gebhart/patrepeval huggingface dataset:
Molecular Dynamics Simulations of Peptide−Surface Interactions (2005)

Proteins, which are bioactive molecules, adsorb on implants placed in the body through complex and poorly understood mechanisms and directly influence biocompatibility. Molecular dynamics modeling using empirical force fields provides one of the most direct methods of theoretically analyzing the behavior of complex molecular systems and is well-suited for the simulation of protein adsorption behavior. To accurately simulate protein adsorption behavior, a force field must correctly represent the thermodynamic driving forces that govern peptide residue-surface interactions. However, since existing force fields were developed without specific consideration of protein-surface interactions, they may not accurately represent this type of molecular behavior. To address this concern, we developed a host-guest peptide adsorption model in the form of a G(4)-X-G(4) peptide (G is glycine, X is a variable residue) to enable determination of the contributions to adsorption free energy of different X residues when adsorbed to functionalized Au-alkanethiol self-assembled monolayers (SAMs). We have previously reported experimental results using surface plasmon resonance (SPR) spectroscopy to measure the free energy of peptide adsorption for this peptide model with X = G and K (lysine) on OH and COOH functionalized SAMs. The objectives of the present research were the development and assessment of methods to calculate adsorption free energy using molecular dynamics simulations with the GROMACS force field for these same peptide adsorption systems, with an oligoethylene oxide (OEG) functionalized SAM surface also being considered. By comparing simulation results to the experimental results, the accuracy of the selected force field to represent the behavior of these molecular systems can be evaluated. From our simulations, the G(4)-G-G(4) and G(4)-K-G(4) peptides showed minimal to no adsorption to the OH SAM surfaces and the G(4)-K-G(4) showed strong adsorption to the COOH SAM surface, which is in agreement with our SPR experiments. Contrary to our experimental results, however, the simulations predicted a relatively strong adsorption of G(4)-G-G(4) peptide to the COOH SAM surface. In addition, both peptides were unexpectedly predicted to adsorb to the OEG surface. These findings demonstrate the need for GROMACS force field parameters to be rebalanced for the simulation of peptide adsorption behavior on SAM surfaces. The developed methods provide a direct means of assessing, modifying, and validating force field performance for the simulation of peptide and protein adsorption to surfaces, without which little confidence can be placed in the simulation results that are generated with these types of systems.
Culture and in vitro hepatogenic differentiation of placenta‐derived stem cells, using placental extract as an alternative to serum (2010)

Our findings revealed that placental extract could be used as a new component for culture of adult stem cells, as well as for development of human-based medium, in translational research for regenerative medicine.
The iron-responsive element binding protein: a method for the affinity purification of a regulatory RNA-binding protein. (1989)

A method of affinity purification of a regulatory protein that binds specific RNA sequences is described. RNAs containing the regulatory sequences are transcribed in vitro from oligonucleotide templates, biotinylated, and incubated with unfractionated cytosol. Specific RNA-protein complexes are bound in solution to avidin, and the resulting complex is bound to biotin-agarose beads. The cytosolic binding protein is released from the RNA in high salt, and a second round of purification yields an essentially homogeneous protein. Using this method, we have identified the protein in human liver that binds iron-responsive RNA regulatory sequences. Iron-responsive elements (IREs) are RNA stem-loops present in the mRNAs encoding ferritin and the transferrin receptor. IREs form the basis for the translational regulation of ferritin gene expression and the regulation of transferrin receptor mRNA degradation rates. The IRE binding protein purified by this technique migrates as a 90-kDa polypeptide on SDS/PAGE. The interaction of the purified protein with IRE-containing RNAs can be detected by gel-mobility shift assays or by covalent crosslinking induced by UV irradiation.
Bifidobacterium carbohydrases‐their role in breakdown and synthesis of (potential) prebiotics (2007)

