High-speed fixed-target serial virus crystallography

We report a method for serial X-ray crystallography at X-ray free-electron lasers (XFELs), which allows for full use of the current 120-Hz repetition rate of the Linear Coherent Light Source (LCLS). Using a micropatterned silicon chip in combination with the high-speed Roadrunner goniometer for sample delivery, we were able to determine the crystal structures of the picornavirus bovine enterovirus 2 (BEV2) and the cytoplasmic polyhedrosis virus type 18 polyhedrin, with total data collection times of less than 14 and 10 min, respectively. Our method requires only micrograms of sample and should therefore broaden the applicability of serial femtosecond crystallography to challenging projects for which only limited sample amounts are available. By synchronizing the sample exchange to the XFEL repetition rate, our method allows for most efficient use of the limited beam time available at XFELs and should enable a substantial increase in sample throughput at these facilities

Investigation into the annotation of protocol sequencing steps in the sequence read archive

BACKGROUND: The workflow for the production of high-throughput sequencing data from nucleic acid samples is complex. There are a series of protocol steps to be followed in the preparation of samples for next-generation sequencing. The quantification of bias in a number of protocol steps, namely DNA fractionation, blunting, phosphorylation, adapter ligation and library enrichment, remains to be determined. RESULTS: We examined the experimental metadata of the public repository Sequence Read Archive (SRA) in order to ascertain the level of annotation of important sequencing steps in submissions to the database. Using SQL relational database queries (using the SRAdb SQLite database generated by the Bioconductor consortium) to search for keywords commonly occurring in key preparatory protocol steps partitioned over studies, we found that 7.10%, 5.84% and 7.57% of all records (fragmentation, ligation and enrichment, respectively), had at least one keyword corresponding to one of the three protocol steps. Only 4.06% of all records, partitioned over studies, had keywords for all three steps in the protocol (5.58% of all SRA records). CONCLUSIONS: The current level of annotation in the SRA inhibits systematic studies of bias due to these protocol steps. Downstream from this, meta-analyses and comparative studies based on these data will have a source of bias that cannot be quantified at present

Genomic landscape and clonal architecture of mouse oral squamous cell carcinomas dictate tumour ecology.

To establish whether 4-nitroquinoline N-oxide-induced carcinogenesis mirrors the heterogeneity of human oral squamous cell carcinoma (OSCC), we have performed genomic analysis of mouse tongue lesions. The mutational signatures of human and mouse OSCC overlap extensively. Mutational burden is higher in moderate dysplasias and invasive SCCs than in hyperplasias and mild dysplasias, although mutations in p53, Notch1 and Fat1 occur in early lesions. Laminin-α3 mutations are associated with tumour invasiveness and Notch1 mutant tumours have an increased immune infiltrate. Computational modelling of clonal dynamics indicates that high genetic heterogeneity may be a feature of those mild dysplasias that are likely to progress to more aggressive tumours. These studies provide a foundation for exploring OSCC evolution, heterogeneity and progression

Modeling Airlift Operations for Humanitarian Aid and Disaster Relief to Support Acquisition Decision-Making

In a fiscally constrained environment, it is crucial that both equipment manufacturers and defence invest in technology that shows marked operational improvement. A priori identification of cost-benefit at the early acquisition stage is often limited and incomplete, leading to poor value propositions. This conundrum motivates the need to develop a method to evaluate technologies such as levels of autonomy, stealth capability, improved engines, etc. and make tradeoffs against operational measures of performance and effectiveness (MOP/Es) rather than solely against vehicle performance characteristics. The objective of this study is to create an environment in which those trades against MOEs could be performed rapidly to inform technology investment and acquisition decision-making. This environment is built on top of representative models of a discrete event simulation of disaster relief airlift operations to compare technology modifications or vehicle acquisition options rapidly against operational measures of effectiveness

Conformal radiotherapy in combination with cetuximab for stage Т1–2 tongue cancer with N1–2b regional metastases detected after preventive lymphadenectomy

The study objective is to analyze the experience of conformal radiotherapy in combination with cetuximab for cervical lymph node (LN) metastasis in patients with early-stage tongue cancer who had undergone multicomponent surgeries.Materials and methods. This retrospective study included 48 patients with primary squamous cell carcinoma of the tongue (Т1–2) that were treated in Nizhny Novgorod Regional Clinical Oncology Dispensary between 2012 and 2019. The experimental group comprised 25 patients who underwent hemiglossectomy with simultaneous preventive cervical lymph node dissection. The control group was composed of 23 patients who underwent hemiglossectomy alone due to the presence of concomitant somatic pathology. Before surgery, none of the patients had any signs of metastatic lesions in the cervical LNs according to the results of clinical and instrumental examinations. After surgery, 100 % of patients from the experimental group were found to have N1–2b cervical LN metastases at histological examination. Patients from the control group developed clinical signs of cervical LN metastasis within a year after operation. All patients underwent radiotherapy. The experimental group was divided into two subgroups: patients from subgroup 1 (n = 11) received cetuximab due to disease progression, whereas patients from subgroup 2 (n = 14) received cisplatin. Participants from the control group received no chemotherapy due to their concomitant somatic disorders and because regional metastasis was not confirmed.Results. In the control group, the time between surgery and patient’s death varied between 8 and 14 months. Patients from subgroups 1 and 2 survived for 12–60 months and 8–48 months respectively. So far, 9 patients from subgroup 1 and 6 patients from subgroup 2 are alive. Among them, 8 participants from subgroup 1 and 4 participants from subgroup 2 have no signs of disease progression. Three patients from subgroup 2 died of cardiovascular diseases (they had no cancer progression within 3 months after the completion of chemotherapy).Conclusion. Preventive lymph node dissection in patients with stage Т1–2 tongue cancer enables early detection of subclinical N1–2b metastases and ensures timely initiation of therapy. Our experience confirmed safety of cetuximab plus radiotherapy used to improve disease control and increase patient’s survival

A new measurement approach of ionizing radiation in irradiated trout (Oncorhynchus mykiss) by Randomly Polymorphic DNA-Polymerase Chain Reaction

Trout (Oncorhynchus mykiss) were irradiated at doses of 0.250, 0.500, 1, 3, 5, 7 and 9 kGy in gamma cell. DNAs were extracted from the irradiated samples before and after storage. 1ERP primers were designed, and RAPD-PCR (Randomly Polymorphic DNA-Polymerase Chain Reaction) was applied to make randomly amplifications on the DNA of the irradiated samples. Agarose gel profiles of irradiated fish were obtained to determine change of band profiles. In addition, DNA fragmentation occurring in each dose was determined by comet assay for the verification of methodology developed in this study. The molecular methodology was developed to estimate ionizing radiation (IR) level in irradiated fish. This methodology allows the analysis of the trout irradiated up to the dose limit of around 0.5 kGy and stored for a period of three months