Search

Plate-based proteomic sample preparation offers a solution to the large sample throughput demands in the biotechnology field where hundreds or thousands of engineered microbes are constructed for testing is routine. Meanwhile, sample preparation methods that work efficiently on broader microbial groups are desirable for new applications of proteomics in other fields, such as microbial communities. Here, we detail a step-by-step protocol that consists of cell lysis in an alkaline chemical buffer (NaOH/SDS) followed by protein precipitation with high-ionic strength acetone in 96-well format. The protocol works for a broad range of microbes (e.g., Gram-negative bacteria, Gram-positive bacteria, non-filamentous fungi) and the resulting proteins are ready for tryptic digestion for bottom-up quantitative proteomic analysis without the need for desalting column cleanup. The yield of protein using this protocol increases linearly with respect to the amount of starting biomass from 0.5-2.0 OD*mL of cells. By using a bench-top automated liquid dispenser, a cost-effective and environmentally-friendly option to eliminating pipette tips and reducing reagent waste, the protocol takes approximately 30 minutes to extract protein from 96 samples. Tests on mock mixtures showed expected results that the biomass composition structure is in close agreement with the experimental design. Lastly, we applied the protocol for the composition analysis of a synthetic community of environmental isolates grown on two different media. This protocol has been developed to facilitate rapid, low-variance sample preparation of hundreds of samples and allow flexibility for future protocol development.

The Global Alliance for Genomics and Health (GA4GH) is a standards-setting organization that is developing a suite of coordinated standards for genomics. The GA4GH Phenopacket Schema is a standard for sharing disease and phenotype information that characterizes an individual person or biosample. The Phenopacket Schema is flexible and can represent clinical data for any kind of human disease including rare disease, complex disease, and cancer. It also allows consortia or databases to apply additional constraints to ensure uniform data collection for specific goals. We present phenopacket-tools, an open-source Java library and command-line application for construction, conversion, and validation of phenopackets. Phenopacket-tools simplifies construction of phenopackets by providing concise builders, programmatic shortcuts, and predefined building blocks (ontology classes) for concepts such as anatomical organs, age of onset, biospecimen type, and clinical modifiers. Phenopacket-tools can be used to validate the syntax and semantics of phenopackets as well as to assess adherence to additional user-defined requirements. The documentation includes examples showing how to use the Java library and the command-line tool to create and validate phenopackets. We demonstrate how to create, convert, and validate phenopackets using the library or the command-line application. Source code, API documentation, comprehensive user guide and a tutorial can be found at https://github.com/phenopackets/phenopacket-tools. The library can be installed from the public Maven Central artifact repository and the application is available as a standalone archive. The phenopacket-tools library helps developers implement and standardize the collection and exchange of phenotypic and other clinical data for use in phenotype-driven genomic diagnostics, translational research, and precision medicine applications.

Study objectiveThe impact of biological sex in peripheral regional anaesthesia is largely unknown. We therefore designed a prospective study in volunteers to investigate the impact of biological sex on pharmacodynamic, pharmacokinetic and morphometric characteristics for peripheral nerve blockade.MethodsThe initial study plan was powered to include 90 volunteers to find a difference of 35 min in duration of sensory block (primary outcome variable) with 80% power and alpha error at 5%. After discussions in ethical review, a pilot study of 2 x 12 volunteers from each sex were studied. Female and male volunteers received ultrasound guided nerve blockade with 3.0 mL ropivacaine 7.5 mg mL-1. Sensory duration of blockade, as the primary outcome, was evaluated by pinprick testing. Secondary outcomes were sensory onset time of blockade, pharmacokinetic characteristics and the visibility of ulnar nerves using ultrasound. Analyses included Mann-Whitney U-statistics with PResultsAfter 24 participants, the median (IQR) duration of sensory blockade was 450 (420; 503) min in women and 480 (450; 510) min in men (P = 0.49). Sensory onset time of blockade, and ultrasound visibility of nerves were also similar between the study groups. The total drug exposure across time (AUC0-infinity) was significantly higher in women (P = 0.017). After a the planned power re-analysis after these 24 study paticipants, which suggested that > 400 subjects would be required with 80% power and alpha error of 5% to find significance for the primary outcome parameter for marginal differences, we terminated the study at this point.ConclusionsWe did not detect significant differences between female and male study participants in terms of pharmacodynamic and morphometric characteristics after ultrasound guided ulnar nerve blocks. Women did show significantly greater pharmacokinetic ropivacaine exposures. The results of this study indicate that peripheral regional block pharmacodynamic characteristics are independent of the biological sex, whereas pharmacokinetic parameters are sex-dependent.

BackgroundNeck pain remains a persistent challenge in modern society and is frequently encountered across a wide range of occupations, particularly those involving repetitive and monotonous tasks. It might be expected that patterns of trapezius muscle activity at work, characterized by few breaks and prolonged periods of sustained muscle activity, are linked to neck pain. However, previous cross-sectional studies have generally failed to establish a definitive association. While some longitudinal studies have suggested that extended periods of heightened muscle activity could be a risk factor for neck pain, these findings often relied on limited participant numbers or specific professional groups. This study aimed to investigate the relationship between trapezius muscle activity and neck pain by pooling data from seven Scandinavian research institutes encompassing a diverse range of occupational backgrounds.MethodsElectromyographic (EMG) data for the upper trapezius muscle, collected during working hours, were coupled with questionnaire responses pertaining to neck pain, individual characteristics, and potential confounding variables for a total of 731 subjects. Additionally, longitudinal data from 258 subjects were available. The various EMG datasets were consolidated into a standardized format, and efforts were made to harmonize inquiries about neck pain. Regression analyses, adjusting for sex and height, were conducted to explore the associations between muscle activity variables and neck pain. An exposure index was devised to quantify the cumulative neck load experienced during working hours and to differentiate between various occupational categories.ResultsThe cross-sectional data displayed a distinct pattern characterized by positive associations for brief periods of sustained muscle activity (SUMA) and negative associations for prolonged SUMA-periods and neck pain. The longitudinal data exhibited a contrasting trend, although it was not as pronounced as the cross-sectional findings. When employing the exposure index, notable differences in cumulative muscle load emerged among occupational groups, and positive associations with longitudinal neck pain were identified.DiscussionThe results suggest that individuals with neck pain experience higher cumulative workloads and extended periods of muscle activity over the long term. In the short term, they appear to compensate by taking frequent short breaks, resulting in a lower cumulative workload. Regardless of their occupation, it is crucial to distribute work breaks throughout the workday to ensure that the cumulative load remains manageable.

