Search

Dairy cattle lameness represents one of the common concerns in intensive and commercial dairy farms. Lameness is characterized by gait-related behavioral changes in cows and multiple approaches are being utilized to associate these changes with lameness conditions including data from accelerometers, and other precision technologies. The objective was to evaluate the use of machine learning algorithms for the identification of lameness conditions in dairy cattle. In this study, 310 multiparous Holstein dairy cows from a herd in Northern Colorado were affixed with a leg-based accelerometer (Icerobotics® Inc, Edinburg, Scotland) to obtain the lying time (min/d), daily steps count (n/d), and daily change (n/d). Subsequently, study cows were monitored for 4 months and cows submitted for claw trimming (CT) were differentiated as receiving corrective claw trimming (CCT) or as being diagnosed with a lameness disorder and consequent therapeutic claw trimming (TCT) by a certified hoof trimmer. Cows not submitted to CT were considered healthy controls. A median filter was applied to smoothen the data by reducing inherent variability. Three different machine learning (ML) models were defined to fit each algorithm which included the conventional features (containing daily lying, daily steps, and daily change derived from the accelerometer), slope features (containing features extracted from each variable in Conventional feature), or all features (3 simple features and 3 slope features). Random forest (RF), Naive Bayes (NB), Logistic Regression (LR), and Time series (ROCKET) were used as ML predictive approaches. For the classification of cows requiring CCT and TCT, ROCKET classifier performed better with accuracy (> 90%), ROC-AUC (> 74%), and F1 score (> 0.61) as compared to other algorithms. Slope features derived in this study increased the efficiency of algorithms as the better-performing models included All features explored. However, further classification of diseases into infectious and non-infectious events was not effective because none of the algorithms presented satisfactory model accuracy parameters. For the classification of observed cow locomotion scores into severely lame and moderately lame conditions, the ROCKET classifier demonstrated satisfactory accuracy (> 0.85), ROC-AUC (> 0.68), and F1 scores (> 0.44). We conclude that ML models using accelerometer data are helpful in the identification of lameness in cows but need further research to increase the granularity and accuracy of classification. [ABSTRACT FROM AUTHOR]

Recent advances in long-read sequencing technologies have enabled the complete assembly of eukaryotic genomes from telomere to telomere by allowing repeated regions to be fully sequenced and assembled, thus filling the gaps left by previous short-read sequencing methods. Furthermore, long-read sequencing can also help characterizing structural variants, with applications in the fields of genome evolution or cancer genomics. For many organisms, the main bottleneck to sequence long reads remains the lack of robust methods to obtain high-molecular-weight (HMW) DNA. For this purpose, we developed an optimized protocol to extract DNA suitable for long-read sequencing from the unicellular green alga Chlamydomonas reinhardtii, based on CTAB/phenol extraction followed by a size selection step for long DNA molecules. We provide validation results for the extraction protocol, as well as statistics obtained with Oxford Nanopore Technologies sequencing. [ABSTRACT FROM AUTHOR]

Viral infections trigger the expression of interferons (IFNs) and interferon stimulated genes (ISGs), which are crucial to modulate an antiviral response. The human guanylate binding protein 1 (GBP1) is an ISG and exhibits antiviral activity against several viruses. In a previous study, GBP1 was described to impair replication of the hepatitis C virus (HCV). However, the impact of GBP1 on the HCV life cycle is still enigmatic. To monitor the expression and subcellular distribution of GBP1 and HCV we performed qPCR, Western blot, CLSM and STED microscopy, virus titration and reporter gene assays. In contrast to previous reports, we observed that HCV induces the expression of GBP1. Further, to induce GBP1 expression, the cells were stimulated with IFNγ. GBP1 modulation was achieved either by overexpression of GBP1-Wt or by siRNA-mediated knockdown. Silencing of GBP1 impaired the release of viral particles and resulted in intracellular HCV core accumulation, while overexpression of GBP1 favored viral replication and release. CLSM and STED analyses revealed a vesicular distribution of GBP1 in the perinuclear region. Here, it colocalizes with HCV core around lipid droplets, where it acts as assembly platform and thereby favors HCV morphogenesis and release. Collectively, our results identify an unprecedented function of GBP1 as a pro-viral factor. As such, it is essential for viral assembly and release acting through tethering factors involved in HCV morphogenesis onto the surface of lipid droplets. Author summary: Morphogenesis and release of the hepatitis C virus (HCV) are still not fully understood. Here we describe a novel so far unprecedented pro-viral function of the interferon stimulated gene (ISG) human guanylate binding protein 1 (GBP1). In contrast to the supposed antiviral effect, we observe that GBP1 favors morphogenesis and release of HCV by acting as an assembly platform on the surface of lipid droplets. This extends our knowledge about the functions of GBP1 and the life cycle of HCV and should be considered for curative approaches targeting innate immunity. [ABSTRACT FROM AUTHOR]

The widespread occurrence of phenotypic plasticity across all domains of life demonstrates its evolutionary significance. However, how plasticity itself evolves and how it contributes to evolution is poorly understood. Here, we investigate the predatory nematode Pristionchus pacificus with its feeding structure plasticity using recombinant-inbred-line and quantitative-trait-locus (QTL) analyses between natural isolates. We show that a single QTL at a core developmental gene controls the expression of the cannibalistic morph. This QTL is composed of several cis-regulatory elements. Through CRISPR/Cas-9 engineering, we identify copy number variation of potential transcription factor binding sites that interacts with a single intronic nucleotide polymorphism. Another intronic element eliminates gene expression altogether, mimicking knockouts of the locus. Comparisons of additional isolates further support the rapid evolution of these cis-regulatory elements. Finally, an independent QTL study reveals evidence for parallel evolution at the same locus. Thus, combinations of cis-regulatory elements shape plastic trait expression and control nematode cannibalism. This study shows that the synergistic effect of multiple cis-regulatory elements at a core developmental gene controls the switch rate of mouth-form plasticity in the free-living nematode Pristionchus pacificus, shedding light on how phenotypic plasticity is genetically controlled in natural populations. [ABSTRACT FROM AUTHOR]

