julilili42/papers huggingface dataset:
The Endometrial Transcription Landscape of MRKH Syndrome
2020-09-24

The Mayer-Rokitansky-Küster-Hauser (MRKH) syndrome (OMIM 277000) is characterized by agenesis of the uterus and upper part of the vagina in females with normal ovarian function. While genetic causes have been identified for a small subset of patients and epigenetic mechanisms presumably contribute to the pathogenic unfolding, too, the etiology of the syndrome has remained largely enigmatic. A comprehensive understanding of gene activity in the context of the disease is crucial to identify etiological components and their potential interplay. So far, this understanding is lacking, primarily due to the scarcity of samples and suitable tissue. In order to close this gap, we profiled endometrial tissue of uterus rudiments in a large cohort of MRKH patients using RNA-seq and thereby provide a genome-wide view on the altered transcription landscape of the MRKH syndrome. Differential and co-expression analyses of the data identified cellular processes and candidate genes that converge on a core network of interconnected regulators that emerge as pivotal for the perturbed expression space. With these results and browsable access to the rich data through an online tool we seek to accelerate research to unravel the underlying biology of the syndrome.
Core Neuropsychological Measures for Obesity and Diabetes Trials: Initial Report
2020-09-24

Obesity and diabetes are known to be related to cognitive abilities. The Core Neuropsychological Measures for Obesity and Diabetes Trials Project aimed to identify the key cognitive and perceptual domains in which performance can influence treatment outcomes, including predicting, mediating, and moderating treatment outcome and to generate neuropsychological batteries comprised of well-validated, easy-to-administer tests that best measure these key domains. The ultimate goal is to facilitate inclusion of neuropsychological measures in clinical studies and trials so that we can gather more information on potential mediators of obesity and diabetes treatment outcomes. We will present the rationale for the project and three options for the neuropsychological batteries to satisfy varying time and other administration constraints. Future directions are discussed. Preprint version of the document is available at https://osf.io/preprints/nutrixiv/7jygx/.
Long-term effects of a food pattern on cardiovascular risk factors and age-related changes of muscular and cognitive function
2020-09-24

Abstract Introduction: The mean age of the German population increased over the last years, which resulted in a higher prevalence of cardiovascular diseases, type 2 diabetes, cognitive impairment, sarcopenia and bone fractures. Current evidence indicates a preservation of human wellbeing in the elderly by a healthy diet, although the recommended macronutrient composition and quality remains unclear and needs further long-term investigation. In this context we investigate the effect of a specific dietary pattern on age-related disorders in a randomized controlled multi-center trial (RCT). Methods: We assess the effect of a specific dietary pattern (NutriAct) with a high proportion of unsaturated fat, plant proteins and fibres (fat 35%–40% of total energy (%E) of which 15%E–20%E monounsaturated fatty acids (MUFA) and 10%E–15%E polyunsaturated fatty acids (PUFA), 15%E–25%E proteins, ≥30 g fibres per day and 35%E–45%E carbohydrates) on age-related impairment of health within a 36-months RCT conducted in the region of Berlin and Potsdam. 502 eligible men (n = 183) and women (n = 319), aged 50 to 80 years, with an increased risk to develop age-related diseases were randomly assigned to either an intervention group focusing on NutriAct dietary pattern or a control group focusing on usual care and dietary recommendations in accordance to the German Nutrition Society (DGE). In the intervention group, 21 nutrition counsellings as well as supplementation of rapeseed oil, oil cake and specific designed foods are used to achieve the intended NutriAct dietary pattern. The primary outcome is a composite endpoint of age-related disorders, including cardiovascular morbidity, decline of cognitive function as well as clinical features of sarcopenia. Secondary outcomes include diet-induced effects on quality of life, depression, frailty, cardiovascular function, bone density, fat distribution pattern, glucose, lipid and energy metabolism, as well as the identification of biomarkers linked with age-related disorders. Discussion: The findings of this trial will provide clinically relevant information regarding dietary effects on age-related impairment of health and will contribute to the definition of the optimal macronutrient composition in the context of healthy aging in the German population.
Gene and Protein Expression in Subjects With a Nystagmus-Associated AHR Mutation
2020-09-24

