gebhart/patrepeval huggingface dataset:
Effects of RE <sup>3+</sup> (RE = La, Ce, Pr, Sm, Dy, Ho, Er, and Tm) on the luminescence of Sr <sub>2</sub> MgSiO <sub>5</sub> :Eu <sup>2+</sup> phosphors (2011)

Abstract Sr 2 MgSiO 5 :Eu 2+ phosphors were synthesized through a high temperature solid state reaction method. The phase and luminescence properties of the samples were characterized by X‐ray diffraction (XRD) and a luminescence spectrometer. The effects of RE 3+ (RE = La, Ce, Pr, Sm, Dy, Ho, Er, and Tm) on the luminescent properties of the samples were studied. The results show that the luminescence spectrum of Sr 2 MgSiO 5 :Eu 2+ is a broad band composed of two emission peaks, at 460 and at 530 nm under near‐ultraviolet excitation. Rare earth ions Re 3+ (RE = La, Ce, Pr, Sm, Dy, Ho, Er, and Tm) have great influence on the emission of Sr 2 MgSiO 5 :Eu 2+ phosphors. The La 3+ ion in Sr 2 MgSiO 5 :Eu 2+ phosphors greatly enhances the emission at 460 and 530 nm.
Characterisation and application of a bovine U6 promoter for expression of short hairpin RNAs (2005)

We have mined data from the bovine genome sequencing project to identify a functional bovine U6 promoter and used the promoter sequence to construct a shRNA expression vector. The use of this native bovine promoter in shRNA expression is an important component of our future development of RNAi therapeutic and transgenic applications in bovine species.
Pemetrexed pharmacokinetics and pharmacodynamics in a phase I/II study of doublet chemotherapy with vinorelbine: implications for further optimisation of pemetrexed schedules (2007)

The purpose of this study was to investigate the utility of plasma pharmacokinetic and pharmacodynamic measures including plasma deoxynucleosides, homocysteine and methylmalonic acid concentrations in understanding the time course and extent of the inhibition of thymidylate synthase (TS) by pemetrexed in the context of a phase I/II combination study with vinorelbine. Eighteen patients received supplementation with folic acid and Vitamin B(12) 1 week before beginning treatment with pemetrexed and vinorelbine administered in a dose-escalating manner on a 21-day cycle. Heparinised blood samples were collected from consenting patients in the first cycle for pharmacokinetic analyses and in the first two cycles for determination of plasma thymidine, deoxyuridine, homocysteine and methylmalonic acid concentrations. These values were correlated with response and toxicity. Plasma deoxyuridine was used as a measure of TS inhibition, and concentrations of deoxyuridine were significantly elevated relative to baseline on days 1 (P<0.01), 2 (P<0.001) and 3 (P<0.05) after treatment at all pemetrexed dose levels (400-700 mg m(-2)). The magnitude of deoxyuridine elevation correlated with pemetrexed area under the plasma concentration-time curve (AUC) (r(2)=0.23, P<0.05). However, deoxyuridine concentrations returned to baseline between 8 and 15 days after treatment with pemetrexed, suggesting that inhibition of TS was not durable. Pemetrexed AUC correlated with the percentage decline (relative to baseline) in both platelets (r(2)=0.58, P<0.001) and leucocytes (r(2)=0.26, P<0.05) at day 8. Baseline homocysteine was also significantly correlated with these measures of haematological toxicity (r(2)=0.37, P<0.01 and r(2)=0.39, P<0.01, respectively). In addition, there was a significant reduction of plasma homocysteine on days 8 (P<0.005) and 15 (P<0.05) in cycle 1 compared to baseline values. The results suggest that the TS inhibitory effects of pemetrexed are short-lived and make the case for a more frequent schedule of administration such as every 2 weeks. The lack of protracted TS inhibition may be due to concomitant vitamin administration, and this may be the mechanism by which vitamins prevent life-threatening toxicity from pemetrexed. Baseline homocysteine concentration remains a predictive marker for haematological toxicity even following folate supplementation.
Novel Therapeutics for The Treatment of Metastatic Melanoma (2009)

