gebhart/patrepeval huggingface dataset:
Microfluidic Generation and Manipulation of Hydrogel Microcapsules for Biomimetic 3D Tissue Culture and Cell Cryopreservation (2016)

Droplet-based microfluidics is a multidisciplinary research field that deals with the multiphase fluid flow in channels of micrometer scale.It has been widely utilized for chemistry, biochemistry, and biotechnology applications.In this dissertation, fundamental numerical and experimental studies were conducted to understand the multiphase fluid flow in the droplet-based microfluidics and to generate and manipulate hydrogel microcapsules for biomimetic 3D culture of cells/tissues and cell cryopreservation.To study the fluid flow in the droplet-based microfluidics, a numerical model was developed using the level set method to track the moving interface between different solutions.The model was validated by experimental data.Numerical studies revealed that significant fluid displacement among multiple fluids could occur during droplet generation due to two mechanisms: shear effect due to viscosity and capillary effect from interfacial tension.These two mechanisms can be scaled by two dimensionless parameters.The quantitative relationship between the degree of fluid displacement and these two dimensionless parameters was determined experimentally.In addition, the multiphase flow could be controlled to generate hydrogel microparticles of various morphologies.The generated hydrogel microcapsules need to be extracted from the carrier oil phase into aqueous solution before they exit the microfluidic device to prevent their aggregation, increase retrieval efficiency, and maintain high cell viability (for cell encapsulation applications).To this end, two on-chip extraction methods were developed.First, a passive approach was established to extract microcapsules confined in the microfluidic Firstly, I would like to express my sincerest and deepest gratitude to my advisor Prof.Xiaoming He for his continuous support on my Ph.D. study
Polymeric Reagents and Catalysts (1986)

R. Bruce Merrifield was honored with the Nobel Prize in Chemistry in 1984 for invention of peptide synthesis in polymer supports. Merrifield peptide synthesis is now used in scores of laboratories to produce natural peptides and, perhaps more importantly, analogs of natural peptides that are vital for the correlation of structures of peptides with their biological activity.
Factors predictive of the development of Levodopa‐induced dyskinesia and wearing‐off in Parkinson's disease (2013)

The Stalevo Reduction in Dyskinesia Evaluation in Parkinson's Disease (STRIDE-PD) study compared the initiation of levodopa (l-dopa) therapy with l-dopa/carbidopa (LC) versus l-dopa/carbidopa/entacapone (LCE) in patients with Parkinson's disease. In the current study, the STRIDE-PD study population was investigated to determine the effect of l-dopa dose and other risk factors on the development of dyskinesia and wearing-off. Patients were randomized to receive LCE (n=373) or LC (n=372). Blinded assessments for dyskinesia and wearing-off were performed at 3-month intervals for the 134- to 208-week duration of the study. The patients were divided into 4 dose groups based on nominal l-dopa dose at the time of onset of dyskinesia (or at study conclusion if there was no dyskinesia): group 1, <400 mg/day (n=157); group 2, 400 mg/day (n=310); group 3, 401 to 600 mg/day (n=201); and group 4, >600 mg/day (n=77). Similar analyses were performed with respect to wearing-off and any motor complication. The times to onset and frequency of dyskinesia, wearing-off, or any motor complication were compared using the log-rank test (overall trend test) and a Cox proportional hazards model (pairwise comparisons). A stepwise Cox proportional hazards model was used to screen predictive factors in a multivariate analysis. The risk of developing dyskinesia and wearing-off increased in an l-dopa dose-dependent manner (P<0.001 for both). Analyses using l-dopa equivalent doses produced comparable results. Factors that were predictive of dyskinesia, in rank order, were: young age at onset, higher l-dopa dose, low body weight, North American geographic region, LCE treatment group, female gender, and more severe Unified Parkinson's Disease Rating Scale (UPDRS) Part II. Multivariate analyses identified similar predictors for wearing-off but included baseline UPDRS Part III and excluded weight and treatment allocation. The risk of developing dyskinesia or wearing-off was closely linked to l-dopa dose. The current results suggest that physicians should use the lowest dose of l-dopa that provides satisfactory clinical control to minimize the risk of both dyskinesia and wearing-off.
Neurobiological Background for Performing Surgical Intervention in the Inferior Thalamic Peduncle for Treatment of Major Depression Disorders (2005)

