### Recent Submissions

• Journal Article

#### Effect of the micro-environment on α-synuclein conversion and implication in seeded conversion assays ﻿

Translational Neurodegeneration. 2020 Jan 17;9(1):5
Abstract Background α-Synuclein is a small soluble protein, whose physiological function in the healthy brain is poorly understood. Intracellular inclusions of α-synuclein, referred to as Lewy bodies (LBs), are pathological hallmarks of α-synucleinopathies, such as Parkinson’s disease (PD) or dementia with Lewy bodies (DLB). Main body Understanding of the molecular basis as well as the factors or conditions promoting α-synuclein misfolding and aggregation is an important step towards the comprehension of pathological mechanism of α-synucleinopathies and for the development of efficient therapeutic strategies. Based on the conversion and aggregation mechanism of α-synuclein, novel diagnostic tests, such as protein misfolding seeded conversion assays, e.g. the real-time quaking-induced conversion (RT-QuIC), had been developed. In diagnostics, α-synuclein RT-QuIC exhibits a specificity between 82 and 100% while the sensitivity varies between 70 and 100% among different laboratories. In addition, the α-synuclein RT-QuIC can be used to study the α-synuclein-seeding-characteristics of different α-synucleinopathies and to differentiate between DLB and PD. Conclusion The variable diagnostic accuracy of current α-synuclein RT-QuIC occurs due to different protocols, cohorts and material etc.. An impact of micro-environmental factors on the α-synuclein aggregation and conversion process and the occurrence and detection of differential misfolded α-synuclein types or strains might underpin the clinical heterogeneity of α-synucleinopathies.
• Journal Article

#### Transcriptome of pleuropodia from locust embryos supports that these organs produce enzymes enabling the larva to hatch ﻿

Frontiers in Zoology. 2020 Jan 16;17(1):4
Abstract Background Pleuropodia are limb-derived glandular organs that transiently appear on the first abdominal segment in embryos of insects from majority of “orders”. They are missing in the genetic model Drosophila and little is known about them. Experiments carried out on orthopteran insects 80 years ago indicated that the pleuropodia secrete a “hatching enzyme” that digests the serosal cuticle to enable the larva to hatch, but evidence by state-of-the-art molecular methods is missing. Results We used high-throughput RNA-sequencing to identify the genes expressed in the pleuropodia of the locust Schistocerca gregaria (Orthoptera). First, using transmission electron microscopy we studied the development of the pleuropodia during 11 stages of the locust embryogenesis. We show that the glandular cells differentiate and start secreting just before the definitive dorsal closure of the embryo and the secretion granules outside the cells become more abundant prior to hatching. Next, we generated a comprehensive embryonic reference transcriptome for the locust and used it to study genome wide gene expression across ten morphologicaly defined stages of the pleuropodia. We show that when the pleuropodia have morphological markers of functional organs and produce secretion, they are primarily enriched in transcripts associated with transport functions. They express genes encoding enzymes capable of digesting cuticular protein and chitin. These include the potent cuticulo-lytic Chitinase 5, whose transcript rises just before hatching. Unexpected finding was the enrichment in transcripts for immunity-related enzymes. This indicates that the pleuropodia are equipped with epithelial immunity similarly as barrier epithelia in postembryonic stages. Conclusions These data provide transcriptomic support for the historic hypothesis that pleuropodia produce cuticle-degrading enzymes and function in hatching. They may also have other functions, such as facilitation of embryonic immune defense. By the genes that they express the pleuropodia are specialized embryonic organs and apparently an important though neglected part of insect physiology.
• Journal Article

#### Pre-treatment with the viral Toll-like receptor 3 agonist poly(I:C) modulates innate immunity and protects neutropenic mice infected intracerebrally with Escherichia coli ﻿

