Searching for patterns in political event sequences: Experiments with the KEDs database

This paper presents an empirical study on the possibility of discovering interesting event sequences and sequential rules in a large database of international political events. A data mining algorithm first presented by Mannila and Toivonen (1996), has been implemented and extended, which is able to search for generalized episodes in such event databases. Experiments conducted with this algorithm on the Kansas Event Data System (KEDS) database, an event data set covering interactions between countries in the Persian Gulf region, are described. Some qualitative and quantitative results are reported, and experiences with strategies for reducing the problem complexity and focusing on the search on interesting subsets of events are described

A randomized multi-center phase II trial of the angiogenesis inhibitor Cilengitide (EMD 121974) and gemcitabine compared with gemcitabine alone in advanced unresectable pancreatic cancer

BACKGROUND: Anti-angiogenic treatment is believed to have at least cystostatic effects in highly vascularized tumours like pancreatic cancer. In this study, the treatment effects of the angiogenesis inhibitor Cilengitide and gemcitabine were compared with gemcitabine alone in patients with advanced unresectable pancreatic cancer. METHODS: A multi-national, open-label, controlled, randomized, parallel-group, phase II pilot study was conducted in 20 centers in 7 countries. Cilengitide was administered at 600 mg/m(2 )twice weekly for 4 weeks per cycle and gemcitabine at 1000 mg/m(2 )for 3 weeks followed by a week of rest per cycle. The planned treatment period was 6 four-week cycles. The primary endpoint of the study was overall survival and the secondary endpoints were progression-free survival (PFS), response rate, quality of life (QoL), effects on biological markers of disease (CA 19.9) and angiogenesis (vascular endothelial growth factor and basic fibroblast growth factor), and safety. An ancillary study investigated the pharmacokinetics of both drugs in a subset of patients. RESULTS: Eighty-nine patients were randomized. The median overall survival was 6.7 months for Cilengitide and gemcitabine and 7.7 months for gemcitabine alone. The median PFS times were 3.6 months and 3.8 months, respectively. The overall response rates were 17% and 14%, and the tumor growth control rates were 54% and 56%, respectively. Changes in the levels of CA 19.9 went in line with the clinical course of the disease, but no apparent relationships were seen with the biological markers of angiogenesis. QoL and safety evaluations were comparable between treatment groups. Pharmacokinetic studies showed no influence of gemcitabine on the pharmacokinetic parameters of Cilengitide and vice versa. CONCLUSION: There were no clinically important differences observed regarding efficacy, safety and QoL between the groups. The observations lay in the range of other clinical studies in this setting. The combination regimen was well tolerated with no adverse effects on the safety, tolerability and pharmacokinetics of either agent

Septation of Infectious Hyphae Is Critical for Appressoria Formation and Virulence in the Smut Fungus Ustilago Maydis

Differentiation of hyphae into specialized infection structures, known as appressoria, is a common feature of plant pathogenic fungi that penetrate the plant cuticle. Appressorium formation in U. maydis is triggered by environmental signals but the molecular mechanism of this hyphal differentiation is largely unknown. Infectious hyphae grow on the leaf surface by inserting regularly spaced retraction septa at the distal end of the tip cell leaving empty sections of collapsed hyphae behind. Here we show that formation of retraction septa is critical for appressorium formation and virulence in U. maydis. We demonstrate that the diaphanous-related formin Drf1 is necessary for actomyosin ring formation during septation of infectious hyphae. Drf1 acts as an effector of a Cdc42 GTPase signaling module, which also consists of the Cdc42-specific guanine nucleotide exchange factor Don1 and the Ste20-like kinase Don3. Deletion of drf1, don1 or don3 abolished formation of retraction septa resulting in reduced virulence. Appressorium formation in these mutants was not completely blocked but infection structures were found only at the tip of short filaments indicating that retraction septa are necessary for appressorium formation in extended infectious hyphae. In addition, appressoria of drf1 mutants penetrated the plant tissue less frequently

