gebhart/patrepeval huggingface dataset:
Induction of Apoptosis and Cell-Cycle Arrest in Human Colon-Cancer Cells by Whole-Grain Alkylresorcinols via Activation of the p53 Pathway (2018)

Colon cancer, one of the leading causes of cancer-associated deaths, is the target of choice for nutrition-based-prevention approaches because of the direct and early contact between the active compounds and the cancerous tissues. We previously reported alkylresorcinols (ARs) as the major active components in wheat bran against human colon cancer. Here, we further investigate the anticancer mechanisms of action of ARs. Our mechanistic studies indicated that AR C15 and AR C17 exert their anticancer activities in colon-cancer cells by inducing apoptosis through PUMA upregulation and mitochondrial-pathway activation, inducing cell-cycle arrest through p21 upregulation, and inhibiting proteasome activity and Mdm2 expression. This cascade of distinct mechanisms was linked to the consequent activation and accumulation of p53. The results of treatment with p53 inhibitor further confirmed that the p53 pathway might play a very important role in AR-induced apoptosis in colon-cancer cells. Altogether these results show that AR C15 and AR C17 can specifically activate the mitochondrial pathway of apoptosis and cause cell-cycle arrest and that inhibition of p53 greatly reduces the activation of this pathway.
Long-term effects of new progressive group balance training for elderly people with increased risk of falling – a randomized controlled trial (2012)

This training program provided important positive short and long-term benefits to gait, balance function, and fear of falling.
The evolution of infectious agents in relation to sex in animals and humans: brief discussions of some individual organisms (2011)

The following series of concise summaries addresses the evolution of infectious agents in relation to sex in animals and humans from the perspective of three specific questions: (1) what have we learned about the likely origin and phylogeny, up to the establishment of the infectious agent in the genital econiche, including the relative frequency of its sexual transmission; (2) what further research is needed to provide additional knowledge on some of these evolutionary aspects; and (3) what evolutionary considerations might aid in providing novel approaches to the more practical clinical and public health issues facing us currently and in the future?
Sex differences in oncogenic mutational processes (2020)

Sex differences have been observed in multiple facets of cancer epidemiology, treatment and biology, and in most cancers outside the sex organs. Efforts to link these clinical differences to specific molecular features have focused on somatic mutations within the coding regions of the genome. Here we report a pan-cancer analysis of sex differences in whole genomes of 1983 tumours of 28 subtypes as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium. We both confirm the results of exome studies, and also uncover previously undescribed sex differences. These include sex-biases in coding and non-coding cancer drivers, mutation prevalence and strikingly, in mutational signatures related to underlying mutational processes. These results underline the pervasiveness of molecular sex differences and strengthen the call for increased consideration of sex in molecular cancer research.
Uptake of Dietary Selenium by Laboratory and Field FeedingPodisus maculiventris(Heteroptera: Pentatomidae) (2017)

Podisus maculiventris (Say) (Hemiptera: Pentatomidae) is a generalist predator commercially available for augmentative biological control of pest insects in a variety of crop and orchard systems. It is exposed to a wide variety of micronutrients based on the soil type, plant, and insect prey items consumed. Bioaccumulation of selenium by adult females of P. maculiventris fed insectary-reared Trichoplusia ni Hübner (Lepidoptera: Noctuidae) larval prey was not statistically significant. However, adult females of P. maculiventris collected from the field that had been feeding primarily on alfalfa weevils (Hypera postica Gyllenhal; Coleoptera: Curculionidae), and those fed an artificial diet, showed significant bioaccumulation of selenium. This is the first report of biomagnification of a trace element across 3 trophic levels involving P. maculiventris.
66 DNA METHYLOME ANALYSIS IN NUCLEAR TRANSFER DONOR CELLS AND ITS RELATIONSHIP TO CLONING EFFICIENCY IN SWINE (2010)

