95 research outputs found
Counting Popular Matchings in House Allocation Problems
We study the problem of counting the number of popular matchings in a given
instance. A popular matching instance consists of agents A and houses H, where
each agent ranks a subset of houses according to their preferences. A matching
is an assignment of agents to houses. A matching M is more popular than
matching M' if the number of agents that prefer M to M' is more than the number
of people that prefer M' to M. A matching M is called popular if there exists
no matching more popular than M. McDermid and Irving gave a poly-time algorithm
for counting the number of popular matchings when the preference lists are
strictly ordered.
We first consider the case of ties in preference lists. Nasre proved that the
problem of counting the number of popular matching is #P-hard when there are
ties. We give an FPRAS for this problem.
We then consider the popular matching problem where preference lists are
strictly ordered but each house has a capacity associated with it. We give a
switching graph characterization of popular matchings in this case. Such
characterizations were studied earlier for the case of strictly ordered
preference lists (McDermid and Irving) and for preference lists with ties
(Nasre). We use our characterization to prove that counting popular matchings
in capacitated case is #P-hard
Triggering the stringent response: signals responsible for activating (p) ppGpp synthesis in bacteria
The stringent response is a conserved bacterial stress response mechanism that allows bacteria to respond to nutritional challenges. It is mediated by the alarmones pppGpp and ppGpp, nucleotides that are synthesized and hydrolyzed by members of the RSH superfamily. Whilst there are key differences in the binding targets for (p)ppGpp between Gram-negative and Gram-positive bacterial species, the transient accumulation of (p)ppGpp caused by nutritional stresses results in a global change in gene expression in all species. The RSH superfamily of enzymes is ubiquitous throughout the bacterial kingdom, and can be split into three main groups: the long-RSH enzymes; the small alarmone synthetases (SAS); and the small alarmone hydrolases (SAH). Despite the prevalence of these enzymes, there are important differences in the way in which they are regulated on a transcriptional and post-translational level. Here we provide an overview of the diverse regulatory mechanisms that are involved in governing this crucial signalling network. Understanding how the RSH superfamily members are regulated gives insights into the varied important biological roles for this signalling pathway across the bacteria
The impact of the stringent response on TRAFAC GTPases and prokaryotic ribosome assembly
Many facets of ribosome biogenesis and function, including ribosomal RNA (rRNA) transcription, 70S assembly and protein translation, are negatively impacted upon induction of a nutrient stress-sensing signalling pathway termed the stringent response. This stress response is mediated by the alarmones guanosine tetra- and penta-phosphate ((p)ppGpp), the accumulation of which leads to a massive cellular response that slows growth and aids survival. The 70S bacterial ribosome is an intricate structure, with assembly both complex and highly modular. Presiding over the assembly process is a group of P-loop GTPases within the TRAFAC (Translation Factor Association) superclass that are crucial for correct positioning of both early and late stage ribosomal proteins (r-proteins) onto the rRNA. Often described as âmolecular switchesâ, members of this GTPase superfamily readily bind and hydrolyse GTP to GDP in a cyclic manner that alters the propensity of the GTPase to carry out a function. TRAFAC GTPases are considered to act as checkpoints to ribosome assembly, involved in binding to immature sections in the GTP-bound state, preventing further r-protein association until maturation is complete. Here we review our current understanding of the impact of the stringent response and (p)ppGpp production on ribosome maturation in prokaryotic cells, focusing on the inhibition of (p)ppGpp on GTPase-mediated subunit assembly, but also touching upon the inhibition of rRNA transcription and protein translation
The stringent response and physiological roles of (pp)pGpp in bacteria
The stringent response is a stress signalling system mediated by the alarmones guanosine tetraphosphate (ppGpp) and guanosine pentaphosphate (pppGpp) in response to nutrient deprivation. Recent research highlights the complexity and broad range of functions that these alarmones control. This Review provides an update on our current understanding of the enzymes involved in ppGpp, pppGpp and guanosine 5âČ-monophosphate 3âČ-diphosphate (pGpp) (collectively (pp)pGpp) turnover, including those shown to produce pGpp and its analogue (pp)pApp. We describe the well-known interactions with RNA polymerase as well as a broader range of cellular target pathways controlled by (pp)pGpp, including DNA replication, transcription, nucleotide synthesis, ribosome biogenesis and function, as well as lipid metabolism. Finally, we review the role of ppGpp and pppGpp in bacterial pathogenesis, providing examples of how these nucleotides are involved in regulating many aspects of virulence and chronic infection
