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Carving Parameterized Unit Tests [article]

Alexander Kampmann, Andreas Zeller
2018 arXiv   pre-print
We present a method to automatically extract ("carve") parameterized unit tests from system executions. The unit tests execute the same functions as the system tests they are carved from, but can do so much faster as they call functions directly; furthermore, being parameterized, they can execute the functions with a large variety of randomly selected input values. If a unit-level test fails, we lift it to the system level to ensure the failure can be reproduced there. Our method thus allows to
more » ... focus testing efforts on selected modules while still avoiding false alarms: In our experiments, running parameterized unit tests for individual functions was, on average, 30~times faster than running the system tests they were carved from.
arXiv:1812.07932v1 fatcat:5evp3v74nngcjemo3v5elexvom

Active Learning of Input Grammars [article]

Matthias Höschele, Alexander Kampmann, Andreas Zeller
2017 arXiv   pre-print
Knowing the precise format of a program's input is a necessary prerequisite for systematic testing. Given a program and a small set of sample inputs, we (1) track the data flow of inputs to aggregate input fragments that share the same data flow through program execution into lexical and syntactic entities; (2) assign these entities names that are based on the associated variable and function identifiers; and (3) systematically generalize production rules by means of membership queries. As a
more » ... ult, we need only a minimal set of sample inputs to obtain human-readable context-free grammars that reflect valid input structure. In our evaluation on inputs like URLs, spreadsheets, or configuration files, our AUTOGRAM prototype obtains input grammars that are both accurate and very readable - and that can be directly fed into test generators for comprehensive automated testing.
arXiv:1708.08731v1 fatcat:gaxqc5gdwbcdvb5uztbpsje3ay

Sample-Free Learning of Input Grammars for Comprehensive Software Fuzzing [article]

Rahul Gopinath, Björn Mathis, Mathias Höschele, Alexander Kampmann, Andreas Zeller
2018 arXiv   pre-print
Generating valid test inputs for a program is much easier if one knows the input language. We present first successes for a technique that, given a program P without any input samples or models, learns an input grammar that represents the syntactically valid inputs for P -- a grammar which can then be used for highly effective test generation for P . To this end, we introduce a test generator targeted at input parsers that systematically explores parsing alternatives based on dynamic tracking
more » ... constraints; the resulting inputs go into a grammar learner producing a grammar that can then be used for fuzzing. In our evaluation on subjects such as JSON, URL, or Mathexpr, our PYGMALION prototype took only a few minutes to infer grammars and generate thousands of valid high-quality inputs.
arXiv:1810.08289v1 fatcat:kkxycyrf6zfanceblal36636ay

JTACO: Test Execution for Faster Bounded Verification [chapter]

Alexander Kampmann, Juan Pablo Galeotti, Andreas Zeller
2014 Lecture Notes in Computer Science  
In bounded program verification a finite set of execution traces is exhaustively checked in order to find violations to a given specification (i.e. errors). SAT-based bounded verifiers rely on SAT-Solvers as their back-end decision procedure, accounting for most of the execution time due to their exponential time complexity. In this paper we sketch a novel approach to improve SAT-based bounded verification. As modern SAT-Solvers work by augmenting partial assignments, the key idea is to
more » ... e some of these partial assignments into JUNIT test cases during the SAT-Solving process. If the execution of the generated test cases succeeds in finding an error, the SAT-Solver is promptly stopped. We implemented our approach in JTACO, an extension to the TACO bounded verifier, and evaluate our prototype by verifying parameterized unit tests of several complex data structures.
doi:10.1007/978-3-319-09099-3_10 fatcat:izzzj4qwnndvlayehfrvpafpbe

