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.

Equation of motion coupled-cluster cumulant approach for intrinsic losses in x-ray spectra

We present a combined equation of motion coupled-cluster cumulant Green's function approach for calculating and understanding intrinsic inelastic losses in core level x-ray absorption spectra (XAS) and x-ray photoemission spectra. The method is based on a factorization of the transition amplitude in the time domain, which leads to a convolution of an effective one-body absorption spectrum and the core-hole spectral function. The spectral function characterizes intrinsic losses in terms of shake-up excitations and satellites using a cumulant representation of the core-hole Green's function that simplifies the interpretation. The one-body spectrum also includes orthogonality corrections that enhance the XAS at the edge.

Autophagy triggered by MAVS inhibits Coxsackievirus A16 replication

Mitochondrial antiviral signaling protein (MAVS), a crucial adaptor protein localized on mitochondria, plays vital roles in various biological processes. Autophagy and apoptosis are two independent and closely linked cell death pathways. But whether MAVS could induce apoptosis and autophagy in rhabdomyosarcoma cells (RD cells) and what is the relationship between autophagy and apoptosis still remains elusive. Here, we reveal that overexpression of MAVS could trigger both apoptosis and autophagy in RD cells. Interestingly, MAVS-induced apoptosis was dependent on the activation of the c-Jun N-terminal kinase (JNK) signaling pathway and inhibition of the extracellular signal-regulated kinase (ERK) signaling pathway. Also, it was found that inhibition of autophagy by 3-methyladenine (3-MA) enhanced MAVS-induced apoptosis resulting in increased cleavage of caspase-3 and poly (ADP-ribose) polymerase (PARP). Meanwhile, autophagy induction by rapamycin resulted in decreased MAVS-induced apoptosis. In addition, we found that MAVS expression was inhibited upon Coxsackievirus A16 (CA16) infection and overexpression of MAVS could inhibit CA16 replication. Collectively, our study provides novel insights into the link between apoptosis and autophagy induced by MAVS overexpression in RD cells and gains a greater understanding of MAVS-induced antiviral functions, which provide new targets for CA16 treatment. Keywords: CA16; MAVS; apoptosis; autophagy.

Streamlined MRM method transfer between instruments assisted with HRMS matching and retention-time prediction

Multiple reaction monitoring (MRM) mode using liquid-chromatography tandem mass spectrometry (e.g., LC-QqQ-MS/MS) has been extensively employed in the small molecule analysis with trace levels in complex samples owing to its high sensitivity. However, most of the reported MRM methods are developed using authentic standards, which are often costly yet not readily available. To address this question, a practical platform for the MRM method transfer between different LC-QqQ-MS/MS instruments, assisted by the high-resolution mass spectrometry (LC-HRMS) and retention time (RT) prediction, has been developed in this study. The reported platform can take advantage of both the high sensitivity of LC-MRM method and ion transition pairs from the previous publications. LC-HRMS can provide the accurate mass measurement of the compounds, though high-quality MS/MS fragments are usually difficult to obtain for chemicals at trace levels. Retention time matching and peaks matching between both instrumental platforms rule out isobaric candidates. With an additional retention time prediction filter from quantitative structure retention relationship (QSRR) model based on random forest feature selection (Pearson r² = 0.63), identification of small molecules is achieved at a high confidence level without using authentic standards. The developed platform has been validated with robustness by examining spiked environmental chemicals in sludge water samples, biological urine, and cell extracts.

The postoperative effect of sevoflurane inhalational anesthesia on cognitive function and inflammatory response of pediatric patients

OBJECTIVE

To investigate the effect of sevoflurane on cognitive function and inflammatory response of children after general anesthesia at different times.

PATIENTS AND METHODS

Ninety-three pediatric patients who underwent general anesthesia surgery were enrolled and divided into groups based on time under general anesthesia: group A (<1 h, n=27), group B (1-3 h, n=36), and group C (≥ 3 h, n=30). Changes in cognitive function and serum inflammatory index were compared.

