Dirk Labudde

Hochschule Mittweida | HSMW · biioinformatics group

This book chapter delves into the field of colorimetric analysis of bloodstains in forensic science, focusing on its application in crime scene investigation. Therefore it provides a comprehensive overview of the biological background of age-induced color changes. The chapter begins with an introduction to the significance of blood evidence in solv...

Short messages stored on mobile devices have become a crucial source of evidence in criminal investigations. However, the high volume of chat messages poses a challenge to the investigator. Topic modelling offers the potential to summarise the short messages compactly, thus effectively supporting the investigator in exploring the vast number of cha...

Fanfiction platforms become very popular. However, since fan fiction stories can also contain content that can be disturbing to readers, it is important to assign appropriate warnings to them. The automatic assignment of 32 trigger labels to fanfiction works is addressed by the Trigger Detection task of PAN’23 in terms of a multi-label document cla...

Digital anthropometric pattern matching encompasses biometric identification on the basis of a combination of anthropometric measurements depicting the proportions of the human body from image or video material. In a previous publication, maximum likelihood density estimation of distributions of anthropometric measurement distances allowed for esti...

Zusammenfassung Der Umgang mit Hatespeech ist bereits seit mehreren Jahren ein Problem im Internet, insbesondere in sozialen Netzwerken. Da die enorme Menge an Kommentaren nicht mehr manuell moderiert werden kann, ist es essenziell, automatische Methoden zur Detektion offensiver Kommentare unterstützend einzusetzen. Doch speziell in Bezug auf die d...

Hass und aggressives Verhalten im Netz werden immer größere Probleme. Der bisher etablierte Versuch zur Lösung des Problems ist das Löschen von Kommentaren, doch um dem grundlegenden Problem entgegenzuwirken, müssen Ursachen für die Entstehung von Hass im Netz bekämpft werden. In diesem Kapitel wird daher neben Grundlagen der Hatespeechanalyse insb...

Video and image material is becoming increasingly ubiquitous thus its potential as evidence in forensic investigations is growing. Once faces are hidden however, the value of surveillance footage is restricted unless there is another biometric trait that can be observed by camera such as linear body measurements. There is much biological evidence f...

Nowadays, a huge amount of information and news articles are available every day. The events of recent years have shown that Fake News can severely shake trust in politics and science. Unfortunately, a decision can only be made about the truthfulness of a fraction of all news and posts. In this respect, the CLEF2022-CheckThat! shared task 3a adress...

Textual social media content and short messages have gained in importance as evidence in criminal investigations. Yet, the large number of textual data poses a great challenge for investigators. Even though text retrieval systems can assist in finding evidential messages, the success of the search still depends on entering appropriate search terms....

In this work, we present a new publicly available offensive language dataset of 10.278 German social media comments collected in the first half of 2021 that were annotated by in total six annotators. With twelve different annotation categories, it is far more comprehensive than other datasets, and goes beyond just hate speech detection. The labels...

During the prosecution process the primary objective is to prove criminal offences to the correct perpetrator to convict them with legal effect. However, in reality this may often be difficult to achieve. Suppose a suspect has been identified and is accused of a bank robbery. Due to the location of the crime, it can be assumed that there is suffici...

Mobile communication devices are a popular means of planning, commissioning and carrying out criminal offenses. In particular, data from messengers such as WhatsApp or Telegram often contain conclusive information. Organized crime also usually involves many devices, but not all of them contain the full history of communication. Rather, it is heavil...

The response of cells to their environment is driven by a variety of proteins and messenger molecules. In eukaryotes, their distribution and location in the cell are regulated by the vesicular transport system. The transport of aquaporin 2 between membrane and storage region is a crucial part of the water reabsorption in renal principal cells, and...

Untersuchung der Eignung von Photogrammetrie und Laserscan zur Digitalisierung in der forensischen Blutspurenmusteranalyse Tommy Bergmann - Sven Becker - Dirk Labudde Die Blutspurenmusteranalyse ist in der forensischen Tatortarbeit nicht mehr wegzudenken. Dabei werden Informationen zu Form und Lage von Blutflecken manuell ermittelt und interpretie...

