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The Graph Traversal Pattern [article]

Marko A. Rodriguez, Peter Neubauer
2010 arXiv   pre-print
A graph is a structure composed of a set of vertices (i.e.nodes, dots) connected to one another by a set of edges (i.e.links, lines). The concept of a graph has been around since the late 19^th century, however, only in recent decades has there been a strong resurgence in both theoretical and applied graph research in mathematics, physics, and computer science. In applied computing, since the late 1960s, the interlinked table structure of the relational database has been the predominant
more » ... ion storage and retrieval model. With the growth of graph/network-based data and the need to efficiently process such data, new data management systems have been developed. In contrast to the index-intensive, set-theoretic operations of relational databases, graph databases make use of index-free, local traversals. This article discusses the graph traversal pattern and its use in computing.
arXiv:1004.1001v1 fatcat:rwikvcbd2vc3vjdy3frberwpce

Constructions from Dots and Lines [article]

Marko A. Rodriguez, Peter Neubauer
2010 arXiv   pre-print
A graph is a data structure composed of dots (i.e. vertices) and lines (i.e. edges). The dots and lines of a graph can be organized into intricate arrangements. The ability for a graph to denote objects and their relationships to one another allow for a surprisingly large number of things to be modeled as a graph. From the dependencies that link software packages to the wood beams that provide the framing to a house, most anything has a corresponding graph representation. However, just because
more » ... t is possible to represent something as a graph does not necessarily mean that its graph representation will be useful. If a modeler can leverage the plethora of tools and algorithms that store and process graphs, then such a mapping is worthwhile. This article explores the world of graphs in computing and exposes situations in which graphical models are beneficial.
arXiv:1006.2361v1 fatcat:5aet52c7vnel5mx3cfi5hojpeu

Sandwich ELISA for quantitative detection of human collagen prolyl 4-hydroxylase

Ekaterina Osmekhina, Antje Neubauer, Katharina Klinzing, Johanna Myllyharju, Peter Neubauer
2010 Microbial Cell Factories  
The highest specific yield of active recombinant C-P4H up to now in cultivation with the Origami strain has been reported by Neubauer et al. [16] .  ... 
doi:10.1186/1475-2859-9-48 pmid:20565744 pmcid:PMC2895579 fatcat:il6itvkah5fvxm6daaef34aw7i

Toward Microbioreactor Arrays

Florian Glauche, Gernot T. John, Sarina Arain, Andreas Knepper, Antje Neubauer, Detlef Goelling, Christine Lang, Norman Violet, Rudibert King, Peter Neubauer
2015 Journal of Laboratory Automation  
In this study, a slow-responding chemo-optical sensor for dissolved oxygen (DO) integrated into a 96-well plate was developed. The slow response time ensures that the measured oxygen value does not change much during plate transport to the microplate reader. The sensor therefore permits at-line DO measurement of microbial cultures. Moreover, it eliminates the necessity of individual optical measurement systems for each culture plate, as many plates can be measured successively. Combined with
more » ... 96-well format, this increases the experimental throughput enormously. The novel sensor plate (Slow OxoPlate) consists of fluorophores suspended in a polymer matrix that were placed into u-bottom 96-well plates. Response time was measured using sodium sulfite, and a t 90 value of 9.7 min was recorded. For application, DO values were then measured in Escherichia coli and Saccharomyces cerevisiae cultures grown under fed-batch-like conditions. Depending on the DO sensor's response time, different information on the oxygenation state of the culture plate was obtained: a fast sensor variant detects disturbance through sampling, whereas the slow sensor indicates oxygen limitation during incubation. A combination of the commercially available OxoPlate and the Slow OxoPlate enables operators of screening facilities to validate their cultivation procedures with regard to oxygen availability.
doi:10.1177/2211068215573924 pmid:25720599 fatcat:rjiseqs7qbembaeupx72vie2yu

Protocol Specialization [chapter]

