Partition Complex Research Articles

DNA supercoiling enhances DNA condensation by ParB proteins.

The ParABS system plays a critical role in bacterial chromosome segregation. The key component of this system, ParB, loads and spreads along DNA to form a local protein-DNA condensate known as a partition complex. As bacterial chromosomes are heavily supercoiled due to the continuous action of RNA polymerases, topoisomerases and nucleoid-associated proteins, it is important to study the impact of DNA supercoiling on the ParB-DNA partition complex formation. Here, we use an in-vitro single-molecule assay to visualize ParB on supercoiled DNA. Unlike most DNA-binding proteins, individual ParB proteins are found to not pin plectonemes on supercoiled DNA, but freely diffuse along supercoiled DNA. We find that DNA supercoiling enhances ParB-DNA condensation, which initiates at lower ParB concentrations than on DNA that is torsionally relaxed. ParB proteins induce a DNA-protein condensate that strikingly absorbs all supercoiling writhe. Our findings provide mechanistic insights that have important implications for our understanding of bacterial chromosome organization and segregation.

Automatic multi-storey building partitioning from point cloud via bidirectional cloth simulation

With the advancements in scanning technology, the rapid acquisition of point cloud spanning multiple storeys of buildings has become feasible. Accurately dividing the building into individual storeys deepens the understanding of the building environment, accelerates the processing of the vast point cloud, and is crucial for numerous fields such as model reconstruction, indoor navigation, and building management. However, it remains a challenge to handle the building with rooms across multiple storeys. This study presents a novel method to partition complex multi-storey building from cluttered point cloud. First, the non-vertical structural elements are detected by taking the difference of height and normal vector as growth conditions. Next, we iteratively employ bidirectional cloth with height variation constraints to simulate the floor and ceiling trend surface. In this step, candidate ceiling patches are obtained through the optimization of a cost function. Finally, the irregular boundary between adjacent storeys that used for partitioning the point cloud is rasterized in terms of the ceilings at lower storey and the floors at upper storey. Each point is orderly classified into the correspond storey with reference to the elevation of the estimated boundary. Through comprehensive evaluation and analysis, our method has demonstrated its effectiveness and adaptability across various datasets. Our method yields superior results compared to the advanced methods, achieving an approximate value of 99 % on the weighted recall, weighted precision and weighted F1-score. Besides, the proposed method is not limited to Manhattan world buildings and requires only the spatial coordinate of points.

In vivo assembly of bacterial partition condensates on circular supercoiled and linear DNA.

In bacteria, faithful DNA segregation of chromosomes and plasmids is mainly mediated by ParABS systems. These systems, consisting of a ParA ATPase, a DNA binding ParB CTPase, and centromere sites parS, orchestrate the separation of newly replicated DNA copies and their intracellular positioning. Accurate segregation relies on the assembly of a high-molecular-weight complex, comprising a few hundreds of ParB dimers nucleated from parS sites. This complex assembles in a multi-step process and exhibits dynamic liquid-droplet properties. Despite various proposed models, the complete mechanism for partition complex assembly remains elusive. This study investigates the impact of DNA supercoiling on ParB DNA binding profiles invivo, using the ParABS system of the plasmid F. We found that variations in DNA supercoiling does not significantly affect any steps in the assembly of the partition complex. Furthermore, physical modeling, leveraging ChIP-seq data from linear plasmids F, suggests that ParB sliding is restricted to approximately 2 Kbp from parS, highlighting the necessity for additional mechanisms beyond ParB sliding over DNA for concentrating ParB into condensates nucleated at parS. Finally, explicit simulations of a polymer coated with bound ParB suggest a dominant role for ParB-ParB interactions in DNA compaction within ParB condensates.

