`Third' Quantization of Vacuum Einstein Gravity and Free Yang-Mills Theories

Based on the algebraico-categorical (:sheaf-theoretic and sheaf cohomological) conceptual and technical machinery of Abstract Differential Geometry, a new, genuinely background spacetime manifold independent, field quantization scenario for vacuum Einstein gravity and free Yang-Mills theories is introduced. The scheme is coined `third quantization' and, although it formally appears to follow a canonical route, it is fully covariant, because it is an expressly functorial `procedure'. Various current and future Quantum Gravity research issues are discussed under the light of 3rd-quantization. A postscript gives a brief account of this author's personal encounters with Rafael Sorkin and his work.Comment: 43 pages; latest version contributed to a fest-volume celebrating Rafael Sorkin's 60th birthday (Erratum: in earlier versions I had wrongly written that the Editor for this volume is Daniele Oriti, with CUP as publisher. I apologize for the mistake.

meCLICK-Seq, a Substrate-Hijacking and RNA Degradation Strategy for the Study of RNA Methylation.

The fates of RNA species in a cell are controlled by ribonucleases, which degrade them by exploiting the universal structural 2'-OH group. This phenomenon plays a key role in numerous transformative technologies, for example, RNA interference and CRISPR/Cas13-based RNA editing systems. These approaches, however, are genetic or oligomer-based and so have inherent limitations. This has led to interest in the development of small molecules capable of degrading nucleic acids in a targeted manner. Here we describe click-degraders, small molecules that can be covalently attached to RNA species through click-chemistry and can degrade them, that are akin to ribonucleases. By using these molecules, we have developed the meCLICK-Seq (methylation CLICK-degradation Sequencing) a method to identify RNA modification substrates with high resolution at intronic and intergenic regions. The method hijacks RNA methyltransferase activity to introduce an alkyne, instead of a methyl, moiety on RNA. Subsequent copper(I)-catalyzed azide-alkyne cycloaddition reaction with the click-degrader leads to RNA cleavage and degradation exploiting a mechanism used by endogenous ribonucleases. Focusing on N6-methyladenosine (m6A), meCLICK-Seq identifies methylated transcripts, determines RNA methylase specificity, and reliably maps modification sites in intronic and intergenic regions. Importantly, we show that METTL16 deposits m6A to intronic polyadenylation (IPA) sites, which suggests a potential role for METTL16 in IPA and, in turn, splicing. Unlike other methods, the readout of meCLICK-Seq is depletion, not enrichment, of modified RNA species, which allows a comprehensive and dynamic study of RNA modifications throughout the transcriptome, including regions of low abundance. The click-degraders are highly modular and so may be exploited to study any RNA modification and design new technologies that rely on RNA degradation.UKRI (BBSRC DTP scholarships to S.M. and H.K.C) and the Jardine Foundation and Cambridge Trust (PhD scholarship to M.E.H.)

A huge intraductal papillary mucinous carcinoma of the bile duct treated by right trisectionectomy with caudate lobectomy

<p>Abstract</p> <p>Background</p> <p>Because intraductal papillary mucinous neoplasm of the bile duct (IPMN-B) is believed to show a better clinical course than non-papillary biliary neoplasms, it is important to make a precise diagnosis and to perform complete surgical resection.</p> <p>Case presentation</p> <p>We herein report a case of malignant IPMN-B treated by right trisectionectomy with caudate lobectomy and extrahepatic bile duct resection. Radiologic images showed marked dilatation of the left medial sectional bile duct (B4) resulting in a bulky cystic mass with multiple internal papillary projections. Duodenal endoscopic examination demonstrated very patulous ampullary orifice with mucin expulsion and endoscopic retrograde cholangiogram confirmed marked cystic dilatation of B4 with luminal filling defects. These findings suggested IPMN-B with malignancy potential. The functional volume of the left lateral section was estimated to be 45%. A planned extensive surgery was successfully performed. The remnant bile ducts were also dilated but had no macroscopic intraluminal tumorous lesion. The histopathological examination yielded the diagnosis of mucin-producing oncocytic intraductal papillary carcinoma of the bile duct with poorly differentiated carcinomas showing neuroendocrine differentiation. The tumor was 14.0 × 13.0 cm-sized and revealed no stromal invasiveness. Resection margins of the proximal bile duct and hepatic parenchyma were free of tumor cell. The patient showed no postoperative complication and was discharged on 10^thpostoperative date. He has been regularly followed at outpatient department with no evidence of recurrence.</p> <p>Conclusion</p> <p>Considering a favorable prognosis of IPMN-B compared to non-papillary biliary neoplasms, this tumor can be a good indication for aggressive surgical resection regardless of its tumor size.</p

