julilili42/papers huggingface dataset:
Scalable 18F Processing Conditions for Copper-Mediated Radiofluorination Chemistry Facilitate "Design of Experiments" (DoE) Optimization Studies and Afford an Improved Synthesis of [18F]Olaparib.
2021-05-07

A convenient, scalable, and azeotropic drying free method for processing [18F]fluoride as base free&lt;br&gt;[18F]TBAF is reported and applied to copper-mediated radiofluorination (CMRF) radiosyntheses. A central&lt;br&gt;feature of this method is that a single production of [18F]TBAF can be divided into small aliquots that can be&lt;br&gt;used to perform multiple small-scale reactions in DoE optimization studies. The results of these studies can&lt;br&gt;then be reliably translated to full batch tracer productions using automated synthesizers. This processing&lt;br&gt;technique was successfully applied to the manual DoE optimization, DoE study validation, and subsequent&lt;br&gt;full-batch automation of the PARP-1 tracer [18F]olaparib. After DoE optimization, we were able to produce&lt;br&gt;[18F]olaparib in high radiochemical yields via both manual (%RCY (CMRF step only) = 78 ± 6 %, n = 4) and&lt;br&gt;automated (up to 80% radiochemical yield (%RCY); 41% activity yield (%AY)) radiosynthesis procedures.&lt;br&gt;This work further demonstrates the power of the DoE approach for improving the radiochemical yields and&lt;br&gt;radiosynthesis performance of clinically relevant tracer productions
Hepatitis E: An update on One Health and clinical medicine
2021-05-08

Abstract The hepatitis E virus (HEV) is one of the main causes of acute hepatitis and the de facto global burden is underestimated. HEV‐related clinical complications are often undetected and are not considered in the differential diagnosis. Convincing findings from studies suggest that HEV is clinically relevant not only in developing countries but also in industrialized countries. Eight HEV genotypes (HEV‐1 to HEV‐8) with different human and animal hosts and other HEV‐related viruses are in circulation. Transmission routes vary by genotype and location, with large waterborne outbreaks in developing countries and zoonotic food‐borne infections in developed countries. An acute infection can be aggravated in pregnant women, organ transplant recipients, patients with pre‐existing liver disease and immunosuppressed patients. HEV during pregnancy affects the fetus and newborn with an increased risk of vertical transmission, preterm and stillbirth, neonatal jaundice and miscarriage. Hepatitis E is associated with extrahepatic manifestations that include neurological disorders such as neuralgic amyotrophy, Guillain‐Barré syndrome and encephalitis, renal injury and haematological disorders. The risk of transfusion‐transmitted HEV is increasingly recognized in Western countries where the risk may be because of a zoonosis. RNA testing of blood components is essential to determine the risk of transfusion‐transmitted HEV. There are currently no approved drugs or vaccines for HEV infections. This review focuses on updating the latest developments in zoonoses, screening and diagnostics, drugs in use and under development, and vaccines.
Beneficial effects of coagulase‐negative Staphylococci on Staphylococcus aureus skin colonization
2021-05-08

Abstract Our skin is constantly exposed to a large number of pathogens while at the same time undergoing selective colonization by commensal microorganisms such as coagulase‐negative Staphylococci. Staphylococcus aureus , however, is a facultative pathogen that is usually absent from healthy skin but frequently colonizes the inflamed skin of atopic dermatitis patients, where it further promotes inflammation. Enhanced S. aureus skin colonization was shown to correlate with a loss of microbiome diversity indicating a role for skin commensals to shape pathogen colonization. Together, keratinocytes and immune cells in the skin need to discriminate commensals from pathogens and orchestrate subsequent immune reactions in response to colonizing microbes. However, the mechanisms how individual commensals cooperate with keratinocytes and the immune system of the skin to prevent pathogen colonization are barely understood. In this review, we discuss the current knowledge on the functional effects of coagulase‐negative staphylococci, the most frequently isolated skin commensals, on S. aureus skin colonization.
The Ambivalent Role of Skin Microbiota and Adrenaline in Wound Healing and the Interplay between Them
2021-05-08

