Improved Approximate String Matching and Regular Expression Matching on Ziv-Lempel Compressed Texts

We study the approximate string matching and regular expression matching problem for the case when the text to be searched is compressed with the Ziv-Lempel adaptive dictionary compression schemes. We present a time-space trade-off that leads to algorithms improving the previously known complexities for both problems. In particular, we significantly improve the space bounds, which in practical applications are likely to be a bottleneck

"Holey Sheets" - Pfaffians and Subdeterminants as D-brane Operators in Large N Gauge Theories

In the AdS/CFT correspondence, wrapped D3-branes (such as "giant gravitons") on the string theory side of the correspondence have been identified with Pfaffian, determinant and subdeterminant operators on the field theory side. We substantiate this identification by showing that the presence of pairs of such operators in a correlation function of a large N gauge theory naturally leads to a modified 't Hooft expansion including also worldsheets with boundaries. This happens independently of supersymmetry or conformal invariance.Comment: 39 pages, 10 figures, harvma

Gravitation with superposed Gauss--Bonnet terms in higher dimensions: Black hole metrics and maximal extensions

Our starting point is an iterative construction suited to combinatorics in arbitarary dimensions d, of totally anisymmetrised p-Riemann 2p-forms (2p\le d) generalising the (1-)Riemann curvature 2-forms. Superposition of p-Ricci scalars obtained from the p-Riemann forms defines the maximally Gauss--Bonnet extended gravitational Lagrangian. Metrics, spherically symmetric in the (d-1) space dimensions are constructed for the general case. The problem is directly reduced to solving polynomial equations. For some black hole type metrics the horizons are obtained by solving polynomial equations. Corresponding Kruskal type maximal extensions are obtained explicitly in complete generality, as is also the periodicity of time for Euclidean signature. We show how to include a cosmological constant and a point charge. Possible further developments and applications are indicated.Comment: 13 pages, REVTEX. References and Note Adde

Faster Approximate String Matching for Short Patterns

We study the classical approximate string matching problem, that is, given strings $P$ and $Q$ and an error threshold $k$, find all ending positions of substrings of $Q$ whose edit distance to $P$ is at most $k$. Let $P$ and $Q$ have lengths $m$ and $n$, respectively. On a standard unit-cost word RAM with word size $w \geq \log n$ we present an algorithm using time $$O(nk \cdot \min(\frac{\log^2 m}{\log n},\frac{\log^2 m\log w}{w}) + n)$$ When $P$ is short, namely, $m = 2^{o(\sqrt{\log n})}$ or $m = 2^{o(\sqrt{w/\log w})}$ this improves the previously best known time bounds for the problem. The result is achieved using a novel implementation of the Landau-Vishkin algorithm based on tabulation and word-level parallelism.Comment: To appear in Theory of Computing System

Distributed phase-covariant cloning with atomic ensembles via quantum Zeno dynamics

We propose an interesting scheme for distributed orbital state quantum cloning with atomic ensembles based on the quantum Zeno dynamics. These atomic ensembles which consist of identical three-level atoms are trapped in distant cavities connected by a single-mode integrated optical star coupler. These qubits can be manipulated through appropriate modulation of the coupling constants between atomic ensemble and classical field, and the cavity decay can be largely suppressed as the number of atoms in the ensemble qubits increases. The fidelity of each cloned qubit can be obtained with analytic result. The present scheme provides a new way to construct the quantum communication network.Comment: 5 pages, 4 figure

Integrating sequence and array data to create an improved 1000 Genomes Project haplotype reference panel

A major use of the 1000 Genomes Project (1000GP) data is genotype imputation in genome-wide association studies (GWAS). Here we develop a method to estimate haplotypes from low-coverage sequencing data that can take advantage of single-nucleotide polymorphism (SNP) microarray genotypes on the same samples. First the SNP array data are phased to build a backbone (or 'scaffold') of haplotypes across each chromosome. We then phase the sequence data 'onto' this haplotype scaffold. This approach can take advantage of relatedness between sequenced and non-sequenced samples to improve accuracy. We use this method to create a new 1000GP haplotype reference set for use by the human genetic community. Using a set of validation genotypes at SNP and bi-allelic indels we show that these haplotypes have lower genotype discordance and improved imputation performance into downstream GWAS samples, especially at low-frequency variants. © 2014 Macmillan Publishers Limited. All rights reserved

Search for black holes and other new phenomena in high-multiplicity final states in proton-proton collisions at root s=13 TeV

Peer reviewe

ACMSD inhibition corrects fibrosis, inflammation, and DNA damage in MASLD/MASH.