A framework for human microbiome research

A variety of microbial communities and their genes (the microbiome) exist throughout the human body, with fundamental roles in human health and disease. The National Institutes of Health (NIH)-funded Human Microbiome Project Consortium has established a population-scale framework to develop metagenomic protocols, resulting in a broad range of quality-controlled resources and data including standardized methods for creating, processing and interpreting distinct types of high-throughput metagenomic data available to the scientific community. Here we present resources from a population of 242 healthy adults sampled at 15 or 18 body sites up to three times, which have generated 5,177 microbial taxonomic profiles from 16S ribosomal RNA genes and over 3.5 terabases of metagenomic sequence so far. In parallel, approximately 800 reference strains isolated from the human body have been sequenced. Collectively, these data represent the largest resource describing the abundance and variety of the human microbiome, while providing a framework for current and future studies

Structure, function and diversity of the healthy human microbiome

Author Posting. © The Authors, 2012. This article is posted here by permission of Nature Publishing Group. The definitive version was published in Nature 486 (2012): 207-214, doi:10.1038/nature11234.Studies of the human microbiome have revealed that even healthy individuals differ remarkably in the microbes that occupy habitats such as the gut, skin and vagina. Much of this diversity remains unexplained, although diet, environment, host genetics and early microbial exposure have all been implicated. Accordingly, to characterize the ecology of human-associated microbial communities, the Human Microbiome Project has analysed the largest cohort and set of distinct, clinically relevant body habitats so far. We found the diversity and abundance of each habitat’s signature microbes to vary widely even among healthy subjects, with strong niche specialization both within and among individuals. The project encountered an estimated 81–99% of the genera, enzyme families and community configurations occupied by the healthy Western microbiome. Metagenomic carriage of metabolic pathways was stable among individuals despite variation in community structure, and ethnic/racial background proved to be one of the strongest associations of both pathways and microbes with clinical metadata. These results thus delineate the range of structural and functional configurations normal in the microbial communities of a healthy population, enabling future characterization of the epidemiology, ecology and translational applications of the human microbiome.This research was supported in part by National Institutes of Health grants U54HG004969 to B.W.B.; U54HG003273 to R.A.G.; U54HG004973 to R.A.G., S.K.H. and J.F.P.; U54HG003067 to E.S.Lander; U54AI084844 to K.E.N.; N01AI30071 to R.L.Strausberg; U54HG004968 to G.M.W.; U01HG004866 to O.R.W.; U54HG003079 to R.K.W.; R01HG005969 to C.H.; R01HG004872 to R.K.; R01HG004885 to M.P.; R01HG005975 to P.D.S.; R01HG004908 to Y.Y.; R01HG004900 to M.K.Cho and P. Sankar; R01HG005171 to D.E.H.; R01HG004853 to A.L.M.; R01HG004856 to R.R.; R01HG004877 to R.R.S. and R.F.; R01HG005172 to P. Spicer.; R01HG004857 to M.P.; R01HG004906 to T.M.S.; R21HG005811 to E.A.V.; M.J.B. was supported by UH2AR057506; G.A.B. was supported by UH2AI083263 and UH3AI083263 (G.A.B., C. N. Cornelissen, L. K. Eaves and J. F. Strauss); S.M.H. was supported by UH3DK083993 (V. B. Young, E. B. Chang, F. Meyer, T. M. S., M. L. Sogin, J. M. Tiedje); K.P.R. was supported by UH2DK083990 (J. V.); J.A.S. and H.H.K. were supported by UH2AR057504 and UH3AR057504 (J.A.S.); DP2OD001500 to K.M.A.; N01HG62088 to the Coriell Institute for Medical Research; U01DE016937 to F.E.D.; S.K.H. was supported by RC1DE0202098 and R01DE021574 (S.K.H. and H. Li); J.I. was supported by R21CA139193 (J.I. and D. S. Michaud); K.P.L. was supported by P30DE020751 (D. J. Smith); Army Research Office grant W911NF-11-1-0473 to C.H.; National Science Foundation grants NSF DBI-1053486 to C.H. and NSF IIS-0812111 to M.P.; The Office of Science of the US Department of Energy under Contract No. DE-AC02-05CH11231 for P.S. C.; LANL Laboratory-Directed Research and Development grant 20100034DR and the US Defense Threat Reduction Agency grants B104153I and B084531I to P.S.C.; Research Foundation - Flanders (FWO) grant to K.F. and J.Raes; R.K. is an HHMI Early Career Scientist; Gordon&BettyMoore Foundation funding and institutional funding fromthe J. David Gladstone Institutes to K.S.P.; A.M.S. was supported by fellowships provided by the Rackham Graduate School and the NIH Molecular Mechanisms in Microbial Pathogenesis Training Grant T32AI007528; a Crohn’s and Colitis Foundation of Canada Grant in Aid of Research to E.A.V.; 2010 IBM Faculty Award to K.C.W.; analysis of the HMPdata was performed using National Energy Research Scientific Computing resources, the BluBioU Computational Resource at Rice University