After skin injury, wound healing sets into motion a dynamic process to repair and replace devitalized tissues. The healing process can be divided into four overlapping phases: hemostasis, inflammation, proliferation, and maturation. Skin microbiota has been reported to participate in orchestrating the wound healing both in negative and positive ways. Many studies reported that skin microbiota can impose negative and positive effects on the wound. Recent findings have shown that many bacterial species on human skin are able to convert aromatic amino acids into so-called trace amines (TAs) and convert corresponding precursors into dopamine and serotonin, which are all released into the environment. As a stress reaction, wounded epithelial cells release the hormone adrenaline (epinephrine), which activates the β2-adrenergic receptor (β2-AR), impairing the migration ability of keratinocytes and thus re-epithelization. This is where TAs come into play, as they act as antagonists of β2-AR and thus attenuate the effects of adrenaline. The result is that not only TAs but also TA-producing skin bacteria accelerate wound healing. Adrenergic receptors (ARs) play a key role in many physiological and disease-related processes and are expressed in numerous cell types. In this review, we describe the role of ARs in relation to wound healing in keratinocytes, immune cells, fibroblasts, and blood vessels and the possible role of the skin microbiota in wound healing.
Agropastoral Economies and Land Use in Bronze Age Western Anatolia
2021-05-08

The Middle and Late Bronze Ages of western Anatolia (modern Turkey) remains poorly understood in comparison with its Mycenaean and Hittite neighbours, especially in agricultural economies and land use. Kaymakci is the largest Middle and Late Bronze Age citadel excavated to date in western Anatolia and new archaeobotanical and zooarchaeological data from the site presented here shed new light on regional agricultural economies and land use. Agricultural practices at Kaymakci focused on barley and bitter vetch farming and pig, caprine, and cattle husbandry within a diverse and extensive economic system that made substantial use of wild plants and animals for food, technology, and fuel. Goats and pigs were managed primarily for meat, while sheep and cattle were managed to produce a range of secondary products. Wood charcoal analysis reconstructs both deciduous and evergreen oak woodlands, which also dominate the contemporary landscape. In regional perspective, Kaymakci is most similar to the northern Aegean agricultural tradition, but with elements of Anatolian practices as well, representing a hybrid position between the Aegean and Anatolian worlds as seen in other lines of archaeological evidence from the site.
A Novel Gaze Gesture Sensor for Smart Glasses Based on Laser Self-Mixing
2021-05-08

The integration of gaze gesture sensors in next-generation smart glasses will improve usability and enable new interaction concepts. However, consumer smart glasses place additional requirements to gaze gesture sensors, such as a low power consumption, high integration capability and robustness to ambient illumination. We propose a novel gaze gesture sensor based on laser feedback interferometry (LFI), which is capable to measure the rotational velocity of the eye as well as the sensor’s distance towards the eye. This sensor delivers a unique and novel set of features with an outstanding sample rate allowing to not only predict a gaze gesture but also to anticipate it. To take full advantage of the unique sensor features and the high sampling rate, we propose a novel gaze symbol classification algorithm based on single sample. At a mean F1-score of 93.44 %, our algorithms shows exceptional classification performance.
Atom-by-atom chemical identification from scanning transmission electron microscopy images in presence of noise and residual aberrations
2021-05-08

The simple dependence of the intensity in annular dark field scanning transmission electron microscopy images on the atomic number provides (to some extent) chemical information about the sample, and even allows an elemental identification in the case of light-element single-layer samples. However, the intensity of individual atoms and atomic columns is affected by residual aberrations and the confidence of an identification is limited by the available signal to noise. Here, we show that matching a simulation to an experimental image by iterative optimization provides a reliable analysis of atomic intensities even in presence of residual non-round aberrations. We compare our new method with other established approaches demonstrating its high reliability for images recorded at limited dose and with different aberrations. This is of particular relevance for analyzing moderately beam-sensitive materials, such as most 2D materials, where the limited sample stability often makes it difficult to obtain spectroscopic information at atomic resolution.
Limited reciprocal surrogacy of bird and habitat diversity and inconsistencies in their representation in Romanian protected areas
2021-05-08

