Accessing the usefulness of atomic adsorption configurations in predicting the adsorption properties of molecules with machine learning

We present a systematic study into the effect of adding atomic adsorption configurations into the training and validation dataset for a neural network's predictions of the adsorption energies of small molecules on single metal and bimetallic, single crystal surfaces. Specifically, we examine the efficacy of models trained with and without H and X atomic adsorption configurations, where X is C, N, or O, to predict XHn adsorption energies. In addition, we compare our machine learning models to traditional simple scaling relationships. We find that models trained with the atomic adsorption configurations outperform models trained with only molecular adsorption configurations, with as much as a 0.37 eV decrease in the MAE. We find that models trained with the atomic adsorption configurations slightly outperform traditional scaling relationships. In general, these results suggest it may be possible to vastly reduce the number of adsorption configurations one needs for training and validation datasets by supplementing said data with the adsorption configurations of composite atoms or smaller molecular fragments.

Combining Deep Learning Neural Networks with Genetic Algorithms to Map Nanocluster Configuration Spaces with Quantum Accuracy at Low Computational Cost

The configuration spaces for bimetallic AuPd nanoclusters of various sizes are explored efficiently and analyzed accurately by combining genetic algorithms with neural networks trained on density functional theory. The methodology demonstrated herein provides an optimizable solution to the problem of searching vast configuration spaces with quantum accuracy in a way that is computationally practical. We implement a machine learning algorithm which learns the density functional theory potential with increasing performance while simultaneously generating and relaxing structures within the system's global configuration space unbiasedly. As a result, the algorithm naturally converges onto the system's energy minima while mapping the configuration space as a function of energy. The algorithm's simple design applies not only to nanocluster configurations, as demonstrated, but to bulk, substrate, and adsorption sites as well, and it is designed to scale. To demonstrate its computational efficiency, we work with AuPd nanoclusters of sizes 15, 20, and 25 atoms. Results focus primarily on evaluating the algorithm's performance; however, several physical insights into possible configurations for these nanoclusters naturally emerge as well, such as geometric Au surface segregation and stoichiometric Au minimization as a function of stability.

NEXMD v2.0 Software Package for Nonadiabatic Excited State Molecular Dynamics Simulations

We present NEXMD version 2.0, the second release of the NEXMD (Nonadiabatic EXcited-state Molecular Dynamics) software package. Across a variety of new features, NEXMD v2.0 incorporates new implementations of two hybrid quantum-classical dynamics methods, namely, Ehrenfest dynamics (EHR) and the Ab-Initio Multiple Cloning sampling technique for Multiconfigurational Ehrenfest quantum dynamics (MCE-AIMC or simply AIMC), which are alternative options to the previously implemented trajectory surface hopping (TSH) method. To illustrate these methodologies, we outline a direct comparison of these three hybrid quantum-classical dynamics methods as implemented in the same NEXMD framework, discussing their weaknesses and strengths, using the modeled photodynamics of a polyphenylene ethylene dendrimer building block as a representative example. We also describe the expanded normal-mode analysis and constraints for both the ground and excited states, newly implemented in the NEXMD v2.0 framework, which allow for a deeper analysis of the main vibrational motions involved in vibronic dynamics. Overall, NEXMD v2.0 expands the range of applications of NEXMD to a larger variety of multichromophore organic molecules and photophysical processes involving quantum coherences and persistent couplings between electronic excited states and nuclear velocity.

Photoexcitation dynamics in perylene diimide dimers

We utilize first-principles theory to investigate photo-induced excited-state dynamics of functionalized perylene diimide. This class of materials is highly suitable for solar energy conversion because of the strong optical absorbance, efficient energy transfer, and chemical tunability. We couple time-dependent density functional theory to a recently developed time-resolved non-adiabatic dynamics approach based on a semi-empirical description. By studying the monomer and dimer, we focus on the role stacking plays on the time-scales associated with excited-state non-radiative relaxation from a high excitonic state to the lowest energy exciton. We predict that the time-scale for energy conversion in the dimer is significantly faster than that in the monomer when equivalent excited states are accounted for. Additionally, for the dimer, the decay from the second to the nearly degenerate lowest energy excited-state involves two time-scales: a rapid decay on the order of ∼10 fs followed by a slower decay of ∼100 fs. Analysis of the spatial localization of the electronic transition density during the internal conversion process points out the existence of localized states on individual monomers, indicating that the strength of thermal fluctuations exceeds electronic couplings between the states such that the exciton hops between localized states throughout the simulation.

