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.

Paraphyly of the Pseudophyllidea (Platyhelminthes: Cestoda): Circumscription of monophyletic clades based on phylogenetic analysis of ribosomal RNA

Phylogenetic relationships of cestodes of the order Pseudophyllidea (Platyhelminthes: Cestoda) were examined using sequences of complete small subunit and partial (D1-D3 region) large subunit nuclear rDNA of members of all pseudophyllidean families. The results provide evidence of paraphyly of the order as indicated by previous molecular phylogenetic analyses based on a much lower number of species sequenced. Pseudophyllidean tapeworms represent an artificial assemblage comprising two unrelated clades. "Bothriocephalidea" is formed by four families sensu Bray et al. (1994), namely Bothriocephalidae, Echinophallidae, Philobythiidae and Triaenophoridae, whereas two other families, Diphyllobothriidae and Cephalochlamydidae, give rise to the "Diphyllobothriidea". The present results indicate that "Bothriocephalidea" forms the most derived clade of all difossate and tetrafossate/bothriate tapeworm lineages which are considered to be basal relative to the rest of tetrafossate/bothridiate and acetabulate cestodes. By contrast, "Diphyllobothriidea", which includes medically important parasites (Diphyllobothrium and Spirometra), appeared more basal, without a clearly resolved position within other difossate tapeworm lineages.

The Singlet−Triplet Gap in Trimethylenmethane and the Ring-Opening of Methylenecyclopropane: A Multireference Brillouin−Wigner Coupled Cluster Study

We performed an ab initio study of the singlet-triplet gap in trimethylenmethane (TMM) and of the ring-opening of methylenecyclopropane by the multireference BWCC method. Since the singlet states of TMM and intermediates between TMM and methylenecyclopropane have a strong multiconfigurational character, it is necessary to use a multireference method. The cc-pVDZ and cc-pVTZ basis sets were used. We compared our results with experiments, where available, and with previous calculations performed by MCSCF and spin-flip coupled-cluster-type methods.

Amygdalar volume and psychiatric symptoms in Alzheimer's disease: an MRI analysis

OBJECTIVES

We measured the volumes of the amygdala to test the hypothesis that the reduction of amygdalar volume may be associated with psychiatric symptoms in Alzheimer's disease.

MATERIALS AND METHODS

Twenty-seven patients underwent neuropsychological investigation including the assessment of general clinical severity by the Mini-Mental State Examination (MMSE) and Neuropsychiatric Inventory (NPI). All patients underwent magnetic resonance imaging (MRI) of the head, from which the volumes of the amygdalae were measured. The obtained values were compared with those of controls (n = 15).

RESULTS

Patients with Alzheimer's dementia showed significant reduction in MRI volumetric measurements compared with controls. We found a significant correlation of MMSE score and absolute amygdala volume (r = 0.62, P < 0.01). Neither the absolute nor relative volume of the amygdala showed any correlation with NPI scores.

CONCLUSIONS

The atrophy of the amygdala does not have a direct association with the existence of neuropsychiatric symptoms. MRI volumetry of the amygdala may be relevant as a marker of dementia severity in Alzheimer's disease.

Correlation of expression of nuclear proteins pKi67 and p63 with lectin histochemical features in head and neck squamous cell cancer

This study represents a combined lectin and immuno-histochemical analysis of normal, dysplastic and malignant squamous epithelia of the upper aerodigestive tract with emphasis on the relation between lectin reactivity and the cells' proliferative/anti-apoptotic potential. Staining by double-labeling to detect pKi67, DeltaNp63alpha, alpha2,3/6-linked sialic acid (NeuNAc) and galectin-3-reactive epitopes was performed on specimens of 8 normal cases, 27 primary tumours and 15 regional lymph node metastases. Normal epithelia expressed alpha2,6-linked NeuNAc in the basal layer, while alpha2,3-linked NeuNAc was observed in suprabasal layers. In normal epithelium pKi67 and DeltaNp63alpha positivity was seen in the basal layer and galectin-3-reactive sites in suprabasal layers. The studied squamous cell carcinomas and their metastases showed a tendency for stratification but with markedly altered architecture. The expression of the studied markers was heterogeneous between the different cancer cases but comparable between the corresponding primary and secondary lesions. Glycophenotypic properties were correlated with the level of differentiation. Tumour cell populations were characterized by occurrence of the p63+/pKi67+ alpha2,3-NeuNAc+ alpha2,6-NeuNAc+ phenotype. Analysis of the expression patterns of pKi67, p63 and galectin-3-reactive epitopes (Gal-3-RE) delineated statistically significant interrelationships (Gal-3-RE vs. p63: r = -0.709; Gal-3-RE vs. pKi67: r = -0.623; pKi67 vs. p63: r = 0.895). Of the studied markers only Gal-3-RE expression was correlated to the differentiation-dependent grading (G1 vs. G2: p = 0.007, G2 vs. G3: p = 0.006, G1 vs. G3: p = 0.002). DeltaNp63alpha expression was statistically different only between G1 and G3 (p = 0.03). No statistically significant differences were detected between the primary tumours and the corresponding regional lymph node metastases. Based on the concept of the sugar code further analysis of cell characteristics such as proliferation together with lectin histochemical features, especially using tissue lectins as probes, is thus warranted.