The success of cloning by somatic cell nuclear transfer is unpredictable due in part to abnormal patterns of DNA methylation and histone modifications in the donor genome. The state of these epigenetic markers appears to regulate the timing and degree of embryonic gene expression by altering chromatin structure. In this study, we sought to determine the pattern of DNA methylation in genetically distinct clonal populations of swine fetal fibroblast donor cells that have previously been demonstrated to have either consistently high or consistently low success at producing healthy cloned pigs. To accomplish this goal, we combined methylated DNA immunoprecipitation using antibodies to 5-methylcytosine with Illumina high throughput sequencing (MeDIP-seq) to detect broad regions of methylated and unmethylated DNA in the 2 populations of donor cells (termed high success v. low success). Size-selected immunoprecipitated DNA samples each had matching input controls. Model-based analysis of ChIP-Seq revealed a total of 272 598 and 261 339 genomic regions enriched for methylated cytosine in high v. low success donor cells, respectively. The majority of these enriched regions (peaks) in high and low success samples coincided in genomic position, but 12.9% of the peaks were unique in high success cells, while 20.4% were unique in low success cells. When intersected with 38 778 predicted CpG islands in the swine genome, 3129 of the total MeDIP peaks (1.1%) overlapped for high success cells as compared to 1836 peaks (0.7%) for the low success cells. Of these intersecting MeDIP-CpG peaks for both groups, 1505 peaks were located in unique locations for high success cells and 205 were unique for low success cells. The chromosomal location of the CpG intersections differed between each cell populations, with the greatest number of overlaps on chromosomes 1 and 3 for high and low success cells, respectively, and the least number of overlaps on chromosomes 9 and 13, respectively. Of the total MeDIP peaks, 6632 (2.4%) from the high success cell population overlapped with predicted swine genes (UCSC Genome Database/Ensembl) compared to 4041 (1.5%) from low success donor cells. Less similar was the percentage of the predicted genes in these methylated regions that were unique to each cell group: 2875 (43.4%) for high success cells v. 338 (8.3%) for low success cells. These results highlight differences in the degree of DNA methylation and the pattern of methylated genes in NT donor cells that produce healthy clones v. those that do not. Such comprehensive genomic analyses of epigenetic markers may provide predictive data to screen for optimal NT donor cells, thereby improving cloning efficiency. This work was supported by the National Institutes of Health NIH R01 RR013438 and Food for the 21st Century at the University of Missouri.
Tissue engineering scaffold for sequential release of vancomycin and rhBMP2 to treat bone infections (2014)

The ability of silica calcium phosphate nanocomposite (SCPC75) for the controlled sequential delivery of vancomycin (Vanc) and rhBMP2 was evaluated. Fourier transform infrared spectroscopy analyses of the SCPC75 showed an increase in the bond energy of the PO4 (-3) due to the interactions with negatively charged moieties of Vanc. Furthermore, a decrease in the bond energy of the Si-O-Si functional groups was observed after rhBMP2 adsorption. In conjunction with the differences in bond site and bond energy at the ceramic/drug interface, significant differences in drug release kinetics and bioceramic dissolution rate were found. UV-vis spectrometry showed a burst release of Vanc in the first 8 h followed by a sustained release stage for up to 28 days. ELISA showed first-order release kinetics of rhBMP2 without burst release. The rhBMP2 release from SCPC75 was associated with a significantly lower rate of Ca and a higher rate of Si dissolutions when compared with Vanc release over identical time periods. Differences in the release kinetic profiles of Vanc and rhBMP2 from the SCPC75-Vanc/SCPC75-rhBMP2 scaffolds at 70/30, 50/50, or 20/80 ratios allowed for sequential drug release profiles that could be exploited to customize doses and release duration of each drug. The released rhBMP2 significantly upregulated MC3T3-E1 expression of collagen type I, osteopontin, and osteocalcin mRNA by 12.6-, 3.3-, and 2.4-fold, respectively. The released Vanc demonstrated bactericidal effects on Staphylococcus aureus in vitro. These results suggest the potential of SCPC75-Vanc-rhBMP2 scaffolds in the treatment of damaged and/or infected bone.
Development of a Highly Efficient Oil Cooler Without Fin and Housing (1990)