Matthias Neubauer, Peter Thiemann
2004 Lecture Notes in Computer Science  
In component-based programming, the programmer assembles applications from prefabricated components. The assembly process has two main steps: adapting a component by tweaking its configuration parameters, and connecting components by gluing output interfaces to input interfaces. While convenient, this approach may give rise to code bloat and inefficiency because prefabricated code is overly general, by necessity. The present work addresses ways to remove unnecessary code during the deployment
more » ... a closed set of components by using program specialization. Our framework models components at the intermediate language level as systems of concurrent functional processes which communicate via channels. Each channel acts as a component connector with the interface determined by the channel's protocol. We present an analysis that determines the minimum protocol required for each process and specify the specialization of a process with respect to a desired protocol, thereby removing unnecessary code. The resulting specialization algorithm is unique in that it processes a concurrent base language, terminates always, and is guaranteed not to expand the program beyond its original size.
doi:10.1007/978-3-540-30477-7_17 fatcat:dxcr3gsttfaaxdl5qmkh7lspn4

Fast Detour Computation for Ride Sharing [article]

Robert Geisberger, Dennis Luxen, Sabine Neubauer, Peter Sanders, Lars Volker
2009 arXiv   pre-print
Todays ride sharing services still mimic a better billboard. They list the offers and allow to search for the source and target city, sometimes enriched with radial search. So finding a connection between big cities is quite easy. These places are on a list of designated origin and distination points. But when you want to go from a small town to another small town, even when they are next to a freeway, you run into problems. You can't find offers that would or could pass by the town easily with
more » ... little or no detour. We solve this interesting problem by presenting a fast algorithm that computes the offers with the smallest detours w.r.t. a request. Our experiments show that the problem is efficiently solvable in times suitable for a web service implementation. For realistic database size we achieve lookup times of about 5ms and a matching rate of 90% instead of just 70% for the simple matching algorithms used today.
arXiv:0907.5269v1 fatcat:l5ttalugfzar3e6244bmdfbztm

Advances in the synthesis of modified NTPs [article]

Maryke Fehlau, Julia Schollmeyer, Peter Neubauer, Anke Kurreck
2021 Zenodo  
Nucleoside triphosphates (NTPs) are building blocks of nucleic acids and play an important role in molecular biology, like PCR and diagnostics, as well as pharmaceutical applications. So far, the golden standard to produce modified NTPs are chemical syntheses. Chemical production routes show limitations due to a low regio- and stereo-selectivity and the need for protection groups. Therefore, they often lead to low yields and are expensive and time consuming. As an alternative, different
more » ... c synthesis pathways have been developed. They offer the advantage of high stereo- and regioselectivity which leads to greatly reduced reaction and purification effort as well as often high product yields. While chemical synthesis routes for NTPs have been discussed extensively a comparison to enzymatic methods in terms of yield, production steps and production times is lacking. The aim of this review is to describe the relevance of NTP analogs in a number of applications and to compare described chemical and enzymatic methods for NTP synthesis. AraCTP was chosen as an example to demonstrate advantages and disadvantages of the different approaches.
doi:10.5281/zenodo.5566311 fatcat:zbtaofpz6rfu5cj7k6gyywfgs4

Functional logic overloading

Matthias Neubauer, Peter Thiemann, Martin Gasbichler, Michael Sperber
2002 SIGPLAN notices  
Functional logic overloading is a novel approach to userdefined overloading that extends Haskell's concept of type classes in significant ways. Whereas type classes are conceptually predicates on types in standard Haskell, they are type functions in our approach. Thus, we can base type inference on the evaluation of functional logic programs. Functional logic programming provides a solid theoretical foundation for type functions and, at the same time, allows for programmable overloading
more » ... on strategies by choosing different evaluation strategies for functional logic programs. Type inference with type functions is an instance of type inference with constrained types, where the underlying constraint system is defined by a functional logic program. We have designed a variant of Haskell which supports our approach to overloading, and implemented a prototype frontend for the language.
doi:10.1145/565816.503294 fatcat:kiujqpbeeffr7a7yaczllzdxlq

An Implementation of Session Types [chapter]

Matthias Neubauer, Peter Thiemann
2004 Lecture Notes in Computer Science  
A session type is an abstraction of a set of sequences of heterogeneous values sent and received over a communication channel. Session types can be used for specifying stream-based Internet protocols. Typically, session types are attached to communication-based program calculi, which renders them theoretical tools which are not readily usable in practice. To transfer session types into practice, we propose an embedding of a core calculus with session types into the functional programming
more » ... e Haskell. The embedding preserves typing. A case study (a client for SMTP, the Simple Mail Transfer Protocol) demonstrates the feasibility of our approach.
doi:10.1007/978-3-540-24836-1_5 fatcat:l7jzxqq7dvfmzihm5uq2kzmhbm

