Knowledge-based design of generate-and-patch problem solvers that solve global resource assignment problems

We present MENDER, a knowledge based system that implements software design techniques that are specialized to automatically compile generate-and-patch problem solvers that satisfy global resource assignments problems. We provide empirical evidence of the superior performance of generate-and-patch over generate-and-test: even with constrained generation, for a global constraint in the domain of '2D-floorplanning'. For a second constraint in '2D-floorplanning' we show that even when it is possible to incorporate the constraint into a constrained generator, a generate-and-patch problem solver may satisfy the constraint more rapidly. We also briefly summarize how an extended version of our system applies to a constraint in the domain of 'multiprocessor scheduling'

An old confusion: Entomophthoromycosis versus mucormycosis and their main differences

Fungal diseases were underestimated for many years. And the global burden of fungal infections is substantial and has increased in recent years. Invasive fungal infections have been linked to several risk factors in humans which basically depend on the individual homeostasis of the patients. However, many fungi can infect even apparently healthy people. Knowledge of these pathogens is critical in reducing or stopping morbidity and/or mortality statistics due to fungal pathogens. Successful therapeutic strategies rely on rapid diagnosis of the causative fungal agent and the underlying disease. However, the terminology of the diseases was updated to existing phylogenetic classifications and led to confusion in the definition of mucormycosis, conidiobolomycosis, and basidiobolomycosis, which were previously grouped under the now-uncommon term zygomycosis. Therefore, the ecological, taxonomic, clinical, and diagnostic differences are addressed to optimize the understanding and definition of these diseases. The term “coenocytic hyphomycosis” is proposed to summarize all fungal infections caused by Mucorales and species of Basidiobolus and Conidiobolus

A stable backbone for the fungi

Fungi are abundant in the biosphere. They have fascinated mankind as far as written history goes and have considerably influenced our culture. In biotechnology, cell biology, genetics, and life sciences in general fungi constitute relevant model organisms. Once the phylogenetic relationships of fungi are stably resolved individual results from fungal research can be combined into a holistic picture of biology. However, and despite recent progress, the backbone of the fungal phylogeny is not yet fully resolved. Especially the early evolutionary history of fungi and the order or below-order relationships within the ascomycetes remain uncertain. Here we present the first phylogenomic study for a eukaryotic kingdom that merges all publicly available fungal genomes and expressed sequence tags (EST) to build a data set comprising 128 genes and 146 taxa. The resulting tree provides a stable phylogenetic backbone for the fungi. Moreover, we present the first formal supertree based on 161 fungal taxa and 128 gene trees. The combined evidences from the trees support the deep-level stability of the fungal groups towards a comprehensive natural system of the fungi. They indicate that the classification of the fungi, especially their alliance with the Microsporidia, requires careful revision. Our analysis is also an inventory of present day sequence information for the fungi. It provides insights into which phylogenenetic conclusions can and which cannot be drawn from the current data and may serve as a guide to direct further sequencing initiatives. Together with a comprehensive animal phylogeny, we provide the second of three pillars to understand the evolution of the multicellular eukaryotic kingdoms, fungi, metazoa, and plants, in the past 1.6 billion years

Reformulating Constraints for Compilability and Efficiency

KBSDE is a knowledge compiler that uses a classification-based approach to map solution constraints in a task specification onto particular search algorithm components that will be responsible for satisfying those constraints (e.g., local constraints are incorporated in generators; global constraints are incorporated in either testers or hillclimbing patchers). Associated with each type of search algorithm component is a subcompiler that specializes in mapping constraints into components of that type. Each of these subcompilers in turn uses a classification-based approach, matching a constraint passed to it against one of several schemas, and applying a compilation technique associated with that schema. While much progress has occurred in our research since we first laid out our classification-based approach [Ton91], we focus in this paper on our reformulation research. Two important reformulation issues that arise out of the choice of a schema-based approach are: (1) compilability-- Can a constraint that does not directly match any of a particular subcompiler's schemas be reformulated into one that does? and (2) Efficiency-- If the efficiency of the compiled search algorithm depends on the compiler's performance, and the compiler's performance depends on the form in which the constraint was expressed, can we find forms for constraints which compile better, or reformulate constraints whose forms can be recognized as ones that compile poorly? In this paper, we describe a set of techniques we are developing for partially addressing these issues

Chemical composition and antimicrobial activity of essential oil from Pyrethrum pulchrum Ledeb.