&lt;div class="htmlview paragraph"&gt;A recent research and development activity brought about and eventually commercialized a new, low-cost oil cooler having a remarkably simple structure for car engines. In particular, the use of heat transfer fins and housing was totally eliminated.&lt;/div&gt; &lt;div class="htmlview paragraph"&gt;A heat exchange core employed in the new oil cooler is comprised merely of a required number of identically designed round plates overlapping each other. Whether this type of oil cooler can maintain required heat transfer rate or not hinges primarily on design and layout of embossed spots and through-holes provided on the individual plates as well as of clearance between those round plates. With design emphasis placed on those important factors, a heat exchange core having a finless structure achieved a heat transfer rate level that stands well comparable with that of conventional oil cooler.&lt;/div&gt; &lt;div class="htmlview paragraph"&gt;This paper describes how the product was developed though efforts to obtain consistent heat transfer rate.&lt;/div&gt;
Millimeter-Scale Robotic Mechanisms Using Carbon Nanotube Composite Structures (2014)

This paper presents a method for fabricating millimeter-scale robotic components for minimally invasive surgery. Photolithographic patterning is used to create a framework of carbon nanotubes (CNTs) that can be infiltrated with a variety of materials, depending on the desired material properties. For the examples shown in this paper, amorphous carbon is used as the infiltration material. The planar frameworks are then stacked to create the 3D device. The detail and precision are affected by large changes in cross section in the direction of stacking. Methods for improving the definition of the 3D object due to changing cross section are discussed. The process is demonstrated in a two-degree-of-freedom (2DOF) wrist mechanism and a 2DOF surgical gripping mechanism, which have the potential of decreasing the size of future minimally invasive surgical instruments.
A TEM Study of Crystalline Boron Nanoribbons (2004)

Extended abstract of a paper presented at Microscopy and Microanalysis 2004 in Savannah, Georgia, USA, August 1–5, 2004.
Cellular Association and Cytotoxicity of Doxorubicin-Loaded Immunoliposomes Targeted via Fab' Fragments of an Anti-CD74 Antibody (2007)

The purpose of our research was to evaluate in vitro therapeutic efficacy of doxorubicin (DXR)-loaded immunoliposomes with Fab' fragments of the anti-CD74 antibody LL1 attached to the surface. LL1 is well suited for targeting purposes because it is internalized very fast by B-lymphoma cells. However, at in vivo application whole antibodies show fast clearance in circulation. Taking this fact into consideration, this study was initiated to elucidate the prospects of using Fab' fragments of LL1 in stead of the whole antibody for future targeting in vivo of DXR-loaded liposomes. The Fab' fragments were covalently attached to the surface of sterically stabilized liposomes by use of a PEG-based heterobifunctinal coupling agent. LL1 Fab' conjugated sterically stabilized DXR liposomes showed approximately six times faster accumulation of the drug in Raji human B-lymphoma cells than nontargeted liposomes. In vitro cytotoxicity, quantitated by a tetrazolium assay, against Raji cells gave IC(50) values of 0.13, 0.45, and 0.11 microM for DXR-loaded immunoliposomes, DXR-loaded liposomes and free drug, respectively. The results from this study suggest that DXR-loaded immunoliposomes targeted with Fab' fragments from the anti-CD74 antibody LL1 could be a useful system for future in vivo experiments.
Harmonic microscopy of isotropic and anisotropic microstructure of the human cornea (2010)

In this study we present combined third-harmonic generation (THG) and second-harmonic generation (SHG) microscopy images of intact human corneas, and we analyze experimentally and theoretically the origin of the THG signal. Multiharmonic microscopy provides detailed images of the cornea microstructure over its entire thickness. A component of the THG signal originates from cellular structures and another one originates from anisotropy changes between successive collagen lamellae in the stroma. This anisotropy-related signal can be specifically detected using circular incident polarization, and provide contrasted images of the stacking and tissue-scale heterogeneity of stromal lamellae. Forward-radiated THG and SHG signals are generally anticorrelated, indicating that maximum THG is obtained from lamellar interfaces whereas maximum SHG is obtained from within lamellae. Polarization-resolved THG imaging reflects the a ernate anisotropy directions of the lamellae. We present a model for THG imaging of layered anisotropic samples and numerical calculations that account for our observations.
Influence of spontaneous polarization and polyimide surface treatment on layer tilt angle in SSFLC cells (1993)

