gebhart/patrepeval huggingface dataset:
Scale Up Pillaring: A Study of the Parameters That Influence the Process (2017)

Pillared clays (PILCs) are interesting materials mostly due to their high basal spacing and surface area, which make them suitable for adsorption and catalysis applications, for example. However, the production of these materials on industrial scale is dependent on research about what parameters influence the process. Thus, the objective of this work was to evaluate what parameters influence the pillaring procedure. For this, pillared clays were synthesized following three series of experiments. In the first series, the effect of the amount of water in a clay suspension was evaluated. The best results were obtained by using diluted suspensions (1 g of clay to 100 mL of water). In the second series, several pillaring methods were tested. In the third series, the amount of pillared clay was raised to 50 g. Fifty grams of pillared clay can be obtained using the pillaring agent synthesized at 60 °C with further aging for 24 h, and this material exhibited high basal spacing (17.6 Å) and surface area (233 m²/g). These values are comparable with the traditional pillaring method using only 3 g of clay.
Anti-IgE Antibody Therapy for Asthma (1999)

Over the past 10 years there have been striking improvements in the treatment of asthma, largely as a result of the earlier and more widespread use of inhaled corticosteroids. The development of new treatments for asthma has proved difficult, although several immunologic approaches are undergoing preclinical and clinical assessment.1 Antileukotrienes are the only new class of drugs to treat asthma that have been introduced in the past 25 years, but their efficacy is somewhat limited and unpredictable, as compared with that of inhaled corticosteroids.Mild asthma can be controlled in most patients by relatively low doses of inhaled corticosteroids, and . . .
Elimination of mouse splenic macrophages correlates with increased susceptibility to experimental disseminated candidiasis. (1994)

To evaluate the role of macrophages in experimental disseminated candidiasis, mouse splenic macrophages were eliminated by i.v. delivery of liposome-entrapped dichloromethylene diphosphonate (L-Cl2MDP). Splenic tissue sections that were immunoperoxidase-stained with mAbs against marginal zone macrophages (MONTS-4), red pulp macrophages (SK39), and neutrophils (SK208) showed that 3 days after L-Cl2MDP treatment, macrophages but not neutrophils were depleted, and circulating neutrophils responded normally to an irritated peritoneum and showed normal phagocytic ability. That is, in response to thioglycollate in the peritoneum, neutrophils migrated in normal numbers to the peritoneal cavity and expressed the normal activation phenotype of high Mac-1 and low Mel-14 Ag levels. These neutrophils also showed normal ability to ingest Candida albicans yeast cells in both in vitro and in vivo assays. However, the spleens from L-Cl2MDP-treated mice lost their ability to bind yeast, which agrees with our previous findings that yeast cells bind specifically to marginal zone macrophages. When macrophage-depleted were systemically challenged with C. albicans, clearance of viable fungal elements from blood was slower, their kidneys had higher recoverable CFU, and both BALB/cByJ and congenitally thymic-deficient (nude) mouse strains did not survive as long as control mice. Mice given L-Cl2MDP recovered most of their macrophage function by 56 days and became normal in their resistance to C. albicans. These results indicate that macrophages play an important role in host resistance to experimental disseminated candidiasis, but the mechanism does not appear to involve T cell functions.
The Art of Critically Reviewing a Medical Article (2010)

Annually about 6 million articles related to the field of medicine are published worldwide. However, only 15% of these are of any use. Average quality score of randomized controlled trials (RCTs) is &lt;50%.
Pharmacokinetic study of [14C]flutrimazole after oral and intravenous administration in dogs. Comparison with clotrimazole. (1992)

