Tile Packing Tomography is NP-hard

Discrete tomography deals with reconstructing finite spatial objects from lower dimensional projections and has applications for example in timetable design. In this paper we consider the problem of reconstructing a tile packing from its row and column projections. It consists of disjoint copies of a fixed tile, all contained in some rectangular grid. The projections tell how many cells are covered by a tile in each row and column. How difficult is it to construct a tile packing satisfying given projections? It was known to be solvable by a greedy algorithm for bars (tiles of width or height 1), and NP-hardness results were known for some specific tiles. This paper shows that the problem is NP-hard whenever the tile is not a bar

Antitumour activity of pembrolizumab in advanced mucosal melanoma: a post-hoc analysis of KEYNOTE-001, 002, 006.

BackgroundMucosal melanoma is an aggressive melanoma with poor prognosis. We assessed efficacy of pembrolizumab in patients with advanced mucosal melanoma in KEYNOTE-001 (NCT01295827), -002 (NCT01704287), and -006 (NCT01866319).MethodsPatients received pembrolizumab 2 mg/kg every 3 weeks (Q3W) or 10 mg/kg Q2W or Q3W. Response was assessed by independent central review per RECIST v1.1.Results1567 patients were treated and 84 (5%) had mucosal melanoma. Fifty-one of 84 were ipilimumab-naive. In patients with mucosal melanoma, the objective response rate (ORR) was 19% (95% CI 11-29%), with median duration of response (DOR) of 27.6 months (range 1.1 + to 27.6). Median progression-free survival (PFS) was 2.8 months (95% CI 2.7-2.8), with median overall survival (OS) of 11.3 months (7.7-16.6). ORR was 22% (95% CI 11-35%) and 15% (95% CI 5-32%) in ipilimumab-naive and ipilimumab-treated patients.ConclusionPembrolizumab provides durable antitumour activity in patients with advanced mucosal melanoma regardless of prior ipilimumab

Ion therapy of prostate cancer: daily rectal dose reduction by application of spacer gel

Background: Ion beam therapy represents a promising approach to treat prostate cancer, mainly due to its high conformity and radiobiological effectiveness. However, the presence of prostate motion, patient positioning and range uncertainties may deteriorate target dose and increase exposure of organs at risk. Spacer gel injected between prostate and rectum may increase the safety of prostate cancer (PC) radiation therapy by separating the rectum from the target dose field. The dosimetric impact of the application of spacer gel for scanned carbon ion therapy of PC has been analyzed at Heidelberg Ion-Beam Therapy Center (HIT). Materials and methods: The robustness of ion therapy treatment plans was investigated by comparison of two data sets of patients treated with and without spacer gel. A research treatment planning system for ion therapy was used for treatment plan optimization and calculation of daily dose distributions on 2 to 9 Computed Tomography (CT) studies available for each of the 19 patients. Planning and daily dose distributions were analyzed with respect to target coverage, maximal dose to the rectum (excluding 1 ml of the greatest dose; Dmax-1 ml) and the rectal volume receiving dose greater than 90% of prescribed target dose (V90Rectum), respectively. Results: The application of spacer gel did substantially diminish rectum dose. Dmax-1 ml on the treatment planning CT was on average reduced from 100.0 ± 1.0% to 90.2 ± 4.8%, when spacer gel was applied. The robustness analysis performed with daily CT studies demonstrated for all analyzed patient cases that application of spacer gel results in a decrease of the daily V90Rectum index, which calculated over all patient cases and CT studies was 10.2 ± 10.4 [ml] and 1.1 ± 2.1 [ml] for patients without and with spacer gel, respectively. Conclusions: The dosimetric benefit of increasing the distance between prostate and rectum using spacer gel for PC treatment with carbon ion beams has been quantified. Application of spacer gel substantially reduced rectal exposure to high treatment dose and, therefore, can reduce the hazard of rectal toxicity in ion beam therapy of PC. The results of this study enable modifications of the PC ion therapy protocol such as dose escalation or hypofractionation