Envy-freeness in 3D hedonic games

We study the problem of fairly partitioning a set of agents into coalitions based on the agents’ additively separable preferences, which can also be viewed as a hedonic game. We study three successively weaker solution concepts, related to envy, weakly justified envy, and justified envy. In a model in which coalitions may have any size, trivial solutions exist for these concepts, which provides a strong motivation for placing restrictions on coalition size. In this paper, we require feasible coalitions to have size three. We study the existence of partitions that are envy-free, weakly justified envy-free, and justified envy-free, and the computational complexity of finding such partitions, if they exist. We impose various restrictions on the agents’ preferences and present a complete complexity classification in terms of these restrictions.

The major Adassil-Medinet fault; a complex evolution of high angle transpressive Variscan shear zones (Western High Atlas, Morocco)

The Western High Atlas is one of the most important sectors of the Variscan foldbelt in Morocco and also of its Alpine intracontinental orogen. Its tectonic evolution is thus essential for the understanding, not only of the Moroccan geology, but also of the interaction between successive orogenic cycles which is one of the focus of this article. Furthermore, as the Moroccan Variscides must be seen in the context of the complex dextral collision between Laurasia and Gondwana, this is also a contribution to the comprehension of the complexity of transpressive regimes and strain partitioning processes.New data show that WNW-ESE sinistral Variscan shear zones (mainly the Addouz-Adassil-Anamrou one - AAAsz), although secondary to the main orogenic scale ENE-WSW dextral shear zones, must be considered in order to understand the Late Paleozoic deformation and its Alpine reactivation. In fact, the concentration of the last stages of the Variscan ductile deformation in the steep and irregular AAAsz played an important role in the initiation and localisation of the minor magmatic events and influenced the geometry and kinematics of the Late Variscan WNW-ESE sinistral shear zones. Furthermore, during the Alpine inversion, the orientation of the AAAsz and related major anisotropies tend to be reactivated, with a major reverse component, giving rise to the irregular Adassil-Medinet fault zone, one of the most important structures of the Western High Atlas.

Phase-separated ParB enforces diverse DNA compaction modes and stabilizes the parS-centered partition complex.

The tripartite ParABS system mediates chromosome segregation in the majority of bacterial species. Typically, DNA-bound ParB proteins around the parS sites condense the chromosomal DNA into a higher-order multimeric nucleoprotein complex for the ParA-driven partition. Despite extensive studies, the molecular mechanism underlying the dynamic assembly of the partition complex remains unclear. Herein, we demonstrate that Bacillus subtilis ParB (Spo0J), through the multimerization of its N-terminal domain, forms phase-separated condensates along a single DNA molecule, leading to the concurrent organization of DNA into a compact structure. Specifically, in addition to the co-condensation of ParB dimers with DNA, the engagement of well-established ParB condensates with DNA allows for the compression of adjacent DNA and the looping of distant DNA. Notably, the presence of CTP promotes the formation of condensates by a low amount of ParB at parS sites, triggering two-step DNA condensation. Remarkably, parS-centered ParB-DNA co-condensate constitutes a robust nucleoprotein architecture capable of withstanding disruptive forces of tens of piconewton. Overall, our findings unveil diverse modes of DNA compaction enabled by phase-separated ParB and offer new insights into the dynamic assembly and maintenance of the bacterial partition complex.

Insights into the molecular mechanism of ParABS system in chromosome partition by HpParA and HpParB.

