The shape and erosion of pebbles

The shapes of flat pebbles may be characterized in terms of the statistical distribution of curvatures measured along their contours. We illustrate this new method for clay pebbles eroded in a controlled laboratory apparatus, and also for naturally-occurring rip-up clasts formed and eroded in the Mont St.-Michel bay. We find that the curvature distribution allows finer discrimination than traditional measures of aspect ratios. Furthermore, it connects to the microscopic action of erosion processes that are typically faster at protruding regions of high curvature. We discuss in detail how the curvature may be reliable deduced from digital photographs.Comment: 10 pages, 11 figure

Estimating survival in patients with gastrointestinal cancers and brain metastases: An update of the graded prognostic assessment for gastrointestinal cancers (GI-GPA).

BackgroundPatients with gastrointestinal cancers and brain metastases (BM) represent a unique and heterogeneous population. Our group previously published the Diagnosis-Specific Graded Prognostic Assessment (DS-GPA) for patients with GI cancers (GI-GPA) (1985-2007, n = 209). The purpose of this study is to update the GI-GPA based on a larger contemporary database.MethodsAn IRB-approved consortium database analysis was performed using a multi-institutional (18), multi-national (3) cohort of 792 patients with gastrointestinal (GI) cancers, with newly-diagnosed BM diagnosed between 1/1/2006 and 12/31/2017. Survival was measured from date of first treatment for BM. Multiple Cox regression was used to select and weight prognostic factors in proportion to their hazard ratios. These factors were incorporated into the updated GI-GPA.ResultsMedian survival (MS) varied widely by primary site and other prognostic factors. Four significant factors (KPS, age, extracranial metastases and number of BM) were used to formulate the updated GI-GPA. Overall MS for this cohort remains poor; 8 months. MS by GPA was 3, 7, 11 and 17 months for GPA 0-1, 1.5-2, 2.5-3.0 and 3.5-4.0, respectively. >30% present in the worst prognostic group (GI-GPA of ≤1.0).ConclusionsBrain metastases are not uncommon in GI cancer patients and MS varies widely among them. This updated GI-GPA index improves our ability to estimate survival for these patients and will be useful for therapy selection, end-of-life decision-making and stratification for future clinical trials. A user-friendly, free, on-line app to calculate the GPA score and estimate survival for an individual patient is available at brainmetgpa.com

The role of historical context in understanding past climate, pollution and health data in trans-disciplinary studies: reply to comments on More et al. 2017

Understanding the context from which evidence emerges is of paramount importance in reaching robust conclusions in scientific inquiries. This is as true of the present as it is of the past. In a trans‐disciplinary study such as More et al. (2017, https://doi.org/10.1002/2017GH000064) and many others appearing in this and similar journals, a proper analysis of context demands the use of historical evidence. This includes demographic, epidemiological, and socio‐economic data—common in many studies of the impact of anthropogenic pollution on human health—and, as in this specific case, also geoarchaeological evidence. These records anchor climate and pollution data in the geographic and human circumstances of history, without which we lose a fundamental understanding of the data itself. This article addresses Hinkley (2018, https://doi.org/10.1002/2018GH000105) by highlighting the importance of context, focusing on the historical and archaeological evidence, and then discussing atmospheric deposition and circulation in the specific region of our study. Since many of the assertions in Bindler (2018, https://doi.org/10.1002/2018GH000135) are congruent with our findings and directly contradict Hinkley (2018), this reply refers to Bindler (2018), whenever appropriate, and indicates where our evidence diverges

What is in a pebble shape?