Circumscribed lesions or electrical stimulation of the ITP, a discrete target easily identified by electrophysiological studies, may improve MDD. Electrical stimulation may have the advantage of being less invasive and more adjustable to patient needs.
Enthalpy and heat capacity changes for the proton dissociation of various buffer components in 0.1 M potassium chloride (1998)

Enthalpy and heat capacity changes for the deprotonation of 18 buffers were calorimetrically determined in 0.1 M potassium chloride at temperatures ranging from 5 to 45 degrees C. The values of the dissociation constant were also determined by means of potentiometric titration. The enthalpy changes for the deprotonation of buffers, except for the phosphate and glycerol 2-phosphate buffers, were found to be characterized by a linear function of temperature. The enthalpy changes for the second dissociation of phosphate and glycerol 2-phosphate where divalent anion is formed on dissociation were fitted with the second order function of temperature rather than the first order. Temperature dependence of buffer pH calculated by using the enthalpy and heat capacity changes obtained was in good agreement with the temperature variation of the pH values actually measured in the temperature range between 0 and 50 degrees C for all the buffers studied. On the basis of the results obtained, a numeric table showing the temperature dependence of pK values for the 18 buffers is presented.
Polymorphisms in IL-8 and the GSTP1 are associated with survival of metastatic colorectal cancer patients treated with CPT-11 (2004)

3606 Background Irinotecan (CPT-11), an analogue of Camptothecins, demonstrates a broad spectrum of antitumor activity. Currently, there are no prognostic molecular markers for CPT-11 efficacy. Therefore, we investigated associations between polymorphisms in genes involved in CPT-11 metabolism (UGT1A1), chemoresistance (GSTP1), DNA repair (XPD, ERCC1, XRCC1, Werner 1074, and Werner 1367), and angiogenesis (IL-8 and COX-2) and survival of patients with metastatic colorectal cancer receiving CPT-11 based chemotherapy. In vivo studies show GSTP1 to detoxify chemotherapeutic agents by glutathione conjugation. In vivo and in vitro studies show IL-8 to possess angiogenic properties and its overexpression is associated with metastasis potential in colorectal cancer. Positional cloning studies identified Werner as the gene responsible for Werner Syndrome (WS), and cells from these patients have been shown to be particularly sensitive to Camptothecin. Methods The gene polymorphisms were tested using PCR-RFLP method on genomic DNA extracted from peripheral blood from metastatic colorectal cancer patients treated with CPT-11. Results 55 patients were collected; 31 males and 24 females; median age 55 (range 34–77) years. The response to CPT-11 was 40% (18/45, 1 pt was inevaluable, and 9 pts are still receiving treatment and were too early to be evaluated), with median survival of 22.9 (95% CI: 18.4, 29.3) months. The median time of follow-up and range was 15.4 (4.7–26.1) months. Individually, IL-8 and GSTP1 showed trends for overall survival (log rank p=0.07 and p=0.077, respectively). A combined analysis of these two genes showed patients carrying two favorable genotypes (homozygous Ile for GSTP1 and T allele for IL-8) had longer survival when compared with those patients carrying no favorable genotypes or only 1 favorable genotype (p=0.005). The Werner Loci polymorphisms also showed a trend for overall survival. Conclusion These data suggest that IL-8, GSTP1, and the Werner Loci polymorphisms may be potential prognostic molecular markers for clinical outcome of metastatic colorectal cancer patients treated with a CPT-11 regimen. Author Disclosure Employment or Leadership Consultant or Advisory Stock Ownership Honoraria Research Funding Expert Testimony Other Remuneration Chiron NCI; NIH; Roche; Lilly; Pharmacia; Bayer; Bristol-Myers Squibb; Chiron; Aventis; Genentech; ImClone; Cellpathway; Newbiotics; Sanofi
Mesogenic polymers. III. Thermal properties and synthesis of three homologous series of thermotropic liquid crystalline “backbone” polyesters (1981)

