gebhart/patrepeval huggingface dataset:
Osteogenic Differentiation and Immune Response of Human Bone-Marrow-Derived Mesenchymal Stem Cells on Injectable Calcium-Silicate-Based Bone Grafts (2010)

Calcium silicate cement (CSC) is biocompatible and possesses in vitro bioactivity. The aim of this study was to improve the handling and enhance osteogenic and immune properties of CSC by the addition of adjuvants to modify the cement. Human bone-marrow-derived mesenchymal stem cells were used to study the osteogenic behavior and immune response of cells on hybrid cements with added gelatin (GLT) and chitosan oligosaccharides (COS), which are analogs of the extracellular matrix components collagen and glycosaminoglycan, respectively. The addition of COS to the liquid phase slightly prolonged the setting time of CSC, whereas GLT in the solid phase significantly (p < 0.05) extended the hydration reaction. However, the addition of GLT appreciably improved the injectability of CSC, compared to COS. Cell viability was higher on CSC-COS than on the CSC control or on CSC-GLT at all culture times. The hybrid bone cements elicited less immune response than the CSC control. Additionally, COS inhibited expression of inducible nitric oxide synthase and interleukin-1 and activated interleukin-10 more effectively than GLT. Osteocalcin production and bone sialoprotein production were higher, and more calcium was detected in human bone-marrow-derived mesenchymal stem cells cultured on a CSC-GLT-COS surface than on CSC, CSC-GLT, or CSC-COS. These synergistic improvements in injectability, immune response, and osteogenesis suggest that the combination of bioactive calcium silicate, GLT, and COS has potential for use in clinical applications.
Metastatic susceptibility locus, an 8p hot-spot for tumour progression disrupted in colorectal liver metastases: 13 candidate genes examined at the DNA, mRNA and protein level (2008)

Our data confirm that genes on 8p21-22 are dysregulated during colorectal cancer progression. Interestingly, however, instead of harbouring a single candidate colorectal metastasis suppressor 8p21-22 appears to be a hot-spot for tumour progression, encoding at least 13 genes with a putative role in carcinoma development. Thus, we propose that this region of 8p comprises a metastatic susceptibility locus involved in tumour progression whose disruption increases metastatic potential.
Effect of clarithromycin on renal excretion of digoxin: Interaction with P-glycoprotein* (1998)

We present a digoxin-clarithromycin interaction in two patients in whom digoxin concentrations were unexpectedly increased. The ratio of renal digoxin clearance to creatinine clearance in one patient was lower during the concomitant administration of clarithromycin (0.64 and 0.73) than that after cessation of clarithromycin administration (1.30 +/- 0.20; mean +/- SD). Because P-glycoprotein could play an important role in the renal secretion of digoxin, we hypothesized that clarithromycin decreases renal digoxin excretion by inhibiting P-glycoprotein-mediated transport. Digoxin transport was evaluated with use of a kidney epithelial cell line, which expresses the human P-glycoprotein on the apical membrane by transfection with MDR1 complementary deoxyribonucleic acid. Clarithromycin inhibited the transcellular transport of digoxin from the basolateral to the apical side in a concentration-dependent manner and concomitantly increased the cellular accumulation of digoxin. These results suggest that clarithromycin may inhibit the P-glycoprotein-mediated tubular secretion of digoxin, and this interaction mechanism may contribute to an increase in the serum digoxin concentration.
Associations between microbial species in subgingival plaque samples (1988)

