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.

Serum-Based Phospho-Neurofilament-Heavy Protein as Theranostic Biomarker in Three Models of Traumatic Brain Injury: An Operation Brain Trauma Therapy Study

Glial fibrillary acidic protein (GFAP) and ubiquitin C-terminal hydrolase (UCH-L1), markers of glial and neuronal cell body injury, respectively, have been previously selected by the Operation Brain Trauma Therapy (OBTT) pre-clinical therapy and biomarker screening consortium as drug development tools. However, traumatic axonal injury (TAI) also represents a major consequence and determinant of adverse outcomes after traumatic brain injury (TBI). Thus, biomarkers capable of assessing TAI are much needed. Neurofilaments (NFs) are found exclusively in axons. Here, we evaluated phospho-neurofilament-H (pNF-H) protein as a possible new TAI marker in serum and cerebrospinal fluid (CSF) across three rat TBI models in studies carried out by the OBTT consortium, namely, controlled cortical impact (CCI), parasagittal fluid percussion (FPI), and penetrating ballistics-like brain injury (PBBI). We indeed found that CSF and serum pNF-H levels are robustly elevated by 24 h post-injury in all three models. Further, in previous studies by OBTT, levetiracetam showed the most promising benefits, whereas nicotinamide showed limited benefit only at high dose (500 mg/kg). Thus, serum samples from the same repository collected by OBTT were evaluated. Treatment with 54 mg/kg intravenously of levetiracetam in the CCI model and 170 mg/kg in the PBBI model significantly attenuated pNF-H levels at 24 h post-injury as compared to respective vehicle groups. In contrast, nicotinamide (50 or 500 mg/kg) showed no reduction of pNF-H levels in CCI or PBBI models. Our current study suggests that pNF-H is a useful theranostic blood-based biomarker for TAI across different rodent TBI models. In addition, our data support levetiracetam as the most promising TBI drug candidate screened by OBTT to date.

Effects of overweight and obesity on motor and mental development in infants and toddlers

BACKGROUND

A consequence of childhood obesity may be poor developmental outcomes.

OBJECTIVES

This study aimed to examine the relationship between weight and developmental delays in young children.

METHODS

We conducted a secondary analysis of the Early Childhood Longitudinal Study Birth Cohort data. Logistic regression models quantified the association between different weight statuses (normal weight <85th, overweight ≥90th, obese ≥95th percentile for weight) and delays in motor and mental development.

RESULTS

Children classified as overweight in both waves had higher percentages of delays in wave 2 (motor [7.5 vs. 6.2-6.4%], mental [8.6 vs. 5.9-6.7%]), as well as wave 1 and/or wave 2 (motor [14.8 vs. 10.9-13.0%], mental [11.9 vs. 9.0-10.1%]), compared with other children. This association was also found in children who were obese at both time points in wave 2 (motor delay [8.9 vs. 4.9-7.3%], mental delay [10.3 vs. 6.0-7.2%]), as well as wave 1 and/or wave 2 (motor delay [14.5 vs. 10.9-12.9%], mental delay [14.1 vs. 9.4-10.1%]). In the adjusted models, children classified as always obese were more likely to have a mental delay in wave 2 (adjusted odds ratio [aOR] 1.89, 95% confidence interval [CI]: 1.21-2.95) as well as wave 1 and/or wave 2 (aOR 1.56, 95% CI: 1.08-2.26). These children were also more likely to have motor delay (aOR 1.47, 95% CI: 1.02-2.13) in wave 1 and/or wave 2.

CONCLUSION

Overweight children are more likely than their normal-weight peers to have motor and mental developmental delays. Preventing obesity during infancy may facilitate reducing developmental delays in young children.

Full Electroresistance Modulation in a Mixed-Phase Metallic Alloy

We report a giant, ∼22%, electroresistance modulation for a metallic alloy above room temperature. It is achieved by a small electric field of 2  kV/cm via piezoelectric strain-mediated magnetoelectric coupling and the resulting magnetic phase transition in epitaxial FeRh/BaTiO_{3} heterostructures. This work presents detailed experimental evidence for an isothermal magnetic phase transition driven by tetragonality modulation in FeRh thin films, which is in contrast to the large volume expansion in the conventional temperature-driven magnetic phase transition in FeRh. Moreover, all the experimental results in this work illustrate FeRh as a mixed-phase model system well similar to phase-separated colossal magnetoresistance systems with phase instability therein.