Mask formulas for cograssmannian Kazhdan-Lusztig polynomials
We give two contructions of sets of masks on cograssmannian permutations that
can be used in Deodhar's formula for Kazhdan-Lusztig basis elements of the
Iwahori-Hecke algebra. The constructions are respectively based on a formula of
Lascoux-Schutzenberger and its geometric interpretation by Zelevinsky. The
first construction relies on a basis of the Hecke algebra constructed from
principal lower order ideals in Bruhat order and a translation of this basis
into sets of masks. The second construction relies on an interpretation of
masks as cells of the Bott-Samelson resolution. These constructions give
distinct answers to a question of Deodhar.Comment: 43 page
Popular matchings in the marriage and roommates problems
Popular matchings have recently been a subject of study in the context of the so-called House Allocation Problem, where the objective is to match applicants to houses over which the applicants have preferences. A matching M is called popular if there is no other matching MâČ with the property that more applicants prefer their allocation in MâČ to their allocation in M. In this paper we study popular matchings in the context of the Roommates Problem, including its special (bipartite) case, the Marriage Problem. We investigate the relationship between popularity and stability, and describe efficient algorithms to test a matching for popularity in these settings. We also show that, when ties are permitted in the preferences, it is NP-hard to determine whether a popular matching exists in both the Roommates and Marriage cases
Young parentsâ experiences of a multi-agency young families project: Findings from a co-produced study
Determination of optimal glucose concentration for microcalorimetric metabolic evaluation of equine spermatozoa
The evolving SARS-CoV-2 epidemic in Africa: Insights from rapidly expanding genomic surveillance
INTRODUCTION
Investment in Africa over the past year with regard to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) sequencing has led to a massive increase in the number of sequences, which, to date, exceeds 100,000 sequences generated to track the pandemic on the continent. These sequences have profoundly affected how public health officials in Africa have navigated the COVID-19 pandemic.
RATIONALE
We demonstrate how the first 100,000 SARS-CoV-2 sequences from Africa have helped monitor the epidemic on the continent, how genomic surveillance expanded over the course of the pandemic, and how we adapted our sequencing methods to deal with an evolving virus. Finally, we also examine how viral lineages have spread across the continent in a phylogeographic framework to gain insights into the underlying temporal and spatial transmission dynamics for several variants of concern (VOCs).
RESULTS
Our results indicate that the number of countries in Africa that can sequence the virus within their own borders is growing and that this is coupled with a shorter turnaround time from the time of sampling to sequence submission. Ongoing evolution necessitated the continual updating of primer sets, and, as a result, eight primer sets were designed in tandem with viral evolution and used to ensure effective sequencing of the virus. The pandemic unfolded through multiple waves of infection that were each driven by distinct genetic lineages, with B.1-like ancestral strains associated with the first pandemic wave of infections in 2020. Successive waves on the continent were fueled by different VOCs, with Alpha and Beta cocirculating in distinct spatial patterns during the second wave and Delta and Omicron affecting the whole continent during the third and fourth waves, respectively. Phylogeographic reconstruction points toward distinct differences in viral importation and exportation patterns associated with the Alpha, Beta, Delta, and Omicron variants and subvariants, when considering both Africa versus the rest of the world and viral dissemination within the continent. Our epidemiological and phylogenetic inferences therefore underscore the heterogeneous nature of the pandemic on the continent and highlight key insights and challenges, for instance, recognizing the limitations of low testing proportions. We also highlight the early warning capacity that genomic surveillance in Africa has had for the rest of the world with the detection of new lineages and variants, the most recent being the characterization of various Omicron subvariants.
CONCLUSION
Sustained investment for diagnostics and genomic surveillance in Africa is needed as the virus continues to evolve. This is important not only to help combat SARS-CoV-2 on the continent but also because it can be used as a platform to help address the many emerging and reemerging infectious disease threats in Africa. In particular, capacity building for local sequencing within countries or within the continent should be prioritized because this is generally associated with shorter turnaround times, providing the most benefit to local public health authorities tasked with pandemic response and mitigation and allowing for the fastest reaction to localized outbreaks. These investments are crucial for pandemic preparedness and response and will serve the health of the continent well into the 21st century
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