Samples of subgingival plaque were taken from 275 active and inactive sites in 35 subjects with destructive periodontal diseases. The predominant cultivable microbiota was determined in each of the samples by characterizing 50 randomly selected isolates recovered on anaerobically incubated Trypticase soy agar supplemented with 5% sheep blood. Microbial associations between species were determined by computing the odds ratio of a site being infected by a “target” species in the presence of an “effector” species. Data are presented for 22 numerically dominant “effector” species and 8 “target” species which consisted of suspected periodontal pathogens. These included Actinobacillus actinomycetemcomitans, Bacteroides forsythus, Bacteroides gingivalis, Bacteroides intermedicus, Bacteroides melaninogenicus, Peptostreptococcus micros, Streptococcus intermedius and Wolinella recta. Positive associations were considered to be relationships in which the odds ratio of detecting a “target” species was >2:1 in the presence of the “effector” species, while negative associations were defined as those in which the odds ratio of detecting the “target” species was < 0.5:1 in the presence of the “effector” species. In general, species of streptococci, an unnamed Actinomyces sp. and Propionibacterium acnes showed a negative association with the 8 suspected pathogens, while many Gram‐negative species tended to show a positive association with these suspected pathogens. There appeared to be specificity in the associations observed. For example, S. intermedius was positively associated with Streptococcus mitis and Streptococcus sanguis I , but negatively associated with Bacteroides forsythus. In contrast, W. recta was negatively associated with S. mitis and Streptococcus sanguis I , but positively associated with Bacteroides forsythus. S. sanguis II, Streptococcus uberis, P. acnes, Capnocytophaga ochracea and an unnamed Actinomyces sp. showed negative associations with 4 of the suspected periodontal pathogens, while B. gingivalis, Fusobacterium nucleatum and the Eubacterium sp. showed only positive or “neutral” associations with the “target” species. Data from this and other investigations suggest that microbial associations might play an important role in controlling the composition of subgingival plaque and, thus, be a major determinant of health or destructive periodontal diseases.
[Quantitative whole-body skeletal scintigraphy with a gamma camera and pinhole collimator]. (1985)

Quantitative evaluation of whole-body bone scans is valuable for the description of metabolic activity in systemic bone disease and provides parameters of whole-body activity retention up to 24 h after injection of the radiopharmacon, of bone to soft tissue relation and of the activity in the epiphysis and diaphysis. A combination of whole-body imaging by a gamma-camera with pinhole collimator and a series of single pictures evaluated by the ROI technique is able to record these parameters with sufficient precision. This is demonstrated by measuring phantoms, and patients with and without bone disease. In 34 patients with systemic bone disease the quantitative parameters are altered partially, the changes however are insufficient for their differential diagnosis.
Protein kinase A regulates RNA polymerase III transcription through the nuclear localization of Maf1 (2006)

Maf1 is an essential and specific mediator of transcriptional repression in the RNA polymerase (pol) III system. Maf1-dependent repression occurs in response to a wide range of conditions, suggesting that the protein itself is targeted by the major nutritional and stress-signaling pathways. We show that Maf1 is a substrate for cAMP-dependent PKA in vitro and is differentially phosphorylated on PKA sites in vivo under normal versus repressing conditions. PKA activity negatively regulates Maf1 function because strains with unregulated high PKA activity block repression of pol III transcription in vivo, and strains lacking all PKA activity are hyperrepressible. Nuclear accumulation of Maf1 is required for transcriptional repression and is regulated by two nuclear localization sequences in the protein. An analysis of PKA phosphosite mutants shows that the localization of Maf1 is affected via the N-terminal nuclear localization sequence. In particular, mutations that prevent phosphorylation at PKA consensus sites promote nuclear accumulation of Maf1 without inducing repression. These results indicate that negative regulation of Maf1 by PKA is achieved by inhibiting its nuclear import and suggest that a PKA-independent activation step is required for nuclear Maf1 to function in the repression of pol III transcription. Finally, we report a previously undescribed phenotype for Maf1 in tRNA gene-mediated silencing of nearby RNA pol II transcription.
The active site of thrombin is altered upon binding to thrombomodulin. Two distinct structural changes are detected by fluorescence, but only one correlates with protein C activation. (1991)

