BioEncoder: A metric learning toolkit for comparative organismal biology.

In the realm of biological image analysis, deep learning (DL) has become a core toolkit, for example for segmentation and classification. However, conventional DL methods are challenged by large biodiversity datasets characterized by unbalanced classes and hard-to-distinguish phenotypic differences between them. Here we present BioEncoder, a user-friendly toolkit for metric learning, which overcomes these challenges by focussing on learning relationships between individual data points rather than on the separability of classes. BioEncoder is released as a Python package, created for ease of use and flexibility across diverse datasets. It features taxon-agnostic data loaders, custom augmentation options, and simple hyperparameter adjustments through text-based configuration files. The toolkit's significance lies in its potential to unlock new research avenues in biological image analysis while democratizing access to advanced deep metric learning techniques. BioEncoder focuses on the urgent need for toolkits bridging the gap between complex DL pipelines and practical applications in biological research.

Effects of obstructive sleep apnea treatment on neurodegenerative biomarker neurofilament light chain and cognitive performance.

Obstructive sleep apnea is associated with cognitive impairment and increased risk for neurodegenerative diseases. Obstructive sleep apnea treatment with positive airway pressure therapy helps to improve cognitive symptoms and reduces long-term dementia risk. To test whether these treatment effects are due to a reduction in neuronal damage, we examined longitudinal changes in the neurodegenerative serum neurofilament light chain and cognitive performance of patients with obstructive sleep apnea. In this study, 17 patients with obstructive sleep apnea completed baseline and follow-up (9 month after starting PAP treatment) investigation of sleep, daytime symptoms, cognitive testing and serum neurofilament light chain measurements. Depending on treatment adherence and efficacy, participants were assigned either to the effective treatment (n = 10) or non-effective treatment group (n = 7). As results at baseline lower mean oxygen saturation during sleep was associated with higher serum neurofilament light chain. Patients in the non-effective treatment group showed a significant increase of age-adjusted percentile of serum neurofilament light chain levels at follow-up, whereas serum neurofilament light chain values remained constant in the effective treatment group. At a functional level, effective treatment leads to an improvement in processing speed, which was not the case in the non-effective treatment group. Longitudinal changes of age-adjusted serum neurofilament light chain levels were associated with changes in cognitive performance. To conclude, this longitudinal observational study showed that effective obstructive sleep apnea treatment positively affects the amount of neuronal damage as well as working memory performance. As cognitive symptoms might not only be attributed to obstructive sleep apnea-related sleep deficiency, but also neurodegeneration, our results underline the importance of treatment adherence and efficacy for the prevention of neuronal damage and cognitive consequences.

Comorbid cerebral amyloid angiopathy in dementia and prodromal stages-Prevalence and effects on cognition.

OBJECTIVES: To determine the contribution of cerebral amyloid angiopathy to cognitive impairment in MCI and dementia. METHODS: Patients with subjective memory impairment (SMI), amnestic and non-amnestic mild cognitive impairment ((n)aMCI), Alzheimer's disease (AD), mixed and vascular dementia (MD/VD) from our memory clinic were included in this retrospective analysis. Patients underwent neuropsychological testing and cranial magnetic resonance imaging (MRI). Magnetic resonance imaging data sets were analyzed regarding the presence of CAA-related MRI biomarkers to determine CAA prevalence. ANOVAs were used to investigate the contribution of CAA to cognitive impairment within diagnostic groups and to determine whether differences in cognitive test performance between the diagnostic groups are mediated by total CAA burden. RESULTS: 475 patients (222 male, 253 female) with SMI (n = 47), naMCI (n = 41), aMCI (n = 189), early AD (n = 9), AD (n = 114), MD (n = 71) and VD (n = 4) were included. Mean age was 73.2 (9.9) years. CAA prevalence was 14.9% in SMI, 14.6% in naMCI, 24.3% in aMCI, 22.2% in early onset AD, 18.4% in late onset AD, 46.5% in MD and 25% in VD. Patients with possible and probable CAA were older than patients without CAA. In particular, diagnosis of aMCI, early onset AD, MD and VD showed high CAA prevalence. In AD but not in aMCI, CAA diagnosis significantly influenced test performance in the CERAD word list recall (F (1,78) = 4505; p = 0.037; partial eta-square = 0.055). Differences in cognitive test performance between the diagnostic groups of naMCI, aMCI, AD and MD were mediated by total CAA burden within AAT simply nouns subtest (F (2,39) = 4059; p = 0.025; partial eta-square = 0.172) and in CERAD verbal fluency test (F (3,129) = 3533; p = 0.017; partial eta-square = 0.076). CONCLUSION: This retrospective analysis demonstrates high prevalence rates of CAA in cognitive diagnoses. Our data suggest that comorbid CAA independently impacts cognitive test performance in the course of AD with presumably stage-dependent effects. Especially in patients with AD comorbid CAA additionally impairs memory function. Total CAA small vessel disease burden further modulates psychometric differences in cognitive test performance between diagnostic groups regarding word finding and word fluency capabilities.