Named entity recognition (NER) constitutes an important step in the processing of unstructured text content for the extraction of information as well as for the computer-supported analysis of large amounts of digital data via machine learning methods. However, NER often relies on domain-specific knowledge, being conducted manually in a time- and hu...

Nowadays, mobile devices play a crucial role in our daily life. In practice, criminals also use mobile devices to communicate. Therefore, they have been becoming an important resource for evidence for law enforcement agencies. Especially, the communication between criminals may provide information that could be important for a criminal investigatio...

In social networks such as Twitter, author profiling plays a big role. It is especially interesting to differentiate between accounts from humans and bots and to make a prediction about the age and the gender of human users. The information can be helpful to analyze possible manipulations, networks and crimes. This paper presents an approach to dif...

With the increasing importance of social media in everyone's life, the risk of its misuse by criminals is also increasing. In particular children are at risk of becoming victims of on-line related crime, especially sexual abuse. For example, sexual predators use online grooming to gain the trust of children and young adults. In this paper, a two-st...

The response of cells to their environment is driven by a variety of proteins and messenger molecules. In eukaryotes their distribution, which is regulated by a vesicular transport system, is important for a tight cellular response. The recycling of aquaporin 2 between membrane and storage region is a crucial part of the body water homeostasis and...

The age estimation of blood traces provides important leads for the chronological assessment of criminal events and their reconstruction. To determine bloodstain age, experimental comparative data from a laboratory environment are used. Under these conditions the utilization of anticoagulants such as EDTA helps to suppress the blood clotting mechan...

Der Charakter der Sammlungs- und Objektforschung lässt sich unter anderem mit dem Begriff „Spurenlesen“ fassen. „Spur“, der erste Bestandteil des Wortes, verankert die Sammlungs- und Objektforschung fest im materiellen Bereich. Ohne materiellen Träger keine Spur. Doch wird die Spur erst durch den Akt des ‚Lesens‘ zur Spur. Die interessegeleitete In...

Durch viele Einzelheiten, die Anthropologen durch logisches Aneinanderreihen einem Knochenpuzzle gleich Stück für Stück zusammensetzen, wird es möglich, aussagekräftige Rückschlüsse zu ziehen. Diese sind dabei behilflich, verstorbene Individuen oder Bevölkerungsgruppen und deren Lebensumstände zu rekonstruieren. Eine umfassende und nachhaltige Fors...

Interpreting the evidence found at a crime scene is essential in reconstructing the circumstances of a crime and, hence, solving it. In this paper a classical hypothesis-driven approach is combined with computer-aided modeling. Hereby, the paper focuses on the advantages of 3D models and their added value in the reconstruction of a case by visually...

In recent years, the automated, efficient and sensitive monitoring of social networks has become increasingly important for the criminal investigation process and crime prevention. Previously, we have shown that the detection of opinion leaders is of great interest in forensic applications to gather important information. In the current work, it is...

While technological advances and improved algorithms enhance most scientific fields, there remains a simple problem in many domains. If a decision has to be made we resort to simple majority votes or utilize agreement measures to determine how unanimous a decision is. Especially in text classification, a text is usually sorted into a specific categ...

Fingerprint analysis played a major role in the investigation of criminal offences for the past 100 years and is often the sole means of criminal identification [YA04]. Electrochemical analysis can yield important additional evidence like fingerprint age, biological age and gender of its creator as well as chemical adhesives [GRW12]. Additional gai...

Mithilfe der so genannten Blutmusteranalyse (engl. BPA – blood pattern analysis) können seit über 100 Jahren forensisch relevante Informationen zur Rekonstruktion eines Tatablaufs am Tatort ermittelt werden. Durch den technischen Fortschritt lässt sich auch auf diesem Gebiet mittlerweile der zeitliche Aufwand und die Präzision der Analysen verbesse...

Announcements of events are regularly spread using the Internet, e.g., via online newspapers or social media. Often, these events involve playing music publicly that is protected by international copyright laws. Authorities entrusted with the protection of the artists' interests have to find unregistered music events in order to fully exercise thei...

Storage and directed transfer of information is the key requirement for the development of life. Yet any information stored on our genes is useless without its correct interpretation. The genetic code defines the rule set to decode this information. Aminoacyl-tRNA synthetases are at the heart of this process. We extensively characterize how these e...