Abstract P2-09-20: Evaluation on the mutation screening by next-generation sequencing in hereditary breast and ovarian cancer: Implementation of recurrent mutation panel

Background: Hereditary disposition accounts for 10-15% in breast cancers and 20-25% in ovarian cancers, in which 5-10% of women have genomic alteration in breast cancer predisposition genes, BRCA1 and BRCA2, while the rest are likely due to less penetrant genes. In specific ethnicities such as Ashkenazi Jewish, three founder mutations have been identified which covers 95 % of all the BRCA mutations identified in this race. These genes are screened prior to the gold standard Sanger Sequencing in order to reduce cost. Sanger Sequencing, however, still has the limitation on the necessity of laborious processing and results interpretation. Moreover, it limits the number of genes that can be analyzed in one setting. With the use of next-generation sequencing (NGS), identification of hereditary breast and ovarian cancer (HBOC) syndrome associated genes, other than BRCA, can be sequenced at the same time but yet a faster turnover time. This allows more timely targeted risk-reducing strategies and interventions to be implemented for mutation positive carriers and their family members.

Methods: In this study cohort, 948 high-risk breast/ovarian patients who met the HBOC selection criteria were recruited for mutation screening by our NGS pipeline. With the inclusion of 90 Sanger-validated known mutation cases, the performance of the NGS pipeline were proven to be comparable to Sanger sequencing. PTEN and TP53, other than BRCA1 and BRCA2, a 4 gene sequencing panel were included in the mutation screening for high-risk patients.

Results: The prevalence of BRCA1/BRCA2 germline mutations was 7.28% in our Chinese cohort and 47.8% of the mutation were recurrent mutations. Based on this finding, we further adopted a new workflow by screening the recurrent mutations including founder mutations from Chinese cohort prior to NGS for those who tested negative. In a testing cohort of 343 cases, the recurrent mutation pick-up rate was 3.5%, this implicated a more cost-effective method for mutation screening in the clinical setting. Moreover, the frequencies of PTEN and TP53 were 0.21% and 0.53% respectively in our population with breast and ovarian cases.

Conclusion: Taken together, our data demonstrated a strategic upfront screening for recurrent mutations in Chinese population which is highly applicable in most of the diagnostic laboratories. Multi-gene sequencing using the NGS technology will be the upcoming strategies for mutation screening for HBOC patients.

Citation Format: Kwong A, Shin VY, Au CH, Law FB, Ho DN, Ip BK, Wong AT, Lau SS, To RM, Choy G, Ford JM, Ma ES, Chan TL. Evaluation on the mutation screening by next-generation sequencing in hereditary breast and ovarian cancer: Implementation of recurrent mutation panel. [abstract]. In: Proceedings of the Thirty-Eighth Annual CTRC-AACR San Antonio Breast Cancer Symposium: 2015 Dec 8-12; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2016;76(4 Suppl):Abstract nr P2-09-20.

Abstract P2-07-03: High-throughput germline mutation screening for hereditary breast cancer in southern Chinese patients by massively parallel DNA sequencing

Introduction: Breast cancer is the most common malignancy and 3rd leading cause of deaths among the female population in Hong Kong. Since the establishment of The Hong Kong Hereditary Breast Cancer Family Registry in 2007, 1344 patients with breast and/or ovarian cancer who met the selection criteria were recruited for genetic testing in Hong Kong. Since 2011 we started to employ next-generation DNA sequencing (NGS) to expedite the analysis workflow and expand the panel of genes for sequencing.

Aim: To evaluate the workflow of NGS in mutation screening of BRCA1, BRCA2, TP53 and PTEN genes, and compared with the sequence data obtained by Sanger sequencing.

Methods: We sequenced BRCA1, BRCA2, TP53 and PTEN genes in peripheral blood samples of 410 patients, 53 positive controls and 107 healthy local individuals using 454 GS Junior System. Generation of barcoded amplicon libraries was streamlined by microfluidic PCR using Fluidigm Access Array System. Sequencing data were analyzed by an in-house developed fully automatic bioinformatics pipeline, which mainly consists of GS Amplicon Variant Analyzer, SAMtools and Ensembl Variant Effect Predictor. All putative mutations identified were validated by Sanger sequencing. Furthermore, the frequency of BRCA1, BRCA2 and PTEN missense variants of unknown significance (VUS) identified in the cohort were compared among 107 healthy local individuals and 1000 Genomes project samples. The VUS were also subjected to a panel of in silico prediction methods including PolyPhen and SIFT.