Fifty years of capacity building in the search for new marine natural products.

The Convention on Biological Diversity, and the Nagoya Protocol in particular, provide a framework for the fair and equitable sharing of benefits arising from the utilization of biological resources and traditional knowledge, and ultimately aim to promote capacity-building in the developing world. However, measuring capacity-building is a challenging task due to its intangible nature. By compiling and analyzing a database of scientific peer-reviewed publications over a period of 50 y (1965 to 2015), we investigated capacity-building in global marine natural product discovery. We used publication and authorship metrics to assess how the capacity to become scientifically proficient, prolific, and independent has changed in bioprospecting countries. Our results show that marine bioprospecting is a dynamically growing field of research with continuously increasing numbers of participating countries, publications, and scientists. Yet despite longstanding efforts to promote equitability and scientific independence, not all countries have similarly increased their capacity to explore marine biodiversity within their national jurisdiction areas. Although developing countries show an increasing trend in the number of publications, a few developed countries still account for almost one-half of all publications in the field. Multiple lines of evidence suggest that economic capacity affects how well countries with species-rich marine ecosystems can scientifically explore those resources. Overall, the capacity-building data analyzed here provides a timely contribution to the ongoing international debate about access to and benefit-sharing of biological resources for countries exploring biodiversity within and outside their national jurisdiction areas.

[Coincidence of normal pressure hydrocephalus and Alzheimer`s disease: therapeutic implications and open questions]. / Zur Koinzidenz von Normaldruckhydrocephalus und Alzheimer-Demenz: therapeutische Implikationen und offene Fragen.

Normal pressure hydrocephalus (NPH) is prevalent in aging patient populations. Despite its clinical relevance, many patients with NPH may not receive adequate treatment. Because of the frequency of Alzheimer`s disease in these patients, there could be overlapping pathophysiological mechanisms that are as yet incompletely understood. Cerebral comorbidities seem to have negative effects on therapeutic response to ventriculoperitoneal shunting. In order to avoid unnecessary and unsuccessful surgery in highly vulnerable elderly patients, they have to be taken into consideration in the diagnostic process.

Predictors of subjective cognitive deficits in patients with mild cognitive impairment.

BACKGROUND: Detailed examination of cognitive deficits in patients with mild cognitive impairment (MCI) yields substantial diagnostic and prognostic value, specifically with respect to memory. Magnitude and characteristics of subjective cognitive deficits, however, often receive less attention in this population at risk for developing dementia. METHODS: We investigated predictors of subjective cognitive deficits in patients with MCI, using a detailed assessment for such impairments associated with different cognitive domains, as well as demographic and clinical variables including magnetic resonance imaging data. RESULTS: The strongest predictor for subjective memory deficits was depressed mood, whereas subjective performance issues associated with attention or executive functions also corresponded to measurable impairments in the respective cognitive domains. Reduced hippocampal thickness and hemispheric entorhinal cortex thickness asymmetry were associated with objective memory impairment but not with subjective deficits or symptoms of depression. CONCLUSIONS: Whereas low objective memory performance and reduced cortical thickness within medial temporal lobe subregions could be associated with neurodegeneration, greater subjective memory deficits in patients with MCI may indicate psychological burden.

On the evolution of trophic position.