There is an increasing interest to positively influence the human intestinal microbiota through the diet by the use of prebiotics and/or probiotics. It is anticipated that this will balance the microbial composition in the gastrointestinal tract in favor of health promoting genera such as Bifidobacterium and Lactobacillus. Carbohydrates like non-digestible oligosaccharides are potential prebiotics. To understand how these bacteria can grow on these carbon sources, knowledge of the carbohydrate-modifying enzymes is needed. Little is known about the carbohydrate-modifying enzymes of bifidobacteria. The genome sequence of Bifidobacterium adolescentis and Bifidobacterium longum biotype longum has been completed and it was observed that for B. longum biotype longum more than 8% of the annotated genes were involved in carbohydrate metabolism. In addition more sequence data of individual carbohydrases from other Bifidobacterium spp. became available. Besides the degradation of (potential) prebiotics by bifidobacterial glycoside hydrolases, we will focus in this review on the possibilities to produce new classes of non-digestible oligosaccharides by showing the presence and (transglycosylation) activity of the most important carbohydrate modifying enzymes in bifidobacteria. Approaches to use and improve carbohydrate-modifying enzymes in prebiotic design will be discussed.
Pore Size Distribution and Apparent Gas Thermal Conductivity of Silica Aerogel (1994)

Silica aerogel is a network of short bonded chains of silica particles, which are fused together. Particles of diameters 2-5 nm and pores of diameter 10-100 nm produce a solid-gas matrix in which the volume fraction of the solid can be less than 5 percent. The small pore size effectively limits the motion of gas molecules and hence reduces the apparent gas conductivity to a very low level. In this paper, we establish a model for the determination of the apparent gas conductivity in terms of the pore sizes. We use the method of gas adsorption-desorption to determine the pore size distribution for silica aerogel. The thermal conductivity is measured by using the hot-wire technique and the experimental data are then used to determine the constants C[sub 1] and n[sub 1] in K = K[sub g][sup o]/[1 + (C[sub 1]/P[sup n1]l[sub ch])]0. 8 refs., 3 figs.
New Activation Modus of STAT3 (2009)

Activation of STAT proteins by cytokines is initiated by their Src homology 2 domain-mediated association with phosphotyrosine residues from the cytoplasmic domain of a receptor. Here, we show that the C terminus of the interleukin-22 receptor (IL-22R) recruits in a tyrosine-independent manner the coiled-coil domain of STAT3. Mutation of all IL-22R cytoplasmic tyrosines did not abolish activation of STAT3, in contrast to that of STAT1 and STAT5. Coimmunoprecipitation and glutathione S-transferase pulldown experiments showed that the coiled-coil domain of STAT3 is constitutively associated with the C-terminal part of IL-22R, and a chimeric STAT3-STAT5 protein containing the coiled-coil domain of STAT3 could be activated by this tyrosine-independent mechanism. Deletion of the C-terminal part of IL-22R dramatically decreased its ability to activate STAT3 and to mediate IL-22 activity in cell lines, demonstrating that preassociation of STAT3 with this cytokine receptor, independent from the interaction between the Src homology 2 domain and phosphotyrosines, is required for its full activity.
Adaptively Reordering Joins during Query Execution (2007)

Traditional query processing techniques based on static query optimization are ineffective in applications where statistics about the data are unavailable at the start of query execution or where the data characteristics are skewed and change dynamically. Several adaptive query processing techniques have been proposed in recent years to overcome the limitations of static query optimizers through either explicit re-optimization of plans during execution or by using a row-routing based approach. In this paper, we present a novel method for processing pipelined join plans that dynamically arranges the join order of both inner and outer-most tables at run-time. We extend the Eddies concept of "moments of symmetry" to reorder indexed nested-loop joins, the join method used by all commercial DBMSs for building pipelined query plans for applications for which low latencies are crucial. Unlike row-routing techniques, our approach achieves adaptability by changing the pipeline itself which avoids the bookkeeping and routing decision associated with each row. Operator selectivities monitored during query execution are used to change the execution plan at strategic points, and the change of execution plans utilizes a novel and efficient technique for avoiding duplicates in the query results. Our prototype implementation in a commercial DBMS shows a query execution speedup of up to 8 times.
Molecular Iodine in Ionic Liquid: A Green Catalytic System for Esterification and Transesterification (2010)

Esterification of carboxylic acids and transesterification of β-ketoesters with alcohols have been developed using a catalytic amount of iodine in polyethylene glycol (PEG) ionic liquid (IL 1000) to afford the corresponding esters in good yields. By simple separation of the ionic-liquid phase containing the iodine, the system of I2/IL 1000 can be reused several times.
TUMOR DORMANCY IN VIVO BY PREVENTION OF NEOVASCULARIZATION (1972)

