Energy landscapes of some matching-problem ensembles

The maximum-weight matching problem and the behavior of its energy landscape is numerically investigated. We apply a perturbation method adapted from the analysis of spin glasses. This gives inside into the complexity of the energy landscape of different ensembles. Erd\"os-Renyi graphs and ring graphs with randomly added edges are considered and two types of distributions for the random edge weighs are used. For maximum-weight matching, fast and scalable algorithms exist, such that we can study large graphs of more than $10^5$ nodes. Our results show that the structure of the energy landscape for standard ensembles of matching is simple, comparable to the energy landscape of a ferromagnet. Nonetheless, for some of the here presented ensembles our results allow for the presence of complex energy landscapes in the spirit of Replica-Symmetry Breaking.Comment: 9 pages, 5 figure

Genome-wide identification of aquaporin encoding genes in Brassica oleracea and their phylogenetic sequence comparison to Brassica crops and Arabidopsis

Aquaporins (AQPs) are essential channel proteins that regulate plant water homeostasis and the uptake and distribution of uncharged solutes such as metalloids, urea, ammonia and carbon dioxide. Despite their importance as crop plants, little is known about AQP gene and protein function in cabbage (Brassica oleracea) and other Brassica species. The recent releases of the genome sequences of B. oleracea and B. rapa allow comparative genomic studies in these species to investigate the evolution and features of Brassica genes and proteins.In this study, we identified all AQP genes in B. oleracea by a genome-wide survey. In total, 67 genes of four plant AQP subfamilies were identified. Their full-length gene sequences and locations on chromosomes and scaffolds were manually curated. The identification of six additional full-length AQP sequences in the B. rapa genome added to the recently published AQP protein family of this species. A phylogenetic analysis of AQPs of A. thaliana, B. oleracea, B. rapa allowed us to follow AQP evolution in closely related species and to systematically classify and (re-) name these isoforms. Thirty-three groups of AQP-orthologous genes were identified between B. oleracea and Arabidopsis and their expression was analyzed in different organs. The two selectivity filters, gene structure and coding sequences were highly conserved within each AQP subfamily while sequence variations in some introns and untranslated regions were frequent. These data suggest a similar substrate selectivity and function of Brassica AQPs compared to Arabidopsis orthologs. The comparative analyses of all AQP subfamilies in three Brassicaceae species give initial insights into AQP evolution in these taxa. Based on the genome-wide AQP identification in B. oleracea and the sequence analysis and reprocessing of Brassica AQP information, our dataset provides a sequence resource for further investigations of the physiological and molecular functions of Brassica crop AQPs

Information on the nuclear periphery from antiprotonic atoms

In the PS209 experiments at CERN two kinds of measurements were performed: the in-beam measurement of X-rays from antiprotonic atoms and the radiochemical, off-line determination of the yield of annihilation products with mass number At — 1 (less by 1 than the target mass). Both methods give observables which allows to study the peripheral matter density composition and distribution. A comparisons of the PS209 results with the theoretical and semiempirical predictions for neutron and proton densities and with the differences Arnp of the rms radii of neutrons and protons obtained in other experiments are also presented

Satzverständnisleistungen von Kindern mit und ohne SSES im TROG-D und einer schweizerdeutschen Adaptation

Background: Certain challenges are associated with identifying children with speech comprehension disorders, as those children typically acquire compensatory strategies of communication, often resul- ting in late identification. In addition, speech therapists in the German-speaking part of Switzerland must employ assessment instruments that are designed for standard German and not for Swiss Ger- man. Those instruments are therefore executed in standard German or must be spontaneously transla- ted into Swiss German. Until now it has been unclear which of these options do the Swiss German-spea- king children justice. Aims: The aim of this study was to compare the sentence comprehension performances of monolingu- al children with and without specific language impairment (SLI) on a test designed in standard German and on a Swiss German translation of the same test. This study also compared the sentence comprehen- sion performances in both versions of the test within the groups. Methods: The sample consists of 481 children living in the canton of Bern (CH). At the time of testing, they were currently attending the grades of kindergarten up to the third grade. The children were tested with the TROG-D (Fox 2013) and with a Swiss German translation of this test. The sequence of the lan- guage versions was randomized. In the statistical analysis, children with SLI (diagnosed through speech language therapist) were matched with children without SLI. Statistical significance was tested by the cal- culation of paired t-tests. Results: The only statistically significant difference in assessment scores occurred in children with SLI compared with children without SLI, when assessed with the Swiss German translation of the test (p<.05, d=.41). The performance in standard German did not differ between groups. Within the groups, no dif- ferences between the sentence comprehension performances in standard German and Swiss German were found. Conclusions: The need for a Swiss German adaptation of the test seems questionable. However, differen- tiation of the sentence comprehension performances between children with and without SLI was only possible in the Swiss German version of the test. This result may be due to the low performance of the children without SLI in the standard German test, but there is insufficient data to confirm this possibi- lity. Further data analyses and controlled studies are needed to clarify the diagnostic issues addressed in the presented study more thoroughly

Independent Recruitment of a Flavin-Dependent Monooxygenase for Safe Accumulation of Sequestered Pyrrolizidine Alkaloids in Grasshoppers and Moths