BackgroundInflammation has been implicated in driving the morbidity associated with subarachnoid hemorrhage (SAH). Despite understanding the important role of inflammation in morbidity following SAH, there is no current effective way to modulate this deleterious response. There is a critical need for a novel approach to immunomodulation that can be safely, rapidly, and effectively deployed in SAH patients. Vagus nerve stimulation (VNS) provides a non-pharmacologic approach to immunomodulation, with prior studies demonstrating VNS can reduce systemic inflammatory markers, and VNS has had early success treating inflammatory conditions such as arthritis, sepsis, and inflammatory bowel diseases. The aim of the Non-invasive Auricular Vagus nerve stimulation for Subarachnoid Hemorrhage (NAVSaH) trial is to translate the use of non-invasive transcutaneous auricular VNS (taVNS) to spontaneous SAH, with our central hypothesis being that implementing taVNS in the acute period following spontaneous SAH attenuates the expected inflammatory response to hemorrhage and curtails morbidity associated with inflammatory-mediated clinical endpoints.Materials and methodsThe overall objectives for the NAHSaH trial are to 1) Define the impact that taVNS has on SAH-induced inflammatory markers in the plasma and cerebrospinal fluid (CSF), 2) Determine whether taVNS following SAH reduces radiographic vasospasm, and 3) Determine whether taVNS following SAH reduces chronic hydrocephalus. Following presentation to a single enrollment site, enrolled SAH patients are randomly assigned twice daily treatment with either taVNS or sham stimulation for the duration of their intensive care unit stay. Blood and CSF are drawn before initiation of treatment sessions, and then every three days during a patient's hospital stay. Primary endpoints include change in the inflammatory cytokine TNF-α in plasma and cerebrospinal fluid between day 1 and day 13, rate of radiographic vasospasm, and rate of requirement for long-term CSF diversion via a ventricular shunt. Secondary outcomes include exploratory analyses of a panel of additional cytokines, number and type of hospitalized acquired infections, duration of external ventricular drain in days, interventions required for vasospasm, continuous physiology data before, during, and after treatment sessions, hospital length of stay, intensive care unit length of stay, and modified Rankin Scale score (mRS) at admission, discharge, and each at follow-up appointment for up to two years following SAH.DiscussionInflammation plays a central role in morbidity following SAH. This NAVSaH trial is innovative because it diverges from the pharmacologic status quo by harnessing a novel non-invasive neuromodulatory approach and its known anti-inflammatory effects to alter the pathophysiology of SAH. The investigation of a new, effective, and rapidly deployable intervention in SAH offers a new route to improve outcomes following SAH.Trial registrationClinical Trials Registered, NCT04557618. Registered on September 21, 2020, and the first patient was enrolled on January 4, 2021.

Cancer continues to pose a significant global health challenge, with gastrointestinal (GI) cancers among the most prevalent and deadly forms. These cancers often lead to high mortality rates and demand the use of potent cytotoxic chemotherapeutics. For example, 5-fluorouracil (5-FU) forms the backbone of chemotherapy regimens for various GI cancers, including colorectal cancer. While these chemotherapeutics efficiently kill cancer cells, they frequently cause off-target effects such as chemotherapy-induced mucositis (CIM), characterized by debilitating symptoms like pain, nausea, and diarrhoea, necessitating medical intervention. In this study, we elucidated the potential of melatonin and misoprostol to reduce 5-FU-induced small intestinal mucositis. Morphological and cellular changes in the jejunum, along with colonic faecal water content were quantified in rats as markers for CIM. Additionally, the effects of melatonin were investigated in vitro on 5-FU treated murine intestinal organoids. The results showed that melatonin prevented villus atrophy in the rat jejunal mucosa and upheld cell viability in murine intestinal organoids. In contrast, misoprostol alone or in combination with melatonin did not significantly affect CIM caused by 5-FU. These in vivo and in vitro experiments provided promising insights that melatonin may be used as a preventive and/or adjuvant combination therapy to prevent and reduce CIM, holding the potential to enhance cancer treatment outcomes and improve patient quality-of-life.

IntroductionPatients with head and neck cancer (PwHNC) benefit from targeted exercise interventions: symptom relief, compensation for dysfunction, improvement in quality of life (QoL). Data on acceptance physical interventions in PwHNC are rare. The 'OSHO #94' trial investigates the short- and medium-term effects of individualized home exercise in PwHNC on QoL, physical activity and functionality. The study includes a feasibility phase (proof of concept) in order to evaluate the acceptance. Here we present the study protocol as well as the feasibility results.Methods and analysisThis prospective, multicentre, single-arm intervention study includes PwHNC ≥18 years of age in aftercare or palliative care with stable remission under immunotherapy. The study opened in January 01, 2021, with estimated completion by December 31, 2024. The PwHNC receive an individualized home exercise program consisting of mobilization, coordination, strengthening and stretching exercises. This should be carried out at least three times a week over 12 weeks for 15 to 30 minutes, supplemented by aerobic training two to three times a week for 30 minutes (intervention). Once weekly telephone calls with a physiotherapist are performed. Subsequently, there is a 12-week follow-up (FU) without exercise specifications/contact. Outcomes are measured before and after the intervention and following the FU. Primary outcome of the feasibility phase (n = 25) was the determination of the dropout rate during the intervention with a termination cut off if more than 30% PwHNC withdrew premature. The primary outcome of the OSHO #94' trial (N = 53) is the change in global QoL score from pre- to post-intervention (EORTC QLQ-C30). Secondary outcomes include clinical and patient-reported measures, training details as well as functional diagnostic data (e.g. level of physical activity, training frequency, flexibility, fall risk and aerobic performance).Results25 PwHNC were enrolled onto the feasibility cohort. Only16% (4/25 patients) did not complete the study. Therefore, recruitment of PwHNC was continued. The dropout rate was adjusted from 30% (N = 60) to 20% (N = 53, calculated sample size n = 42 PwHNC and 20% (n = 11) to dropout).ConclusionsIndividualized home exercise programs in PwHNC in aftercare seem feasible. Consequently, the aim is now to evaluate the short and medium-term effects of individualized home exercise.

Background and aimCalibrated pelvic X-ray images are needed in the preoperative planning of total hip arthroplasty (THA) to predict component sizes. Errors and mismatch in the size of one or more components are reported, which can lead to clinically relevant complications. Our aim is to investigate whether we can solve the fundamental problem of X-ray calibration and whether traditional X-ray still has a place in preoperative planning despite improved radiological alternatives.MethodsBased on geometric and radiographic principles, we estimate that the magnification factor is adapted to the X-ray device and depends strongly on the source-image distance of the device. We analyse the errors of the various calibration methods and investigate which narrow range can be expected to show that the center of rotation is sufficiently accurate. Based on the results of several CT-scans we defined an adapted magnification factor and validated the degree of measurement accuracy.ResultsThe true magnification of objects on X-ray images depends mainly on the device settings. Stem size prediction is possible to a limited extent, with an error margin of 4.3%. Components can be predicted with a safety margin of one size up and down as with CT or 3D images. The prerequisite is that the source-image distance is greater than or equal to 120 cm, the table-image distance is known, and the object-image distance is estimated according to the patient's BMI. We defined a device-adapted magnification factor that simplifies the templating routine and can be used to obtain the most reliable preoperative dimensional measurements that can be expected from X-ray images. We found the error margin of the magnification factor with the highest degrees of prediction and precision.ConclusionPreoperative planning is reliable and reproducible using X-ray images if calibration is performed with the device-adapted magnification factor suggested in this paper.