RESULTS

The occurrence of postoperative cognitive dysfunction (POCD) in group A and B was lower than in group C and the difference was statistically significant (p<0.05). The levels of caspase-3, TNF-α, and IL-6 in the POCD group at the different time points were significantly higher than in the non-POCD group and the differences were statistically significant (p<0.05). Caspase-3, TNF-α, and IL-6 levels in the POCD group at the different time points significantly changed and were highest during the recovery period, while there were no significant changes in the non-POCD group at the different time points.

CONCLUSIONS

The prolonged sevoflurane inhalational anesthesia time (≥ 3 h) enhanced the occurrence of POCD and was related to the expression levels of serum caspase-3, TNF-α, and IL-6.

Phase Space Dynamics of a Plasma Wakefield Dechirper for Energy Spread Reduction

Plasma-based accelerators have made impressive progress in recent years. However, the beam energy spread obtained in these accelerators is still at the ∼1% level, nearly one order of magnitude larger than what is needed for challenging applications like coherent light sources or colliders. In plasma accelerators, the beam energy spread is mainly dominated by its energy chirp (longitudinally correlated energy spread). Here we demonstrate that when an initially chirped electron beam from a linac with a proper current profile is sent through a low-density plasma structure, the self-wake of the beam can significantly reduce its energy chirp and the overall energy spread. The resolution-limited energy spectrum measurements show at least a threefold reduction of the beam energy spread from 1.28% to 0.41% FWHM with a dechirping strength of ∼1  (MV/m)/(mm pC). Refined time-resolved phase space measurements, combined with high-fidelity three-dimensional particle-in-cell simulations, further indicate the real energy spread after the dechirper is only about 0.13% (FWHM), a factor of 10 reduction of the initial energy spread.

[Antiviral effect of hepatitis B virus S gene-specific anti-gene locked nucleic acid in transgenic mice]

Objective: To investigate the antiviral effect of hepatitis B virus (HBV) S gene-specific anti-gene locked nucleic acid (LNA) in transgenic mice. Methods: A total of 30 HBV transgenic mice were randomly divided into blank control group (5% glucose + liposome), unrelated sequence control group, lamivudine control group, antisense LNA control group, and anti-gene LNA group, with 6 mice in each group. The mice in the lamivudine group were given lamivudine by gavage, and LNA was injected via the caudal vein. Quantitative real-time PCR was used to measure serum HBV DNA, ELISA was used to measure serum HBsAg, RT-PCR was used to measure HBV S mRNA level in the liver, and immunohistochemistry was used to measure the level of HBsAg in hepatocytes. Results: At 3, 5, and 7 days after treatment, there were significant changes in the inhibition rates of HBV DNA (37.18%, 50.27%, and 61.46%, respectively) and HBsAg (30.17%, 44.00%, and 57.76%, respectively) achieved by anti-gene LNA (P < 0.01), and there were significant differences between the anti-gene LNA group and the other four control groups (P < 0.05). In the anti-gene LNA group, the relative mRNA expression of HBV S gene was 0.33 and the percentage of HBsAg-positive hepatocytes was 31%, which were significantly different from these two indices in the control groups (P < 0.05). There were no abnormal changes in liver/renal biochemical parameters and HE staining results. Conclusion: Anti-gene LNA targeting at HBV S gene has a strong antiviral effect in transgenic mice, which provides theoretical and experimental bases for gene therapy for HBV.

