gebhart/patrepeval huggingface dataset:
Behavior of Transplanted Bone Marrow-derived GFP Mesenchymal Cells in Osteochondral Defect as a Simulation of Autologous Transplantation (2005)

To elucidate the behavior of autologously transplanted mesenchymal cells in osteochondral defects, we followed transplanted cells using green fluorescent protein (GFP) transgenic rats, in which all cells express GFP signals in their cytoplasm and nuclei as transplantation donors. Bone marrow-derived mesenchymal cells, which contain mesenchymal stem cells (MSCs), were obtained from transgenic rats. Then, dense mesenchymal cell masses created by hanging-drop culture were transplanted and fixed with fibrin glue into osteochondral defects of wild-type rats. At 24 weeks after surgery, the defects were repaired with hyaline-like cartilage and subchondral bone. GFP positive cells, indicating transplanted mesenchymal-derived cells, were observed in the regenerated tissues for 24 weeks although GFP positive cells decreased in number with time. Because GFP causes no immunological rejection and requires no chemicals for visualization, transplantation between transgenic and wild-type rats can be regarded as a simulation of autologous transplantation, and the survivability of transplanted cells are able to be followed easily and reliably. Thus, the behavior of transplanted mesenchymal cells was able to be elucidated in vivo by this strategy, and the results could be essential in future tissue engineering for the regeneration of osteochondral defects with original hyaline cartilage and subchondral bone.
Grafting of in vitro cultured melanocytes onto laser-ablated lesions in vitiligo (1998)

A variety of grafting procedures using autologous melanocytes have achieved promising results in the treatment of vitiligo. We here report on the preparation of an adequate graft recipient bed by pulsed Erbium-YAG laser skin ablation. In particular, for irregular lesions on delicate sites, which cannot be approached by utilization of suction blisters or dermabrasion, this technique may offer a distinct advantage.
Poly(oxazoline)s with Telechelic Antimicrobial Functions (2004)

Poly(2-alkyl-1,3-oxazoline)s (alkyl = methyl, ethyl) with terminal quarternary ammonium groups were synthesized. It could be shown by NMR and ESI-MS that the termination of the living polymerization with N,N-dimethylalkyl(butyl to hexadecyl)amines was quantitative. The novel functions were investigated regarding their antimicrobial potential toward the bacterium Staphylococcus aureus revealing that only quarternary ammonium functions with 12 and more carbons are antibacterial. Using a novel bifunctional initiator, 3-[(tert-butoxycarbonyl)amino]benzyl-p-toluenesulfonate, poly(oxazoline) with a primary amino group at the starting end and an antimicrobial function at the terminal could be synthesized, as confirmed by NMR and ESI-MS measurements. Comparing the bioactivity of polymers with different functions at the starting end and terminated with dimethyldodecylamine revealed that the starting group has a great effect on the antibacterial properties of the distant terminal. The minimal inhibitory concentrations varied from 0.1 mM for polymer derivatives with a BOC-NH-phenyl starting group to 4 mM for poly(oxazoline)s with a free primary amine at the starting end.
Dimerization with Cannabinoid Receptors Allosterically Modulates Delta Opioid Receptor Activity during Neuropathic Pain (2012)

The diversity of receptor signaling is increased by receptor heteromerization leading to dynamic regulation of receptor function. While a number of studies have demonstrated that family A G-protein-coupled receptors are capable of forming heteromers in vitro, the role of these heteromers in normal physiology and disease has been poorly explored. In this study, direct interactions between CB(1) cannabinoid and delta opioid receptors in the brain were examined. Additionally, regulation of heteromer levels and signaling in a rodent model of neuropathic pain was explored. First we examined changes in the expression, function and interaction of these receptors in the cerebral cortex of rats with a peripheral nerve lesion that resulted in neuropathic pain. We found that, following the peripheral nerve lesion, the expression of both cannabinoid type 1 receptor (CB(1)R) and the delta opioid receptor (DOR) are increased in select brain regions. Concomitantly, an increase in CB(1)R activity and decrease in DOR activity was observed. We hypothesize that this decrease in DOR activity could be due to heteromeric interactions between these two receptors. Using a CB(1)R-DOR heteromer-specific antibody, we found increased levels of CB(1)R-DOR heteromer protein in the cortex of neuropathic animals. We subsequently examined the functionality of these heteromers by testing whether low, non-signaling doses of CB(1)R ligands influenced DOR signaling in the cortex. We found that, in cortical membranes from animals that experienced neuropathic pain, non-signaling doses of CB(1)R ligands significantly enhanced DOR activity. Moreover, this activity is selectively blocked by a heteromer-specific antibody. Together, these results demonstrate an important role for CB(1)R-DOR heteromers in altered cortical function of DOR during neuropathic pain. Moreover, they suggest the possibility that a novel heteromer-directed therapeutic strategy for enhancing DOR activity, could potentially be employed to reduce anxiety associated with chronic pain.
Theoretical study of the secondary structures of unionized Poly(γ-D-glutamic acid) (2004)