The Development of an Academic Engagement Intervention for Academically Dismissed Students

"Reclaim the W" is an academic recovery program at a medium-sized midwestern university that offers undergraduates who have been academically dismissed a chance to reenroll at the institution. In this article we describe the Reclaim the W program and its target population of academically at-risk undergraduates. We then outline the first two phases of the process we used to develop an intervention for students in the Reclaim the W program, which we call Engage to Excel (E²). In the first phase we collected data from focus groups with academically at-risk students and professional staff who serve these students. This qualitative data informed the creation of the E² intervention for students in the Reclaim the W program. In the second phase we identified key components of the quasi-experimental E² intervention and outlined the student outcomes that will be evaluated during the intervention. Finally, we highlight research and practice implications of the E² intervention.

Triphenylene-Derived Electron Acceptors and Donors on Ag(111): Formation of Intermolecular Charge-Transfer Complexes with Common Unoccupied Molecular States

Over the past years, ultrathin films consisting of electron donating and accepting molecules have attracted increasing attention due to their potential usage in optoelectronic devices. Key parameters for understanding and tuning their performance are intermolecular and molecule-substrate interactions. Here, the formation of a monolayer thick blend of triphenylene-based organic donor and acceptor molecules from 2,3,6,7,10,11-hexamethoxytriphenylene (HAT) and 1,4,5,8,9,12-hexaazatriphenylenehexacarbonitrile (HATCN), respectively, on a silver (111) surface is reported. Scanning tunneling microscopy and spectroscopy, valence and core level photoelectron spectroscopy, as well as low-energy electron diffraction measurements are used, complemented by density functional theory calculations, to investigate both the electronic and structural properties of the homomolecular as well as the intermixed layers. The donor molecules are weakly interacting with the Ag(111) surface, while the acceptor molecules show a strong interaction with the substrate leading to charge transfer and substantial buckling of the top silver layer and of the adsorbates. Upon mixing acceptor and donor molecules, strong hybridization occurs between the two different molecules leading to the emergence of a common unoccupied molecular orbital located at both the donor and acceptor molecules. The donor acceptor blend studied here is, therefore, a compelling candidate for organic electronics based on self-assembled charge-transfer complexes.

Competing adsorption mechanisms of pyridine on Cu, Ag, Au, and Pt(110) surfaces

We explore the adsorption of pyridine on Cu, Ag, Au, and Pt(110) surfaces using density functional theory. To account for the van der Waals interaction, we use the optB86b-vdW, optB88-vdW, optPBE-vdW, revPBE-vdW, and rPW86-vdW2 functionals. For comparison, we also run calculations using the generalized gradient approximation-PBE (Perdew-Burke-Ernzerhof) functional. We find the most stable adsorption site to depend on both metal and functional, with two energetically favorable adsorption sites, namely, a vertically oriented site and a flat pyridine site. We calculate that every functional predicts pyridine to lie in the vertical configuration on the coinage metals at a low coverage. On Pt(110), by contrast, we calculate all the functionals-except rPW86-vdW2-to predict pyridine to lie flat at a low coverage. By analyzing these differences for these adsorption configurations, along with various geometric and electronic properties of the adsorbate/substrate system, we access in detail the performance of the 6 functionals we use. We also characterize the nature of the bonding of pyridine on the coinage metals from weak to strong physisorption, depending on the functional used. On Pt(110), we characterize the nature of the bonding of pyridine as ranging from strong physisorption to strong chemisorption depending again on the functional used, illustrating both the importance of the van der Waals interaction to this system and that this system can make a stringent test for computational methods.

Pressure-induced superconductivity in Ba0.5Sr0.5Fe2As2

High-pressure electrical resistance measurements have been performed on single crystal Ba(0.5)Sr(0.5)Fe(2)As(2) platelets to pressures of 16 GPa and temperatures down to 10 K using designer diamond anvils under quasi-hydrostatic conditions with an insulating steatite pressure medium. The resistance measurements show evidence of pressure-induced superconductivity with an onset transition temperature at ∼31 K and zero resistance at ∼22 K for a pressure of 3.3 GPa. The transition temperature decreases gradually with increasing pressure before completely disappearing for pressures above 12 GPa. The present results provide experimental evidence that a solid solution of two 122-type materials, i.e., Ba(1-x)Sr(x)Fe(2)As(2) (0 < x < 1), can also exhibit superconductivity under high pressure.