Canagliflozin and renal outcomes in type 2 diabetes and nephropathy

BACKGROUND Type 2 diabetes mellitus is the leading cause of kidney failure worldwide, but few effective long-term treatments are available. In cardiovascular trials of inhibitors of sodium–glucose cotransporter 2 (SGLT2), exploratory results have suggested that such drugs may improve renal outcomes in patients with type 2 diabetes. METHODS In this double-blind, randomized trial, we assigned patients with type 2 diabetes and albuminuric chronic kidney disease to receive canagliflozin, an oral SGLT2 inhibitor, at a dose of 100 mg daily or placebo. All the patients had an estimated glomerular filtration rate (GFR) of 30 to <90 ml per minute per 1.73 m2 of body-surface area and albuminuria (ratio of albumin [mg] to creatinine [g], >300 to 5000) and were treated with renin–angiotensin system blockade. The primary outcome was a composite of end-stage kidney disease (dialysis, transplantation, or a sustained estimated GFR of <15 ml per minute per 1.73 m2), a doubling of the serum creatinine level, or death from renal or cardiovascular causes. Prespecified secondary outcomes were tested hierarchically. RESULTS The trial was stopped early after a planned interim analysis on the recommendation of the data and safety monitoring committee. At that time, 4401 patients had undergone randomization, with a median follow-up of 2.62 years. The relative risk of the primary outcome was 30% lower in the canagliflozin group than in the placebo group, with event rates of 43.2 and 61.2 per 1000 patient-years, respectively (hazard ratio, 0.70; 95% confidence interval [CI], 0.59 to 0.82; P=0.00001). The relative risk of the renal-specific composite of end-stage kidney disease, a doubling of the creatinine level, or death from renal causes was lower by 34% (hazard ratio, 0.66; 95% CI, 0.53 to 0.81; P<0.001), and the relative risk of end-stage kidney disease was lower by 32% (hazard ratio, 0.68; 95% CI, 0.54 to 0.86; P=0.002). The canagliflozin group also had a lower risk of cardiovascular death, myocardial infarction, or stroke (hazard ratio, 0.80; 95% CI, 0.67 to 0.95; P=0.01) and hospitalization for heart failure (hazard ratio, 0.61; 95% CI, 0.47 to 0.80; P<0.001). There were no significant differences in rates of amputation or fracture. CONCLUSIONS In patients with type 2 diabetes and kidney disease, the risk of kidney failure and cardiovascular events was lower in the canagliflozin group than in the placebo group at a median follow-up of 2.62 years

Finishing the euchromatic sequence of the human genome

The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers ∼99% of the euchromatic genome and is accurate to an error rate of ∼1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human enome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead

Untersuchung FLT3-ITD-abhängiger Signalsignaturen in der akuten myeloischen Leukämie