Poly(γ-D-glutamic acid), 1, the only natural γ-peptides, have many important biological functions. The secondary structures of a hexamer model of unionized γDPGA, 3, have been studied by a quantum mechanical method (B3LYP/6-31G*), including the solvent effect using the SCIPCM model. Frequency calculations were carried out using the HF/6-31G* method. Calculations indicate that a right-handed 19-helix is the most stable secondary structure. The calculated electronic circular dichroism spectrum of the right-handed 19-helix agrees with the experimental spectrum quite well, which further supports the above prediction. A right-handed 14-helical structure is also found to be quite stable in the gas phase.
High brightness visible (660 nm) resonant-cavity light-emitting diode (1998)

Visible (660 nm) resonant-cavity light-emitting (RCLEDs) have been fabricated. The top-emitting devices employed two AlGaAs-AlAs-Bragg mirrors and GaInP-AlGaInP quantum-well active layers. The device performance was characterized as a function of the device diameters, ranging from 24 to 202 μm. The larger devices exhibited a nearly linear increase of output power with injected current with 8.4-mW emission at 120 mA. A maximum external efficiency of 4.8% was measured at 4 mA on the 84-μm aperture devices. All devices exhibited a narrow emission at 659-661 nm with a linewidth around 3 nm. The results show that RCLED's are promising low-cost light sources for plastic fiber transmission as well as display applications.
Exosome Function: From Tumor Immunology to Pathogen Biology (2008)

Exosomes are the newest family member of 'bioactive vesicles' that function to promote intercellular communication. Exosomes are derived from the fusion of multivesicular bodies with the plasma membrane and extracellular release of the intraluminal vesicles. Recent studies have focused on the biogenesis and composition of exosomes as well as regulation of exosome release. Exosomes have been shown to be released by cells of hematopoietic and non-hematopoietic origin, yet their function remains enigmatic. Much of the prior work has focused on exosomes as a source of tumor antigens and in presentation of tumor antigens to T cells. However, new studies have shown that exosomes might also promote cell-to-cell spread of infectious agents. Moreover, exosomes isolated from cells infected with various intracellular pathogens, including Mycobacterium tuberculosis and Toxoplasma gondii, have been shown to contain microbial components and can promote antigen presentation and macrophage activation, suggesting that exosomes may function in immune surveillance. In this review, we summarize our understanding of exosome biogenesis but focus primarily on new insights into exosome function. We also discuss their possible use as disease biomarkers and vaccine candidates.
Ribosome activity and modification of 16S RNA are influenced by deletion of ribosomal protein S20 (1993)

A spontaneous mutant of Escherichia coli K-12 was isolated that shows an increased misreading ability of all three nonsense codons together with an inability to grow at 42 degrees C. It is demonstrated that the mutation is a deletion of the gene rpsT, coding for ribosomal protein S20. The loss of this protein not only influences the decoding properties of the ribosome; the modification pattern of 16S ribosomal RNA is also changed. This leads to a deficiency in the ability of the mutant to associate its 30S subunits with 50S subunits to form 70S ribosomes. It is suggested that two modified bases, m5C and m6(2)A, are directly or indirectly essential for association of subunits to functional ribosomes in the rpsT mutant strain. Two other modifications were also studied; m2G which is not affected at all and m3U which is undermodified in both active and inactive subunits and, therefore, not involved in subunit association.
Comment on “Hydrocarbon emissions characterization in the Colorado Front Range: A pilot study” by Gabrielle Pétron et al. (2012)