Effect of subacute ibuprofen dosing on rectal mucosal prostaglandin E2 levels in healthy subjects with a history of resected polyps

Nonsteroidal antiinflammatory drugs are among the most promising chemopreventive agents for colorectal cancer. Although the mechanism by which nonsteroidal antiinflammatory drugs exert such effects remains to be further characterized, their best known pharmacological effect is inhibition of prostaglandin synthetase, which leads to decreases in tissue prostaglandin levels. We conducted a randomized, double-blind, controlled study to examine the effect of daily ibuprofen treatment on the rectal mucosal prostaglandin E2 (PGE2) levels in healthy subjects with a history of resected polyps. Study participants (n = 27) completed a 2-week run-in period and were then randomized to take a single, daily dose of ibuprofen (300 or 600 mg) or of a placebo for 4 weeks. Rectal biopsy specimens were taken before and after the run-in period and at 2 and 4 weeks after the ibuprofen/placebo treatment. Notably large between- and within-subject variability in the rectal mucosal PGE2 content was seen. The changes in PGE2 levels after ibuprofen/placebo treatment correlated with the baseline PGE2 content. After adjustment of the baseline values, 2 weeks of 300 mg/day of ibuprofen treatment resulted in significantly more suppression of PGE2 levels than that observed after the placebo treatment (55% versus 22% suppression from baseline; P = 0.033). Although other ibuprofen treatment schedules and doses appeared to result in suppression in the PGE2 levels, the suppression was not statistically significant because of the large variability in this measurement. Because lower doses are associated with fewer adverse effects, a dose of 300 mg of ibuprofen/day should be considered for future Phase II chemoprevention studies. Stratifying study participants, based on their baseline PGE2 levels and inclusion of a larger number of study subjects, are recommended for future trials where the rectal mucosal PGE2 level is to be used as a surrogate end point biomarker.

Plasma alpha-tocopherol concentrations after supplementation with water- and fat-soluble vitamin E

The objective of this study was to examine differences in plasma alpha-tocopherol concentrations after oral administration of pharmacologic doses of vitamin E to normal healthy subjects as RRR-alpha-tocopheryl glycol 1000 succinate (TPGS; water-miscible form) and RRR-alpha-tocopheryl acetate (TA; fat-soluble form). The study was designed to evaluate the administration of three different single doses and multiple doses for 4 wk with both preparations. Administration of 400 IU (269 mg), 800 IU (537 mg), and 1200 IU (807 mg) TPGS as a single dose resulted in slight elevation of plasma alpha-tocopherol concentrations. Administration of multiple daily doses at all three amounts of TPGS for 28 consecutive days resulted in a slight elevation of plasma alpha-to-copherol concentrations. A significant increase in plasma alpha-to-copherol concentrations was observed after ingestion of a single dose or equivalent multiple doses of TA at all three doses. As reported in the literature, in cases of cholestasis and other forms of lipid malabsorption, oral administration of TPGS is the treatment of choice. It appears that for normal adults and patients with normal lipid absorption, fat-soluble forms of vitamin E are preferable for therapeutic and prophylactic uses.

Streptococcal preseptal cellulitis complicated by the toxic Streptococcus syndrome

BACKGROUND

After decades of decline in the incidence of severe infections secondary to group A streptococci, a dramatic increase in the frequency and severity of infections with these organisms has been reported since 1984, including a "toxic Streptococcus syndrome," resembling staphylococcal toxic shock syndrome. To the authors' knowledge, this entity has never been described after ocular infection.

METHODS

In a previously healthy 3-year-old boy, preseptal cellulitis developed secondary to minor trauma to the eyelid, progressing rapidly to hypotension, respiratory distress, and an erythrodermic desquamating rash. Ocular and blood cultures grew group A beta-hemolytic streptococci. Appropriate antibiotic coverage and management of systemic manifestations led to rapid improvement, although necrosis developed in the right upper anterior eyelid, requiring skin grafts.

RESULTS

More than 3 years since the incident, the patient is free of infection and has a good cosmetic result after skin grafting and revisions for scarring and adhesions.

CONCLUSIONS

Streptococcal preseptal cellulitis is not unusual, particularly after trauma. Ophthalmologists must be aware of the re-emergence of more virulent organisms with increased potential for morbidity and mortality.

