julilili42/papers huggingface dataset:
Tracking activity patterns of a multispecies community of gymnotiform weakly electric fish in their neotropical habitat without tagging
2020-01-01

Field studies on freely behaving animals commonly require tagging and often are focused on single species. Weakly electric fish generate a species- and individual-specific electric organ discharge (EOD) and therefore provide a unique opportunity for individual tracking without tagging. We here present and test tracking algorithms based on recordings with submerged electrode arrays. Harmonic structures extracted from power spectra provide fish identity. Localization of fish based on weighted averages of their EOD amplitudes is found to be more robust than fitting a dipole model. We apply these techniques to monitor a community of three species, Apteronotus rostratus, Eigenmannia humboldtii, and Sternopygus dariensis, in their natural habitat in Darién, Panamá. We found consistent upstream movements after sunset followed by downstream movements in the second half of the night. Extrapolations of these movements and estimates of fish density obtained from additional transect data suggest that some fish cover at least several hundreds of meters of the stream per night. Most fish, including Eigenmannia, were traversing the electrode array solitarily. From in-situ measurements of the decay of the EOD amplitude with distance of individual animals we estimated that fish can detect conspecifics at distances of up to 2 m. Our recordings also emphasize the complexity of natural electrosensory scenes resulting from the interactions of the EODs of different species. Electrode arrays thus provide an unprecedented window into the so-far hidden nocturnal activities of multispecies communities of weakly electric fish at an unmatched level of detail.
Evaluation of Efficacy of a New Cryoprobe for Transbronchial Cryobiopsy: A Randomized, Controlled in vivo Animal Study
2020-01-01

&lt;b&gt;&lt;i&gt;Background:&lt;/i&gt;&lt;/b&gt; Forceps biopsy (FB) is still the most popular procedure for the bronchoscopic sampling of lung tissue. However, it has limitations like inadequate sample size and crush artifacts. Cryobiopsy (CB) has been introduced to obtain bronchoscopic biopsies with improved diagnostic yield compared to FB. Limitations of CB are the need to retract the cryoprobe en bloc with bronchoscope because samples are larger than the working channel and the variations of the freezing power of the reusable CB (rCB). Therefore, 3 new disposable cryoprobes (dCB) have been developed with different outer diameters: 1.1 mm (CB11-S) that can be retracted through the working channel of the bronchoscope, 1.7 mm (CB17) and 2.4 mm (CB24n), respectively. &lt;b&gt;&lt;i&gt;Objectives:&lt;/i&gt;&lt;/b&gt; The aim was to evaluate the new cryoprobes with regard to feasibility, specimen area, specimen quality and complications. &lt;b&gt;&lt;i&gt;Methods:&lt;/i&gt;&lt;/b&gt; We compared biopsy samples of the new probes with those obtained by FB and by rCB in an in vivo (porcine) model. A flexible bronchoscope was used to perform biopsy at 4 different locations at the upper and lower lobes of the right and left lung, respectively. The biopsies were taken under fluoroscopic control. The biopsy tool and activation times were allocated randomly. Altogether 204 biopsy procedures were performed. &lt;b&gt;&lt;i&gt;Results:&lt;/i&gt;&lt;/b&gt; The sample quality of the dCB was superior to that of FB (all &lt;i&gt;p&lt;/i&gt; &amp;#x3c; 0.05) and not significantly different to the rCB sample quality. Mean specimen sample area of all CB was significantly larger compared to FB (&lt;i&gt;p&lt;/i&gt; &amp;#x3c; 0.05). The sample area of the small cryoprobe (CB11-S) was significantly smaller compared to the other CB probes (&lt;i&gt;p&lt;/i&gt; &amp;#x3c; 0.05). No severe bleedings occurred. Pneumothoraces were detected in 3 of the 7 pigs. &lt;b&gt;&lt;i&gt;Conclusion:&lt;/i&gt;&lt;/b&gt; We conclude that CB with the new single-use instruments are feasible and represent a viable option to improve the diagnostic accuracy of histopathological evaluation compared to FB.
The FOXJ1 target Cfap206 is required for sperm motility, mucociliary clearance of the airways and brain development
2020-01-01