Feralization is the process of domesticated animals returning to the wild and it is considered the counterpart of domestication. Molecular genetic changes are well documented in domesticated organisms but understudied in feral populations. In this study, the genetic differentiation between domestic and feral cats was inferred by analysing whole-genome sequencing data of two geographically distant feral cat island populations, Dirk Hartog Island (Australia) and Kaho'olawe (Hawaii) as well as domestic cats and European wildcats. The study investigated population structure, genetic differentiation, genetic diversity, highly differentiated genes, and recombination rates. Genetic structure analyses linked both feral cat populations to North American domestic and European cat populations. Recombination rates in feral cats were lower than in domestic cats but higher than in wildcats. For Australian and Hawaiian feral cats, 105 and 94 highly differentiated genes compared to domestic cats respectively, were identified. Annotated genes had similar functions, with almost 30% of the divergent genes related to nervous system development in both feral groups. Twenty mutually highly differentiated genes were found in both feral populations. Evolution of highly differentiated genes was likely driven by specific demographic histories, the relaxation of the selective pressures associated with domestication, and adaptation to novel environments to a minor extent. Random drift was the prevailing force driving highly divergent regions, with relaxed selection in feral populations also playing a significant role in differentiation from domestic cats. The study demonstrates that feralization is an independent process that brings feral cats on a unique evolutionary trajectory.

Prior research has identified that school absences harm children's academic achievement. However, this literature is focused on brief periods or single school years and does not consistently account for the dynamic nature of absences across multiple school years. This study examined dynamic trajectories of children's authorised and unauthorised absences throughout their compulsory school career in England. It investigated the consequences of these absence trajectories for children's achievement at the end of compulsory schooling. We analyse linked administrative data on children's absences and achievement from the National Pupil Database and survey data from the Millennium Cohort Study for a representative sample of children born in 2000/2001 in England (N = 7218). We used k-means clustering for longitudinal data to identify joint authorised-unauthorised absence trajectories throughout compulsory schooling and a regression-with-residuals approach to examine the link between absence trajectories and achievement. We identified five distinct absence trajectories: (1) 'Consistently Low Absences', (2) 'Consistently Moderate Authorised Absences', (3) 'Moderately Increasing Unauthorised Absences', (4) 'Strongly Increasing Unauthorised Absences', and (5) 'Strongly Increasing Authorised Absences'. We found substantial differences between trajectory groups in GCSE achievement, even when accounting for significant risk factors of school absences. Compared to 'Consistently Low Absences', 'Strongly Increasing Unauthorised Absences' reduced achievement by -1.23 to -1.48 standard deviations, while 'Strongly Increasing Authorised Absences' reduced achievement by -0.72 to -1.00 SD for our continuous outcomes. 'Moderately Increasing Unauthorised Absences' (-0.61 to -0.70 SD) and 'Consistently Moderate Authorised Absences' (-0.13 to -0.21 SD) also negatively affected achievement compared to 'Consistently Low Absences'. Our research underscores the critical importance of examining entire trajectories of absenteeism and differentiating between types of absences to fully grasp their associations with academic outcomes and design targeted interventions accordingly.

BackgroundIn Germany, skin cancer screening (SCS) is available free of charge every two years to all those with statutory health insurance over the age of 35. General Practitioners (GP) can carry out the screening if they have completed an 8-hour training course. GPs play a crucial role in the implementation of SCS and act as gatekeepers between initial patient contact and referral to dermatologists.ObjectiveTo record how comprehensively GPs carry out SCS in terms of patient information and body examination, as well as to explore GPs opinions on the feasibility of SCS.MethodsA cross-sectional survey was conducted. A questionnaire was sent to GPs with permission to perform SCS in two regions of Germany (Bavaria and Saxony) between August and September 2021. Data were analyzed using descriptive analysis. Subgroup analysis was performed according to regions (federal state, location of physician´s office), professional experience (experience in years, number of monthly screenings, age) and gender. Open questions were evaluated using qualitative content analysis.ResultsIn the survey, 204 GPs responded. Genitalia (40.7%, 83/203), anal fold (62.3%, 127/204) and oral mucosa (66.7%, 136/204) were the least examined body regions during screening. Information on risks (false-positive findings: 18.6%, 38/203; false-negative findings: 13.2%, 27/203; overdiagnosis: 7.8%, 16/203) and benefits (48.0%, 98/202) were not always provided. GPs who performed screenings more frequently were more likely to provide information about the benefits of SCS (p10 vs. ConclusionUncertainties in the implementation of the SCS should be addressed by offering refresher courses. Good networking between GPs and dermatologists is essential to improve SCS quality.

Current strategies to hold surface warming below a certain level, e. g., 1.5 or 2°C, advocate limiting total anthropogenic cumulative carbon emissions to ∼0.9 or ∼1.25 Eg C (1018 grams carbon), respectively. These allowable emission budgets are based on a near-linear relationship between cumulative emissions and warming identified in various modeling efforts. The IPCC assesses this near-linear relationship with high confidence in its Summary for Policymakers (§D1.1 and Figure SPM.10). Here we test this proportionality in specially designed simulations with a latest-generation Earth system model (ESM) that includes an interactive carbon cycle with updated terrestrial ecosystem processes, and a suite of CMIP simulations (ZecMIP, ScenarioMIP). We find that atmospheric CO2 concentrations can differ by ∼100 ppmv and surface warming by ∼0.31°C (0.46°C over land) for the same cumulated emissions (≈1.2 Eg C, approximate carbon budget for 2°C target). CO2 concentration and warming per 1 Eg of emitted carbon (Transient Climate Response to Cumulative Carbon Emissions; TCRE) depend not just on total emissions, but also on the timing of emissions, which heretofore have been mainly overlooked. A decomposition of TCRE reveals that oceanic heat uptake is compensating for some, but not all, of the pathway dependence induced by the carbon cycle response. The time dependency clearly arises due to lagged carbon sequestration processes in the oceans and specifically on land, viz., ecological succession, land-cover, and demographic changes, etc., which are still poorly represented in most ESMs. This implies a temporally evolving state of the carbon system, but one which surprisingly apportions carbon into land and ocean sinks in a manner that is independent of the emission pathway. Therefore, even though TCRE differs for different pathways with the same total emissions, it is roughly constant when related to the state of the carbon system, i. e., the amount of carbon stored in surface sinks. While this study does not fundamentally invalidate the established TCRE concept, it does uncover additional uncertainties tied to the carbon system state. Thus, efforts to better understand this state dependency with observations and refined models are needed to accurately project the impact of future emissions.