Die globale Vernetzung und die damit verbundene Veränderung des Kommunikationsverhaltens in der modernen Informationsgesellschaft ermöglicht die Kommunikation prinzipiell aller Menschen untereinander, unabhängig von Ort und Zeit. Auch (Cyber)Kriminelle nutzen diese Möglichkeiten, um potentielle Opfer auszuspähen oder sich mit anderen Gleichgesinnte...

Introduction During the last 20 years forensic imaging became increasingly more important due to the wider distribution and advancements of radiological techniques, such as computed tomography and magnetic resonance imaging. The databank on a knowledge-based case collection (WiFas) was developed to make the results and knowledge gained from these n...

Protein folding and structure prediction are two sides of the same coin. Contact maps and the related techniques of constraint-based structure reconstruction can be considered as unifying aspects of both processes. We present the Structural Relevance (SR) score which quantifies the information content of individual contacts and residues in the cont...

Due to the increasing digitalisation multi-label classification gains in importance in many areas. In this paper we propose a method to classify blurbs into eight basic book genre using an ensemble of classifier chains composed of radial support vector machines using word em-beddings and author information as features. Five models were tested using...

In this paper an approach for the automatic detection of offensive language in German twitter posts, so called tweets, based on a data set provided by the organizers from the GermEval2019 contest is presented. Two different approaches were used. The first one is based on a document-term-matrix and the second one uses fastText to represent tweets as...

Protein folding and structure prediction are two sides of the same coin. We propose contact maps and the related techniques of constraint-based structure reconstruction as unifying aspect of both processes. The presented Structural Relevance (SR) score quantifies the contribution of individual contacts and residues to structural integrity. It is de...

The lantibiotic nisin is used as a food additive to effectively inactivate a broad spectrum of Gram-positive bacteria such as Listeria monocytogenes. In total, 282 L. monocytogenes field isolates from German ready-to-eat food products, food-processing environments and patient samples and 39 Listeria reference strains were evaluated for their suscep...

With the rapid growth of public protein structure databases, computational techniques for storing as well as comparing proteins in an efficient manner are still in demand. Proteins play a major role in virtually all processes in life, and comparing their three-dimensional structures is essential to understanding the functional and evolutionary rela...

Genetic code and translation are key to all life. As a consequence, all kingdoms and species share the enzymes known as aminoacyl-tRNA synthetases, which link amino acids to their codons. For life to flourish, it is vital that these enzymes correctly implement the genetic code and hence correctly recognize amino acids. There are many theories on th...

Background: Machine learning strategies are prominent tools for data analysis. Especially in life sciences, they have become increasingly important to handle the growing datasets collected by the scientific community. Meanwhile, algorithms improve in performance, but also gain complexity, and tend to neglect interpretability and comprehensiveness o...

Dieses Lehrbuch soll Studierenden den Einstieg in die Gebiete der Forensik und Bioinformatik gleichermaßen erleichtern. Anhand eines fiktiven Falls, der sich durch das gesamte Buch zieht, wird die Bioinformatik und deren Grundlagen in das Gebiet der Forensik übertragen. Der Fall deckt eine Vielzahl an biologischen Spuren, sowie deren klassische Ana...

p-Hydroxybenzoate hydroxylase (PHBH; EC 1.14.13.2) is a microbial group A flavoprotein monooxygenase that catalyzes the ortho-hydroxylation of 4-hydroxybenzoate to 3,4-dihydroxybenzoate with the stoichiometric consumption of NAD(P)H and oxygen. PHBH and related enzymes lack a canonical NAD(P)H-binding domain and the way they interact with the pyrid...

Announcements of events are regularly spread using the Internet, e.g., via online newspapers or social media. Often, these events involve playing music publicly that is protected by international copyright laws. Authorities entrusted with the protection of the artists’ interests have to find unregistered music events in order to fully exercise thei...

Im Zusammenhang mit körperlicher Gewalt und deren Klassifizierung im rechtsmedizinischen Umfeld kommt der Begutachtung der Haut und deren Schädigung eine Schlüsselposition zu. So sollte die rechtsmedizinische Begutachtung von Spuren von Gewalteinwirkungen auf den menschlichen Körper hierarchisch von der Makro- zur Detailspur erfolgen. Grundsätzlich...