Cilia are complex cellular protrusions consisting of hundreds of proteins. Defects in ciliary structure and function, many of which have not been characterised molecularly, cause ciliopathies, a heterogeneous group of human syndromes. Here we report on the FOXJ1 target gene Cfap206, orthologues of which so far have only been studied in Chlamydomonas and Tetrahymena. In mouse and Xenopus, Cfap206 was co-expressed with and dependent on Foxj1. CFAP206 protein localised to the basal body and to the axoneme of motile cilia. In Xenopus crispant larvae ciliary beat frequency of skin multiciliated cells was enhanced and bead transport across the epidermal mucociliary epithelium was reduced. Likewise, Cfap206 knockout mice revealed ciliary phenotypes. Electron tomography of immotile knockout mouse sperm flagella indicated a role in radial spokes formation reminiscent of FAP206 function in Tetrahymena. Male infertility, hydrocephalus and impaired mucociliary clearance of the airways in the absence of laterality defects in Cfap206 mutant mice suggests that Cfap206 may represent a candidate for the subgroup of human primary ciliary dyskinesia caused by radial spoke defects.
Analysis of brain atrophy and local gene expression in genetic frontotemporal dementia
2020-01-01

Abstract Frontotemporal dementia is a heterogeneous neurodegenerative disorder characterized by neuronal loss in the frontal and temporal lobes. Despite progress in understanding which genes are associated with the aetiology of frontotemporal dementia, the biological basis of how mutations in these genes lead to cell loss in specific cortical regions remains unclear. In this work, we combined gene expression data for 16 772 genes from the Allen Institute for Brain Science atlas with brain maps of grey matter atrophy in symptomatic C9orf72, GRN and MAPT mutation carriers obtained from the Genetic Frontotemporal dementia Initiative study. No significant association was seen between C9orf72, GRN and MAPT expression and the atrophy patterns in the respective genetic groups. After adjusting for spatial autocorrelation, between 1000 and 5000 genes showed a negative or positive association with the atrophy pattern within each individual genetic group, with the most significantly associated genes being TREM2, SSBP3 and GPR158 (negative association in C9Orf72, GRN and MAPT respectively) and RELN, MXRA8 and LPA (positive association in C9Orf72, GRN and MAPT respectively). An overrepresentation analysis identified a negative association with genes involved in mitochondrial function, and a positive association with genes involved in vascular and glial cell function in each of the genetic groups. A set of 423 and 700 genes showed significant positive and negative association, respectively, with atrophy patterns in all three maps. The gene set with increased expression in spared cortical regions was enriched for neuronal and microglial genes, while the gene set with increased expression in atrophied regions was enriched for astrocyte and endothelial cell genes. Our analysis suggests that these cell types may play a more active role in the onset of neurodegeneration in frontotemporal dementia than previously assumed, and in the case of the positively associated cell marker genes, potentially through emergence of neurotoxic astrocytes and alteration in the blood–brain barrier, respectively.
Bubble formation in nanopores: a matter of hydrophobicity, geometry, and size
2020-01-01

This review focuses on the phase behaviour of liquids in nanoscale confinement, which promotes drying by a combination of hydrophobicity, small size, and high degree of confinement. In these conditions, the vapour phase can form at exceptionally large pressures or low temperatures as compared to bulk vaporisation, giving rise to the unexpected formation of bubbles. A general framework is introduced which allows to understand the main effects of confinement on the thermodynamics and on the kinetics of drying. The relevance of such phenomena is discussed in the realm of biological nanopores, specifically ion channels, and in nanoporous materials. The emergence of nanoscale effects not accounted for in macroscopic theories is discussed together with the open challenges in this rapidly expanding field.
Electrospun nanofibers for biomedical applications
2020-01-01