Journal of Neuroinflammation. 2020 Jan 17;17(1):24
Abstract Background Individuals with impaired immunity are more susceptible to infections than immunocompetent subjects. No vaccines are currently available to induce protection against E. coli meningoencephalitis. This study evaluated the potential of poly(I:C) pre-treatment to induce trained immunity. Poly(I:C) was administered as a non-specific stimulus of innate immune responses to protect immunocompetent and neutropenic wild-type mice from a subsequent challenge by the intracranial injection of E. coli K1. Methods Three days prior to infection, mice received an intraperitoneal injection of poly(I:C) or vehicle. Kaplan-Meier survival curves were analyzed. In short-term experiments, bacterial titers and the inflammatory response were characterized in the blood, cerebellum, and spleen homogenates. NK cell subpopulations in the brain and spleen were analyzed by flow cytometry. Numbers of microglia and activation scores were evaluated by histopathology. Results Pre-treatment with 200 μg poly(I:C) increased survival time, reduced mortality, and enhanced bacterial clearance in the blood, cerebellum, and spleen at early infection in neutropenic mice. Poly(I:C)-mediated protection correlated with an augmented number of NK cells (CD45+NK1.1+CD3−) and Iba-1+ microglial cells and a higher production of IFN-γ in the brain. In the spleen, levels of CCL5/RANTES and IFN-γ were increased and sustained in surviving poly(I:C)-treated animals for 14 days after infection. In immunocompetent animals, survival time was not significantly prolonged in poly(I:C)-treated animals although poly(I:C) priming reduced brain bacterial concentrations compared with vehicle-injected animals at early infection. Conclusions Pre-treatment with the viral TLR3 agonist poly(I:C) modulated innate immune responses and strengthened the resistance of neutropenic mice against E. coli K1 meningoencephalitis.
• Journal Article

#### Evaluation of sex differences in dietary behaviours and their relationship with cardiovascular risk factors: a cross-sectional study of nationally representative surveys in seven low- and middle-income countries ﻿

Nutrition Journal. 2020 Jan 13;19(1):3
Abstract Background Cardiovascular diseases (CVD) are the leading causes of death for men and women in low-and-middle income countries (LMIC). The nutrition transition to diets high in salt, fat and sugar and low in fruit and vegetables, in parallel with increasing prevalence of diet-related CVD risk factors in LMICs, identifies the need for urgent action to reverse this trend. To aid identification of the most effective interventions it is crucial to understand whether there are sex differences in dietary behaviours related to CVD risk. Methods From a dataset of 46 nationally representative surveys, we included data from seven countries that had recorded the same dietary behaviour measurements in adults; Bhutan, Eswatini, Georgia, Guyana, Kenya, Nepal and St Vincent and the Grenadines (2013–2017). Three dietary behaviours were investigated: positive salt use behaviour (SUB), meeting fruit and vegetable (F&V) recommendations and use of vegetable oil rather than animal fats in cooking. Generalized linear models were used to investigate the association between dietary behaviours and waist circumference (WC) and undiagnosed and diagnosed hypertension and diabetes. Interaction terms between sex and dietary behaviour were added to test for sex differences. Results Twenty-four thousand three hundred thirty-two participants were included. More females than males reported positive SUB (31.3 vs. 27.2% p-value < 0.001), yet less met F&V recommendations (13.2 vs. 14.8%, p-value< 0.05). The prevalence of reporting all three dietary behaviours in a positive manner was 2.7%, varying by country, but not sex. Poor SUB was associated with a higher prevalence of undiagnosed hypertension for females (13.1% vs. 9.9%, p-value = 0.04), and a higher prevalence of undiagnosed diabetes for males (2.4% vs. 1.5%, p-value = 0.02). Meeting F&V recommendations was associated with a higher prevalence of high WC (24.4% vs 22.6%, p-value = 0.01), but was not associated with undiagnosed or diagnosed hypertension or diabetes. Conclusion Interventions to increase F&V intake and positive SUBs in the included countries are urgently needed. Dietary behaviours were not notably different between sexes. However, our findings were limited by the small proportion of the population reporting positive dietary behaviours, and further research is required to understand whether associations with CVD risk factors and interactions by sex would change as the prevalence of positive behaviours increases.
• Journal Article