The relationship of food comminution and individual age in Tupaia belangeri is investigated. It is hypothesized that with increasing age the performance of the molar dentition decreases due to progressive tooth wear. While this relationship is well-documented for herbivores, age-related test series are largely lacking for insectivorous mammals. 15 individuals of Tupaia belangeri were fed exclusively with mealworms, and their faeces were analyzed for the number and size of chitin particles. The exoskeleton of a mealworm is resistant to digestive fluids in the gastrointestinal tract, and the size of individual chitin particles indicates the effectiveness of mechanical comminution that occurs in the oral cavity during mastication. It is hypothesized that a more precise occlusion of the dentition results in smaller particle size. Although individuals of all ages (juvenile, adult, and senile) were able to effectively process mealworms with their dentition prior to digestion, a larger area of very large chitin particles (98% quantile of all particles in senile animals as compared to in the same quantile in adults) in the feces of senile animals was detected. Even though the particle size of indigestible material is irrelevant for the digestive process, these findings either document somatic senescence in the functionality of the teeth, or alternatively a change in chewing behaviour with age. [ABSTRACT FROM AUTHOR]

Parallel test versions require a comparable degree of difficulty and must capture the same characteristics using different items. This can become challenging when dealing with multivariate items, which are for example very common in language or image data. Here, we propose a heuristic to identify and select similar multivariate items for the generation of equivalent parallel test versions. This heuristic includes: 1. inspection of correlations between variables; 2. identification of outlying items; 3. application of a dimension-reduction method, such as for example principal component analysis (PCA); 4. generation of a biplot, in case of PCA of the first two principal components (PC), and grouping the displayed items; 5. assigning of the items to parallel test versions; and 6. checking the resulting test versions for multivariate equivalence, parallelism, reliability, and internal consistency. To illustrate the proposed heuristic, we applied it exemplarily on the items of a picture naming task. From a pool of 116 items, four parallel test versions were derived, each containing 20 items. We found that our heuristic can help to generate parallel test versions that meet requirements of the classical test theory, while simultaneously taking several variables into account. [ABSTRACT FROM AUTHOR]

The purpose of this study was to develop a method of estimating pulsatile ocular blood volume (POBV) from measurements taken during an ophthalmic exam, including axial length and using a tonometer capable of measuring intraocular pressure (IOP) and ocular pulse amplitude (OPA). Unpublished OPA data from a previous invasive study was used in the derivation, along with central corneal thickness (CCT) and axial length (AL), as well as IOP from the PASCAL dynamic contour tonometer (DCT) and intracameral (ICM) measurements of IOP for 60 cataract patients. Intracameral mean pressure was set to 15, 20, and 35 mmHg (randomized sequence) in the supine position, using a fluid-filled manometer. IOP and OPA measurements were acquired at each manometric setpoint (DCT and ICM simultaneously). In the current study, ocular rigidity (OR) was estimated using a published significant relationship of OR to the natural log of AL in which OR was invasively measured through fluid injection. Friedenwald's original pressure volume relationship was then used to derive the estimated POBV, delivered to the choroid with each heartbeat as a function of OR, systolic IOP (IOPsys), diastolic IOP (IOPdia), and OPA, according to the derived equation POBV = log (IOPsys/IOPdia) / OR. Linear regression analyses were performed comparing OPA to OR and calculated POBV at each of the three manometric setpoints. POBV was also compared to OPA/IOPdia with all data points combined. Significance threshold was p < 0.05. OR estimated from AL showed a significant positive relationship to OPA for both DCT (p < 0.011) and ICM (p < 0.006) at all three manometric pressure setpoints, with a greater slope for lower IOP. Calculated POBV also showed a significant positive relationship to OPA (p < 0.001) at all three setpoints with greater slope at lower IOP, and a significant negative relationship with IOPdia. In the combined analysis, POBV showed a significant positive relationship to OPA/ IOPdia (p < 0.001) in both ICM and DCT measurements with R2 = 0.9685, and R2 = 0.9589, respectively. POBV provides a straight-forward, clinically applicable method to estimate ocular blood supply noninvasively. Higher IOP in combination with lower OPA results in the lowest values of POBV. The simplified ratio, OPA/ IOPdia, may also provide a useful clinical tool for evaluating changes in ocular blood supply in diseases with a vascular component, such as diabetic retinopathy and normal tension glaucoma. Future studies are warranted. [ABSTRACT FROM AUTHOR]

The beating of cilia and flagella, which relies on an efficient conversion of energy from ATP-hydrolysis into mechanical work, offers a promising way to propel synthetic cargoes. Recent experimental realizations of such micro-swimmers, in which micron-sized beads are propelled by isolated and demembranated flagella from the green algae Chlamydomonas reinhardtii (C. reinhardtii), revealed a variety of propulsion modes, depending in particular on the calcium concentration. Here, we investigate theoretically and numerically the propulsion of a bead as a function of the flagellar waveform and the attachment geometries between the bead and the flagellum. To this end, we take advantage of the low Reynolds number of the fluid flows generated by the micro-swimmer, which allows us to neglect fluid inertia. By describing the flagellar waveform as a superposition of a static component and a propagating wave, and using resistive-force theory, we show that the asymmetric sideways attachment of the flagellum to the bead makes a contribution to the rotational velocity of the micro-swimmer that is comparable to the contribution caused by the static component of the flagellar waveform. Remarkably, our analysis reveals the existence of a counter-intuitive propulsion regime in which an increase in the size of the cargo, and hence its drag, leads to an increase in some components of the velocity of the bead. Finally, we discuss the relevance of the uncovered mechanisms for the fabrication of synthetic, bio-actuated medical micro-robots for targeted drug delivery. [ABSTRACT FROM AUTHOR]