Dormant solid tumors were produced in vivo by prevention of neovascularization. When small fragments of anaplastic Brown-Pearce carcinoma were implanted directly on the iris in susceptible rabbits, they always vascularized. A characteristic growth pattern, consisting of prevascular, vascular, and late phases, was observed, which terminated with destruction of the eye within 2 wk. The beginning of exponential volume increase was shown to coincide with vascularization of the implant, as demonstrated by perfusion with intravenous fluorescein and by histologic sections. In contrast, implants placed in the anterior chamber, at a distance from the iris, did not become vascularized. After initial growth into spheroids, they remained arrested at a small size comparable to prevascular iris implants, for periods as long as 6 wk. Although dormant in terms of expansion, these avascular tumors contained a population of viable and mitotically active tumor cells. When reimplanted on the iris, vascularization was followed by rapid, invasive growth. These observations suggest that neovascularization is a necessary condition for malignant growth of a solid tumor. When a small mass of tumor cells is prevented from eliciting new vessel ingrowth from surrounding host tissues, population dormancy results. These data suggest that the specific blockade of tumor-induced angiogenesis may be an effective means of controlling neoplastic growth.
SAR and Factor IXa Crystal Structure of a Dual Inhibitor of Factors IXa and Xa. (2005)

Abstract For Abstract see ChemInform Abstract in Full Text.
Low-voltage high-performance silicon photonic devices and photonic integrated circuits operating up to 30 Gb/s (2011)

We present high performance silicon photonic circuits (PICs) defined for off-chip or on-chip photonic interconnects, where PN depletion Mach-Zehnder modulators and evanescent-coupled waveguide Ge-on-Si photodetectors were monolithically integrated on an SOI wafer with CMOS-compatible process. The fabricated silicon PIC(off-chip) for off-chip optical interconnects showed operation up to 30 Gb/s. Under differential drive of low-voltage 1.2 V(pp), the integrated 1 mm-phase-shifter modulator in the PIC(off-chip) demonstrated an extinction ratio (ER) of 10.5dB for 12.5 Gb/s, an ER of 9.1dB for 20 Gb/s, and an ER of 7.2 dB for 30 Gb/s operation, without adoption of travelling-wave electrodes. The device showed the modulation efficiency of V(π)L(π) ~1.59 Vcm, and the phase-shifter loss of 3.2 dB/mm for maximum optical transmission. The Ge photodetector, which allows simpler integration process based on reduced pressure chemical vapor deposition exhibited operation over 30 Gb/s with a low dark current of 700 nA at -1V. The fabricated silicon PIC(intra-chip) for on-chip (intra-chip) photonic interconnects, where the monolithically integrated modulator and Ge photodetector were connected by a silicon waveguide on the same chip, showed on-chip data transmissions up to 20 Gb/s, indicating potential application in future silicon on-chip optical network. We also report the performance of the hybrid silicon electronic-photonic IC (EPIC), where a PIC(intra-chip) chip and 0.13μm CMOS interface IC chips were hybrid-integrated.
Biology, Models, and the Analysis of Tumor Xenograft Experiments (2011)

Advances in statistical modeling and analysis technology have improved our ability to derive valid inferences from tumor xenograft experiments. Further challenges in this area include the modeling of intertumor heterogeneity and the development of robust statistical models that describe key parameters in the underlying tumor biology.
Moesin expression is a marker of basal breast carcinomas (2007)

Basal breast cancers (BBCs) have a high risk of metastasis, recurrence and death. Formal subtype definition relies on gene expression but can be approximated by protein expression. New markers are needed to help in the management of the basal subtype of breast cancer. In a previous transcriptional analysis of breast cell lines we found that Moesin expression was a potential basal marker. We show here that Moesin protein expression is a basal marker in breast tumors. In a tissue microarray (TMA) containing 547 sporadic breast cancers, of which 108 were profiled for gene expression, Moesin was expressed in 31% of all tumors and in 82% of the basal tumors. To confirm that Moesin expression remained associated with the basal phenotype in specific types of BBCs, we analyzed Moesin expression in 2 other TMAs containing 40 medullary breast cancers (MBCs) and 27 BRCA1-associated breast cancers (BRCA1-BCs), respectively. Moesin was strongly expressed in MBCs (87%; p = 2.4 x 10(-5)) and in BRCA1-BCs (58%; p = 1.3 x 10(-5)) as compared with non-MBCs and sporadic cases. Moesin-expressing tumors display features of BBCs, such as high proliferation rate, hormone receptors negativity, expression of putative basal/myoepithelial markers (CAV1, CD10, CK5/6, CK14, EGFR, P53, P-cadherin and SMA). Survival analysis showed a reduced specific survival and metastasis-free survival in Moesin-expressing tumors by log-rank test (p(SS) = 0.014 and p(MFS) = 0.014). In multivariate analysis, Moesin expression was nearly an independent prognostic marker of poor outcome as shown by Cox proportional hazard model in patients without lymph node metastasis (p = 0.052, HR = 2.38, CI 95[0.99-5.69]).
Effect of electroreduction pretreatment in aqueous media on hydropyrolysis of a bituminous coal (1990)