Virtuelle PC Pools für Computerpraktika am Beispiel der Materialwissenschaften

Steffen Kampmann, David Bodesheim, Alexander Croy, Thomas Schied, Rafael Gutierrez, Arezoo Dianat, Gianaurelio Cuniberti
2021 Lessons Learned  
Computerpraktika stellen einen wichtigen Bestandteil vieler Lehrveranstaltungen dar, welche die Grundlagen und Details von computergestützten Methoden vermitteln sollen. In den Materialwissenschaften spielen solche Methoden eine zunehmend wichtige Rolle. Typischerweise setzen die Praktika eine physische Präsenz in den PC Pools voraus, u.a. da eine Vielzahl von verschiedenen Programmen lokal installiert und bereitgestellt werden muss. Um Computerpraktika auch in der Online-Lehre vollumfänglich
more » ... d weitestgehend unabhängig von den Gegebenheiten der Studierenden einsetzen zu können, wurde im Wintersemester 2020/21 ein virtueller PC Pool auf Basis von virtuellen Maschinen mit Web-basiertem Zugang eingerichtet. Dieser virtuelle PC Pool wurde in verschiedenen Lehrveranstaltungen erfolgreich eingesetzt und kann auch bei hybriden Lehrformaten in verschiedenen Disziplinen verwendet werden.
doi:10.25369/ll.v1i1/2.17 fatcat:wtok2u2yjfakri2pfhd63dqfzi

Abstracting failure-inducing inputs

Rahul Gopinath, Alexander Kampmann, Nikolas Havrikov, Ezekiel O. Soremekun, Andreas Zeller
2020 Proceedings of the 29th ACM SIGSOFT International Symposium on Software Testing and Analysis  
A program fails. Under which circumstances does the failure occur? Starting with a single failure-inducing input (łThe input ((4)) failsž) and an input grammar, the ddset algorithm uses systematic tests to automatically generalize the input to an abstract failureinducing input that contains both (concrete) terminal symbols and (abstract) nonterminal symbols from the grammarÐfor instance, ł((⟨expr⟩))ž, which represents any expression ⟨expr⟩ in double parentheses. Such an abstract
more » ... input can be used (1) as a debugging diagnostic, characterizing the circumstances under which a failure occurs (łThe error occurs whenever an expression is enclosed in double parenthesesž); (2) as a producer of additional failure-inducing tests to help design and validate fixes and repair candidates (łThe inputs ((1)), ((3 * 4)), and many more also failž). In its evaluation on real-world bugs in JavaScript, Clojure, Lua, and UNIX command line utilities, ddset's abstract failure-inducing inputs provided to-the-point diagnostics, and precise producers for further failure inducing inputs. CCS CONCEPTS · Software and its engineering → Software testing and debugging; · Theory of computation → Grammars and context-free languages; Active learning.
doi:10.1145/3395363.3397349 dblp:conf/issta/GopinathKHSZ20 fatcat:5ficvzekxzfatbfxyszfieeize

Microstructural Characterization of the Anisotropy and Cyclic Deformation Behavior of Selective Laser Melted AlSi10Mg Structures

Mustafa Awd, Felix Stern, Alexander Kampmann, Daniel Kotzem, Jochen Tenkamp, Frank Walther
2018 Metals  
The laser-based fusion of metallic powder allows construction of components with arbitrary complexity. In selective laser melting, the rapid cooling of melt pools in the direction of the component building causes significant anisotropy of the microstructure and properties. The objective of this work is to investigate the influence of build anisotropy on the microstructure and mechanical properties in selective laser melted AlSi10Mg. The alloy is comprehensively used in the automotive industry
more » ... d has been one of the most frequently investigated Al alloys in additive manufacturing. Using specimens produced in three different building orientations with respect to the build platform, the anisotropy of the microstructure and defects will be investigated using scanning electron microscopy and microcomputed tomography. The analysis showed a seven-times higher pore density for the 90°-specimen compared to the 0°-specimen. The scanning electron microscopy revealed the influence of the direction of the cooling gradient on the constitution of the eutectic phase. Mechanical properties are produced in quasi-static and fatigue tests of variable and constant loading amplitudes. Specimens of 0° showed 8% higher tensile strength compared to 90°-specimens, while fracture strain was reduced almost 30% for the 45°-specimen. The correlation between structural anisotropy and mechanical properties illustrates the influence of the building orientation during selective laser melting on foreseen fields of application.
doi:10.3390/met8100825 fatcat:ernju4xivrfjbfqzh6gckoyyhi