The association of thrombin with thrombomodulin, a non-enzymatic endothelial cell surface receptor, alters the substrate specificity of thrombin. Complex formation converts thrombin from a procoagulant to an anticoagulant enzyme. Structure-function analysis of this change in specificity is facilitated by the availability of two soluble proteolytic derivatives of thrombomodulin, one consisting of the six repeated growth factor-like domains of thrombomodulin (GF1-6) and the other containing only the fifth and sixth such domains (GF5-6). Both derivatives can bind to thrombin and block fibrinogen clotting activity, though only the larger GF1-6 can stimulate the activation of protein C. To ascertain whether the substrate specificity change from fibrinogen to protein C is accompanied by structural changes in the active site of the enzyme, fluorescent dyes were positioned at different locations within the active site. A 5-dimethylaminonaphthalene-1-sulfonyl (dansyl) dye was covalently attached to the active site serine to form dansyl-thrombin, while either a fluorescein or an anilinonaphthalene-6-sulfonic acid (ANS) dye was attached covalently to the active site histidine of thrombin via a D-Phe-Pro-Arg linkage. The environment of the dansyl dye was altered in a similar fashion when either GF1-6 or GF5-6 bound to thrombin, since a similar reduction in dansyl emission intensity was elicited by these two thrombomodulin derivatives (25 and 32%, respectively). These spectral changes, and all others in this study, were saturable and reached a maximum when the ratio of thrombomodulin derivative to thrombin was close to 1. The environments of the fluorescein and ANS dyes were also altered when GF1-6 bound to thrombin because binding resulted in emission intensity changes of -13% and +18%, respectively. In contrast, no fluorescence changes were observed when the fluorescein and ANS thrombin derivatives were titrated with GF5-6. Thus, the structure of the active site was altered by thrombomodulin both immediately adjacent to the active site serine and also more than 15 A away from it. However, the structural change far from Ser-195 was only elicited by thrombomodulin species that stimulate thrombin-dependent activation of protein C.
On Generalized Reed–Solomon Codes Over Commutative and Noncommutative Rings (2013)

In this paper, we study generalized Reed-Solomon codes (GRS codes) over commutative and noncommutative rings, we show that the classical Welch-Berlekamp and Guruswami-Sudan decoding algorithms still hold in this context, and we investigate their complexities. Under some hypothesis, the study of noncommutative GRS codes over finite rings leads to the fact that GRS codes over commutative rings have better parameters than their noncommutative counterparts. Also, GRS codes over finite fields have better parameters than their commutative rings counterparts. But we also show that given a unique decoding algorithm for a GRS code over a finite field, there exists a unique decoding algorithm for a GRS code over a truncated power series ring with a better asymptotic complexity. Moreover, we generalize a lifting decoding scheme to obtain new unique and list decoding algorithms designed to work when the base ring is, for example, a Galois ring or a truncated power series ring or the ring of square matrices over the latter ring.
Composition-based statistics and translated nucleotide searches: Improving the TBLASTN module of BLAST (2006)

TBLASTN is widely used, as it is common to wish to compare proteins to chromosomes or to libraries of mRNAs. Composition-based statistics improve the statistical accuracy, and therefore the reliability, of TBLASTN results. The algorithms used by TBLASTN are not widely known, and some of the most important are reported here. The data used to test TBLASTN are available for download and may be useful in other studies of translated search algorithms.
Differential expression of cysteine-rich intestinal protein in liver and intestine in CCl4-induced inflammation (1996)

Cysteine-rich intestinal protein (CRIP) is a double zinc finger (LIM domain) protein that is developmentally regulated but has an unknown function. CRIP is highly expressed in the intestine, but expression is low in liver. To determine if CRIP expression is regulated under altered physiological status, we used CCl4-induced injury as a model to produce hepatic injury and systemic effects associated with inflammation. Since CRIP is a zinc finger protein and zinc decreases the hepatic response to CCl4, the effect of supplemental dietary zinc (300 mg/kg diet) was also examined. Our results show that this supplemental level of dietary zinc did not affect the index of hepatic injury (plasma alanine aminotransferase), indicating zinc did not have a protective effect. Liver CRIP mRNA increased with CCl4 and CRIP protein was shown by immunohistochemistry to be localized in hepatocytes near the vascular supply. In the intestine, CCl4 caused a transient decrease in CRIP mRNA, but supplemental dietary zinc treatment prevented this decrease. These current results show that CRIP expression changes in response to cellular damage due to acute hepatic injury and are consistent with a functional role for CRIP in proliferation, differentiation, or turnover.
Oxalate:formate exchange (1989)