The Presence and involvement of interleukin-17 in apical periodontitis

Apical periodontitis (AP) is a chronic inflammatory disease characterized by periapical tissue inflammation and destruction of the associated alveolar bone. It is caused by microbial infections within the root canal and the resultant host immune responses in the periapical tissues. The proinflammatory cytokine interleukin (IL)-17 has been shown to play an important role in many inflammatory diseases. There is increasing evidence of the presence of IL-17 in AP, which might be associated with disease pathogenesis. Moreover, several animal studies indicate the potential role of IL-17 in periapical inflammation and the resultant bone resorption in AP. This article reviews recent studies regarding the collective in vitro, in vivo and clinical evidence of the presence and involvement of IL-17 in AP. A search related to IL-17 in apical periodontitis was conducted on PubMed, EMBASE and Web of Science databases using keywords and controlled vocabulary. Two independent reviewers first screened titles and abstracts and then the full texts that were included. A total of 25 papers were identified, of the 25 included articles, 7 involved laboratory studies on cell cultures, 11 involved animal experimentations, and 7 were observational studies using human clinical samples. In conclusion, evidence for the presence of IL-17 in AP from human and animal models is clear. However, there is relatively little information currently available that would highlight the specific role of IL-17 in AP.

[Morphological classification of acute isolated pontine infarction and it's clinical relevance]

Objective: To investigate a diffusion weighted imaging (DWI)-based morphological classification for acute isolated pontine infarcts (AIPI) and to assess differences in clinical characteristics, risk factors and functional outcomes among the different morphologies. Methods: All participants from SMART cohort with DWI-proven AIPI were included and categorized into 3 groups: basilar artery branch disease (BABD) group, small artery disease (SAD) group and large-artery-occlusive disease (LAOD) group, according to lesion extent of the transverse axial plane and basilar artery atherosclerosis severity. The clinical characteristics, vascular risk factors and 6-month's functional outcome was analyzed among 3 groups. Results: Of the 1 129 patients enrolled, 175 had AIPI. BABD was the most frequent subtype of AIPI (46.3%), followed by SAD (36.0%) and LAOD (17.7%). Neurological impairment on admission was more severe in the LAOD and BABD group than SAD group (P<0.001). In terms of risk factors, the percentage of hypertension was significant different among three groups (P<0.05). The average National Institute of Health stroke scale was 3.49 for SAD group, 5.93 for LAOD group, 5.97 for BABD group, and the differences were significant (P<0.001). The Poor outcome (mRS>2) was found in only 13.7% of patients at 6-month post-stroke and there was no difference among 3 groups. Conclusions: According to the morphological classification, BABD is the most frequent subtype of AIPI. The differences of the clinical characteristics and risk factors among three groups indicate that differences observed in morphology might have distinct pathophysiologic mechanisms. AIPI can be reliably classified based on morphology using clinical magnetic resonance images.

[Clinical experience and next-generation sequencing analysis of encephalitis caused by pseudorabies virus]

Objective: To detect potential pathogens including pseudorabies virus in patients with encephalitis of unknown etiology in China and describe novel encephalitic entities. Methods: Patients with clinically suspected infectious encephalitis were enrolled in a multicenter study to identify the pathogens in PUMCH Encephalitis Program.Next-generation sequencing(NGS) of cerebrospinal fluid (CSF) was used in patients with encephalitis of unknown etiology enrolled from 2016 to 2017.The patients diagnosed as PRV encephalitis were studied to describe this novel entity. Results: The four patients(3 male, 1 male, 38-54 years old) had occupational exposure to raw park when working in the production or marketing of pork and at least one got injured during pork-cutting.Two of them were confirmed with NGS of CSF, and anti-PRV antibodies were positive in 3 patients whose serum was available for serological analysis.They all presented with an acute onset of fever, convulsion, loss of consciousness and respiratory failure within 1 to 4 days and rapidly deteriorated even on extensive treatment.All the patients needed ICU admission and 3 needed mechanical ventilation.Two patients also had bilateral retinitis.Neuroimaging revealed symmetric gray matter lesions including limbic system, basal ganglia and midbrain without obvious hemorrhage.Lumbar puncture revealed elevated intracranial pressure and lymphocytic pleocytosis [(6-64)×10(6)/L] of CSF.The patients failed to response to the treatment of acyclovir combined with intravenous immunoglobulin and steroids.Modified Rankin Score was 3, 5, 5 and 6 (died) for the 4 patients respectively on last follow-up. Conclusions: PRV could be a cause of severe encephalitis.The patients with suspected pseudorabies encephalitis (PRE) need to be tested for PRV DNA timely.Severe encephalitis with bilateral involvement of limbic system, basal ganglion, thalamus and midbrain in patient with occupational exposure indicate this emerging infectious encephalitis.

