Makespan Scheduling of Unit Jobs with Precedence Constraints in O(1.995n)O(1.995^n) time

In a classical scheduling problem, we are given a set of $n$ jobs of unitlength along with precedence constraints and the goal is to find a schedule ofthese jobs on $m$ identical machines that minimizes the makespan. This problemis well-known to be NP-hard for an unbounded number of machines. Using standard3-field notation, it is known as $P|\text{prec}, p_j=1|C_{\max}$. We present an algorithm for this problem that runs in $O(1.995^n)$ time.Before our work, even for $m=3$ machines the best known algorithms ran in$O^\ast(2^n)$ time. In contrast, our algorithm works when the number ofmachines $m$ is unbounded. A crucial ingredient of our approach is an algorithmwith a runtime that is only single-exponential in the vertex cover of thecomparability graph of the precedence constraint graph. This heavily relies oninsights from a classical result by Dolev and Warmuth (Journal of Algorithms1984) for precedence graphs without long chains.<br

Analysis of Released Circulating Tumor Cells During Surgery for Non-Small Cell Lung Cancer:are they what they appear to be?

Purpose: Tumor cells from patients with lung cancer are expelled from the primary tumor into the blood, but difficult to detect in the peripheral circulation. We studied the release of circulating tumor cells (CTCs) during surgery to test the hypothesis that CTC counts are influenced by hemodynamic changes (caused by surgical approach) and manipulation. Experimental Design: Patients undergoing video-assisted thoracic surgery (VATS) or open surgery for (suspected) primary lung cancer were included. Blood samples were taken before surgery (T0) from the radial artery (RA), from both the RA and pulmonary vein (PV) when the PV was located (T1) and when either the pulmonary artery (T2 open) or the PV (T2VATS) was dissected. The CTCs were enumerated using the CellSearch system. Single-cell whole-genome sequencing was performed on isolated CTCs for aneuploidy. Results: CTCs were detected in 58 of 138 samples (42%) of 31 patients. CTCs were more often detected in the PV (70%) compared with the RA (22%, P <0.01) and in higher counts ( P <0.01). After surgery, the RA but not the PV showed less often CTCs (P = 0.02). Type of surgery did not influence CTC release. Only six of 496 isolated CTCs showed aneuploidy, despite matched primary tumor tissue being aneuploid. Euploid so-called CTCs had a different morphology than aneuploid. Conclusions: CTCs defined by CellSearch were identified more often and in higher numbers in the PV compared with the RA, suggesting central clearance. The majority of cells in the PV were normal epithelial cells and outnumbered CTCs. Release of CTCs was not influenced by surgical approach

Characterization of ERG, AR and PTEN gene status in circulating tumor cells from patients with castration-resistant prostate cancer

Hormone-driven expression of the ERG oncogene after fusion with TMPRSS2 occurs in 30% to 70% of therapy-naive prostate cancers. Its relevance in castration-resistant prostate cancer (CRPC) remains controversial as ERG is not expressed in some TMPRSS2-ERG androgen-independent xenograft models. However, unlike these models, CRPC patients have an increasing prostate-specific antigen, indicating active androgen receptor signaling. Here, we collected blood every month from 89 patients (54 chemotherapy-naive patients and 35 docetaxel-treated patients) treated in phase I/phase II clinical trials of an orally available, highly specific CYP17 inhibitor, abiraterone acetate, that ablates the synthesis of androgens and estrogens that drive TMPRSS2-ERG fusions. We isolated circulating tumor cells (CTC) by anti-epithelial cell adhesion molecule immunomagnetic selection followed by cytokeratin and CD45 immunofluorescence and 4',6diamidino-2-phenylindole staining. We used multicolor fluorescence in situ hybridization to show that CRPC CTCs, metastases, and prostate tissue invariably had the same ERG gene status as therapy-naive tumors (n = 31). We then used quantitative reverse transcription-PCR to show that ERG expression was maintained in CRPC. We also observed homogeneity in ERG gene rearrangement status in CTCs (n = 48) in contrast to significant heterogeneity of AR copy number gain and PTEN loss, suggesting that rearrangement of ERG may be an earlier event in prostate carcinogenesis. We finally report a significant association between ERG rearrangements in therapy-naive tumors, CRPCs, and CTCs and magnitude of prostate-specific antigen decline (P = 0.007) in CRPC patients treated with abiraterone acetate. These data confirm that CTCs are malignant in origin and indicate that hormone-regulated expressio