Background: Like other countries in sub-Saharan Africa, Madagascar has a high burden of stroke. The Malagasy population is unique in sharing both African and Asian ancestry. The proportion of ischemic and hemorrhagic stroke types is unknown for this population. Aim: Our aim was to establish the proportion of stroke types and known risk factors for the Malagasy population. Methods: We conducted a single-center, tertiary-level hospital-based case series. We included all patients with a CT-imaging confirmed stroke who presented at the emergency ward of the study hospital between January 1, 2017, and November 20, 2018. Results: Of 223 patients with CT-confirmed stroke, 57.4% (128/223, 95% CI: 51–64%) had an ischemic stroke and 42.6% (95/223, 95% CI: 36–49%) had an intracranial hemorrhage. The majority (89.5%; 85/95, 95% CI: 83–96%) of intracranial hemorrhages were intracerebral; 4.2% (4/95, 95% CI: 0–8%) had a subdural hematoma, 5.3% (5/95, 95% CI: 1–10%) had a subarachnoid hemorrhage, there was one isolated intraventricular hemorrhage (1.1%; 1/95, 95% CI: -1-3%). The prevalence of hypertension among stroke patients was high (86.6%; 187/216, 95% CI: 82–91%). Conclusions: Our study is the first to report the proportion of stroke types and known risk factors in Madagascar. We find that the proportion of hemorrhagic strokes was unexpectedly higher than that reported from other countries in sub-Saharan Africa. Our findings highlight the need for a country-specific approach to stroke prevention, treatment, and rehabilitation and provide guidance on public health resource allocation in Madagascar. [ABSTRACT FROM AUTHOR]

We propose a new method for the classification task of distinguishing atrial fibrillation (AFib) from regular atrial tachycardias including atrial flutter (AFlu) based on a surface electrocardiogram (ECG). Recently, many approaches for an automatic classification of cardiac arrhythmia were proposed and to our knowledge none of them can distinguish between these two. We discuss reasons why deep learning may not yield satisfactory results for this task. We generate new and clinically interpretable features using mathematical optimization for subsequent use within a machine learning (ML) model. These features are generated from the same input data by solving an additional regression problem with complicated combinatorial substructures. The resultant can be seen as a novel machine learning model that incorporates expert knowledge on the pathophysiology of atrial flutter. Our approach achieves an unprecedented accuracy of 82.84% and an area under the receiver operating characteristic (ROC) curve of 0.9, which classifies as "excellent" according to the classification indicator of diagnostic tests. One additional advantage of our approach is the inherent interpretability of the classification results. Our features give insight into a possibly occurring multilevel atrioventricular blocking mechanism, which may improve treatment decisions beyond the classification itself. Our research ideally complements existing textbook cardiac arrhythmia classification methods, which cannot provide a classification for the important case of AFib↔AFlu. The main contribution is the successful use of a novel mathematical model for multilevel atrioventricular block and optimization-driven inverse simulation to enhance machine learning for classification of the arguably most difficult cases in cardiac arrhythmia. A tailored Branch-and-Bound algorithm was implemented for the domain knowledge part, while standard algorithms such as Adam could be used for training. [ABSTRACT FROM AUTHOR]

Author(s): Zacharia Mtema 1,2,3, Joel Changalucha 1, Sarah Cleaveland 2, Martin Elias 4, Heather M. Ferguson 1,2, Jo E. B. Halliday 2, Daniel T. Haydon 2, Gurdeep Jaswant 5, Rudovick [...]

Purpose: To determine the impact of 18F-fluorodeoxyglucose (FDG) positron emission tomography/computed tomography (PET/CT) on clinical management in patients with suspected mycotic aortic aneurysms (MAA). Materials and methods: For this observational cohort study 101 PET/CT were acquired in 50 patients, thereof 50 for the initial diagnosis/baseline scan, 51 for follow-up. Impact on patient management was defined in three categories: PET/CT results were "confirmed" (by clinical follow-up), "suspected" (conclusive, not confirmed), or "misleading" (proven wrong by follow-up). For clinical follow-up patient data were recorded at the time of imaging, and at the latest recorded clinical visit. It included patient demographics, clinical information, laboratory data, results of microbiology and other diagnostic procedures, information about treatment, and patient's general health condition. Results: In four patients (8%) no clinical follow-up was feasible, the other 46 patients were clinically followed for a median of 898 days (IQR 320–4105). The combined evaluation of all 101 PET/CT demonstrated an impact on patient management in 78,5% of cases (48,5% confirmed, 30% suspected). Results of 21,5% of the PET/CT examinations were misleading. Respective values at baseline and at follow-up were: impact on patient management in 82% and 74,5% (70% and 27.5% confirmed, and 12% and 47% suspected), misleading cases in 18% and 25.5%. Conclusion: In MAA, PET/CT has a high impact on patient management, which is more pronounced with baseline than with follow-up examinations. However, PET/CT results may be misleading in a smaller proportion of cases. [ABSTRACT FROM AUTHOR]

Interruptions in nonlinear wave propagation, commonly referred to as wave breaks, are typical of many complex excitable systems. In the heart they lead to lethal rhythm disorders, the so-called arrhythmias, which are one of the main causes of sudden death in the industrialized world. Progress in the treatment and therapy of cardiac arrhythmias requires a detailed understanding of the triggers and dynamics of these wave breaks. In particular, two very important questions are: 1) What determines the potential of a wave break to initiate re-entry? and 2) How do these breaks evolve such that the system is able to maintain spatiotemporally chaotic electrical activity? Here we approach these questions numerically using optogenetics in an in silico model of human atrial tissue that has undergone chronic atrial fibrillation (cAF) remodelling. In the lesser studied sub-threshold illumination régime, we discover a new mechanism of wave break initiation in cardiac tissue that occurs for gentle slopes of the restitution characteristics. This mechanism involves the creation of conduction blocks through a combination of wavefront-waveback interaction, reshaping of the wave profile and heterogeneous recovery from the excitation of the spatially extended medium, leading to the creation of re-excitable windows for sustained re-entry. This finding is an important contribution to cardiac arrhythmia research as it identifies scenarios in which low-energy perturbations to cardiac rhythm can be potentially life-threatening. Author summary: Electric turbulence in the heart is associated with complex spatiotemporal dynamics of nonlinear excitation waves. This life-threatening state is initiated by wavebreaks and maintained by self-organized vortices of abnormal excitation. Control over this state is achieved via defibrillation, a method whose efficacy relies on understanding the role of electric vortices in the onset and perpetuation of the turbulent state. However, in biological tissue, these vortices remain largely elusive in experiments due to limitations of visualisation. In order to study the spatiotemporal evolution of vortices in the heart precisely, reversibly and in real-time, we apply computational cardiac optogenetics on a mathematical model for human atrial tissue. Our study demonstrates a heretofore unidentified mechanism of wavebreak initiation, in the absence of standard markers of excitable medium vulnerability. This finding is an important contribution to cardiac arrhythmia research as it identifies how low-energy perturbations to cardiac rhythm can be potentially life-threatening, and render a defibrillation strategy to backfire. [ABSTRACT FROM AUTHOR]