Role of Microbial Hydrolysis in Anaerobic Digestion

Theresa Menzel, Peter Neubauer, Stefan Junne
2020 Energies  
There is a growing need of substrate flexibility for biobased production of energy and value-added products that allows the application of variable biodegradable residues within a circular economy. It can be used to balance fluctuating energy provision of other renewable sources. Hydrolysis presents one of the biggest limitations during anaerobic digestion. Methods to improve it will result in broader process applicability and improved integration into regional material cycles. Recently, one
more » ... us of anaerobic digestion research has been directed to systems with a separate hydrolysis–acidogenesis stage as it might be promised to improve process performance. Conditions can be adjusted to each class of microorganisms individually without harming methanogenic microorganisms. Extensive research of separate biomass pretreatment via biological, chemical, physical or mixed methods has been conducted. Nevertheless, several methods lack economic efficiency, have a high environmental impact or focus on specific substrates. Pretreatment via a separate hydrolysis stage as cell-driven biotransformation in a suspension might be an alternative that enables high yields, flexible feeding and production, and a better process control. In this review, we summarize existing technologies for microbial hydrolytic biotransformation in a separate reactor stage and the impacts of substrate, operational parameters, combined methods and process design as well as remaining challenges.
doi:10.3390/en13215555 fatcat:zlj7wp7owvdy7pilvj7hqyubxa

Parameterized LR Parsing

Peter Thiemann, Matthias Neubauer
2004 Electronical Notes in Theoretical Computer Science  
Neubauer / Electronic Notes in Theoretical ComputerScience 110 (2004) 115-132 121 P. Thiemann, M. Neubauer / Electronic Notes in Theoretical ComputerScience 110 (2004) 115-132 123  ... 
doi:10.1016/j.entcs.2004.06.007 fatcat:ux46jwggyjb4teqtmt66nqz64u

Type classes with more higher-order polymorphism

Matthias Neubauer, Peter Thiemann
2002 SIGPLAN notices  
We propose an extension of Haskell's type class system with lambda abstractions in the type language. Type inference for our extension relies on a novel constrained unification procedure called guided higher-order unification. This unification procedure is more general than Haskell's kind-preserving unification but less powerful than full higher-order unification. The main technical result is the soundness and completeness of the unification rules for the fragment of lambda calculus that we admit on the type level.
doi:10.1145/583852.581496 fatcat:2jx6xxhihzh2fkoqrxbqljnjea

Social Work and Social Living

1953 American Journal of Psychiatry  
Peter B. Neusauer, M. D., Council Child Development Center, New York, City. Ein PsycuoLtoc Ertest pas KZ (A Psychologist Experiences Life in a Concentration Camp). Second edition. By Viktor E.  ...  Peter B. Neusauer, M.D., Council Child Development Center, New York City. Tueory AND Practice oF SociaL Caszg Work. By Gordon Hamilton. (New York: Columbia Uni- versity Press, 1951. Price: $4.00.)  ... 
doi:10.1176/ajp.110.5.396-a fatcat:f3dslepwrzc43bzadt4x7qbuii

Optimisation of substrate feeding in shake flask cultures of Pichia pastoris for recombinant protein production

Myllyharju Johanna, Neubauer Antje, Hämäläinen Eija-Riitta, Vasala Antti, Krause Mirja, Ruottinen Maria, Bollok Monika, Neubauer Peter
2006 Microbial Cell Factories  
doi:10.1186/1475-2859-5-s1-p32 doaj:be40e628232a42a2a8aef035d3f724fa fatcat:7egrxa3mlradtifqhspnvif5nu

Adaptive Monitoring of Biotechnological Processes Kinetics

Velislava Lyubenova, Maya Ignatova, Olympia Roeva, Stefan Junne, Peter Neubauer
2020 Processes  
[Google Scholar] [CrossRef] Neubauer, P.; Lin, H.Y.; Mathiszik, B.  ...  [Google Scholar] Junne, S.; Klingner, A.; Kabisch, J.; Schweder, T.; Neubauer, P.  ... 
doi:10.3390/pr8101307 fatcat:kuratng2zbgcpe5fpxzwgwojam
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