On-line algorithms for polynomially solvable satisfiability problems

AbstractGiven a propositional Horn formula, we show how to maintain on-line information about its satisfiability during the insertion of new clauses. A data structure is presented which answers each satisfiability question in O(1) time and inserts a new clause of length q in O(q) amortized time. This significantly outperforms previously known solutions of the same problem. This result is extended also to a particular class of non-Horn formulae already considered in the literature, for which the space bound is improved. Other operations are considered, such as testing whether a given hypothesis is consistent with a satisfying interpretation of the given formula and determining a truth assignment which satisfies a given formula. The on-line time and space complexity of these operations is also analyzed

Apical endosomes isolated from kidney collecting duct principal cells lack subunits of the proton pumping ATPase.

Endocytic vesicles that are involved in the vasopressin-stimulated recycling of water channels to and from the apical membrane of kidney collecting duct principal cells were isolated from rat renal papilla by differential and Percoll density gradient centrifugation. Fluorescence quenching measurements showed that the isolated vesicles maintained a high, HgCl2-sensitive water permeability, consistent with the presence of vasopressin-sensitive water channels. They did not, however, exhibit ATP-dependent luminal acidification, nor any N-ethylmaleimide-sensitive ATPase activity, properties that are characteristic of most acidic endosomal compartments. Western blotting with specific antibodies showed that the 31- and 70-kD cytoplasmically oriented subunits of the vacuolar proton pump were not detectable in these apical endosomes from the papilla, whereas they were present in endosomes prepared in parallel from the cortex. In contrast, the 56-kD subunit of the proton pump was abundant in papillary endosomes, and was localized at the apical pole of principal cells by immunocytochemistry. Finally, an antibody that recognizes the 16-kD transmembrane subunit of oat tonoplast ATPase cross-reacted with a distinct 16-kD band in cortical endosomes, but no 16-kD band was detectable in endosomes from the papilla. This antibody also recognized a 16-kD band in affinity-purified H+ ATPase preparations from bovine kidney medulla. Therefore, early endosomes derived from the apical plasma membrane of collecting duct principal cells fail to acidify because they lack functionally important subunits of a vacuolar-type proton pumping ATPase, including the 16-kD transmembrane domain that serves as the proton-conducting channel, and the 70-kD cytoplasmic subunit that contains the ATPase catalytic site. This specialized, non-acidic early endosomal compartment appears to be involved primarily in the hormonally induced recycling of water channels to and from the apical plasma membrane of vasopressin-sensitive cells in the kidney collecting duct

A novel approach to represent and compare RNA secondary structures

Structural information is crucial in ribonucleic acid (RNA) analysis and functional annotation; nevertheless, how to include such structural data is still a debated problem. Dot-bracket notation is the most common and simple representation for RNA secondary structures but its simplicity leads also to ambiguity requiring further processing steps to dissolve. Here we present BEAR (Brand nEw Alphabet for RNA), a new context-aware structural encoding represented by a string of characters. Each character in BEAR encodes for a specific secondary structure element (loop, stem, bulge and internal loop) with specific length. Furthermore, exploiting this informative and yet simple encoding in multiple alignments of related RNAs, we captured how much structural variation is tolerated in RNA families and convert it into transition rates among secondary structure elements. This allowed us to compute a substitution matrix for secondary structure elements called MBR (Matrix of BEAR-encoded RNA secondary structures), of which we tested the ability in aligning RNA secondary structures. We propose BEAR and the MBR as powerful resources for the RNA secondary structure analysis, comparison and classification, motif finding and phylogeny

The Use of Premixed Calcium Silicate Bioceramic Sealer with Warm Carrier-Based Technique: A 2-Year Study for Patients Treated in a Master Program

Background: Recently several calcium silicate flowable sealers have been introduced as endodontic materials for the root canal. This clinical study tested the use of a new premixed calcium silicate bioceramic sealer in association with the Thermafil warm carrier-based technique (TF). Epoxy-resin-based sealer with the warm carrier-based technique was the control group. Methodology: Healthy consecutive patients (n = 85) requiring 94 root canal treatments were enrolled in this study and assigned to one filling group (Ceraseal-TF n = 47, AH Plus-TF n = 47) in accordance with operator training and best clinical practice. Periapical X-rays were taken preoperatively, after root canal filling and after 6, 12 and 24 months. Two evaluators blindly assessed the periapical index (PAI) and sealer extrusion in the groups (k = 0.90). Healing rate and survival rate were also evaluated. Chi-square tests was used to analyze significant differences between the groups. Multilevel analysis was performed to evaluate the factors associated with healing status. Results: A total of 89 root canal treatments in 82 patients were analyzed at the end-line (24 months). The total drop-out was 3.6% (3 patients; 5 teeth). A total of 91.1% of healed teeth (PAI 1-2) was observed in Ceraseal-TF, with 88.6% in AH Plus-TF. No significant difference was observed on healing outcome and survival among the two filling groups (p > 0.05). Apical extrusion of the sealers occurred in 17 cases (19.0%). Of these, 6 occurred in Ceraseal-TF (13.3%) and 11 in AH Plus-TF (25.0%). Three Ceraseal extrusions were radiographically undetectable after 24 months. All the AH Plus extrusions did not change during the evaluation time. Conclusions: The combined use of the carrier-based technique and premixed CaSi-based bioceramic sealer showed clinical results comparable with carrier-based technique and epoxy-resin-based sealer. The radiographical disappearance of apically extruded Ceraseal is a possible event in the first 24 months

webPDBinder: a server for the identification of ligand binding sites on protein structures