Metastatic malignant melanoma is an incurable disease with a median survival of 8.5 months and a probability of surviving 5 years after the diagnosis of less than 5%. To date, no systemic therapy has meaningfully changed these survival end points. Currently, in the USA the FDA has approved three agents for the treatment of metastatic melanoma: hydroxyurea, dacarbazine and interleukin-2. None of these have demonstrated a meaningfully prolonged survival of patients with metastatic melanoma. Therefore, a number of innovative therapeutic strategies have been pursued to improve outcomes, including immune therapy, tyrosine kinase inhibitors and angiogenesis inhibitors. Herein, we review some of the recent advances in novel therapeutic developments for the treatment of metastatic melanoma.
Design and Application of Genome-Scale Reconstructed Metabolic Models (2008)

In this chapter, the process for the reconstruction of genome-scale metabolic networks is described, and some of the main applications of such models are illustrated. The reconstruction process can be viewed as an iterative process where information obtained from several sources is combined to construct a preliminary set of reactions and constraints. This involves steps such as genome annotation; identification of the reactions from the annotated genome sequence and available literature; determination of the reaction stoichiometry; definition of compartmentation and assignment of localization; determination of the biomass composition; measurement, calculation, or fitting of energy requirements; and definition of additional constraints. The reaction and constraint sets, after debugging, may be integrated into a stoichiometric model that can be used for simulation using tools such as Flux Balance Analysis (Section 3.8). From the flux distributions obtained, physiologic parameters such as growth yields or minimal medium components can be calculated, and their distance from similar experimental data provides a basis from where the model may need to be improved.
HicA of <i>Escherichia coli</i> Defines a Novel Family of Translation-Independent mRNA Interferases in Bacteria and Archaea (2008)

Toxin-antitoxin (TA) loci are common in free-living bacteria and archaea. TA loci encode a stable toxin that is neutralized by a metabolically unstable antitoxin. The antitoxin can be either a protein or an antisense RNA. So far, six different TA gene families, in which the antitoxins are proteins, have been identified. Recently, Makarova et al. (K. S. Makarova, N. V. Grishin, and E. V. Koonin, Bioinformatics 22:2581-2584, 2006) suggested that the hicAB loci constitute a novel TA gene family. Using the hicAB locus of Escherichia coli K-12 as a model system, we present evidence that supports this inference: expression of the small HicA protein (58 amino acids [aa]) induced cleavage in three model mRNAs and tmRNA. Concomitantly, the global rate of translation was severely reduced. Using tmRNA as a substrate, we show that HicA-induced cleavage does not require the target RNA to be translated. Expression of HicB (145 aa) prevented HicA-mediated inhibition of cell growth. These results suggest that HicB neutralizes HicA and therefore functions as an antitoxin. As with other antitoxins (RelB and MazF), HicB could resuscitate cells inhibited by HicA, indicating that ectopic production of HicA induces a bacteriostatic rather than a bactericidal condition. Nutrient starvation induced strong hicAB transcription that depended on Lon protease. Mining of 218 prokaryotic genomes revealed that hicAB loci are abundant in bacteria and archaea.
Simple source of Li metal for evaporators in ultrahigh vacuum (UHV) applications (1994)

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QCD corrections to the reaction p W + + X (1989)

The complete order c~ QCD corrections to the cross section and differential distributions for p +/5-, W + 7 + X are presented. At the quark level this involves the computation of the contributions from the reactions q + 4 ~ W + ~ + g and q(q) + g --' W + 7 + q(q). We discuss how these corrections modify the factorization property of the lowest order ampli- tude and give results for future experiments at CERN and Fermilab.
Synthesis of2H- and3H-labeledN-cyclopropylmethyl-7α-[(R)-1-hydroxy-1-methyl-3-(2thienyl)-propyl]-6,14-endoethano-6,7,8,14-tetrahydro nororipavine (2005)

A procedure for deuterium and tritium labeling of the titled compound, an analgesic agent, was developed. A secondary amine intermediate was acylated to an acylamide, then the carbonyl function was reduced by LiAlD4 to yield the tertiary amine. In the tritium-labeled synthesis, the process utilized a bromo-substituted precursor, which was subsequently reduced with 3H2 in the presence of a Pd/C catalyst. The labeled compounds were successfully applied in pharmacokinetic and pharmacological studies. Copyright © 2005 John Wiley & Sons, Ltd.
Nanospring Pressure Sensors Grown by Glancing Angle Deposition (2006)

