Testable uniqueness conditions for empirical assessment of undersampling levels in total variation-regularized X-ray CT

We study recoverability in fan-beam computed tomography (CT) with sparsity and total variation priors: how many underdetermined linear measurements suffice for recovering images of given sparsity? Results from compressed sensing (CS) establish such conditions for, e.g., random measurements, but not for CT. Recoverability is typically tested by checking whether a computed solution recovers the original. This approach cannot guarantee solution uniqueness and the recoverability decision therefore depends on the optimization algorithm. We propose new computational methods to test recoverability by verifying solution uniqueness conditions. Using both reconstruction and uniqueness testing we empirically study the number of CT measurements sufficient for recovery on new classes of sparse test images. We demonstrate an average-case relation between sparsity and sufficient sampling and observe a sharp phase transition as known from CS, but never established for CT. In addition to assessing recoverability more reliably, we show that uniqueness tests are often the faster option.Comment: 18 pages, 7 figures, submitte

Isoquinolinequinone N-oxides as anticancer agents effective against drug resistant cell lines

The isoquinolinequinone (IQQ) pharmacophore is a privileged framework in known cytotoxic natural product families, caulibugulones and mansouramycins. Exploiting both families as a chemical starting point, we report on the structured development of an IQQ N-oxide anticancer framework which exhibits growth inhibition in the nM range across melanoma, ovarian and leukaemia cancer cell lines. A new lead compound (16, R6 = benzyl, R7 = H) exhibits nM GI50 values against 31/57 human tumour cell lines screened as part of the NCI60 panel and shows activity against doxorubicin resistant tumour cell lines. An electrochemical study highlights a correlation between electropositivity of the IQQ N-oxide framework and cytotoxicity. Adduct binding to sulfur based biological nucleophiles glutathione and cysteine was observed in vitro. This new framework possesses significant anticancer potential

Pseudocholinesterase as a biomarker for untreated Wilson's disease

The aim of this study was to demonstrate that pseudocholinesterase (CHE) serum level is a useful diagnostic biomarker for untreated Wilson's disease (WD). Between 2013 and 2019, about 75 patients were referred to the outpatient department of the University of Düsseldorf with suspected Wilson's disease. In 31 patients with suspected Wilson's disease (WD-SUS-group), WD was excluded by means of investigations other than analysis of blood and urine. A total of 27 parameters of blood and urine in these 31 patients were compared to those of 20 de novo patients with manifest WD (WD-DEF-group), which parameter showed the highest significance level of difference between the WD-DEF-group and the WD-SUS-group. Thereafter, receiver operating characteristics (ROC-curves) were analyzed to evaluate which parameter showed the largest area under the curve (AUC) to detect WD. Finally, a logistic regression analysis was performed to analyze which combination of parameters allowed the best classification of the 51 patients either into the WD-DEF-group or into the WD-SUS-group. CHE showed the highest significance level for a difference between the WD-DEF- and WD-SUS-group, had the highest AUC, and, in combination with ceruloplasmin, allowed 100% correct classification. Without CHE, no other combination of parameters reached this level of correct classification. After the initiation of treatment, which regularly results in an improvement in CHE, the high diagnostic accuracy of this biomarker was lost. Cholinesterase turns out to be an excellent biomarker for differentiation between untreated de novo patients with manifest WD and heterozygotic gene carriers

Using Entropy Maximization to Understand the Determinants of Structural Dynamics beyond Native Contact Topology

Comparison of elastic network model predictions with experimental data has provided important insights on the dominant role of the network of inter-residue contacts in defining the global dynamics of proteins. Most of these studies have focused on interpreting the mean-square fluctuations of residues, or deriving the most collective, or softest, modes of motions that are known to be insensitive to structural and energetic details. However, with increasing structural data, we are in a position to perform a more critical assessment of the structure-dynamics relations in proteins, and gain a deeper understanding of the major determinants of not only the mean-square fluctuations and lowest frequency modes, but the covariance or the cross-correlations between residue fluctuations and the shapes of higher modes. A systematic study of a large set of NMR-determined proteins is analyzed using a novel method based on entropy maximization to demonstrate that the next level of refinement in the elastic network model description of proteins ought to take into consideration properties such as contact order (or sequential separation between contacting residues) and the secondary structure types of the interacting residues, whereas the types of amino acids do not play a critical role. Most importantly, an optimal description of observed cross-correlations requires the inclusion of destabilizing, as opposed to exclusively stabilizing, interactions, stipulating the functional significance of local frustration in imparting native-like dynamics. This study provides us with a deeper understanding of the structural basis of experimentally observed behavior, and opens the way to the development of more accurate models for exploring protein dynamics