The webPDBinder (http://pdbinder.bio.uniroma2.it/PDBinder) is a web server for the identification of small ligand-binding sites in a protein structure. webPDBinder searches a protein structure against a library of known binding sites and a collection of control non-binding pockets. The number of similarities identified with the residues in the two sets is then used to derive a propensity value for each residue of the query protein associated to the likelihood that the residue is part of a ligand binding site. The predicted binding residues can be further refined using conservation scores derived from the multiple alignment of the PFAM protein family. webPDBinder correctly identifies residues belonging to the binding site in 77% of the cases and is able to identify binding pockets starting from holo or apo structures with comparable performances. This is important for all the real world cases where the query protein has been crystallized without a ligand and is also difficult to obtain clear similarities with bound pockets from holo pocket libraries. The input is either a PDB code or a user-submitted structure. The output is a list of predicted binding pocket residues with propensity and conservation values both in text and graphical format

DBATE: database of alternative transcripts expression

The use of high-throughput RNA sequencing technology (RNA-seq) allows whole transcriptome analysis, providing an unbiased and unabridged view of alternative transcript expression. Coupling splicing variant-specific expression with its functional inference is still an open and difficult issue for which we created the DataBase of Alternative Transcripts Expression (DBATE), a web-based repository storing expression values and functional annotation of alternative splicing variants. We processed 13 large RNA-seq panels from human healthy tissues and in disease conditions, reporting expression levels and functional annotations gathered and integrated from different sources for each splicing variant, using a variant-specific annotation transfer pipeline. The possibility to perform complex queries by cross-referencing different functional annotations permits the retrieval of desired subsets of splicing variant expression values that can be visualized in several ways, from simple to more informative. DBATE is intended as a novel tool to help appreciate how, and possibly why, the transcriptome expression is shaped. DATABASE URL: http://bioinformatica.uniroma2.it/DBATE/

Phosfinder: a web server for the identification of phosphate-binding sites on protein structures

Phosfinder is a web server for the identification of phosphate binding sites in protein structures. Phosfinder uses a structural comparison algorithm to scan a query structure against a set of known 3D phosphate binding motifs. Whenever a structural similarity between the query protein and a phosphate binding motif is detected, the phosphate bound by the known motif is added to the protein structure thus representing a putative phosphate binding site. Predicted binding sites are then evaluated according to (i) their position with respect to the query protein solvent-excluded surface and (ii) the conservation of the binding residues in the protein family. The server accepts as input either the PDB code of the protein to be analyzed or a user-submitted structure in PDB format. All the search parameters are user modifiable. Phosfinder outputs a list of predicted binding sites with detailed information about their structural similarity with known phosphate binding motifs, and the conservation of the residues involved. A graphical applet allows the user to visualize the predicted binding sites on the query protein structure. The results on a set of 52 apo/holo structure pairs show that the performance of our method is largely unaffected by ligand-induced conformational changes. Phosfinder is available at http://phosfinder.bio.uniroma2.it

Evaluation of potential miRNA sponge effects of SARS genomes in human

: To date the coronavirus family is composed of seven different viruses which were commonly known as cold viruses until the appearance of the severe acute respiratory coronavirus (SARS-CoV) in 2002, the middle east respiratory syndrome coronavirus (MERS) in 2012 and the severe acute respiratory coronavirus 2 (SARS-CoV-2) which caused the COVID-19 global pandemic in 2019. Using bioinformatic approaches we tested the potential interactions of human miRNAs, expressed in pulmonary epithelial cells, with the available coronavirus genomes. Putative miRNA binding sites were then compared between pathogenic and non pathogenic virus groups. The pathogenic group shares 6 miRNA binding sites that can be potentially involved in the sequestration of miRNAs already known to be associated with deep vein thrombosis. We then analysed ∼100k SARS-CoV-2 variant genomes for their potential interaction with human miRNAs and this study highlighted a group of 97 miRNA binding sites which is present in all the analysed genomes. Among these, we identified 6 miRNA binding sites specific for SARS-CoV-2 and the other two pathogenic viruses whose down-regulation has been seen associated with deep vein thrombosis and cardiovascular diseases. Interestingly, one of these miRNAs, namely miR-20a-5p, whose expression decreases with advancing age, is involved in cytokine signaling, cell differentiation and/or proliferation. We hypothesize that depletion of poorly expressed miRNA could be related with disease severity

Experimental implementation of an adiabatic quantum optimization algorithm

We report the realization of a nuclear magnetic resonance computer with three quantum bits that simulates an adiabatic quantum optimization algorithm. Adiabatic quantum algorithms offer new insight into how quantum resources can be used to solve hard problems. This experiment uses a particularly well suited three quantum bit molecule and was made possible by introducing a technique that encodes general instances of the given optimization problem into an easily applicable Hamiltonian. Our results indicate an optimal run time of the adiabatic algorithm that agrees well with the prediction of a simple decoherence model.Comment: REVTeX, 5 pages, 4 figures, improved lay-out; accepted for publication in Physical Review Letter

Local comparison of protein structures highlights cases of convergent evolution in analogous functional sites

We performed an exhaustive search for local structural similarities in an ensemble of non-redundant protein functional sites. With the purpose of finding new examples of convergent evolution, we selected only those matching sites composed of structural regions whose residue order is inverted in the relative protein sequences