The trophic structure of food webs is primarily determined by the variation in trophic position among species and individuals. Temporal dynamics of food web structure are central to our understanding of energy and nutrient fluxes in changing environments, but little is known about how evolutionary processes shape trophic position variation in natural populations. We propose that trophic position, whose expression depends on both environmental and genetic determinants of the diet variation in individual consumers, is a quantitative trait that can evolve via natural selection. Such evolution can occur either when trophic position is correlated with other heritable morphological and behavioural traits under selection, or when trophic position is a target of selection, which is possible if the fitness effects of prey items are heterogeneously distributed along food chains. Recognising trophic position as an evolving trait, whose expression depends on the food web context, provides an important conceptual link between behavioural foraging theory and food web dynamics, and a useful starting point for the integration of ecological and evolutionary studies of trophic position.

Dietary-based developmental plasticity affects juvenile survival in an aquatic detritivore.

Developmental plasticity is ubiquitous in natural populations, but the underlying causes and fitness consequences are poorly understood. For consumers, nutritional variation of juvenile diets is probably associated with plasticity in developmental rates, but little is known about how diet quality can affect phenotypic trajectories in ways that might influence survival to maturity and lifetime reproductive output. Here, we tested how the diet quality of a freshwater detritivorous isopod (Asellus aquaticus), in terms of elemental ratios of diet (i.e. carbon : nitrogen : phosphorus; C : N : P), can affect (i) developmental rates of body size and pigmentation and (ii) variation in juvenile survival. We reared 1047 individuals, in a full-sib split-family design (29 families), on either a high- (low C : P, C : N) or low-quality (high C : P, C : N) diet, and quantified developmental trajectories of body size and pigmentation for every individual over 12 weeks. Our diet contrast caused strong divergence in the developmental rates of pigmentation but not growth, culminating in a distribution of adult pigmentation spanning the broad range of phenotypes observed both within and among natural populations. Under low-quality diet, we found highest survival at intermediate growth and pigmentation rates. By contrast, survival under high-quality diet survival increased continuously with pigmentation rate, with longest lifespans at intermediate growth rates and high pigmentation rates. Building on previous work which suggests that visual predation mediates the evolution of cryptic pigmentation in A. aquaticus, our study shows how diet quality and composition can generate substantial phenotypic variation by affecting rates of growth and pigmentation during development in the absence of predation.

Norepinephrine is a negative regulator of the adult periventricular neural stem cell niche.

The limited proliferative capacity of neuroprogenitor cells (NPCs) within the periventricular germinal niches (PGNs) located caudal of the subventricular zone (SVZ) of the lateral ventricles together with their high proliferation capacity after isolation strongly implicates cell-extrinsic humoral factors restricting NPC proliferation in the hypothalamic and midbrain PGNs. We comparatively examined the effects of norepinephrine (NE) as an endogenous candidate regulator of PGN neurogenesis in the SVZ as well as the periventricular hypothalamus and the periaqueductal midbrain. Histological and neurochemical analyses revealed that the pattern of NE innervation of the adult PGNs is inversely associated with their in vivo NPC proliferation capacity with low NE levels coupled to high NPC proliferation in the SVZ but high NE levels coupled to low NPC proliferation in hypothalamic and midbrain PGNs. Intraventricular infusion of NE decreased NPC proliferation and neurogenesis in the SVZ-olfactory bulb system, while pharmacological NE inhibition increased NPC proliferation and early neurogenesis events in the caudal PGNs. Neurotoxic ablation of NE neurons using the Dsp4-fluoxetine protocol confirmed its inhibitory effects on NPC proliferation. Contrarily, NE depletion largely impairs NPC proliferation within the hippocampus in the same animals. Our data indicate that norepinephrine has opposite effects on the two fundamental neurogenic niches of the adult brain with norepinephrine being a negative regulator of adult periventricular neurogenesis. This knowledge might ultimately lead to new therapeutic approaches to influence neurogenesis in hypothalamus-related metabolic diseases or to stimulate endogenous regenerative potential in neurodegenerative processes such as Parkinson's disease.

[Insomnia in the context of neurological diseases]. / Insomnie im Rahmen neurologischer Erkrankungen.

