326 research outputs found
The Direct and Enantioselective Organocatalytic α-Oxidation of Aldehydes
The first direct enantioselective catalytic α-oxidation of carbonyls has been accomplished. The use of enamine catalysis has provided a new organocatalytic strategy for the enantioselective oxyamination of aldehydes, to generate α-oxyaldehydes, important chiral synthons for natural product and medicinal agent synthesis. The use of l-proline as the asymmetric catalyst has been found to mediate the oxidation of a large variety of aldehyde substrates with nitrosobenzene serving as the electrophilic oxidant. A diverse spectrum of aldehyde substrates can also be accommodated in this new organocatalytic transformation. While catalyst quantities of 2 mol % were generally employed in this study, successful oxidations conducted using catalyst loadings as low as 0.5 mol % are described
Efficient Certified Resolution Proof Checking
We present a novel propositional proof tracing format that eliminates complex
processing, thus enabling efficient (formal) proof checking. The benefits of
this format are demonstrated by implementing a proof checker in C, which
outperforms a state-of-the-art checker by two orders of magnitude. We then
formalize the theory underlying propositional proof checking in Coq, and
extract a correct-by-construction proof checker for our format from the
formalization. An empirical evaluation using 280 unsatisfiable instances from
the 2015 and 2016 SAT competitions shows that this certified checker usually
performs comparably to a state-of-the-art non-certified proof checker. Using
this format, we formally verify the recent 200 TB proof of the Boolean
Pythagorean Triples conjecture
Alternative splicing substantially diversifies the transcriptome during early photomorphogenesis and correlates with the energy availability in arabidopsis
Plants use light as source of energy and information to detect diurnal rhythms and seasonal changes. Sensing changing light conditions is critical to adjust plant metabolism and to initiate developmental transitions. Here we analyzed transcriptome-wide alterations in gene expression and alternative splicing (AS) of etiolated seedlings undergoing photomorphogenesis upon exposure to blue, red, or white light. Our analysis revealed massive transcriptome reprograming as reflected by differential expression of ~20% of all genes and changes in several hundred AS events. For more than 60% of all regulated AS events, light promoted the production of a presumably protein-coding variant at the expense of an mRNA with nonsense-mediated decay-triggering features. Accordingly, AS of the putative splicing factor REDUCED RED-LIGHT RESPONSES IN CRY1CRY2 BACKGROUND 1 (RRC1), previously identified as a red light signaling component, was shifted to the functional variant under light. Downstream analyses of candidate AS events pointed at a role of photoreceptor signaling only in monochromatic but not in white light. Furthermore, we demonstrated similar AS changes upon light exposure and exogenous sugar supply, with a critical involvement of kinase signaling. We propose that AS is an integration point of signaling pathways that sense and transmit information regarding the energy availability in plants
Molecular Details of Retinal Guanylyl Cyclase 1/GCAP-2 Interaction
The rod outer segment guanylyl cyclase 1 (ROS-GC1) is an essential component of photo-transduction in the retina. In the light-induced signal cascade, membrane-bound ROS-GC1 restores cGMP levels in the dark in a calcium-dependent manner. With decreasing calcium concentration in the intracellular compartment, ROS-GC1 is activated via the intracellular site by guanylyl cyclase-activating proteins (GCAP-1/-2). Presently, the exact activation mechanism is elusive. To obtain structural insights into the ROS-GC1 regulation by GCAP-2, chemical cross-linking/mass spectrometry studies using GCAP-2 and three ROS-GC1 peptides were performed in the presence and absence of calcium. The majority of cross-links were identified with the C-terminal lobe of GCAP-2 and a peptide comprising parts of ROS-GC1's catalytic domain and C-terminal extension. Consistently with the cross-linking results, surface plasmon resonance and fluorescence measurements confirmed specific binding of this ROS-GC peptide to GCAP-2 with a dissociation constant in the low micromolar range. These results imply that a region of the catalytic domain of ROS-GC1 can participate in the interaction with GCAP-2. Additional binding surfaces upstream of the catalytic domain, in particular the juxtamembrane domain, can currently not be excluded
Comprehensive vascular imaging using optical coherence tomography-based angiography and photoacoustic tomography
Studies have proven the relationship between cutaneous vasculature abnormalities and dermatological disorders, but to image vasculature noninvasively in vivo, advanced optical imaging techniques are required. In this study, we imaged a palm of a healthy volunteer and three subjects with cutaneous abnormalities with photoacoustic tomography (PAT) and optical coherence tomography with angiography extension (OCTA). Capillaries in the papillary dermis that are too small to be discerned with PAT are visualized with OCTA. From our results, we speculate that the PA signal from the palm is mostly from hemoglobin in capillaries rather than melanin, knowing that melanin concentration in volar skin is significantly smaller than that in other areas of the skin. We present for the first time OCTA images of capillaries along with the PAT images of the deeper vessels, demonstrating the complementary effective imaging depth range and the visualization capabilities of PAT and OCTA for imaging human skin in vivo. The proposed imaging system in this study could significantly improve treatment monitoring of dermatological diseases associated with cutaneous vasculature abnormalities
