NWChem: Past, present, and future.

Specialized computational chemistry packages have permanently reshaped the landscape of chemical and materials science by providing tools to support and guide experimental efforts and for the prediction of atomistic and electronic properties. In this regard, electronic structure packages have played a special role by using first-principle-driven methodologies to model complex chemical and materials processes. Over the past few decades, the rapid development of computing technologies and the tremendous increase in computational power have offered a unique chance to study complex transformations using sophisticated and predictive many-body techniques that describe correlated behavior of electrons in molecular and condensed phase systems at different levels of theory. In enabling these simulations, novel parallel algorithms have been able to take advantage of computational resources to address the polynomial scaling of electronic structure methods. In this paper, we briefly review the NWChem computational chemistry suite, including its history, design principles, parallel tools, current capabilities, outreach, and outlook.

Polypharmacology Within the Full Kinome: a Machine Learning Approach.

Protein kinases generate nearly a thousand different protein products and regulate the majority of cellular pathways and signal transduction. It is therefore not surprising that the deregulation of kinases has been implicated in many disease states. In fact, kinase inhibitors are the largest class of new cancer therapies. Understanding polypharmacology within the full kinome, how drugs interact with many different kinases, would allow for the development of safer and more efficacious cancer therapies. A full understanding of these interactions is not experimentally feasible making highly accurate computational predictions extremely useful and important. This work aims at making a machine learning model useful for investigating the full kinome. We evaluate many feature sets for our model and get better performance over molecular docking with all of them. We demonstrate that you can achieve a nearly 60% increase in success rate at identifying binding compounds using our model over molecular docking scores.

Gaussian Basis Set and Planewave Relativistic Spin-Orbit Methods in NWChem.

Relativistic spin-orbit density functional theory (DFT) methods have been implemented in the molecular Gaussian DFT and pseudopotential planewave DFT modules of the NWChem electronic-structure program. The Gaussian basis set implementation is based upon the zeroth-order regular approximation (ZORA) while the planewave implementation uses spin-orbit pseudopotentials that are directly generated from the atomic Dirac-Kohn-Sham wave functions or atomic ZORA-Kohn-Sham wave functions. Compared to solving the full Dirac equation these methods are computationally efficient but robust enough for a realistic description of relativistic effects such as spin-orbit splitting, molecular orbital hybridization, and core effects. Both methods have been applied to a variety of small molecules, including I2, IF, HI, Br2, Bi2, AuH, and Au2, using various exchange-correlation functionals. Our results are in good agreement with experiment and previously reported calculations.

Vibrational spectroscopy of anionic nitrate complexes of UO22+ and Eu3+ isolated in the gas phase.

Wavelength-selective infrared multiple photon photo-dissociation (IRMPD) was used to generate spectra of anionic nitrate complexes of UO(2)(2+) and Eu(3+) in the mid-infrared region. Similar spectral patterns were observed for both species, including splitting of the antisymmetric O-N-O stretch into high and low frequency components with the magnitude of the splitting consistent with attachment of nitrate to a strong Lewis acid center. The frequencies measured for [UO(2)(NO(3))(3)](-) were within a few cm(-1) of those measured in the condensed phase, the best agreement yet achieved for a comparison of IRMPD with condensed phase absorption spectra. In addition, experimentally-determined values were in good general agreement with those predicted by DFT calculations, especially for the antisymmetric UO(2) stretch. The spectrum from the [UO(2)(NO(3))(3)](-) was compared with that of [Eu(NO(3))(4)](-), which showed that nitrate was bound more strongly to the Eu(3+) metal center, consistent with its higher charge. The spectrum of a unique uranyl-oxo species having an elemental composition [UO(9)N(2)](-) was also acquired, that contained nitrate absorptions suggestive of a [UO(2)(NO(3))(2)(O)](-) structure; the spectrum lacked bands indicative of nitrite and superoxide that would be indicative of an alternative [UO(2)(NO(3))(NO(2))(O(2))](-) structure.