This trial involved a comparative study using 6 Beagle dogs on the pharmacokinetics of 14C-labelled 1-[(2-fluorophenyl)(4-fluorophenyl)phenylmethyl]-1H-imidazole (flutrimazole, CAS 119006-77-8) and [14C]clotrimazole labelled in the imidazole ring. On the basis of a cross-over trial, each animal received a dose of 5 mg/kg (approx. 100 microCi) [14C]flutrimazole and [14C]clotrimazole, both intravenously and orally. The levels in plasma, urine and faeces of the total radioactivity, unchanged drug and the [14C]imidazole formed by metabolization of the unchanged drug were determined. Flutrimazole presented a biological half-life (t1/2) of 14.4 +/- 3.8 h and a clearance (Cl) of 6.7 +/- 0.8 l/h, while the values for clotrimazole were very different: t1/2 4.6 +/- 0.8 h and Cl: 13.6 +/- 1.0 l/h. After oral administration a fraction of absorbed dose (f) of 78 +/- 21% and bioavailability of 8.9 +/- 6.1% were calculated for flutrimazole. For clotrimazole, these were: 52 +/- 10% and 4.9 +/- 1.9%, respectively. Both drugs showed a significant first-pass effect, with 90% of the absorbed dose being metabolized before reaching the systemic circulation. The total recovery of radioactivity in faeces and urine 5 days after i.v. and oral administration was 58% and 68%, respectively, for [14C]flutrimazole, and 81% and 79% for [14C]clotrimazole. In both cases, most of the radioactivity was recovered in the faeces. The high radioactivity obtained in faeces after i.v. administration of both drugs confirms biliary elimination. For both flutrimazole and clotrimazole, less than 1% of the total recovered in the urine after i.v. administration was recovered as unchanged drug.(ABSTRACT TRUNCATED AT 250 WORDS)
Filterability of blood cells: Methods and clinical applications (1990)

It could be claimed that expansion in clinical aspects of haemorheology has largely been fueled by the development of a simple test of blood flow properties, i.e., analysis of filterability. With time, the level of sophistication in equipment, theory and sample preparation has increased. Theories for the development of flow in the filter have been described and these enable cellular parameters, such as transit times, to be calculated from experimental data. These theories can be quite general, and applied to filtration of red or white cells. Ideally, experimental design requires an understanding of cell behaviour at the filter and of the effects of factors such as the sample concentration and volume, and the presence of different types of cells or subpopulations. Otherwise, results are susceptible to misinterpretation, particularly if impurities or mixed populations of cells are present. It is thus very important to know accurately the constituents of the test suspension. In clinical applications the trend has been to move away from whole blood filtration, toward use of relatively pure suspension of separated red cells and white cells. In the area of red cell filtration this has led to reappraisal of some previously reported abnormalities. The relatively new study of white cell filtration should benefit from previous experience, but there is the added problem of the reactivity of the cells under test, and their mixed nature. In any case, critical evaluation of the meaning and clinical relevance of results is necessary.
Cell Surface and Transcriptional Characterization of Human Adipose‐Derived Adherent Stromal (hADAS) Cells (2005)

Adult human subcutaneous adipose tissue contains cells with intriguing multilineage developmental plasticity, much like marrow-derived mesenchymal stem cells. Putative stem or progenitor cells from fat have been given many different names in the literature, reflecting an early and evolving consensus regarding their phenotypic characterization. The study reported here used microarrays to evaluate over 170 genes relating to angiogenesis and extracellular matrix in undifferentiated, early-passage human adipose-derived adherent stromal (hADAS) cells isolated from three separate donors. The hADAS populations unanimously transcribed 66% of the screened genes, and 83% were transcribed by at least two of the three populations. The most highly transcribed genes relate to functional groupings such as cell adhesion, matrix proteins, growth factors and receptors, and proteases. The transcriptome of hADAS cells demonstrated by this work reveals many similarities to published profiles of bone marrow mesenchymal stem cells (MSCs). In addition, flow analysis of over 24 hADAS cell surface proteins (n = 7 donors) both confirms and expands on the existing literature and reveals strong intergroup correlation, despite an inconsistent nomenclature and the lack of standardized protocols for cell isolation and culture. Finally, based on flow analysis and reverse transcription polymerase chain reaction studies, our results suggest that hADAS cells do not express several proteins that are implicated as markers of "stemness" in other stem cell populations, including telomerase, CD133, and the membrane transporter ABCG2.
Fibroblast growth factor expression during skeletal fracture healing in mice (2009)