Safety of Administering Live Vaccines During Pregnancy: A Systematic Review and Meta-Analysis of Pregnancy Outcomes

Almudena Laris-González, Daniel Bernal-Serrano, Alexander Jarde, Beate Kampmann
2020 Vaccines  
Live-attenuated vaccines (LAV) are currently contraindicated during pregnancy, given uncertain safety records for the mother–infant pair. LAV might, however, play an important role to protect them against serious emerging diseases, such as Ebola and Lassa fever. For this systematic review we searched relevant databases to identify studies published up to November 2019. Controlled observational studies reporting pregnancy outcomes after maternal immunization with LAV were included. The ROBINS-I
more » ... ool was used to assess risk of bias. Pooled odds ratios (OR) were obtained under a random-effects model. Of 2831 studies identified, fifteen fulfilled inclusion criteria. Smallpox, rubella, poliovirus, yellow fever and dengue vaccines were assessed in these studies. No association was found between vaccination and miscarriage (OR 0.98, 95% CI 0.87–1.10), stillbirth (OR 1.04, 95% CI 0.74–1.48), malformations (OR 1.09, 95% CI 0.98–1.21), prematurity (OR 0.99, 95% CI 0.90–1.08) or neonatal death (OR 1.06, 95% CI 0.68–1.65) overall. However, increased odds of malformations (OR 1.24; 95% CI 1.03–1.49) and miscarriage after first trimester immunization (OR 4.82; 95% CI 2.38–9.77) was found for smallpox vaccine. Thus, we did not find evidence of harm related to LAV other than smallpox with regards to pregnancy outcomes, but quality of evidence was very low. Overall risks appear to be small and have to be balanced against potential benefits for the mother-infant pair.
doi:10.3390/vaccines8010124 pmid:32168941 pmcid:PMC7157743 fatcat:nkxdoakd4bfh5ap6qo5z3wlhkm

Mislocalization and clearance of neuronal Rhes as a novel hallmark of tauopathies [article]

Alexander J Ehrenberg, Kun Leng, Israel Hernandez, CAroline Lew, William W Seeley, Salvatore Spina, Bruce L Miller, Helmut Heinsen, Martin Kampmann, Kenneth Kosik, Lea T. Grinberg
2020 medRxiv   pre-print
The farnesyltransferase inhibitor lonafarnib reduces tau inclusion burden and atrophy in familial tauopathy models by inhibiting farnesylation on the Ras GTPase, Rhes, and activating autophagy. While hinting at a role of Rhes in tau aggregation, it is unclear how translatable these results are for sporadic forms of tauopathy. We used a combination of quantitative pathology using multiplex immunofluorescence for Rhes, several tau post-translational modifications, and single nucleus RNA sequence
more » ... nalysis to interrogate Rhes presence and distribution in human cortical neurons and Rhes relation to tau and TDP-43 changes. snRNA data suggest that Rhes is found in all cortical neuron subpopulations, not only in striatum cells. Histologic investigation in hippocampal formation from multiple postmortem cases in five different tauopathies and healthy controls and TDP-43 proteinopathy showed that nearly all neurons in control brains display a pattern of diffuse cytoplasmic Rhes positivity. However, in the presence of abnormal tau, but not TDP-43 inclusions, the patterns of neuronal cytoplasmic Rhes tend to present as either punctiform or fully absent. Our findings reinforce the relevance of the link between Rhes changes and tau pathology suggested by in vivo and in vitro models of tauopathy and support a potential clinical application of lonafarnib to tauopathies.
doi:10.1101/2020.10.27.20220954 fatcat:qlmyfrwlfvf7nj7xzzgdbjbba4

Tau Internalization is Regulated by 6-O Sulfation on Heparan Sulfate Proteoglycans (HSPGs) [article]