Comparative analysis of alpha2,3/2,6-linked N-acetylneuraminic acid and cytokeratin expression in head and neck squamous cell carcinoma

Head and neck squamous cell cancer (HNSCC) requires precise characterization of their biological properties to better stratify treatment approaches. Some biological features of tumor cells are related to altered glycosylation of their surface. This study characterized alpha2,3/6-N-acetylneuraminic acid (NeuNAc) expression in adult squamous epithelia of primary and metastatic HNSCC in relation to expression of well established differentiation markers, such as cytokeratins. The expression of NeuNAc was assessed by plant lectins: Maackia amurensis agglutinin type 2 (MAA) and Sambucus nigra agglutinin (SNA) specific for alpha2,3NeuNAc and alpha2,6NeuNAc, respectively. Double labeling studies at the single-cell level were performed to compare alpha2,3/6NeuNAc linkage with expression of intermediate filaments. In studied normal adult epithelia, predominantly basal expression of alpha2,6NeuNAc and suprabasal expression of alpha2,3NeuNAc was seen, showing their differentiation-dependent linkage. The cells with markers of terminal differentiation (i.e. CK10+ alpha2,3NeuNAc+ alpha2,6NeuNAc-) prevailed in HNSCC, with increasing proportion from differentiation grade G1 to G3. High proportions of cytokeratin pCK37+ carcinoma cells occurred in all studied tumors and were accompanied by a hypersialylated phenotype (i.e. alpha2,3 NeuNAc+ alpha2,6NeuNAc+) not generally seen in non-transformed epithelia. It is hypothesized that these cells could be the pool for tumor spreading in the organism. Monitoring HNSCC using multiparameter phenotype analysis can produce new data important for the understanding of the biological behavior of HNSCC, and useful for the treatment rationalization.

Diagnostic relevance of Langerin detection in cells from bronchoalveolar lavage of patients with pulmonary Langerhans cell histiocytosis, sarcoidosis and idiopathic pulmonary fibrosis

The diagnosis of pulmonary Langerhans cell histiocytosis might be refined by demonstrating reliability of a new cell marker, i.e., Langerin (CD207), used on bronchoalveolar lavage fluid. For this purpose, we collected material from patients with this disease and also with sarcoidosis and idiopathic pulmonary fibrosis as controls. In addition to the immunocytochemical detection of Langerin, we examined the expression profiles of CD1a and the macrophage tandem-repeat mannose receptor (CD206). To test accessibility of Langerin, a C-type lectin, for mannosides, we employed reverse lectin histochemistry using mannose-containing neoglycoproteins. The analysis revealed a significantly increased percentage of CD1a- and Langerin-positive cells in pulmonary Langerhans cell histiocytosis in comparison with both other studied diseases. No expression of the 175-kDa mannose-binding lectin (CD206) in Langerhans cells was observed. Evidently, binding sites on the cells were not accessible for the mannose-containing neoglycoligand. These results provide evidence for the usefulness of Langerin-directed immuno- and glycohistochemical monitoring of bronchoalveolar lavage fluid in the diagnosis of pulmonary Langerhans cell histiocytosis.

Volumetry of striatum and pallidum in man--anatomy, cytoarchitecture, connections, MRI and aging

BACKGROUND

For comparing of the pathological and normal healthy state it is essential to obtain sufficient amount of the volumetric data. Nevertheless most of the publicized works use only few healthy controls opposite to the patients for the measuring of the basal ganglia volume. Further essential condition is to take into account the effect of age to the basal ganglia volume in such analysis.