Fibroblast growth factors (FGFs) are important signaling molecules that regulate many stages of endochondral bone development. During the healing of a skeletal fracture, several features of endochondral bone development are reactivated. To better understand the role of FGFs in skeletal fracture healing, we quantitatively evaluated the temporal expression patterns of Fgfs, Fgf receptors (Fgfrs), and molecular markers of bone development over a 14-day period following long bone fracture in a mouse model. These studies identify distinct groups of FGFs that are differentially expressed and suggest active stage-specific roles for FGF signaling during the fracture repair process.
Factors involved in the transformation of previously non-transformable Clostridium perfringens type B (1996)

The pre-shock incubation of cells plus DNA and the methylation state of plasmid DNA were found to play a role in the electroporation-based transformation of Clostridium perfringens 3626B.Following pre-shock incubation, the highest number of C. per-f?ingens 3626B transformants was obtained when plasmid pGK201 was both dam+ dcm+ modified, while no transformants were obtained when pGK201 was not methylated or only dcm methylated.This is consistent with the observation that plasmid pGK201 was protected against digestion by C. petfringens 3626B cell-associated nucleases for up to 3 min when methylated by both methylases.C. perfringens 3626B was successfully transformed only within a narrow cell recovery rate window.The ermAM gene associated with pGK201 and pAK102 was found to integrate into the chromosome of C. perfringens strains 13A and 3626B.
Toward a Small Molecule, Biomimetic Carbonic Anhydrase Model: Theoretical and Experimental Investigations of a Panel of Zinc(II) Aza-Macrocyclic Catalysts (2012)

A panel of five zinc-chelated aza-macrocycle ligands and their ability to catalyze the hydration of carbon dioxide to bicarbonate, H(2)O + CO(2) → H(+) + HCO(3)(–), was investigated using quantum-mechanical methods and stopped-flow experiments. The key intermediates in the reaction coordinate were optimized using the M06-2X density functional with aug-cc-pVTZ basis set. Activation energies for the first step in the catalytic cycle, nucleophilic CO(2) addition, were calculated from gas-phase optimized transition-state geometries. The computationally derived trend in activation energies was found to not correspond with the experimentally observed rates. However, activation energies for the second, bicarbonate release step, which were estimated using calculated bond dissociation energies, provided good agreement with the observed trend in rate constants. Thus, the joint theoretical and experimental results provide evidence that bicarbonate release, not CO(2) addition, may be the rate-limiting step in CO(2) hydration by zinc complexes of aza-macrocyclic ligands. pH-independent rate constants were found to increase with decreasing Lewis acidity of the ligand-Zn complex, and the trend in rate constants was correlated with molecular properties of the ligands. It is suggested that tuning catalytic efficiency through the first coordination shell of Zn(2+) ligands is predominantly a balance between increasing charge-donating character of the ligand and maintaining the catalytically relevant pK(a) below the operating pH.
Design and characterization of α-melanotropin peptide analogs cyclized through rhenium and technetium metal coordination (1998)

alpha-Melanocyte stimulating hormone (alpha-MSH) analogs, cyclized through site-specific rhenium (Re) and technetium (Tc) metal coordination, were structurally characterized and analyzed for their abilities to bind alpha-MSH receptors present on melanoma cells and in tumor-bearing mice. Results from receptor-binding assays conducted with B16 F1 murine melanoma cells indicated that receptor-binding affinity was reduced to approximately 1% of its original levels after Re incorporation into the cyclic Cys4,10, D-Phe7-alpha-MSH4-13 analog. Structural analysis of the Re-peptide complex showed that the disulfide bond of the original peptide was replaced by thiolate-metal-thiolate cyclization. A comparison of the metal-bound and metal-free structures indicated that metal complexation dramatically altered the structure of the receptor-binding core sequence. Redesign of the metal binding site resulted in a second-generation Re-peptide complex (ReCCMSH) that displayed a receptor-binding affinity of 2.9 nM, 25-fold higher than the initial Re-alpha-MSH analog. Characterization of the second-generation Re-peptide complex indicated that the peptide was still cyclized through Re coordination, but the structure of the receptor-binding sequence was no longer constrained. The corresponding 99mTc- and 188ReCCMSH complexes were synthesized and shown to be stable in phosphate-buffered saline and to challenges from diethylenetriaminepentaacetic acid (DTPA) and free cysteine. In vivo, the 99mTcCCMSH complex exhibited significant tumor uptake and retention and was effective in imaging melanoma in a murine-tumor model system. Cyclization of alpha-MSH analogs via 99mTc and 188Re yields chemically stable and biologically active molecules with potential melanoma-imaging and therapeutic properties.
Activation of pyruvate dehydrogenase in adipose tissue by insulin. Evidence for an effect of insulin on pyruvate dehydrogenase phosphate phosphatase (1975)

