A 2-Approximation Algorithm for the Complementary Maximal Strip Recovery Problem

The Maximal Strip Recovery problem (MSR) and its complementary (CMSR) are well-studied NP-hard problems in computational genomics. The input of these dual problems are two signed permutations. The goal is to delete some gene markers from both permutations, such that, in the remaining permutations, each gene marker has at least one common neighbor. Equivalently, the resulting permutations could be partitioned into common strips of length at least two. Then MSR is to maximize the number of remaining genes, while the objective of CMSR is to delete the minimum number of gene markers. In this paper, we present a new approximation algorithm for the Complementary Maximal Strip Recovery (CMSR) problem. Our approximation factor is 2, improving the currently best 7/3-approximation algorithm. Although the improvement on the factor is not huge, the analysis is greatly simplified by a compensating method, commonly referred to as the non-oblivious local search technique. In such a method a substitution may not always increase the value of the current solution (it sometimes may even decrease the solution value), though it always improves the value of another function seemingly unrelated to the objective function

Isomorphism and Similarity for 2-Generation Pedigrees

We consider the emerging problem of comparing the similarity between (unlabeled) pedigrees. More specifically, we focus on the simplest pedigrees, namely, the 2-generation pedigrees. We show that the isomorphism testing for two 2-generation pedigrees is GI-hard. If the 2-generation pedigrees are monogamous (i.e., each individual at level-1 can mate with exactly one partner) then the isomorphism testing problem can be solved in polynomial time. We then consider the problem by relaxing it into an NP-complete decomposition problem which can be formulated as the Minimum Common Integer Pair Partition (MCIPP) problem, which we show to be FPT by exploiting a property of the optimal solution. While there is still some difficulty to overcome, this lays down a solid foundation for this research

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

Genomic Scaffold Filling Revisited

The genomic scaffold filling problem has attracted a lot of attention recently. The problem is on filling an incomplete sequence (scaffold) I into I\u27, with respect to a complete reference genome G, such that the number of adjacencies between G and I\u27 is maximized. The problem is NP-complete and APX-hard, and admits a 1.2-approximation. However, the sequence input I is not quite practical and does not fit most of the real datasets (where a scaffold is more often given as a list of contigs). In this paper, we revisit the genomic scaffold filling problem by considering this important case when, (1) a scaffold S is given, the missing genes X = c(G) - c(S) can only be inserted in between the contigs, and the objective is to maximize the number of adjacencies between G and the filled S\u27 and (2) a scaffold S is given, a subset of the missing genes X\u27 subset X = c(G) - c(S) can only be inserted in between the contigs, and the objective is still to maximize the number of adjacencies between G and the filled S\u27\u27. For problem (1), we present a simple NP-completeness proof, we then present a factor-2 greedy approximation algorithm, and finally we show that the problem is FPT when each gene appears at most d times in G. For problem (2), we prove that the problem is W[1]-hard and then we present a factor-2 FPT-approximation for the case when each gene appears at most d times in G

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

Alcohol misuse, health-related behaviors, and burnout among clinical therapists in China during the early Covid-19 pandemic: A Nationwide survey

ObjectivesThis study aimed to assess the extent of alcohol use and misuse among clinical therapists working in psychiatric hospitals in China during the early COVID-19 Pandemic, and to identify associated factors.MethodsAn anonymous nationwide survey was conducted in 41 tertiary psychiatric hospitals. We collected demographic data as well as alcohol use using the Alcohol Use Disorders Identification Test-Consumption (AUDIT-C) and burnout using the Maslach Burnout Inventory Human Services Survey.ResultsIn total, 396 clinical therapists completed the survey, representing 89.0% of all potential participants we targeted. The mean age of participants was 33.8 years old, and more than three-quarters (77.5%) were female. Nearly two-fifths (39.1%) self-reported as current alcohol users. The overall prevalence of alcohol misuse was 6.6%. Nearly one-fifth (19.9%) reported symptoms of burnout with high emotional exhaustion in 46 (11.6%), and high depersonalization in 61 (15.4%). Multiple logistic regression showed alcohol use was associated with male gender (OR = 4.392; 95% CI =2.443–7.894), single marital status (OR = 1.652; 95% CI =0.970–2.814), smoking habit (OR = 3.847; 95%CI =1.160–12.758) and regular exercise (OR = 2.719; 95%CI =1.490–4.963). Alcohol misuse was associated with male gender (OR = 3.367; 95% CI =1.174–9.655), a lower education level (OR = 3.788; 95%CI =1.009–14.224), smoking habit (OR = 4.626; 95%CI =1.277–16.754) and high burnout (depersonalization, OR = 4.848; 95%CI =1.433–16.406).ConclusionDuring the COVID-19 pandemic, clinical therapists’ alcohol consumption did not increase significantly. Male gender, cigarette smoking, and burnout are associated with an increased risk of alcohol misuse among clinical therapists. Targeted intervention is needed when developing strategies to reduce alcohol misuse and improve clinical therapists’ wellness and mental health

Comparative Spectroscopic and Electrochemical Properties of Bis (octakis (dodecylthio) naphthalocyaninato) europium (III) and Bis (tetra-tert-butylnaphthalocyaninato) europium (III) Complexes

Bis(substituted-2,3-naphthalocyaninato)europium(III) complexes:  bis(octakis(dodecylthio)-2,3-naphthalocyaninato)europium(III) {Eu[2,3-Nc(SC12H25)8]2, 1} and bis(tetra-tert-butyl-2,3-naphthalocyaninato)europium(III) {Eu[2,3-Nc(t-Bu)4]2, 2} have been synthesized by cyclic tetramerization of naphthalonitriles with Eu(acac)3·H2O in the presence of 1,8-diazabicyclo[5.4.0]undec-7-ene (DBU) in refluxing n-octanol. These compounds were characterized by UV−visible, magnetic circular dichroism (MCD), near-IR, IR, EPR, and mass spectroscopies. The absorption and MCD spectra of 1 showed splitting of the Q band, with peaks at 700 and 784 nm, red shifted from the Q band of 2 at 763 nm. The absorption and MCD spectral band deconvolution calculations of complex 1 gave two A terms in the Q-band region. The A terms are assigned to 2A2 → 2E1 transitions. Cyclic voltammograms of 1 and 2 showed reversible oxidation couples at E1/2 = −0.28 V (for 2) and −0.25 V (for 1) vs ferrocenium/ferrocene (Fc+/Fc). The second oxidation exhibited a complicated behavior for both complexes. The reduction couples for 2 were observed at E1/2 = −0.61, −1.64, −1.97, and −2.42 V, and for 1 they were observed at E1/2 = −0.62, −1.60, −1.86, and −2.27 V vs Fc+/Fc. Spectral changes observed on chemical oxidation and reduction of the complexes are presented, and the behaviors of 1 and 2 are compared