Abstract Because it is impossible to comprehensively characterize biodiversity at all levels of organization, conservation prioritization efforts need to rely on surrogates. As species distribution maps of relished groups as well as high-resolution remotely sensed data increasingly become available, both types of surrogates are commonly used. A good surrogate should represent as much of biodiversity as possible, but it often remains unclear to what extent this is the case. Here, we aimed to address this question by assessing how well bird species and habitat diversity represent one another. We conducted our study in Romania, a species-rich country with high landscape heterogeneity where bird species distribution data have only recently started to become available. First, we prioritized areas for conservation based on either 137 breeding bird species or 36 habitat classes, and then evaluated their reciprocal surrogacy performance. Second, we examined how well these features are represented in already existing protected areas. Finally, we identified target regions of high conservation value for the potential expansion of the current network of reserves (as planned under the new EU Biodiversity Strategy for 2030). We found that bird species were a better surrogate for habitat diversity than vice versa. Highly ranked areas based on habitat diversity were represented better than areas based on bird species, which varied considerably between species. Our results highlight that taxonomic and environmental (i.e., habitat types) data may perform rather poorly as reciprocal surrogates, and multiple sources of data are required for a full evaluation of protected areas expansion.
Clinical Validation of Saliency Maps for Understanding Deep Neural Networks in Ophthalmology
2021-05-09

Abstract Deep neural networks (DNNs) have achieved physician-level accuracy on many imaging-based medical diagnostic tasks, for example classification of retinal images in ophthalmology. However, their decision mechanisms are often considered impenetrable leading to a lack of trust by clinicians and patients. To alle-viate this issue, a range of explanation methods have been proposed to expose the inner workings of DNNs leading to their decisions. For imaging-based tasks, this is often achieved via saliency maps. The quality of these maps are typically evaluated via perturbation analysis without experts involved. To facilitate the adoption and success of such automated systems, however, it is crucial to validate saliency maps against clinicians. In this study, we used three different network architectures and developed ensembles of DNNs to detect diabetic retinopathy and neovascular age-related macular degeneration from retinal fundus images and optical coherence tomography scans, respectively. We used a variety of explanation methods and obtained a comprehensive set of saliency maps for explaining the ensemble-based diagnostic decisions. Then, we systematically validated saliency maps against clinicians through two main analyses — a direct comparison of saliency maps with the expert annotations of disease-specific pathologies and perturbation analyses using also expert annotations as saliency maps. We found the choice of DNN architecture and explanation method to significantly influence the quality of saliency maps. Guided Backprop showed consistently good performance across disease scenarios and DNN architectures, suggesting that it provides a suitable starting point for explaining the decisions of DNNs on retinal images.
The evolution and changing ecology of the African hominid oral microbiome
2021-05-10

Significance The microbiome plays key roles in human health, but little is known about its evolution. We investigate the evolutionary history of the African hominid oral microbiome by analyzing dental biofilms of humans and Neanderthals spanning the past 100,000 years and comparing them with those of chimpanzees, gorillas, and howler monkeys. We identify 10 core bacterial genera that have been maintained within the human lineage and play key biofilm structural roles. However, many remain understudied and unnamed. We find major taxonomic and functional differences between the oral microbiomes of Homo and chimpanzees but a high degree of similarity between Neanderthals and modern humans, including an apparent Homo -specific acquisition of starch digestion capability in oral streptococci, suggesting microbial coadaptation with host diet.
The impact of severe rare chronic neurological disease in childhood on the quality of life of families—a study on MLD and PCH2
2021-05-10