Mid-infrared vibrational spectra of discrete acetone-ligated cerium hydroxide cations.

Cerium(iii) hydroxy reactive sites are responsible for several important heterogeneous catalysis processes, and understanding the reaction chemistry of substrate molecules like CO, H(2)O, and CH(3)OH as they occur in heterogeneous media is a challenging task. We report here the first infrared spectra of model gas-phase cerium complexes and use the results as a benchmark to assist evaluation of the accuracy of ab initio calculations. Complexes containing [CeOH](2+) ligated by three- and four-acetone molecules were generated by electrospray ionization and characterized using wavelength-selective infrared multiple photon dissociation (IRMPD). The C[double bond, length as m-dash]O stretching frequency for the [CeOH(acetone)(4)](2+) species appeared at 1650 cm(-1) and was red-shifted by 90 cm(-1) compared to unligated acetone. The magnitude of this shift for the carbonyl frequency was even greater for the [CeOH(acetone)(3)](2+) complex: the IRMPD peak consisted of two dissociation channels, an initial elimination of acetone at 1635 cm(-1), and elimination of acetone concurrent with a charge separation producing [CeO(acetone)](+) at 1599 cm(-1), with the overall frequency centered at 1616 cm(-1). The increasing red shift observed as the number of acetone ligands decreases from four to three is consistent with transfer of more electron density per ligand in the less coordinated complexes. The lower frequency measured for the elimination/charge separation process is likely due to a combination of: (a) anharmonicity resulting from population of higher vibrational states, and (b) absorption by the initially formed photofragment [CeOH(acetone)(2)](2+). The C-C stretching frequency in the complexes is also influenced by coordination to the metal: it is blue-shifted compared to bare acetone, indicating a slight strengthening of the C-C bond in the complex, with the intensity of the absorption decreasing with decreasing ligation. Density functional theory (DFT) calculations using three different functionals (VWN, B3LYP, and PBE0) were used to predict the infrared spectra of the complexes. Calculated frequencies for the carbonyl stretch are within 40 cm(-1) of the IRMPD of the three-acetone complex measured using the single acetone loss, and within 60 cm(-1) of the measurement for the four-acetone complexes. The B3LYP functionals provided the best agreement with the measured spectra, with the VWN modestly lower and PBE0 modestly higher. The C-C stretching frequencies calculated using B3LYP are higher in energy than the measured values by approximately 30 cm(-1), and reproduce the observed trend which shows that the C-C stretching frequency decreases with increasing ligation. Agreement between C-C frequency and calculation was not as good using the VWN functional, but still within 70 cm(-1). The results provide an evaluation of changes in the acceptor properties of the metal center as ligands are added, and of the utility of DFT for modeling f-block coordination complexes.

Vaccination against Salmonella enteritidis in Dutch commercial layer flocks with a vaccine based on a live Salmonella gallinarum 9R strain: evaluation of efficacy, safety, and performance of serologic Salmonella tests.

This study describes a field trial in which 80 commercial layer flocks, with an increased risk of Salmonella enteritidis (SE) infection and placed on farms with a certified Standardized Biosecurity Programme (SBP) or a request for a SBP certificate, were vaccinated with a vaccine based on a live attenuated Salmonella gallinarum (SG) 9R strain. An evaluation is presented of the efficacy of the vaccine against SE infections, the effect on the performance of serologic Salmonella tests, and the spread of the vaccine strain to the egg content. For the efficacy study, assessment of the flock level occurrence of SE infections in the vaccinated group of 80 flocks was compared with that of a nonvaccinated group of 1854 flocks hatched in the same period. This control group was examined according to the compulsory control programme in The Netherlands. An evaluation was done of the performance of serologic Salmonella tests and the spread of the vaccine strain to the inner egg content of five of the vaccinated flocks. Findings demonstrated the flock level occurrence of SE infections in the vaccinated group (2/80 = 2.5%) to be significantly (P = 0.01) lower than that of the nonvaccinated group (214/1854 = 11.5%). Vaccination resulted in 59.0% positive test results in lipopolysaccharide BD enzyme-linked immunosorbent assay (ELISA) for detecting antibodies against Salmonella serogroups B and D and 0% positive test results in the rapid plate agglutination test for detecting antibodies against S. pullorum (SP)/SG. The mean specificities of two blocking ELISAs (gm- and i-double antibody sandwich ELISAs) based on the flagellar antigen of SE and Salmonella typhimurium (ST) on the same sera were 99.6% and 96.1%, respectively. The vaccine strain could not be isolated from any of the 450 pools of 10 eggs. On the basis of these results, we concluded that vaccination with a vaccine based on an attenuated SG 9R strain contributes to the reduction of SE infections in commercial layer flocks. Furthermore, serologic monitoring of SE, ST, and SP/SG can still be carried out on flocks vaccinated with an attenuated SG 9R strain. Additionally, we found no indication of the spread of the vaccine strain to the egg content.