1. The mechanism by which insulin activates pyruvate dehydrogenase in rat epididymal adipose tissue was further investigated. 2. When crude extracts, prepared from tissue segments previously exposed to insulin (2m-i.u/ml) for 2min, were supplemented with Mg-2+, Ca-2+, glucose and hexokinase and incubated at 30 degrees C, they displayed an enhanced rate of increase in pyruvate dehydrogenase activity compared with control extracts. 3. When similar extracts were instead supplemented with fluoride, ADP, creatine phosphate and creatine kinase, the rate of decrease in pyruvate dehydrogenase activity observed during incubation at 30 degrees C was unaffected by insulin treatment. 4. It is suggested that insulin increases the fraction of pyruvate dehydrogenase present in the tissue in the active dephospho form by increasing the activity of pyruvate dehydrogenase phosphate phosphatase.
RUNX1 and GATA-1 coexpression and cooperation in megakaryocytic differentiation (2003)

Megakaryocytic and erythroid lineages derive from a common bipotential progenitor and share many transcription factors, most prominently factors of the GATA zinc-finger family. Little is known about transcription factors unique to the megakaryocytic lineage that might program divergence from the erythroid pathway. To identify such factors, we used the K562 system in which megakaryocyte lineage commitment is dependent on sustained extracellular regulatory kinase (ERK) activation and is inhibited by stromal cell contact. During megakaryocytic induction in this system, the myeloid transcription factor RUNX1 underwent up-regulation, dependent on ERK signaling and inhibitable by stromal cell contact. Immunostaining of healthy human bone marrow confirmed a strong expression of RUNX1 and its cofactor, core-binding factor beta (CBFbeta), in megakaryocytes and a minimal expression in erythroblasts. In primary human hematopoietic progenitor cultures, RUNX1 and CBFbeta up-regulation preceded megakaryocytic differentiation, and down-regulation of these factors preceded erythroid differentiation. Functional studies showed cooperation among RUNX1, CBFbeta, and GATA-1 in the activation of a megakaryocytic promoter. By contrast, the RUNX1-ETO leukemic fusion protein potently repressed GATA-1-mediated transactivation. These functional interactions correlated with physical interactions observed between GATA-1 and RUNX1 factors. Enforced RUNX1 expression in K562 cells enhanced the induction of the megakaryocytic integrin proteins alphaIIb and alpha2. These results suggest that RUNX1 may participate in the programming of megakaryocytic lineage commitment through functional and physical interactions with GATA transcription factors. By contrast, RUNX1-ETO inhibition of GATA function may constitute a potential mechanism for the blockade of erythroid and megakaryocytic differentiation seen in leukemias with t(8;21).
P2Z purinoreceptor ligation induces activation of caspases with distinct roles in apoptotic and necrotic alterations of cell death (1999)

Myeloic cells express a peculiar surface receptor for extracellular ATP, called the P2Z/P2X7 purinoreceptor, which is involved in cell death signalling. Here, we investigated the role of caspases, a family of proteases implicated in apoptosis and the cytokine secretion. We observed that extracellular ATP induced the activation of multiple caspases including caspase-1, -3 and -8, and subsequent cleavage of the caspase substrates PARP and lamin B. Using caspase inhibitors, it was found that caspases were specifically involved in ATP-induced apoptotic damage such as chromatin condensation and DNA fragmentation. In contrast, inhibition of caspases only marginally affected necrotic alterations and cell death proceeded normally whether or not nuclear damage was blocked. Our results therefore suggest that the activation of caspases by the P2Z receptor is required for apoptotic but not necrotic alterations of ATP-induced cell death.
Evolutionary Chemistry Approach toward Finding Novel Inhibitors of the Type 2 Diabetes Target Glucose-6-phosphate Translocase (2005)