On Tackling the Limits of Resolution in SAT Solving
The practical success of Boolean Satisfiability (SAT) solvers stems from the
CDCL (Conflict-Driven Clause Learning) approach to SAT solving. However, from a
propositional proof complexity perspective, CDCL is no more powerful than the
resolution proof system, for which many hard examples exist. This paper
proposes a new problem transformation, which enables reducing the decision
problem for formulas in conjunctive normal form (CNF) to the problem of solving
maximum satisfiability over Horn formulas. Given the new transformation, the
paper proves a polynomial bound on the number of MaxSAT resolution steps for
pigeonhole formulas. This result is in clear contrast with earlier results on
the length of proofs of MaxSAT resolution for pigeonhole formulas. The paper
also establishes the same polynomial bound in the case of modern core-guided
MaxSAT solvers. Experimental results, obtained on CNF formulas known to be hard
for CDCL SAT solvers, show that these can be efficiently solved with modern
MaxSAT solvers
CLPM: A Cross-Linked Peptide Mapping Algorithm for Mass Spectrometric Analysis
BACKGROUND: Protein-protein, protein-DNA and protein-RNA interactions are of central importance in biological systems. Quadrapole Time-of-flight (Q-TOF) mass spectrometry is a sensitive, promising tool for studying these interactions. Combining this technique with chemical crosslinking, it is possible to identify the sites of interactions within these complexes. Due to the complexities of the mass spectrometric data of crosslinked proteins, new software is required to analyze the resulting products of these studies. RESULT: We designed a Cross-Linked Peptide Mapping (CLPM) algorithm which takes advantage of all of the information available in the experiment including the amino acid sequence from each protein, the identity of the crosslinker, the identity of the digesting enzyme, the level of missed cleavage, and possible chemical modifications. The algorithm does in silico digestion and crosslinking, calculates all possible mass values and matches the theoretical data to the actual experimental data provided by the mass spectrometry analysis to identify the crosslinked peptides. CONCLUSION: Identifying peptides by their masses can be an efficient starting point for direct sequence confirmation. The CLPM algorithm provides a powerful tool in identifying these potential interaction sites in combination with chemical crosslinking and mass spectrometry. Through this cost-effective approach, subsequent efforts can quickly focus attention on investigating these specific interaction sites
Natural Image Coding in V1: How Much Use is Orientation Selectivity?
Orientation selectivity is the most striking feature of simple cell coding in
V1 which has been shown to emerge from the reduction of higher-order
correlations in natural images in a large variety of statistical image models.
The most parsimonious one among these models is linear Independent Component
Analysis (ICA), whereas second-order decorrelation transformations such as
Principal Component Analysis (PCA) do not yield oriented filters. Because of
this finding it has been suggested that the emergence of orientation
selectivity may be explained by higher-order redundancy reduction. In order to
assess the tenability of this hypothesis, it is an important empirical question
how much more redundancies can be removed with ICA in comparison to PCA, or
other second-order decorrelation methods. This question has not yet been
settled, as over the last ten years contradicting results have been reported
ranging from less than five to more than hundred percent extra gain for ICA.
Here, we aim at resolving this conflict by presenting a very careful and
comprehensive analysis using three evaluation criteria related to redundancy
reduction: In addition to the multi-information and the average log-loss we
compute, for the first time, complete rate-distortion curves for ICA in
comparison with PCA. Without exception, we find that the advantage of the ICA
filters is surprisingly small. Furthermore, we show that a simple spherically
symmetric distribution with only two parameters can fit the data even better
than the probabilistic model underlying ICA. Since spherically symmetric models
are agnostic with respect to the specific filter shapes, we conlude that
orientation selectivity is unlikely to play a critical role for redundancy
reduction
A SAT Approach to Clique-Width
Clique-width is a graph invariant that has been widely studied in
combinatorics and computer science. However, computing the clique-width of a
graph is an intricate problem, the exact clique-width is not known even for
very small graphs. We present a new method for computing the clique-width of
graphs based on an encoding to propositional satisfiability (SAT) which is then
evaluated by a SAT solver. Our encoding is based on a reformulation of
clique-width in terms of partitions that utilizes an efficient encoding of
cardinality constraints. Our SAT-based method is the first to discover the
exact clique-width of various small graphs, including famous graphs from the
literature as well as random graphs of various density. With our method we
determined the smallest graphs that require a small pre-described clique-width.Comment: proofs in section 3 updated, results remain unchange
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