Early virological response may predict treatment response in sofosbuvir-based combination therapy of chronic hepatitis c in a multi-center “real-life” cohort

Background: The combination of sofosbuvir (SOF), ribavirin (RBV) and peg-interferon-alfa-2a (peg-IFN-alfa-2a) as well as the combination of SOF and RBV for the treatment of patients infected with hepatitis c virus (HCV) has improved rates of sustained virological response (SVR) considerably in recent trials. However, there is only limited data concerning the efficacy and safety in a “real-life” cohort. Methods: We analyzed a cohort of 119 patients with chronic HCV infection treated at four investigational sites in Germany. All patients received either a combination treatment of SOF, RBV and peg-IFN-alfa-2a or SOF and RBV. Results: The rates of SVR at 12 weeks after end of treatment (SVR 12) were as follows: Among 76 patients with genotype 1 infection the SVR 12 rate was 74 % (n = 56), among 14 patients with genotype 2 infection the SVR 12 rate was 79 % (n = 11), among 24 patients with genotype 3 infection the SVR 12 rate was 92 % (n = 22) and among 5 patients with genotype 4 infection the SVR 12 rate was 80 % (n = 4). Of all 26 patients with a relapse in our cohort, 69 % (n = 18) of these patients presented with liver cirrhosis and 58 % (n = 15) were treatment experienced. Notably, the level of HCV-RNA after 4 weeks of treatment was a significant predictor of treatment response in genotype 1 patients. Patients with HCV-RNA levels ≥ 12 IU ml-1 after 4 weeks of treatment achieved SVR 12 only in 30 % (n = 17/56, p < 0.0001) of cases and treatment response was even lower with SVR 12 of 25 % (n = 5/20, p = 0.0016) in the subgroup of patients with cirrhosis. Conclusion: We observed a high rate of SVR 12 with SOF-based treatment regimes, however probably due to the high number of patients with liver cirrhosis and prior treatment experience, treatment response rates were lower than in previously published trials. In genotype 1 patients the analysis of early virological response may predict treatment response in SOF-based combination therapies

Mandipropamid as a chemical inducer of proximity for in vivo applications

Direct control of protein interactions by chemically induced protein proximity holds great potential for both cell and synthetic biology as well as therapeutic applications. Low toxicity, orthogonality and excellent cell permeability are important criteria for chemical inducers of proximity (CIPs), in particular for in vivo applications. Here, we present the use of the agrochemical mandipropamid (Mandi) as a highly efficient CIP in cell culture systems and living organisms. Mandi specifically induces complex formation between a sixfold mutant of the plant hormone receptor pyrabactin resistance 1 (PYR1) and abscisic acid insensitive (ABI). It is orthogonal to other plant hormone-based CIPs and rapamycin-based CIP systems. We demonstrate the applicability of the Mandi system for rapid and efficient protein translocation in mammalian cells and zebrafish embryos, protein network shuttling and manipulation of endogenous proteins

Risk assessment of new sequencing data on GM maize event MIR604

In 2009 and 2010, the EFSA GMO Panel concluded the assessment of genetically modified (GM) maizes MIR604, MIR604 × GA21, MIR604 × Bt11 and MIR604 × GA21 × Bt11. These maizes were found to be as safe as their conventional counterparts and other appropriate comparators with respect to potential effects on human and animal health and the environment. On 23 July 2015, the European Commission (EC) received from Syngenta new nucleic acid sequencing data on maize event MIR604 and updated bioinformatic analyses using the new sequencing data. EC tasked EFSA to analyse these data and to indicate whether the previous conclusions of the EFSA GMO Panel on the above-listed GM maizes remain valid. The EFSA GMO Panel used the appropriate principles described in its guidelines for the risk assessment of GM plants to analyse the received data. The new sequencing data indicated a single base pair difference compared to the sequencing data originally provided, located in a non-coding region of the insert. which had already been present in the original plant material used for the risk assessment. Thus, with the exception of bioinformatics analyses, the studies performed for the risk assessment remain valid. The new sequencing data and the bioinformatic analyses performed on the new sequence did not give rise to safety issues. Therefore, the GMO Panel concludes that the original risk assessment of event MIR604 as a single and as a part of stacked events remains valid