A novel near-infrared nanomaterial with high quantum efficiency and its applications in real time in vivo imaging

Fluorescence imaging signal is severely limited by the quantum efficiency and emission wavelength. To overcome these challenges, novel NIR-emitting K₅NdLi₂F₁₀ nanoparticles under NIR excitation was introduced as fluorescence imaging probe for the first time. The photostability of K₅NdLi₂F₁₀ nanoparticles in the water, phosphate buffer saline, fetal bovine serum and living mice was investigated. The fluorescence signal was detected with depths of 3.5 and 2.0 cm in phantom and pork tissue, respectively. Fluorescence spectrum with a significant signal-to-background ratio of 10:1 was captured in living mice. Moreover, clear NIR images were virtualized for the living mice after intravenous injection. The imaging ability of nanoparticles in tumor-beard mice were evaluated, the enrichment of K₅NdLi₂F₁₀ nanoparticles in tumor site due to the enhanced permeability and retention effect was confirmed. The systematic studies of toxicity, bio-distribution and in-vivo dynamic imaging suggest that these materials give high biocompatibility and low toxicity. These NIR-emitting nanoparticles with high quantum efficiency, high penetration and low toxicity might facilitate tumor identification in deep tissues more sensitively.

Abstract P3-04-01: Molecular determinants of post-mastectomy breast cancer recurrence

Introduction

The management of breast cancer (BC) patients who undergo mastectomy in the setting of 1-3 positive lymph nodes has been controversial. This retrospective Translational Breast Cancer Research Consortium study evaluated the molecular aberrations associated with locoregional recurrence (LRR) or distant metastasis (DM) compared to controls in an effort to identify molecular predictors associated with recurrence.

Methods/Materials

We identified 115 HER2 negative, therapy naïve, T 1-3 and N 0-1 BC patients treated with mastectomy and no post mastectomy radiation therapy from 1997 to present with available FFPE tissue blocks. The cohort included 32 patients with LRR, 34 with DM, and 49 controls (without recurrence) who were matched for stage, grade, hormone receptor status, age ≤ or &gt; 50, chemotherapy receipt, and margin status. Matched primary and recurrent LRR samples were available for 3 patients. Hybrid capture next generation sequencing (NGS) of 142 cancer related genes and RNAseq were performed to identify DNA/RNA alterations associated with LRR or DM. The frequency of common alterations on NGS was compared with Fisher's exact test. Expression of each gene from mRNA-Seq was treated as an explanatory variable. Immunohistochemistry (IHC) was performed for PTEN, Ki-67 and cleaved caspase 3 (CC3). PTEN loss and percentage of Ki-67 and CC3 positive cells were compared between groups with Fisher's exact test and nonparametric methods, respectively.

Results

RNAseq was performed on 115 patients; there was no difference in RNA expression levels between the groups. DNA analysis was performed on 57 patients (17 LRR, 15 DM and 25 controls), NF1 mutation rate was significantly elevated in both the LRR (24%) and DM (27%) samples compared to controls 0%; (p=0.0070). The mitogen activated protein kinase (MAPK) pathway was significantly mutated in both LRR (47%) and DM (40%) samples compared to the controls 0%; (p&lt;0.0001). There was no significant difference in the rate of alterations of the PI3K/Akt/mTOR pathway among the three groups. Of three patients with matched primary vs LRR samples, one had concordant mutations. The second patient had additional mutations in the LRR, including gain of a NF1 mutation. The third patient had complete discordance of mutations identified in primary and LRR and had gain of HER2 amplification, suggestive of a new primary. There was no significant association between the groups and the loss of PTEN expression or CC3 expression. There was a significant difference between Ki 67 positive cells in patients with LRR (mean 29%), DM (mean 26%) versus controls (mean 14%, p= 0.0011). HR+ patients were significantly more likely to have a positive PTEN, lower Ki-67 and lower CC3 expression, p=0.0004, p&lt;0.0001, and p&lt;0.0001 respectively.