The American lobster (Homarus americanus) is an economically important species in the western Atlantic and its climate-driven range shift northward along the east coast of the United States is well documented. The thermal tolerance of lab-reared postlarvae of this species has been extensively investigated to better understand settlement and recruitment dynamics. However, there have been few studies focused on wild-caught postlarvae, and even fewer that have analyzed lab-rearing conditions in context of diet. In this study, we investigated gene transcriptional changes in postlarvae caught in the wild, as well as postlarvae reared in the laboratory on a brine shrimp diet or a wild-sourced zooplankton diet. We found between wild-caught and brine shrimp-reared larvae 3,682 differentially expressed genes, and between wild and zooplankton-reared postlarvae 3,939 differentially expressed genes. Between the two lab-reared groups fed different diets 2,603 genes were differentially expressed. We also exposed individuals in all rearing groups to chronic temperature treatments of 8°C and 26°C and found that both temperature extremes elicit 68-95% fewer transcriptional changes in wild postlarvae compared to either lab-reared group. In wild postlarvae, we identified differential expression of transcripts within the FoxO signaling pathway, a signaling pathway with a central role in cellular physiology, as potential molecular markers for cold tolerance in the American lobster. These findings contextualize the current literature on lab-reared postlarvae as containing conservative estimates for in situ organisms and can be used to inform population distribution modeling efforts. They also provide evidence for the need to adjust lab-rearing techniques or source wild larval crustaceans to augment studies of larval biology.

PurposeOut-of-hospital cardiac arrest (OHCA) carries a relatively poor prognosis and requires multimodal prognostication to guide clinical decisions. Identification of previously unrecognized metabolic routes associated with patient outcome may contribute to future biomarker discovery. In OHCA, inhaled xenon elicits neuro- and cardioprotection. However, the metabolic effects remain unknown.Materials and methodsIn this post-hoc study of the randomised, 2-group, single-blind, phase 2 Xe-Hypotheca trial, 110 OHCA survivors were randomised 1:1 to receive targeted temperature management (TTM) at 33°C with or without inhaled xenon during 24 h. Blood samples for nuclear magnetic resonance spectroscopy metabolic profiling were drawn upon admission, at 24 and 72 h.ResultsAt 24 h, increased lactate, adjusted hazard-ratio 2.25, 95% CI [1.53; 3.30], pConclusionsIn OHCA patients receiving TTM with or without xenon, high lactate and alanine and decreased BCAAs and S-HDL-CE associated with increased mortality. It remains to be established whether current observations on BCAAs, and possibly alanine and lactate, could reflect neural damage via their roles in the metabolism of the neurotransmitter glutamate. Xenon did not significantly alter the measured metabolic profile, a potentially beneficial attribute in the context of compromised ICU patients.Trial registrationTrial Registry number: ClinicalTrials.gov Identifier: NCT00879892.

The Arctic faces increasing exposure to environmental chemicals such as metals, posing health risks to humans and wildlife. Biomonitoring of polar bears (Ursus maritimus) can be used to quantify chemicals in the environment and in traditional foods consumed by the Inuit. However, typically, these samples are collected through invasive or terminal methods. The biomonitoring of feces could be a useful alternative to the current metal monitoring method within the Arctic. Here, we aim to 1) quantify the relationship between concentrations of metals in the feces and tissues (muscle, liver, and fat) of polar bears using predictive modeling, 2) develop an easy-to-use conversion tool for use in community-based monitoring programs to non-invasively estimate contaminant concentrations in polar bears tissues and 3) demonstrate the application of these models by examining potential exposure risk for humans from consumption of polar bear muscle. Fecal, muscle, liver, and fat samples were harvested from 49 polar bears through a community-based monitoring program. The samples were analyzed for 32 metals. Exploratory analysis indicated that mean metal concentrations generally did not vary by age or sex, and many of the metals measured in feces were positively correlated with the internal tissue concentration. We developed predictive linear regression models between internal (muscle, liver, fat) and external (feces) metal concentrations and further explored the mercury and methylmercury relationships for utility risk screening. Using the cross-validated regression coefficients, we developed a conversion tool that contributes to the One Health approach by understanding the interrelated health of humans, wildlife, and the environment in the Arctic. The findings support using feces as a biomonitoring tool for assessing contaminants in polar bears. Further research is needed to validate the developed models for other regions in the Arctic and assess the impact of environmental weathering on fecal metal concentrations.

The Hedgehog (HH) pathway is crucial for embryonic development, and adult homeostasis. Its dysregulation is implicated in multiple diseases. Existing cellular models used to study HH signal regulation in mammals do not fully recapitulate the complexity of the pathway. Here we show that Spinal Cord Organoids (SCOs) can be applied to quantitively study the activity of the HH pathway. During SCO formation, the specification of different categories of neural progenitors (NPC) depends on the intensity of the HH signal, mirroring the process that occurs during neural tube development. By assessing the number of NPCs within these distinct subgroups, we are able to categorize and quantify the activation level of the HH pathway. We validate this system by measuring the effects of mutating the HH receptor PTCH1 and the impact of HH agonists and antagonists on NPC specification. SCOs represent an accessible and reliable in-vitro tool to quantify HH signaling and investigate the contribution of genetic and chemical cues in the HH pathway regulation.

BackgroundPredicting and explaining species occurrence using environmental characteristics is essential for nature conservation and management. Species distribution models consider species occurrence as the dependent variable and environmental conditions as the independent variables. Suitable conditions are estimated based on a sample of species observations, where one assumes that the underlying environmental conditions are known. This is not always the case, as environmental variables at broad spatial scales are regularly extrapolated from point-referenced data. However, treating the predicted environmental conditions as accurate surveys of independent variables at a specific point does not take into account their uncertainty.MethodsWe present a joint hierarchical Bayesian model where models for the environmental variables, rather than a set of predicted values, are input to the species distribution model. All models are fitted together based only on point-referenced observations, which results in a correct propagation of uncertainty. We use 50 plant species representative of the Dutch flora in natural areas with 8 soil condition predictors taken during field visits in the Netherlands as a case study. We compare the proposed model to the standard approach by studying the difference in associations, predicted maps, and cross-validated accuracy.FindingsWe find that there are differences between the two approaches in the estimated association between soil conditions and species occurrence (correlation 0.64-0.84), but the predicted maps are quite similar (correlation 0.82-1.00). The differences are more pronounced in the rarer species. The cross-validated accuracy is substantially better for 5 species out of the 50, and the species can also help to predict the soil characteristics. The estimated associations tend to have a smaller magnitude with more certainty.ConclusionThese findings suggests that the standard model is often sufficient for prediction, but effort should be taken to develop models which take the uncertainty in the independent variables into account for interpretation.