This article provides an overview of the prevalence, cause and treatment of insomnia in common neurological diseases (restless legs syndrome, stroke, multiple sclerosis, Parkinson´s disease and Alzheimer´s disease) with an additional focus on the bidirectional relationship between sleep and neurological disorders.Insomnia is prevalent, but frequently unrecognized in the context of neurological diseases. Although it is widely known that sleep has a relevant impact on quality of life in general and cerebral function in particular, sleep disorders receive little attention in the prevention and treatment of neurological diseases.

The role of plasticity in the evolution of cryptic pigmentation in a freshwater isopod.

Cryptic pigmentation of prey is often thought to evolve in response to predator-mediated selection, but pigmentation traits can also be plastic, and change with respect to both abiotic and biotic environmental conditions. In such cases, identifying the presence of, and drivers of trait plasticity is useful for understanding the evolution of crypsis. Previous work suggests that cryptic pigmentation of freshwater isopods (Asellus aquaticus) has evolved in response to predation pressure by fish in habitats with varying macrophyte cover and coloration. However, macrophytes can potentially influence the distribution of pigmentation by altering not only habitat-specific predation susceptibility, but also dietary resources and abiotic conditions. The goals of this study were to experimentally test how two putative agents of selection, namely macrophytes and fish, affect the pigmentation of A. aquaticus, and to assess whether pigmentation is plastic, using a diet manipulation in a common garden. We performed two experiments: (a) in an outdoor mesocosm experiment, we investigated how different densities of predatory fish (0/30/60 three-spined stickleback [Gasterosteus aculeatus] per mesocosm) and macrophytes (presence/absence) affected the abundance, pigmentation and body size structure of isopod populations. (b) In a subsequent laboratory experiment, we reared isopods in a common garden experiment on two different food sources (high/low protein content) to test whether variation in pigmentation of isopods can be explained by diet-based developmental plasticity. We found that fish presence strongly reduced isopod densities, particularly in the absence of macrophytes, but had no effect on pigmentation or size structure of the populations. However, we found that isopods showed consistently higher pigmentation in the presence of macrophytes, regardless of fish presence or absence. Our laboratory experiment, in which we manipulated the protein content of the isopods' diet, revealed strong plasticity of pigmentation and weak plasticity of growth rate. The combined results of both experiments suggest that pigmentation of A. aquaticus is a developmentally plastic trait and that multiple environmental factors (e.g. macrophytes, diet and predation) might jointly influence the evolution of cryptic pigmentation of A. aquaticus in nature on relatively short time-scales.

Memory-induced acceleration and slowdown of barrier crossing.

We study the mean first-passage time τMFP for the barrier crossing of a single massive particle with non-Markovian memory by Langevin simulations in one dimension. In the Markovian limit of short memory time τΓ, the expected Kramers turnover between the overdamped (high-friction) and the inertial (low-friction) limits is recovered. Compared to the Markovian case, we find barrier crossing to be accelerated for intermediate memory time, while for long memory time, barrier crossing is slowed down and τMFP increases with τΓ as a power law τMFP∼τΓ2. Both effects are derived from an asymptotic propagator analysis: while barrier crossing acceleration at intermediate memory can be understood as an effective particle mass reduction, slowing down for long memory is caused by the slow kinetics of energy diffusion. A simple and globally accurate heuristic formula for τMFP in terms of all relevant time scales of the system is presented and used to establish a scaling diagram featuring the Markovian overdamped and the Markovian inertial regimes, as well as the non-Markovian intermediate memory time regime where barrier crossing is accelerated and the non-Markovian long memory time regime where barrier crossing is slowed down.

MAPT mutation associated with frontotemporal dementia and parkinsonism (FTDP-17).

We present a 56-year-old patient suffering from frontotemporal dementia with parkinsonism linked to chromosome 17 (FTDP-17). The history included a three-generation pedigree and the patient was found to be a mutation carrier. The diagnosis was hindered by late appearance of the hypokinetic movement disorder. For clinicians, it is important to consider rare neurodegenerative disease variants in early-onset familial dementia syndromes with behavioral, cognitive, and motor symptoms.

The nonmotor features of Parkinson's disease: pathophysiology and management advances.