Climate drives the geography of marine consumption by changing predator communities

Este artículo contiene 7 páginas, 3 figuras, 1 tabla.The global distribution of primary production and consumption by humans (fisheries) is well-documented, but we have no map linking the central ecological process of consumption within food webs to temperature and other ecological drivers. Using standardized assays that span 105° of latitude on four continents, we show that rates of bait consumption by generalist predators in shallow marine ecosystems are tightly linked to both temperature and the composition of consumer assemblages. Unexpectedly, rates of consumption peaked at midlatitudes (25 to 35°) in both Northern and Southern Hemispheres across both seagrass and unvegetated sediment habitats. This pattern contrasts with terrestrial systems, where biotic interactions reportedly weaken away from the equator, but it parallels an emerging pattern of a subtropical peak in marine biodiversity. The higher consumption at midlatitudes was closely related to the type of consumers present, which explained rates of consumption better than consumer density, biomass, species diversity, or habitat. Indeed, the apparent effect of temperature on consumption was mostly driven by temperature-associated turnover in consumer community composition. Our findings reinforce the key influence of climate warming on altered species composition and highlight its implications for the functioning of Earth’s ecosystems.We acknowledge funding from the Smithsonian Institution and the Tula Foundation.Peer reviewe

Synthesis and evaluation of quinoline-5,8-diones and isoquinoline-5,8-diones as anticancer agents

This thesis outlines the design and synthesis of novel chemical routes towards a nascent class of functionalised quinoline-5,8-diones and isoquinoline-5,8-diones. The structured approach adopted is predicted to lead to advancements in the two frameworks, expanding the structural diversity of both the quinoline-5,8-diones and isoquinoline-5,8-diones families with bioactivity evaluation. Chapters 4, 5, 6, 7 and 8 are focused on the development and biological screening of the quinoline-5,8-dione library; Chapters 9 and 10 construct and evaluate the isoquinoline-5,8-dione library. Initial route development furnished versatile quinoline-5,8-dione and isoquinoline-5,8-dione frameworks in high yields employing robust methodologies. Synthetic exploration into the regioselective addition of carbon, nitrogen, and oxygen to the quinone moiety was investigated yielding 85 novel analogues. The use of directing group strategies, Lewis acid coordination and blocking groups provided access to regioselective reactions. Antimicrobial screening was undertaken in collaboration with the Community for Open Antimicrobial Drug Discovery (CO-ADD). The quinoline-5,8-dione library exhibited potent antibacterial and antifungal MIC values, outperforming known antimicrobial agents’ vancomycin and fluconazole, respectively. Preliminary in vitro toxicology studies revealed that all analogues are not haemolytic, and multiple analogues are not cytotoxic to the human kidney cell line HEK293. Anticancer screening was undertaken in in collaboration with the National Cancer Institute (NCI) in Maryland US. Although the quinoline-5,8-dione library were not effective anticancer agents, the isoquinoline-5,8-dione family possessed nanomolar anticancer GI50 values across multiple human tumour cell lines. Multidrug resistant ovarian cancer cell lines NCI/ADR-RES and IGROV 1 were responsive to the series in the nanomolar range. Lead isoquinoline-5,8-dione N-oxide 10.21 exhibits a mean GI50 of 0.21 μM across 60 cancer cell lines. Extended mechanistic work incorporated molecular modelling, electrochemical assays and COMPARE analysis to rationalise the potent in vitro bioactivity and identities future biological targets

Divalent metal ions promote the formation of the 5′-splice site recognition complex in a self-splicing group II intron