The clinical significance of soluble E-cadherin in nonsmall cell lung cancer

Aim: Aberrant expression of the epithelial transmembrane adhesion molecule E-cadherin (E-cad) has been associated with many human malignancies. In the present study the clinical significance of serum levels of soluble E-cadherin (sE-cad) in newly diagnosed patients with non small cell lung cancer (NSCLC) was investigated. Material and Methods: An enzyme linked immunospecific assay (ELISA) to determine the circulating levels of sE-cad in 20 newly diagnosed patients with NSCLC as well as in 29 healthy volunteers (control group) was used. Results: NSCLC patients exerted increased circulating levels of sE-cad compared with individuals of the control group (p < 0.001). An association was also detected between serum sE-cad levels and the development of distant metastases. On the contrary, no statistically significant correlation could be established with histological type, gender and smoking habits. Patients with increased sE-cad levels at diagnosis had worser outcome, although multivariate analysis failed to demonstrate that sE-cad levels represent an independent prognostic factor of survival. Conclusion: Our data suggest that E-cad plays a role in the pathogenesis of NSCLC. sE-cad levels may be further studied as a potential prognostic biomarker.Цель: нарушения экспрессии трансмембранной молекулы адгезии эпителия Е-кадерина (Е-cad) ассоциированы со злокачеcтвенными новообразованиями у человека. Цель исследования — оценить клиническое значение содержания секретируемого Е-кадерина (sE-cad) в сыворотке крови больных с диагнозом немелкоклеточного рака легкого (НМКРЛ). Материалы и методы: для определения уровня циркулирующего sE-cad в сыворотке крови 20 больных с НМКРЛ и 29 здоровых доноров применили метод ELISA. Результаты: у больных с НМКРЛ выявлено значительное повышение содержания циркулирующего sE-cad в сыворотке крови по сравнению с таковым в контрольной группе (p < 0,001). Установлена связь между уровнем sE-cad в сыворотке крови и появлением периферических метастазов. Не выявлено статистически достоверной корреляции между гистологическим типом опухоли, полом больного и курением. У пациентов с повышенным содержанием sE-cad наблюдалась тенеденция к худшему исходу заболевания, хотя результаты статистического анализа не подтвердили прогностического значения sE-cad. Выводы: полученные данные позволили предположить, что E-cad участвует в патогенезе НМКРЛ. Оценка содержания sE-cad в качестве прогностического биомаркера нуждается в дальнейшем исследовании

High-dimensional wave atoms and compression of seismic datasets

Wave atoms are a low-redundancy alternative to curvelets, suitable for high-dimensional seismic data processing. This abstract extends the wave atom orthobasis construction to 3D, 4D, and 5D Cartesian arrays, and parallelizes it in a shared-memory environment. An implementation of the algorithm for NVIDIA CUDA capable graphics processing units (GPU) is also developed to accelerate computation for 2D and 3D data. The new transforms are benchmarked against the Fourier transform for compression of data generated from synthetic 2D and 3D acoustic models.National Science Foundation (U.S.); Alfred P. Sloan Foundatio

Transition Radiation Spectra of Electrons from 1 to 10 GeV/c in Regular and Irregular Radiators

We present measurements of the spectral distribution of transition radiation generated by electrons of momentum 1 to 10 GeV/c in different radiator types. We investigate periodic foil radiators and irregular foam and fiber materials. The transition radiation photons are detected by prototypes of the drift chambers to be used in the Transition Radiation Detector (TRD) of the ALICE experiment at CERN, which are filled with a Xe, CO2 (15 %) mixture. The measurements are compared to simulations in order to enhance the quantitative understanding of transition radiation production, in particular the momentum dependence of the transition radiation yield.Comment: 18 pages, 15 figures, submitted to Nucl. Instr. Meth. Phys. Res.

