Zoonotic origin and transmission of Middle East respiratory syndrome coronavirus in the UAE

Since the emergence of Middle East respiratory syndrome coronavirus (MERS-CoV) in 2012, there have been a number of clusters of human-to-human transmission. These cases of human-to-human transmission involve close contact and have occurred primarily in healthcare settings, and they are suspected to result from repeated zoonotic introductions. In this study, we sequenced whole MERS-CoV genomes directly from respiratory samples collected from 23 confirmed MERS cases in the United Arab Emirates (UAE). These samples included cases from three nosocomial and three household clusters. The sequences were analysed for changes and relatedness with regard to the collected epidemiological data and other available MERS-CoV genomic data. Sequence analysis supports the epidemiological data within the clusters, and further, suggests that these clusters emerged independently. To understand how and when these clusters emerged, respiratory samples were taken from dromedary camels, a known host of MERS-CoV, in the same geographic regions as the human clusters. Middle East respiratory syndrome coronavirus genomes from six virus-positive animals were sequenced, and these genomes were nearly identical to those found in human patients from corresponding regions. These data demonstrate a genetic link for each of these clusters to a camel and support the hypothesis that human MERS-CoV diversity results from multiple zoonotic introductions.

Regulatory network analysis of LINC00472, a long noncoding RNA downregulated by DNA hypermethylation in colorectal cancer

Colorectal cancer (CRC), one of the common malignant cancers in the world, is caused by accumulated alterations of genetic and epigenetic factors over a long period of time. Along with that protein-coding genes being identified as oncogenes or tumor suppressors in CRC, a number of lncRNAs have also been found to be associated with CRC. Considering the important regulatory role of lncRNAs, the first goal of this study was to identify CRC-associated lncRNAs from a public database. One such lncRNA, LINC00472, was verified to be downregulated in CRC cell lines and cancer tissues compared with adjacent tissues. In addition, the down-regulation of LINC00472 seemed to be caused by DNA hypermethylation at its promoter region. Furthermore, the expression of LINC00472 and DNA methylation of promoter were significantly correlated with clinicopathological features. And DNA hypermethylation of LINC00472 may serve as a better diagnostic biomarker than its expression for CRC. Finally, we predicted the functions of LINC00472 and constructed a regulatory network and found LINC00472 may be involved in cell cycle and cell proliferation processes. Our results may provide a clue to further research into the function and regulatory mechanism of LINC00472 in CRC.

Nanoladder Cantilevers Made from Diamond and Silicon

We present a "nanoladder" geometry that minimizes the mechanical dissipation of ultrasensitive cantilevers. A nanoladder cantilever consists of a lithographically patterned scaffold of rails and rungs with feature size ∼100 nm. Compared to a rectangular beam of the same dimensions, the mass and spring constant of a nanoladder are each reduced by roughly 2 orders of magnitude. We demonstrate a low force noise of 158_-42⁺⁶² zN and 190_-33⁺⁴² zN in a 1 Hz bandwidth for devices made from silicon and diamond, respectively, measured at temperatures between 100-150 mK. As opposed to bottom-up mechanical resonators like nanowires or nanotubes, nanoladder cantilevers can be batch-fabricated using standard lithography, which is a critical factor for applications in scanning force microscopy.

Diagnostic Accuracy of Amino Acid and FDG-PET in Differentiating Brain Metastasis Recurrence from Radionecrosis after Radiotherapy: A Systematic Review and Meta-Analysis

BACKGROUND

Current studies that analyze the usefulness of amino acid and FDG-PET in distinguishing brain metastasis recurrence and radionecrosis after radiation therapy are limited by small cohort size.

PURPOSE

Our aim was to assess the diagnostic accuracy of amino acid and FDG-PET in differentiating brain metastasis recurrence from radionecrosis after radiation therapy.

DATA SOURCES

Studies were retrieved from PubMed, Embase, and the Cochrane Library.

STUDY SELECTION

Fifteen studies were included from the literature. Each study used PET to differentiate radiation necrosis from tumor recurrence in contrast-enhancing lesions on follow-up brain MR imaging after treating brain metastasis with radiation therapy.