PURPOSE OF REVIEW: In recent years progress has been made in the detection and evaluation of nonmotor symptoms in Parkinson's disease. The pathophysiology is better understood and new treatment is available, which will be discussed in this review. RECENT FINDINGS: The most intriguing recent finding is the fact that Parkinson's disease may be a spreading disease. From the environment a toxin, bacteria, or virus may start in genetically susceptible patients a cascade of α-synuclein aggregation which reaches via the olfactory and the enteric system of the gut the brain where further spreading causes symptoms, such as sleep disturbances, motor impairment, and neuropsychiatric symptoms. New treatment should address the abnormal α-synuclein folding. If this would be achieved premotor signs, such as hyposmia, rapid eye movement-sleep behavior disorder, constipation, or depression may be a kind of biomarkers which allow together with other diagnostic tools, such as parenchymal sonography, iodobenzamide-scintigraphy and dopamine transporter scans the prediction whether somebody might be under way to develop the full-blown Parkinson's disease syndrome. SUMMARY: Parkinson's disease seems to be a spreading disease which causes not only a dopaminergic deficit as major cause for the movement disorder but also impairs function of many other brain centers which leads to a multitransmitter malfunction.

Desulfurization and denitrogenation of heavy gas oil by Rhodococcus erythropolis ATCC 4277.

Some of the noxious atmospheric pollutants such as nitrogen and sulfur dioxides come from the fossil fuel combustion. Biodesulfurization and biodenitrogenation are processes which remove those pollutants through the action of microorganisms. The ability of sulfur and nitrogen removal by the strain Rhodococcus erythropolis ATCC 4277 was tested in a biphasic system containing different heavy gas oil concentrations in a batch reactor. Heavy gas oil is an important fraction of petroleum, because after passing through, the vacuum distillation is incorporated into diesel oil. This strain was able to remove about 40% of the nitrogen and sulfur present in the gas heavy oil. Additionally, no growth inhibition occurred even when in the presence of pure heavy gas oil. Results present in this work are considered relevant for the development of biocatalytic processes for nitrogen and sulfur removal toward building feasible industrial applications.

Subthalamic nucleus but not entopeduncular nucleus deep brain stimulation enhances neurogenesis in the SVZ-olfactory bulb system of Parkinsonian rats.

Introduction: Deep brain stimulation (DBS) is a highly effective treatment option in Parkinson's disease. However, the underlying mechanisms of action, particularly effects on neuronal plasticity, remain enigmatic. Adult neurogenesis in the subventricular zone-olfactory bulb (SVZ-OB) axis and in the dentate gyrus (DG) has been linked to various non-motor symptoms in PD, e.g., memory deficits and olfactory dysfunction. Since DBS affects several of these non-motor symptoms, we analyzed the effects of DBS in the subthalamic nucleus (STN) and the entopeduncular nucleus (EPN) on neurogenesis in 6-hydroxydopamine (6-OHDA)-lesioned hemiparkinsonian rats. Methods: In our study, we applied five weeks of continuous bilateral STN-DBS or EPN-DBS in 6-OHDA-lesioned rats with stable dopaminergic deficits compared to 6-OHDA-lesioned rats with corresponding sham stimulation. We injected two thymidine analogs to quantify newborn neurons early after DBS onset and three weeks later. Immunohistochemistry identified newborn cells co-labeled with NeuN, TH and GABA within the OB and DG. As a putative mechanism, we simulated the electric field distribution depending on the stimulation site to analyze direct electric effects on neural stem cell proliferation. Results: STN-DBS persistently increased the number of newborn dopaminergic and GABAergic neurons in the OB but not in the DG, while EPN-DBS does not impact neurogenesis. These effects do not seem to be mediated via direct electric stimulation of neural stem/progenitor cells within the neurogenic niches. Discussion: Our data support target-specific effects of STN-DBS on adult neurogenesis, a putative modulator of non-motor symptoms in Parkinson's disease.

Brief report: Adult hippocampal precursor cells shorten S-phase and total cell cycle length during neuronal differentiation.

