Sheaves on fibered threefolds and quiver sheaves

This paper classifies a class of holomorphic D-branes, closely related to framed torsion-free sheaves, on threefolds fibered in resolved ADE surfaces over a general curve C, in terms of representations with relations of a twisted Kronheimer--Nakajima-type quiver in the category Coh(C) of coherent sheaves on C. For the local Calabi--Yau case C\cong\A^1 and special choice of framing, one recovers the N=1 ADE quiver studied by Cachazo--Katz--Vafa.Comment: 13 pages, 2 figures, minor change

Noncommutative resolutions of ADE fibered Calabi-Yau threefolds

In this paper we construct noncommutative resolutions of a certain class of Calabi-Yau threefolds studied by F. Cachazo, S. Katz and C. Vafa. The threefolds under consideration are fibered over a complex plane with the fibers being deformed Kleinian singularities. The construction is in terms of a noncommutative algebra introduced by V. Ginzburg, which we call the "N=1 ADE quiver algebra"

Structure of a large social network

We study a social network consisting of over $10^4$ individuals, with a degree distribution exhibiting two power scaling regimes separated by a critical degree $k_{\rm crit}$, and a power law relation between degree and local clustering. We introduce a growing random model based on a local interaction mechanism that reproduces all of the observed scaling features and their exponents. Our results lend strong support to the idea that several very different networks are simultenously present in the human social network, and these need to be taken into account for successful modeling.Comment: 5 pages, 5 figure

Wall Crossing of BPS States on the Conifold from Seiberg Duality and Pyramid Partitions

In this paper we study the relation between pyramid partitions with a general empty room configuration (ERC) and the BPS states of D-branes on the resolved conifold. We find that the generating function for pyramid partitions with a length n ERC is exactly the same as the D6/D2/D0 BPS partition function on the resolved conifold in particular Kaehler chambers. We define a new type of pyramid partition with a finite ERC that counts the BPS degeneracies in certain other chambers. The D6/D2/D0 partition functions in different chambers were obtained by applying the wall crossing formula. On the other hand, the pyramid partitions describe T^3 fixed points of the moduli space of a quiver quantum mechanics. This quiver arises after we apply Seiberg dualities to the D6/D2/D0 system on the conifold and choose a particular set of FI parameters. The arrow structure of the dual quiver is confirmed by computation of the Ext group between the sheaves. We show that the superpotential and the stability condition of the dual quiver with this choice of the FI parameters give rise to the rules specifying pyramid partitions with length n ERC.Comment: 23 pages, 8 figures. CMP versio

Opposite prognostic roles of HIF1α and HIF2α expressions in bone metastatic clear cell renal cell cancer

BACKGROUND Prognostic markers of bone metastatic clear cell renal cell cancer (ccRCC) are poorly established. We tested prognostic value of HIF1α/HIF2α and their selected target genes in primary tumors and corresponding bone metastases. RESULTS Expression of HIF2α was lower in mRCC both at mRNA and protein levels (p/mRNA/=0.011, p/protein/=0.001) while HIF1α was similar to nmRCC. At the protein level, CAIX, GAPDH and GLUT1 were increased in mRCC. In all primary RCCs, low HIF2α and high HIF1α as well as CAIX, GAPDH and GLUT1 expressions correlated with adverse prognosis, while VEGFR2 and EPOR gene expressions were associated with favorable prognosis. Multivariate analysis confirmed high HIF2α protein expression as an independent risk factor. Prognostic validation of HIFs, LDH, EPOR and VEGFR2 in RNA-Seq data confirmed higher HIF1α gene expression in primary RCC as an adverse (p=0.07), whereas higher HIF2α and VEGFR2 expressions as favorable prognostic factors. HIF1α/HIF2α-index (HIF-index) proved to be an independent prognostic factor in both the discovery and the TCGA cohort. PATIENTS AND METHODS Expressions of HIF1α and HIF2α as well as their 7 target genes were analysed on the mRNA and protein level in 59 non-metastatic ccRCCs (nmRCC), 40 bone metastatic primary ccRCCs (mRCC) and 55 corresponding bone metastases. Results were validated in 399 ccRCCs from the TCGA project. CONCLUSIONS We identified HIF2α protein as an independent marker of the metastatic potential of ccRCC, however, unlike HIF1α, increased HIF2α expression is a favorable prognostic factor. The HIF-index incorporated these two markers into a strong prognostic biomarker of ccRCC