Das Blut gilt als Lebenselixier – ein Symbol der fortdauernden Vitalität des menschlichen Körpers. Mephisto, eine der Hauptfiguren von Goethes Faust, erkannte: „Blut ist ein ganz besonderer Saft.“ In der Umgangssprache stehen Wörter wie heißblütig oder blutjung für besonders kraft- und temperamentvolle Menschentypen, während blutarm und ausgeblutet...

Proteins are chains of amino acids which adopt a three-dimensional structure and are then able to catalyze chemical reactions or propagate signals in organisms. Without external influence, many proteins fold into their native structure, and a small number of Early Folding Residues (EFR) have previously been shown to initiate the formation of second...

Statistical characterization of EFR. For each presented feature the mean (μ) and standard deviation (σ) of both the EFR and LFR category is reported. It was tested whether the differences of a feature between EFR and LFR state is significant. pburied refers to the p-value of the test on residues buried according their RASA value, this was done beca...

Comparison of EFR and functional residues. For each presented feature the distribution of values is compared between functional and non-functional residues as well as EFR and functional residues. The corresponding p-values and significance level are stated for buried residues. Mean values are shown for EFR (μearly) and functional residues (μfunc)....

Start2Fold dataset as JSON file. Machine-readable JSON version of the dataset. Provides protein name, Start2Fold identifier, PDB identifier, UniProt identifier, number of EFR, range of residues numbers, and the secondary structure element composition for each dataset entry. (JSON)

Correlation matrix of computed features. Depicts correlations of analyzed correlation. The bigger the circle, the higher the association of both variables. Blue refers to positive correlation, whereas red represents a negative correlation. (TIF)

Network descriptors. Depiction of the used network descriptors: betweenness, closeness, clustering coefficient, and distinct neighborhood count. (TIF)

Summary of the aaRS dataset. Sequence conservation [93, 94] and EFoldMine [9] predictions for the aaRS protozyme regions [46–48] are presented. Encompassed are the average values for all residues, residues in the protozyme region, for positions predicted to be EFR, functional residues, ATP binding residues, and amino acid binding sites. (XLSX)

Detailed description of aaRS class I structures. For each renumbered position, it is stated whether it is functional [48] or an EFR. Furthermore given are the sequence conservation [93, 94], the number of backing sequences [48], and the average EFoldMine score [9]. (CSV)

Detailed description of aaRS class II structures. For each renumbered position, it is stated whether it is functional [48] or an EFR. Furthermore given are the sequence conservation [93, 94], the number of backing sequences [48], and the average EFoldMine score [9]. (CSV)

Table of computed features for the Start2Fold dataset. Contains for all residues the set of computed features as well as the annotation of Early Folding and functional residues. (CSV)

EFR dataset summary. Summarizes identifiers [23] of each entry as well as the number of residues in the corresponding protein chain, the number of EFR and functional residues as well as the cardinality of the intersection of both sets. To assess the relevance of the observed intersection it was compared to the expected intersection. Negative shift...

Start2Fold dataset as table. Summary table of all protein chains used for the analysis. Provides Start2Fold identifier, PDB identifier, evaluated HDX experiments, number of EFR, UniProt identifier, and identifiers of functional residues derived from UniProt. The last column contains the features in the UniProt XML file considered functional for thi...

Background: Machine learning strategies are prominent tools for data analysis. Especially in life sciences, they have become increasingly important to handle the growing datasets collected by the scientific community. Meanwhile, algorithms improve in performance, but also gain complexity, and tend to neglect interpretability and comprehensiveness o...

In recent years, the automated, efficient and sensitive monitoring of social networks has become increasingly important for criminal investigations and crime prevention. Previously, we have shown that the detection of opinion leaders is of great interest in forensic applications. In the present study, it is argued that state of the art opinion lead...

Micro-pollutants such as 17β-Estradiol (E2) have been detected in different water resources and their negative effects on the environment and organisms have been observed. Aptamers are established as a possible detection tool, but the underlying ligand binding is largely unexplored. In this study, a previously described 35-mer E2-specific aptamer w...

Micro-pollutants such as 17β-Estradiol (E2) have been detected in different water resources and their negative effects on the environment and organisms have been observed. Aptamers are established as a possible detection tool, but the underlying ligand binding is largely unexplored. In this study, a previously described 35-mer E2-specific aptamer w...