Recently, a consanguineous family was identified in Israel with three children affected by Infantile Nystagmus and Foveal Hypoplasia, following an autosomal recessive mode of inheritance. A homozygous stop mutation c.1861C > T; p.Q621<sup>∗</sup> in the aryl hydrocarbon receptor (<i>AHR</i>) gene (<i>AHR</i>; MIM 600253) was identified that co-segregated with the disease in the larger family. AHR is the first gene to be identified causing an autosomal recessive Infantile Nystagmus-related disease in humans. The goal of this study is to delineate the molecular basis of this newly discovered human genetic disorder associated with a rare <i>AHR</i> gene mutation. The gene and protein expression levels of <i>AHR</i> and selected <i>AHR</i> targets from leukocyte cultures of healthy subjects and the patients were analyzed. We observed significant variation between mRNA and protein expression of CYP1A1, CYP1B1, and TiPARP under rest and AHR-induced conditions. The CYP1A1 enzymatic activity in induced leukocytes also differs significantly between the patients and healthy volunteers. Intriguingly, the heterozygous subjects demonstrate CYP1A1 and TiPARP gene and protein expression similar to homozygous patients. In contrast, CYP1B1 inducibility and expression vary between hetero- and homozygous subjects. Similarity and differences in gene and protein expression between heterozygotes and homozygous patients can give us a hint as to which metabolic pathway/s might be involved in the Nystagmus etiology. Thus, we have a unique human model for AHR deficiency that will allow us the opportunity to study the biochemical basis of this rare human mutation, as well as the involvement of AHR in other physiological processes.
A neural correlate of sensory consciousness in a corvid bird
2020-09-25

Consciousness shared Humans have tended to believe that we are the only species to possess certain traits, behaviors, or abilities, especially with regard to cognition. Occasionally, we extend such traits to primates or other mammals—species with which we share fundamental brain similarities. Over time, more and more of these supposed pillars of human exceptionalism have fallen. Nieder et al. now argue that the relationship between consciousness and a standard cerebral cortex is another fallen pillar (see the Perspective by Herculano-Houzel). Specifically, carrion crows show a neuronal response in the palliative end brain during the performance of a task that correlates with their perception of a stimulus. Such activity might be a broad marker for consciousness. Science , this issue p. 1626 ; see also p. 1567
Retrieving scattering clouds and disequilibrium chemistry in the atmosphere of HR 8799e
2020-09-25

Context. Clouds are ubiquitous in exoplanet atmospheres and they represent a challenge for the model interpretation of their spectra. When generating a large number of model spectra, complex cloud models often prove too costly numerically, whereas more efficient models may be overly simplified. Aims. We aim to constrain the atmospheric properties of the directly imaged planet HR 8799e with a free retrieval approach. Methods. We used our radiative transfer code petitRADTRANS for generating the spectra, which we coupled to the PyMultiNest tool. We added the effect of multiple scattering which is important for treating clouds. Two cloud model parameterizations are tested: the first incorporates the mixing and settling of condensates, the second simply parameterizes the functional form of the opacity. Results. In mock retrievals, using an inadequate cloud model may result in atmospheres that are more isothermal and less cloudy than the input. Applying our framework on observations of HR 8799e made with the GPI, SPHERE, and GRAVITY, we find a cloudy atmosphere governed by disequilibrium chemistry, confirming previous analyses. We retrieve that . Other models have not yet produced a well constrained C/O value for this planet. The retrieved C/O values of both cloud models are consistent, while leading to different atmospheric structures: either cloudy or more isothermal and less cloudy. Fitting the observations with the self-consistent Exo-REM model leads to comparable results, without constraining C/O. Conclusions. With data from the most sensitive instruments, retrieval analyses of directly imaged planets are possible. The inferred C/O ratio of HR 8799e is independent of the cloud model and thus appears to be a robust. This C/O is consistent with stellar, which could indicate that the HR 8799e formed outside the CO2 or CO iceline. As it is the innermost planet of the system, this constraint could apply to all HR 8799 planets.
Enzyme-Constrained Models and Omics Analysis of Streptomyces coelicolor Reveal Metabolic Changes that Enhance Heterologous Production.
2020-09-25