Abstract Details of the thermal behavior, including transition temperatures, transition heats and transition entropies, are reported for three series of nematic liquid‐crystalline “backbone” polyesters having the general structure magnified image All polysters described above were examined by differential scanning calorimetry and were found to have reproducible thermal behavior once the polymer had been annealed by heating to the isotropic phase and then subsequently cooled. Enantiotropic nematic phases were found for all 30 polysters studied. Many polymers showed multiple endotherms on melting to the nematic phase. Plots of solid–nematic and nematic–isotropic transition temperatures versus number of carbon atoms in the diacid segment ( x ) for each ( y ) reveal an even–odd alternation reminiscent of trends in homologous series of small‐molecule liquid crystals. Enthalpies for the solid → nematic and nematic → isotropic transitions do not show such a precise alternation.
Noninvasive tests of CYP3A enzymes (1994)

Cytochromes P450 belonging to the CYP 3A gene subfamily account for up to 2 5% of the total cyto­chrome P450 present in adult human liver, and account for the majority of cytochrome P450 present in human small bowel. The importance of the CYP3A enzymes is most established with respect to the metabolism of xenobiotics, particularly medications. The number of drugs metabolized chiefly by CYP3A enzymes is expanding rapidly and includes a wide variety of compounds in many different therapeutic classes (reviewed in Guengerich, 1992a; Watkins, 1992; Wrighton and Stevens, 1992). Several pharma­ceutical companies are now screening new chemical entities in development to determine whether they are metabolized by CYP3A enzymes. The finding that a drug is a substrate for CYP3A enzymes has three major implications. First, because CYP3A enzymes are relatively abundant in the intestinal mucosa (Kolars et al., 1992; Watkins et al., 198 7), CYP3A substrates may have poor oral bioavailability due to extensive 'first pass' metabolism at the level of the intestine (Kolars et al., 1991). Second, CYP3A substrates may be susceptible to certain drug interactions because some CYP3A enzymes are induced or inhibited by certain medications (reviewed in Watkins, 1992; Wrighton and Stevens, 1992). For example, the im­munosuppressant cyclosporine A and the antihis­tamine terfenadine have been shown to be metabolized chiefly by CYP3A4 (Kronbach et al., 1988; Combalbert et al., 1989; Chui-ho et al., 1993). This enzyme has been shown to be inhibited by erythromycin and ketoconazole (Pichard et al., 1990), and this appears to be the reason that patients receiving these drugs may develop toxic responses when treated with cyclosporine A or terfenadine. Conversely, CYP3A4 is inducible by treatment with antiseizure drugs and the antibiotic rifampicin (Pichard et al., 1990), and this appears to explain why patients treated with these medications require increased dosing of cyclosporine A. In drug development, the discovery that a new chemical entity is largely metabolized by CYP3A enzymes there­fore suggests the potential for similar drug inter­actions.
Structures of the potassium-saturated, 2:1, and intermediate, 1:1, forms of a quadruplex DNA (2000)

Potassium can stabilize the formation of chair- or edge-type quadruplex DNA structures and appears to be the only naturally occurring cation that can do so. As quadruplex DNAs may be important in the structure of telomere, centromere, triplet repeat and other DNAs, information about the details of the potassium-quadruplex DNA interactions are of interest. The structures of the 1:1 and the fully saturated, 2:1, potassium-DNA complexes of d(GGTTGGTGTGGTTGG) have been determined using the combination of experimental NMR results and restrained molecular dynamics simulations. The refined structures have been used to model the interactions at the potassium binding sites. Comparison of the 1:1 and 2:1 potassium:DNA structures indicates how potassium binding can determine the folding pattern of the DNA. In each binding site potassium interacts with the carbonyl oxygens of both the loop thymine residues and the guanine residues of the adjacent quartet.
Structure determination of the head–tail connector of bacteriophage ϕ29 (2001)