PURPOSE

The goal of our study was (1) to give the current review of the structure, neurotransmitters, connections and general integration of the basal ganglia in the pathways of the central nervous system, (2) aggregate sufficient amount of volumetric data by virtue of MRI and post-mortem studies, and appoint volumes of the striatum and pallidum, (3) evaluate aging of these structures in adult healthy patients. Another goal was (4) to inspect the correlations between the size of the basal ganglia and volume characteristics of the brain, cranial capacity or frequently measured dimensions within CNS. In the spite of the fact that it is not possible to measure all of these dimensions for clinicians who want to determine if the structure is "normal" or not. Another goal was (5) to find a simple measure, which could serve as the indicator of the real size of structure of the interest.

METHODS

By virtue of the classical anatomical methods and MRI examination we appointed volumes of the striatum (furthermore divided into the complex of the caudatum--nucleus accumbens--CD-Acc and putamen) and pallidum in the sample of 108 healthy adults (18-89 years old). From another measurements we calculated the cranial capacity and volume characteristics of each brain.

RESULTS

In a general view that does not respect changes due to age neither volumetric difference between two sexes nor interhemispheric difference was significant for absolute volumes of the striatum, CD-Acc complex, putamen and pallidum. In the case of the striatum, significant correlation between size and age was found (p < 0.0001) for absolute volumes in both sexes. In men, striatum showed a decrease about 14.3% in volume in the 20-50-year age range (about 4.8% per decade). In woman, the age related shrinkage is about 16.9% (about 5.6% per decade). Dependence on age was not statistically proven for volume of female complex CD-Acc (p = 0.061). Age related decrease of female putamen was about 23.15% in the 20-50 year age range (7.7% per decade). In men, the seizure decrease of the caudate--accumbens complex amounts 16.2%, in the same age range (5.4% per decade). Similarly, volume of the putamen in men decreases up to 12.3% between 20-50 years of age (4.1% per decade). In men, the pallidum showed a decrease about 21.6% in volume in the 20-50-year age range (7.2% per decade). In women, it amounts only 11.5% (3.8% per decade). Plane of the striatum in the level of the commissura anterior showed high correlation with total striatal volume (p < 0.0001, r = 0.668). The percentual portion of striatal volume at the level of the commissura anterior (1 cm thick slice) does not differ statistically between males and females. In our data it gives 28.56% (SD = 3.05). Correlation between the striatal planes and age was significant in both sexes (in women: p = 0.007, r = 0.348, and in men: p = 0.029, r = 0.349) as in the case of the correlation between striatal volume and age.

CONCLUSIONS

Our findings suggest that age mirror differently on separate structures in the brain. We have found unequal volume decrease within both sexes even particular nuclei. Our findings also suggest that decrease of the basal ganglia volume in the dependence on age is not linear but it is composed from periods without changes and periods with reduction of its size. In the case of the striatum, behaviour of changes looks similar (with only 5 years), while in the case of the pallidum this situation is markedly different. Our observations may suggest intersexual singularity in the aging of brain structures. From one MRI, from one frontal slice in the level of the commissura anterior is possible to reduce total volume of the striatum for every examined individual. Simple graph shows interval, where the normal value of this plain should be in dependency on age and sex of the examined patient. Another graph allows reducing from this plane the total volume of the striatum. These findings can be the quick and reliable aid in better diagnostics of different diseases.

Training appropriate laboratory workers for rural health centres in Papua New Guinea

Many rural health centres in developing countries continue to treat patients without the help of any laboratory tests. The result is often inaccurate diagnosis, wasteful use of multiple drugs, and increasing drug resistance of pathogens. It is unlikely that there will ever be sufficient funds to employ a full-time laboratory worker at each of the many small remote health centres in Papua New Guinea. It is also doubtful whether staff and health extension officers who run such centres have the appropriate knowledge to adequately utilize full-time laboratory personnel. It is feasible, however, to train selected health workers in courses of three to four months' duration to perform a few simple laboratory tests part-time, in addition to their clinical duties. Suitable tests are those where the result does not require skilled interpretation. For most such tests, the result is the diagnosis. After the clinical staff have received the laboratory diagnosis, they are free to decide whether it fits the clinical picture. If so, they can then find the appropriate treatment to prescribe in standard treatment books. The present paper describes the experience in setting up and operating laboratory training for health centre staff in Milne Bay Province, Papua New Guinea. Costs and initial results of the program are discussed.