Jennifer Rauch, John J. Chen, Alexander W. Sorum, Gregory M. Miller, Tal Sharf, Stephanie K. See, Linda C. Hsieh-Wilson, Martin Kampmann, Kenneth S. Kosik
2017 bioRxiv   pre-print
The misfolding and accumulation of tau protein into intracellular aggregates known as neurofibrillary tangles is a pathological hallmark of neurodegenerative diseases such as Alzheimers disease. However, while tau propagation is a known marker for disease progression, exactly how tau propagates from one cell to another and what mechanisms govern this spread are still unclear. Here, we report that cellular internalization of tau is regulated by quaternary structure and have developed a cellular
more » ... ssay to screen for genetic modulators of tau uptake. Using CRISPRi technology we have tested 3200 genes for their ability to regulate tau entry and identified enzymes in the heparan sulfate proteoglycan biosynthetic pathway as key regulators. We show that 6-O-sulfation is critical for tau-heparan sulfate interactions and that this modification regulates uptake in human central nervous system cell lines, iPS-derived neurons, and mouse organotypic brain slice culture. Together, these results suggest novel strategies to halt tau transmission.
doi:10.1101/167874 fatcat:nqta3ijxazgsveqzvbuhx3afrm

Patterns of neuronal Rhes as a novel hallmark of tauopathies

Alexander J. Ehrenberg, Kun Leng, Kaitlyn N. Letourneau, Israel Hernandez, Caroline Lew, William W. Seeley, Salvatore Spina, Bruce Miller, Helmut Heinsen, Martin Kampmann, Kenneth S. Kosik, Lea T. Grinberg
2021 Acta Neuropathologica  
The farnesyltransferase inhibitor, Lonafarnib, reduces tau inclusions and associated atrophy in familial tauopathy models through activation of autophagy, mediated by the inhibition of farnesylation of the Ras GTPase, Rhes. While hinting at a role of Rhes in tau aggregation, it is unclear how translatable these results are for sporadic forms of tauopathy. We examined histological slides of allocortex and neocortex from multiple postmortem cases in five different tauopathies, FTLD-TDP, and
more » ... y controls using immunofluorescence for Rhes, several tau post-translational modifications, and phospho-TDP-43. Single nucleus RNA data suggest that Rhes is found in all cortical neuron subpopulations but not in glia. Histologic investigation showed that nearly all neurons in control brains display a pattern of diffuse cytoplasmic Rhes positivity. However, in the presence of abnormal tau, but not abnormal TDP-43, the patterns of neuronal cytoplasmic Rhes tend to present as either punctiform or entirely absent. This observation reinforces the relevance of findings that link Rhes changes and tau pathology from the in vivo and in vitro models of tauopathy. The results here support a potential clinical application of Lonafarnib to tauopathies.
doi:10.1007/s00401-021-02279-2 pmid:33677647 pmcid:PMC8418783 fatcat:tp7565vgq5fw3hkutq3ewjdjau

The Lonafarnib target, Rhes, is uniquely dysregulated in tauopathies: A human postmortem study

Alexander J. Ehrenberg, Kun Leng, Kaitlin Letourneau, Israel Hernandez, Caroline Lew, William W. Seeley, Salvatore Spina, Bruce L. Miller, Helmut Heinsen, Martin Kampmann, Kenneth S. Kosik, Lea T. Grinberg
2021 Alzheimer's & Dementia  
The farnesyltransferase inhibitor, Lonafarnib, is capable of reducing tau lesions and associated atrophy in tauopathy models through activity on the Ras GTPase, Rhes (Hernandez I et al., 2019). While hinting at a role of Rhes in tau proteino-
doi:10.1002/alz.056685 fatcat:yiz2hz73hrehfipivvbeebcy34

Compact and highly active next-generation libraries for CRISPR-mediated gene repression and activation