Conclusions

In this matched cohort analysis, mutations in the MAPK pathway, specifically NF1, were associated with both LRR and DM, suggesting that alterations in this pathway are associated with a more aggressive tumor phenotype. However, there were no molecular features that discriminated between those likely to recur locally alone versus distantly. Further study is needed to validate these findings, and to determine whether targeting alterations in this pathway could decrease the risk of recurrence.

Citation Format: Keene KS, King T, Hwang ES, Peng B, McGuire K, Tapia C, Zhang H, Bae S, Nakhlis F, Klauber-Demore N, Meszoely I, Sabel MS, Willey SC, Eterovic KA, Hudis C, Wolff A, De Los Santos J, Thompson A, Mills GB, Meric-Bernstam F. Molecular determinants of post-mastectomy breast cancer recurrence [abstract]. In: Proceedings of the 2017 San Antonio Breast Cancer Symposium; 2017 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2018;78(4 Suppl):Abstract nr P3-04-01.

Differential research of inflammatory and related mediators in BPH, histological prostatitis and PCa

Prostate cancer (PCa) is one of the most common male malignancies in the world. It was aimed to investigate differential expression of inflammatory and related factors in benign prostatic hyperplasia (BPH), prostate cancer (PCa), histological prostatitis (HP) and explore the role of Inducible nitric oxide synthase (iNOS), (VEGF) Vascular endothelial growth factor, androgen receptor (AR) and IL-2, IL-8 and TNF-α in the occurrence and development of prostate cancer. RT-PCR was used to detect the mRNA expression level of iNOS, VEGF, AR and IL-2, IL-8 and TNF-α in BPH, PCa and BPH+HP. Western blotting and immunohistochemical staining were used to detect the protein levels of various proteins in three diseases. The results showed the mRNA and protein levels of iNOS, VEGF and IL-2, IL-8 and TNF-α were significantly increased in PCa and BPH+HP groups compared with BPH group (p < .05), while the AR was significantly lower than those in PCa and BPH+HP groups (p < .05). There was no significant difference in the mRNA and protein levels of iNOS, VEGF, AR and IL-2, IL-8 and TNF-α between PCa and BPH+HP groups (p > .05). iNOS, VEGF, AR and IL-2, IL-8 and TNF-α are involved in the malignant transformation of prostate tissue and play an important role in the development and progression of Prostate cancer (PCa).

The effectiveness of anterior cervical decompression and fusion for the relief of dizziness in patients with cervical spondylosis: a multicentre prospective cohort study

AIMS

Cervical spondylosis is often accompanied by dizziness. It has recently been shown that the ingrowth of Ruffini corpuscles into diseased cervical discs may be related to cervicogenic dizziness. In order to evaluate whether cervicogenic dizziness stems from the diseased cervical disc, we performed a prospective cohort study to assess the effectiveness of anterior cervical discectomy and fusion on the relief of dizziness.

PATIENTS AND METHODS

Of 145 patients with cervical spondylosis and dizziness, 116 underwent anterior cervical decompression and fusion and 29 underwent conservative treatment. All were followed up for one year. The primary outcomes were measures of the intensity and frequency of dizziness. Secondary outcomes were changes in the modified Japanese Orthopaedic Association (mJOA) score and a visual analogue scale score for neck pain.

RESULTS

There were significantly lower scores for the intensity and frequency of dizziness in the surgical group compared with the conservative group at different time points during the one-year follow-up period (p = 0.001). There was a significant improvement in mJOA scores in the surgical group.

CONCLUSION

This study indicates that anterior cervical surgery can relieve dizziness in patients with cervical spondylosis and that dizziness is an accompanying manifestation of cervical spondylosis. Cite this article: Bone Joint J 2018;100-B:81-7.