Abstract Background Rare and severe neurological disorders in childhood not only heavily affect the life perspective of the patients, but also their caregivers and families. The aim of this study was to investigate the impact of such diseases on the family, especially on the quality of life and life perspectives of parents, but also on the families’ everyday life, based on the model of two diseases which have been well described in recent years with respect to symptoms and course: metachromatic leukodystrophy (MLD) and pontocerebellar hypoplasia type 2 (PCH2). PCH2 is a primary severe developmental disorder, while children with MLD initially develop normally and then progressively deteriorate. Methods Using a semi-standardized questionnaire, 43 families with children suffering from MLD (n = 30) or PCH2 (n = 19) reported data on the severity of the illness/symptoms, on family support and the care situation, as well as on the circumstances of non-affected siblings and the parents’ work situation. In addition, the quality of life of parents and general family functioning was assessed using the PedsQLTM Family Impact Module [23]. Results for the latter were compared to published data from families with children without any chronic condition using student’s t-tests for independent samples. Potential factors influencing the PedsQLTM scores were analyzed using Spearman’s rank correlation. Results Parents of children with MLD and PCH2 reported significantly lower health-related quality of life (HRQOL) compared to parents of healthy children ( P &lt; 0.001). Mothers showed significantly poorer HRQOL ( P &lt; 0.05) and were significantly more dissatisfied with their professional development ( P &lt; 0.05) than fathers, and this was seen in relation to their child's disease. Neither the form of disease (‘primary’ symptomatic PCH2 or ‘secondary’ symptomatic MLD), nor the severity of the child’s illness (in terms of gross motor and speech function) had a specific impact on HRQOL in families. However, the time from diagnosis and advanced symptoms in the terminal disease stage were experienced as especially distressing. Conclusions This study illustrates that MLD and PCH2 affect mothers in particular, but also the entire family. This underlines the need for personalized care and counselling of parents and families, especially following diagnosis and during the end stage in a child with a severe, rare chronic neurological disorder.
Number processing outside awareness? Systematically testing sensitivities of direct and indirect measures of consciousness
2021-05-10

Abstract In priming research, it is often argued that humans can discriminate stimuli outside consciousness. For example, the semantic meaning of numbers can be processed even when the numbers are so strongly masked that participants are not aware of them. These claims are typically based on a certain pattern of results: Direct measures indicate no conscious awareness of the masked stimuli, while indirect measures show clear priming effects of the same stimuli on reaction times or neurophysiological measures. From this pattern, preserved (unconscious) processing in the indirect task is concluded. However, this widely used standard reasoning is problematic and leads to spurious claims of unconscious processing. Such problems can be avoided by comparing sensitivities of direct and indirect measures. Many studies are affected by these problems, such that a reassessment of the literature is needed. Here, we investigated whether numbers can be processed unconsciously. In three experiments, we replicated and extended well-established effects of number priming over a wide range of stimulus visibilities. We then compared the standard reasoning to a sensitivity analysis, where direct and indirect effects are compared using the same metric. Results show that the sensitivities of indirect measures did not exceed those of direct measures, thereby indicating no evidence for preserved unconscious processing when awareness of the stimuli is low. Instead, it seems that at low visibility there is residual processing that affects direct and indirect measures to a similar degree. This suggests that similar processing modes cause those effects in direct and indirect measures.
Development and Evaluation of Deep Learning-Accelerated Single-Breath-Hold Abdominal HASTE at 3 T Using Variable Refocusing Flip Angles
2021-05-10