The chemical composition and antimicrobial activity of the essential oil from the aerial parts of Pyrethrum pulchrum Ledeb. were investigated. Dried plant material was hydro-distillated yielding 0.1% of essential oil. The oil was analyzed by GC-MS techniques. Fifty-five compounds were identified representing 99.7% of the total oil composition. Camphor was the predominant compound (33.9%) followed by linalool (21.1%) and α-pinene (9.0%). The antimicrobial activity of the oil was determined using the disk diffusion method against Gram-positive bacteria (Bacillus subtilis, Staphylococcus aureus and Enterococcus faecalis), Gram-negative bacteria (Pseudomonas aeruginosa and Escherichia coli), Mycobacterium vaccae and fungi (Candida albicans, Sporidiobolus salmonicolor and Penicillum notatum). The essential oil of P. pulchrum displays an intermediate activity against selected bacteria

Microfluidic Impedance Biosensor Chips Using Sensing Layers Based on DNA-Based Self-Assembled Monolayers for Label-Free Detection of Proteins

A microfluidic chip for electrochemical impedance spectroscopy (EIS) is presented as bio-sensor for label-free detection of proteins by using the example of cardiac troponin I. Troponin I is one of the most specific diagnostic serum biomarkers for myocardial infarction. The microfluidic impedance biosensor chip presented here consists of a microscope glass slide serving as base plate, sputtered electrodes, and a polydimethylsiloxane (PDMS) microchannel. Electrode functionalization protocols were developed considering a possible charge transfer through the sensing layer, in addition to analyte-specific binding by corresponding antibodies and reduction of nonspecific protein adsorption to prevent false-positive signals. Reagents tested for self-assembled monolayers (SAMs) on gold electrodes included thiolated hydrocarbons and thiolated oligonucleotides, where SAMs based on the latter showed a better performance. The corresponding antibody was covalently coupled on the SAM using carbodiimide chemistry. Sampling and measurement took only a few minutes. Application of a human serum albumin (HSA) sample, 1000 ng/mL, led to negligible impedance changes, while application of a troponin I sample, 1 ng/mL, led to a significant shift in the Nyquist plot. The results are promising regarding specific detection of clinically relevant concentrations of biomarkers, such as cardiac markers, with the newly developed microfluidic impedance biosensor chip

Microfluidic Impedance Biosensor Chip with DNA-Based Self-Assembled Monolayers for Label-Free Detection of Cardiac Biomarker Troponin I

A microfluidic chip for electrochemical impedance spectroscopy (EIS) is presented as biosensor for the detection of cardiac troponin I (cTnI), which is one of the most specific diagnostic serum biomarkers for myocardial infarction. Impedimetric biosensors enable the detection of a variety of analytes, including small molecules, proteins, and cells. As analyte detection is direct and label-free, they allow fast detection of biomarkers, which is essential in the diagnosis of cardiac infarctions to promote a positive outcome. The EIS chip presented here consists of a microscope glass slide serving as base plate, sputtered electrodes, and a polydimethylsiloxane (PDMS) microchannel. The electrode design mainly consists of a working electrode and a counter electrode made of gold. A silver reference electrode can be included, if required. Protocols for electrode functionalization were developed considering a low initial impedance in addition to analyte-specific binding by corresponding antibodies and reduction of non-specific protein adsorption to prevent false-positive signals. Reagents tested for self-assembled monolayers (SAM) on gold electrodes included hydrocarbons with thiol groups and thiolated oligonucleotides. The optimized coating used thiolated single-strand DNA (ssDNA) and 1,4-benzenedithiol on the working electrode and 1,4-benzenedithiol on the counter electrode. After hybridization with corresponding ssDNA carrying an amino group, the reaction with glutaric anhydride led to carboxyl groups, on which anti-cTnI antibody was covalently coupled using carbodiimide chemistry. The PDMS microchannel was bonded on the glass slide with the functionalized electrodes, and the completed EIS chip was connected to the readout system. Sampling with human serum albumin (HSA), 1000 ng/mL, led to negligible signal changes, while sampling with cTnI, 1 ng/mL, led to a significant signal shift in the Nyquist plot. Sampling and measurement took only a few minutes. The results were promising regarding a future cost-effective biosensor array chip for the rapid detection of clinically relevant biomarkers in real samples

Open-Access-Projekte wissenschaftlicher Einrichtungen aus Berlin und Brandenburg 2016

Im Spätsommer 2016 begannen die Planungen der Open-Access-Teams der Freien Universität, der Humboldt-Universität und der Technischen Universität Berlin für die internationale Open Access Week 2016. In einem Call for Posters wurden Berliner und Brandenburger Open-Access-Projekte dazu aufgerufen, ihre Aktivitäten in einer Ausstellung vorzustellen. Die Publikation dokumentiert die Posterausstellung und Podiumsdiskussion zur Open Access Week 2016. Sie enthält 30 Poster inklusive Beschreibungen und Links zu den Originalversionen in Druckqualität, ergänzt um Fotos einer Abendveranstaltung bei Wikimedia Deutschland.In late summer 2016 the open access teams of the Freie Universität, the Humboldt-Universität and the Technische Universität Berlin started their plans for the international Open Access Week 2016. In a call for posters, open access projects from Berlin and Brandenburg were requested to present their activities in a poster exhibition. The publication documents the poster exhibition and panel discussion during the Open Access Week 2016. It contains all posters including abstracts and links to the original versions in print quality, supplemented by photos from the Wikimedia event