Aufgrund der starken Heterogenität und Komplexität der akuten myeloischen Leukämie ist diese bis heute nicht zufriedenstellend zu behandeln. Die bestmögliche Therapie wird mittlerweile zunehmend auf die Erkrankung des Einzelnen angepasst. Vermehrt gewinnen Tyrosinkinase-Inhibitoren in der Therapie an Bedeutung. Diese Inhibitoren hemmen Proteine auf zellulärer Ebene. Bei etwa 30% der AML-Patienten lassen sich Mutationen des FLT3-Gens nachweisen. Das Gen kodiert für die fms like tyrosine kinase 3, eine Rezeptor-Tyrosinkinase an der Zelloberfläche von unreifen Blutzellen des Knochenmarks. Durch Mutationen des FLT3 Gens erhalten diese Zellen einen Proliferationsvorteil gegenüber den physiologischen Blutzellen. Am häufigsten kommt es zu in frame-Insertionen des FLT3-Gens, vor allem im Bereich der juxtamembranen Domäne: sogenannte interne Tandemduplikationen (ITD). Weiterhin kommen zu einem geringeren Teil Punktmutationen einzelner Codons, zum Beispiel im Bereich des activation loops oder im Bereich des gatekeepers vor. Durch das Auftreten der Punktmutationen, die entweder bereits zum Zeitpunkt der Diagnose vorliegen oder erst während einer Therapie mit einem Tyrosinkinase-Inhibitor entstehen können, verändert sich das Bindungsverhalten vieler solcher gegen FLT3 gerichteten Inhibitoren. Durch Letzteres kann ein mögliches Therapieversagen beispielsweise während der Behandlung mit AC220 (Quizartinib) erklärt werden (Smith et al.). In der vorliegenden Dissertationsschrift sind Unterschiede der Signalwege zwischen FLT3-ITD und FLT3-ITD mit der zusätzlichen gatekeeper-Punktmutation F691L herausgearbeitet. Dafür wurden die beiden FLT3-Mutationen in den Vektor pMy-IRES-GFP eingebracht und retroviral in Ba/F3-Zellen transduziert. Nach Überprüfung der Expression von FLT3 ITD und dem Wachstumsverhalten unter Zugabe von AC220 (Quizartinib), wurden verschiedene Signalkaskaden von FLT3 mittels Western Blot untersucht. Hierbei zeigten sich sowohl Unterschiede für die Expression von phosphoryliertem ERK als auch von phosphoryliertem STAT5. Durch verschieden starke Expressionen der FLT3130kDa- und FLT3160kDA-Varianten wurde eine unterschiedliche Lokalisation von FLT3-ITD in Zellen mit und ohne die Mutation F691L postuliert. Allerdings ließ sich diese experimentell mittels Immunfluoreszenz nicht belegen, da die Methode für die verwendeten Suspensionszellen nicht ausreichend geeignet war. In den durchgeführten Versuchen zum Wachstumsverhalten der Zellen bei der Verwendung von Kinaseinhibitoren konnte bei der Verwendung des SYK-Inhibitors R406 eine dosisabhängige Proliferationshemmung der FLT3-ITD-mutierten Ba/F3- und 32D-Zellen beobachtet werden. Die Hemmung von FLT3 durch R406 wurde in der Literatur bereits beschrieben (Braselmann et al.). Die abschließenden Experimente der Massenspektrometrie mit SILAC Markierung lassen mit der Detektion von mehreren hundert signifikant regulierten phosphorylierten Proteinen in den beiden FLT3-ITD-exprimierenden Populationen auf die Aktivierung unterschiedlicher Signalwege schließen. Durch das Vergleichen einzelner Teilexperimente ergaben sich Proteine, deren Phosphorylierung mehrfach in die gleiche Richtung reguliert war. Für Zellen, die zusätzlich zur ITD-Mutation die Mutation F691L besaßen, konnten insgesamt sieben hoch-regulierte, phosphorylierte Proteine ermittelt werden, bei denen ein zellulärer Effekt durch die Phosphorylierung der entsprechenden Aminosäurereste in der Literatur beschrieben ist. Das im Western Blot nachgewiesene, in Zellen mit der Mutation F691L stärker phosphorylierte STAT5 ist aller Voraussicht nach Ursache der nachgewiesenen verstärkten Phosphorylierung von RPS6 im Experiment der globalen Phosphorylierung. Die PIM-Kinasen als Substrate einer STAT5-induzierten Transkription phosphorylieren RPS6 an Serin 235. Dies führt seinerseits zu einer verstärkten Translation von mRNA weiterer Gene. Die genauen Zusammenhänge der hier ermittelten Unterschiede müssen jedoch weiter untersucht werden. In Zukunft könnte zudem die Untersuchung der beiden Proteine SHP 1 oder HSP90 weitere Aufschlüsse über die unterschiedlichen Signalwege geben. Für beide Proteine