gebhart/patrepeval huggingface dataset:
Fluorescence‐Energy Transfer in Human Estradiol 17β‐Dehydrogenase‐NADPH Complex and Studies on the Coenzyme Binding (1996)

Fluorescence spectroscopy was used to examine the interaction between human estradiol 17 beta-dehydrogenase (estrogenic 17 beta-hydroxysteroid dehydrogenase, 17 beta-HSD) and the cofactor NADPH. After the binding of NADPH to the enzyme, there was an emission enhancement at 436 nm following an excitation at 295 nm, as compared to the cofactor alone. This phenomenon was attributed to a radiationless transfer of excitation energy from 17 beta-HSD to the enzyme-bound cofactor. The distance of 2.69 nm, between the bound NADPH and the sole tryptophan residue (Trp46) within one subunit, has been determined using fluorescence energy transfer. This result coincides very well with the same distance, recently calculated from the crystallographic coordinates obtained by Ghosh et al. [Ghosh, D., Pletnev, V. Z., Zhu, D.-W., Wawrzak, Z., Duax, W. L., Pangborn, W., Labrie, F. & Lin, S.-X. (1995) Structure 3, 503-513]. Compared to free NADPH, the fluorescence emission of enzyme-bound NADPH was increased in intensity and its maximum blue-shifted from 457 nm to 436 nm. Binding of NADPH to 17 beta-HSD was studied by fluorescence titration. The enzyme binds two molecules of NADPH with a Kd = 0.73 +/- 0.2 microM. The dissociation constant was further confirmed by the method of coenzyme protection against cold inactivation of the enzyme. The binding was little altered in the presence of estradiol-17 beta. The environment of tryptophan residues on the surface of the enzyme is discussed.
Longitudinal Changes in Ferritin During Chronic Transfusion: A Report From the Stroke Prevention Trial in Sickle Cell Anemia (STOP) (2002)

There was strong intrapatient correlation between serum ferritin levels and volume transfused but wide interpatient variability early during chronic transfusion therapy. Intrapatient correlation declined at transfusion volumes of more than 250 mL/kg. Direct iron store assessment is needed to determine the clinical significance of serum ferritin variability.
Studies on taxane synthesis. II. Syntheses of 3,8,11,11-tetramethyl-4-oxo- and 4,8,11,11-tetramethyl-3-oxo-bicyclo[5.3.1]undec-8-enes corresponding to the A- and B-rings of taxane diterpenes. (1988)

Two types of tetramethylbicyclo [5.3.1] undec-8-enes 2 and 3 were synthesized from oc-ionone as a model for taxane synthesis.Introduction of the requisite cis-arrangement of substituents at the C-1 and C-7 positions was carried out by catalytic hydrogenation of the α, β-unsaturated ketone 12. Treatment of the hydroxy ester 27 and 16 with diethyl azodicarboxylate and triphenylphosphine led to regioselective dehydration giving 33 and 43, respectively.Intramolecular cyclization of 41 and 49 with lithium diisopropylamide followed by reductive desulfurization with Na-Hg produced the eight-membered ring ketones 2 and 3, respectively, in good yields.
Does Incomplete Recovery From First Lifetime Major Depressive Episode Herald a Chronic Course of Illness? (2000)

Resolution of major depressive episodes with residual subthreshold depressive symptoms, even the first lifetime episode, appears to be the first step of a more severe, relapsing, and chronic future course. When ongoing subthreshold symptoms continue after major depressive episodes, the illness is still active, and continued treatment is strongly recommended.
Electrochemical Properties of Oxide Anode Materials for SOFC (2001)

An oxide material, which can tolerate carbon deposition, would be a potential candidate for the SOFC anode. Electrochemical properties of n-type doped strontium titanates, whose electronic conductivity and chemical stability are high, were investigated by means of both impedance spectroscopy and steady state polarization technique. The specific interfacial resistances of SrTi0.97Nb0.03O3, La0.1Sr0.9TiO3 and La0.2Sr0.8TiO3 were 7.0×102 Ωcm2, 5.1×102 Ωcm2 and 3.5×102 Ωcm2 at 1073 K in 50%H2-2.3%H2O-Ar, respectively. The performances of these oxide anodes are much inferior to Ni/YSZ. This result indicates that the electronic conduction of the oxide-anode might not control the performance.
Combining Machine Learning and Enhanced Sampling Techniques for Efficient and Accurate Calculation of Absolute Binding Free Energies (2020)