Abstract— The influence of the spontaneous polarization of liquid‐crystal materials and polyimide surface treatments on layer tilt angle in surface‐stabilized ferroelectric liquid‐crystal (SSFLC) cells has been studied by x‐ray diffraction. For the case of liquid‐crystal molecules with the same core structure, the layer tilt angle is not influenced by the magnitude of the spontaneous polarization of the liquid crystals (P s ). Three kinds of polyimides which result in different pre‐tilt angles for the typical nematic material result in the same layer tilt angle for the ferroelectric liquid‐crystal materials. The layer tilt angle vs. molecular tilt angle characteristics are expressed by a universal straight line and its slope is less than unity.
Biochemical Analysis of Potential Sites for Protein 4.1-mediated Anchoring of the Spectrin-Actin Skeleton to the Erythrocyte Membrane (1998)

Erythrocyte protein 4.1 has been hypothesized to link the spectrin-actin junctional complex directly to the cytoplasmic domain of glycophorin C, but this bridging function has never been directly demonstrated. Because an alternative protein-mediated bridge between the junctional complex and the cytoplasmic domain of band 3 is also plausible, we have undertaken to characterize the membrane sites to which protein 4.1 can anchor the spectrin and actin skeleton. We demonstrate that proteolytic removal of the cytoplasmic domain of band 3 has minimal effect on the ability of protein 4.1 to promote 125I-labeled spectrin and actin binding to KI-stripped erythrocyte membrane vesicles. We also show that quantitative blockade of all band 3 sites with either monoclonal or polyclonal antibodies to band 3 is equally ineffective in preventing protein 4.1-mediated association of spectrin and actin with the membrane. In contrast, obstruction of protein 4.1 binding to its docking site on the cytoplasmic pole of glycophorin C is demonstrated to reduce the same protein 4.1 bridging function by approximately 85%. We conclude from these data that (i) glycophorin C contributes the primary anchoring site of the protein 4.1-mediated bridge to the spectrin-actin skeleton; (ii) band 3 is incapable of serving the same function; and (iii) additional minor protein 4.1 bridging sites may exist on the human erythrocyte membrane.
Experimental studies on the role of antibody fragments in cancer radio-immunotherapy: Influence of radiation dose and dose rate on toxicity and anti-tumor efficacy (1998)

Whereas bivalent fragments have been widely used for radio-immunotherapy, no systematic study has been published on the therapeutic performance of monovalent conjugates in vivo. The aim of our study was, therefore, to determine the therapeutic performance of (131)I-labeled Fab as compared to bivalent conjugates and to analyze factors that influence dose-limiting organ toxicity and anti-tumor efficacy. The maximum tolerated doses (MTDs) and dose-limiting organ toxicities of the (131)I-labeled anti-CEA antibody MN-14 [IgG, F(ab')2 and Fab] were determined in nude mice bearing s.c. human colon cancer xenografts. Mice were treated with or without bone marrow transplantation (BMT) or inhibition of the renal accretion of antibody fragments by D-lysine or combinations thereof. Toxicity and tumor growth were monitored. Radiation dosimetry was calculated from biodistribution data. With all 3 (131)I-labeled immunoconjugates [IgG, F(ab')2 and Fab], the red marrow was the only dose-limiting organ; MTDs were 260 microCi for IgG, 1,200 microCi for F(ab')2 and 3 mCi for Fab, corresponding to blood doses of 17 Gy, 9 Gy and 4 Gy, respectively. However, initial dose rates were 10 times higher with Fab as compared to IgG and 3 times higher as compared to F(ab')2. The MTD of all 3 immunoconjugates was increased by BMT by approximately 30%. In accordance with renal doses below 10 Gy, no signs of nephrotoxicity were observed. Despite lower absorbed tumor doses, at equitoxic dosing, Fab fragments were more effective at controlling tumor growth than the respective bivalent fragment or IgG, probably due to higher intratumoral dose rates. Our data indicate that the improved anti-tumor effectiveness of antibody fragments as compared to IgG and the higher myelotoxicity at comparably lower red marrow doses are most likely due to the higher initial dose rates observed with antibody fragments.
One-Pot Syntheses of the First Series of Emulsion Based Hierarchical Hybrid Organic−Inorganic Open-Cell Monoliths Possessing Tunable Functionality (Organo−Si(HIPE) Series) (2007)