Determination of Oltipraz in serum by high-performance liquid chromatography with optical absorbance and mass spectrometric detection

Three methods have been developed for the analysis of Oltipraz in serum. A method suitable for routine use employs spiking with a homologous internal standard, off-line solid-phase extraction, high-performance liquid chromatographic separation, and optical absorbance detection at 450 nm. Method detection limit is about 1 ng/ml. A second method, less susceptible to bias from co-eluting interferences, uses a stable isotope-labeled internal standard, similar extraction and separation, and detection by thermospray mass spectrometry. Method detection limit is about 0.2 ng/ml. A third method was developed which can be used without specially synthesized internal standards. It uses on-line solid-phase extraction, with quantification by comparison with external standards. Method detection limit is about 3 ng/ml. Good agreement was observed between these methods and with similar and different methods run in other laboratories. Calibration curves were linear over the entire range which was investigated, i.e., up to 500 ng/ml. Coefficients of variation were similar for all three methods, being about 5%.

Clinical pharmacology studies of oltipraz--a potential chemopreventive agent

Pharmacological studies on Oltipraz [4-methyl-5(pyrazinyl-2)-1-2-dithiole-3-thione)] were conducted with normal healthy subjects using various doses and schedules. Administration of single doses (1, 2 and 3 mg/kg) resulted in detectable drug levels in the serum (mean peak serum concentrations 16, 61 and 205 ng, respectively) and urine. The t1/2 was short (4.4, 4.1 and 5.3 hours respectively) and no steady state was achieved after multiple daily doses for 12 days. Introduction of a loading dose during the first day produced a steady state when 1.5 and 2.0 mg/kg/day were used. Daily administration of Oltipraz sustained the steady state with insignificant variations. Consumption of a high fat diet increased the serum and urine concentrations of Oltipraz (30-60%) compared to the low fat diet. Two subjects experienced flatulence during the administration of the drug. One subject developed numbness and pain in the thumbs with occurrence of small purplish-black spots resembling those observed in subacute endocarditis. These changes disappeared 10 days after discontinuation of the drug. No changes in peripheral blood counts, biochemical profile or thyroid function tests were observed after four weeks of Oltipraz. Further studies with a larger number of healthy subjects are needed for clarification of the safety and biological efficacy of small doses of Oltipraz during chronic administration.

Determination of glycyrrhetinic acid in human plasma by high-performance liquid chromatography

A high-performance liquid chromatographic (HPLC) method has been developed for measuring 18 beta-glycyrrhetinic acid (GRA) in human plasma in the range of 0.1-3 micrograms/ml. The acetate ester of GRA is added to the plasma as an internal standard, plasma proteins are denatured with urea to release GRA, and the GRA and the internal standard are extracted in an ion-pairing solid-phase extraction process. An isocratic, reversed-phase HPLC separation is used, followed by ultraviolet absorbance detection at 248 nm. The results from the analysis of five GRA-fortified plasma pools show a mean relative standard deviation of 7% and are accurate to within 10%. With evaporative concentration of the extract, the limit of detection for GRA in plasma is approximately 10 ng/ml.

Plasma tocopherol concentrations in response to supplemental vitamin E

Normal healthy volunteers were studied after various doses of dl-alpha-tocopherol were ingested on different schedules. Administration of 440, 880, or 1320 mg (400, 800, or 1200 IU) of dl-alpha-tocopherol as a single dose resulted in elevation of plasma alpha-tocopherol concentrations that peaked at 12-24 h. Chronic administration of dl-alpha-tocopherol (440, 880, or 1320 mg/d for 28 d) resulted in a steady state that occurred by days 4-5 of supplementation. Discontinuation of the treatment after day 28 was associated with a decline of plasma alpha-tocopherol, which returned to the pretreatment concentrations between 12 and 20 d. The plasma elevation of alpha-tocopherol was affected by dietary fat intake. Individuals consuming a high-fat diet showed significantly greater plasma alpha-tocopherol concentrations as compared with those fed a low-fat diet. The results of this study indicate that plasma kinetics of alpha-tocopherol are similar when supplements of 440, 880, or 1320 mg dl-alpha-tocopherol are given to normal, healthy individuals.

Alteration of retinol-binding-protein concentrations by the synthetic retinoid fenretinide in healthy human subjects

Normal subjects received fenretinide (HPR), 200 mg/d, on three schedules. Schedule 1 was treatment for 28 d. Schedule 2 consisted of 14 d of treatment, 3 d hiatus, and a second drug course of 14 d, 10,000 IU vitamin A was administered during the 3-d hiatus. Schedule 3 was 14 d of treatment followed by a rest period of 7 d and then 14 d of treatment. Increase in plasma HPR was accompanied by an even higher increase in the metabolite N-(4-methoxyphenyl)-all-trans-retinamide (MPR). The administration of HPR was associated with a significant reduction in retinol-binding protein (RBP), which returned to pretreatment values after the drug treatment was discontinued. Reduction of plasma retinol was also observed. Use of interrupted schedules with resting periods of 3 and 7 d changed HPR, MPR, and RBP concentrations in plasma. Addition of vitamin A did not affect the pattern of the measured variables in the plasma.