IntroductionMicrovascular dysfunction (MVD) is a hallmark feature of chronic graft dysfunction in patients that underwent orthotopic heart transplantation (OHT) and is the main contributor to impaired long-term graft survival. The aim of this study was to determine the effect of MVD on functional and structural properties of cardiomyocytes isolated from ventricular biopsies of OHT patients.MethodsWe included 14 patients post-OHT, who had been transplanted for 8.1 years [5.0; 15.7 years]. Mean age was 49.6 ± 14.3 years; 64% were male. Coronary microvasculature was assessed using guidewire-based coronary flow reserve(CFR)/index of microvascular resistance (IMR) measurements. Ventricular myocardial biopsies were obtained and cardiomyocytes were isolated using enzymatic digestion. Cells were electrically stimulated and subcellular Ca2+ signalling as well as mitochondrial density were measured using confocal imaging.ResultsMVD measured by IMR was present in 6 of 14 patients with a mean IMR of 53±10 vs. 12±2 in MVD vs. controls (CTRL), respectively. CFR did not differ between MVD and CTRL. Ca2+ transients during excitation-contraction coupling in isolated ventricular cardiomyocytes from a subset of patients showed unaltered amplitudes. In addition, Ca2+ release and Ca2+ removal were not significantly different between MVD and CTRL. However, mitochondrial density was significantly increased in MVD vs. CTRL (34±1 vs. 29±2%), indicating subcellular changes associated with MVD.ConclusionIn-vivo ventricular microvascular dysfunction post OHT is associated with preserved excitation-contraction coupling in-vitro, potentially owing to compensatory changes on the mitochondrial level or due to the potentially reversible cause of the disease.

Whether a saccade is accurate and has reached the target cannot be evaluated during its execution, but relies on post-saccadic feedback. If the eye has missed the target object, a secondary corrective saccade has to be made to align the fovea with the target. If a systematic post-saccadic error occurs, adaptive changes to the oculomotor behavior are made, such as shortening or lengthening the saccade amplitude. Systematic post-saccadic errors are typically attributed internally to erroneous motor commands. The corresponding adaptive changes to the motor command reduce the error and the need for secondary corrective saccades, and, in doing so, restore accuracy and efficiency. However, adaptive changes to the oculomotor behavior also occur if a change in saccade amplitude is beneficial for task performance, or if it is rewarded. Oculomotor learning thus is more complex than reducing a post-saccadic position error. In the current study, we used a novel oculomotor learning paradigm and investigated whether human participants are able to adapt their oculomotor behavior to improve task performance even when they attribute the error externally. The task was to indicate the intended target object among several objects to a simulated human-machine interface by making eye movements. The participants were informed that the system itself could make errors. The decoding process depended on a distorted landing point of the saccade, resulting in decoding errors. Two different types of visual feedback were added to the post-saccadic scene and we compared how participants used the different feedback types to adjust their oculomotor behavior to avoid errors. We found that task performance improved over time, regardless of the type of feedback. Thus, error feedback from the simulated human-machine interface was used for post-saccadic error evaluation. This indicates that 1) artificial visual feedback signals and 2) externally caused errors might drive adaptive changes to oculomotor behavior.

Accurate monitoring of gastro-enteric and other diseases in large populations poses a challenge for public health management. Sewage represents a larger population, is freely obtainable and non-subject to ethical approval. Metagenomic sequencing offers simultaneous, multiple-target analysis. However, no study has demonstrated the sensitivity of metagenomics for detecting bacteria in sewage. In this study, we spot-released 1013 colony-forming units (CFU) of Staphyloccus hyicus (non-pathogenetic strain 842J-88). The strain was flushed down a toilet into the sewer in the catchment area of a public wastewater treatment plant (WWTP), serving a population of 36,000 people. Raw sewage was continuously sampled at the WWTP's inlet over 30- and 60-minute intervals for a total period of seven hours. The experiment was conducted twice with one week in-between release days and under comparable weather conditions. For the metagenomics analyses, the pure single isolate of S. hyicus was sequenced, assembled and added to a large database of bacterial reference sequences. All sewage samples were analyzed by shotgun metagenome sequencing and mapped against the reference database. S. hyicus was identified in duplicate samples at both of two release days and these sequence fragment counts served as a proxy to estimate the minimum number of sick people or sensitivity required in order to observe at least one sick person at 95% probability. We found the sensitivity to be in the range 41-140 and 16-36 sick people at release days 1 and 2, respectively. The WWTP normally serves 36,000 people giving a normalized sensitivity in the range of one in 257 to 2,250 persons.

Multiple sensorimotor loops converge in the motor cortex to create an adaptable system capable of context-specific sensorimotor control. Afferent inhibition provides a non-invasive tool to investigate the substrates by which procedural and cognitive control processes interact to shape motor corticospinal projections. Varying the transcranial magnetic stimulation properties during afferent inhibition can probe specific sensorimotor circuits that contribute to short- and long-latency periods of inhibition in response to the peripheral stimulation. The current study used short- (SAI) and long-latency (LAI) afferent inhibition to probe the influence of verbal and spatial working memory load on the specific sensorimotor circuits recruited by posterior-anterior (PA) and anterior-posterior (AP) TMS-induced current. Participants completed two sessions where SAI and LAI were assessed during the short-term maintenance of two- or six-item sets of letters (verbal) or stimulus locations (spatial). The only difference between the sessions was the direction of the induced current. PA SAI decreased as the verbal working memory load increased. In contrast, AP SAI was not modulated by verbal working memory load. Visuospatial working memory load did not affect PA or AP SAI. Neither PA LAI nor AP LAI were sensitive to verbal or spatial working memory load. The dissociation of short-latency PA and AP sensorimotor circuits and short- and long-latency PA sensorimotor circuits with increasing verbal working memory load support multiple convergent sensorimotor loops that provide distinct functional information to facilitate context-specific supraspinal control.