DATA ANALYSIS

Data were analyzed with a bivariate random-effects model. Sensitivity, specificity, positive likelihood ratio, negative likelihood ratio, and diagnostic odds ratio were pooled, and a summary receiver operating characteristic curve was fit to the data.

DATA SYNTHESIS

The overall pooled sensitivity, specificity, positive likelihood ratio, negative likelihood ratio, and diagnostic odds ratio of PET were 0.85, 0.88, 7.0, 0.17, and 40, respectively. The area under the receiver operating characteristic curve was 0.93. On subgroup analysis of different tracers, amino acid and FDG-PET had similar diagnostic accuracy. Meta-regression analysis demonstrated that the method of quantification based on patient, lesion, or PET scan (based on lesion versus not, P = .07) contributed to the heterogeneity.

LIMITATIONS

Our study was limited by small sample size, and 60% of the included studies were of retrospective design.

CONCLUSIONS

Amino acid and FDG-PET had good diagnostic accuracy in differentiating brain metastasis recurrence from radionecrosis after radiation therapy.

Growth of magnetic nanowires along freely selectable 〈hkl〉 crystal directions

The production of nanowire materials, uniformly oriented along any arbitrarily chosen crystal orientation, is an important, yet unsolved, problem in material science. Here, we present a generalizable solution to this problem. The solution is based on the technique of glancing angle deposition combined with a rapid switching of the deposition direction between crystal symmetry positions. Using iron-cobalt as an example, we showcase the simplicity and capabilities of the process in one-step fabrications of 〈100〉, 〈110〉, 〈111〉, 〈210〉, 〈310〉, 〈320〉, and 〈321〉-oriented nanowires, three-dimensional nanowire spirals, core-shell heterostructures, and axial hybrids. Our results provide a new capability for tailoring the properties of nanowires, and should be generalizable to any material that can be grown as a single-crystal biaxial film.

Identification of the Beagle 2 lander on Mars

The 2003 Beagle 2 Mars lander has been identified in Isidis Planitia at 90.43° E, 11.53° N, close to the predicted target of 90.50° E, 11.53° N. Beagle 2 was an exobiology lander designed to look for isotopic and compositional signs of life on Mars, as part of the European Space Agency Mars Express (MEX) mission. The 2004 recalculation of the original landing ellipse from a 3-sigma major axis from 174 km to 57 km, and the acquisition of Mars Reconnaissance Orbiter High Resolution Imaging Science Experiment (HiRISE) imagery at 30 cm per pixel across the target region, led to the initial identification of the lander in 2014. Following this, more HiRISE images, giving a total of 15, including red and blue-green colours, were obtained over the area of interest and searched, which allowed sub-pixel imaging using super high-resolution techniques. The size (approx. 1.5 m), distinctive multilobed shape, high reflectivity relative to the local terrain, specular reflections, and location close to the centre of the planned landing ellipse led to the identification of the Beagle 2 lander. The shape of the imaged lander, although to some extent masked by the specular reflections in the various images, is consistent with deployment of the lander lid and then some or all solar panels. Failure to fully deploy the panels-which may have been caused by damage during landing-would have prohibited communication between the lander and MEX and commencement of science operations. This implies that the main part of the entry, descent and landing sequence, the ejection from MEX, atmospheric entry and parachute deployment, and landing worked as planned with perhaps only the final full panel deployment failing.

[The Value of SMI in the Evaluation of interventional therapy of liver cancer]