Calculating absolute binding free energies is challenging and important. In this paper, we test some recently developed metadynamics-based methods and develop a new combination with a Hamiltonian replica-exchange approach. The methods were tested on 18 chemically diverse ligands with a wide range of different binding affinities to a complex target; namely, human soluble epoxide hydrolase. The results suggest that metadynamics with a funnel-shaped restraint can be used to calculate, in a computationally affordable and relatively accurate way, the absolute binding free energy for small fragments. When used in combination with an optimal pathlike variable obtained using machine learning or with the Hamiltonian replica-exchange algorithm SWISH, this method can achieve reasonably accurate results for increasingly complex ligands, with a good balance of computational cost and speed. An additional benefit of using the combination of metadynamics and SWISH is that it also provides useful information about the role of water in the binding mechanism.
Dancers of the Ivory Coast (1962)

A project is afoot in the Ivory Coast to form a national theatre, one that would include dance, drama and the making of films.Though an ambitious undertaking for any country, it is especially so for a new nation when economic, social, and educational problems loom large.Yet this enterprise is not considered a frivolous, cultural teather in the cap.Its aim is to help create a national image; to put the Ivory Coast on the map, show its multifaceted culture, and give encouragement to its musicians, writers, dancers, and other artistic people.As more and more contacts are made on the cultural level, nations of diverse background and training find they share a more equal footing and have better grounds for mutual understanding and appreciation. In these early stages in the Ivory Coast, nothing concrete has been done about film making; the drama finds expression in numerous small acting companies touring in station wagons; but the dance has already come to a natural flowering, making it the most potent and exciting component in the national-theatre scheme.Recently, Thomas Skelton, an expert in stage lighting who also has specialized in presenting Oriental and other non-Western groups to the United States, was invited by the Ivory Coast Government to tour the country and see whether the talent and experience of native dancers could be extended to the international scene.
Elevated Nitric Oxide Concentration in the Seminal Plasma of Infertile Males: Nitric Oxide Inhibits Sperm Motility (1996)

These findings indicate that nitric oxide concentration in the seminal plasma of infertile males is elevated and that nitric oxide is an inhibitor of sperm motion.
Rapid Inactivation Determines the Rectification and [K<sup>+</sup>]<sub>o</sub>Dependence of the Rapid Component of the Delayed Rectifier K<sup>+</sup>Current in Cardiac Cells (1997)

Two characteristic features of the rapid component of the cardiac delayed rectifier current (IKr) are prominent inward rectification and an unexpected reduction in activating current with decreased [K+]o. Similar features are observed with heterologous expression of HERG, the gene thought to encode the channel carrying IKr, moreover, recent studies indicate that the mechanism underlying rectification of HERG current is the inactivation that channels rapidly undergo during depolarizing pulses. The present studies were designed to determine the mechanism of IKr rectification and [K+]o sensitivity in the mouse atrial myocyte cell line, AT-1 cells. Reducing [Mg2+]i to 0, which reverses inward rectification of some K+ channels, did not alter IKr current-voltage relationships, although it did decrease sensitivity to the IKr blockers dofetilide and quinidine 2- to 5-fold. To determine the presence and extent of fast inactivation of IKr in AT-1 cells, a brief hyperpolarizing pulse (20 ms to -120 mV) was applied during long depolarizations. Immediately after this pulse, a very large outward current that decayed rapidly to the previous activating current baseline was observed. This outward current component was blocked by the IKr-specific inhibitor dofetilide, indicating that it represented recovery from fast inactivation during the hyperpolarizing step, with fast reinactivation during the return to depolarized potential. With removal of inactivation using this approach, current-voltage relationships for IKr ([K+]o, 1 to 20 mmol/L) were linar and reversed close to the predicted Nernst potential for K+. In addition, decreased [K+]o decreased the time constants for open-->inactivated and inactivated-->open transitions. Thus, in these cardiac myocytes, as with heterologously expressed HERG, IKr undergoes fast inactivation that determines its characteristic inward rectification. These studies demonstrate that the mechanism underlying decreased activating current observed at low [K+]o is more extensive fast inactivation.
Role of the liver in regulating numbers of circulating neutrophils (2001)