The ParABS system, composed of ParA (an ATPase), ParB (a DNA binding protein), and parS (a centromere-like DNA), regulates bacterial chromosome partition. The ParB-parS partition complex interacts with the nucleoid-bound ParA to form the nucleoid-adaptor complex (NAC). In Helicobacter pylori, ParA and ParB homologs are encoded as HpSoj and HpSpo0J (HpParA and HpParB), respectively. We determined the crystal structures of the ATP hydrolysis deficient mutant, HpParAD41A, and the HpParAD41A-DNA complex. We assayed the CTPase activity of HpParB and identified two potential DNA binding modes of HpParB regulated by CTP, one is the specific DNA binding by the DNA binding domain and the other is the non-specific DNA binding through the C-terminal domain under the regulation of CTP. We observed an interaction between HpParAD41A and the N-terminus fragment of HpParB (residue 1-10, HpParBN10) and determined the crystal structure of the ternary complex, HpParAD41A-DNA-HpParBN10 complex which mimics the NAC formation. HpParBN10 binds near the HpParAD41A dimer interface and is clamped by flexible loops, L23 and L34, through a specific cation-π interaction between Arg9 of HpParBN10 and Phe52 of HpParAD41A. We propose a molecular mechanism model of the ParABS system providing insight into chromosome partition in bacteria.

The complexity of subcube partition relates to the additive structure of the support

The subcube partition of a Boolean function is a partition of {0,1}n into the union of subcubes ∪iCi, such that the value of the function f is the same on each vector of Ci, i.e. for every i and x,y∈Ci, f(x)=f(y). The complexity of it denotes by HSCP(f) is the minimum number of subcubes in a subcube partition which computes the Boolean function f. We give a lower bound of the complexity of subcube partitions of Boolean function which relates the additive behaviour of the support and the influence of the function.

On negative mass, partition function and entropy

This work examines some aspects related to the existence of negative mass. The requirement for the partition function to converge leads to two distinct approaches. Initially, convergence is achieved by assuming a negative absolute temperature, which results in an imaginary partition function and complex entropy. Subsequently, convergence is maintained by keeping the absolute temperature positive while introducing an imaginary velocity. This modification leads to a positive partition function and real entropy. It seems the utilization of imaginary velocity may yield more plausible physical results compared to the use of negative temperature, at least for the partition function and entropy.

Dynamic ParB-DNA interactions initiate and maintain a partition condensate for bacterial chromosome segregation.

In most bacteria, chromosome segregation is driven by the ParABS system where the CTPase protein ParB loads at the parS site to trigger the formation of a large partition complex. Here, we present in vitro studies of the partition complex for Bacillus subtilis ParB, using single-molecule fluorescence microscopy and AFM imaging to show that transient ParB-ParB bridges are essential for forming DNA condensates. Molecular Dynamics simulations confirm that condensation occurs abruptly at a critical concentration of ParB and show that multimerization is a prerequisite for forming the partition complex. Magnetic tweezer force spectroscopy on mutant ParB proteins demonstrates that CTP hydrolysis at the N-terminal domain is essential for DNA condensation. Finally, we show that transcribing RNA polymerases can steadily traverse the ParB-DNA partition complex. These findings uncover how ParB forms a stable yet dynamic partition complex for chromosome segregation that induces DNA condensation and segregation while enabling replication and transcription.

Joint DNN partitioning and task offloading in mobile edge computing via deep reinforcement learning

As Artificial Intelligence (AI) becomes increasingly prevalent, Deep Neural Networks (DNNs) have become a crucial tool for developing and advancing AI applications. Considering limited computing and energy resources on mobile devices (MDs), it is a challenge to perform compute-intensive DNN tasks on MDs. To attack this challenge, mobile edge computing (MEC) provides a viable solution through DNN partitioning and task offloading. However, as the communication conditions between different devices change over time, DNN partitioning on different devices must also change synchronously. This is a dynamic process, which aggravates the complexity of DNN partitioning. In this paper, we delve into the issue of jointly optimizing energy and delay for DNN partitioning and task offloading in a dynamic MEC scenario where each MD and the server adopt the pre-trained DNNs for task inference. Taking advantage of the characteristics of DNN, we first propose a strategy for layered partitioning of DNN tasks to divide the task of each MD into subtasks that can be either processed on the MD or offloaded to the server for computation. Then, we formulate the trade-off between energy and delay as a joint optimization problem, which is further represented as a Markov decision process (MDP). To solve this, we design a DNN partitioning and task offloading (DPTO) algorithm utilizing deep reinforcement learning (DRL), which enables MDs to make optimal offloading decisions. Finally, experimental results demonstrate that our algorithm outperforms existing non-DRL and DRL algorithms with respect to processing delay and energy consumption, and can be applied to different DNN types.