Curve counting via stable pairs in the derived category

For a nonsingular projective 3-fold $X$, we define integer invariants virtually enumerating pairs $(C,D)$ where $C\subset X$ is an embedded curve and $D\subset C$ is a divisor. A virtual class is constructed on the associated moduli space by viewing a pair as an object in the derived category of $X$. The resulting invariants are conjecturally equivalent, after universal transformations, to both the Gromov-Witten and DT theories of $X$. For Calabi-Yau 3-folds, the latter equivalence should be viewed as a wall-crossing formula in the derived category. Several calculations of the new invariants are carried out. In the Fano case, the local contributions of nonsingular embedded curves are found. In the local toric Calabi-Yau case, a completely new form of the topological vertex is described. The virtual enumeration of pairs is closely related to the geometry underlying the BPS state counts of Gopakumar and Vafa. We prove that our integrality predictions for Gromov-Witten invariants agree with the BPS integrality. Conversely, the BPS geometry imposes strong conditions on the enumeration of pairs.Comment: Corrected typos and duality error in Proposition 4.6. 47 page

Contrastive focus and emphasis

The paper puts forward a discourse-semantic account of the notoriously evasive phenomena of contrastivity and emphasis. Based on new evidence from Chadic, it is argued that occurrences of focus that are treated in terms of ‘contrastive focus’, ‘kontrast’ (Vallduví-Vilkuna 1998) or ‘identificational focus’ (É. Kiss 1998) in the literature should not be analyzed in familiar semantic terms as involving the introduction and subsequent exclusion of alternatives. Rather, an adequate analysis must take into account discourse-semantic notions like ‘hearer expectation’ or ‘discourse expectability’ of the focused content in a given discourse situation. The less expected the focus content is judged to be for the hearer, relative to the Common Ground, the more likely a speaker is to mark the focus constituent by means of special grammatical devices, thus giving rise to emphasis

Reconstructive periodontal therapy with simultaneous ridge augmentation. A clinical and histological case series report

Treatment of intrabony periodontal defects with a combination of a natural bone mineral (NBM) and guided tissue regeneration (GTR) has been shown to promote periodontal regeneration in intrabony defects. In certain clinical situations, the teeth presenting intrabony defects are located at close vicinity of the resorbed alveolar ridge. In these particular cases, it is of clinical interest to simultaneously reconstruct both the intrabony periodontal defect and the resorbed alveolar ridge, thus allowing insertion of endosseous dental implants. The aim of the present study was to present the clinical and histological results obtained with a new surgical technique designed to simultaneously reconstruct the intrabony defect and the adjacently located resorbed alveolar ridge. Eight patients with chronic advanced periodontitis displaying intrabony defects located in the close vicinity of resorbed alveolar ridges were consecutively enrolled in the study. After local anesthesia, mucoperiosteal flaps were raised, the granulation tissue removed, and the roots meticulously scaled and planed. A subepithelial connective tissue graft was harvested from the palate and sutured to the oral flap. The intrabony defect and the adjacent alveolar ridge were filled with a NBM and subsequently covered with a bioresorbable collagen membrane (GTR). At 11–20 months (mean, 13.9 ± 3.9 months) after surgery, implants were placed, core biopsies retrieved, and histologically evaluated. Mean pocket depth reduction measured 3.8 ± 1.7 mm and mean clinical attachment level gain 4.3 ± 2.2 mm, respectively. Reentry revealed in all cases a complete fill of the intrabony component and a mean additional vertical hard tissue gain of 1.8 ± 1.8 mm. The histologic evaluation indicated that most NBM particles were surrounded by bone. Mean new bone and mean graft area measured 17.8 ± 2.8% and 32.1 ± 8.3%, respectively. Within their limits, the present findings indicate that the described surgical approach may be successfully used in certain clinical cases to simultaneously treat intrabony defects and to reconstruct the resorbed alveolar ridge

Identifying Resistance Mechanisms against Five Tyrosine Kinase Inhibitors Targeting the ERBB/RAS Pathway in 45 Cancer Cell Lines

Because of the low overall response rates of 10-47% to targeted cancer therapeutics, there is an increasing need for predictive biomarkers. We aimed to identify genes predicting response to five already approved tyrosine kinase inhibitors. We tested 45 cancer cell lines for sensitivity to sunitinib, erlotinib, lapatinib, sorafenib and gefitinib at the clinically administered doses. A resistance matrix was determined, and gene expression profiles of the subsets of resistant vs. sensitive cell lines were compared. Triplicate gene expression signatures were obtained from the caArray project. Significance analysis of microarrays and rank products were applied for feature selection. Ninety-five genes were also measured by RT-PCR. In case of four sunitinib resistance associated genes, the results were validated in clinical samples by immunohistochemistry. A list of 63 top genes associated with resistance against the five tyrosine kinase inhibitors was identified. Quantitative RT-PCR analysis confirmed 45 of 63 genes identified by microarray analysis. Only two genes (ANXA3 and RAB25) were related to sensitivity against more than three inhibitors. The immunohistochemical analysis of sunitinib-treated metastatic renal cell carcinomas confirmed the correlation between RAB17, LGALS8, and EPCAM and overall survival. In summary, we determined predictive biomarkers for five tyrosine kinase inhibitors, and validated sunitinib resistance biomarkers by immunohistochemistry in an independent patient cohort. © 2013 Pénzváltó et al