer remain at risk for relapse following standard therapy. Vaccines targeting HER-2/neu to prevent relapse are in various phases of clinical testing. Many vaccines incorporate the HER-2/neu HLA-A2-binding peptide p369-377 (KIFGSLAFL), because it has been shown that CTLs specific for this epitope can directly kill HER-2/neu-overexpressing breast cancer cells. Thus, understanding how tumors process this epitope may be important for identifying those patients who would benefit from immunization. Proteasome preparations were used to determine if p369-377 was processed from larger HER-2/neu-derived fragments. HPLC, mass spectrometry, cytotoxicity assays, IFN-γ ELISPOT, and human breast cancer cell lines were used to assess the proteolytic fragments. Processing of p369-377 was not detected by purified 20S proteasome and immunoproteasome, indicating that tumor cells may not be capable of processing this Ag from the HER-2/neu protein and presenting it in the context of HLA class I. Instead, we show that other extracellular domain HER-2/neu peptide sequences are consistently processed by the proteasomes. One of these sequences, p373-382 (SLAFLPESFD), bound HLA-A2 stronger than did p369-377. CTLs specific for p373-382 recognized both p373-382 and p369-377 complexed with HLA-A2. CTLs specific for p373-382 also killed human breast cancer cell lines at higher levels than did CTLs specific for p369-377. Conversely, CTLs specific for p369-377 recognized p373-382. Peptide p373-382 is a candidate epitope for breast cancer vaccines, as it is processed by proteasomes and binds HLA-A2.
The ABC Transporter BcatrB Affects the Sensitivity of Botrytis cinerea to the Phytoalexin Resveratrol and the Fungicide Fenpiclonil (2001)

During pathogenesis, fungal pathogens are exposed to a variety of fungitoxic compounds. This may be particularly relevant to Botrytis cinerea, a plant pathogen that has a broad host range and, consequently, is subjected to exposure to many plant defense compounds. In practice, the pathogen is controlled with fungicides belonging to different chemical groups. ATP-binding cassette (ABC) transporters might provide protection against plant defense compounds and fungicides by ATP-driven efflux mechanisms. To test this hypothesis, we cloned BcatrB, an ABC transporter-encoding gene from B. cinerea. This gene encodes a 1,439 amino acid protein with nucleotide binding fold (NBF) and transmembrane (TM) domains in a [NBF-TM6]2 topology. The amino acid sequence has 31 to 67% identity with ABC transporters from various fungi. The expression of BcatrB is up regulated by treatment of B. cinerea germlings with the grapevine phytoalexin resveratrol and the fungicide fenpiclonil. BcatrB replacement mutants are not affected in saprophytic growth on different media but are more sensitive to resveratrol and fenpiclonil than the parental isolate. Furthermore, virulence of deltaBcatrB mutants on grapevine leaves was slightly reduced. These results indicate that BcatrB is a determinant in sensitivity of B. cinerea to plant defense compounds and fungicides.
Spin Flop Switching of the Guided Synthetic Antiferromagnet MRAM (2006)

A magnetoresistance random access memory (MRAM) with a guided synthetic antiferromagnet (SAF) and direct writing scheme is presented to reduce the writing time. The MRAM cell includes not only the balanced SAF trilayers but also one more guiding layer, which is weakly exchange-coupled with one of the SAF layers. The two orthogonally oriented digital and word lines are aligned at 45deg with respect to the easy axis of the cell. With the exchange-coupling field from the guiding layer, the MRAM cell can be written directly by the combined field induced by current of the digital and word line. However, the cell cannot be switched by any single field induced by either current due to the balanced SAF structure before saturation. The switching field has been reduced and the writing operation margin has been improved with the use of the exchange-coupling field. Both simulation and the experiments have been carried out to verify this scheme. The write operation margin-H <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">disturb</sub> /H <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">sw</sub> of more than 4.3 has been achieved for the magnetic tunnel junction MRAM cell
Ex vivo expansion of murine marrow cells with interleukin-3 (IL-3), IL- 6, IL-11, and stem cell factor leads to impaired engraftment in irradiated hosts (1996)

In vitro incubation of bone marrow cells with cytokines has been used as an approach to expand stem cells and to facilitate retroviral integration. Expansion of hematopoietic progenitor cells has been monitored by different in vitro assays and in a few instances by in vivo marrow renewal in myeloablated hosts. This is the first report of studies, using two competitive transplant models, in which cytokine-treated cells, obtained from nonpretreated donors (eg, 5-fluorouracil), were competed with normal cells. A basic assumption is that the expansion of progenitors assayed in vitro as high- and low-proliferative potential colony-forming cells (HPP- and LPP-CFCs) indicates an expansion of stem cells which will repopulate in vivo. This study shows that culture of marrow cells with four cytokines (stem cell factor, interleukin-3 [IL-3], IL-6, IL-11) induces significant expansion and proliferation of HPP-CFC and LPP-CFC. Cell-cycle analysis showed that these hematopoietic progenitors were induced to actively cell cycle by culture with these cytokines. In the first competitive transplant model, which uses Ly5.2/Ly5.1 congenic mice, cytokine-cultured Ly5.2 cells competed with noncultured Ly5.1 cells led to 5% +/- 1% engraftment at 12 weeks and to 4% +/- 2% engraftment at 22 weeks posttransplantation for the cytokine exposed cells. Noncultured Ly5.2 cells competed with cultured Ly5.1 cells led to 70% +/- 1% engraftment at 12 weeks and to 93% +/- 2% engraftment at 22 weeks posttransplantation. In the second model, which uses BALB/c marrow of opposite genders, cultured male cells lead to 13% +/- 9% engraftment at 10 weeks and 2% +/- 1% engraftment at 14 weeks posttransplantation; noncultured male cells lead to 70% +/- 2% and 95% +/- 2% engraftment at 10 and 14 weeks posttransplantation, respectively. Data presented here from two different competitive transplant studies show a defect of cytokine expanded marrow related to cell cycle activation which manifests as defective long-term repopulating capability in irradiated host mice. The engraftment defect is more profound at longer time intervals, suggesting that the most striking effect may be on long-term repopulating cells.