Objective: To evaluate the value of super microvascular imaging(SMI) for evaluating the effect of interventional therapy of liver cancer. Methods: A total of 30 patients with 40 leisions were enrolled in this study, from the tumor intervention department in the third affiliated hospital of suzhou university.This patients were underwent TACE, after the treatment 1 month, CDFI, SMI, and CT were study respectively. Using the continuity correction McNemar matching chi-square test, with P < 0.05 for the standard , CDFI and SMI shows the difference in monitoring the microvascular imaging in and around the tumors leisions. Results: A total of 30 patients, 12 cases were primary liver cancer (7 cases combined with liver cirrhosis), 18cases were metastatic liver cancer; 30 cases including 25 single and 5 multiple. Significant difference were found between CT and SMI in detecting blood flows inside the lesion (χ² = 8.642 9, P < 0.05), and were also found between CT and CDFI in detecting blood flows inside the lesion (χ² = 16.961 5, P < 0.05). The AUROC, sensitivity, specificity, accuracy, PPV and NPV of CDFI were 0.647, 29.4%、100%、29.4%、100%、20.0%, while in SMI were 0.809, 61.8%、100%、61.7%、100%、31.5%, respectively. Conclusions: SMI SMI can detect the microvascular inside the lesions. This new method was superior to CDFI, achieving the same effect as CT.

The rs4238326 polymorphism in ALDH1A2 gene potentially associated with non-post traumatic knee osteoarthritis susceptibility: a two-stage population-based study

OBJECTIVE

A recent genome-wide association study reported significant associations of genetic variants within the ALDH1A2 gene with osteoarthritis (OA) of the hand in European populations. However, these findings have not been well generalized to other joints, or to other populations.

METHODS

We performed a two-stage population-based case-control study including 196 non-post traumatic knee OA cases and 442 controls in the first stage and independent 143 non-post traumatic knee OA cases and 238 controls in the second stage in a Chinese population by genotyping eight tagging polymorphisms in ALDH1A2.

RESULTS

In the first stage, the single nucleotide polymorphism (SNP) rs4238326 was found to be potentially associated with knee OA risk (additive model: odds ratio [OR] = 0.70; 95% confidence interval [95% CI] = 0.49-1.01; P = 0.055), which was further confirmed in the second stage with similar effect (additive model: OR = 0.60; 95% CI = 0.38-0.95; P = 0.029). After combining the two stages, we found that the variant C allele of rs4238326 was probably associated with decreased risk of knee OA (additive model: OR = 0.65; 95% CI = 0.49-0.86; P = 0.003). Furthermore, interaction analyses showed that rs4238326 interacted multiplicatively with age to contribute to knee OA risk (interaction P = 0.041).

CONCLUSIONS

These findings indicate that the SNP rs4238326 in ALDH1A2 gene may potentially modify individual susceptibility to knee OA in the Chinese population. Beyond that, further studies are warranted to validate and extend our findings, and future functional studies are required to clarify the possible mechanisms.

Long-term response in patient with recurrent oropharyngeal carcinoma treated with cetuximab, docetaxel and cisplatin (TPEx) as first-line treatment followed by cetuximab maintenance

BACKGROUND

Cetuximab, an anti-EGFR monoclonal antibody in combination with platinum and 5FU is the standard of care in first-line treatment of patients with recurrent head and neck squamous cell carcinoma (HNSCC), with an expected median outcome of 10months. For this population, development of efficacious and safer therapies is still needed.

CASE REPORT

A 62-year-old male with a first recurrence of human papillomavirus positive stage IVA (T3N2bM0) adenocarcinoma of the glossotonsillar sulcus not amenable to locoregional curative treatment was offered chemotherapy as part of the TPEx clinical trial. He was treated by cetuximab (loading dose 400mg/m² on day 1 cycle 1, then 250mg/m² weekly), and chemotherapy (cisplatin 75mg/m² and docetaxel 75mg/m², on day 1). Cycles were repeated every 21days for 4 cycles (TPEx regimen) with systematic granulocyte colony-stimulating factor support at each cycle. Bi-monthly maintenance cetuximab 500mg/m² was then administered. The patient showed a clinical complete response according to RECIST 1.1 criteria after 5months maintenance, with progression-free survival of 25months. Relapses that followed were treated with stereotactic irradiation, radiofrequency ablation, cetuximab and paclitaxel. The patient is alive eleven years after cancer diagnosis and remains controlled for his disease, with a cumulative period of 59months of cetuximab administration (equivalence of 121 injections).