In the Gram-negative anaerobe, Oxalobacter formigenes, the generation of metabolic energy depends on the transport and decarboxylation of oxalate. We have now used assays of reconstitution to study the movements of oxalate and to characterize the exchange of oxalate with formate, its immediate metabolic derivative. Membranes of O. formigenes were solubilized with octyl-beta-D-glucopyranoside in the presence of 20% glycerol and Escherichia coli phospholipid, and detergent extracts were reconstituted by detergent dilution. [14C]Oxalate was taken up by proteoliposomes loaded with unlabeled oxalate, but not by similarly loaded liposomes or by proteoliposomes containing sulfate in place of oxalate. Oxalate transport did not depend on the presence of sodium or potassium, nor was it affected by valinomycin (1 microM), nigericin (1 microM), or a proton conductor, carbonylcyanide-p-trifluoromethoxyphenylhydrazone (5 microM) when potassium was at equal concentration on either side of the membrane. Such data suggest the presence of an overall neutral oxalate self-exchange, independent of common cations or anions. Kinetic analysis of the reaction in proteoliposomes gave a Michaelis constant (Kt) for oxalate transport of 0.24 mM and a maximal velocity (Vmax) of 99 mumol/min/mg of protein. A direct exchange of oxalate and formate was indicated by the observations that formate inhibited oxalate transport and that delayed addition of formate released [14C]oxalate accumulated during oxalate exchange. Moreover, [14C]formate was taken up by oxalate-loaded proteoliposomes (but not liposomes), and this heterologous reaction could be blocked by external oxalate. Further studies, using formate-loaded proteoliposomes, suggested that the heterologous exchange was electrogenic. Thus, for assays in which N-methylglucamine served as both internal and external cation, formate-loaded particles took up oxalate at a rate of 2.4 mumol/min/mg of protein. When external or internal N-methylglucamine was replaced by potassium in the presence of valinomycin, there was, respectively, a 7-fold stimulation or an 8-fold inhibition of oxalate accumulation, demonstrating that net negative charge moved in parallel with oxalate during the heterologous exchange. The work summarized here suggests the presence of an unusually rapid and electrogenic oxalate2-:formate1- antiport in membranes of O. formigenes. Since a proton is consumed during the intracellular decarboxylation that converts oxalate into formate plus CO2, antiport of oxalate and formate would play a central role in a biochemical cycle consisting of (a) oxalate influx, (b) oxalate decarboxylation, and (c) formate efflux.(ABSTRACT TRUNCATED AT 400 WORDS)
Text Clustering with Seeds Affinity Propagation (2010)

Based on an effective clustering algorithm-Affinity Propagation (AP)-we present in this paper a novel semisupervised text clustering algorithm, called Seeds Affinity Propagation (SAP). There are two main contributions in our approach: 1) a new similarity metric that captures the structural information of texts, and 2) a novel seed construction method to improve the semisupervised clustering process. To study the performance of the new algorithm, we applied it to the benchmark data set Reuters-21578 and compared it to two state-of-the-art clustering algorithms, namely, k-means algorithm and the original AP algorithm. Furthermore, we have analyzed the individual impact of the two proposed contributions. Results show that the proposed similarity metric is more effective in text clustering (F-measures ca. 21 percent higher than in the AP algorithm) and the proposed semisupervised strategy achieves both better clustering results and faster convergence (using only 76 percent iterations of the original AP). The complete SAP algorithm obtains higher F-measure (ca. 40 percent improvement over k-means and AP) and lower entropy (ca. 28 percent decrease over k-means and AP), improves significantly clustering execution time (20 times faster) in respect that k-means, and provides enhanced robustness compared with all other methods.
Infants Fed a Lower Calorie Formula With 2<i>′</i>FL Show Growth and 2<i>′</i>FL Uptake Like Breast‐Fed Infants (2015)