Results of the application and demonstration calculations

CORTEX - Research and Innovation Action (RIA) This project has received funding from the European Union's Horizon 2020 research and innovation programme under grant agreement No 754316.Publisher PD

Scientific Opinion on application EFSA‐GMO‐BE‐2013‐117 for authorisation of genetically modified maize MON 87427 × MON 89034 × NK603 and subcombinations independently of their origin, for food and feed uses, import and processing submitted under Regulation (EC) No 1829/2003 by Monsanto Company

Scientific opinionRequestor: Competent Authority of BelgiumQuestion number: EFSA-Q-2013-00765In this opinion, the EFSA Panel on Genetically Modified Organisms (GMO Panel) assessed the three-event stack maize MON 87427 9 MON 89034 9 NK603 and its three subcombinations, independently of their origin. The GMO Panel has previously assessed the three single events combined to produce this three-event stack maize and did not identify safety concerns. No new data on the single events, leading to modification of the original conclusions on their safety, were identified. Based on the molecular, agronomic, phenotypic and compositional characteristics, the combination of the single maize events and of the newly expressed proteins in the three-event stack maize did not give rise to issues regarding food and feed safety or nutrition. In the case of accidental release of viable grains of maize MON 87427 9 MON 89034 9 NK603 into the environment, the three-event stack maize would not raise environmental safety concerns. The GMO Panel concludes that the threeevent stack maize is as safe and as nutritious as the non-GM comparator and the tested non-GM reference varieties in the context of its scope. The GMO Panel considered that its previous conclusions on the two-event stack maize MON 89034 9 NK603 remain valid. For the two maize subcombinations for which no experimental data were provided the GMO Panel assessed the likelihood of interactions among the single events, and concluded that their combination would not raise safety concerns. These two subcombinations are therefore expected to be as safe as the single events, the previously assessed maize MON 89034 9 NK603 and maize MON 87427 9 MON 89034 9 NK603. Since the post-market environmental monitoring plan for the three-event stack maize does not include any provisions for the two subcombinations not previously assessed, the GMO Panel recommended the applicant to revise the plan accordingly

Technical Note on the quality of DNA sequencing for the molecular characterisation of genetically modified plants

As part of the risk assessment (RA) requirements for genetically modified (GM) plants, according to Regulation (EU) No 503/2013 and the EFSA guidance on the RA of food and feed from GM plants (EFSA GMO Panel, 2011), applicants need to perform a molecular characterisation of the DNA sequences inserted in the GM plant genome. The European Commission has mandated EFSA to develop a technical note to the applicants on, and checking of, the quality of the methodology, analysis and reporting covering complete sequencing of the insert and flanking regions, insertion site analysis of the GM event, and generational stability and integrity. This Technical Note puts together requirements and recommendations for when DNA sequencing is part of the molecular characterisation of GM plants, in particular for the characterisation of the inserted genetic material at each insertion site and flanking regions, the determination of the copy number of all detectable inserts, and the analysis of the genetic stability of the inserts, when addressed by Sanger sequencing or NGS. This document reflects the current knowledge in scientific‐technical methods for generating and verifying, in a standardised manner, DNA sequencing data in the context of RA of GM plants. From 1 October 2018, this Technical Note will replace the JRC guideline of 2016 (updated April 2017) related to the verification and quality assessment of the sequencing of the insert(s) and flanking regions. It does not take into consideration the verification and validation of the detection method which remains under the remit of the JRC