The brains of smaller animals are smaller than those of their larger relatives, but it is not clear whether their adaptive behavioral flexibility is more limited. Previous interspecific comparisons found that aspects of web construction behavior of very small orb weaving spiders (0.005 mg) were no less precise than those of much larger related orb weavers (30 mg), but the behaviors tested were relatively simple. Here we perform a more sensitive intraspecific test involving the multiple behavioral adjustments of orb web designs made by Leucauge argyra to confinement in very small spaces. Web adjustments of spiderlings as small as ~0.1 mg were compared to previously published observations of ~80 mg conspecific adults. Spiderlings in constrained spaces made all of the complex adjustments made by adults in at least seven independent web design variables, and their adjustments were no less precise. Rough estimates based on previously published data on total brain volumes and the mean diameters of neuron cell bodies suggested that spiderlings and adult females of Leucauge may have similar numbers of neurons, due to spiderlings having smaller neurons and a greater percentage of body tissues dedicated to the brain. We speculate that this neural similarity may explain why L. argyra spiderlings showed no behavioral deficits compared with adults. [ABSTRACT FROM AUTHOR]

A major factor contributing to the etiology of depression is a neurochemical imbalance of the dopaminergic and serotonergic systems, which is caused by persistently high levels of circulating stress hormones. Here, a computational model is proposed to investigate the interplay between dopaminergic and serotonergic-kynurenine metabolism under cortisolemia and its consequences for the onset of depression. The model was formulated as a set of nonlinear ordinary differential equations represented with power-law functions. Parameter values were obtained from experimental data reported in the literature, biological databases, and other general information, and subsequently fine-tuned through optimization. Model simulations predict that changes in the kynurenine pathway, caused by elevated levels of cortisol, can increase the risk of neurotoxicity and lead to increased levels of 3,4-dihydroxyphenylaceltahyde (DOPAL) and 5-hydroxyindoleacetaldehyde (5-HIAL). These aldehydes contribute to alpha-synuclein aggregation and may cause mitochondrial fragmentation. Further model analysis demonstrated that the inhibition of both serotonin transport and kynurenine-3-monooxygenase decreased the levels of DOPAL and 5-HIAL and the neurotoxic risk often associated with depression. The mathematical model was also able to predict a novel role of the dopamine and serotonin metabolites DOPAL and 5-HIAL in the ethiology of depression, which is facilitated through increased cortisol levels. Finally, the model analysis suggests treatment with a combination of inhibitors of serotonin transport and kynurenine-3-monooxygenase as a potentially effective pharmacological strategy to revert the slow-down in monoamine neurotransmission that is often triggered by inflammation. Author summary: According to the World Health Organization, major depressive disorder (MDD) was in 2014 the fourth leading cause of disability in people between the ages of 15 and 44 years. MDD is responsible for about 1 million suicides per year and associated with a number of other medical conditions such as coronary disease, diabetes, and Alzheimer's disease. While MDD has been studied for a long time, molecular details of its pathophysiology are still scarce. Computational models offer a powerful opportunity to assist neuropsychiatric disorder research, as they permit the representation of large sets of physiological, cellular and biochemical phenomena through mathematical equations that can be simulated in a very efficient fashion and have the capacity to provide testable hypotheses. Here, we introduce a computational model of relevant biochemical pathways associated with high levels of circulating stress hormone, as they are observed in MDD. The model captures known observations well and demonstrates how increased levels of internally produced toxic agents, such as various kynurenines, DOPAL and 5-HIAL, can lead to dysregulation of key enzymes. These insights suggest new hypotheses for model-driven experiments, as well as novel potential targets for pharmacological intervention. [ABSTRACT FROM AUTHOR]

In the case of airborne diseases, pathogen copies are transmitted by droplets of respiratory tract fluid that are exhaled by the infectious that stay suspended in the air for some time and, after partial or full drying, inhaled as aerosols by the susceptible. The risk of infection in indoor environments is typically modelled using the Wells-Riley model or a Wells-Riley-like formulation, usually assuming the pathogen dose follows a Poisson distribution (mono-pathogen assumption). Aerosols that hold more than one pathogen copy, i.e. poly-pathogen aerosols, break this assumption even if the aerosol dose itself follows a Poisson distribution. For the largest aerosols where the number of pathogen in each aerosol can sometimes be several hundred or several thousand, the effect is non-negligible, especially in diseases where the risk of infection per pathogen is high. Here we report on a generalization of the Wells-Riley model and dose-response models for poly-pathogen aerosols by separately modeling each number of pathogen copies per aerosol, while the aerosol dose itself follows a Poisson distribution. This results in a model for computational risk assessment suitable for mono-/poly-pathogen aerosols. We show that the mono-pathogen assumption significantly overestimates the risk of infection for high pathogen concentrations in the respiratory tract fluid. The model also includes the aerosol removal due to filtering by the individuals which becomes significant for poorly ventilated environments with a high density of individuals, and systematically includes the effects of facemasks in the infectious aerosol source and sink terms and dose calculations. [ABSTRACT FROM AUTHOR]