This is the first report of infants fed 2'FL-fortified formulas with a caloric density similar to HM. Growth and 2'FL uptake were similar to those of HM-fed infants.
Ionophore‐Based Biphasic Chemical Sensing in Droplet Microfluidics (2019)

Droplet microfluidics is an enabling platform for high-throughput screens, single-cell studies, low-volume chemical diagnostics, and microscale material syntheses. Analytical methods for real-time and in situ detection of chemicals in the droplets will benefit these applications, but they remain limited. Reported herein is a novel heterogeneous chemical sensing strategy based on functionalization of the oil phase with rationally combined sensing reagents. Sub-nanoliter oil segments containing pH-sensitive fluorophores, ionophores, and ion-exchangers enable highly selective and rapid fluorescence detection of physiologically important electrolytes (K<sup>+</sup> , Na<sup>+</sup> , and Cl<sup>-</sup> ) and polyions (protamine) in sub-nanoliter aqueous droplets. Electrolyte analysis in whole blood is demonstrated without suffering from optical interference from the sample matrix. Moreover, an oil phase doped with an aza-BODIPY dye allows indication of H<sub>2</sub> O<sub>2</sub> in the aqueous droplets, exemplifying sensing of targets beyond ionic species.
A stable graphite negative electrode for the lithium–sulfur battery (2015)

Efficient, reversible lithium intercalation into graphite in ether-based electrolytes is enabled through a protective electrode binder, polyacrylic acid sodium salt (PAA-Na). In turn, this enables the creation of a stable "lithium-ion-sulfur" cell, using a lithiated graphite negative electrode with a sulfur positive electrode, using the common DME:DOL solvent system suited to the electrochemistry of the lithium-sulfur battery. Graphite-sulfur lithium-ion cells show average coulombic efficiencies of ∼99.5%, compared with <95% for lithium-sulfur cells, and significantly better capacity retention, taking into account cell balancing considerations. The high efficiency derives from the considerably better interfacial stability of the graphite electrode, which suppresses the polysulfide redox shuttle and self-discharge.
Defect-free Ge-on-insulator with (100), (110), and (111) orientations by growth-direction-selected rapid-melting growth (2010)

Defect-free Ge-on-insulator (GOI) with various crystal orientations is essential to realize high-speed and multifunctional devices. Seeded rapid-melting growth of GOI is investigated as a function of seed-orientations and growth-directions. From (100)-oriented Si seeds, Ge growth with a (100) orientation propagates for all growth-directions, however, rotational-growth is observed for some directions when Si seeds with (110) and (111) orientations are used. Such rotational-growth can be completely suppressed by selecting the growth-directions deviating from ⟨111⟩ by more than 35°. Transmission-electron-microscopy observation shows no-stacking fault and no-dislocations. Consequently, defect-free GOI with (100), (110), and (111) orientation is achieved, which demonstrates high-hole mobility (∼1100 cm2/V s).
Optimal combining for RAKE reception in mobile cellular CDMA forward links (2002)

Two methods for multipath combining are compared for RAKE reception of a CDMA cellular forward-link traffic channel. Combining based on estimation of the signal-to-interference ratio of the output of each tap of the RAKE receiver is shown to provide significant performance improvement in comparison with the more commonly considered combiner that is based on measurement of the signal strength. The performance of RAKE receivers using the two methods of combining is considered for several fading, multipath channels.
Effects of Price, Brand, and Store Information on Buyers’ Product Evaluations (1991)

The authors report a study of the effects of price, brand, and store information on buyers’ perceptions of product quality and value, as well as their willingness to buy. Hypotheses are derived from a conceptual model positing the effects of extrinsic cues (price, brand name, and store name) on buyers’ perceptions and purchase intentions. Moreover, the design of the experiment allows additional analyses on the relative differential effects of price, brand name, and store name on the three dependent variables. Results indicate that price had a positive effect on perceived quality, but a negative effect on perceived value and willingness to buy. Favorable brand and store information positively influenced perceptions of quality and value, and subjects’ willingness to buy. The major findings are discussed and directions for future research are suggested.