Group II introns are ribozymes occurring in genes of plants, fungi, lower eukaryotes, and bacteria. These large RNA molecular machines, ranging in length from 400 to 2500 nucleotides, are able to catalyze their own excision from pre-mRNA, as well as to reinsert themselves into RNA or sometimes even DNA. The intronic domain 1 contains two sequences (exon binding sites 1 and 2, EBS1 and EBS2) that pair with their complementary regions at the 3'-end of the 5'-exon (intron binding sites 1 and 2, IBS1 and IBS2) such defining the 5'-splice site. The correct recognition of the 5'-splice site stands at the beginning of the two steps of splicing and is thus crucial for catalysis. It is known that metal ions play an important role in folding and catalysis of ribozymes in general. Here, we characterize the specific metal ion requirements for the formation of the 5'-splice site recognition complex from the mitochondrial yeast group II intron Sc.ai5gamma. Circular dichroism studies reveal that the formation of the EBS1.IBS1 duplex does not necessarily require divalent metal ions, as large amounts of monovalent metal ions also promote the duplex, albeit at a 5000 times higher concentration. Nevertheless, micromolar amounts of divalent metal ions, e.g. Mg2+ or Cd2+, strongly promote the formation of the 5'-splice site. These observations illustrate that a high charge density independent of the nature of the ion is needed for binding EBS1 to IBS1, but divalent metal ions are presumably the better players

Differences in the time course of recovery from brain and liver dysfunction in conventional long-term treatment of Wilson disease

BACKGROUND: The aim of this study was to demonstrate that both neurological and hepatic symptoms respond to copper chelation therapy in Wilson disease (WD). However, the time course of their recovery is different. METHODS: Eighteen patients with neurological WD from a single specialized center who had been listed for liver transplantation during the last ten years and two newly diagnosed homozygous twins were recruited for this retrospective study. The mean duration of conventional treatment was 7.3 years (range: 0.25 to 36.2 years). A custom Wilson disease score with seven motor items, three non-motor items, and 33 biochemical parameters of the blood and urine, as well as the MELD score, was determined at various checkup visits during treatment. These data were extracted from the charts of the patients. RESULTS: Treatment was initiated with severity-dependent doses (≥900 mg) of D-penicillamine (DPA) or triethylene-tetramin-dihydrochloride (TRIEN). The motor score improved in 10 and remained constant in 8 patients. Worsening of neurological symptoms was observed only in two patients who developed comorbidities (myasthenia gravis or hemispheric stroke). The neurological symptoms continuously improved over the years until the majority of patients became only mildly affected. In contrast to this slow recovery of the neurological symptoms, the MELD score and liver enzymes had already started to improve after 1 month and rapidly improved over the next 6 months in 19 patients. The cholinesterase levels continued to increase significantly (p < 0.0074) even further. One patient whose MELD score indicated further progression of liver disease received an orthotopic liver transplantation 3 months after the diagnosis of WD and the onset of DPA treatment. CONCLUSIONS: Neurological and hepatic symptoms both respond to copper chelation therapy. For patients with acute liver failure, the first 4 months are critical. This is the time span in which patients have to wait either for a donor organ or until significant improvement has occurred under conventional therapy. For patients with severe neurological symptoms, it is important that they are treated with fairly high doses over several years

Contemporary genetic structure and postglacial demographic history of the black scorpionfish, Scorpaena porcus, in the Mediterranean and the Black Seas

Understanding the distribution of genetic diversity in the light of past demographic events linked with climatic shifts will help to forecast evolutionary trajectories of ecosystems within the current context of climate change. In this study, mitochondrial sequences and microsatellite loci were analysed using traditional population genetic approaches together with Bayesian dating and the more recent approximate Bayesian computation scenario testing. The genetic structure and demographic history of a commercial fish, the black scorpionfish, Scorpaena porcus, was investigated throughout the Mediterranean and Black Seas. The results suggest that the species recently underwent population expansions, in both seas, likely concomitant with the warming period following the Last Glacial Maximum, 20 000 years ago. A weak contemporaneous genetic differentiation was identified between the Black Sea and the Mediterranean Sea. However, the genetic diversity was similar for populations of the two seas, suggesting a high number of colonizers entered the Black Sea during the interglacial period and/or the presence of a refugial population in the Black Sea during the glacial period. Finally, within seas, an east/west genetic differentiation in the Adriatic seems to prevail, whereas the Black Sea does not show any structured spatial genetic pattern of its population. Overall, these results suggest that the Black Sea is not that isolated from the Mediterranean, and both seas revealed similar evolutionary patterns related to climate change and changes in sea level