Determining the function of proteins remains a key task of modern biology. Classical genetic approaches to knocking out protein function in plants still face limitations, such as the time-consuming nature of generating homozygous transgenic lines or the risk of non-viable loss-of-function phenotypes. We aimed to overcome these limitations by acting downstream of the protein level. Chimeric E3 ligases degrade proteins of interest in mammalian cell lines, Drosophila melanogaster embryos, and transgenic tobacco. We successfully recruited the 26S proteasome pathway to directly degrade a protein of interest located in plant nuclei. This success was achieved via replacement of the interaction domain of the E3 ligase adaptor protein SPOP (Speckle-type POZ adapter protein) with a specific anti-GFP nanobody (VHHGFP4). For proof of concept, the target protein CENH3 of A. thaliana fused to EYFP was subjected to nanobody-guided proteasomal degradation in planta. Our results show the potential of the modified E3-ligase adapter protein VHHGFP4-SPOP in this respect. We were able to point out its capability for nucleus-specific protein degradation in plants. [ABSTRACT FROM AUTHOR]

Shedding of DNA of pathogenic Leptospira spp. has been documented in naturally infected cats in several countries, but urinary shedding of infectious Leptospira spp. has only recently been proven. The climate in Southern Chile is temperate rainy with high annual precipitations which represents ideal preconditions for survival of Leptospira spp., especially during spring and summer. The aims of this study were to investigate shedding of pathogenic Leptospira spp. in outdoor cats in Southern Chile, to perform molecular characterization of isolates growing in culture, and to assess potential risk factors associated with shedding. Urine samples of 231 outdoor cats from rural and urban areas in southern Chile were collected. Urine samples were investigated for pathogenic Leptospira spp. by 4 techniques: qPCR targeting the lipL32 gene, immunomagnetic separation (IMS)-coupled qPCR (IMS-qPCR), direct culture and IMS-coupled culture. Positive urine cultures were additionally confirmed by PCR. Multilocus sequence typing (MLST) was used to molecularly characterize isolates obtained from positive cultures. Overall, 36 urine samples (15.6%, 95% confidence interval (CI) 11.4–20.9) showed positive results. Eighteen (7.8%, 95% CI 4.9–12.1), 30 (13%, 95% CI 9.2–18), 3 (1.3%, 0.3–3.9) and 4 cats (1.7%; 95% CI 0.5–4.5) were positive in qPCR, IMS-qPCR, conventional culture, and IMS-coupled culture, respectively. MLST results of 7 culture-positive cats revealed sequences that could be assigned to sequence type 17 (6 cats) and sequence type 27 (1 cat) corresponding to L. interrogans (Pathogenic Leptospira Subgroup 1). Shedding of pathogenic Leptospira spp. by cats might be an underestimated source of infection for other species including humans. The present study is the first one reporting growth of leptospires from feline urine in culture in naturally infected cats in South-America and characterisation of culture-derived isolates. So far, very few cases of successful attempts to culture leptospires from naturally infected cats are described worldwide. [ABSTRACT FROM AUTHOR]

Species of the perennial woody plant genus Betula dominate subalpine forests and play a significant role in preserving biological diversity. In addition to their conventional benefits, birches synthesize a wide range of secondary metabolites having pharmacological significance. Methyl salicylate (MeSA) is one of these naturally occurring compounds constitutively produced by different birch species. MeSA is therapeutically important in human medicine for muscle injuries and joint pain. However, MeSA is now mainly produced synthetically due to a lack of information relating to MeSA biosynthesis and regulation. In this study, we performed a comprehensive bioinformatics analysis of two candidate genes mediating MeSA biosynthesis, SALICYLIC ACID METHYLTRANSFERASE (SAMT) and SALICYLIC ACID-BINDING PROTEIN 2 (SABP2), of high (B. lenta, B. alleghaniensis, B. medwediewii, and B. grossa) and low (B. pendula, B. utilis, B. alnoides, and B. nana) MeSA-producing birch species. Phylogenetic analyses of SAMT and SABP2 genes and homologous genes from other plant species confirmed their evolutionary relationships. Multiple sequence alignments of the amino acid revealed the occurrence of important residues for substrate specificity in SAMT and SABP2. The analysis of cis elements in different birches indicated a functional multiplicity of SAMT and SABP2 and provided insights into the regulation of both genes. We successfully developed six prominent single nucleotide substitution markers that were validated with 38 additional birch individuals to differentiate high and low MeSA-producing birch species. Relative tissue-specific expression analysis of SAMT in leaf and bark tissue of two high and two low MeSA-synthesizing birches revealed a high expression in the bark of both high MeSA-synthesizing birches. In contrast, SABP2 expression in tissues revealed indifferent levels of expression between species belonging to the two groups. The comparative expression and bioinformatics analyses provided vital information that could be used to apply plant genetic engineering technology in the mass production of organic MeSA. [ABSTRACT FROM AUTHOR]

Background: Brown adipose tissue (BAT) is a specialized form of adipose tissue, able to increase energy expenditure by heat generation in response to various stimuli. Recently, its pathological activation has been implicated in the pathogenesis of cancer cachexia. To establish a causal relationship, we retrospectively investigated the longitudinal changes in BAT and cancer in a large FDG-PET/CT cohort. Methods: We retrospectively analyzed 13 461 FDG-PET/CT examinations of n = 8 409 patients at our institution from the winter months of 2007–2015. We graded the activation strength of BAT based on the anatomical location of the most caudally activated BAT depot into three tiers, and the stage of the cancer into five general grades. We validated the cancer grading by an interreader analysis and correlation with histopathological stage. Ambient temperature data (seven-day average before the examination) was obtained from a meteorological station close to the hospital. Changes of BAT, cancer, body mass index (BMI) and temperature between the different examinations were examined with Spearman's test and a mixed linear model for correlation, and with a causal inference algorithm for causality. Results: We found n = 283 patients with at least two examinations and active BAT in at least one of them. There was no significant interaction between the changes in BAT activation, cancer burden or BMI. Temperature changes exhibited a strong negative correlation with BAT activity (ϱ = -0.57, p<0.00001). These results were confirmed with the mixed linear model. Causal inference revealed a link of Temperature ➜ BAT in all subjects and also of BMI ➜ BAT in subjects who had lost weight and increased cancer burden, but no role of cancer and no causal links of BAT ➜ BMI. Conclusions: Our data did not confirm the hypothesis that BAT plays a major role in cancer-mediated weight loss. Temperature changes are the main driver of incidental BAT activity on FDG-PET scans. [ABSTRACT FROM AUTHOR]