Many biosynthetic gene clusters (BGCs) require heterologous expression to realize their genetic potential, including silent and metagenomic BGCs. Although the engineered <i>Streptomyces coelicolor</i> M1152 is a widely used host for heterologous expression of BGCs, a systemic understanding of how its genetic modifications affect the metabolism is lacking and limiting further development. We performed a comparative analysis of M1152 and its ancestor M145, connecting information from proteomics, transcriptomics, and cultivation data into a comprehensive picture of the metabolic differences between these strains. Instrumental to this comparison was the application of an improved consensus genome-scale metabolic model (GEM) of <i>S. coelicolor</i>. Although many metabolic patterns are retained in M1152, we find that this strain suffers from oxidative stress, possibly caused by increased oxidative metabolism. Furthermore, precursor availability is likely not limiting polyketide production, implying that other strategies could be beneficial for further development of <i>S. coelicolor</i> for heterologous production of novel compounds.
Cerium Pyrazolates Grafted onto Mesoporous Silica SBA-15: Reversible CO2 Uptake and Catalytic Cycloaddition of Epoxides and Carbon Dioxide
2020-09-25

The activation and catalytic conversion of CO<sub>2</sub> is a current topic relating to molecular chemistry and materials science alike. As a transdisciplinary field of research, surface organometallic chemistry (SOMC) might be applicable to perform synergistically, thus striking a new path in sustainable chemistry. Both ceric and cerous rare-earth-metal pyrazolates, which were recently shown to reversibly insert CO<sub>2</sub> and to promote the catalytic cycloaddition of epoxides and carbon dioxide, were grafted onto large-pore mesoporous silica SBA-15<sub>500</sub>, thermally pretreated at 500 °C. The obtained hybrid materials [Ce(Me<sub>2</sub>pz)<sub>4</sub>]<sub>2</sub>@SBA-15<sub>500</sub>, Ce(Me<sub>2</sub>pz)<sub>4</sub>(thf)@SBA-15<sub>500</sub>, Ce<sub>4</sub>(Me<sub>2</sub>pz)<sub>12</sub>@SBA-15<sub>500</sub>, and [Ce(Me<sub>2</sub>pz)<sub>3</sub>(thf)]<sub>2</sub>@SBA-15<sub>500</sub> (Me<sub>2</sub>pz = 3,5-dimethylpyrazolato) were characterized by DRIFTS (diffuse reflectance infrared Fourier transform spectroscopy), solid-state <sup>1</sup>H/<sup>13</sup>C NMR spectroscopy, elemental analysis, ICP/OES, and N<sub>2</sub> physisorption. The lanthanum(III)-based material [La(Me<sub>2</sub>pz)<sub>3</sub>(thf)]<sub>2</sub>@SBA-15<sub>500</sub> was synthesized for better assessment of the cerous materials being highly sensitive to oxidation. To mimic ceric surface species, Ce[OSi(O<i>t</i>Bu)<sub>3</sub>]<sub>3</sub>Cl was treated with 1 equiv of K(Me<sub>2</sub>pz), generating the mixed pyrazolyl/siloxy complex KCe[OSi(O<i>t</i>Bu)<sub>3</sub>]<sub>4</sub>(Me<sub>2</sub>pz) featuring a cerium(IV)-bonded terminal pyrazolato ligand. All hybrid materials show efficient and reversible carbon dioxide uptake of maximum 20 wt % in the solid state. When combined with tetra-<i>n</i>-butylammonium bromide (TBAB), the hybrid materials catalyze the cycloaddition of CO<sub>2</sub> and epoxides, displaying good conversion of various epoxides and reusability.
Academisation of the Midwifery Profession and the Implementation of Higher Education in the Context of the New Requirements for Licensure
2020-09-25

Abstract The academization of the midwifery profession poses great challenges for Germany, especially due to the tight timelines: Corresponding courses of study can in principle be offered at both universities and technical colleges – although contrary to the recommendations of the Science Council. This means that there is a heterogeneity in midwifery qualifications and promotes a discussion regarding coherent study concepts. This process must be accompanied with great care so that midwifery courses of study are not designed to be of poorer quality than other courses of study due to a lack of financial resources. First concepts are already available and will be discussed and examined below.
Comparison of environmental tracers including organic micropollutants as groundwater exfiltration indicators into a small river of a karstic catchment
2020-09-25