Atomic many-body effects for the p-shell photoelectron spectra of transition metals.

Ab initio theoretical results for the 2p- and 3p-hole states of an Mn(2+) ion are reported in order to determine the importance of atomic contributions to the photoelectron spectra of bulk MnO. A combined treatment of relativity and electron correlation reveals important physical effects that have been neglected in virtually all previous work. The many-body and relativistic effects included in the atomic model are able, without any ad hoc empirical parameters, to explain most of the features of the MnO photoelectron spectra. In particular, it is not necessary to invoke charge transfer to explain the complex p-level spectra.

Results of a Salmonella enteritidis vaccination field trial in broiler-breeder flocks in The Netherlands.

From August 1995 until December 1997, the effect of adding Salmonella enteritidis (SE) vaccination to a certified standardized biosecurity program in a situation of increased infection risk was examined in a field trial in The Netherlands. In this field trial, two groups of broiler-breeder flocks with increased infection risk were vaccinated, one group with VAC-T/TALOVAC logSE(group A) and the second group with SALENVAC (group B). The determination of increased infection risk in groups A and B was based on an SE infection history; flocks were either previously infected and treated (PIT) or had other risk factors than previously infected and treated (OPIT). SE infections in both vaccinated groups were assessed by monitoring according to the Dutch salmonella control program. Under field conditions, designation of a vaccinated and a control group on the farm was not possible. In the same period as the vaccinated groups, 608 nonvaccinated flocks (group C) were hatched and monitored according to the Dutch salmonella control program. The flock level occurrence of SE infection in the vaccinated groups was compared with the flock level occurrence of SE infection in the nonvaccinated group on the basis of comparability of infection risk. In group C, whether or not flocks had infection risk PIT was known and for risk factor OPIT, only whether or not a flock had been placed on a previously contaminated farm (= risk of reinfection) was known. The proportion of SE-infected flocks with risk factor PIT in the vaccinated groups was not significantly different from that in the nonvaccinated group C. Only the proportion of SE-infected flocks with a risk of reinfection in the vaccinated group B (0) was significantly lower (P = 0.02) than in the nonvaccinated group C (18%). The fact that no significant result was found in favor of group A is because of the small number of flocks in this part of the study. On the basis of the conditions of the setup of this trial, it can only be concluded that there is an indication that vaccination contributes in the reduction of SE reinfection in broiler breeder flocks.

Serological detection of chicken flocks naturally infected with Salmonella enteritidis, using an enzyme-linked immunosorbent assay based on monoclonal antibodies against the flagellar antigen.