Cells have the ability to detect electric fields and respond to them with directed migratory movement. Investigations identified genes and proteins that play important roles in defining the migration efficiency. Nevertheless, the sensing and transduction mechanisms underlying directed cell migration are still under discussion. We use Dictyostelium discoideum cells as model system for studying eukaryotic cell migration in DC electric fields. We have defined the temporal electric persistence to characterize the memory that cells have in a varying electric field. In addition to imposing a directional bias, we observed that the electric field influences the cellular kinematics by accelerating the movement of cells along their paths. Moreover, the study of vegetative and briefly starved cells provided insight into the electrical sensing of cells. We found evidence that conditioned medium of starved cells was able to trigger the electrical sensing of vegetative cells that would otherwise not orient themselves in the electric field. This observation may be explained by the presence of the conditioned medium factor (CMF), a protein secreted by the cells, when they begin to starve. The results of this study give new insights into understanding the mechanism that triggers the electrical sensing and transduces the external stimulus into directed cell migration. Finally, the observed increased mobility of cells over time in an electric field could offer a novel perspective towards wound healing assays. [ABSTRACT FROM AUTHOR]

Spontaneous electroencephalogram (EEG) and auditory evoked potentials (AEP) have been suggested to monitor the level of consciousness during anesthesia. As both signals reflect different neuronal pathways, a combination of parameters from both signals may provide broader information about the brain status during anesthesia. Appropriate parameter selection and combination to a single index is crucial to take advantage of this potential. The field of machine learning offers algorithms for both parameter selection and combination. In this study, several established machine learning approaches including a method for the selection of suitable signal parameters and classification algorithms are applied to construct an index which predicts responsiveness in anesthetized patients. The present analysis considers several classification algorithms, among those support vector machines, artificial neural networks and Bayesian learning algorithms. On the basis of data from the transition between consciousness and unconsciousness, a combination of EEG and AEP signal parameters developed with automated methods provides a maximum prediction probability of 0.935, which is higher than 0.916 (for EEG parameters) and 0.880 (for AEP parameters) using a cross-validation approach. This suggests that machine learning techniques can successfully be applied to develop an improved combined EEG and AEP parameter to separate consciousness from unconsciousness. [ABSTRACT FROM AUTHOR]

Research based on secondary analysis of data stored in electronic health records (EHR) has gained popularity, but whether the data are consistent with those collected under a study setting is unknown. The objective is to assess the agreement between data obtained in a prospective study and routine-care data extracted retrospectively from the EHR. We compared the data collected in a longitudinal lifestyle intervention study with those recorded in the EHR system over 5 years. A total of 225 working adults were recruited at an academic institution between 2008–2012, whose EHR data were also available during the same time period. After aligning the participants' study visit dates with their hospital encounter dates, data on blood pressure, body mass index (BMI), and laboratory measurements (including high-density lipoprotein (HDL), low-density lipoprotein (LDL), triglycerides, and total cholesterol) were compared via a paired t-test for equivalence with pre-specified margins. Summary statistics were used to compare smoking status and medication prescriptions. Overall, data were consistent between the two sources (i.e., BMI, smoking status, medication prescriptions), whereas some differences were found in cholesterol measurements (i.e., HDL and total cholesterol), possibly due to different lab assays and subject's fasting status. In conclusion, some EHR data are fairly consistent with those collected in a clinical study, whereas others may require further examination. Researchers should evaluate the consistency and quality of EHR data and compare them with other sources of data when possible. [ABSTRACT FROM AUTHOR]

Objectives: To compare objective and subjective image quality of bronchial structures between a 512-pixel and a 1024-pixel image matrix for chest CT in phantoms and in patients. Materials and methods: First, a two-size chest phantom was imaged at two radiation doses on a 192-slice CT scanner. Datasets were reconstructed with 512-, 768-, and 1024-pixel image matrices and a sharp reconstruction kernel (Bl64). Image sharpness and normalized noise power spectrum (nNPS) were quantified. Second, chest CT images of 100 patients were reconstructed with 512- and 1024-pixel matrices and two blinded readers independently assessed objective and subjective image quality. In each patient dataset, the highest number of visible bronchi was counted for each lobe of the right lung. A linear mixed effects model was applied in the phantom study and a Welch's t-test in the patient study. Results: Objective image sharpness and image noise increased with increasing matrix size and were highest for the 1024-matrix in phantoms and patients (all, P<0.001). nNPS was comparable among the three matrices. Objective image noise was on average 16% higher for the 1024-matrix compared to the 512-matrix in patients (P<0.0001). Subjective evaluation in patients yielded improved sharpness but increased image noise for the 1024- compared to the 512-matrix (both, P<0.001). There was no significant difference between highest-order visible bronchi (P>0.07) and the overall bronchial image quality between the two matrices (P>0.22). Conclusion: Our study demonstrated superior image sharpness and higher image noise for a 1024- compared to a 512-pixel matrix, while there was no significant difference in the depiction and subjective image quality of bronchial structures for chest CT. [ABSTRACT FROM AUTHOR]