Max A Horlbeck, Luke A Gilbert, Jacqueline E Villalta, Britt Adamson, Ryan A Pak, Yuwen Chen, Alexander P Fields, Chong Yon Park, Jacob E Corn, Martin Kampmann, Jonathan S Weissman
2016 eLife  
Genes were then partitioned into one of the 13 sublibraries defined by (Kampmann et al., 2015) , compressed into the indicated 7 groupings.  ...  We calculated the growth phenotype (g) for each sgRNA (Bassik et al., 2013; Kampmann et al., 2013) and averaged these values across two screen replicates (Figure 3 -figure supplement 1 and Supplementary  ... 
doi:10.7554/elife.19760 pmid:27661255 pmcid:PMC5094855 fatcat:fqi3vp4ovreqlaoe4baasrnb6i

Tau Internalization is Regulated by 6-O Sulfation on Heparan Sulfate Proteoglycans (HSPGs)

Jennifer N. Rauch, John J. Chen, Alexander W. Sorum, Gregory M. Miller, Tal Sharf, Stephanie K. See, Linda C. Hsieh-Wilson, Martin Kampmann, Kenneth S. Kosik
2018 Scientific Reports  
The misfolding and accumulation of tau protein into intracellular aggregates known as neurofibrillary tangles is a pathological hallmark of neurodegenerative diseases such as Alzheimer's disease. However, while tau propagation is a known marker for disease progression, exactly how tau propagates from one cell to another and what mechanisms govern this spread are still unclear. Here, we report that cellular internalization of tau is regulated by quaternary structure and have developed a cellular
more » ... assay to screen for genetic modulators of tau uptake. Using CRISPRi technology we have tested 3200 genes for their ability to regulate tau entry and identified enzymes in the heparan sulfate proteoglycan biosynthetic pathway as key regulators. We show that 6-O-sulfation is critical for tauheparan sulfate interactions and that this modification regulates uptake in human central nervous system cell lines, iPS-derived neurons, and mouse organotypic brain slice culture. Together, these results suggest novel strategies to halt tau transmission. The Microtubule-Associated Protein Tau (MAPT or tau) is an intrinsically disordered protein that under pathological conditions aggregates into filamentous inclusions known as neurofibrillary tangles (NFTs) 1 . While the composition and structure of NFTs are well characterized 2,3 , the in vivo process of aggregation is not well understood. The presence of NFTs is characteristic of a number of human diseases, collectively termed tauopathies. In tauopathies, such as Alzheimer's disease (AD), NFT pathology advances in a predictable pattern throughout the brain affecting regions involved in learning and memory 4 . This progression of NFT pathology correlates with cognitive decline in patients and permits neuropathological diagnoses of patients in different stages of AD 5 . peer-reviewed)
doi:10.1038/s41598-018-24904-z pmid:29686391 pmcid:PMC5913225 fatcat:hgtqr3uhlnhc5bzw2ljtuj4vtu

Sn-Doped Hematite for Photoelectrochemical Water Splitting: The Effect of Sn Concentration

Siyuan Zhang, Hamidreza Hajiyani, Alexander G. Hufnagel, Jonathan Kampmann, Benjamin Breitbach, Thomas Bein, Dina Fattakhova-Rohlfing, Rossitza Pentcheva, Christina Scheu
2019 Zeitschrift fur physikalische Chemie (Munchen. 1991)  
Hematite-based photoanodes have been intensively studied for photoelectrochemical water oxidation. The n-type dopant Sn has been shown to benefit the activity of hematite anodes. We demonstrate in this study that Sn-doped hematite thin films grown by atomic layer deposition can achieve uniform doping across the film thickness up to at least 32 mol%, far exceeding the equilibrium solubility limit of less than 1 mol%. On the other hand, with the introduction of Sn doping, the hematite crystallite
more » ... size decreases and many twin boundaries form in the film, which may contribute to the low photocurrent observed in these films. Density functional theory calculations with a Hubbard U term show that Sn doping has multiple effects on the hematite properties. With increasing Sn4+ content, the Fe2+ concentration increases, leading to a reduction of the band gap and finally to a metallic state. This goes hand in hand with an increase of the lattice constant.
doi:10.1515/zpch-2019-1482 fatcat:ctbbq32dsnbhtbfsq4aoqmldcm
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