The Dutch Salmonella enteritidis monitoring and eradication programme for poultry prescribes a periodic examination of all breeding flocks for the presence of S. enteritidis. For the first years of the programme this was done by bacteriological examination of 50 faecal samples per visit per flock. In this study we compare the results of bacteriological examination of faecal samples taken at 1580 visits from 545 flocks with those of a S. enteritidis enzyme-linked immunosorbent assay (ELISA) applied on 24 serum samples per visit per flock. Two flocks were found positive for S. enteritidis by bacteriological examination; both flocks were also detected by ELISA. Ten flocks, bacteriologically negative for S. enteritidis were found positive by ELISA. S. enteritidis was isolated from three of these flocks by repeated and extensive bacteriological examination for verification. Verification was not possible in the fourth ELISA positive flock. S. enteritidis infections were likely in three other flocks because of the farm histories. On the basis of the results of this study it was decided to use this ELISA, starting from April 1992, as screening technique in the Dutch S. enteritidis programme instead of bacteriological examination of faecal samples. The ELISA is regarded as a flock test; an extensive, confirmatory bacteriological investigation for S. enteritidis is carried out in ELISA positive flocks to decide whether the flocks are truly infected.

Immunotherapy of bovine ocular squamous cell carcinoma: isolation, culture and characterization of lymphocytes present in the tumor.

Bovine ocular squamous cell carcinoma (BOSCC) is sensitive to intralesional immunotherapy with BCG or recombinant human IL-2 (rhIL-2). The mechanism of tumor regression is as yet unclear. Alterations in the concentration of IL-2 (and possibly other factors) in the tumor, due to regional injection or induction by BCG, may induce killer cell activity and thus tumor regression. To investigate this, lymphocytes were isolated by mechanical fractionation of biopsies of BOSCC. Growth, phenotypical, and functional characteristics were studied. TIL could be isolated and grown from all biopsies of BOSCC. An estimated increase in cell number of 50-150 fold was observed during 5-7 weeks of culture. FACS analysis of a limited number of the TIL cultures showed a characteristic shift in phenotypes until day 28 of culture. CD2+ cells (50-70%), and as a consequence of this CD2- cells, remained stable in number. The number of CD8+ cells increased. CD4+ cells were detected in low numbers by day 28. Prolonged culture resulted in an increase of CD2- gamma delta + cells, CD2+4-8- cells, and occasionally of both CD8+ and CD2+ cells. In 51Cr release assays TIL showed cytotoxicity for BOSCC-derived tumor cell lines in general, which increased transiently by cocultivation with tumor cells. Killing of YAC-1, and P815 was far less efficient. Preferential killing of autologous cell lines was not seen. In conclusion, TIL from bovine ocular squamous cell carcinomas can be cultured in the presence of rhIL-2, which induces cytotoxic activity for BOSCC-derived tumor cells. Cells responsible for killing in vitro and potentially for regression of the tumor after immunotherapy with BCG or rhIL2 cannot yet be identified. Depletion and blocking experiments are being conducted in order to identify the cells (CD2+8+, CD2-gamma delta + or other CD2 +/-) responsible for killing.

Immunotherapy of bovine ocular squamous cell carcinoma by repeated intralesional injections of live bacillus Calmette-Guérin (BCG) or BCG cell walls.

UNLABELLED: Thirty cows of the Dutch Friesian and the Maas-Rijn-Ijssel breed with histologically confirmed ocular squamous cell carcinoma were treated by repeated intralesional injection of live bacillus Calmette-Guérin (BCG) (n = 14) or a BCG cell-wall vaccine (n = 16). Complete regression of the primary tumour was observed in 64% and 57% of the animals respectively. In the 2-year follow-up period there was no recurrence of primary tumours. This sharply contrasts with the recurrence frequency (40%-50%) after complete remission induced by a single intralesional injection with BCG, observed in an earlier study. In 1 animal a new primary tumour developed. At necropsy metastases were present in 33% of the treated animals: in 3 of 17 animals that showed complete regression of the primary tumour and in 7 of 13 animals with partial regression or progressive disease. This did not differ significantly from results obtained after a single treatment (27%). Delayed-type hypersensitivity to M. bovis purified protein derivative (PPD) was more persistent in animals showing regression of the primary tumour than in non-responding animals. Of the animals with a positive PPD response 6 months after treatment, 79% showed tumour regression. Regression was observed in only 28% of the animals not responding to PPD after the same period of time. IN CONCLUSION: (a) recurrence of the primary tumour was not observed after repeated BCG treatment; (b) the frequency of metastases was not decreased compared to results obtained with a single treatment; (c) regression was correlated with a positive delayed-type hypersensitivity reaction to PPD (P less than 0.05) 6 months after treatment; (d) no significant differences were observed when the clinical results of treatment with live BCG and the BCG cell wall vaccine were compared.