Arrays of Cr zigzag nanosprings and slanted nanorods, 15-55 nm and 40-80-nm-wide, respectively, were grown on SiO2/Si substrates by glancing angle deposition. The arrays exhibit a reversible change in resistivity upon loading and unloading, by 50% for nanosprings and 5% for nanorods, indicating their potential as pressure sensors. The resistivity drop is due to a compression of nanosprings (by a measured 19% for an applied external force of 10(-10) N per spring), which causes them to physically touch their neighbors, providing a path for electric current to flow between nanosprings. Repeated loading and unloading at large loads (> or =1 MPa) results in irreversible plastic deformation and a degradation of the pressure sensitivity.
Retrieval of Aerosol Complex Refractive Index by Combining Cavity Ring Down Aerosol Spectrometer Measurements with Full Size Distribution Information (2007)

Cavity ring down aerosol extinction measurements are combined with size distribution measurements to provide a multi-parameter basis for the retrieval of the aerosol complex refractive index. We show that two distinct size distributions of small particles (< 300 nm) suffice to obtain robust convergence of the Mie theory fit of the extinction function. Experiments are performed both for purely scattering and for absorbing aerosol. Thus this method provides a perspective to use cavity ring down aerosol spectroscopy in field and laboratory measurements that often suffer from low particle concentrations and a lack of large particles.
Characterization of the bovine pregnancy-associated glycoprotein gene family – analysis of gene sequences, regulatory regions within the promoter and expression of selected genes (2009)

PAGs represent a relatively large gene family in the bovine genome. The proximal promoter regions of these genes display differences in putative TF binding sites, likely contributing to observed differences in spatial and temporal expression. We also discovered that boPAG-2 is the most abundant of all boPAG transcripts and provided evidence for the role of ETS and DDVL TFs in its regulation. These experiments mark the crucial first step in discerning the complex transcriptional regulation operating within the boPAG gene family.
An Internet-enabled Knowledge Discovery Process (1999)

A holistic approach, in the form of a process, is proposed in order to discover marketing intelligence from Internet data. The Internet-enabled knowledge discovery process contains the steps human resource identification, problem specification, data prospecting, domain knowledge elicitation, methodology identification, data pre-processing, pattern discovery, and knowledge post-processing. It also involves the three types of expertise required during a project, namely a web administrator, a marketing expert, and a data mining specialist. To show the validity and applicability of the proposed approach, the electronic commerce marketing scenarios of customer attraction, customer retention, cross-sales, and churn are tackled with the outlined process, respectively.
Phase 1 Study of Anti-CTGF Monoclonal Antibody in Patients with Diabetes and Microalbuminuria (2010)

Treatment of microalbuminuric DKD subjects using FG-3019 was well tolerated and associated with a decrease in albuminuria. The data demonstrate a saturable pathway for drug elimination, minimal infusion adverse events, and no significant drug-attributable adverse effects over the year of follow-up. Changes in albuminuria were promising but require validation in a prospective, randomized, blinded study.
Personal computer based Fourier transform ion cyclotron resonance mass spectrometer (1988)

An IBM PC AT compatible computer is used to host the interface of a Fourier transform ion cyclotron resonance mass spectrometer or FTMS. A common fast memory bank for both ion-excitation waveform and data acquisition is reserved in the computer’s system memory space. All the digital electronics circuitry is assembled on an IBM PC AT extension board. Neither an external frequency synthesizer nor a waveform digitizer is needed. Ion-excitation waveforms can be generated in either frequency-sweeping or inverse-Fourier transform modes. Both excitation and data acquisition can be carried out at eight megawords per second.
Gas fIIIed lipid bilayers as imaging contrast agents (1994)

Gas bubbles are highly efficient reflectors of sound and are therefore useful as contrast agents for diagnostic ultrasound. In general, in order to pass through the pulmonary circulation and provide contrast for the systemic circulation the gas bubbles must be of defined diameter and stabilized by a coating material. Our group has developed gas bubbles which are stabilized within lipid bilayers. These bubbles may be formed with stable size and gas content. In vivo studies in rabbit and porcine models show sustained ventricular enhancement, increased arterial doppler signal following intravenous injection and myocardial perfusion enhancement following injection into the aortic root of pigs. Preliminary toxicity studies suggest that the therapeutic index (LD50 dose divided by imaging dose) is greater than 400 to 1. For therapy, these agents may be used to increase the capture of ultrasonic energy for hyperthermia to augment local tissue heating. An exciting new class of agents based upon gas fIIIed lipid bilayers has been developed. Work is presently underway to take these agents into clinical trials.
Effect of pharmacological chaperones on brain tyrosine hydroxylase and tryptophan hydroxylase 2 (2010)

