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.

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.

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.

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.

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.

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.

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.

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.

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.

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).

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.

Protection of chicks against salmonella infection induced by spray application of intestinal microflora in the hatchery.

The efficacy of spray application of intestinal microflora of the adult bird in protection of broilers against salmonella infections was studied in 3 experiments under laboratory and field conditions. In chicks treated soon after hatching (in the hatchers at approximately 30 per cent hatch or in the chick delivery boxes in the hatchery) with crop-caecum homogenate or a mixture of aerobically and strict anaerobically cultured intestinal flora, very good results were achieved. A very obvious protective effect against a high infection dose (3 X 10(6) c.f.u.S. infantis bacteria per chick) and complete protection against natural infection with different salmonella types was induced. A significant improvement of growth rate was observed in broilers treated by spray in the hatchery and reared for 7 weeks under field conditions in an environment heavily contaminated with different salmonella types.

Protection of chicks against Salmonella infantis infection induced by strict anaerobically cultured intestinal microflora.

In two experiments newly hatched broilers were orally inoculated either with intestinal microfloras cultured under different conditions or with a suspension of intestinal homogenate and challenged with high doses (3 X 10(5) c.f.u. per chick) of Salmonella infantis organisms. Inocula were prepared from intestinal material of mature SPF WL hens under aerobic or strictly anaerobic conditions (less than 5 ppm oxygen), and protected against atmospheric oxygen during storage. A very significant reduction of the number of Salmonella infantis bacteria in caecal content was achieved one and two weeks after challenge in those groups of chicks which were inoculated with anaerobically cultured flora or with intestinal homogenate. In order to induce protection, obligate anaerobes had to be accompanied by facultative anaerobes. Amprolium or Monensin dit not interfere with protection. Protection induced by intestinal microflora depends on anaerobiosis during preparation, culturing, storage, and application of the protective bacteria. Starvation on the first day of life appeared to have a negative effect on protection.

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.

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.

The influence of the incubation period and the amount of antigen on the haemagglutination inhibition titres to Newcastle disease virus.

An investigation was made into the significance of incubation period and amount of antigen used in the haemagglutination inhibition (HI) test for Newcastle disease virus in chicken serum. Also the results of a manually performed macrotest were compared with those of an automated microtest. Both incubation period and amount of antigen greatly influenced the HI titres. In incubating sera the titres increased up to 75 or 120 minutes when respectively 2 or 4 haemagglutinating units per volume were used. By contrast they became stable after 45 minutes' incubation with 8 units per volume. It was concluded that the latter combination gave optimum results. There were no significant differences between the results obtained with the macro and the micro technique.

[Campylobacter fetus subspecies jejuni in chickens (author's transl)]. / Campylobacter fetus subspecies jejuni bij pluimvee.

A bacteriological examination of 239 chickens coming from 89 commerical flocks yielded a high incidence of Campylobacter fetus subspecies jejuni isolations. From 30.1% of the birds or 41.6% of the flocks this micro-organism was isolated from 28.6% of the jejunal contents and 11.2% of the bile samples respectively. In contrast this agent could not be isolated from the skin or peritoneal cavity of 750 carcasses of broilers (13 flocks) before of after freezing in. No correlation could be found between the isolation of Campylobacter fetus ssp jejuni and the diagnosed disease condition of the birds examined.

[Drug residues in poultry (author's transl)]. / Residuen van geneesmiddelen bij pluimvee

The following microbiological tests: the Bacillus subtilis BGA (Bundes-Gesundheitsamt) test and Sarcina lutea test as well as the test bacteria Bacillus stearothermophilus var. calidolactis and E. coli were used to examine whether drug residues were detectable in broiler chickens during and after treatment with various drugs. With the exception of the occidiostat Esb3, residues were not found to be present using the two above tests. On the other hand, residues of a number of drugs were detected in some interior organs and faeces during treatment when the other test bacteria were used. Residues were no longer detected in the faeces, however, within twelve hours after treatment had been discontinued.