The elaboration of organo-silica-based hybrid monoliths exhibiting a hierarchical trimodal porous structure (micro-, synthesis, many organic functionalities that can act as network modifiers (methyl, dinitrophenylamino, benzyl, and mercaptopropyl) or co-network formers (pyrrol) have been anchored to the amorphous silica porous network. The resulting materials have been thoroughly characterized via a large set of techniques: SEM, TEM, SAXS, mercury porosimetry, nitrogen adsorption isotherms, FTIR, 29Si MAS NMR, and XPS. These sol-gel-derived hierarchical open-cell functional hybrid monoliths exhibit macroscopic void spaces ranging from 5 ím up to 30 ím and their accessible micro-and mesoporosities reveal hexagonal organization for the dinitrophenylamino-, benzyl-, and pyrrol-based hybrids. The average condensation degree for these hybrid networks ranges between 86 and 90%, yielding shaped monoliths with both good integrity and sufficient mechanical properties to be usable as functional catalytic or chromatographic supports. Also, function accessibility has been demonstrated through heterogeneous nucleation of Pd metallic nanoparticles.
Stress Suppressor Screening Leads to Detection of Regulation of Cyclic di-AMP Homeostasis by a Trk Family Effector Protein in Streptococcus pneumoniae (2018)

Cyclic di-AMP (c-di-AMP) is a newly discovered bacterial second messenger. However, regulation of c-di-AMP homeostasis is poorly understood. In <i>Streptococcus pneumoniae</i>, a sole diadenylate cyclase, CdaA, produces c-di-AMP and two phosphodiesterases, Pde1 and Pde2, cleave the signaling dinucleotide. To expand our knowledge of the pneumococcal c-di-AMP signaling network, we performed whole-genome sequencing of Δ<i>pde1</i> Δ<i>pde2</i> heat shock suppressors. In addition to their effects on surviving heat shock, these suppressor mutations restored general stress resistance and improved growth in rich medium. Mutations in CdaA or in the potassium transporter TrkH paired with an insertion leading to a frameshift at the C terminus of CdaA significantly reduced c-di-AMP levels. These observations indicate that the elevated c-di-AMP levels in the Δ<i>pde1</i> Δ<i>pde2</i> mutant enhance susceptibility of <i>S. pneumoniae</i> to the stress conditions. Interestingly, we have previously shown that TrkH complexes with a Trk family c-di-AMP-binding protein, CabP, to mediate potassium uptake. In this study, we found that deletion of <i>cabP</i> significantly reduced pneumococcal c-di-AMP levels. This is the first observation that a c-di-AMP effector protein modulates bacterial c-di-AMP homeostasis.<b>IMPORTANCE</b> Second messengers, including c-di-AMP, are prevalent among bacterial species. In <i>S. pneumoniae</i>, c-di-AMP phosphodiesterase-encoding gene null mutants are attenuated during mouse models of infection, but the role of c-di-AMP signaling in pneumococcal pathogenesis is enigmatic. In this work, we found that heat shock suppressor mutations converge on undermining c-di-AMP toxicity by changing intracellular c-di-AMP concentrations. These mutations improve the growth and restore the stress response generally in c-di-AMP phosphodiesterase-deficient pneumococci, thereby demonstrating the essentiality for tight regulation of c-di-AMP homeostasis in order to respond to stress. Likewise, this work demonstrates that a c-di-AMP effector protein, CabP, affects c-di-AMP homeostasis, which provides new perception into c-di-AMP regulation. This study has implications for c-di-AMP-producing bacteria since many species contain CabP homologs.
Predictive risk factors for hospitalization and response to colchicine in patients with COVID-19 (2022)

This model could serve to identify high-risk subjects who will particularly benefit from early colchicine therapy.