Formalin-Fixed, Paraffin-Embedded–Targeted Locus Capture:A Next-Generation Sequencing Technology for Accurate DNA-Based Gene Fusion Detection in Bone and Soft Tissue Tumors

Chromosomal rearrangements are important drivers in cancer, and their robust detection is essential for diagnosis, prognosis, and treatment selection, particularly for bone and soft tissue tumors. Current diagnostic methods are hindered by limitations, including difficulties with multiplexing targets and poor quality of RNA. A novel targeted DNA-based next-generation sequencing method, formalin-fixed, paraffin-embedded–targeted locus capture (FFPE-TLC), has shown advantages over current diagnostic methods when applied on FFPE lymphomas, including the ability to detect novel rearrangements. We evaluated the utility of FFPE-TLC in bone and soft tissue tumor diagnostics. FFPE-TLC sequencing was successfully applied on noncalcified and decalcified FFPE samples (n = 44) and control samples (n = 19). In total, 58 rearrangements were identified in 40 FFPE tumor samples, including three previously negative samples, and none was identified in the FFPE control samples. In all five discordant cases, FFPE-TLC could identify gene fusions where other methods had failed due to either detection limits or poor sample quality. FFPE-TLC achieved a high specificity and sensitivity (no false positives and negatives). These results indicate that FFPE-TLC is applicable in cancer diagnostics to simultaneously analyze many genes for their involvement in gene fusions. Similar to the observation in lymphomas, FFPE-TLC is a good DNA-based alternative to the conventional methods for detection of rearrangements in bone and soft tissue tumors.</p

Catalytic Transformations of Alkynes via Ruthenium Vinylidene and Allenylidene Intermediates

NOTICE: This is the peer reviewed version of the following book chapter: Varela J. A., González-Rodríguez C., Saá C. (2014). Catalytic Transformations of Alkynes via Ruthenium Vinylidene and Allenylidene Intermediates. In: Dixneuf P., Bruneau C. (eds) Ruthenium in Catalysis. Topics in Organometallic Chemistry, vol 48, pp. 237-287. Springer, Cham. [doi: 10.1007/3418_2014_81]. This article may be used for non-commercial purposes in accordance with Springer Verlag Terms and Conditions for self-archiving.Vinylidenes are high-energy tautomers of terminal alkynes and they can be stabilized by coordination with transition metals. The resulting metal-vinylidene species have interesting chemical properties that make their reactivity different to that of the free and metal π-coordinated alkynes: the carbon α to the metal is electrophilic whereas the β carbon is nucleophilic. Ruthenium is one of the most commonly used transition metals to stabilize vinylidenes and the resulting species can undergo a range of useful transformations. The most remarkable transformations are the regioselective anti-Markovnikov addition of different nucleophiles to catalytic ruthenium vinylidenes and the participation of the π system of catalytic ruthenium vinylidenes in pericyclic reactions. Ruthenium vinylidenes have also been employed as precatalysts in ring closing metathesis (RCM) or ring opening metathesis polymerization (ROMP). Allenylidenes could be considered as divalent radicals derived from allenes. In a similar way to vinylidenes, allenylidenes can be stabilized by coordination with transition metals and again ruthenium is one of the most widely used metals. Metalallenylidene complexes can be easily obtained from terminal propargylic alcohols by dehydration of the initially formed metal-hydroxyvinylidenes, in which the reactivity of these metal complexes is based on the electrophilic nature of Cα and Cγ, while Cβ is nucleophilic. Catalytic processes based on nucleophilic additions and pericyclic reactions involving the π system of ruthenium allenylidenes afford interesting new structures with high selectivity and atom economy

Targeted locus amplification to develop robust patient-specific assays for liquid biopsies in pediatric solid tumors

