Minimum Degree up to Local Complementation: Bounds, Parameterized Complexity, and Exact Algorithms

The local minimum degree of a graph is the minimum degree that can be reached by means of local complementation. For any n, there exist graphs of order n which have a local minimum degree at least 0.189n, or at least 0.110n when restricted to bipartite graphs. Regarding the upper bound, we show that for any graph of order n, its local minimum degree is at most 3n/8+o(n) and n/4+o(n) for bipartite graphs, improving the known n/2 upper bound. We also prove that the local minimum degree is smaller than half of the vertex cover number (up to a logarithmic term). The local minimum degree problem is NP-Complete and hard to approximate. We show that this problem, even when restricted to bipartite graphs, is in W[2] and FPT-equivalent to the EvenSet problem, which W[1]-hardness is a long standing open question. Finally, we show that the local minimum degree is computed by a O*(1.938^n)-algorithm, and a O*(1.466^n)-algorithm for the bipartite graphs

Acoustic cues to tonal contrasts in Mandarin: Implications for cochlear implants

The present study systematically manipulated three acoustic cues-fundamental frequency (f0), amplitude envelope, and duration-to investigate their contributions to tonal contrasts in Mandarin. Simplified stimuli with all possible combinations of these three cues were presented for identification to eight normal-hearing listeners, all native speakers of Mandarin from Taiwan. The f0 information was conveyed either by an f0-controlled sawtooth carrier or a modulated noise so as to compare the performance achievable by a clear indication of voice f0 and what is possible with purely temporal coding of f0. Tone recognition performance with explicit f0 was much better than that with any combination of other acoustic cues (consistently greater than 90% correct compared to 33%-65%; chance is 25%). In the absence of explicit f0, the temporal coding of f0 and amplitude envelope both contributed somewhat to tone recognition, while duration had only a marginal effect. Performance based on these secondary cues varied greatly across listeners. These results explain the relatively poor perception of tone in cochlear implant users, given that cochlear implants currently provide only weak cues to f0, so that users must rely upon the purely temporal (and secondary) features for the perception of tone. (c) 2008 Acoustical Society of America

Permutation complexity of the fixed points of some uniform binary morphisms

An infinite permutation is a linear order on the set N. We study the properties of infinite permutations generated by fixed points of some uniform binary morphisms, and find the formula for their complexity.Comment: In Proceedings WORDS 2011, arXiv:1108.341

EphA4 signaling regulates phospholipase Cgamma1 activation, cofilin membrane association, and dendritic spine morphology

Specialized postsynaptic structures known as dendritic spines are the primary sites of glutamatergic innervation at synapses of the CNS. Previous studies have shown that spines rapidly remodel their actin cytoskeleton to modify their shape and this has been associated with changes in synaptic physiology. However, the receptors and signaling intermediates that restructure the actin network in spines are only beginning to be identified. We reported previously that the EphA4 receptor tyrosine kinase regulates spine morphology. However, the signaling pathways downstream of EphA4 that induce spine retraction on ephrin ligand binding remain poorly understood. Here, we demonstrate that ephrin stimulation of EphA4 leads to the recruitment and activation of phospholipase Cgamma1 (PLCgamma1) in heterologous cells and in hippocampal slices. This interaction occurs through an Src homology 2 domain of PLCgamma1 and requires the EphA4 juxtamembrane tyrosines. In the brain, PLCgamma1 is found in multiple compartments of synaptosomes and is readily found in postsynaptic density fractions. Consistent with this, PLC activity is required for the maintenance of spine morphology and ephrin-induced spine retraction. Remarkably, EphA4 and PLC activity modulate the association of the actin depolymerizing/severing factor cofilin with the plasma membrane. Because cofilin has been implicated previously in the structural plasticity of spines, this signaling may enable cofilin to depolymerize actin filaments and restructure spines at sites of ephrin-EphA4 contact

S-, P- and D-wave resonances in positronium-sodium and positronium-potassium scattering

Scattering of positronium (Ps) by sodium and potassium atoms has been investigated employing a three-Ps-state coupled-channel model with Ps(1s,2s,2p) states using a time-reversal-symmetric regularized electron-exchange model potential fitted to reproduce accurate theoretical results for PsNa and PsK binding energies. We find a narrow S-wave singlet resonance at 4.58 eV of width 0.002 eV in the Ps-Na system and at 4.77 eV of width 0.003 eV in the Ps-K system. Singlet P-wave resonances in both systems are found at 5.07 eV of width 0.3 eV. Singlet D-wave structures are found at 5.3 eV in both systems. We also report results for elastic and Ps-excitation cross sections for Ps scattering by Na and K.Comment: 9 pages, 5 figures, Accepted in Journal of Physics

Statistical identification of gene association by CID in application of constructing ER regulatory network