#### Enhanced genome assembly and a new official gene set for Tribolium castaneum ﻿

BMC Genomics. 2020 Jan 14;21(1):47
Abstract Background The red flour beetle Tribolium castaneum has emerged as an important model organism for the study of gene function in development and physiology, for ecological and evolutionary genomics, for pest control and a plethora of other topics. RNA interference (RNAi), transgenesis and genome editing are well established and the resources for genome-wide RNAi screening have become available in this model. All these techniques depend on a high quality genome assembly and precise gene models. However, the first version of the genome assembly was generated by Sanger sequencing, and with a small set of RNA sequence data limiting annotation quality. Results Here, we present an improved genome assembly (Tcas5.2) and an enhanced genome annotation resulting in a new official gene set (OGS3) for Tribolium castaneum, which significantly increase the quality of the genomic resources. By adding large-distance jumping library DNA sequencing to join scaffolds and fill small gaps, the gaps in the genome assembly were reduced and the N50 increased to 4753kbp. The precision of the gene models was enhanced by the use of a large body of RNA-Seq reads of different life history stages and tissue types, leading to the discovery of 1452 novel gene sequences. We also added new features such as alternative splicing, well defined UTRs and microRNA target predictions. For quality control, 399 gene models were evaluated by manual inspection. The current gene set was submitted to Genbank and accepted as a RefSeq genome by NCBI. Conclusions The new genome assembly (Tcas5.2) and the official gene set (OGS3) provide enhanced genomic resources for genetic work in Tribolium castaneum. The much improved information on transcription start sites supports transgenic and gene editing approaches. Further, novel types of information such as splice variants and microRNA target genes open additional possibilities for analysis.
• Journal Article

#### Global exponential stability and existence of periodic solutions of fuzzy wave equations ﻿

Advances in Difference Equations. 2020 Jan 07;2020(1):13
Abstract In this paper, the global exponential stability and the existence of periodic solutions of fuzzy wave equations are investigated. By variable substitution the system of partial differential equations (PDEs) is transformed from second order to first order. Some sufficient conditions that ensure the global exponential stability and the existence of periodic solution of the system are obtained by an analysis that uses a suitable Lyapunov functional. In addition, a concrete example is given to show the effectiveness of the results.
• Journal Article

#### Towards the restoration of the Mesoamerican Biological Corridor for large mammals in Panama: comparing multi-species occupancy to movement models ﻿

Movement Ecology. 2020 Jan 09;8(1):3
Abstract Background Habitat fragmentation is a primary driver of wildlife loss, and the establishment of biological corridors is a conservation strategy to mitigate this problem. Identifying areas with high potential functional connectivity typically relies on the assessment of landscape resistance to movement. Many modeling approaches exist to estimate resistance surfaces but to date only a handful of studies compared the outputs resulting from different methods. Moreover, as many species are threatened by fragmentation, effective biodiversity conservation requires that corridors simultaneously meet the needs of multiple species. While many corridor planning initiatives focus on single species, we here used a combination of data types and analytical approaches to identify and compare corridors for several large mammal species within the Panama portion of the Mesoamerican Biological Corridor. Methods We divided a large mammal assemblage into two groups depending on the species sensitivity to habitat disturbance. We subsequently used cost-distance methods to produce multi-species corridors which were modeled on the basis of (i) occupancy of nine species derived from camera trapping data collected across Panama, and (ii) step selection functions based on GPS telemetry data from white-lipped peccary Tayassu pecari, puma Puma concolor, and ocelot Leopardus pardalis. In addition to different data sources and species groups, we also used different transformation curves to convert occupancy and step-selection results into landscape resistance values. Results Corridors modeled differed between sensitive and tolerant species, between the data sets, and between the transformation curves. There were more corridors identified for tolerant species than for sensitive species. For tolerant species, several corridors developed with occupancy data overlapped with corridors produced with step selection functions, but this was not the case for sensitive species. Conclusion Our study represents the first comparison of multispecies corridors parametrized with step selection functions versus occupancy models. Given the wide variability in output corridors, our findings underscore the need to consider the ecological requirements of several species. Our results also suggest that occupancy models can be used for estimating connectivity of generalist species. Finally, this effort allowed to identify important corridors within the MBC (i) at a country scale and (ii) for several species simultaneously to accurately inform the local authorities in conservation planning. The approach we present is reproducible in other sites and/or for other species.
• Journal Article