Neutrophils (polymorphonuclear leukocytes [PMNs]) carry potent destructive enzymes that can destroy invasive bacteria or damage normal tissue. PMNs have a half-life of only 6 hours in the blood, but the details of this homeostasis are unknown. In a rat model of endotoxemia, P-selectin was selectively up-regulated in hepatic sinusoids and veins where it was necessary for phagocytosis of PMNs by Kupffer cells in the liver, as opposed to the spleen or the lungs. Apoptotic PMNs appeared in the lungs and spleen only after inactivation of Kupffer cells by gadolinium chloride (GdCl(3)). Blocking of Fas protein reduced the number of apoptotic cells in the liver; binding of annexin V to phosphatidylserine (PS) reduced the number of PMNs phagocytosed by Kupffer cells. The results support a clearance pathway in which apoptosis and phagocytosis are effected by Kupffer cells after P-selectin-mediated sequestration. (Blood. 2001;98:1226-1230)
A Normalized Statistical Metric Space for Hidden Markov Models (2012)

In this paper, we present a normalized statistical metric space for hidden Markov models (HMMs). HMMs are widely used to model real-world systems. Like graph matching, some previous approaches compare HMMs by evaluating the correspondence, or goodness of match, between every pair of states, concentrating on the structure of the models instead of the statistics of the process being observed. To remedy this, we present a new metric space that compares the statistics of HMMs within a given level of statistical significance. Compared with the Kullback-Leibler divergence, which is another widely used approach for measuring model similarity, our approach is a true metric, can always return an appropriate distance value, and provides a confidence measure on the metric value. Experimental results are given for a sample application, which quantify the similarity of HMMs of network traffic in the Tor anonymization system. This application is interesting since it considers models extracted from a system that is intentionally trying to obfuscate its internal workings. In the conclusion, we discuss applications in less-challenging domains, such as data mining.
New insights into smectite illitization: A zoned K-bentonite revisited (2009)

The illitization reaction in a thick K-bentonite bed located in upper Cretaceous marine shale in the Montana disturbed belt was studied by X-ray diffraction, chemical analysis, and thermal gravimetric analysis. Modeling of the experimental XRD patterns from oriented clay specimens in air-dried and glycolated states shows that at each sample location in the bentonite bed a mixture of R0 illite-smectite (I-S) and R1 I-S coexist. Each of these phases in all samples consists of the same or similar content of illite and expandable layers independent on location in the bed. In particular, the illite content in the R0 I-S and the R1 I-S from the <0.5 μm fractions is equal to 30 and 62%, respectively. The main difference between the samples at different locations is the different weight concentrations of the coexisting I-S phases. The R1 I-S content decreases progressively from the lower and upper contacts of the bed to its center. The reverse trend was observed for the R0 I-S. The layer unit-cell parameter b increases from samples located near the middle of the bed toward samples near the bed margins. The DTG patterns of the samples contain two endothermic maxima at about 640 and 470 °C, corresponding to cis-vacant (cv) illite and trans-vacant (tv) smectite layers coexisting in the R1 I-S and R0 I-S.
Optimized spiral imaging for measurement of myocardial <i>T</i><sub>2</sub> relaxation (2003)

Microcirculation oxygen levels and blood volumes should be reflected in measurements of myocardial T(2) relaxation. This work describes the optimization of a spiral imaging strategy for robust myocardial T(2) measurement to minimize the standard deviation of T(2) measurement (sigmaT(2)). Theoretical and experimental studies of blurring at muscle/blood interfaces enabled the derivation of parameter sets which reduce sigma T(2) to the level of 5%. T(2) relaxation mapping within healthy volunteers provided estimation of residual sigmaT(2) within the optimized technique. The standard deviation in T(2) measurement across regions of interest (ROIs) in different locations is about 9%. The standard deviation in T(2) measurement in an ROI across different time points is about 5%.
Generation and Characterization of Severe Combined Immunodeficiency Rats (2012)