Objective Deep learning (DL) reconstruction enables substantial acceleration of image acquisition while maintaining diagnostic image quality. The aims of this study were to overcome the drawback of specific absorption rate (SAR)–related limitations at 3 T and to develop a DL-accelerated single-breath-hold half-Fourier acquisition single-shot turbo spin echo (HASTE) sequence for 2-dimesional T2-weighted fat-suppressed magnetic resonance imaging of the abdomen at 3 T using a variable flip angle (FA) evolution for the refocusing radiofrequency pulses, as well as to evaluate its feasibility and image quality in comparison to state-of-the-art T2-weighted fat-suppressed imaging technique (BLADE). Materials and Methods First, a suitable FA evolution with low cardiac motion–related signal loss (CRSL) and low SAR was determined through a prospective volunteer study with 11 participants. Image quality and diagnostic confidence with 5 different FA evolutions of a HASTE DL were assessed to identify the most suitable FA evolution. Second, the identified FA evolution was implemented clinically and evaluated in 51 patients undergoing a clinically indicated liver magnetic resonance imaging at 3 T. Two radiologists assessed the HASTE DL and standard sequences regarding overall image quality, noise, contrast, sharpness, artifacts, CRSL, and diagnostic confidence using a Likert scale ranging from 1 to 4, with 4 being the best. Comparative analyses were conducted to assess the differences between HASTE DL (acquisition time, 21 seconds; single breath-hold) and the routinely used T2-weighted BLADE sequence (acquisition time, 4 minutes; respiratory triggering). Results From the volunteer study, the FA evolution characterized by the control points 130-90-110-130 degrees (HASTE DL ) was identified as optimal among the 5 evolutions evaluated and was implemented in our clinical protocol. In all 51 patients, HASTE DL was successfully acquired at 3 T and showed excellent image quality (median, 4; interquartile range, 3–4). Although BLADE was rated significantly higher for overall image quality, noise, contrast, sharpness, artifacts, CRSL, and diagnostic confidence than HASTE DL , no differences were found concerning the number (n = 102) and measured diameter of the detected hepatic lesions between the 2 sequences BLADE and HASTE DL . Conclusions The proposed single-breath-hold abdominal HASTE DL with variable refocusing FAs is feasible at 3 T within SAR limits and yields high image quality and diagnostic confidence as compared with a standard T2-weighted acquisition technique, at a 10th of the acquisition time.
Universal Spectrum Explorer: A Standalone (Web-)Application for Cross-Resource Spectrum Comparison
2021-05-10

Here, we present the Universal Spectrum Explorer (USE), a web-based tool based on IPSA for cross-resource (peptide) spectrum visualization and comparison (https://www.proteomicsdb.org/use/). Mass spectra under investigation can be either provided manually by the user (table format) or automatically retrieved from online repositories supporting access to spectral data via the universal spectrum identifier (USI), or requested from other resources and services implementing a newly designed REST interface. As a proof of principle, we implemented such an interface in ProteomicsDB thereby allowing the retrieval of spectra acquired within the ProteomeTools project or real-time prediction of tandem mass spectra from the deep learning framework Prosit. Annotated mirror spectrum plots can be exported from the USE as editable scalable high-quality vector graphics. The USE was designed and implemented with minimal external dependencies allowing local usage and integration into other web sites (https://github.com/kusterlab/universal_spectrum_explorer).
Mass-Transfer-Limited Biodegradation at Low Concentrations—Evidence from Reactive Transport Modeling of Isotope Profiles in a Bench-Scale Aquifer
2021-05-10

Organic contaminant degradation by suspended bacteria in chemostats has shown that isotope fractionation decreases dramatically when pollutant concentrations fall below the (half-saturation) Monod constant. This masked isotope fractionation implies that membrane transfer is slow relative to the enzyme turnover at μg L<sup>-1</sup> substrate levels. Analogous evidence of mass transfer as a bottleneck for biodegradation in aquifer settings, where microbes are attached to the sediment, is lacking. A quasi-two-dimensional flow-through sediment microcosm/tank system enabled us to study the aerobic degradation of 2,6-dichlorobenzamide (BAM), while collecting sufficient samples at the outlet for compound-specific isotope analysis. By feeding an anoxic BAM solution through the center inlet port and dissolved oxygen (DO) above and below, strong transverse concentration cross-gradients of BAM and DO yielded zones of low (μg L<sup>-1</sup>) steady-state concentrations. We were able to simulate the profiles of concentrations and isotope ratios of the contaminant plume using a reactive transport model that accounted for a mass-transfer limitation into bacterial cells, where apparent isotope enrichment factors *ε decreased strongly below concentrations around 600 μg/L BAM. For the biodegradation of organic micropollutants, mass transfer into the cell emerges as a bottleneck, specifically at low (μg L<sup>-1</sup>) concentrations. Neglecting this effect when interpreting isotope ratios at field sites may lead to a significant underestimation of biodegradation.