Multiple factors are involved in the pathogenesis of non-alcoholic fatty liver disease (NAFLD), but the exact immunological mechanisms that cause inflammation and fibrosis of the liver remain enigmatic. In this current study, cellular samples of a cohort of NAFLD patients (peripheral blood mononuclear cells (PBMC): n = 27, liver samples: n = 15) and healthy individuals (PBMC: n = 26, liver samples: n = 3) were analyzed using 16-color flow cytometry, and the frequency and phenotype of 23 immune cell subtypes was assessed. PBMC of NAFLD patients showed decreased frequencies of total CD3+, CD8+ T cells, CD56dim NK cells and MAIT cells, but elevated frequencies of CD4+ T cells and Th2 cells compared to healthy controls. Intrahepatic lymphocytes (IHL) of NAFLD patients showed decreased frequencies of total T cells, total CD8+ T cells, Vd2+γδ T cells, and CD56bright NK cells, but elevated frequencies of Vδ2-γδ T cells and CD56dim NK cells compared to healthy controls. The activating receptor NKG2D was significantly less frequently expressed among iNKT cells, total NK cells and CD56dim NK cells of PBMC of NAFLD patients compared to healthy controls. More strikingly, hepatic fibrosis as measured by fibroscan elastography negatively correlated with the intrahepatic frequency of total NK cells (r2 = 0,3737, p = 0,02). Hepatic steatosis as measured by controlled attenuation parameter (CAP) value negatively correlated with the frequency of circulating NKG2D+ iNKT cells (r2 = 0,3365, p = 0,0047). Our data provide an overview of the circulating and intrahepatic immune cell composition of NAFLD patients, and point towards a potential role of NK cells and iNKT cells for the regulation of hepatic fibrosis and steatosis in NAFLD. [ABSTRACT FROM AUTHOR]

The scientific method has been guiding biological research for a long time. It not only prescribes the order and types of activities that give a scientific study validity and a stamp of approval but also has substantially shaped how we collectively think about the endeavor of investigating nature. The advent of high-throughput data generation, data mining, and advanced computational modeling has thrown the formerly undisputed, monolithic status of the scientific method into turmoil. On the one hand, the new approaches are clearly successful and expect the same acceptance as the traditional methods, but on the other hand, they replace much of the hypothesis-driven reasoning with inductive argumentation, which philosophers of science consider problematic. Intrigued by the enormous wealth of data and the power of machine learning, some scientists have even argued that significant correlations within datasets could make the entire quest for causation obsolete. Many of these issues have been passionately debated during the past two decades, often with scant agreement. It is proffered here that hypothesis-driven, data-mining–inspired, and “allochthonous” knowledge acquisition, based on mathematical and computational models, are vectors spanning a 3D space of an expanded scientific method. The combination of methods within this space will most certainly shape our thinking about nature, with implications for experimental design, peer review and funding, sharing of result, education, medical diagnostics, and even questions of litigation. [ABSTRACT FROM AUTHOR]

Anti-α4β7 therapy with vedolizumab (VDZ) has been suggested as possible immune intervention in HIV. Relatively little is known about the α4β7-integrin (α4β7) expression of different T-cell subsets in different anatomical compartments of healthy individuals, patients with HIV or inflammatory bowel disease (IBD). Surface expression of α4β7 as well as the frequency of activation, homing and exhaustion markers of T cells were assessed by multicolour flow cytometry in healthy volunteers (n = 15) compared to HIV infected patients (n = 52) or patients diagnosed with ulcerative colitis (UC) (n = 14), 6 of whom treated with vedolizumab. In addition, lymph nodal cells (n = 6), gut-derived cells of healthy volunteers (n = 5) and patients with UC (n = 6) were analysed. Additionally, we studied longitudinal PBMC samples of an HIV patient who was treated with vedolizumab for concomitant UC. Overall, only minor variations of the frequency of α4β7 on total CD4+ T cells were detectable regardless of the disease status or (VDZ) treatment status in peripheral blood and the studied tissues. Peripheral α4β7+ CD4+ T cells of healthy individuals and patients with UC showed a higher activation status and were more frequently CCR5+ than their α4β7- counterparts. Also, the frequency of α4β7+ cells was significantly lower in peripheral blood CD4+ effector memory T cells of HIV-infected compared to healthy individuals and this reduced frequency did not recover in HIV patients on ART. Conversely, the frequency of peripheral blood naïve α4β7+ CD4+ T cells was significantly reduced under VDZ treatment. The results of the current study will contribute to the understanding of the dynamics of α4β7 expression pattern on T cells in HIV and UC and will be useful for future studies investigating VDZ as possible HIV cure strategy. [ABSTRACT FROM AUTHOR]

Aims: More than mild paravalvular aortic regurgitation (pAR) negatively impacts prognosis after transcatheter aortic valve implantation (TAVI). “Newer generation” transcatheter heart valves (THVs) including Direct Flow Medical, Medtronic Evolut R, Boston Lotus, and Edwards SAPIEN 3 valve system promise to improve outcome by reducing the rate of TAVI-related issues such as pAR. Aim was to evaluate and compare the hemodynamic performance with AR index of “early” vs. “newer generation” THVs and its impact on outcome. Methods and results: In 805 patients undergoing TAVI, the degree of pAR was assessed using imaging modalities (angiography, echocardiography) and hemodynamic measurements (aortic regurgitation index, ARI ratio). Severity of pAR and outcome were assessed according to the VARC-2 criteria. 805 patients underwent TAVI with use of the CoreValve (n = 400), SAPIEN XT (n = 48), Direct Flow Medical (n = 38), Evolut R (n = 114), Lotus (n = 104), or SAPIEN 3 (n = 101) prosthesis. TTE post TAVI revealed that a total of 7.3% of the patients showed moderate/severe pAR. The occurrence of greater than mild pAR occurred less frequently in patients treated with “newer generation” THVs (p<0.001): CoreValve (11.3%), SAPIEN XT (12.5%), Direct Flow Medical (5.3%), Evolut R (5.3%), Lotus (0.0%), and SAPIEN 3 (0.0%). The AR index was significantly higher (p<0.001) in patients receiving “newer generation” prostheses compared to those in whom “earlier generation” THVs were used. However, the ARI was only predictive of cumulative all-cause mortality at 1 and 3 years in “early generation”, but not in “newer generation” THVs. In the overall cohort, 30-day and 1-year mortality was 4.8% and 20.1%, respectively. In patients treated with “newer generation” devices, the respective mortality rates remained substantially below those of patients treated with “earlier generation” THVs (30-day mortality: 2.5% vs. 6.7%, p< 0.001; 1-year mortality: 11.2% vs. 27.2%, p<0.001). Conclusion: TAVI with use of “newer generation” THVs showed significantly reduced pAR and improved outcomes compared to “early generation” devices that could at least in part be explained by more favorable hemodynamics [ABSTRACT FROM AUTHOR]