Pétron et al. (2012) have recently observed and analyzed alkane concentrations in air in Colorado's Weld County and used them to estimate the volume of methane vented from oil and gas operations in the Denver‐Julesburg Basin. They conclude that “the emissions of the species we measured are most likely underestimated in current inventories”, often by large factors. However, their estimates of methane venting, and hence of other alkane emissions, rely on unfounded assumptions about the composition of vented natural gas. We show that relaxing those assumptions results in much greater uncertainty. We then exploit previously unused observations reported in Pétron et al. (2012) to constrain methane emissions without making assumptions about the composition of vented gas. This results in a new set of estimates that are consistent with current inventories but inconsistent with the estimates in Pétron et al. (2012). The analysis also demonstrates the value of the mobile air sampling method employed in Pétron et al. (2012).
The Influence of Crystallization Conditions on Radiation Effects in Polyethylene - I. Crystallization from Dilute Solution and from the Melt (1961)

Samples of Marlex 50 crystallized from dilute solution (yielding single crystals) and in the bulk form were irradiated by high-energy electrons and the solubilities compared. The single-crystal specimens remained fully soluble after a dose of 20 megarads, which rendered the bulk two-thirds to three-quarters insoluble. Since the initial free-radical concentration was identical and the chemical changes induced were not widely different in the two kinds of specimens, it is suggested that intramolecular crosslinks, occurring in a larger number in the single crystals, are responsible for this behavior. At high doses the same solubility limit is approached by both specimens, which is ascribed to the possibility of chain cutting becoming increasingly ineffective in the single crystal. In the light of these findings, the limitations of the conventional treatment of radiation effects are discussed and the possible significance of the present results for morphological problems is pointed out. A number of further effects are reported in connection with melting behavior and spin resonance spectra that are at variance with results in the literature.
A Simple Hanging Drop Cell Culture Protocol for Generation of 3D Spheroids (2011)

Studies of cell-cell cohesion and cell-substratum adhesion have historically been performed on monolayer cultures adherent to rigid substrates. Cells within a tissue, however, are typically encased within a closely packed tissue mass in which cells establish intimate connections with many near-neighbors and with extracellular matrix components. Accordingly, the chemical milieu and physical forces experienced by cells within a 3D tissue are fundamentally different than those experienced by cells grown in monolayer culture. This has been shown to markedly impact cellular morphology and signaling. Several methods have been devised to generate 3D cell cultures including encapsulation of cells in collagen gels or in biomaterial scaffolds. Such methods, while useful, do not recapitulate the intimate direct cell-cell adhesion architecture found in normal tissues. Rather, they more closely approximate culture systems in which single cells are loosely dispersed within a 3D meshwork of ECM products. Here, we describe a simple method in which cells are placed in hanging drop culture and incubated under physiological conditions until they form true 3D spheroids in which cells are in direct contact with each other and with extracellular matrix components. The method requires no specialized equipment and can be adapted to include addition of any biological agent in very small quantities that may be of interest in elucidating effects on cell-cell or cell-ECM interaction. The method can also be used to co-culture two (or more) different cell populations so as to elucidate the role of cell-cell or cell-ECM interactions in specifying spatial relationships between cells. Cell-cell cohesion and cell-ECM adhesion are the cornerstones of studies of embryonic development, tumor-stromal cell interaction in malignant invasion, wound healing, and for applications to tissue engineering. This simple method will provide a means of generating tissue-like cellular aggregates for measurement of biomechanical properties or for molecular and biochemical analysis in a physiologically relevant model.
Physiological preparation for studying the response of subcutaneously implanted glucose and oxygen sensors (1989)