<p>Abstract</p> <p>Background</p> <p>A variety of high-throughput techniques are now available for constructing comprehensive gene regulatory networks in systems biology. In this study, we report a new statistical approach for facilitating <it>in silico </it>inference of regulatory network structure. The new measure of association, coefficient of intrinsic dependence (CID), is model-free and can be applied to both continuous and categorical distributions. When given two variables X and Y, CID answers whether Y is dependent on X by examining the conditional distribution of Y given X. In this paper, we apply CID to analyze the regulatory relationships between transcription factors (TFs) (X) and their downstream genes (Y) based on clinical data. More specifically, we use estrogen receptor α (ERα) as the variable X, and the analyses are based on 48 clinical breast cancer gene expression arrays (48A).</p> <p>Results</p> <p>The analytical utility of CID was evaluated in comparison with four commonly used statistical methods, Galton-Pearson's correlation coefficient (GPCC), Student's <it>t</it>-test (STT), coefficient of determination (CoD), and mutual information (MI). When being compared to GPCC, CoD, and MI, CID reveals its preferential ability to discover the regulatory association where distribution of the mRNA expression levels on X and Y does not fit linear models. On the other hand, when CID is used to measure the association of a continuous variable (Y) against a discrete variable (X), it shows similar performance as compared to STT, and appears to outperform CoD and MI. In addition, this study established a two-layer transcriptional regulatory network to exemplify the usage of CID, in combination with GPCC, in deciphering gene networks based on gene expression profiles from patient arrays.</p> <p>Conclusion</p> <p>CID is shown to provide useful information for identifying associations between genes and transcription factors of interest in patient arrays. When coupled with the relationships detected by GPCC, the association predicted by CID are applicable to the construction of transcriptional regulatory networks. This study shows how information from different data sources and learning algorithms can be integrated to investigate whether relevant regulatory mechanisms identified in cell models can also be partially re-identified in clinical samples of breast cancers.</p> <p>Availability</p> <p>the implementation of CID in R codes can be freely downloaded from <url>http://homepage.ntu.edu.tw/~lyliu/BC/</url>.</p

Possible association between ABCC8 C49620T polymorphism and type 2 diabetes in a Nigerian population

The association between ABCC8 gene C49620T polymorphism and type 2 diabetes (T2D) in populations of diverse ethnic backgrounds has been reported. However, such occurrence in an African population is yet to be established. This case-control study involving 73 T2D and 75 non-diabetic (ND) patients investigated the occurrence of this polymorphism among T2D patients in Nigeria and assessed its relationship with body lipids of patients. Demographic and clinical characteristics of patients were collected and lipid profile indices including total cholesterol (TC), triglyceride (TG), low density lipoprotein (LDL) and high density lipoprotein (HDL) were assayed. Restriction fragment length polymorphism-PCR (RFLP-PCR) was employed to genotype the ABCC8-C49620T polymorphism using PstI restriction enzyme. This study revealed significantly (p 0.05) of T2D for the unadjusted codominant, dominant and recessive models. Following age adjustment, the mutant genotypes (CT and TT) showed significant (p<0.05) risk of T2D for all the models with the recessive model presenting the greatest risk of T2D (OR: 2.39, 95% CI: 1.16-4.91, p<0.018). The TT genotype significantly (p<0.05) associated with high level of HDL and reduced levels of TC, TG and LDL in non-diabetic patients but was not associated with any of the demographic and clinical characteristics among T2D patients. ABCC8 C49620T polymorphism showed possible association with T2D marked by predominance of the mutant TT genotype in T2D patients. However, the relationship between TT genotype and lipid abnormalities for possible beneficial effect on people suffering from T2D is unclear

Low back pain as the presenting sign in a patient with primary extradural melanoma of the thoracic spine - A metastatic disease 17 Years after complete surgical resection

Primary spinal melanomas are extremely rare lesions. In 1906, Hirschberg reported the first primary spinal melanoma, and since then only 40 new cases have been reported. A 47-year-old man was admitted suffering from low back pain, fatigue and loss of body weight persisting for three months. He had a 17-year-old history of an operated primary spinal melanoma from T7-T9, which had remained stable for these 17 years. Routine laboratory findings and clinical symptoms aroused suspicion of a metastatic disease. Multislice computed tomography and magnetic resonance imaging revealed stage-IV melanoma with thoracic, abdominal and skeletal metastases without the recurrence of the primary process. Transiliac crest core bone biopsy confirmed the diagnosis of metastatic melanoma. It is important to know that in all cases of back ore skeletal pain and unexplained weight loss, malignancy must always be considered in the differential diagnosis, especially in the subjects with a positive medical history. Patients who have back, skeletal, or joint pain that is unresponsive to a few weeks of conservative treatment or have known risk factors with or without serious etiology, are candidates for imaging studies. The present case demonstrates that complete surgical resection alone may result in a favourable outcome, but regular medical follow-up for an extended period, with the purpose of an early detection of a metastatic disease, is highly recommended

Author Correction: Elucidating causative gene variants in hereditary Parkinson’s disease in the Global Parkinson’s Genetics Program (GP2)

Correction to: npj Parkinson’s Disease, published online 27 June 2023 In this article the Global Parkinson’s Genetics Program (GP2) members names and affiliations were missing in the main author list of the Original article which are listed in the below