Phenylalanine hydroxylase (PAH), tyrosine hydroxylase (TH) and the tryptophan hydroxylases (TPH1 and TPH2) are structurally and functionally related enzymes that share a number of ligands, such as amino acid substrates, pterin cofactors and inhibitors. We have recently identified four compounds (I-IV) with pharmacological chaperone effect for PAH and phenylketonuria mutants (Pey et al. (2008) J. Clin. Invest. 118, 2858-2867). We have now investigated the effect of these compounds on the brain enzymes TH and TPH2, comparative to hepatic PAH. As assayed by differential scanning fluorimetry each of the purified human PAH, TH and TPH2 was differently stabilized by the compounds and only 3-amino-2-benzyl-7-nitro-4-(2-quinolyl)-1,2-dihydroisoquinolin-1-one (compound III) stabilized the three enzymes. We also investigated the effect of compounds II-IV in wild-type mice upon oral loading with 5 mg/kg/day. Significant effects were obtained by treatment with compound III - which increased total TH activity in mouse brain extracts by 100% but had no measurable effects either on TPH activity nor on monoamine neurotransmitter metabolites dopamine, dihydroxyphenylacetic acid, homovanillic acid, serotonin and 5-hydroxyindolacetic acid - and with 5,6-dimethyl-3-(4-methyl-2-pyridinyl)-2-thioxo-2,3-dihydrothieno[2,3-d]pyrimidin-4(1H)-one (compound IV) - which led to a 10-30% decrease of these metabolites. Our results indicate that pharmacological chaperones aiming the stabilization of one of the aromatic amino acid hydroxylases should be tested on other members of the enzyme family. Moreover, compound III stabilizes in vitro the human TH mutant R202H, associated to autosomal recessive L-DOPA-responsive dystonia, revealing the potential of pharmacological chaperones for the treatment of disorders associated with TH misfolding.
Management of Resistant Pseudarthrosis of Long Bones (1988)

A retrospective review was undertaken of 15 patients with long-bone pseudarthrosis with long-standing nonunion. These patients were referred to a tertiary care center after their fractures failed to unite after numerous surgical attempts as well as a course of electrical stimulation. Fourteen patients had nonunion of the tibia, and one had nonunion of a humerus fracture. Twelve were originally Gustillo Grade II or III fractures, and four sustained multiple injuries. The average duration of nonunion before presentation to the clinic was 22.5 months. Five patients presented as infected nonunions. Each nonunion was analyzed with specific reference to injury mechanism, skin and bone conditions, presence of infection, primary treatment protocol, and selection criteria for treatment with electrical stimulation. Review of the data revealed that the most common factor associated with failure of electrical stimulation treatment was inappropriate patient selection, according to criteria previously published for the use of these techniques. Treatment modalities consisted of intramedullary fixation in three, open reduction and internal fixation using Arbeitsgemeinschaft fur Osteosynthesefragen (AO) technique in nine, and external fixation in three. All patients were bone grafted. The mean follow-up duration was 1.5 years. Nonunions were healed in fourteen patients. Twelve were fully weight bearing at six months, and one at 12 months. Success was defined as restoration of a functional extremity, giving a success rate of 87%. A thorough reevaluation of the original treatment regimen and a return to basic principles of operative fracture management and bone grafting can yield excellent results, even in patients with recalcitrant nonunion.
Botanical Galactagogues (2008)

Herbs have a long history of use in all cultures to stimulate milk production both in women and in dairy animals. It is estimated that about 15% of breastfeeding women in the United States have used botanical galactagogues. This article discusses some of the herbs commonly used as galactagogues and also makes some suggestions on how studies might be conducted to bridge the gap between common uses and lack of studies on the safety and effectiveness of these herbs in lactation. Coverage in this article includes Trigonella foenum-graecum (fenugreek) seed, Galega officinalis (goat’s rue) herb, Foeniculum vulgare (fennel) seed, Vitex agnus-castus (chaste tree) seed, Epilobium spp. (fireweed) herb, Pimpinella anisum (anise) seed, Cnicus benedictus (blessed thistle) herb, Silybum marianum (milk thistle) herb, Urtica dioica (stinging nettle) herb, and Gossypium spp. (cotton) root.
Pathogen Occurrence and Antimicrobial Susceptibility of Urinary Tract Infection Cases during a 20-Year Period (1983 - 2002) at a Single Institution in Japan (2005)