Determination of BHV1 specific immune reactivity in naturally infected and vaccinated animals by lymphocyte proliferation assays.

The in vitro BHV1-specific lymphocyte stimulation assay was used to investigate immune reactivity of cattle after natural infection or vaccination with BHV1. Proliferative responses to live virus were shown in tests with peripheral blood lymphocytes of seropositive field virus-infected animals and of vaccinated animals. Nineteen out of 36 seropositive field virus-infected animals did not show in vitro responses. Nine out of 12 animals showed, at least transient, responsiveness after vaccination. Antibody titers were maintained throughout the observation period. T cell activity is believed to play a role in protection against BHV1 infection. The in vitro proliferative assay, however, can not discriminate between BHV1 seropositive and seronegative field virus-infected animals. After vaccination, the BHV1-specific lymphocyte responses of at least one animal disappeared. Both observations may point to the fact that T cell memory is generated, or at least systemically present, to a limited extent.

Failure of an in vitro lymphoproliferative assay specific for bovine herpes virus type 1 to detect immunised or latently infected animals.

The in vitro lymphoproliferative assay specific for bovine herpes virus type 1 (BHV1) was tested for its ability to predict whether an animal was protected against challenge with virulent BHV1 and for its ability to identify animals latently infected with the virus. Three animals that had been in contact with a field strain of the virus, three that had been vaccinated with a modified live-virus vaccine seven weeks previously, six that had been vaccinated in the same way five months previously, and seven control animals that had had no previous contact with the virus were challenged with virulent BHV1. The 12 animals that had had previous contact with BHV1 all resisted the challenge well or fairly well, but six of them did not react positively in the in vitro lymphoproliferative assay. It was concluded that the assay did not give consistent evidence of the immune status of the animals. Four animals that had had previous contact with a field strain of BHV1 were treated with dexamethasone; they excreted BHV1 irrespective of whether they showed a positive response in the in vitro lymphoproliferative assay.

Local interleukin-2 therapy in bovine ocular squamous cell carcinoma. A pilot study.

Five cows bearing bovine ocular squamous cell carcinoma (BOSCC) were treated with low doses of recombinant human interleukin-2 (rhIL-2). A dose of 2500 U rhIL-2 was injected intralesionally and another 2500 U were injected into the subparotid regional lymph node once a day during a period of 5 consecutive days. This cycle of 5 days was repeated after an interval of 2 days. Total regression of the tumor was observed in three out of five animals. One cow showed tumor regression (greater than 80%) accompanied by metastases to the regional lymph node that were observed from the fifth week after the beginning of the treatment. Growth of the tumor of the fifth animal was retarded after treatment. In vitro proliferation of peripheral blood lymphocytes was investigated in two animals and tumor-infiltrating lymphocytes in one animal during incubation in various rhIL-2 concentrations. Cytotoxic activity of both cell populations against P815, Yac-1 and BOSCC-derived cell lines increased during incubation with rhIL-2. Cultured BOSCC-infiltrating lymphocytes showed predominant killing of the BOSCC-derived autologous cell line after 4 weeks of culture. Preliminary phenotype analysis did not give conclusive results with respect to the types of cells responsible for killing.

Reduction of salmonella infection of broilers by spray application of intestinal microflora: a longitudinal study.