Abstract Understanding groundwater–surface water (GW–SW) interactions is vital for water management in karstic catchments due to its impact on water quality. The objective of this study was to evaluate and compare the applicability of seven environmental tracers to quantify and localize groundwater exfiltration into a small, human‐impacted karstic river system. Tracers were selected based on their emission source to the surface water either as (a) dissolved, predominantly geogenic compounds (radon‐222, sulphate and electrical conductivity) or (b) anthropogenic compounds (predominantly) originating from wastewater treatment plant (WWTP) effluents (carbamazepine, tramadol, sodium, chloride). Two contrasting sampling approaches were compared (a) assuming steady‐state flow conditions and (b) considering the travel time of the water parcels (Lagrangian sampling) through the catchment to account for diurnal changes in inflow from the WWTP. Spatial variability of the concentrations of all tracers indicated sections of preferential groundwater inflow. Lagrangian sampling techniques seem highly relevant for capturing dynamic concentration patterns of WWTP‐derived compounds. Quantification of GW inflow with the finite element model FINIFLUX, based on observed in‐stream Rn activities led to plausible fluxes along the investigated river reaches (0.265 m 3 s −1 ), while observations of other natural or anthropogenic environmental tracers produced less plausible water fluxes. Important point sources of groundwater exfiltration can be ascribed to locations where the river crosses geological fault lines. This indicates that commonly applied concepts describing groundwater–surface water interactions assuming diffuse flow in porous media are difficult to transfer to karstic river systems whereas concepts from fractured aquifers may be more applicable. In general, this study helps selecting the best suited hydrological tracer for GW exfiltration and leads to a better understanding of processes controlling groundwater inflow into karstic river systems.
Exploring the role of individual learning in animal tool-use
2020-09-25

The notion that tool-use is unique to humans has long been refuted by the growing number of observations of animals using tools across various contexts. Yet, the mechanisms behind the emergence and sustenance of these tool-use repertoires are still heavily debated. We argue that the current animal behaviour literature is biased towards a social learning approach, in which animal, and in particular primate, tool-use repertoires are thought to require social learning mechanisms (copying variants of social learning are most often invoked). However, concrete evidence for a widespread dependency on social learning is still lacking. On the other hand, a growing body of observational and experimental data demonstrates that various animal species are capable of acquiring the forms of their tool-use behaviours via individual learning, with (non-copying) social learning regulating the frequencies of the behavioural forms within (and, indirectly, between) groups. As a first outline of the extent of the role of individual learning in animal tool-use, a literature review of reports of the spontaneous acquisition of animal tool-use behaviours was carried out across observational and experimental studies. The results of this review suggest that perhaps due to the pervasive focus on social learning in the literature, accounts of the individual learning of tool-use forms by naïve animals may have been largely overlooked, and their importance under-examined.
Special Report on the Impact of the COVID-19 Pandemic on Clinical EEG and Research and Consensus Recommendations for the Safe Use of EEG
2020-09-25

Introduction The global COVID-19 pandemic has affected the economy, daily life, and mental/physical health. The latter includes the use of electroencephalography (EEG) in clinical practice and research. We report a survey of the impact of COVID-19 on the use of clinical EEG in practice and research in several countries, and the recommendations of an international panel of experts for the safe application of EEG during and after this pandemic. Methods Fifteen clinicians from 8 different countries and 25 researchers from 13 different countries reported the impact of COVID-19 on their EEG activities, the procedures implemented in response to the COVID-19 pandemic, and precautions planned or already implemented during the reopening of EEG activities. Results Of the 15 clinical centers responding, 11 reported a total stoppage of all EEG activities, while 4 reduced the number of tests per day. In research settings, all 25 laboratories reported a complete stoppage of activity, with 7 laboratories reopening to some extent since initial closure. In both settings, recommended precautions for restarting or continuing EEG recording included strict hygienic rules, social distance, and assessment for infection symptoms among staff and patients/participants. Conclusions The COVID-19 pandemic interfered with the use of EEG recordings in clinical practice and even more in clinical research. We suggest updated best practices to allow safe EEG recordings in both research and clinical settings. The continued use of EEG is important in those with psychiatric diseases, particularly in times of social alarm such as the COVID-19 pandemic.
Solid‐State Preparation and Luminescence Investigation of Rare Earth Iodide Carbodiimide Nitrides RE2I(CN2)N (RE = La, Gd) and LaI(CN2)
2020-09-25