Severe combined immunodeficiency (SCID) mice, the most widely used animal model of DNA-PKcs (Prkdc) deficiency, have contributed enormously to our understanding of immunodeficiency, lymphocyte development, and DNA-repair mechanisms, and they are ideal hosts for allogeneic and xenogeneic tissue transplantation. Here, we use zinc-finger nucleases to generate rats that lack either the Prkdc gene (SCID) or the Prkdc and Il2rg genes (referred to as F344-scid gamma [FSG] rats). SCID rats show several phenotypic differences from SCID mice, including growth retardation, premature senescence, and a more severe immunodeficiency without "leaky" phenotypes. Double-knockout FSG rats show an even more immunocompromised phenotype, such as the abolishment of natural killer cells. Finally, xenotransplantation of human induced pluripotent stem cells, ovarian cancer cells, and hepatocytes shows that SCID and FSG rats can act as hosts for xenogeneic tissue grafts and stem cell transplantation and may be useful for preclinical testing of new drugs.
Antitumoral Effects of Liarozole in Androgen-Dependent and Independent R3327-Dunning Prostate Adenocarcinomas (1994)

We examined the in vivo antitumoral effects of liarozole against androgen-dependent and independent Dunning rat prostatic tumors. Liarozole, applied as a dietary admixture, at a dose of 120 mg./100 gm. food, equivalent to 100 mg./kg. per day, inhibited the growth of the slow growing, well-differentiated, androgen-dependent Dunning-H tumor (median tumor volume decrease of 60%). At the same dose it also significantly reduced the growth of the androgen-independent, moderately differentiated PIF-1 (-60%) and androgen-independent, anaplastic AT-6 tumors (-73%). The growth of AT-6 sq tumor showing squamous metaplasia was unaffected by liarozole. When administered by oral gavage, liarozole at 40 (-82%) mg./kg. twice a day was as effective as castration (-92%) in reducing the androgen-dependent, poorly differentiated Dunning R3327-G tumor. Liarozole, administered by gavage, twice a day, also significantly reduced median tumor volume in the androgen-independent, AT-6 sq (-90% at 60 mg./kg., twice a day). This difference between liarozole administration by gavage and food admixture will have to be taken into account in further experimental studies. Inhibition of the growth of several androgen-dependent and, chiefly, androgen-independent Dunning prostate carcinoma sublines that differ widely in their histological degree of differentiation and growth rate suggests that liarozole may be a suitable agent for evaluation in second line treatment of hormone refractory prostate carcinoma in patients who relapse after androgen ablation.
On the dynamic range of coefficients generated in transform processing of digitised image data (1985)

It is well known that the transform operation results in a large expansion of the numerical range of values encountered when input data is subjected to a one- or more dimensional transformation. It is usually assumed that the dynamic range expansion factor is Nc, where N is the transform order and c its dimension, but it is demonstrated here that this result is only true under very restricted conditions, and that, in general, coefficient dynamic range expansion is not only transform dependent, but is often significantly greater than the above value. It is suggested that this effect may influence the transform processing operation in feature extraction and coding applications to a greater degree than has previously been realised.
Stem cell gene therapy, position effects and chromatin insulators (1997)