The Nurmi concept for diminishing salmonella infection of poultry by application of gastrointestinal microflora from adult birds into newly hatched chicks was tested in a field study in which 8 million broilers were involved. Half of the 284 flocks was treated in the hatchery by spray application of an undefined microflora propagated in SPF chicks. A significant reduction in salmonella-contaminated flocks, as well as in the number of infected broilers in these flocks was demonstrated. No undesirable side effects were detected. It was concluded that hygienic improvements in transportation and slaughtering of broilers are needed in order to maintain the reduced salmonella contamination rate.

Therapeutic efficacy of medicating drinking water with spectinomycin and lincomycin-spectinomycin in experimental Escherichia coli infection in poultry.

Although no microbiological activity was found in blood plasma during treatment of broilers through the drinking water with spectinomycin or lincomycin-spectinomycin, these drugs proved highly effective in treating experimentally induced colibacillosis. This efficacy may be produced by a metabolite or a degradation product of spectinomycin that reaches the infection site in the respiratory tract and interferes with adherence of bacteria.

Therapeutic efficacy of doxycycline hyclate in experimental Escherichia coli infection in broilers.

Treatment of experimentally induced colibacillosis in broilers with doxycycline hyclate through the drinking water was just effective at a dose of 200 mg/kg body weight (1000 ppm). The achieved therapeutic effects were similar to those of tetracycline at the same dose and of flumequine at a dose of 19 mg/kg body weight (100 ppm).

Additional studies on the therapeutic efficacy of sulphadimidine sodium in experimental Escherichia coli infection of broilers.

In contrast with the recommended dose of 2,000 ppm sulphadimidine sodium in the drinking water for treatment of broilers against colibacillosis, it appeared that under experimental conditions, treatment at 500 ppm (60 mg/kg body weight) gave the best therapeutic effects. At higher concentrations, drinking water consumption and body weight gain were reduced significantly. During treatment high blood plasma-concentrations were measured.

Peripheral nerve P2 basic protein and the Guillain-Barré syndrome. In vitro demonstration of P2-specific antibody-secreting cells.

An immune response to the peripheral nerve basic protein P2 may be operative in the pathogenesis of the Guillain-Barré syndrome (GBS). A method is described for the purification of P2 of human origin. Purified P2 was used to investigate whether lymphocytes derived from peripheral blood of GBS patients are capable of producing P2-specific antibodies after stimulation with the antigen in vitro. Peripheral blood lymphocytes (PBL) from 5 GBS patients, from 3 patients with chronic idiopathic polyradiculoneuropathy (CIP) and from 3 normal controls were cultured in vitro in the presence of P2. PBL from the 5 GBS patients were shown to generate an antigen (P2)-specific antibody response. Contrariwise, PBL from the 3 CIP patients as well as from the 3 normal controls did not show this specific response.

Some pharmacokinetic aspects of four sulphonamides and trimethoprim, and their therapeutic efficacy in experimental Escherichia coli infection in poultry.

Pharmacokinetic studies in broilers and layers of different sulphonamides indicate a good absorption and a long elimination half-life (of sulphaquinoxaline, sulphadimidine and to a lesser degree sulphadiazine) resulting in high plasma concentrations during drinking water medication in the recommended therapeutic doses. In contrast drinking water medication with high concentrations of trimethoprim (up to 1,320 mg/liter) resulted in a maximal mean plasma concentration of 1.2 micrograms/ml. Very good therapeutic effects were demonstrated in broilers experimentally infected with a sulphonamide-susceptible E. coli strain when treated with sulphaquinoxaline (200 mg/liter), sulphadimidine sodium (2 gram/liter), sulphachloropyridazine 30 per cent (1 gram/liter) and to a lesser degree sulphadiazine sodium (250 mg/liter). Synergism was demonstrated between trimethoprim and sulphadiazine (1:5). The combination of trimethoprim with sulphaquinoxaline (1:3) did not induce better therapeutic effects than sulphaquinoxaline in proportional doses. However, significant synergism was demonstrated between trimethoprim and both sulphonamides in treatment of experimental infection with sulphonamide-resistant E. coli. No signs resembling sulphonamide intoxication were observed during these studies.