Stack and Queue Layouts via Layered Separators

It is known that every proper minor-closed class of graphs has bounded stack-number (a.k.a. book thickness and page number). While this includes notable graph families such as planar graphs and graphs of bounded genus, many other graph families are not closed under taking minors. For fixed $g$ and $k$, we show that every $n$-vertex graph that can be embedded on a surface of genus $g$ with at most $k$ crossings per edge has stack-number $\mathcal{O}(\log n)$; this includes $k$-planar graphs. The previously best known bound for the stack-number of these families was $\mathcal{O}(\sqrt{n})$, except in the case of $1$-planar graphs. Analogous results are proved for map graphs that can be embedded on a surface of fixed genus. None of these families is closed under taking minors. The main ingredient in the proof of these results is a construction proving that $n$-vertex graphs that admit constant layered separators have $\mathcal{O}(\log n)$ stack-number.Comment: Appears in the Proceedings of the 24th International Symposium on Graph Drawing and Network Visualization (GD 2016

Genotyping isolates of the entomopathogenic fungus Beauveria bassiana sensu lato by multi-locus polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) analysis

Multi-locus denaturing gradient gel electrophoresis (DGGE) analysis was developed to investigate the genotypes of Beauveria bassiana sensu lato. Sensitive tests indicated all isolates with one or more nucleotide differences at EF-1 and Bloc could be distinguished by DGGE except for one pair of strains that differed at four nucleotide positions. Ten, twelve and five genotypes were identified at the EF-1, Bloc and ITS locus, respectively, among seventeen isolates, which together differentiated 13 genotypes. These results demonstrated that multi-locus DGGE is a potentially useful molecular marker for genotyping, identifying and tracking the fates of experimentally released strains of B. bassiana sensu lato. Moreover, by multi-locus DGGE for scanning B. bassiana sensu lato isolates with different multilocus sequences, genetic diversity of B. bassiana sensu lato was effectively investigated with substantially reduced time and cost in subsequent DNA sequencing

A natural product-like JAK2/STAT3 inhibitor induces apoptosis of malignant melanoma cells

The JAK2/STAT3 signaling pathway plays a critical role in tumorigenesis, and has been suggested as a potential molecular target for anti-melanoma therapeutics. However, few JAK2 inhibitors were being tested for melanoma therapy. In this study, eight amentoflavone analogues were evaluated for their activity against human malignant melanoma cells. The most potent analogue, compound 1, inhibited the phosphorylation of JAK2 and STAT3 in human melanoma cells, but had no discernible effect on total JAK2 and STAT3 levels. A cellular thermal shift assay was performed to identify that JAK2 is engaged by 1 in cell lysates. Moreover, compound 1 showed higher antiproliferative activity against human melanoma A375 cells compared to a panel of cancer and normal cell lines. Compound 1 also activated caspase-3 and cleaved PARP, which are markers of apoptosis, and suppressed the anti-apoptotic Bcl-2 level. Finally, compound 1 induced apoptosis in 80% of treated melanoma cells. To our knowledge, compound 1 is the first amentoflavone-based JAK2 inhibitor to be investigated for use as an anti-melanoma agent.published_or_final_versio

Relaxed 2-D Principal Component Analysis by LpL_p Norm for Face Recognition

A relaxed two dimensional principal component analysis (R2DPCA) approach is proposed for face recognition. Different to the 2DPCA, 2DPCA-$L_1$ and G2DPCA, the R2DPCA utilizes the label information (if known) of training samples to calculate a relaxation vector and presents a weight to each subset of training data. A new relaxed scatter matrix is defined and the computed projection axes are able to increase the accuracy of face recognition. The optimal $L_p$-norms are selected in a reasonable range. Numerical experiments on practical face databased indicate that the R2DPCA has high generalization ability and can achieve a higher recognition rate than state-of-the-art methods.Comment: 19 pages, 11 figure

A randomised, open label, active comparator trial assessing the effects of 26 weeks of liraglutide or sitagliptin on cardiovascular function in young obese adults with type 2 diabetes

Aim To compare the effects of a glucagon‐like peptide‐1 receptor agonist and a dipeptidyl peptidase‐4 inhibitor on magnetic resonance imaging‐derived measures of cardiovascular function. Materials and methods In a prospective, randomized, open‐label, blinded endpoint trial liraglutide (1.8 mg) and sitagliptin (100 mg) were compared in asymptomatic, non‐insulin treated young (aged 18‐50 years) adults with obesity and type 2 diabetes. The primary outcome was difference in circumferential peak early diastolic strain rate change (PEDSR), a biomarker of cardiac diastolic dysfunction 26 weeks after randomization. Secondary outcomes included other indices of cardiac structure and function, HbA1c and body weight. Results Seventy‐six participants were randomized (54% female, mean ± SD age 44 ± 6 years, diabetes duration 4.4 years, body mass index 35.3 ± 6.1 kg m−2), of whom 65% had ≥1 cardiovascular risk factor. Sixty‐one participants had primary outcome data available. There were no statistically significant between‐group differences (intention‐to‐treat; mean [95% confidence interval]) in PEDSR change (−0.01 [−0.07, +0.06] s−1), left ventricular ejection fraction (−1.98 [−4.90, +0.94]%), left ventricular mass (+1.14 [−5.23, +7.50] g) or aortic distensibility (−0.35 [−0.98, +0.28] mmHg−1 × 10−3) after 26 weeks. Reductions in HbA1c (−4.57 [−9.10, −0.37] mmol mol−1) and body weight (−3.88 [−5.74, −2.01] kg) were greater with liraglutide. Conclusion There were no differences in cardiovascular structure or function after short‐term use of liraglutide and sitagliptin in younger adults with obesity and type 2 diabetes. Longer studies in patients with more severe cardiac dysfunction may be necessary before definitive conclusions can be made about putative pleiotropic properties of incretin‐based therapies