The complexity of morphogenesis poses a fundamental challenge to understanding the mechanisms governing the formation of biological patterns and structures. Over the past century, numerous processes have been identified as critically contributing to morphogenetic events, but the interplay between the various components and aspects of pattern formation have been much harder to grasp. The combination of traditional biology with mathematical and computational methods has had a profound effect on our current understanding of morphogenesis and led to significant insights and advancements in the field. In particular, the theoretical concepts of reaction–diffusion systems and positional information, proposed by Alan Turing and Lewis Wolpert, respectively, dramatically influenced our general view of morphogenesis, although typically in isolation from one another. In recent years, agent-based modeling has been emerging as a consolidation and implementation of the two theories within a single framework. Agent-based models (ABMs) are unique in their ability to integrate combinations of heterogeneous processes and investigate their respective dynamics, especially in the context of spatial phenomena. In this review, we highlight the benefits and technical challenges associated with ABMs as tools for examining morphogenetic events. These models display unparalleled flexibility for studying various morphogenetic phenomena at multiple levels and have the important advantage of informing future experimental work, including the targeted engineering of tissues and organs. [ABSTRACT FROM AUTHOR]

While there is a burgeoning interest in the effects of nutrition on systemic inflammatory diseases, how dietary macronutrient balance impacts local chronic inflammatory diseases in the mouth has been largely overlooked. Here, we used the Geometric Framework for Nutrition to test how the amounts of dietary macronutrients and their interactions, as well as carbohydrate type (starch vs sucrose vs resistant starch) influenced periodontitis-associated alveolar bone height in mice. Increasing intake of carbohydrates reduced alveolar bone height, while dietary protein had no effect. Whether carbohydrate came from sugar or starch did not influence the extent of alveolar bone height. In summary, the amount of carbohydrate in the diet modulated periodontitis-associated alveolar bone height independent of the source of carbohydrates. [ABSTRACT FROM AUTHOR]

We describe in this paper the experimental procedure, the data treatment and the quantification of the black body correction: an experimental approach to compensate for scattering and systematic biases in quantitative neutron imaging based on experimental data. The correction algorithm is based on two steps; estimation of the scattering component and correction using an enhanced normalization formula. The method incorporates correction terms into the image normalization procedure, which usually only includes open beam and dark current images (open beam correction). Our aim is to show its efficiency and reproducibility: we detail the data treatment procedures and quantitatively investigate the effect of the correction. Its implementation is included within the open source CT reconstruction software MuhRec. The performance of the proposed algorithm is demonstrated using simulated and experimental CT datasets acquired at the ICON and NEUTRA beamlines at the Paul Scherrer Institut. [ABSTRACT FROM AUTHOR]

Background: The study of Onchocerca volvulus has been limited by its host range, with only humans and non-human primates shown to be susceptible to the full life cycle infection. Small animal models that support the development of adult parasites have not been identified. Methodology/Principal findings: We hypothesized that highly immunodeficient NSG mice would support the survival and maturation of O. volvulus and alteration of the host microenvironment through the addition of various human cells and tissues would further enhance the level of parasite maturation. NSG mice were humanized with: (1) umbilical cord derived CD34+ stem cells, (2) fetal derived liver, thymus and CD34+ stem cells or (3) primary human skeletal muscle cells. NSG and humanized NSG mice were infected with 100 O. volvulus infective larvae (L3) for 4 to 12 weeks. When necropsies of infected animals were performed, it was observed that parasites survived and developed throughout the infection time course. In each of the different humanized mouse models, worms matured from L3 to advanced fourth stage larvae, with both male and female organ development. In addition, worms increased in length by up to 4-fold. Serum and urine, collected from humanized mice for identification of potential biomarkers of infection, allowed for the identification of 10 O. volvulus-derived proteins found specifically in either the urine or the serum of the humanized O. volvulus-infected NSG mice. Conclusions/Significance: The newly identified mouse models for onchocerciasis will enable the development of O. volvulus specific biomarkers, screening for new therapeutic approaches and potentially studying the human immune response to infection with O. volvulus. [ABSTRACT FROM AUTHOR]

Endometriosis affects various aspects of women’s lives. We searched for predictors for patient satisfaction with medical support (PSwMS) in women with endometriosis. The study was designed as a multi-centre retrospective cohort study. We approached women with histologically confirmed endometriosis from 2010 until 2016, comparing women satisfied to women dissatisfied with medical support. We analysed data on characteristics of endometriosis, PSwMS and the influence of disease characteristics on PSwMS. Information on satisfaction with medical support was collected through a standardized questionnaire. After exclusion of 73 women because of inchoately filled in questionnaires, data from 498 women was evaluated. Altogether, it was observed that 54.6% (n = 272) of the study participants were satisfied with medical support and 45.4% (n = 226) were not. Feeling adequately informed by the time of diagnosis (p < 0.001), taking women’s mental troubles seriously (p < 0.001) and supporting women in handling their pain (p < 0.001) were significantly associated with satisfaction. We found adequate information to be the most distinctive indicator for PSwMS. Further, acknowledging psychological distress and supporting women in handling their symptoms rather than to alleviate them, positively affect PSwMS. To achieve PSwMS, healthcare providers have to give adequate information on endometriosis and its management. [ABSTRACT FROM AUTHOR]