Short telomeres are associated with cardiovascular disease (CVD). We aimed to investigate, if genetically determined telomere-length effects CVD-risk in the Heinz-Nixdorf-Recall study (HNRS) population. We selected 14 single-nucleotide polymorphisms (SNPs) associated with telomere-length (p

IntroductionBiliary tract cancer (BTC) is a lethal disease with a bad overall survivability, partly arising from inadequate therapeutic alternatives, detection at a belated stage, and a resistance to common therapeutic approaches. Ferroptosis is a form of programmed cell death that depends on reactive oxygen species (ROS) and iron, causing excessive peroxidation of polyunsaturated fatty acids (PUFAs). Therefore, the objective of this investigation is, whether ferroptosis can be induced in BTC in vitro and whether this induction is dependent on specific molecular markers.MethodsThe study conducted resazurin assay and IC25/50 calculation to explore the possible cytotoxic outcomes of different classes of ferroptosis-inducing substances (FINs) on a comprehensive in vitro model of 11 BTC cell lines. Combinatory treatments with different cell death inhibitors were performed to evaluate the magnitude of ferroptosis induction. To ascertain whether ferroptotic cell death occurred, liperfluo and iron assay kits were employed to evaluate lipid ROS and intracellular iron abundance. Potential biomarkers of ferroptosis sensitivity were then assessed via western blot analysis, a rtPCR panel and functional assay kits.ResultsThe study found that different FINs reduced cell viability in a cell line-dependent manner. In addition, we measured increased lipid ROS and intracellular Fe2+ levels upon exposure to FINs in BTC cells. Combining FINs with inhibitors of ferroptosis, necroptosis or apoptosis suggests the occurrence of ferroptotic events in BTC cell lines CCC-5, HuH-28 and KKU-055. Furthermore, we found that BTC cells display a heterogeneous profile regarding different molecular genes/markers of ferroptosis. Subsequent analysis revealed that sensitivity of BTC cells towards IKE and RSL3 positively correlated with CD71 and SLC7A11 protein expression.ConclusionOur results demonstrate that induction of ferroptosis is a promising approach to inhibit BTC cell growth and that the sensitivity of BTC cells towards ferroptosis induction might be dependent on molecular markers such as CD71 and SLC7A11.

Entomological sampling and storage conditions often prioritise efficiency, practicality and conservation of morphological characteristics, and may therefore be suboptimal for DNA preservation. This practice can impact downstream molecular applications, such as the generation of high-throughput genomic libraries, which often requires substantial DNA input amounts. Here, we use a practical Tn5 transposase tagmentation-based library preparation method optimised for 96-well plates and low yield DNA extracts from insect legs that were stored under sub-optimal conditions for DNA preservation. The samples were kept in field vehicles for extended periods of time, before long-term storage in ethanol in the freezer, or dry at room temperature. By reducing DNA input to 6ng, more samples with sub-optimal DNA yields could be processed. We matched this low DNA input with a 6-fold dilution of a commercially available tagmentation enzyme, significantly reducing library preparation costs. Costs and workload were further suppressed by direct post-amplification pooling of individual libraries. We generated medium coverage (>3-fold) genomes for 88 out of 90 specimens, with an average of approximately 10-fold coverage. While samples stored in ethanol yielded significantly less DNA compared to those which were stored dry, these samples had superior sequencing statistics, with longer sequencing reads and higher rates of endogenous DNA. Furthermore, we find that the efficiency of tagmentation-based library preparation can be improved by a thorough post-amplification bead clean-up which selects against both short and large DNA fragments. By opening opportunities for the use of sub-optimally preserved, low yield DNA extracts, we broaden the scope of whole genome studies of insect specimens. We therefore expect these results and this protocol to be valuable for a range of applications in the field of entomology.

Brain dynamics is highly non-stationary, permanently subject to ever-changing external conditions and continuously monitoring and adjusting internal control mechanisms. Finding stationary structures in this system, as has been done recently, is therefore of great importance for understanding fundamental dynamic trade relationships. Here we analyse electroencephalographic recordings (EEG) of 13 subjects with unresponsive wakefulness syndrome (UWS) during rest and while being influenced by different acoustic stimuli. We compare the results with a control group under the same experimental conditions and with clinically healthy subjects during overnight sleep. The main objective of this study is to investigate whether a stationary correlation pattern is also present in the UWS group, and if so, to what extent this structure resembles the one found in healthy subjects. Furthermore, we extract transient dynamical features via specific deviations from the stationary interrelation pattern. We find that (i) the UWS group is more heterogeneous than the two groups of healthy subjects, (ii) also the EEGs of the UWS group contain a stationary cross-correlation pattern, although it is less pronounced and shows less similarity to that found for healthy subjects and (iii) deviations from the stationary pattern are notably larger for the UWS than for the two groups of healthy subjects. The results suggest that the nervous system of subjects with UWS receive external stimuli but show an overreaching reaction to them, which may disturb opportune information processing.

AimsIn a high-income country, Australia, it is unclear how raised systolic blood pressure (SBP) ranks among other risk factors regarding the overall and cardiovascular disease (CVD) burden, and whether the situation has changed over time.MethodsWe analysed the 2019 Global Burden of Disease (GBD) data, with focus on Australia. We assessed ten leading risk factors for all-cause and CVD deaths and disability-adjusted life-years (DALYs) and compared findings with the Australian Burden of Diseases Study.ResultsFrom 1990 to 2019, raised SBP remained the leading risk factor for attributable all-cause deaths (followed by dietary risks and tobacco use), accounting for 29,056/75,235 (95% Uncertainty Interval (UI) [24,863 to 32,915]) deaths in 1990; 21,845/76,893 [17,678 to 26,044] in 2010; and 25,498/90,393 [20,152 to 30,851] in 2019. Contributions of raised SBP to cardiovascular deaths for both sexes were 54.0% [45.8 to 61.5] in 1990, 44.0% [36.7 to 51.3] in 2010 and 43.7% [36.2 to 51.6] in 2019, respectively. The contribution of raised SBP to cardiovascular deaths declined between 1990 and 2010 but exhibited an increase in males from 2010 onwards, with figures of 52.6% [44.7 to 60.0] in 1990, 43.1% [36.0 to 50.5] in 2010 and 43.5% [35.7 to 51.4] in 2019. The contribution of raised SBP to stroke deaths and DALYs in males aged 25-49 years were higher than other age groups, in excess of 60% and increasing steeply between 2010 and 2019.ConclusionRaised SBP continues to be the leading risk factor for all-cause and cardiovascular deaths in Australia. We urge cross-disciplinary stakeholder engagement to implement effective strategies to detect, treat and control raised blood pressure as a central priority to mitigate the CVD burden.

We present a Deep Learning approach to predict 3D folding structures of RNAs from their nucleic acid sequence. Our approach combines an autoregressive Deep Generative Model, Monte Carlo Tree Search, and a score model to find and rank the most likely folding structures for a given RNA sequence. We show that RNA de novo structure prediction by deep learning is possible at atom resolution, despite the low number of experimentally measured structures that can be used for training. We confirm the predictive power of our approach by achieving competitive results in a retrospective evaluation of the RNA-Puzzles prediction challenges, without using structural contact information from multiple sequence alignments or additional data from chemical probing experiments. Blind predictions for recent RNA-Puzzle challenges under the name "Dfold" further support the competitive performance of our approach.