Partition complex structure can arise from sliding and bridging of ParB dimers

In many bacteria, chromosome segregation requires the association of ParB to the parS-containing centromeric region to form the partition complex. However, the structure and formation of this complex have been unclear. Recently, studies have revealed that CTP binding enables ParB dimers to slide along DNA and condense the centromeric region through the formation of DNA bridges. Using semi-flexible polymer simulations, we demonstrate that these properties can explain partition complex formation. Transient ParB bridges organize DNA into globular states or hairpins and helical structures, depending on bridge lifetime, while separate simulations show that ParB sliding reproduces the multi-peaked binding profile observed in Caulobacter crescentus. Combining sliding and bridging into a unified model, we find that short-lived ParB bridges do not impede sliding and can reproduce both the binding profile and condensation of the nucleoprotein complex. Overall, our model elucidates the mechanism of partition complex formation and predicts its fine structure.

Atypical low-copy number plasmid segregation systems, all in one?

Plasmid families harbor different maintenances functions, depending on their size and copy number. Low copy number plasmids rely on active partition systems, organizing a partition complex at specific centromere sites that is actively positioned using NTPase proteins. Some low copy number plasmids lack an active partition system, but carry atypical intracellular positioning systems using a single protein that binds to the centromere site but without an associated NTPase. These systems have been studied in the case of the Escherichia coli R388 and of the Staphylococcus aureus pSK1 plasmids. Here we review these two systems, which appear to be unrelated but share common features, such as their distribution on plasmids of medium size and copy number, certain activities of their centromere-binding proteins, StbA and Par, respectively, as well as their mode of action, which may involve dynamic interactions with the nucleoid-packed chromosome of their hosts.

Learning Needle Pick-and-Place Without Expert Demonstrations

We introduce a novel approach for learning a complex multi-stage needle pick-and-place manipulation task for surgical applications using Reinforcement Learning without expert demonstrations or explicit curriculum. The proposed method is based on a recursive decomposition of the original task into a sequence of sub-tasks with increasing complexity and utilizes an actor-critic algorithm with deterministic policy output. In this work, exploratory bottlenecks have been used by a human expert as convenient boundary points for partitioning complex tasks into simpler subunits. Our method has successfully learnt a policy for the needle pick-and-place task, whereas the state-of-the-art TD3+HER method is unable to achieve success without the help of expert demonstrations. Comparison results show that our method achieves the highest performance with a 91% average success rate.

Partition complexes and trees

We construct a functor from the partition complex of a finite set A A to a category of trees with leaves labelled by A A and prove that it is homotopy initial. This construction and our proof are elementary and require very few preliminaries, but imply an equivalence between different bar constructions of an operad in great generality.

Keep your distance: Land division with separation

This paper is part of an ongoing endeavor to bring the theory of fair division closer to practice by handling requirements from real-life applications. We focus on two requirements originating from the division of land estates: (1) each agent should receive a plot of a usable geometric shape, and (2) plots of different agents must be physically separated. With these requirements, the classic fairness notion of proportionality is impractical, since it may be impossible to attain any multiplicative approximation of it. In contrast, the ordinal maximin share approximation, introduced by Budish in 2011, provides meaningful fairness guarantees. We prove upper and lower bounds on achievable maximin share guarantees when the usable shapes are squares, fat rectangles, or arbitrary axis-aligned rectangles, and explore the algorithmic and query complexity of finding fair partitions in this setting. Our work makes use of tools and concepts from computational geometry such as independent sets of rectangles and guillotine partitions.

The dynamics of partition protein B (ParB) spreading on the DNA and bridging-induced DNA condensation.