Low efficiency of gene transfer is the main obstacle for a clinically effective gene therapy at the level of the pluripotent hematopoietic stem cell. Another important aspect of stem cell gene therapy, the actual expression of the transduced genes, has only been investigated adequately in very few studies, mainly for globin genes. Transcriptional silencing and position effects due to negative effects of surrounding chromatin on the expression of randomly integrated vector sequences may seriously jeopardize the success of current gene therapy strategies, even if transduction efficiency can be significantly improved. We propose the incorporation of chromatin insulators in the design of gene therapy vectors to overcome the problem of position effects. Chromatin insulators are protein-binding DNA elements that lack intrinsic promoter/enhancer activity but shelter genes from transcriptional influence of surrounding chromatin. The best characterized insulators are from Drosophila. We hypothesize that the important cellular function of chromatin organization is evolutionarily conserved and that human homologs to Drosophila insulator binding proteins such as the suppressor of Hairy-wing exist and can be cloned. Using these putative proteins, it should be possible to identify corresponding minimal binding sites with insulator activity. The design and incorporation of effective chromatin insulator sequences in the next generation of gene therapy vectors should lead to improved and more predictable expression of therapeutic transgenes and constitute an important step toward clinically effective gene therapy.
The General Approach to Cystic Fibrosis Pulmonary Infection in Spain (1996)

The ACLFQ (Asociación Cientifica de Lucha contra la Fibrosis Quίstica) organization was generally working on the assumption of a total number of about 2000 patients for the whole country. The real number of well-identified patients currently registered in the different CF Units is 996. This figure is based on the data obtained by us from fifteen reference hospitals where the cases of smaller institutions are collected. The Social Security organization in Spain assures a practical 100% coverage of the population, so that only few clinically relevant cases are expected to remain undetected in children. The real number of cases needs to be documented by an extensive neonatal screening at national level.
<i>Ab initio</i>energetics of<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" display="inline"><mml:mrow><mml:mtext>La</mml:mtext><mml:mi>B</mml:mi><mml:msub><mml:mtext>O</mml:mtext><mml:mn>3</mml:mn></mml:msub><mml:mrow><mml:mo>(</mml:mo><mml:mrow><mml:mn>001</mml:mn></mml:mrow><mml:mo>)</mml:mo></mml:mrow></mml:mrow></mml:math>(<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" display="inline"><mml:mrow><mml:mi>B</mml:mi><mml:mo>=</mml:mo><mml:mtext>Mn</mml:mtext></mml:mrow></mml:math>, Fe, Co, and Ni) for solid oxide fuel cell cathodes (2009)

$\text{La}B{\text{O}}_{3}$ ($B=\text{Mn}$, Fe, Co, and Ni) perovskites form a family of materials of significant interest for cathodes of solid oxide fuel cells (SOFCs). In this paper ab initio methods are used to study both bulk and surface properties of relevance for SOFCs, including vacancy formation and oxygen binding energies. A thermodynamic approach and the density functional theory plus $U$ method are combined to obtain energies relevant for SOFC conditions ($T\ensuremath{\approx}800\text{ }\ifmmode^\circ\else\textdegree\fi{}\text{C}$, $P{\text{O}}_{2}\ensuremath{\approx}0.2\text{ }\text{atm}$). The impact of varying ${U}_{\text{eff}}$ $({U}_{\text{eff}}=U\ensuremath{-}J)$ on energy and electronic structure is explored in detail and it is shown that optimal ${U}_{\text{eff}}$ values yield significantly better agreement with experimental energies than ${U}_{\text{eff}}=0$ (which corresponds to the standard generalized gradient approximation). $\text{La}B{\text{O}}_{3}$ oxygen vacancy formation energies are predicted to be in the order $\text{Fe}>\text{Mn}>\text{Co}>\text{Ni}$ (where the largest implies most difficult to form a vacancy). It is shown that (001) $B{\text{O}}_{2}$ terminated surfaces have 1--2 eV lower vacancy formation energies and therefore far higher vacancy concentrations than the bulk. The stable surface species at low temperature are predicted to be the superoxide $\text{O}_{2}{}^{\ensuremath{-}}$ for $B=\text{Mn}$, Fe, Co and a peroxide $\text{O}_{2}{}^{2\ensuremath{-}}$ with a surface oxygen for $B=\text{Ni}$. Entropy effects are predicted to stabilize the monomer oxygen surface state for all $B$ cations at higher temperatures. Overall oxygen coverage of the (001) $B{\text{O}}_{2}$ surface is predicted to be quite low at SOFC operating conditions. These results will aid in understanding the oxygen reduction reaction on perovskite SOFC cathodes.