Studies have shown that certain vocal fold pathologies are more common in one sex than the other. This is often explained by differences in the composition of the lamina propria and anatomical differences between female and male vocal folds, resulting in e.g. different fundamental frequencies. Here, we investigated a potential sex-specific voice frequency effect in an in vitro setting using vocal fold fibroblasts from one male and one female donor with and without cigarette smoke extract (CSE) addition. After exposure to either male or female vibration frequency with or without CSE, cells and supernatants were harvested. Gene and protein analysis were performed by means of qPCR, western blot, ELISA and Luminex. We found that exposure of cells to both male and female vibration pattern did not elicit significant changes in the expression of extracellular matrix-, inflammation-, and fibrosis-related genes, compared to control cells. The addition of CSE to vibration downregulated the gene expression of COL1A1 in cells exposed to the female vibration pattern, as well as induced MMP1 and PTGS2 in cells exposed to both female and male vibration pattern. The protein expression of MMP1 and COX2 was found to be significantly upregulated only in cells exposed to CSE and female vibration pattern. To conclude, different vibration patterns alone did not cause different responses of the cells. However, the female vibration pattern in combination with CSE had a tendency to elicit/maintain more pro-inflammatory responses in cells than the male vibration pattern.

BackgroundThe COVID-19 pandemic revealed a need for better collaboration among research, care, and management in Germany as well as globally. Initially, there was a high demand for broad data collection across Germany, but as the pandemic evolved, localized data became increasingly necessary. Customized dashboards and tools were rapidly developed to provide timely and accurate information. In Saxony, the DISPENSE project was created to predict short-term hospital bed capacity demands, and while it was successful, continuous adjustments and the initial monolithic system architecture of the application made it difficult to customize and scale.MethodsTo analyze the current state of the DISPENSE tool, we conducted an in-depth analysis of the data processing steps and identified data flows underlying users' metrics and dashboards. We also conducted a workshop to understand the different views and constraints of specific user groups, and brought together and clustered the information according to content-related service areas to determine functionality-related service groups. Based on this analysis, we developed a concept for the system architecture, modularized the main services by assigning specialized applications and integrated them into the existing system, allowing for self-service reporting and evaluation of the expert groups' needs.ResultsWe analyzed the applications' dataflow and identified specific user groups. The functionalities of the monolithic application were divided into specific service groups for data processing, data storage, predictions, content visualization, and user management. After composition and implementation, we evaluated the new system architecture against the initial requirements by enabling self-service reporting to the users.DiscussionBy modularizing the monolithic application and creating a more flexible system, the challenges of rapidly changing requirements, growing need for information, and high administrative efforts were addressed.ConclusionWe demonstrated an improved adaptation towards the needs of various user groups, increased efficiency, and reduced burden on administrators, while also enabling self-service functionalities and specialization of single applications on individual service groups.

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) evades the innate immune machinery through multiple viral proteins, including nonstructural protein 1 (NSP1). While NSP1 is known to suppress translation of host mRNAs, the mechanisms underlying its immune evasion properties remain elusive. By integrating RNA-seq, ribosome footprinting, and ChIP-seq in A549 cells we found that NSP1 predominantly represses transcription of immune-related genes by favoring Histone 3 Lysine 9 dimethylation (H3K9me2). G9a/GLP H3K9 methyltransferase inhibitor UNC0638 restored expression of antiviral genes and restricted SARS-CoV-2 replication. Our multi-omics study unravels an epigenetic mechanism underlying host immune evasion by SARS-CoV-2 NSP1. Elucidating the factors involved in this phenomenon, may have implications for understanding and treating viral infections and other immunomodulatory diseases.

Pathologists routinely use immunohistochemical (IHC)-stained tissue slides against MelanA in addition to hematoxylin and eosin (H&E)-stained slides to improve their accuracy in diagnosing melanomas. The use of diagnostic Deep Learning (DL)-based support systems for automated examination of tissue morphology and cellular composition has been well studied in standard H&E-stained tissue slides. In contrast, there are few studies that analyze IHC slides using DL. Therefore, we investigated the separate and joint performance of ResNets trained on MelanA and corresponding H&E-stained slides. The MelanA classifier achieved an area under receiver operating characteristics curve (AUROC) of 0.82 and 0.74 on out of distribution (OOD)-datasets, similar to the H&E-based benchmark classification of 0.81 and 0.75, respectively. A combined classifier using MelanA and H&E achieved AUROCs of 0.85 and 0.81 on the OOD datasets. DL MelanA-based assistance systems show the same performance as the benchmark H&E classification and may be improved by multi stain classification to assist pathologists in their clinical routine.

ObjectivesWe set out to evaluate the effect of postnatal exposure to tenofovir-containing antiretroviral therapy on bone mineral density among breastfeeding women living with HIV.DesignIMPAACT P1084s is a sub-study of the PROMISE randomized trial conducted in four African countries (ClinicalTrials.gov number NCT01066858).MethodsIMPAACT P1084s enrolled eligible mother-infant pairs previously randomised in the PROMISE trial at one week after delivery to receive either maternal antiretroviral therapy (Tenofovir disoproxil fumarate / Emtricitabine + Lopinavir/ritonavir-maternal TDF-ART) or administer infant nevirapine, with no maternal antiretroviral therapy, to prevent breastmilk HIV transmission. Maternal lumbar spine and hip bone mineral density were measured using dual-energy x-ray absorptiometry (DXA) at postpartum weeks 1 and 74. We studied the effect of the postpartum randomization on percent change in maternal bone mineral density in an intention-to-treat analysis with a t-test; mean and 95% confidence interval (95%CI) are presented.ResultsAmong 398/400 women included in this analysis, baseline age, body-mass index, CD4 count, mean bone mineral density and alcohol use were comparable between study arms. On average, maternal lumbar spine bone mineral density declined significantly through week 74 in the maternal TDF-ART compared to the infant nevirapine arm; mean difference (95%CI) -2.86 (-4.03, -1.70) percentage points (p-value

BackgroundGenome-wide association studies have identified multiple genomic loci associated with coronary artery disease, but most are common variants in non-coding regions that provide limited information on causal genes and etiology of the disease. To overcome the limited scope that common variants provide, we focused our investigation on low-frequency and rare sequence variations primarily residing in coding regions of the genome.Methods and resultsUsing samples of individuals of European ancestry from ten cohorts within the Cohorts for Heart and Aging Research in Genomic Epidemiology (CHARGE) consortium, both cross-sectional and prospective analyses were conducted to examine associations between genetic variants and myocardial infarction (MI), coronary heart disease (CHD), and all-cause mortality following these events. For prevalent events, a total of 27,349 participants of European ancestry, including 1831 prevalent MI cases and 2518 prevalent CHD cases were used. For incident cases, a total of 55,736 participants of European ancestry were included (3,031 incident MI cases and 5,425 incident CHD cases). There were 1,860 all-cause deaths among the 3,751 MI and CHD cases from six cohorts that contributed to the analysis of all-cause mortality. Single variant and gene-based analyses were performed separately in each cohort and then meta-analyzed for each outcome. A low-frequency intronic variant (rs988583) in PLCL1 was significantly associated with prevalent MI (OR = 1.80, 95% confidence interval: 1.43, 2.27; P = 7.12 × 10-7). We conducted gene-based burden tests for genes with a cumulative minor allele count (cMAC) ≥ 5 and variants with minor allele frequency (MAF) < 5%. TMPRSS5 and LDLRAD1 were significantly associated with prevalent MI and CHD, respectively, and RC3H2 and ANGPTL4 were significantly associated with incident MI and CHD, respectively. No loci were significantly associated with all-cause mortality following a MI or CHD event.ConclusionThis study identified one known locus (ANGPTL4) and four new loci (PLCL1, RC3H2, TMPRSS5, and LDLRAD1) associated with cardiovascular disease risk that warrant further investigation.