BackgroundLiquid biopsies combine minimally invasive sample collection with sensitive detection of residual disease. Pediatric malignancies harbor tumor-driving copy number alterations or fusion genes, rather than recurrent point mutations. These regions contain tumor-specific DNA breakpoint sequences. We investigated the feasibility to use these breakpoints to design patient-specific markers to detect tumor-derived cell-free DNA (cfDNA) in plasma from patients with pediatric solid tumors.Materials and methodsRegions of interest (ROI) were identified through standard clinical diagnostic pipelines, using SNP array for CNAs, and FISH or RT-qPCR for fusion genes. Using targeted locus amplification (TLA) on tumor organoids grown from tumor material or targeted locus capture (TLC) on FFPE material, ROI-specific primers and probes were designed, which were used to design droplet digital PCR (ddPCR) assays. cfDNA from patient plasma at diagnosis and during therapy was analyzed.ResultsTLA was performed on material from 2 rhabdomyosarcoma, 1 Ewing sarcoma and 3 neuroblastoma. FFPE-TLC was performed on 8 neuroblastoma tumors. For all patients, at least one patient-specific ddPCR was successfully designed and in all diagnostic plasma samples the patient-specific markers were detected. In the rhabdomyosarcoma and Ewing sarcoma patients, all samples after start of therapy were negative. In neuroblastoma patients, presence of patient-specific markers in cfDNA tracked tumor burden, decreasing during induction therapy, disappearing at complete remission and re-appearing at relapse.ConclusionWe demonstrate the feasibility to determine tumor-specific breakpoints using TLA/TLC in different pediatric solid tumors and use these for analysis of cfDNA from plasma. Considering the high prevalence of CNAs and fusion genes in pediatric solid tumors, this approach holds great promise and deserves further study in a larger cohort with standardized plasma sampling protocols

Immunomagnetic separation technologies

The largest difficulty one faces in the development of technology for detection of circulating tumor cells (CTCs) is whether or not tumor cells are present in the blood and at what frequency. Although the introduction of the validated CellSearch system for CTC enumeration has facilitated CTC research the question remains whether CTC are missed or whether the CTC that are reported are indeed clinically relevant. To fulfill the promise of CTC as a real-time liquid biopsy they will need to be present in the blood volume tested and need to be isolated without losing the ability to test the presence of treatment targets. To characterize a sufficiently large number of CTCs in the majority of cancer patients the volume of blood needed is simply too large to process without enrichment prior to detection. Here, we review the detection of CTCs by flow cytometry and fluorescence microscopy with and without immunomagnetic enrichment

Significant and Sustained Antitumor Activity in Post-Docetaxel, Castration-Resistant Prostate Cancer With the CYP17 Inhibitor Abiraterone Acetate

Purpose: The principal objective of this trial was to evaluate the antitumor activity of abiraterone acetate, an oral, specific, irreversible inhibitor of CYP17 in docetaxel-treated patients with castration-resistant prostate cancer (CRPC). Patients and Methods: In this multicenter, two-stage, phase II study, abiraterone acetate 1,000 mg was administered once daily continuously. The primary end point was achievement of a prostate-specific antigen (PSA) decline of ≥ 50% in at least seven of 35 patients. Per an attained phase II design, more than 35 patients could be enrolled if the primary end point was met. Secondary objectives included: PSA declines of ≥ 30% and ≥ 90%; rate of RECIST (Response Evaluation Criteria in Solid Tumors) responses and duration on study; time to PSA progression; safety and tolerability; and circulating tumor cell (CTC) enumeration. Results: Docetaxel-treated patients with CRPC (N = 47) were enrolled. PSA declines of ≥ 30%, ≥ 50% and ≥ 90% were seen in 68% (32 of 47), 51% (24 of 47), and 15% (seven of 47) of patients, respectively. Partial responses (by RECIST) were reported in eight (27%) of 30 patients with measurable disease. Median time to PSA progression was 169 days (95% CI, 113 to 281 days). The median number of weeks on study was 24, and 12 (25.5%) of 47 patients remained on study ≥ 48 weeks. CTCs were enumerated in 34 patients; 27 (79%) of 34 patients had at least five CTCs at baseline. Eleven (41%) of 27 patients had a decline from at least five to less than 5 CTCs, and 18 (67%) of 27 had a ≥ 30% decline in CTCs after starting treatment with abiraterone acetate. Abiraterone acetate was well tolerated. Conclusion: Abiraterone acetate has significant antitumor activity in post-docetaxel patients with CRPC. Randomized, phase III trials of abiraterone acetate are underway to define the future role of this agent