The head-tail connector of bacteriophage phi29 is composed of 12 36 kDa subunits with 12-fold symmetry. It is the central component of a rotary motor that packages the genomic dsDNA into preformed proheads. This motor consists of the head-tail connector, surrounded by a phi29-encoded, 174-base, RNA and a viral ATPase protein, both of which have fivefold symmetry in three-dimensional cryo-electron microscopy reconstructions. DNA is translocated into the prohead through a 36 A diameter pore in the center of the connector, where the DNA takes the role of a motor spindle. The helical nature of the DNA allows the rotational action of the connector to be transformed into a linear translation of the DNA. The crystal structure determination of connector crystals in space group C2 was initiated by molecular replacement, using an approximately 20 A resolution model derived from cryo-electron microscopy. The model phases were extended to 3.5 A resolution using 12-fold non-crystallographic symmetry averaging and solvent flattening. Although this electron density was not interpretable, the phases were adequate to locate the position of 24 mercury sites of a thimerosal heavy-atom derivative. The resultant 3.2 A single isomorphous replacement phases were improved using density modification, producing an interpretable electron-density map. The crystallographically refined structure was used as a molecular-replacement model to solve the structures of two other crystal forms of the connector molecule. One of these was in the same space group and almost isomorphous, whereas the other was in space group P2(1)2(1)2. The structural differences between the oligomeric connector molecules in the three crystal forms and between different monomers within each crystal show that the structure is relatively flexible, particularly in the protruding domain at the wide end of the connector. This domain probably acts as a bearing, allowing the connector to rotate within the pentagonal portal of the prohead during DNA packaging.
Cyclic AMP-dependent phosphorylation of a brain inositol trisphosphate receptor decreases its release of calcium. (1988)

We report the stoichiometric phosphorylation of an inositol 1,4,5-trisphosphate receptor-binding protein from rat brain by the cAMP-dependent protein kinase but not by protein kinase C or Ca2+/calmodulin-dependent protein kinase. This phosphorylation event does not markedly alter [3H]inositol 1,4,5-trisphosphate-binding characteristics. However, inositol 1,4,5-trisphosphate is only 10% as potent in releasing 45Ca2+ from phosphorylated, as compared with native, cerebellar microsomes. Phosphorylation of the inositol 1,4,5-trisphosphate-binding protein by the cAMP-dependent protein kinase may provide a biochemical substrate for second-messenger cross talk.
Catalytic Function of PLA2G6 Is Impaired by Mutations Associated with Infantile Neuroaxonal Dystrophy but Not Dystonia-Parkinsonism (2010)

These results indicate that different alterations in PLA2G6 function produce the different disease phenotypes of NBIA/INAD and dystonia-parkinsonism. INAD/NBIA is caused by loss of the ability of PLA2G6 to catalyze fatty acid release from phospholipids, which predicts accumulation of PLA2G6 phospholipid substrates and provides a mechanistic explanation for the accumulation of membranes in neuroaxonal spheroids previously observed in histopathological studies of INAD/NBIA. In contrast, dystonia-parkinsonism mutations do not appear to directly impair catalytic function, but may modify substrate preferences or regulatory mechanisms for PLA2G6.
Characterization and mode of action of xylanases ␁and some accessory enzymes (1992)

Three endo-(l,4)-β-D-xylanases; (Endo I, Endo II, and Endo III), a (1,4)-β-xylosidase and an (1,4)-β-D-arabinoxylan arabinofuranohydrolase (AXH) were purified from a culture filtrate produced by Aspergillus awamori CMI 142717. In addition to these enzymes, an acetyl xylan esterase (AE) was purified from a culture filtrate produced by Aspergillus niger DS 16813.The enzymes were characterized by determining specific activities, molecular weight, isoelectric point, kinetic parameters (K m ,V max ), optimum pH and optimum temperature.Arabinoxylan oligosaccharides were derived from alkali-extracted wheat arabinoxylans by complete digestion with Endo I and III. The structures of unknown oligosaccharides were elucidated by 1H-n.m.r. spectroscopy. From these structures a model was proposed for the mode of action of Endo I and Endo III towards arabinoxylans. The same oligosaccharides were also used to specify the action of (1,4)-β-xylosidase, AXH and two α-L-arabinofuranosidases towards these arabinofuranosylated arabinoxylan oligosaccharides.The interaction between the purified enzymes was studied by degradation of xylans from rice bran, oat spelt, wheat-flour, larchwood, and birchwood by single and combined actions of these enzymes on these substrates. The cooperativity was monitored by the amount of reducing sugars and by the types of products released.
Controlling charge balance and exciton recombination by bipolar host in single-layer organic light-emitting diodes (2010)