Closest string with outliers

Background: Given n strings s1, …, sn each of length ℓ and a nonnegative integer d, the CLOSEST STRING problem asks to find a center string s such that none of the input strings has Hamming distance greater than d from s. Finding a common pattern in many – but not necessarily all – input strings is an important task that plays a role in many applications in bioinformatics. Results: Although the closest string model is robust to the oversampling of strings in the input, it is severely affected by the existence of outliers. We propose a refined model, the CLOSEST STRING WITH OUTLIERS (CSWO) problem, to overcome this limitation. This new model asks for a center string s that is within Hamming distance d to at least n – k of the n input strings, where k is a parameter describing the maximum number of outliers. A CSWO solution not only provides the center string as a representative for the set of strings but also reveals the outliers of the set. We provide fixed parameter algorithms for CSWO when d and k are parameters, for both bounded and unbounded alphabets. We also show that when the alphabet is unbounded the problem is W[1]-hard with respect to n – k, ℓ, and d. Conclusions: Our refined model abstractly models finding common patterns in several but not all input strings

Late presentation of superior mesenteric artery syndrome following scoliosis surgery: a case report

<p>Abstract</p> <p>Introduction</p> <p>Obstruction of the third part of the duodenum by the superior mesenteric artery (SMA) can occur following surgical correction of scoliosis. The condition most commonly occurs in significantly underweight patients with severe deformities during the first few days to a week following spinal surgery.</p> <p>Case presentation</p> <p>We present the atypical case of a patient with normal body habitus and a 50° adolescent idiopathic thoracolumbar scoliosis who underwent anterior spinal arthrodesis with instrumentation and developed SMA syndrome due to progressive weight loss several weeks postoperatively. The condition manifested with recurrent vomiting, abdominal distension, marked dehydration, and severe electrolyte disorder. Prolonged nasogastric decompression and nasojejunal feeding resulted in resolution of the symptoms with no recurrence at follow-up. The spinal instrumentation was retained and a solid spinal fusion was achieved with good spinal balance in both the coronal and sagittal planes.</p> <p>Conclusion</p> <p>SMA syndrome can occur much later than previously reported and with potentially life-threatening symptoms following scoliosis correction. Early recognition of the condition and institution of appropriate conservative measures is critical to prevent the development of severe complications including the risk of death.</p

Swiftly Computing Center Strings

Hufsky F, Kuchenbecker L, Jahn K, Stoye J, Böcker S. Swiftly Computing Center Strings. BMC Bioinformatics. 2011;12(1): 106

Malignant B Cells Induce the Conversion of CD4+CD25− T Cells to Regulatory T Cells in B-Cell Non-Hodgkin Lymphoma

Recent evidence has demonstrated that regulatory T cells (Treg) were enriched in the tumor sites of patients with B-cell non-Hodgkin lymphoma (NHL). However, the causes of enrichment and suppressive mechanisms need to be further elucidated. Here we demonstrated that CD4+CD25+FoxP3+CD127lo Treg were markedly increased and their phenotypes were different in peripheral blood (PB) as well as bone marrow (BM) from newly diagnosed patients with B-cell NHL compared with those from healthy volunteers (HVs). Involved lymphatic tissues also showed higher frequencies of Treg than benign lymph nodes. Moreover, the frequencies of Treg were significantly higher in involved lymphatic tissues than those from PB as well as BM in the same patients. Suppression mediated by CD4+CD25+ Treg co-cultured with allogeneic CFSE-labeled CD4+CD25− responder cells was also higher in involved lymphatic tissues from B-cell NHL than that mediated by Treg from HVs. In addition, we found that malignant B cells significantly induced FoxP3 expression and regulatory function in CD4+CD25− T cells in vitro. In contrast, normal B cells could not induce the conversion of CD4+CD25− T cells to Treg. We also showed that the PD-1/B7-H1 pathway might play an important role in Treg induction. Taken together, our results suggest that malignant B cells induce the conversion of CD4+CD25− T cells to Treg, which may play a role in the pathogenesis of B-cell NHL and represent a promising therapeutic target