Results: Among 410 patients, there were 7 in BRCA1, 6 in BRCA2 and 1 in TP53 mutations found, including 1 novel recurrent BRCA2 (c.7007G&gt;T) and 1 novel founder BRCA2 (c.5164_5165delAG) mutations. Based on multiple criteria, 12 in BRCA1, 12 in BRCA2 and 1 in PTEN VUS could be prioritized for further investigation. The bioinformatics pipeline was extensively evaluated with Sanger-validated controls. The evaluation determined minimum sequencing coverage needed in this sequencing platform for accurate analysis. The pipeline accuracy was demonstrated by successful detecting mutations from 53 positive controls, including single nucleotide variants, insertions and deletions in different sequence context.

Conclusion: BRCA1, BRCA2, TP53 and PTEN mutation screening of 410 patients were expedited by high-throughput DNA sequencing. This method could detect 14 positive cases, including recurrent mutations, in a shorter period of time when compared with Sanger full gene sequencing. High-risk patients who are negative for the gene panel may need further investigation other than screening for BRCA1/2. The in-house developed bioinformatics pipeline was validated to detect various types of mutations and potentially become a conventional platform for genetic screening.

Citation Information: Cancer Res 2013;73(24 Suppl): Abstract nr P2-07-03.

Multimodal approach in the management of 1163 ureteric stone cases

One thousand one hundred and sixty three patients (male-852, female-311) with ureteric calculi requiring intervention were treated between April 1988 to July 1992. Four hundred and eleven cases were treated by ESWL Monotherapy, 414 by stone manipulation plus ESWL, 301 by retrograde ureteroscopic lithotripsy, 36 by percutaneous antegrade ureteroscopic lithotripsy and 1 case by open ureterolithotomy. There were 25 failures of the initial procedures. Only three cases that failed primary procedures required open surgery. Other complications include minor ureteric mucosal perforation (3%), infection (3%), transient moderate to gross haematuria (20%), loin ache (26.4%), irritative urination (34.4%) and low grade fever (30.1%). Current modalities used in the treatment of ureteric calculi produce good results and there is generally no primary role for any open surgery.

Effects of Eight Herbicides on In Vitro Hatching of Heterodera glycines

Laboratory studies were conducted to evaluate effects of selected herbicides on hatching of free eggs of the soybean cyst nematode, Heterodera glycines. The herbicides used were Atrazine (atrazine), Basagran (bentazon), Bladex (cyanazine), Blazer (acifluorfen), Command (clomazone), Lasso (alachlor), Sonalan (ethalfluralin), and Treflan (trifluralin). Treatments comprised two concentrations of commercial herbicide formulations and deionized water and 3.14 mM zinc sulfate as negative and positive controls, respectively. Eggs were extracted from females and cysts, surface disinfested, and incubated in herbicide or control solutions at 25 +/- 2 C in darkness. Hatched second-stage juveniles were counted every other day for 24 days. Hatching of H. glycines eggs in 50 and 500 mug/ml Blazer was 42 to 67% less than that in deionized water and 6l to 78% less than that in zinc sulfate solution. Zinc sulfate significantly increased hatching activity in 50 mug/ml but not 500 mug/ml Blazer. The other herbicides tested at various concentrations had no significant effect on egg hatching. The specific component of Blazer inhibiting egg hatching is unknown. Suppression of hatching by Blazer indicates that this postemergence soybean herbicide may have a potential role in managing H. glycines.

Expression of epithelial and extracellular matrix protein markers in meningiomas

In an attempt to characterize the dual mesenchymal and epithelial differentiating potential of meningiomas, cryostat sections from 50 meningiomas of diverse histological subtypes were examined immunohistochemically with a panel of markers for epithelial and mesenchymal differentiation. The overall positivities were: keratins 50%, epithelial membrane antigen 94%, human milk fat globules 38%, carcinoembryonic antigen 4% (secretory meningiomas only), desmoplakins 64%, collagen I 82%, procollagen I 96%, collagen III 74%, collagen IV 60%, laminin 54%, fibronectin 98% and vimentin 98%. Such production of keratins was not found in many previous immunohistochemical analyses of meningiomas with paraffin sections. The extracellular matrix proteins were present in a pericellular distribution suggestive of their being produced by the tumour cells. The potential of dual epithelial and mesenchymal differentiation in meningiomas was further examined in seven cases established on short-term cultures. Morphologically, subcultured tumour cells resembled fibroblasts and in five cases revealed similar epithelial and mesenchymal immunohistochemical profiles as for direct tumour immunostaining. In two cases, cells from the primary cultures revealed a fine skeleton of intercellular matrix proteins stainable by immunohistochemical methods, providing further proof that meningioma cells possess the capability to elaborate extracellular matrix proteins, a major mesenchymal function akin to that of fibroblasts.