Recent findings reveal the importance of tryptophan-initiated de novo nicotinamide adenine dinucleotide (NAD <sup>+</sup> ) synthesis in the liver, a process previously considered secondary to biosynthesis from nicotinamide. The enzyme α-amino-β-carboxymuconate-ε-semialdehyde decarboxylase (ACMSD), primarily expressed in the liver and kidney, acts as a modulator of de novo NAD <sup>+</sup> synthesis. Boosting NAD <sup>+</sup> levels has previously demonstrated remarkable metabolic benefits in mouse models. In this study, we aimed to investigate the therapeutic implications of ACMSD inhibition in the treatment of metabolic dysfunction-associated steatotic liver disease/steatohepatitis (MASLD/MASH). In vitro experiments were conducted in primary rodent hepatocytes, Huh7 human liver carcinoma cells and induced pluripotent stem cell-derived human liver organoids (HLOs). C57BL/6J male mice were fed a western-style diet and housed at thermoneutrality to recapitulate key aspects of MASLD/MASH. Pharmacological ACMSD inhibition was given therapeutically, following disease onset. HLO models of steatohepatitis were used to assess the DNA damage responses to ACMSD inhibition in human contexts. Inhibiting ACMSD with a novel specific pharmacological inhibitor promotes de novo NAD <sup>+</sup> synthesis and reduces DNA damage ex vivo, in vivo, and in HLO models. In mouse models of MASLD/MASH, de novo NAD <sup>+</sup> biosynthesis is suppressed, and transcriptomic DNA damage signatures correlate with disease severity; in humans, Mendelian randomization-based genetic analysis suggests a notable impact of genomic stress on liver disease susceptibility. Therapeutic inhibition of ACMSD in mice increases liver NAD <sup>+</sup> and reverses MASLD/MASH, mitigating fibrosis, inflammation, and DNA damage, as observed in HLO models of steatohepatitis. Our findings highlight the benefits of ACMSD inhibition in enhancing hepatic NAD <sup>+</sup> levels and enabling genomic protection, underscoring its therapeutic potential in MASLD/MASH. Enhancing NAD <sup>+</sup> levels has been shown to induce remarkable health benefits in mouse models of metabolic dysfunction-associated steatotic liver disease/steatohepatitis (MASLD/MASH), yet liver-specific NAD <sup>+</sup> boosting strategies remain underexplored. Here, we present a novel pharmacological approach to enhance de novo synthesis of NAD <sup>+</sup> in the liver by inhibiting α-amino-β-carboxymuconate-ε-semialdehyde decarboxylase (ACMSD), an enzyme highly expressed in the liver. Inhibiting ACMSD increases NAD <sup>+</sup> levels, enhances mitochondrial respiration, and maintains genomic stability in hepatocytes ex vivo and in vivo. These molecular benefits prevent disease progression in both mouse and human liver organoid models of steatohepatitis. Our preclinical study identifies ACMSD as a promising target for MASLD/MASH management and lays the groundwork for developing ACMSD inhibitors as a clinical treatment

Size Doesn't Matter: Towards a More Inclusive Philosophy of Biology

notes: As the primary author, O’Malley drafted the paper, and gathered and analysed data (scientific papers and talks). Conceptual analysis was conducted by both authors.publication-status: Publishedtypes: ArticlePhilosophers of biology, along with everyone else, generally perceive life to fall into two broad categories, the microbes and macrobes, and then pay most of their attention to the latter. ‘Macrobe’ is the word we propose for larger life forms, and we use it as part of an argument for microbial equality. We suggest that taking more notice of microbes – the dominant life form on the planet, both now and throughout evolutionary history – will transform some of the philosophy of biology’s standard ideas on ontology, evolution, taxonomy and biodiversity. We set out a number of recent developments in microbiology – including biofilm formation, chemotaxis, quorum sensing and gene transfer – that highlight microbial capacities for cooperation and communication and break down conventional thinking that microbes are solely or primarily single-celled organisms. These insights also bring new perspectives to the levels of selection debate, as well as to discussions of the evolution and nature of multicellularity, and to neo-Darwinian understandings of evolutionary mechanisms. We show how these revisions lead to further complications for microbial classification and the philosophies of systematics and biodiversity. Incorporating microbial insights into the philosophy of biology will challenge many of its assumptions, but also give greater scope and depth to its investigations

Potential Benefits of Limited Clinical and Radiographic Follow-up After Surgical Treatment of Ankle Fractures

Introduction: Ankle fractures are one of the most prevalent musculoskeletal injuries, with a significant number requiring surgical treatment. Postoperative complications requiring additional interventions frequently occur during the early postoperative period. We hypothesize that there is a limited need for routine clinical and radiographic follow-up once the fracture is deemed healed. Methods: IRB approval was obtained at four academic trauma centers. A retrospective chart review was done to identify adults with healed unimalleolar and bimalleolar ankle fractures treated surgically with at least 12 months of follow-up. Based on postoperative radiographs, changes in fracture alignment and implant position from radiographic union to final follow-up were documented. The average reimbursement for a final follow-up clinic visit and a set of ankle radiographs were estimated. Results: A total of 140 patients met inclusion criteria. The mean age at injury was 49.5 years, and 67.9% of patients were female. The mean time to healing was 82.2 days (±33.5 days). After radiographic healing, one patient had radiographic changes but was asymptomatic and full weight bearing at their final follow-up. On average, our institution was reimbursed $46 to$49 for a follow-up clinic visit and $364 to$497 for a set of ankle radiographs. Conclusion: Given the average time to healing, there is limited utility in routine radiographic and clinical follow-up beyond 16 weeks in asymptomatic patients. In our series, this would result in a savings of $950 to$1,200 per patient. However, after ankle fractures were deemed healed, 0.7% patients had radiographic evidence of a change in implant position. Documenting this change did not modify the immediate course of fracture treatment. Surgeons will need to balance the need for routine follow-up with the potential economic benefits in reducing costs to the healthcare system