This article contributes to a more adequate modelling of emotions encoded in speech, by addressing four fallacies prevalent in traditional affective computing: First, studies concentrate on few emotions and disregard all other ones ('closed world'). Second, studies use clean (lab) data or real-life ones but do not compare clean and noisy data in a comparable setting ('clean world'). Third, machine learning approaches need large amounts of data; however, their performance has not yet been assessed by systematically comparing different approaches and different sizes of databases ('small world'). Fourth, although human annotations of emotion constitute the basis for automatic classification, human perception and machine classification have not yet been compared on a strict basis ('one world'). Finally, we deal with the intrinsic ambiguities of emotions by interpreting the confusions between categories ('fuzzy world'). We use acted nonsense speech from the GEMEP corpus, emotional 'distractors' as categories not entailed in the test set, real-life noises that mask the clear recordings, and different sizes of the training set for machine learning. We show that machine learning based on state-of-the-art feature representations (wav2vec2) is able to mirror the main emotional categories ('pillars') present in perceptual emotional constellations even in degradated acoustic conditions.

This longitudinal study aimed to explore anxiety and depressive symptoms, individual resources, and job demands in a multi-country sample of 612 healthcare workers (HCWs) during the COVID-19 pandemic. Two online surveys were distributed to HCWs in seven countries (Germany, Andorra, Ireland, Spain, Italy, Romania, Iran) during the first (May-October 2020, T1) and the second (February-April 2021, T2) phase of the pandemic, assessing sociodemographic characteristics, contact with COVID-19 patients, anxiety and depressive symptoms, self-compassion, sense of coherence, social support, risk perception, and health and safety at the workplace. HCWs reported a significant increase in depressive and anxiety symptoms. HCWs with high depressive or anxiety symptoms at T1 and T2 reported a history of mental illness and lower self-compassion and sense of coherence over time. Risk perception, self-compassion, sense of coherence, and social support were strong independent predictors of depressive and anxiety symptoms at T2, even after controlling for baseline depressive or anxiety symptoms and sociodemographic variables. These findings pointed out that HCWs during the COVID-19 outbreak experienced a high burden of psychological distress. The mental health and resilience of HCWs should be supported during disease outbreaks by instituting workplace interventions for psychological support.

Beall's list is widely used to identify potentially predatory journals. With this study, we aim to investigate the impact of Beall's list on the perception of listed journals as well as on the publication and citation behavior of the scientific community. We performed comprehensive bibliometric analyses of data extracted from the ISSN database, PubMed, PubMed Central (PMC), Crossref, Scopus and Web of Science. Citation analysis was performed by data extracted from the Crossref Cited-by database. At the time of analysis, Beall's list consisted of 1,289 standalone journals and 1,162 publishers, which corresponds to 21,735 individual journals. Of these, 3,206 (38.8%) were located in the United States, 2,484 in India (30.0%), and 585 in United Kingdom (7.1%). The majority of journals were listed in the ISSN database (n = 8,266), Crossref (n = 5,155), PubMed (n = 1,139), Scopus (n = 570), DOAJ (n = 224), PMC (n = 135) or Web of Science (n = 50). The number of articles published by journals on Beall's list as well as on the DOAJ continuously increased from 2011 to 2017. In 2018, the number of articles published by journals on Beall's list decreased. Journals on Beall's list were more often cited when listed in Web of Science (CI 95% 5.5 to 21.5; OR = 10.7) and PMC (CI 95% 6.3 to 14.1; OR = 9.4). It seems that the importance of Beall's list for the scientific community is overestimated. In contrast, journals are more likely to be selected for publication or citation when indexed by commonly used and renowned databases. Thus, the providers of these databases must be aware of their impact and verify that good publication practice standards are being applied by the journals listed.

Fasciola hepatica is one of the economically most important endoparasites in cattle production. The aim of the present work was to evaluate the relevance of production level on the associations of on-farm presence of F. hepatica with farm-level milk yield, milk fat, and milk protein in Holstein cows, a specialised dairy breed, and in Simmental cows, a dual purpose breed. Furthermore, we investigated whether differential associations were present depending on breed. Data from 560 dairy farms across Germany housing 93,672 cows were analysed. The presence of F. hepatica antibodies was determined via ELISA on bulk tank milk samples. Quantile regression was applied to model the median difference in milk yield, milk fat, and milk protein depending on the interaction of breed and fluke occurrence. Whereas a reduction in milk yield (-1,206 kg, p < 0.001), milk fat (-22.9 kg, p = 0.001), and milk protein (-41.6 kg, p

[This corrects the article DOI: 10.1371/journal.pone.0271610.].

IntroductionDespite guideline recommendations, inpatients with mental health disorders often do not receive appropriate treatment after discharge. This leads to high readmission rates, problems with medication adherence, increased risk of chronicity and suicide, and exclusion from the labour market accompanied by high individual and social costs. The causes are both system-related, such as limited treatment availability, and patient-related, such as ambivalent motivation to continue treatment and lack of information about available treatment options. The aim of this trial is to assess the feasibility of a Care Transition Intervention (CTI) which supports patients in the psychosocial follow-up treatment process after discharge from a psychotherapy ward.Methods and analysisFifty patients with depression and/or anxiety who are treated as inpatients at a psychotherapy ward will be included and randomised into two groups with a 1:1 ratio. In the intervention group, patients will receive five CTI sessions with a Care Transition Navigator before and after discharge. The sessions will focus on individual patient support including a) identification and tackling of barriers to initiate follow-up treatment, b) reflection on the inpatient stay and individual progress, with focus on the helpful aspects and c) motivation of patients to organise and take up outpatient treatment. Patients in the control group will receive treatment-as-usual during discharge. We will evaluate the following outcomes: effectiveness of recruitment strategies, patient acceptance of randomisation, practicability of implemented workflows, feasibility of data collection, and clinical outcomes.