A genetic algorithm (GA), driven by experimentally determined biological activities as a feedback fitness function, was used to propose novel small molecules as inhibitors of glucose-6-phosphate translocase (G6PT) in iterative rounds of evolutionary optimization. A straightforward polymer-supported synthetic sequence was implemented to synthesize molecules proposed by the GA, and the biological activities of the compounds were determined by a microsomal assay. Additional compound design strategies were integrated, such as Tanimoto similarity-based selection of starting materials and transfer of favored structure elements into a new chemical scaffold to identify more active and selective inhibitors.
Thioesterases: A new perspective based on their primary and tertiary structures (2010)

Thioesterases (TEs) are classified into EC 3.1.2.1 through EC 3.1.2.27 based on their activities on different substrates, with many remaining unclassified (EC 3.1.2.-). Analysis of primary and tertiary structures of known TEs casts a new light on this enzyme group. We used strong primary sequence conservation based on experimentally proved proteins as the main criterion, followed by verification with tertiary structure superpositions, mechanisms, and catalytic residue positions, to accurately define TE families. At present, TEs fall into 23 families almost completely unrelated to each other by primary structure. It is assumed that all members of the same family have essentially the same tertiary structure; however, TEs in different families can have markedly different folds and mechanisms. Conversely, the latter sometimes have very similar tertiary structures and catalytic mechanisms despite being only slightly or not at all related by primary structure, indicating that they have common distant ancestors and can be grouped into clans. At present, four clans encompass 12 TE families. The new constantly updated ThYme (Thioester-active enzYmes) database contains TE primary and tertiary structures, classified into families and clans that are different from those currently found in the literature or in other databases. We review all types of TEs, including those cleaving CoA, ACP, glutathione, and other protein molecules, and we discuss their structures, functions, and mechanisms.
28 GHz propagation measurements for outdoor cellular communications using steerable beam antennas in New York city (2013)

The millimeter wave frequency spectrum offers unprecedented bandwidths for future broadband cellular networks. This paper presents the world's first empirical measurements for 28 GHz outdoor cellular propagation in New York City. Measurements were made in Manhattan for three different base station locations and 75 receiver locations over distances up to 500 meters. A 400 megachip-per-second channel sounder and directional horn antennas were used to measure propagation characteristics for future mm-wave cellular systems in urban environments. This paper presents measured path loss as a function of the transmitter - receiver separation distance, the angular distribution of received power using directional 24.5 dBi antennas, and power delay profiles observed in New York City. The measured data show that a large number of resolvable multipath components exist in both non line of sight and line of sight environments, with observed multipath excess delay spreads (20 dB) as great as 1388.4 ns and 753.5 ns, respectively. The widely diverse spatial channels observed at any particular location suggest that millimeter wave mobile communication systems with electrically steerable antennas could exploit resolvable multipath components to create viable links for cell sizes on the order of 200 m.
Postsynthetic Metalation of Bipyridyl-Containing Metal–Organic Frameworks for Highly Efficient Catalytic Organic Transformations (2014)

We have designed highly stable and recyclable single-site solid catalysts via postsynthetic metalation of the 2,2'-bipyridyl-derived metal-organic framework (MOF) of the UiO structure (bpy-UiO). The Ir-functionalized MOF (bpy-UiO-Ir) is a highly active catalyst for both borylation of aromatic C-H bonds using B2(pin)2 (pin = pinacolate) and ortho-silylation of benzylicsilyl ethers; the ortho-silylation activity of the bpy-UiO-Ir is at least 3 orders of magnitude higher than that of the homogeneous control. The Pd-functionalized MOF (bpy-UiO-Pd) catalyzes the dehydrogenation of substituted cyclohexenones to afford phenol derivatives with oxygen as the oxidant. Most impressively, the bpy-UiO-Ir was recycled and reused 20 times for the borylation reaction without loss of catalytic activity or MOF crystallinity. This work highlights the opportunity in designing highly stable and active catalysts based on MOFs containing nitrogen donor ligands for important organic transformations.