Electrospinning is a versatile and effective technique widely used to manufacture nanofibrous structures from a diversity of materials (synthetic, natural or inorganic). The electrospun nanofibrous meshes’ composition, morphology, porosity, and surface functionality support the development of advanced solutions for many biomedical applications. The Special Issue on “Electrospun Nanofibers for Biomedical Applications” assembles a set of original and highly-innovative contributions showcasing advanced devices and therapies based on or involving electrospun meshes. It comprises 13 original research papers covering topics that span from biomaterial scaffolds’ structure and functionalization, nanocomposites, antibacterial nanofibrous systems, wound dressings, monitoring devices, electrical stimulation, bone tissue engineering to first-in-human clinical trials. This publication also includes four review papers focused on drug delivery and tissue engineering applications.
Effekt: Capability-passing style for type- and effect-safe, extensible effect handlers in Scala
2020-01-01

Abstract Effect handlers are a promising way to structure effectful programs in a modular way. We present the Scala library Effekt , which is centered around capability passing and implemented in terms of a monad for multi-prompt delimited continuations. Effekt is the first library implementation of effect handlers that supports effect safety and effect polymorphism without resorting to type-level programming. We describe a novel way of achieving effect safety using intersection types and path-dependent types. The effect system of our library design fits well into the programming paradigm of capability passing and is inspired by the effect system of Zhang &amp; Myers (2019, Proc. ACM Program. Lang. 3 (POPL), 5:1-5:29). Capabilities carry an abstract type member, which represents an individual effect type and reflects the use of the capability on the type level. We represent effect rows as the contravariant intersection of effect types. Handlers introduce capabilities and remove components of the intersection type. Reusing the existing type system of Scala, we get effect subtyping and effect polymorphism for free.
Appraisal Theories for Emotion Classification in Text
2020-01-01

Automatic emotion categorization has been predominantly formulated as text classification in which textual units are assigned to an emotion from a predefined inventory, for instance following the fundamental emotion classes proposed by Paul Ekman (fear, joy, anger, disgust, sadness, surprise) or Robert Plutchik (adding trust, anticipation). This approach ignores existing psychological theories to some degree, which provide explanations regarding the perception of events. For instance, the description that somebody discovers a snake is associated with fear, based on the appraisal as being an unpleasant and non-controllable situation. This emotion reconstruction is even possible without having access to explicit reports of a subjective feeling (for instance expressing this with the words "I am afraid."). Automatic classification approaches therefore need to learn properties of events as latent variables (for instance that the uncertainty and the mental or physical effort associated with the encounter of a snake leads to fear). With this paper, we propose to make such interpretations of events explicit, following theories of cognitive appraisal of events, and show their potential for emotion classification when being encoded in classification models. Our results show that high quality appraisal dimension assignments in event descriptions lead to an improvement in the classification of discrete emotion categories. We make our corpus of appraisal-annotated emotion-associated event descriptions publicly available.
Carbon turnover and microbial activity in an artificial soil under imposed cyclic drainage and imbibition
2020-01-01

Abstract Water table fluctuations generate temporally and spatially dynamic physicochemical conditions that drive biogeochemical hot spots and hot moments in the vadose zone. However, their role in the cycling of soil C remains poorly known. Here, we present results from unvegetated column experiments filled with 45 cm of artificial soil containing 10% humus, and inoculated with a natural microbial extract. In one series of three replicate columns, five cycles, each consisting of a 4‐wk drainage followed by a 4‐wk imbibition period, were imposed, whereas in a second series, the water table remained static. Depth‐resolved O 2 concentration profiles and headspace CO 2 effluxes were markedly different between the two regimes. In the fluctuating regime, drainage periods yielded 2.5 times greater CO 2 effluxes than imbibition periods. At the end of the experiment, the fluctuating water table columns exhibited a distinct zone of organic C (OC) depletion in the depth interval of 8–20 cm that was not observed under the static regime. Although this zone showed elevated levels of adenosine triphosphate (ATP), the microbial biomass was actually lower than at the corresponding depth interval of the static regime. A vertically stratified microbial community established in all columns that depended on oxygenation with depth. The 16S ribosomal RNA (rRNA) gene analyses showed a slightly higher diversity in the soil exposed to moisture fluctuations, but there was no clear difference in major taxa and microbial community composition between treatments. These results thus suggest that the localized enhancement of OC degradation induced by the water table fluctuations was driven by a more active, rather than a more abundant or compositionally very different, microbial community.
Systematic Investigation of Polyurethane Biomaterial Surface Roughness on Human Immune Responses in vitro
2020-01-01