Tolerability of the synthetic retinoid Fenretinide (HPR)

Fenretinide, N-(4-hydroxyphenyl)retinamide (HPR), is a synthetic retinoid which has been proven effective in inducing cell differentiation and in inhibiting carcinogen induced mammary tumors in rodents. Because of its efficacy and low toxicity in animals, HPR has been proposed for chemopreventive evaluation in humans. Thus, a randomized trial has been conducted to select a dose which can be administered over a lengthy period of time and with acceptable toxicity. The retinoid was administered orally to patients already operated on for breast cancer in daily doses of 100, 200 and 300 mg for 6 months and subsequently at 200 mg for another 6 months. No acute toxicity was found. Dermatological toxicity was minimal and no liver function abnormalities were observed. Nausea and headaches were infrequent and always mild. Menstrual irregularities were recorded with similar frequency in the treatment and placebo groups and appeared to be more age related than drug dependent. After 6 months of treatment one of 25 patients taking 300 mg HPR daily experienced impaired night vision, confirmed by the electroretinogram, and resolved by interruption of treatment. Because the 300 mg daily dose is possibly associated with impaired dark adaptation, the recommended dose for chemoprevention trials of HPR is 200 mg per day.

Fractures of the distal phalanges

A prospective study of 110 patients with fractures of the distal phalanx indicates that less than one in three patients with such injuries will have recovered after six months. Less than one half of distal phalangeal fractures will have united by then. Factors that carry a poor prognosis include osteolysis of fractured fragments, subungual haematomas and non-union of fractures.

Bioavailability of beta-carotene in humans

Normal healthy volunteers were studied after they ingested various beta-carotene doses. Daily administration of 15 or 45 mg beta-carotene resulted in significant increase in plasma beta-carotene levels. The extent of increase and the pattern of plasma beta-carotene levels showed substantial interindividual variation. Absorption of beta-carotene was affected by dietary fat concentration. Individuals placed on a high-fat diet showed significant increases in plasma beta-carotene as compared with those placed on a low-fat diet. Pharmacological doses of beta-carotene (45 and 90 mg) were used in intermittent schedules (5-6 d intervals) without altering the steady state of beta-carotene plasma levels. Yellowing of the skin occasionally occurred during daily dosing with 45 mg beta-carotene without evidence of toxicity. The observed individual variation in bioavailability of beta-carotene raises questions regarding clinical use of this micronutrient. It appears that determination of target plasma beta-carotene concentrations is essential for effective use of this compound in prevention or treatment.

Fractures of the Distal Phalanges

A prospective study of 110 patients with fractures of the distal phalanx indicates that less than one in three patients with such injuries will have recovered after six months. Less than one half of distal phalangeal fractures will have united by then.

Factors that carry a poor prognosis include osteolysis of fractured fragments, subungual haematomas and non-union of fractures.

Pneumococcal vaccination in children with acute lymphocytic leukemia

Sixty-three children with ALL in CCR and treated according to a standard therapy protocol were immunized with the 14-valent pneumococcal vaccine. Forty-six children were vaccinated 1, 3, or 6 months following initial induction remission; 15 were vaccinated 4-6 weeks following successful completion of 30 months of antileukemia therapy; and two were vaccinated at the time of diagnosis. Response to the vaccine was suboptimal and by the 6-month follow-up there were only two serotypes for which more than half the patients tested had greater than or equal to 300 ng antibodies N/ml.

Outcome of hepatitis in children with acute leukemia

The cases of 31 children with acute leukemia and concurrent hepatitis were evaluated for the outcome of their hepatitis. Thirteen of these children had hepatitis B and 18 children had a non-B hepatitis. Chronic hepatitis developed in more than half of the children with acute hepatitis, with the majority of cases being of the chronic, active type. A majority of these children had received at least one blood transfusion in the preceding year. No relationship was seen between the development of chronicity of the liver disease and the management of the acute hepatitis or the state of underlying disease. With the potential for a cure for acute leukemia increasing, a method of reducing the sequelae of hepatitis in children with leukemia is needed.