wurden Phosphorylierungen detektiert, die in den untersuchten Zellen mit FLT3-ITD bzw. der zusätzlichen Punktmutation F691L unterschiedlich reguliert sind.Acute myeloid leukemia is characterized by a distinct heterogeneity and complexity. Therefore, no coherent satisfying treatment exists. Recently, the respective therapy is mainly adjusted to the individual patient and tyrosine kinase inhibitors (TKI) become more important. These inhibitors block specific proteins on a cellular level. About 30% of all adult AML patients exhibit mutations of the FLT3-gene. The gene encodes the fms like tyrosine kinase 3, a cell surface receptor tyrosine kinase of immature blood cells in the bone marrow. Through mutations of the FLT3 gene, these cells gain an advantage in proliferation compared to physiologic blood cells. The most common mutations of the FLT3 gene are in-frame insertions, mostly located in the part that encodes the juxtamembrane domain. Those mutations are known as internal tandem duplications (ITD). To a lesser extent, there are point mutations of several codons e.g., in the area of the activation loop or localized at the gatekeeper. These point mutations change the binding capacity of FTL3 targeting TKIs and are present at the time of AML diagnosis or can develop during treatment with TKIs. As a consequence, the respective cells may not respond to treatment with e.g. AC220 (Quizartinib) anymore resulting in a therapeutic failure (Smith et al.). The objective of this work was to investigate the signaling pathways of FLT3-ITD and FLT3 ITD plus the additional gatekeeper point mutation F691L describing similarities and differences. Therefore, these two mutations were introduced into the vector pMy IRES GFP and retroviral transduced into murine Ba/F3 cells. Subsequently, the expression was checked for FLT3 and the proliferation of the transduced cells during treatment with AC220 was observed. Afterwards, several signaling pathways were analyzed by Western blotting. In these experiments, differences in expression of phosphorylated ERK and phosphorylated STAT5 could be shown for the mutations of interest. An observed difference in expression of FLT3130kDa and FLT3160kDa variants led to the conclusion of varying FLT3-ITD localizations depending on the additional point mutation F691L. However, this hypothesis could not be verified by the performed immunofluorescence experiments since this method was not suitable for the used suspension cells. In the proliferation assay, the SYK inhibitor R406 has shown to be a potent inhibitor of FLT3 ITD mutated BA/F3 and 32D cells whereas, proliferations of FLT3- wildtype cells could only be inhibited at much higher R406 concentrations. This is in contrast to Braselmann, who showed previously an inhibitory effect for R406 on FLT3. (Braselmann et al.). The concluding mass spectrometry experiments with SILAC-labeled cells showed several hundred significantly regulated phosphorylated proteins in both FLT3-ITD expressing populations implying an activation of different signaling pathways. By comparing parts of these experiments, several proteins could be identified whose changes in phosphorylation went multiple times into the same direction. For the population with both mutations (FLT3-ITD and F691L) seven upregulated, phosphorylated proteins have been detected for which a phosphorylation of the specific amino acid residue has been described in the literature already. In Western blots, STAT5 was more phosphorylated when cells expressed FLT3 carrying the F691L in addition to the ITD mutation. This could explain why RPS6 was detected to be stronger phosphorylated in the global phosphorylation experiment. PIM kinases as target proteins of a STAT5 induced transcription can phosphorylate serine 235 of RPS6 resulting in an enhanced transcription of mRNA. The exact impact has to be examined in future experiments. The two proteins SHP-1 and HSP90 represent further targets for a better understanding of the differently activated pathways. Differential phosphorylation of both proteins has been detected in FLT3-ITD and in FLT3-ITD plus the TKD mutation F691L expressing cells