CONCLUSION

This case report demonstrated that TPEx regimen, by synergistic interaction between taxanes and cetuximab, followed by bimonthly cetuximab maintenance may lead to patient complete remission within the first year of treatment. Furthermore, prolonged intermittent treatment with cetuximab seems to participate in the improved survival associated with preserved quality of life. Key favorable prognostic factors may be moderate tumor differentiation, oropharyngeal location, HPV p16 positive tumor status.

Temporal model for quasi-phase matching in high-order harmonic generation

We present a model for quasi-phase matching (QPM) in high-order harmonic generation (HHG). Using a one-dimensional description, we analyze the time-dependent, ultrafast wave-vector balance to calculate the on-axis harmonic output versus time, from which we obtain the output pulse energy. Considering, as an example, periodically patterned argon gas, as may be provided with a grid in a cluster jet, we calculate the harmonic output during different time intervals within the drive laser pulse duration. We find that identifying a suitable single spatial period is not straightforward due to the complex and ultrafast plasma dynamics that underlies HHG at increased intensities. The maximum on-axis harmonic pulse energy is obtained when choosing the QPM period to phase match HHG at the leading edge of the drive laser pulse.

Abstract PD8-03: Differences in the mutational landscape in African Americans and Caucasians with triple negative breast cancer

Background-Triple negative breast cancer (TNBC) occurs at a higher frequency in African American (AA) premenopausal women compared with Caucasians. It is unclear if the biology and clinical outcome of TNBC is different in AA versus Caucasians. In this study, we sought to evaluate differences in the molecular pathology of TNBC in a large cohort of AA and Caucasians.

Methods-Using publicly available data from The Cancer Genome Atlas, we identified all patients with TNBC who had information on race. We analyzed the differences in clinical characteristics and tumor somatic mutations by race from whole exome sequencing using student's t test or one-way ANOVA for continuous variables and chi square or Fisher's test for categorical variables. Exome sequencing was performed with coverage of ≥70% and at a depth of 20x.

Results-A total of 1104 primary breast cancer patients were identified, of which 178 (16%) had TNBC. Overall, TNBC was more frequent in AA than in Caucasians (33.3% versus 14.9%; p value &lt;0.001). More AA than Caucasians were classified as basal-like from PAM50 gene expression analysis (34.8% versus 16.1%; p value 0.001). No differences in the TNBC cohort were observed, 91% of AA were basal-like versus 81% of Caucasians (p value 0.842). Median tumor somatic mutation counts were higher in AA (39.5) versus Caucasians (34) (p value 0.022). However, no racial differences in the mutation counts in TNBC were observed (AA=56, Caucasians=60, p value 0.399). Somatic mutation analysis revealed racial differences in specific high prevalence (&gt;5%) genes in all patients- [TP53 alterations: 46% in AA versus 27% in Caucasians; p value &lt;0.001, PIK3CA alterations: 23% in AA versus 34% in Caucasians; p value 0.019, and MLL3 alterations: 12% in AA versus 6% in Caucasians; p value 0.028]. The TNBC patients did not have any specific high prevalence (&gt;5%) genes associated with racial differences. AA with breast cancer had a shorter time to progression (TTP) (hazard ratio 1.62, p value 0.014) and worse disease free survival (DFS) than Caucasians. However, racial difference in TTP or DFS were not observed in the TNBC patients.

Conclusion-The mutational landscape of breast cancer may be different between AA and Caucasians, but appears to be similar in both races in the cohort with TNBC. Our findings have 2 implications: racial disparities in breast cancer may largely be due to differences in those with hormone receptor positive disease, and secondly, the higher frequency of TNBC in AA is unlikely due to differences in molecular features, but other modifiable factors.

Citation Format: Ademuyiwa FO, Tao Y, Luo J. Differences in the mutational landscape in African Americans and Caucasians with triple negative breast cancer [abstract]. In: Proceedings of the 2016 San Antonio Breast Cancer Symposium; 2016 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2017;77(4 Suppl):Abstract nr PD8-03.

Quantitative chemoproteomic profiling reveals multiple target interactions of spongiolactone derivatives in leukemia cells

Identifying the covalent targets of a natural product-derivative in cancer cells.