A physiological preparation has been developed for studying the response of glucose end oxygen sensors chronically implanted in subcutaneous tissues. The preparation employs a chamber permanently mounted on the back of a rat that supports the growth of vascularized subcutaneous tissue around the sensors and is used in conjunction with chronic intravascular catheters for blood sampling and fluid infusion. A total of 26 glucose and oxygen sensors were implanted in nine chambers. At 10 days, the tissue surrounding the sensors was cellular, well vascularized and permeable. Glucose sensors responded to glucose infusions with a 10-15 minute lag.
c‐fos and estrogen receptor gene expression pattern in the rat uterine epithelium during the estrous cycle (2003)

Different studies in ovariectomized estrogen treated animals support the idea that c-fos plays a role in the proliferation of uterine epithelial cells. However, these studies invite us to reassess the role played by c-fos in epithelial cell types of the endometrium during the estrous cycle. The present study was undertaken to determine the c-fos and estrogen receptor (ER) gene expression pattern in the rat uterine epithelium during the estrous cycle in which natural and cyclic changes of steroid hormones occur, and correlate these changes with the proliferation status of this cellular types. Proliferation was assessed during the estrous cycle using bromodeoxyuridine incorporation to DNA. ERalpha and beta proteins were assessed by immunohistochemistry. The regulation of c-fos gene expression in the uterus of intact animals during the estrous cycle was evaluated using both in situ hybridization and immunohistochemistry. Estradiol (E(2)) and progesterone (P(4)) plasma levels were assessed by radioimmunoassay. The results indicated that luminal (LE) and glandular epithelia (GE) presented maximal proliferation during the metestrus (M) and the diestrus (D) days. However, during the proestrus (P) day only LE presented proliferation, and during the estrus (E) day only the stromal cells proliferated. A marked immunostaining for ERalpha was detected in both LE and GE cells during the early phases of the cycle but diminished on the P and the E day. In contrast, ERbeta was undetectable in both epithelia during all stages of the cycle. The highest c-fos mRNA level was detected in both epithelia on the M day, followed by a significant reduction during the other days of the cycle. The highest protein content was observed on the M and D days, and the minimal value was detected on the E day. The c-Fos protein level in LE was increased during M and D days, presenting a high correlation with the cellular proliferation pattern of this cell type. In conclusion, the overall results indicate that c-Fos protein presented a good correlation with uterine epithelial cell proliferation of LE. In the case of GE, the same tendency was observed, although no significant correlation was found. Both in LE and GE, c-fos mRNA did not strictly correlate with its protein levels. c-fos seems to have a postranscriptional regulation in uterine epithelial cells during the rat's estrous cycle.
Superhydrophilic Smart Coating for Self-Cleaning Application on Glass Substrate (2018)

In general, superhydrophilic coating on glass substrate possesses water contact angle (WCA) below 10° and contains high self-cleaning properties in outdoor environment as compared to noncoated glass substrate panels. In this study, the superhydrophilic coating behavior on glass substrate has been developed. The micro- and nanosized titanium dioxide (TiO 2 ) particles have been utilized to improve the surface roughness, and the polypropylene glycol (PPG) has been utilized to increase the surface energy of glass substrates. The wettability of coating surface shows the coating possess water contact angle (WCA) as low as 5° and suddenly reduce to 0° after 10 s. Superhydrophilic coated glass clearly shows excellent dirt repellent against dilute ketchup solution due to the absence of dirt streak on the glass surface. Meanwhile, the dirt streak is present on the bare glass surface indicating its weak self-cleaning property. The developed superhydrophilic coating on glass substrate was also found to have great antifog property compared to the bare glass substrate. Superhydrophilic surfaces have showed free tiny droplet even at 130°C of hot boiling bath for 10 min and completely dry after 1 min. The superhydrophilic coating surfaces have demonstrated free water streak after impacting with harsh water spraying for 5 min confirming that the superhydrophilic coating on glass substrate is antiwater streak.
A Putative α-Helical Structure Which Overlaps the Capsid-p2 Boundary in the Human Immunodeficiency Virus Type 1 Gag Precursor Is Crucial for Viral Particle Assembly (1998)