#### Eumelanin and pheomelanin pigmentation in mollusc shells may be less common than expected: insights from mass spectrometry ﻿

Frontiers in Zoology. 2019 Dec 23;16(1):47
Abstract Background The geometric patterns that adorn the shells of many phylogenetically disparate molluscan species are comprised of pigments that span the visible spectrum. Although early chemical studies implicated melanin as a commonly employed pigment, surprisingly little evidence generated with more recent and sensitive techniques exists to support these observations. Results Here we present the first mass spectrometric investigations for the presence of eumelanin and pheomelanin in 13 different molluscan species from three conchiferan classes: Bivalvia, Cephalopoda and Gastropoda. In the bivalve Mytilus edulis we demonstrate that eumelanin mainly occurs in the outermost, non-mineralised and highly pigmented layer of the shell (often referred to as the periostracum). We also identified eumelanin in the shells of the cephalopod Nautilus pompilius and the marine gastropods Clanculus pharaonius and Steromphala adriatica. In the terrestrial gastropod Cepaea nemoralis we verify the presence of pheomelanin in a mollusc shell for the first time. Surprisingly, in a large number of brown/black coloured shells we did not find any evidence for either type of melanin. Conclusions We recommend methods such as high-performance liquid chromatography with mass spectrometric detection for the analysis of complex biological samples to avoid potential false-positive identification of melanin. Our results imply that many molluscan species employ as yet unidentified pigments to pattern their shells. This has implications for our understanding of how molluscs evolved the ability to pigment and pattern their shells, and for the identification of the molecular mechanisms that regulate these processes.
• Journal Article

#### TRITEX: chromosome-scale sequence assembly of Triticeae genomes with open-source tools ﻿

Genome Biology. 2019 Dec 18;20(1):284
Abstract Chromosome-scale genome sequence assemblies underpin pan-genomic studies. Recent genome assembly efforts in the large-genome Triticeae crops wheat and barley have relied on the commercial closed-source assembly algorithm DeNovoMagic. We present TRITEX, an open-source computational workflow that combines paired-end, mate-pair, 10X Genomics linked-read with chromosome conformation capture sequencing data to construct sequence scaffolds with megabase-scale contiguity ordered into chromosomal pseudomolecules. We evaluate the performance of TRITEX on publicly available sequence data of tetraploid wild emmer and hexaploid bread wheat, and construct an improved annotated reference genome sequence assembly of the barley cultivar Morex as a community resource.
• Journal Article

#### The prognostic capacities of CBP and p300 in locally advanced rectal cancer ﻿

World Journal of Surgical Oncology. 2019 Dec 19;17(1):224
Abstract Background CREB-binding protein (CBP) and p300 represent histone acetyltransferases (HATs) and transcriptional coactivators that play essential roles in tumour initiation and progression. Both proteins are generally thought to function as tumour suppressors, although their distinct roles in colorectal cancer (CRC) remain inconsistent and ambiguous. Thus, we analysed the expression of these two HATs in human tissue samples from patients with locally advanced rectal cancer via immunohistochemistry and evaluated their potential impacts on future CRC diagnosis and treatment. Methods In our analysis, we included ninety-three (n = 93) patients diagnosed with adenocarcinoma in the upper third of the rectum. None of the patients received preoperative chemoradiotherapy, but the patients did undergo primary resection of the tumour within the phase II GAST-05 trial. By using H-scores, the expression of both proteins was visualised via immunohistochemistry in resected specimens from the patients. CBP and p300 expression were correlated with clinical and follow-up data. Results Our analysis showed that high expression of CBP was significantly associated with prolonged cancer-specific survival (CSS; p = 0.002). In univariate analysis, CBP was an independent prognostic parameter for CSS (p = 0.042). High nuclear CBP expression was observed in two-thirds of patients. In contrast, we could not find any significant correlation between the expression of p300 and cancer-specific survival in this cohort of patients (p = 0.09). We did not observe any cooperation between CBP and p300 in our analysis. Conclusions High expression of CBP was significantly associated with improved oncological outcomes. This finding could help to stratify patients in the future for CRC treatment. Histone deacetylase (HDAC) inhibitors are increasingly playing a role in oncological treatment and could additionally become therapeutic options in CRC. Our findings need to be further evaluated and verified in future clinical analyses.
• Journal Article