Zoledronic Acid Preserves Bone Structure and Increases Survival but Does Not Limit Tumour Incidence in a Prostate Cancer Bone Metastasis Model

Background The bisphosphonate, zoledronic acid (ZOL), can inhibit osteoclasts leading to decreased osteoclastogenesis and osteoclast activity in bone. Here, we used a mixed osteolytic/osteoblastic murine model of bone-metastatic prostate cancer, RM1(BM), to determine how inhibiting osteolysis with ZOL affects the ability of these cells to establish metastases in bone, the integrity of the tumour-bearing bones and the survival of the tumour-bearing mice. Methods The model involves intracardiac injection for arterial dissemination of the RM1(BM) cells in C57BL/6 mice. ZOL treatment was given via subcutaneous injections on days 0, 4, 8 and 12, at 20 and 100 µg/kg doses. Bone integrity was assessed by micro-computed tomography and histology with comparison to untreated mice. The osteoclast and osteoblast activity was determined by measuring serum tartrate-resistant acid phosphatase 5b (TRAP 5b) and osteocalcin, respectively. Mice were euthanased according to predetermined criteria and survival was assessed using Kaplan Meier plots. Findings Micro-CT and histological analysis showed that treatment of mice with ZOL from the day of intracardiac injection of RM1(BM) cells inhibited tumour-induced bone lysis, maintained bone volume and reduced the calcification of tumour-induced endochondral osteoid material. ZOL treatment also led to a decreased serum osteocalcin and TRAP 5b levels. Additionally, treated mice showed increased survival compared to vehicle treated controls. However, ZOL treatment did not inhibit the cells ability to metastasise to bone as the number of bone-metastases was similar in both treated and untreated mice. Conclusions ZOL treatment provided significant benefits for maintaining the integrity of tumour-bearing bones and increased the survival of tumour bearing mice, though it did not prevent establishment of bone-metastases in this model. From the mechanistic view, these observations confirm that tumour-induced bone lysis is not a requirement for establishment of these bone tumours

Promiscuous targeting of bromodomains by bromosporine identifies BET proteins as master regulators of primary transcription response in leukemia

Bromodomains (BRDs) have emerged as compelling targets for cancer therapy. The development of selective and potent BET (bromo and extra-terminal) inhibitors and their significant activity in diverse tumor models have rapidly translated into clinical studies and have motivated drug development efforts targeting non-BET BRDs. However, the complex multidomain/subunit architecture of BRD protein complexes complicates predictions of the consequences of their pharmacological targeting. To address this issue, we developed a promiscuous BRD inhibitor [bromosporine (BSP)] that broadly targets BRDs (including BETs) with nanomolar affinity, creating a tool for the identification of cellular processes and diseases where BRDs have a regulatory function. As a proof of principle, we studied the effects of BSP on leukemic cell lines known to be sensitive to BET inhibition and found, as expected, strong antiproliferative activity. Comparison of the modulation of transcriptional profiles by BSP after a short exposure to the inhibitor resulted in a BET inhibitor signature but no significant additional changes in transcription that could account for inhibition of other BRDs. Thus, nonselective targeting of BRDs identified BETs, but not other BRDs, as master regulators of context-dependent primary transcription response.The Structural Genomics Consortium is a registered charity (no. 1097737) that receives funds from AbbVie, Bayer Pharma AG, Boehringer Ingelheim, Canada Foundation for Innovation, Eshelman Institute for Innovation, Genome Canada, Innovative Medicines Initiative (EU/EFPIA) (ULTRA-DD grant 115766), Janssen, Merck & Co., Novartis Pharma AG, Ontario Ministry of Economic Development and Innovation, Pfizer, São Paulo Research Foundation (FAPESP), Takeda, and Wellcome Trust (092809/Z/10/Z). P.F., S.P., and C.-Y.W. were supported by a Wellcome Career Development Fellowship (095751/Z/11/Z). A.-C.G. is the Canada Research Chair in Functional Proteomics and the Lea Reichmann Chair in Cancer Proteomics and was supported by the Canadian Institutes of Health Research (foundation grant FDN143301). J.-P.L. was supported by a Cancer Research Society (Canada) Scholarship for the Next Generation of Scientists