Serious crime scenes or disaster sites with many victimsafter natural disasters, airplane crashes or terrorist attacksrequire extensive and comprehensive investigations to clarify allcircumstances leading to the event, to identify the victims andto find the responsible people. The results of investigations donot only serve to prosecute the perpetra...

Micro pollutants such as 17β-Estradiol (E2) have been detected in low concentrations in different water resources and their negative effects on the environment and organisms are observed. In this study, a previously described 35-mer E2-specific aptamer was used to investigate the underlying binding characteristics between E2 and the aptamer through...

The origin of the machinery that realizes protein biosynthesis in all organisms is still unclear. One key component of this machinery are aminoacyl tRNA synthetases (aaRS), which ligate tRNAs to amino acids while consuming ATP. Sequence analyses revealed that these enzymes can be divided into two complementary classes. Both classes differ significa...

Binding mode definition. Binding modes M1 and M2 are defined based on the complexed ligand: ligands that bind to the adenosine phosphate moiety (highlighted in red, only in contact when adenosine phosphate is part of the ligand) of the binding site (M1), no ligands or ligands that bind exclusively to the aminoacyl part (green) of the binding site (...

Core-interaction patterns. Both aaRS classes contain highly conserved patterns, responsible for proper binding of the adenosine phosphate part of the ligand. Class I aaRS share a highly conserved set of backbone hydrogen interactions with the ligand: the Backbone Brackets. Class II active sites contain a pattern of two arginine residues grasping th...

Origin organisms of aaRS Class I and Class II structures in the dataset. The organisms of origin for aaRS Class I (A) and Class II (B) structures in the dataset. The inner circles correspond to the superkingdom of the organism. The outer circle depicts the partition into specific species (combining different strains). Sections representing eukaryot...

Class II sequences in FASTA format. Protein sequences of Class II aaRS structures used to construct the structure-guided MSA in FASTA format. (FASTA)

Secondary structure of Backbone Brackets adjacent residues. WebLogo [75] representation of secondary structure elements around the Backbone Brackets residues (274 and 1361) annotated by DSSP [123]: helices (blues), strands (red), and unordered (black). Unassigned states are represented by the character “C”. The height of each character corresponds...

Dataset preparation. (DOCX)

Selection of representative entries. (DOCX)

Dataset as JSON file. Machine-readable JSON version of the dataset. Additionally enriched with protein sequence, sequence cluster identifier, and representative types for each dataset entry. (JSON)

Backbone Brackets failed mapping. List of structures where the mapping of the Backbone Brackets motif was not possible. (TXT)

Arginine Tweezers failed mapping. List of structures where the mapping of the Arginine Tweezers motif was not possible. (TXT)

Renumbering table for Class II structures. Formatted table that contains all sequence positions of the Class II MSA and annotations of sequence motifs, Arginine Tweezers residues, and ligand binding regions (rows). Each renumbered sequence position is related to its original sequence position for every structure in the dataset (columns). (XLSX)

Secondary structure of Arginine Tweezers adjacent residues. WebLogo [75] representation of secondary structure elements around the Arginine Tweezers residues (698 and 1786) annotated by DSSP [123]: helices (blues), strands (red), and unordered (black). Unassigned states are represented by the letter “C”. The height of each character corresponds to...

Distributions of alpha carbon distances for Backbone Brackets and Arginine Tweezers. Distributions of alpha carbon distances for Class I Backbone Brackets motif and Class II Arginine Tweezers motif in adenosine phosphate bound (M1) and unbound state (M2). The alpha carbon distance of the Backbone Brackets differs significantly between the two state...

Distributions of side chain angles for Backbone Brackets and Arginine Tweezers. Distributions of side chain angle θ for Class I Backbone Brackets motif and Class II Arginine Tweezers motif in adenosine phosphate bound (M1) and unbound state (M2). The side chain angles of the Arginine Tweezers differs differs significantly between the two states (Ma...

Alignments of Backbone Brackets and Arginine Tweezers. Structural backbone-only alignments of relevant binding site motifs computed with Fit3D [122]. Alignments are grouped by structures derived from adenosine phosphate bound (M1) and unbound state (M2) for aaRS Class I and Class II. (A,C) The Class