We propose to characterize the shapes of flat pebbles in terms of the statistical distribution of curvatures measured along the pebble contour. This is demonstrated for the erosion of clay pebbles in a controlled laboratory apparatus. Photographs at various stages of erosion are analyzed, and compared with two models. We find that the curvature distribution complements the usual measurement of aspect ratio, and connects naturally to erosion processes that are typically faster at protruding regions of high curvature.Comment: Phys. Rev. Lett. (to appear

Biosynthesis of coral settlement cue tetrabromopyrrole in marine bacteria by a uniquely adapted brominase-thioesterase enzyme pair

Author Posting. © The Author(s), 2016. This is the author's version of the work. It is posted here by permission of National Academy of Sciences for personal use, not for redistribution. The definitive version was published in Proceedings of the National Academy of Sciences of United States of America 113 (2016): 3797-3802, doi: 10.1073/pnas.1519695113.Halogenated pyrroles (halopyrroles) are common chemical moieties found in bioactive bacterial natural products. The halopyrrole moieties of mono- and di- halopyrrole-containing compounds arise from a conserved mechanism in which a proline-derived pyrrolyl group bound to a carrier protein is first halogenated then elaborated by peptidic or polyketide extensions. This paradigm is broken during the marine pseudoalteromonad bacterial biosynthesis of the coral larval settlement cue tetrabromopyrrole (1), which arises from the substitution of the proline-derived carboxylate by a bromine atom. To understand the molecular basis for decarboxylative bromination in the biosynthesis of 1, we sequenced two Pseudoalteromonas genomes and identified a conserved four-gene locus encoding the enzymes involved its complete biosynthesis. Through total in vitro reconstitution of the biosynthesis of 1 using purified enzymes and biochemical interrogation of individual biochemical steps, we show that all four bromine atoms in 1 are installed by the action of a single flavin-dependent halogenase- Bmp2. Tetrabromination of the pyrrole induces a thioesterase-mediated offloading reaction from the carrier protein and activates the biosynthetic intermediate for decarboxylation. Insights into the tetrabrominating activity of Bmp2 were obtained from the high-resolution crystal structure of the halogenase contrasted against structurally homologous halogenase Mpy16 that forms only a dihalogenated pyrrole in marinopyrrole biosynthesis. Structure-guided mutagenesis of the proposed substrate-binding pocket of Bmp2 led to a reduction in the degree of halogenation catalyzed. Our study provides a biogenetic basis for the biosynthesis of 1, and sets a firm foundation for querying the biosynthetic potential for the production of 1 in marine (meta)genomes.This work was jointly supported by the US National Science Foundation (OCE-1313747) and the US National Institute of Environmental Health Sciences (P01-ES021921) through the Ocean and Human Health Program to B.S.M., and the US National Institute of Allergy and Infectious Disease R01-AI47818 to B.S.M. and R21- AI119311 to K.E.W. and T.J.M., the Mote Protect Our Reef Grant Program (POR-2012-3), the Dart Foundation, the Smithsonian Competitive Grants Program for Science to V.J.P., the Howard Hughes Medical Institute to J.P.N., the US National Institutes of Health (NIH) Marine Biotechnology Training Grant predoctoral fellowship to A.E. (T32-GM067550), the Helen Hay Whitney Foundation postdoctoral fellowship to V.A., and a Swiss National Science Foundation (SNF) postdoctoral Fellowship to S.D.2016-09-2

Subject-oriented plural method meets BPMN: a case study

Subject-oriented approach to business process management focuses on the subjects and their interactions with the aim to capture more accurate process information with increased fidelity. In a common setting, business processes are modeled by process engineers or modeling experts who often create their processes in a top-down fashion. However, this may pose risks to the acceptance and adoption of these models in practice, particularly in knowledge-centric environments. The Plural method follows a subject-oriented approach and allows process participants, rather than a centralized group of process engineers, to model and maintain their processes in a decentralized way. It guides process participants to focus on the roles and their interactions in terms of message exchanges. This study investigates the use of BPMN 2.0 for the Plural method. With the aim to show the applicability of the notation for a subject-oriented approach and report on the benefits and limitations of the new edition of the Plural method in general, we performed a case study in an industry company. Guided by a coordinator, 11 process participants modeled four processes that they participate by following the Plural method. These models were also compared with the classical models developed prior to the application of the Plural method to better understand the influence. Analyses showed that the application of the Plural resulted in more complete process models. However, there are concerns regarding the understandability of these models when compared with their classical counterparts. It has been shown that the Plural method is a powerful tool for process discovery and modeling, but an improvement on its models is needed to obtain full value of the framework