Several insect lineages have developed diverse strategies to sequester toxic pyrrolizidine alkaloids from food-plants for their own defense. Here, we show that in two highly divergent insect taxa, the hemimetabolous grasshoppers and the holometabolous butterflies, an almost identical strategy evolved independently for safe accumulation of pyrrolizidine alkaloids. This strategy involves a pyrrolizidine alkaloid N-oxygenase that transfers the pyrrolizidine alkaloids to their respective N-oxide, enabling the insects to avoid high concentrations of toxic pyrrolizidine alkaloids in the hemolymph. We have identified a pyrrolizidine alkaloid N-oxygenase, which is a flavin-dependent monooxygenase, of the grasshopper Zonocerus variegatus. After heterologous expression in E. coli, this enzyme shows high specificity for pyrrolizidine alkaloids of various structural types and for the tropane alkaloid atropine as substrates, a property that has been described previously for a pyrrolizidine alkaloid N-oxygenase of the arctiid moth Grammia geneura. Phylogenetic analyses of insect flavin-dependent monooxygenase sequences suggest that independent gene duplication events preceded the establishment of this specific enzyme in the lineages of the grasshoppers and of arctiid moths. Two further flavin-dependent monooxygenase sequences have been identified from Z. variegatus sharing amino acid identities of approximately 78% to the pyrrolizidine alkaloid N-oxygenase. After heterologous expression, both enzymes are also able to catalyze the N-oxygenation of pyrrolizidine alkaloids, albeit with a 400-fold lower specific activity. With respect to the high sequence identity between the three Z. variegatus sequences this ability to N-oxygenize pyrrolizidine alkaloids is interpreted as a relict of a former bifunctional ancestor gene of which one of the gene copies optimized this activity for the specific adaptation to pyrrolizidine alkaloid containing food plants

Molecularly defined diffuse leptomeningeal glioneuronal tumor (DLGNT) comprises two subgroups with distinct clinical and genetic features

Diffuse leptomeningeal glioneuronal tumors (DLGNT) represent rare CNS neoplasms which have been included in the 2016 update of the WHO classification. The wide spectrum of histopathological and radiological features can make this enigmatic tumor entity difficult to diagnose. In recent years, large-scale genomic and epigenomic analyses have afforded insight into key genetic alterations occurring in multiple types of brain tumors and provide unbiased, complementary tools to improve diagnostic accuracy. Through genome-wide DNA methylation screening of &gt; 25,000 tumors, we discovered a molecularly distinct class comprising 30 tumors, mostly diagnosed histologically as DLGNTs. Copy-number profiles derived from the methylation arrays revealed unifying characteristics, including loss of chromosomal arm 1p in all cases. Furthermore, this molecular DLGNT class can be subdivided into two subgroups [DLGNT methylation class (MC)-1 and DLGNT methylation class (MC)-2], with all DLGNT-MC-2 additionally displaying a gain of chromosomal arm 1q. Co-deletion of 1p/19q, commonly seen in IDH-mutant oligodendroglioma, was frequently observed in DLGNT, especially in DLGNT-MC-1 cases. Both subgroups also had recurrent genetic alterations leading to an aberrant MAPK/ERK pathway, with KIAA1549:BRAF fusion being the most frequent event. Other alterations included fusions of NTRK1/2/3 and TRIM33:RAF1, adding up to an MAPK/ERK pathway activation identified in 80% of cases. In the DLGNT-MC-1 group, age at diagnosis was significantly lower (median 5 vs 14 years, p &lt; 0.01) and clinical course less aggressive (5-year OS 100, vs 43% in DLGNT-MC-2). Our study proposes an additional molecular layer to the current histopathological classification of DLGNT, of particular use for cases without typical morphological or radiological characteristics, such as diffuse growth and radiologic leptomeningeal dissemination. Recurrent 1p deletion and MAPK/ERK pathway activation represent diagnostic biomarkers and therapeutic targets, respectively—laying the foundation for future clinical trials with, e.g., MEK inhibitors that may improve the clinical outcome of patients with DLGNT

Glioblastomas with primitive neuronal component harbor a distinct methylation and copy‑number profle with inactivation of TP53, PTEN, and RB1

Glioblastoma IDH-wildtype presents with a wide histological spectrum. Some features are so distinctive that they are considered as separate histological variants or patterns for the purpose of classification. However, these usually lack defined (epi-)genetic alterations or profiles correlating with this histology. Here, we describe a molecular subtype with overlap to the unique histological pattern of glioblastoma with primitive neuronal component. Our cohort consists of 63 IDH-wildtype glioblastomas that harbor a characteristic DNA methylation profile. Median age at diagnosis was 59.5 years. Copy-number variations and genetic sequencing revealed frequent alterations in TP53, RB1 and PTEN, with fewer gains of chromosome 7 and homozygous CDKN2A/B deletions than usually described for IDH-wildtype glioblastoma. Gains of chromosome 1 were detected in more than half of the cases. A poorly differentiated phenotype with frequent absence of GFAP expression, high proliferation index and strong staining for p53 and TTF1 often caused misleading histological classification as carcinoma metastasis or primitive neuroectodermal tumor. Clinically, many patients presented with leptomeningeal dissemination and spinal metastasis. Outcome was poor with a median overall survival of only 12 months. Overall, we describe a new molecular subtype of IDH-wildtype glioblastoma with a distinct histological appearance and genetic signature.publishedVersio