Urinary tract infections are one of the most common infectious diseases diagnosed in outpatients as well as in hospitalized patients. Recently, urinary tract infections have become more complicated and difficult to treat. Therefore, the present study analyzed the occurrence and antimicrobial susceptibility of uropathogens isolated at Kobe University Hospital between 1983 and 2002. This study was performed with three patient groups: urology inpatients, urology outpatients, and inpatients of other departments. During the 20-year study period, we studied 15,925 urine isolates obtained from those patients who were diagnosed with urinary tract infection. Overall, Enterococcus faecalis was the most frequently isolated pathogen, followed by Pseudomonas aeruginosa and Escherichia coli. The frequency of Staphylococcus aureus increased over time, corresponding to an increase in the occurrence of methicillin-resistant S. aureus (MRSA). In addition, the rate of isolation of Serratia marcescens also increased over time, especially among patients with urinary tract catheters. Our results demonstrate that the uropathogens isolated at a single institution have shown a trend of increasing resistance to various classes of antimicrobial agents. In addition, serious problems should be anticipated in the treatment of multidrug-resistant P. aeruginosa, fluoroquinolone-resistant E. coli, and arbekacin-resistant MRSA.
Association of CRHR1 and CRHR2 with major depressive disorder and panic disorder in a Japanese population (2012)

Major depressive disorder (MDD) and panic disorder (PD) are common and disabling medical disorders with stress and genetic components. Dysregulation of the stress response of the hypothalamic-pituitary-adrenal axis, including the corticotrophin-releasing hormone (CRH) signaling via primary receptors (CRHR1 and CRHR2), is considered to play a major role for onset and recurrence in MDD and PD. To confirm the association of CRHR1 and CRHR2 with MDD and PD, we investigated 12 single nucleotide polymorphisms (SNPs) (rs4076452, rs7209436, rs110402, rs242924, rs242940, and rs173365 for CRHR1 and rs4722999, rs3779250, rs2267710, rs1076292, rs2284217, and rs226771 for CRHR2) in MDD patients (n = 173), PD patients (n = 180), and healthy controls (n = 285). The SNP rs110402 and rs242924 in the CRHR1 gene and the rs3779250 in the CRHR2 gene were associated with MDD. The SNP rs242924 in the CRHR1 gene was also associated with PD. The T-A-T-G-G haplotype consisting of rs7209436 and rs173365 in CRHR1 was positively associated with MDD. The T-A haplotype consisting of rs7209436 and rs110402 in CRHR1 was positively associated with MDD. The C-C haplotype consisting of rs4722999 and rs37790 in CRHR1 was associated with PD. These results provide support for an association of CRHR1 and CRHR2 with MDD and PD.
On rectangle packing: maximizing benefits (2004)

We consider the following rectangle packing problem: Given a set of rectangles, each of which is associated with a profit, we are requested to pack a subset of the rectangles into a bigger rectangle to maximize the total profit of rectangles packed. The rectangles may not overlap and may or may not be rotated. This problem is strongly NP-hard even for packing squares with identical profits. A simple (3 + e)-approximation algorithm is presented. We further improve the algorithm by showing a worst-case ratio of at most 5/2 + e. Finally we devise a (2 + e)-approximation algorithm. A number of restricted cases are also considered.
Stem Cells from Human Trabecular Meshwork Hold the Potential to Develop into Ocular and Non-Ocular Lineages After Long-Term Storage (2019)

Stem cells from the eye hold a great potential for vision restoration and can also be used for regeneration in other tissues. In this study, we characterized the stem cell properties of Trabecular meshwork stem cells (TMSCs) after long-term cryopreservation (∼8 years). TMSCs derived from four donors were examined for their viability and proliferation, as well as stem cell marker expression. Spheroid formation, colony formation, and multipotency were investigated. We observed that TMSCs were fully viable with variable proliferation ability. They expressed the stem cell markers CD90, CD166, CD105, CD73, OCT4, SSEA4, Notch1, <i>KLF4</i>, <i>ABCG2</i>, Nestin, and HNK1 detected by flow cytometry, quantitative polymerase chain reaction, or immunofluorescent staining. They could form spheroids and colonies after thawing. All TMSCs were able to differentiate into osteocytes, neural cells, and trabecular meshwork (TM) cells, but not adipocytes. Differentiated TM cells responded to dexamethasone treatment with increased expression of <i>myocilin</i> and angiopoietin-like 7 (<i>ANGPTL7</i>). In a nutshell, our study demonstrated that TMSCs retain their stem cell properties after long-term cryopreservation and hence can be an effective cell therapy source for various clinical applications.