@article{HafemeisterSchulzeBortfeldtetal., author = {Hafemeister, Tim and Schulze, Paul and Bortfeldt, Ralf and Simmet, Christian and Jung, Markus and Fuchs-Kittowski, Frank and Schulze, Martin}, title = {Boar Semen Shipping for Artificial Insemination: Current Status and Analysis of Transport Conditions with a Major Focus on Vibration Emissions}, series = {Animals}, volume = {12}, journal = {Animals}, number = {10}, editor = {Tsakmakidis, Ioannis A.}, publisher = {MDPI}, issn = {2076-2615}, doi = {10.3390/ani12101331}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:523-15816}, pages = {1 -- 13}, abstract = {In the modern pig reproduction system, artificial insemination (AI) doses are delivered from AI centers to sow farms via logistics vehicles. In this study, six breeding companies in three countries (Brazil, Germany, and the USA) were interviewed about their delivery process. It was found that there is currently no comprehensive monitoring system for the delivery of semen. The entire process "shipping of boar semen" was documented using Business Process Model and Notation (BPMN). Although it is not currently known which vibrations occur at all, it is suspected that vibration emissions affect the quality of boar semen. For this reason, a prototype of a measuring system was developed to calculate a displacement index (Di), representing vibration intensities. Vibrations were analyzed in standardized road trials (n = 120) on several road types (A: smooth asphalt pavement, B: rough asphalt pavement, C: cobblestone, and D: dirt road) with different speeds (30, 60, 90, 120, and 150 km/h). A two-way ANOVA showed significant differences in mean Di, depending on road surface and speed as well as an interaction of both factors (p < 0.001). A field study on a reference delivery from a German AI center to several sow farms indicated that 33\% of the observed roads are in good quality and generate only a few vibrations (Di ≤ 1), while 40\% are of a moderate quality with interrupted surfaces (Di = 1-1.5). However, 25\% of the roads show markedly increased vibrations (Di ≥ 1.5), as a consequence of bad conditions on cobblestones or unpaved roads. Overall, more attention should be paid to factors affecting sperm quality during transport. In the future, an Internet of Things (IoT) based solution could enable complete monitoring of the entire transport process in real time, which could influence the courier's driving behavior based on road conditions in order to maintain the quality of the transported AI doses.}, subject = {Insemination}, language = {en} } @article{HafemeisterSchulzeSimmetetal., author = {Hafemeister, Tim and Schulze, Paul and Simmet, Christian and Jung, Markus and Fuchs-Kittowski, Frank and Schulze, Martin}, title = {Intensity and Duration of Vibration Emissions during Shipping as Interacting Factors on the Quality of Boar Semen Extended in Beltsville Thawing Solution}, series = {Animals}, volume = {13}, journal = {Animals}, number = {5}, editor = {Tsakmakidis, Ioannis A.}, publisher = {MDPI}, issn = {2076-2615}, doi = {10.3390/ani13050952}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:523-16783}, pages = {1 -- 11}, abstract = {In the modern pig reproduction system, boar semen is a high-quality but perishable product that is distributed from only a few central boar stations to the sow farms. Like all parts of the production chain, the shipment of boar semen can affect sperm quality to varying degrees. In the present study, the loss of quality in response to increasing intensities and duration of vibration emissions was examined, and interaction of both factors was found. During normal transport conditions, vibration emissions are expected to be low, resulting in a low loss of quality. Nevertheless, the duration of transport should also be considered for the maintenance of boar semen quality at a high level. Abstract Vibration emissions during the transport of boar semen for artificial insemination (AI) affect sperm quality. In the present study, the common influence of the following factors was investigated: vibrations (displacement index (Di) = 0.5 to 6.0), duration of transport (0 to 12 h) and storage time (days 1 to 4). Normospermic ejaculates were collected from 39 fertile Pietrain boars (aged 18.6 ± 4.5 months) and diluted in a one-step procedure with an isothermic (32 °C) BTS (Minit{\"u}b) extender (n = 546 samples). Sperm concentration was adjusted to 22 × 106 sperm·mL-1. Extended semen (85 ± 1 mL) was filled into 95 mL QuickTip Flexitubes (Minit{\"u}b). For transport simulation on day 0, a laboratory shaker IKA MTS 4 was used. Total sperm motility (TSM) was evaluated on days 1 to 4. Thermo-resistance test (TRT), mitochondrial activity (MITO) and plasma membrane integrity (PMI) were assessed on day 4. Sperm quality dropped with increasing vibration intensity and transport duration, and the effect was enhanced by a longer storage time. A linear regression was performed using a mixed model, accounting for the boar as a random effect. The interaction between Di and transport duration significantly (p < 0.001) explained data for TSM (-0.30 ± 0.03\%), TRT (-0.39 ± 0.06\%), MITO (-0.45 ± 0.06\%) and PMI (-0.43 ± 0.05\%). Additionally, TSM decreased by 0.66 ± 0.08\% with each day of storage (p < 0.001). It can be concluded that boar semen extended in BTS should be transported carefully. If this is not possible or the semen doses are transported a long way, the storage time should be reduced to a minimum.}, subject = {Insemination}, language = {en} } @article{TauschLokaSchulzeetal., author = {Tausch, Simon H. and Loka, Tobias P. and Schulze, Jakob M. and Andrusch, Andreas and Klenner, Jeanette and Dabrowski, Piotr Wojciech and Lindner, Martin S. and Nitsche, Andreas and Renard, Bernhard Y.}, title = {PathoLive—Real-Time Pathogen Identification from Metagenomic Illumina Datasets}, series = {Life}, volume = {12}, journal = {Life}, number = {9}, editor = {Cai, Yudong}, publisher = {MDPI}, issn = {2075-1729}, doi = {10.3390/life12091345}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:523-16024}, pages = {1 -- 17}, abstract = {Over the past years, NGS has become a crucial workhorse for open-view pathogen diagnostics. Yet, long turnaround times result from using massively parallel high-throughput technologies as the analysis can only be performed after sequencing has finished. The interpretation of results can further be challenged by contaminations, clinically irrelevant sequences, and the sheer amount and complexity of the data. We implemented PathoLive, a real-time diagnostics pipeline for the detection of pathogens from clinical samples hours before sequencing has finished. Based on real-time alignment with HiLive2, mappings are scored with respect to common contaminations, low-entropy areas, and sequences of widespread, non-pathogenic organisms. The results are visualized using an interactive taxonomic tree that provides an easily interpretable overview of the relevance of hits. For a human plasma sample that was spiked in vitro with six pathogenic viruses, all agents were clearly detected after only 40 of 200 sequencing cycles. For a real-world sample from Sudan, the results correctly indicated the presence of Crimean-Congo hemorrhagic fever virus. In a second real-world dataset from the 2019 SARS-CoV-2 outbreak in Wuhan, we found the presence of a SARS coronavirus as the most relevant hit without the novel virus reference genome being included in the database. For all samples, clinically irrelevant hits were correctly de-emphasized. Our approach is valuable to obtain fast and accurate NGS-based pathogen identifications and correctly prioritize and visualize them based on their clinical significance: PathoLive is open source and available on GitLab and BioConda.}, subject = {Metagenom}, language = {en} }