It has been widely shown that biomaterial surface topography can modulate host immune response, but a fundamental understanding of how different topographies contribute to pro‐inflammatory or anti‐inflammatory responses is still lacking. To investigate the impact of surface topography on immune response, we undertook a systematic approach by analyzing immune response to eight grades of medical grade polyurethane of increasing surface roughness in three in vitro models of the human immune system. Polyurethane specimens were produced with defined roughness values by injection molding according to the VDI 3400 industrial standard. Specimens ranged from 0.1 μ m to 18 μ m in average roughness (Ra), which was confirmed by confocal scanning microscopy. Immunological responses were assessed with THP‐1‐derived macrophages, human peripheral blood mononuclear cells (PBMCs), and whole blood following culture on polyurethane specimens. As shown by the release of pro‐inflammatory and anti‐inflammatory cytokines in all three models, a mild immune response to polyurethane was observed, however, this was not associated with the degree of surface roughness. Likewise, the cell morphology (cell spreading, circularity, and elongation) in THP‐1‐derived macrophages and the expression of CD molecules in the PBMC model on T cells (HLA‐DR and CD16), NK cells (HLA‐DR), and monocytes (HLA‐DR, CD16, CD86, and CD163) showed no influence of surface roughness. In summary, this study shows that modifying surface roughness in the micrometer range on polyurethane has no impact on the pro‐inflammatory immune response. Therefore, we propose that such modifications do not affect the immunocompatibility of polyurethane, thereby supporting the notion of polyurethane as a biocompatible material.
First Trimester Screening for Common Trisomies and Microdeletion 22q11.2 Syndrome Using Cell-Free DNA: A Prospective Clinical Study
2020-01-01

Objectives: The aims of the study were to assess the false-positive and uninformative test rate with first trimester cell-free DNA (cfDNA) screening for common trisomies and microdeletion 22q11.2 (22q11.2DS) and to examine women’s attitudes toward such an approach. Methods: This is a prospective study at the Prenatal Medicine Department of the University of Tübingen, Germany, at 11–13 weeks. In all pregnancies, a detailed ultrasound examination was carried out, followed by a cfDNA analysis for common trisomies and 22q11.2DS. In cases where the cfDNA analysis indicated 22q11.2DS, invasive prenatal diagnostic testing and parental testing were performed. After delivery, a detailed neonatal clinical examination was carried out including further genetic testing. Prior to counselling about the study, we asked the pregnant women who were potentially eligible for the study to anonymously report on their knowledge about 22q11.2DS. Results: A total of 1,127 pregnancies were included in the final analysis of the study. The first cfDNA test was uninformative in 15 (1.33%) pregnancies. In 10 (0.89%) cases, the test remained uninformative, even after the second blood sample. There were 3 (0.27%) cases with a positive cfDNA test for 22q11.2DS. In all, 983 women returned the anonymous questionnaire prior to study participation. Only 80 (8.1%) women responded that they felt familiar or very familiar with 22q11.2DS. Conclusion: The addition of 22q11.2DS in first trimester cfDNA screening for common trisomies is feasible. The uninformative test rate for common trisomies and 22q11.2DS is 0.9%, and the false-positive rate for 22q11.2DS is 0.3%. Awareness and education around 22q11.2DS should be improved.
Diagnostic Accuracy of Electrical Impedance Spectroscopy in Non-melanoma Skin Cancer
2020-01-01