The capsid (CA) and nucleocapsid domains of the human immunodeficiency virus type 1 Gag polyprotein are separated by the p2 spacer peptide, which is essential for virus replication. Previous studies have revealed that p2 has an important role in virus morphogenesis. In this paper, we show that a crucial assembly determinant maps to the highly conserved N terminus of p2, which is predicted to form part of an alpha-helix that begins in CA. A mutational analysis indicates that the ability of the N terminus of p2 to adopt an alpha-helical structure is essential for its function during virus assembly. To prevent CA-p2 processing, it was necessary to mutate both the CA-p2 cleavage site and an internal cleavage site within p2. Virions produced by the double mutant lacked a conical core shell and instead contained a thin electron-dense shell about 10 nm underneath the virion membrane. These results suggest that p2 is transiently required for proper assembly, but needs to be removed from the C terminus of CA to weaken CA-CA interactions and allow the rearrangement of the virion core shell during virus maturation.
Response of Staphylococcus aureus Isolates from Bovine Mastitis to Exogenous Iron Sources (2002)

Staphylococcus aureus can survive in conditions of extremely low iron concentration. The ability of S. aureus to use two exogenous hydroxamate types of siderophores (desferrioxamine and ferrichrome) and four iron-containing proteins found in cattle (hemin, hemoglobin, ferritin, and lactoferrin) were tested on 16 reference and clinical isolates. For all strains tested, ferrichrome and desferrioxamine showed strong growth-promoting activities in a disk diffusion assay and in liquid medium. The heme proteins hemin and hemoglobin were also found to support growth in culture media lacking other iron sources, while lactoferrin failed to do so. On media containing the iron chelator dipyridyl, ferritin induced a growth inhibition effect that was further enhanced in the presence of lactoferrin in seven of the 13 tested strains. Staphylococcus aureus was able to bind hemin and the level of binding activity was not increased after growth in iron-rich or -poor media. Dot-blot competition tests showed that biotin-labeled lactoferrin binds to S. aureus, and this binding can be inhibited by unlabeled lactoferrin. Expression of lactoferrin-binding activity was independent of the level of iron in the medium and the iron saturation status of lactoferrin. For each strain tested, ligand blots showed lactoferrin-binding proteins of molecular weights ranging from 32 to 92 kDa. Possible functions of these lactoferrin-binding proteins could not be related to iron acquisition mechanism in S. aureus.
Identification of a key molecular regulator of liver metastasis in human pancreatic carcinoma using a novel quantitative model of metastasis in NOD/SCID/γcnull (NOG) mice (2007)

We developed a reliable new model system for assaying liver metastasis using NOD/SCID/gamma(c)(null) (NOG) mice. Seven human pancreatic cancer cell lines were examined for their ability to form diverse metastatic foci in the livers of NOD/SCID and NOG mice. Capan-2 and PL45 showed no metastasis when seeded at up to 10(5) cells in both strains, and no BxPC-3 metastasis was observed in NOD/SCID mice. The NOD/SCID mouse model detected liver metastasis only in the AsPC-1 cell line when inoculated with >10(3) cells. In contrast, when inoculated with only 10(2) MIA PaCa-2, AsPC-1 and PANC-1 cells, liver metastasis was evident in 71.4% (5/7), 57.1% (4/7) and 37.5% (3/8) of the NOG mice, respectively. Capan-1 and BxPC-3 cells metastasized when seeded at 10(3) cells in 50% (5/10) and in 12.5% (1/8) of the mice, respectively. Using the NOG mouse model system, we established a highly metastatic cell line, liver metastasized-BxPC-3 (LM-BxPC-3), from liver metastatic foci formed by the relatively poorly metastatic parental BxPC-3 cell line. The gene expression profiles of parental and LM-BxPC-3 cells were compared, and we identified forty-five genes that were either upregulated or downregulated >4-fold in the LM-BxPC-3 cell line. We validated 9 candidate protein-coding sequences, and examined the correlation between their expression pattern and the in vivo liver metastatic potential of all 7 pancreatic cancer cell lines. Only S100A4 expression correlated with the ability to form liver metastases, as evaluated in our quantitative model of metastasis in NOG mice. These results suggested that S100A4 is a key regulator of liver metastasis in pancreatic cancer, and demonstrated the feasibility of using the quantitative metastasis model to search for and develop new anti-cancer therapies and novel drugs against this and other key molecules.