Non-adiabatic holonomic quantum computation in linear system-bath coupling

Non-adiabatic holonomic quantum computation in decoherence-free subspaces protects quantum information from control imprecisions and decoherence. For the non-collective decoherence that each qubit has its own bath, we show the implementations of two non-commutable holonomic single-qubit gates and one holonomic nontrivial two-qubit gate that compose a universal set of non-adiabatic holonomic quantum gates in decoherence-free-subspaces of the decoupling group, with an encoding rate of $\frac{N-2}{N}$. The proposed scheme is robust against control imprecisions and the non-collective decoherence, and its non-adiabatic property ensures less operation time. We demonstrate that our proposed scheme can be realized by utilizing only two-qubit interactions rather than many-qubit interactions. Our results reduce the complexity of practical implementation of holonomic quantum computation in experiments. We also discuss the physical implementation of our scheme in coupled microcavities.Comment: 2 figures; accepted by Sci. Re

IsoTree: A New Framework for De novo Transcriptome Assembly from RNA-seq Reads

High-throughput sequencing of mRNA has made the deep and efficient probing of transcriptome more affordable. However, the vast amounts of short RNA-seq reads make de novo transcriptome assembly an algorithmic challenge. In this work, we present IsoTree, a novel framework for transcripts reconstruction in the absence of reference genomes. Unlike most of de novo assembly methods that build de Bruijn graph or splicing graph by connecting $k-mers$ which are sets of overlapping substrings generated from reads, IsoTree constructs splicing graph by connecting reads directly. For each splicing graph, IsoTree applies an iterative scheme of mixed integer linear program to build a prefix tree, called isoform tree. Each path from the root node of the isoform tree to a leaf node represents a plausible transcript candidate which will be pruned based on the information of paired-end reads. Experiments showed that in most cases IsoTree performs better than other leading transcriptome assembly programs. IsoTree is available at https://github.com/Jane110111107/IsoTree

Can a permutation be sorted by best short swaps?

A short swap switches two elements with at most one element caught between them. Sorting permutation by short swaps asks to find a shortest short swap sequence to transform a permutation into another. A short swap can eliminate at most three inversions. It is still open for whether a permutation can be sorted by short swaps each of which can eliminate three inversions. In this paper, we present a polynomial time algorithm to solve the problem, which can decide whether a permutation can be sorted by short swaps each of which can eliminate 3 inversions in O(n) time, and if so, sort the permutation by such short swaps in O(n^2) time, where n is the number of elements in the permutation. A short swap can cause the total length of two element vectors to decrease by at most 4. We further propose an algorithm to recognize a permutation which can be sorted by short swaps each of which can cause the element vector length sum to decrease by 4 in O(n) time, and if so, sort the permutation by such short swaps in O(n^2) time. This improves upon the O(n^2) algorithm proposed by Heath and Vergara to decide whether a permutation is so called lucky

The Longest Common Exemplar Subsequence Problem

In this paper, we propose to find order conserved subsequences of genomes by finding longest common exemplar subsequences of the genomes. The longest common exemplar subsequence problem is given by two genomes, asks to find a common exemplar subsequence of them, such that the exemplar subsequence length is maximized. We focus on genomes whose genes of the same gene family are in at most s spans. We propose a dynamic programming algorithm with time complexity O(s4 s mn) to find a longest common exemplar subsequence of two genomes with one genome admitting s span genes of the same gene family, where m, n stand for the gene numbers of those two given genomes. Our algorithm can be extended to find longest common exemplar subsequences of more than one genomes

Dual-enhanced word representations based on knowledge base

In this paper, we propose an approach for enhancing word representations twice based on large-scale knowledge bases. In the first layer of enhancement, we use the knowledge base as another contextual form corresponding to the corpus and add it to the training of distributed semantics including neural network based and matrix-based. In the second layer, we utilize local features of the knowledge base to enhance the word representations by mutual reinforcement between the keyword and the strongly associated words. We evaluate our approach not only on the well-known datasets but also on a brand-new dataset, IQ-Synonym-323. The results show that our approach compares favorably to other word representations

Unsupervised Segmentation of Chinese Corpus Using Accessor Variety (Extended Abstract)

Haodi Feng City University of Hong Kong [email protected] Kang Chen and Technology TsingHua University, Beijing, PRC Chunyu Kit Department of Chinese, Translation and Linguistics Xiaotie Deng City University of Hong Kong Abstract Chinese texts are di#erent from English texts in that they have no spaces to mark the boundaries of words. This makes the segmentation a special issue in Chinese texts processing. Since the amount of Chinese texts grows rapidly, especially due to the fast increase of the Internet, the number of Chinese words is also increasing fast. Those segmentation methods that depend on an existing dictionary thus have an obvious defect when they are used to segment texts which may contain words unknown to the dictionary

Stimulus-Responsive Metal–Organic Framework Signal-Reporting System for Photoelectrochemical and Fluorescent Dual-Mode Detection of ATP

Dual-mode bioanalysis integrating photoelectrochemical (PEC) and other modes is emerging and allows signal cross-checking for more reliable results. Metal–organic frameworks (MOFs) have been shown to be attractive materials in various biological applications. This work presents the utilization of MOF encapsulation and stimuli-responsive decapsulation for dual-mode PEC and fluorescence (FL) bioanalysis. Photoactive dye methylene violet (MV) was encapsulated in zeolitic imidazolate framework-90 (ZIF-90) to form an MV@ZIF-90 hybrid material, and MV could be released by adenosine triphosphate (ATP)-induced ZIF-90 disintegration. The released MV not only had FL emission but also had a sensitization effect on the ZnIn2S4 (ZnInS) photoanode. Based on the MV-dependent sensitization effect and FL emission characteristic, a dual-mode PEC–FL strategy was established for ATP detection with low detection limits, that is, 3.2 and 4.1 pM for PEC and FL detection, respectively. This study features and will inspire the construction and implementation of smart MOF materials for dual-mode bioanalysis

Lamellar Keratoplasty Using Acellular Bioengineering Cornea (BioCorneaVet^TM) for the Treatment of Feline Corneal Sequestrum: A Retrospective Study of 62 Eyes (2018–2021)

To retrospectively evaluate the effectiveness and outcome of lamellar keratoplasty using acellular bioengineering cornea (BioCorneaVetTM) for the treatment of feline corneal sequestrum (FCS). The medical records of cats diagnosed with FCS that underwent lamellar keratoplasty with BioCorneaVetTM between 2018 and 2021 with a minimum of 3 months of follow-up were reviewed. Follow-up examinations were performed weekly for 3 months, and then optical coherence tomography (OCT) examination was performed on select patients at 0, 3, 6, and 12 months post-operatively. A total of 61 cats (30 left eyes and 32 right eyes) were included. The Persian breed was overrepresented, 48/61 (78.69%). Four different thicknesses of acellular bioengineering cornea were used (200, 300, 400, or 450 microns), and the mean graft size was 8.23 mm (range, 5.00–12.00 mm). Minor complications were composed of partial dehiscence, and protrusion of the graft occurred in 7/62 eyes (11.29%). The median postoperative follow-up was 12.00 months (range, 3–41 months). A good visual outcome was achieved in 60/62 eyes (96.77%), and a mild to moderate corneal opacification occurred in 2/62 (3.23%). No recurrence of corneal sequestrum was observed. From the results, lamellar keratoplasty using acellular bioengineering cornea (BioCorneaVetTM) is an effective treatment for FCS, providing a good tectonic support and natural collagen framework, and resulting in satisfactory visual and cosmetic effects