New rare earth iodide carbodiimide nitride compounds with the composition RE 2 I(CN 2 )N (RE = La, Gd) were successfully synthesized by multilateral solid‐state metathesis reaction from RE triiodides, LiN and Li 2 (CN 2 ). The crystal structures of RE 2 I(CN 2 )N were refined from X‐ray powder diffraction data with the space group Cmmm . LaI(CN 2 ) was prepared from a mixture of LaI 3 and Li 2 (CN 2 ). The crystal structure was determined by X‐ray single‐crystal diffraction on a colorless crystal with the orthorhombic space group Cmcm . The luminescence investigation of Ce 3+ ‐doped LaI(CN 2 ) was carried out by excitation at 390 nm and reveals a broad emission band in the blue range of the visible spectrum.
GBA-Associated Synucleinopathies: Prime Candidates for Alpha-Synuclein Targeting Compounds
2020-09-25

With disease-modifying compounds targeting alpha-synuclein available in clinical trials, patient stratification according to alpha-synuclein-specific enrichment strategies is a much-needed prerequisite. Such a scenario will be exemplified for <i>GBA</i>, one major genetic risk factor that is specifically associated with the alpha-synucleinopathies: Parkinson's disease and dementia with Lewy bodies.
Case Report First-in-Man Method Description: Left Ventricular Unloading With iVAC2L During Veno-Arterial Extracorporeal Membrane Oxygenation: From Veno-Arterial Extracorporeal Membrane Oxygenation to ECMELLA to EC-iVAC®
2020-09-25

Veno-arterial extracorporeal membrane oxygenation (V-A ECMO) is increasingly used in bi-ventricular failure with cardiogenic shock to maintain systemic perfusion. Nonetheless, it tends to increase left ventricular (LV) afterload and myocardial oxygen demand. In order to mitigate these negative effects on the myocardium, an Impella CP® (3.5 L/min Cardiac Output) can be used in conjunction with V-A ECMO (ECMELLA approach). We implemented this strategy in a patient with severe acute myocarditis complicated by cardiogenic shock. Due to a hemolysis crisis, Impella CP® had to be substituted with PulseCath iVAC2L®, which applies pulsatile flow to unload the LV. A subsequent improvement in LV systolic function was noted, with increased LV ejection fraction (LVEF), LV end-diastolic diameter (LVEDD) reduction, and a reduction in plasma free hemoglobin. This case documents the efficacy of iVAC2L in replacing Impella CP as a LV vent during V-A ECMO, with less hemolysis.
Images of the unseen: Extrapolating visual representations for abstract and concrete words in a data-driven computational model
2020-09-25

Theories of grounded cognition assume that conceptual representations are grounded in sensorimotor experience. However, abstract concepts such as jealousy or childhood have no directly associated referents with which such sensorimotor experience can be made; therefore, the grounding of abstract concepts has long been a topic of debate. Here, we propose (a) that systematic relations exist between semantic representations learned from language on the one hand and perceptual experience on the other hand, (b) that these relations can be learned in a bottom-up fashion, and (c) that it is possible to extrapolate from this learning experience to predict expected perceptual representations for words even where direct experience is missing. To test this, we implement a data-driven computational model that is trained to map language-based representations (obtained from text corpora, representing language experience) onto vision-based representations (obtained from an image database, representing perceptual experience), and apply its mapping function onto language-based representations for abstract and concrete words outside the training set. In three experiments, we present participants with these words, accompanied by two images: the image predicted by the model and a random control image. Results show that participants' judgements were in line with model predictions even for the most abstract words. This preference was stronger for more concrete items and decreased for the more abstract ones. Taken together, our findings have substantial implications in support of the grounding of abstract words, suggesting that we can tap into our previous experience to create possible visual representation we don't have.