Electrical impedance spectroscopy is a non-invasive technique that can help clinicians in diagnosing malignant skin tumours. Depending on the cellular irregularity of the lesion, electrical impedance spectroscopy can reveal changes in the structure and form of the cells, using a harmless electrical current applied to the skin. A score between 0 and 10 is generated by the electrical impedance spectrometer, where 0 is considered benign and 10 is malignant. This prospective study was conducted in 101 patients with a total of 200 skin lesions; 62 benign and 138 malignant. There was a significant difference between the electrical impedance of malignant and benign lesions (p < 0.001). The sensitivity, specificity, positive predictive value and negative predictive value of electrical impedance spectroscopy for non-melanoma skin cancer were 94.2%, 41.9%, 78.3% and 76.5%, respectively, when the cut-off for the electrical impedance spectroscopy score was set at between 5 and 6. The area under the curve in receiver operating characteristics analyses was 0.758.
Skin manifestations in spondyloarthritis
2020-01-01

Spondyloarthritides (SpA) like psoriatic arthritis, axial spondyloarthritis/ankylosing spondylitis, reactive arthritis and inflammatory bowel disease (IBD)-associated SpA can present with characteristic skin manifestations. These SpA-associated skin disorders may precede joint involvement, reflect a loss of efficacy of a current systemic treatment or can even be treatment associated. Cutaneous manifestations in SpA not only add additional morbidity with physical impact but also impose a psychosocial burden on affected patients. Psoriasis (PsO) – the main skin disease in SpA – has a variety of clinical presentations, including plaque-type PsO, inverse PsO, guttate PsO, erythrodermic PsO, nail PsO and pustular types. SpA associated with IBD presents with neutrophilic and granulomatous skin disorders, including pyoderma gangrenosum, hidradenitis suppurativa and cutaneous Crohn’s disease. Reactive arthritides has a favourable prognosis and may feature keratoderma blenorrhagicum or balanitis circinatum as typical skin manifestations. Immunologically, SpA-associated skin diseases share interleukin (IL)-17 and IL-23 dysregulation but show distinctive genetic and immunological profiles. Therefore, they vary in their treatment responses to targeted therapies with biologicals or small molecules. In this review, we highlight the clinical presentation of skin manifestations in SpA and discuss therapeutic approaches in this interdisciplinary field.
Reduction of coercive measures under routine conditions in psychiatric hospitals 2004–2019: Strong effects in old age psychiatry, much less in general psychiatry
2020-01-01

Abstract Background Many interventions to reduce the use of seclusion and restraint have been suggested in the last decades. Evidence-based interventions in old age psychiatry are different from those in general psychiatry. A common database for psychiatric hospitals introduced in 2004 allowed to examine the use of seclusion and restraint over 16 years under routine conditions. Methods A registry for coercive measures in the Federal State of Baden-Wuerttemberg has been available since 2015, and comprises all 32 hospitals licensed to admit involuntary patients. A study group had collected data prospectively since 2004 from a subsample of these hospitals. We analyzed the mean percentage of patients subjected to coercive measures and the mean cumulative duration of these interventions in ICD-10 diagnostic groups in psychiatric hospitals from 2004 to 2019 among a total of 1,038,239 admissions. Results The proportion of cases affected by coercive measures dropped significantly from 28.4 to 10.5% in patients with ICD-10 F0 disorders, while rates in patients with other diagnoses decreased insignificantly from 7.0 to 5.4%. The cumulated duration of coercive measures per affected case also dropped significantly among patients with F0 disorders, while changes in patients with other diagnoses remained insiginficant. Conclusions The use of coercive measures in patients with organic disorders could be reduced by about 50% in a State of 11 million inhabitants within 15 years, while in contrast no substantial reduction occurred among all other diagnostic groups. Specific interventions to reduce coercive interventions seem to be particularly successful for this patient group.