julilili42/papers huggingface dataset:
First large‐scale provenance study of pigments reveals new complex behavioural patterns during the Upper Palaeolithic of south‐western Germany
2020-09-28

The use of red iron‐based earth pigments, or ochre, is a key component of early symbolic behaviours for anatomically modern humans and possibly Neanderthals. We present the first ochre provenance study in Central Europe showing long‐term selection strategies by inhabitants of cave sites in south‐western Germany during the Upper Palaeolithic (43–14.5 ka). Ochre artefacts from Hohle Fels, Geißenklösterle and Vogelherd, and local and extra‐local sources, were investigated using neutron activation analysis (NAA), X‐ray diffraction (XRD) and scanning electron microscopy (SEM). The results show that local ochre sources were continuously and systematically accessed for c .29 500 years, with periodic events of long‐distance (about &gt; 300 km) ochre acquisition during the Aurignacian ( c .35–43 ka), suggesting higher mobility than previously suspected. The results reveal previously unknown long‐term, complex spatio‐temporal behavioural patterns during the earliest presence of Homo sapiens in Europe.
Work-Related Psychosocial Demands and Resources in General Practice Teams in Germany. A Team-Based Ethnography
2020-09-28

General practices are established microenterprises in Germany providing a variety of preventive and therapeutic health care services and procedures in a challenging working environment. For example, general practice teams are confronted increasingly with work-related demands, which have been associated with poor psychological and physical outcomes. It is therefore important to gain a better understanding of issues related to occupational health and safety for personnel working in the primary care setting. This study aims to gain an in-depth understanding of psychosocial demands and resources in the primary care setting. We applied an ethnographic design, comprising a combination of participating observations, individual interviews with general practitioners (GPs) (N = 6), and focus group discussion with practice assistants and administrative staff (N = 19) in five general practices in Germany. A grounded theory approach was applied to analyze all data. Our results identified psychosocial demands and resources exemplified mainly along two typical tasks in GP practices: the issuing of medical prescriptions and blood sampling. Main psychosocial demands included factors related to work content and tasks, organization of work, and the working environment. For example, daily routines across all practices were characterized by a very high work intensity including disturbances, interruptions, delegation, and the division of labor between GPs and practice staff. Work-related resources comprised the staff’s influence on aspects related to work organization and social support. The triangulation of methods and data formats allowed the disclosure of interconnectedness between these factors. Although work processes in general practices are complex and required to comply with legal regulations, there are opportunities for practice owners and practice teams to establish working procedures in ways that reduce psychosocial risks and strengthen work-related resources.
ColwelliaandMarinobactermetapangenomes reveal species-specific responses to oil and dispersant exposure in deepsea microbial communities
2020-09-28

Abstract Over 7 million liters of Corexit EC9500A and EC9527A were applied to the Gulf of Mexico in response to the Deepwater Horizon oil spill. The impacts of dispersants remain under debate and negative, positive, and inconclusive impacts have been reported. Here, metatrancriptomics was applied in the context of metapangenomes to microcosms that simulated environmental conditions comparable to the hydrocarbon-rich 1,100 m deep plume. Within this microcosm study, negative effects of dispersants on microbial hydrocarbon degradation were previously reported based on activity measurements and geochemical data. Transcriptional enrichment of Colwellia , a potential dispersant degrader, followed variable time-dependent trajectories due to interactions between oil, dispersants, and nutrients. The Colwellia metapangenome captured a mixture of environmental responses linked to the Colwellia psychrerythraea 34H genome and to the genomes of other members of the Colwellia genus. The activation of genes involved in lipid degradation, nitrogen metabolism, and membrane composition under oil or nutrient availability, suggested an opportunistic growth strategy for Colwellia . In contrast, transcripts of Marinobacter , a natural hydrocarbon degrader, increased only in oil treatments. Marinobacter transcripts largely recruited to the accessory metapangenome of Marinobacter sp. C18, the closest genomic reference. A complex response involving carbon and lipid metabolism, chemotaxis and a type IV secretion system suggested active energy-dependent processes in Marinobacter . These findings highlight chemistry-dependent responses in the metabolism of key hydrocarbon-degrading bacteria and underscore that dispersant-driven selection could temper the ability of the community to respond to hydrocarbon injection.
Pregnant women do not display impaired memory formation across one night of sleep
2020-09-28