Cell cycle analyses of adult hippocampal neural stem and precursor cells in vivo are challenging, as there is no temporal or local discrimination of different precursor cell populations. All commonly used techniques to determine the cell cycle length of proliferating cells in the adult hippocampus do not allow discrimination between different cell types. Here, we introduce a novel procedure to precisely calculate cell cycle phase lengths of distinct precursor cell populations in vivo and thereby demonstrate a large heterogeneity of cell cycle kinetics within the pool of adult hippocampal precursor cells. Proliferating NeuroD1(+) cells exhibited a significantly faster S-phase progression (T(s) = 10.1 ± 0.6 hours) and shorter total cell cycle length (T(c) = 22.6 ± 0.1 hours) than NeuroD1(-) cells (T(s) = 13.5 ± 0.8 hours, T(c) = 27.0 ± 0.5 hours; p < .05). Dividing glial fibrillary acidic protein (GFAP(+)) cells also showed significantly shorter mean T(s) of 9.7 ± 0.6 hours and T(c) of 22.8 ± 0.5 hours compared to the rest of uncommitted NeuroD1(-) precursors (p < .01). Together, NeuroD1(+) neuronal progenitors and mitotic GFAP(+) radial glia-like cells divide significantly faster than amplifying neural progenitor cells by accelerating their S-phase. S-phase duration seems to determine cell cycle length in the adult hippocampus.

Training with Odors Impacts Hippocampal Thickness in Patients with Mild Cognitive Impairment.

BACKGROUND: The olfactory system is affected early in Alzheimer's disease and olfactory loss can already be observed in patients with mild cognitive impairment (MCI). Olfactory training is effective for improving olfactory and cognitive function by stimulating the olfactory pathway, but its effect on patients with MCI remains unclear. OBJECTIVE: The aim of this randomized, prospective, controlled, blinded study was to assess whether a 4-month period of olfactory training (frequent short-term sniffing various odors) may have an effect on olfactory function, cognitive function, and morphology of medial temporal lobe (MTL) subregions and olfactory bulb in MCI patients. METHODS: A total of thirty-seven MCI patients were randomly assigned to the training group or a placebo group, which were performed twice a day for 4 months. Olfactory assessments, cognitive tests and magnetic resonance imaging were performed at the baseline and follow-up period. RESULTS: After the training, there was an increase in odor discrimination, and increased cortical thickness of bilateral hippocampus (CA23DG and CA1) and mean MTL. Additionally, the change of olfactory score was positively associated with change of volume of olfactory bulb and hippocampus; the change of global cognition was positively associated with change of cortical thickness of hippocampus, entorhinal cortex and mean MTL; the change of cortical thickness of entorhinal cortex was positively associated with change of executive function. CONCLUSION: Olfactory training was associated with an increase in cortical thickness of the hippocampus but not olfactory bulb volume in patients with MCI. Olfactory training may serve as an early intervention of preventing hippocampal atrophy.

A pragmatic methodical framework for the user-centred development of an electronic process support for the sleep laboratory patients' management.

Objective: Limited capacities and ineffective care pathways result in long waiting times for patients and sporadic treatment controls in sleep medicine. As one objective of the 'Telesleep Medicine' project, a portal should be developed, which supports sleep specialists in an efficient and resource-saving patient management. On account of the limited project timeframe, the 'classical' user-centred design and evaluation methods could not be comprehensively implemented. Therefore, a pragmatic methodical framework was developed. Methods: For the iterative development of the portal, a combination of low-cost and quick-to-implement methods was used. In chronological order, these were: context interviews, personas, the development of an as-is model, a web search of design standards and good design aspects of similar systems, the development of a to-be model, the creation of an overarching mind map, and the iterative creation of mockups with simplified usability walkthroughs. Results: The feasibility of the pragmatic methodological framework for the development of a prototype for the portal was demonstrated. The used method combination resulted in a prototype based on the needs and requirements of the sleep specialists, taking into account their specific workflow and the technical implementation conditions. Conclusions: The presented pragmatic methodological framework can be a valuable resource for developers of comparable projects. The combination of methods worked well together regarding the limited timeframe and resources for concept development. For the future, we plan to implement and test the portal in the clinical field and thus enrich our framework with additional methods.