#### Read-SpaM: assembly-free and alignment-free comparison of bacterial genomes with low sequencing coverage ﻿

BMC Bioinformatics. 2019 Dec 17;20(Suppl 20):638
Abstract Background In many fields of biomedical research, it is important to estimate phylogenetic distances between taxa based on low-coverage sequencing reads. Major applications are, for example, phylogeny reconstruction, species identification from small sequencing samples, or bacterial strain typing in medical diagnostics. Results We adapted our previously developed software program Filtered Spaced-Word Matches (FSWM) for alignment-free phylogeny reconstruction to take unassembled reads as input; we call this implementation Read-SpaM. Conclusions Test runs on simulated reads from semi-artificial and real-world bacterial genomes show that our approach can estimate phylogenetic distances with high accuracy, even for large evolutionary distances and for very low sequencing coverage.
• Journal Article

#### PedCAPNETZ – prospective observational study on community acquired pneumonia in children and adolescents ﻿

BMC Pulmonary Medicine. 2019 Dec 09;19(1):238
Abstract Background Pediatric community acquired pneumonia (pedCAP) is one of the leading causes for childhood morbidity accounting for up to 20% of pediatric hospital admissions in high income countries. In spite of its high morbidity, updated epidemiological and pathogen data after introduction of preventive vaccination and novel pathogen screening strategies are limited. Moreover, there is a need for validated recommendations on diagnostic and treatment regimens in pedCAP. Through collection of patient data and analysis of pathogen and host factors in a large sample of unselected pedCAP patients in Germany, we aim to address and substantially improve this situation. Methods pedCAPNETZ is an observational, multi-center study on pedCAP. Thus far, nine study centers in hospitals, outpatient clinics and practices have been initiated and more than 400 patients with radiologically confirmed pneumonia have been enrolled, aiming at a total of 1000 study participants. Employing an online data base, information on disease course, treatment as well as demographical and socioeconomical data is recorded. Patients are followed up until day 90 after enrollment; Comprehensive biosample collection and a central pedCAPNETZ biobank allow for in-depth analyses of pathogen and host factors. Standardized workflows to assure sample logistics and data management in more than fifteen future study centers have been established. Discussion Through comprehensive epidemiological, clinical and biological analyses, pedCAPNETZ fills an important gap in pediatric and infection research. To secure dissemination of the registry, we will raise clinical and scientific awareness at all levels. We aim at participating in decision making processes for guidelines and prevention strategies. Ultimately, we hope the results of the pedCAPNETZ registry will help to improve care and quality of life in pedCAP patients in the future.
• Journal Article

#### Pharmacotherapy of borderline personality disorder: what has changed over two decades? A retrospective evaluation of clinical practice ﻿

BMC Psychiatry. 2019 Dec 12;19(1):393
Abstract Background The purpose of this study was to assess the pharmacological treatment strategies of inpatients with borderline personality disorder between 2008 and 2012. Additionally, we compared pharmacotherapy during this period to a previous one (1996 to 2004). Methods Charts of 87 patients with the main diagnosis of borderline personality disorder receiving inpatient treatment in the University Medical Center of Goettingen, Germany, between 2008 and 2012 were evaluated retrospectively. For each inpatient treatment, psychotropic drug therapy including admission and discharge medication was documented. We compared the prescription rates of the interval 2008–2012 with the interval 1996–2004. Results 94% of all inpatients of the interval 2008–2012 were treated with at least one psychotropic drug at time of discharge. All classes of psychotropic drugs were applied. We found high prescription rates of naltrexone (35.6%), quetiapine (19.5%), mirtazapine (18.4%), sertraline (12.6%), and escitalopram (11.5%). Compared to 1996–2004, rates of low-potency antipsychotics, tri−/tetracyclic antidepressants and mood stabilizers significantly decreased while usage of naltrexone significantly increased. Conclusions In inpatient settings, pharmacotherapy is still highly prevalent in the management of BPD. Prescription strategies changed between 1996 and 2012. Quetiapine was preferred, older antidepressants and low-potency antipsychotics were avoided. Opioid antagonists are increasingly used and should be considered for further investigation.
• Journal Article