Electroreduotion of coal is studied in aqueous tetrabutylammonium hydroxide (TBAOH) solution and tetrabutylammonium tetrafluoroborate (TBABF4) -THF-H2O solution by using platinum as anode and Hg pool as cathode. The electrolysis in aqueous TBAOH solution seems to have little effect on the following HyPy although the pyridine extractable yield of reduced coal increases. In an undivided cell the re-oxidation of the reduced coal occurs. Cathodic reduction in TBABF4-THF-H2O solution gives a pronounced effect on HyPy. Higher conversion (60.9%) and total oil yield (50.6%) (THF soluble + oil formed in HyPy) are obtained in a divided cell as compared with 42.1% and 28.4% for untreated coal, respectively. The electroreduction pretreatment of coal enhances the rate of oil formation and the oil yield in HyPy of the reduced coal, indicating that the reduced coal can be depolymerized more easily due to the solvolysis and hydrogenation.
Long-term engraftment of hepatocytes transplanted on biodegradable polymer sponges (1997)

Hepatocyte transplantation may provide an alternative to orthotopic liver transplantation to treat liver failure. However, suitable systems to transplant hepatocytes and promote long-term engraftment must be developed. In this study, highly porous, biodegradable sponges were fabricated from poly (L-lactic acid) (PLA), and poly (DL-lacticco-glycolic acid) (PLGA), and utilized to transplant hepatocytes into the mesentery of three groups of Lewis rats. The portal vein was shunted to the inferior vena cava in one group of rats (PCS). The second group of animals received a PCS and a 70% hepatectomy on the day of sponge-hepatocyte implantation (PCS + HEP), and the control group (CON) received no surgical stimulation. The sponges were vascularized by ingrowth of fibrovascular tissue over the first 7 days in vivo. Approximately 95-99% of the implanted hepatocytes (determined utilizing computer-assisted image analysis) died in all three experimental groups during this time. The number of engrafted hepatocytes in the CON group further decreased over the next 7 days to 1.3 +/- 1.1% of the original cell number. However, the number of engrafted hepatocytes in the PCS and PCS + HEP increased over this time to 6 +/- 1% and 5 +/- 2%, respectively. The number of engrafted hepatocytes in the PCS group continued to increase over the next 2.5 months to a value of 26 +/- 12% of the initial cell number, and a large number of engrafted hepatocytes was still present at 6 months. These results indicate that stable new tissues can be engineered by transplanting hepatocytes on biodegradable sponges into heterotopic locations if appropriate stimulation is provided.
Gas Adsorption Sites in a Large-Pore Metal-Organic Framework (2005)

The primary adsorption sites for Ar and N2 within metal-organic framework-5, a cubic structure composed of Zn4O(CO2)6 units and phenylene links defining large pores 12 and 15 angstroms in diameter, have been identified by single-crystal x-ray diffraction. Refinement of data collected between 293 and 30 kelvin revealed a total of eight symmetry-independent adsorption sites. Five of these are sites on the zinc oxide unit and the organic link; the remaining three sites form a second layer in the pores. The structural integrity and high symmetry of the framework are retained throughout, with negligible changes resulting from gas adsorption.
Listeriolysin O Expressed in a Bacterial Vaccine Suppresses CD4+CD25high Regulatory T Cell Function In Vivo (2007)