Highly efficient single-layer organic light-emitting diodes with reduced efficiency roll-off are demonstrated by using a bipolar host material of 2,5-bis(2-(9H-carbazol-9-yl)phenyl)-1,3,4-oxadiazole (o-CzOXD) doped with iridium complexes as the emissive layer. For example, the green single-layer device, employing fac-tris(2-phenylpyridine)iridium Ir(ppy)3 as dopant, shows a peak current efficiency of 45.57 cd A−1, corresponding to external quantum efficiency (EQE) of 12.42%, and still exhibits efficiencies of 45.26 cd A−1 and 40.42 cd A−1 at luminance of 1000 and 10 000 cd m−2, respectively. In addition, the yellow and red single-layer devices, with bis(2-(9,9- diethyl-9H-fluoren-2-yl)-1-phenyl-1H-benzoimidazol-N,C3)iridium(acetylacetonate) (fbi)2Ir(acac) and bis(1-phenylisoquinolinolato-C2,N)iridium(acetylacetonate) (piq)2Ir(acac) as emitter, also show high EQE of 7.04% and 7.28%, respectively. The transport properties of o-CzOXD film are well investigated by current-voltage measurement, from which both hole and electron mobility are determined. It is found that the o-CzOXD shows appealing bipolar transport character, which is favor for the balanced charge distribution in the whole doped zone. More importantly, the multifunctional role of hole trapping and electron transporting of the iridium complex in o-CzOXD further balances the charge carriers and broadens the recombination zone. As a result, the recombination of electrons and holes is significantly improved and the triplet-triplet annihilation and triplet-polaron quenching processes are effectively suppressed, eventually leading to the high efficiency as well as the reduced efficiency roll-off.
Generic structure storage and retrieval (1985)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTGeneric structure storage and retrievalMichael F. Lynch, John M. Barnard, and Stephen M. WelfordCite this: J. Chem. Inf. Comput. Sci. 1985, 25, 3, 264–270Publication Date (Print):August 1, 1985Publication History Published online1 May 2002Published inissue 1 August 1985https://doi.org/10.1021/ci00047a024RIGHTS & PERMISSIONSArticle Views60Altmetric-Citations12LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InReddit PDF (2 MB) Get e-Alerts
The prevalence of immunization to Duffy antigens in a population of known racial distribution (1989)

A retrospective study at our hospital determined the race or ethnicity of patients seen in an 8‐year period who had formed antibodies to Duffy antigens. During that time, 9876 serologic investigations had been performed as a result of a positive direct or indirect antiglobulin test. Among these samples, sera from 45 previously transfused or pregnant patients contained anti‐Fy a and two contained anti‐Fy3. Twenty‐nine of the sera that contained anti‐Fy a (62%) were from blacks, 12 (25%) were from whites, and 6 (13%) were from Hispanics. Both examples of anti‐Fy3 were made by black patients. Red cells (RBCs) from 21 of the black patients were Fy(a−b−), those from 7 were Fy(a−b+), and those from 1 could not be phenotyped. RBCs from 17 of the non‐black patients were Fy(a−b+) and those from 1 could not be phenotyped. The population of transfused patients evaluated in this study was 47 percent black, 29 percent white, and 24 percent Hispanic. Calculations based on an expected Fy(a−) frequency of 88 percent in blacks, 33 percent in whites, and 20 percent in Hispanics predict that the racial makeup of the Fy(a−) population at our hospital would be 73 percent black, 18 percent white, and 9 percent Hispanic, which is not significantly different (p = 0.25) from the racial makeup of the patients forming anti‐Fy a and ‐Fy3. These data indicate that blacks make antibodies to Duffy antigens as frequently as non‐blacks.