#### A Case Report: Building communities with training and resources for Open Science trainers ﻿

LIBER Quarterly 2018; 29(1)
To foster responsible research and innovation, research communities, institutions, and funders are shifting their practices and requirements towards Open Science. Open Science skills are becoming increasingly essential for researchers. Indeed general awareness of Open Science has grown among EU researchers, but the practical adoption can be further improved. Recognizing a gap between the needed and the provided training offer, the FOSTER project offers practical guidance and training to help researchers learn how to open up their research within a particular domain or research environment. Aiming for a sustainable approach, FOSTER focused on strengthening the Open Science training capacity by establishing and supporting a community of trainers. The creation of an Open Science training handbook was a first step towards bringing together trainers to share their experiences and to create an open and living knowledge resource. A subsequent series of train-the-trainer bootcamps helped trainers to find inspiration, improve their skills and to intensify exchange within a peer group. Four trainers, who attended one of the bootcamps, contributed a case study on their experiences and how they rolled out Open Science training within their own institutions. On its platform the project provides a range of online courses and resources to learn about key Open Science topics. FOSTER awards users gamification badges when completing courses in order to provide incentives and rewards, and to spur them on to even greater achievements in learning. The paper at hand describes FOSTER Plus’ training strategies, shares the lessons learnt and provides guidance on how to reuse the project’s materials and training approaches.
• Journal Article

#### Mothers’ experiences of quality of care and potential benefits of implementing the WHO safe childbirth checklist: a case study of Aceh Indonesia ﻿

BMC Pregnancy and Childbirth. 2019 Dec 03;19(1):461
Abstract Background In an effort to mitigate missed opportunities to provide high-quality care, the World Health Organization (WHO) has developed the Safe Childbirth Checklist (SCC) to support health providers perform essential tasks. Our qualitative study is a baseline assessment of quality of care (QoC) perceived by mothers who gave birth at health facilities aiming to highlight areas where implementing the SCC can potentially improve the QoC as well as areas that are not part of the SCC yet require improvement. Methods Assessing the overall experience of care, our qualitative study focuses on 8 out of 29 items in the checklist that are related to the personal interactions between healthcare provider and mothers. Using a set of semi-structured questions, we interviewed 26 new mothers who gave institutional births in Aceh province in Indonesia. Results Our findings revealed some gaps where implementing the SCC can potentially improve safety and QoC. They include communicating danger signs at critical points during birth and after discharge, encouraging breastfeeding, and providing mothers with information on family planning. Moreover, taking a qualitative approach allowed us to identify additional aspects such as need for clarity at the point of admission, maintaining dignity, and protecting mothers’ rights in the decision-making process to be also essential for better QoC. Conclusions Our study highlights the need to actively listen to and engage with the experiences of women in the adaptation and implementation of the checklist. While our findings indicate that implementing the SCC has the potential to improve the quality of maternal care and overall birth experience, a more holistic understanding of the lived experiences of women and the dynamics of their interactions with health facilities, care providers, and their birth companions can complement the implementation of the checklist.
• Journal Article

#### Health-related quality of life in early-onset-scoliosis patients treated with growth-friendly implants is influenced by etiology, complication rate and ambulatory ability ﻿