The ParABS system plays an essential role in prokaryotic chromosome segregation. After loading at the parS site on the genome, ParB proteins rapidly redistribute to distances of ∼15 kb away from the loading site and form a partition complex. It has remained puzzling how this large-distance spreading can occur along DNA that is loaded with hundreds of proteins as well as its mechanism in DNA condensation. Using in vitro single-molecule fluorescence imaging, we here show that ParB proteins can load onto the DNA distantly of parS loading site by a novel ParB-ParB recruitment. We observe the proteins loading in-cis and in-trans whereby, at low tensions within the DNA, newly recruited ParB can bypass roadblocks as it gets loaded to spatially proximal but genomically distant DNA regions. Moreover, we investigate the detailed mechanism of ParB-induced DNA-condensation, where previously spread ParB proteins can fix distant genomic regions in close proximity via transient loop formation. We investigate this process in the light of polymer-polymer phase-separation (PPPS) and detect which molecular domains are involved in this bridging-induced condensation. ParB-ParB recruitment and ParB-DNA condensation explains how ParB can form a bacterial segregation apparatus involving substantial genomic distance during chromosome segregation which is vital for the bacterial cell cycle.

Partitioning real-time workloads on multi-core virtual machines

Modern real-time virtual machines and containers are starting to make it possible to support the execution of real-time applications in virtualized environments. Real-time scheduling theory already provides techniques for analyzing the schedulability of real-time applications executed in virtual machines, but most of the previous work focused on global scheduling while, excluding a few exceptions, the problem of partitioning real-time workloads on multi-core VMs has not been properly investigated yet. This paper discusses and presents a set of partitioning algorithms, based on both mathematical optimization and some heuristics, to tackle the problem of online admission control and partitioning. An experimental evaluation shows that some of the heuristic algorithms can be effectively used in practical settings, being capable to partition complex task sets in short times and introducing an allocation overhead near to the optimum one.

Distinct architectural requirements for the parS centromeric sequence of the pSM19035 plasmid partition machinery.

Three-component ParABS partition systems ensure stable inheritance of many bacterial chromosomes and low-copy-number plasmids. ParA localizes to the nucleoid through its ATP-dependent nonspecific DNA-binding activity, whereas centromere-like parS-DNA and ParB form partition complexes that activate ParA-ATPase to drive the system dynamics. The essential parS sequence arrangements vary among ParABS systems, reflecting the architectural diversity of their partition complexes. Here, we focus on the pSM19035 plasmid partition system that uses a ParBpSM of the ribbon-helix-helix (RHH) family. We show that parSpSM with four or more contiguous ParBpSM-binding sequence repeats is required to assemble a stable ParApSM-ParBpSM complex and efficiently activate the ParApSM-ATPase, stimulating complex disassembly. Disruption of the contiguity of the parSpSM sequence array destabilizes the ParApSM-ParBpSM complex and prevents efficient ATPase activation. Our findings reveal the unique architecture of the pSM19035 partition complex and how it interacts with nucleoid-bound ParApSM-ATP.

On the use of deep learning and parallelism techniques to significantly reduce the HEVC intra-coding time

It is well-known that each new video coding standard significantly increases in computational complexity with respect to previous standards, and this is particularly true for the HEVC and VVC video coding standards. The development of techniques for reducing the required complexity without affecting the rate/distortion (R/D) performance is therefore always a topic of intense research interest. In this paper, we propose a combination of two powerful techniques, deep learning and parallel computing, to significantly reduce the complexity of the HEVC encoding engine. Our experimental results show that a combination of deep learning to reduce the CTU partitioning complexity with parallel strategies based on frame partitioning is able to achieve speedups of up to 26times when 16 threads are used. The R/D penalty in terms of the BD-BR metric depends on the video content, the compression rate and the number of OpenMP threads, and was consistently between 0.35 and 10% for the video sequence test set used in our experiments