CD4(+)CD25(high) regulatory T cells (Treg) protect the host from autoimmune diseases but are also obstacles against cancer therapies. An ideal cancer vaccine would stimulate specific cytotoxic responses and reduce/suppress Treg function. In this study, we showed that Escherichia coli expressing listeriolysin O and OVA (E. coli LLO/OVA) demonstrated remarkable levels of protection against OVA-expressing tumor cells. By contrast, E. coli expressing OVA only (E. coli OVA) showed poor protection. High-avidity OVA-specific CTL were induced in E. coli LLO/OVA-vaccinated mice, and CD8(+) depletion--but not NK cell depletion, abolished the antitumor activity of the E. coli LLO/OVA vaccine. Phenotypic analysis of T cells following vaccination with either vaccine revealed preferential generation of CD44(high)CD62L(low) CD8(+) effector memory T cells over CD44(high)CD62L(high) central memory T cells. Unexpectedly, CD4(+) depletion turned E. coli OVA into a vaccine as effective as E. coli LLO/OVA suggesting that a subset of CD4(+) cells suppressed the CD8(+) T cell-mediated antitumor response. Further depletion experiments demonstrated that these suppressive cells consisted of CD4(+)CD25(high) regulatory T cells. We therefore assessed these vaccines for Treg function and found that although CD4(+)CD25(high) expansion and Foxp3 expression within this population was similar in all groups of mice, Treg cells from E. coli LLO/OVA-vaccinated animals were unable to suppress conventional T cells proliferation. These findings provide the first evidence that LLO expression affects Treg cell function and may have important implications for enhancing antitumor vaccination strategies in humans.
Direct Human Cartilage Repair Using Three-Dimensional Bioprinting Technology (2012)

Current cartilage tissue engineering strategies cannot as yet fabricate new tissue that is indistinguishable from native cartilage with respect to zonal organization, extracellular matrix composition, and mechanical properties. Integration of implants with surrounding native tissues is crucial for long-term stability and enhanced functionality. In this study, we developed a bioprinting system with simultaneous photopolymerization capable for three-dimensional (3D) cartilage tissue engineering. Poly(ethylene glycol) dimethacrylate (PEGDMA) with human chondrocytes were printed to repair defects in osteochondral plugs (3D biopaper) in layer-by-layer assembly. Compressive modulus of printed PEGDMA was 395.73±80.40 kPa, which was close to the range of the properties of native human articular cartilage. Printed human chondrocytes maintained the initially deposited positions due to simultaneous photopolymerization of surrounded biomaterial scaffold, which is ideal in precise cell distribution for anatomic cartilage engineering. Viability of printed human chondrocytes increased 26% in simultaneous polymerization than polymerized after printing. Printed cartilage implant attached firmly with surrounding tissue and greater proteoglycan deposition was observed at the interface of implant and native cartilage in Safranin-O staining. This is consistent with the enhanced interface failure strength during the culture assessed by push-out testing. Printed cartilage in 3D biopaper had elevated glycosaminoglycan (GAG) content comparing to that without biopaper when normalized to DNA. These observations were consistent with gene expression results. This study indicates the importance of direct cartilage repair and promising anatomic cartilage engineering using 3D bioprinting technology.
Age-related Macular Degeneration Is Associated with Atherosclerosis (1995)

Age-related macular degeneration is the most frequent cause of blindness in the elderly. A vascular basis of the disease has been suggested, but not confirmed. The association between atherosclerosis and this type of macular degeneration was investigated in 104 subjects with and 1,324 subjects without macular degeneration as part of the population-based Rotterdam Study. The study was performed between March 1990 and July 1993 in a suburb of Rotterdam, the Netherlands. Macular degeneration was assessed on fundus photographs. Carotid atherosclerosis was ultrasonographically evaluated by measurement of the common carotid intima-media thickness and by assessment of the presence of atherosclerotic plaques. Atherosclerosis in arteries of the lower extremities was studied by determination of the ankle-arm systolic blood pressure ratio. In subjects younger than age 85 years, plaques in the carotid bifurcation were associated with a 4.7 times increased prevalence odds of macular degeneration (95% confidence interval (CI) 1.8-12.2); those with plaques in the common carotid artery showed an increased prevalence odds of 2.5 (95% CI 1.4-4.5). The intima-media thickness of the common carotid arteries was not significantly different. Lower extremity arterial disease (ankle-arm index less than 0.90 on at least one side) was associated with a 2.5 times increased prevalence odds (95% CI 1.4-4.5). These findings suggest that atherosclerosis may be involved in the etiology of age-related macular degeneration.