BMC Musculoskeletal Disorders. 2019 Dec 07;20(1):588
Abstract Background Progressive Early-Onset Scoliosis (EOS) in children may lead to surgical interventions with growth-friendly implants, which require repeated lengthening procedures in order to allow adequate growth. Quality of life was studied using the validated German version of the EOS-Questionnaire (EOSQ-24-G) in surgically treated EOS children with different lengthening modalities. Methods EOSQ-24-G and the KINDLR questionnaire were given to families with EOS children who had been treated by either vertical expandable prosthetic titanium rib implants and repetitive lengthening surgeries every 6 months or children who had received a magnetically expansion controlled implant, which was externally lengthened every 3 months. Results were compared according to differences between the two tests, and with possible influencing factors such as surgical method, severity of scoliosis, relative improvement of curvature, etiology, weight, age, travelling distance, complications, ambulatory ability and others. Results 56 children with an average curve angle of 69° corrected to 33° (52%; average age 5.6 yrs) answered the EOSQ-24-G and the KINDLR after an average follow-up of 3.9 years. Health-related quality of life (HRQoL) was not affected by the initial scoliosis correction, the number of surgeries or the implant type. However, there was a negative correlation with non-ambulatory status, complications during treatment and for children with a neuromuscular scoliosis. Conclusion Using the validated EOSQ-24-G, no statistically significant differences were found between the group of children receiving repetitive surgeries and children with external lengthening procedures without surgery. However, results were influenced by the etiology, complication rate or ambulatory ability. Level of Evidence/Clinical relevance Therapeutic Level IV
• Journal Article

#### Improvement and use of CRISPR/Cas9 to engineer a sperm-marking strain for the invasive fruit pest Drosophila suzukii ﻿

BMC Biotechnology. 2019 Dec 05;19(1):85
Abstract Background The invasive fruit pest Drosophila suzukii was reported for the first time in Europe and the USA in 2008 and has spread since then. The adoption of type II clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated (Cas) as a tool for genome manipulation provides new ways to develop novel biotechnologically-based pest control approaches. Stage or tissue-specifically expressed genes are of particular importance in the field of insect biotechnology. The enhancer/promoter of the spermatogenesis-specific beta-2-tubulin (β2t) gene was used to drive the expression of fluorescent proteins or effector molecules in testes of agricultural pests and disease vectors for sexing, monitoring, and reproductive biology studies. Here, we demonstrate an improvement to CRISPR/Cas-based genome editing in D. suzukii and establish a sperm-marking system. Results To improve genome editing, we isolated and tested the D. suzukii endogenous promoters of the small nuclear RNA gene U6 to drive the expression of a guide RNA and the Ds heat shock protein 70 promoter to express Cas9. For comparison, we used recombinant Cas9 protein and in vitro transcribed gRNA as a preformed ribonucleoprotein. We demonstrate the homology-dependent repair (HDR)-based genome editing efficiency by applying a previously established transgenic line that expresses DsRed ubiquitously as a target platform. In addition, we isolated the Ds_β2t gene and used its promoter to drive the expression of a red fluorescence protein in the sperm. A transgenic sperm-marking strain was then established by the improved HDR-based genome editing. Conclusion The deployment of the endogenous promoters of the D. suzukii U6 and hsp70 genes to drive the expression of gRNA and Cas9, respectively, enabled the effective application of helper plasmid co-injections instead of preformed ribonucleoproteins used in previous reports for HDR-based genome editing. The sperm-marking system should help to monitor the success of pest control campaigns in the context of the Sterile Insect Technique and provides a tool for basic research in reproductive biology of this invasive pest. Furthermore, the promoter of the β2t gene can be used in developing novel transgenic pest control approaches and the CRISPR/Cas9 system as an additional tool for the modification of previously established transgenes.
• Journal Article

#### Comparative knowledge, attitudes, and practices regarding anthrax, brucellosis, and rabies in three districts of northern Tanzania ﻿

BMC Public Health. 2019 Dec 03;19(1):1625
Abstract Background Knowledge, attitudes, and practices (KAP) surveys regarding zoonotic diseases are crucial to understanding the extent of knowledge among citizens and for guiding health-related education programs. Method Employing a structured questionnaire, we interviewed residents (n = 388) in three districts of northern Tanzania (Karatu n = 128, Monduli n = 114, Babati n = 146) to assess knowledge, attitudes and reported practices regarding three zoonotic diseases that occur in the region (anthrax, brucellosis, and rabies). We used generalized linear mixed effects models and multi-model inference to identify demographic correlates of knowledge. Results Proportional average district- and disease- specific knowledge scores ranged from 0.14–0.61. We found positive correlations between age and knowledge of symptoms, causes and treatments of anthrax (three districts), brucellosis (three districts), and rabies (one district). Gender, ethnic identity, formal education and ownership of livestock or dogs had variable effects on knowledge among the interviewed population. Risk perceptions regarding different diseases varied across districts and were positively correlated with knowledge of the specific diseases. Direct interactions with livestock and domestic dogs were reported to occur across all demographic groups, suggesting that most people living in rural settings of our study area are potentially exposed to zoonotic diseases. Behaviors which may favor transmission of specific pathogens (such as consumption of raw milk or meat) were occasionally reported and varied by district. Wildlife was generally regarded as negative or neutral with regard to overall veterinary and human health. Conclusion The combination of variable knowledge about zoonotic diseases in the three districts, reported occurrence of practices that are conducive to pathogen transmission, and previously documented circulation of pathogens causing anthrax, brucellosis and rabies in our study system, call for health education programs embedded in a holistic One Health approach.
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#### Unlocking the Digital Potential of Scholarly Monographs in 21st Century Research ﻿

LIBER QUARTERLY 2017; 27(1) p.194-211
In the light of new digital production and dissemination practices, the scholarly publishing system has seen significant and also disruptive changes, especially in STM (science, technology and medicine) and with regard to the predominant format “journal article.” The digital transformation also holds true for those disciplines that continue to rely on the scholarly monograph as a publication format and means for reputation building, namely the Humanities and the Social Sciences with a qualitative approach (HSS). In our paper we analyse the reasons why the monograph has not yet reached its full potential in the digital paradigm, especially in the uptake of Open Access and innovative publishing options. We highlight some of the principal underlying factors for this, and suggest how especially practices, now more widespread in HSS but arising from the Digital Humanities, could play a role in moving forward the rich digitality of the scholarly monograph.
• Journal Article

#### Mechanical power at a glance: a simple surrogate for volume-controlled ventilation ﻿

Intensive Care Medicine Experimental. 2019 Nov 27;7(1):61
Abstract Background Mechanical power is a summary variable including all the components which can possibly cause VILI (pressures, volume, flow, respiratory rate). Since the complexity of its mathematical computation is one of the major factors that delay its clinical use, we propose here a simple and easy to remember equation to estimate mechanical power under volume-controlled ventilation: Mechanical Power=VE×Peak Pressure+PEEP+F/620$$\mathrm{Mechanical}\ \mathrm{Power}=\frac{\mathrm{VE}\times \left(\mathrm{Peak}\ \mathrm{Pressure}+\mathrm{PEEP}+F/6\right)}{20}$$ where the mechanical power is expressed in Joules/minute, the minute ventilation (VE) in liters/minute, the inspiratory flow (F) in liters/minute, and peak pressure and positive end-expiratory pressure (PEEP) in centimeter of water. All the components of this equation are continuously displayed by any ventilator under volume-controlled ventilation without the need for clinician intervention. To test the accuracy of this new equation, we compared it with the reference formula of mechanical power that we proposed for volume-controlled ventilation in the past. The comparisons were made in a cohort of mechanically ventilated pigs (485 observations) and in a cohort of ICU patients (265 observations). Results Both in pigs and in ICU patients, the correlation between our equation and the reference one was close to the identity. Indeed, the R2 ranged from 0.97 to 0.99 and the Bland-Altman showed small biases (ranging from + 0.35 to − 0.53 J/min) and proportional errors (ranging from + 0.02 to − 0.05). Conclusions Our new equation of mechanical power for volume-controlled ventilation represents a simple and accurate alternative to the more complex ones available to date. This equation does not need any clinical intervention on the ventilator (such as an inspiratory hold) and could be easily implemented in the software of any ventilator in volume-controlled mode. This would allow the clinician to have an estimation of mechanical power at a simple glance and thus increase the clinical consciousness of this variable which is still far from being used at the bedside. Our equation carries the same limitations of all other formulas of mechanical power, the most important of which, as far as it concerns VILI prevention, are the lack of normalization and its application to the whole respiratory system (including the chest wall) and not only to the lung parenchyma.