Abstract Forgetfulness is a common complaint of pregnant women, who also often report impaired nocturnal sleep. Considering sleep's well‐known beneficial role in consolidating newly encoded memory content, we hypothesized that pregnant women would display detrimental changes in objective sleep measures and associated memory deficits. We compared the consolidation of declarative as well as procedural memory across sleep in 21 healthy, third‐trimester pregnant women versus 20 matched non‐pregnant controls. Subjects encoded and were tested on visuospatial and procedural memory tasks before and after, respectively, a night of sleep spent at home. The emergence of gist‐based memories was tested with the Deese‐Roediger‐McDermott (DRM) paradigm. Sleep was polysomnographically recorded and subjective sleep quality was assessed with questionnaires. Although pregnant in comparison to non‐pregnant women reported markedly impaired subjective sleep quality and efficiency, quantitative changes were limited to increases in wakefulness after sleep onset and reductions in rapid eye movement (REM) sleep. Retention of newly learned memory contents, which is believed to reflect sleep‐associated memory consolidation, was comparable between groups, as was the formation of gist‐based memories. The findings indicate that subjective deteriorations in sleep quality experienced by pregnant women are not necessarily linked to objective impairments. They raise the possibility that sufficient slow wave sleep towards the end of pregnancy allows for normal sleep‐related memory consolidation. Although these results were obtained in a small number of pregnant women in very good health and should be corroborated in larger samples, they challenge the assumption of poor sleep and impaired memory as hallmarks of the “pregnancy brain”.
FHL-1 interacts with human RPE cells through the α5β1 integrin and confers protection against oxidative stress
2020-09-28

Abstract Retinal pigment epithelial (RPE) cells that underlie the neurosensory retina are essential for the maintenance of photoreceptor cells and hence vision. Interactions between the RPE and their basement membrane, i.e . the inner layer of Bruch’s membrane, are essential for RPE cell health and function, but the signals induced by Bruch’s membrane engagement, and their contributions to RPE cell fate determination remain poorly defined. Here, we studied the functional role of the soluble complement regulator and component of Bruch’s membrane, Factor H-like protein 1 (FHL-1). Human primary RPE cells adhered to FHL-1 in a manner that was eliminated by either mutagenesis of the integrin-binding RGD motif in FHL-1 or by using competing antibodies directed against the α5 and β1 integrin subunits. The results obtained from primary RPE cells were replicated using the hTERT-RPE cell line. RNAseq expression analysis of hTERT-RPE cells bound to FHL-1 showed an increased expression of the heat-shock protein genes HSPA6, CRYAB, HSPA1A and HSPA1B when compared to cells bound to fibronectin (FN) or laminin (LA). Pathway analysis implicated changes in EIF2 signalling, the unfolded protein response, and mineralocorticoid receptor signalling as putative pathways. Subsequent cell survival assays using H 2 O 2 to induce oxidative stress-induced cell death showed hTERT-RPE cells had significantly greater protection when bound to FHL-1 or LA compared to plastic or FN. These data show a non-canonical role of FHL-1 in protecting RPE cells against oxidative stress and identifies a novel interaction that has implications for ocular diseases such as age-related macular degeneration.
Assessing the Influence of Soil Quality on Rainfed Wheat Yield
2020-09-28

Soil quality assessment based on crop yields and identification of key indicators of it can be used for better management of agricultural production. In the current research, the weighted additive soil quality index (SQIw), factor analysis (FA) and multiple linear regression (MLR) method are used to assess the soil quality of rainfed winter wheat fields with two soil orders on 53.20 km2 of agricultural land in western Iran. A total of 18 soil quality indicators were determined for 100 soil samples (0-20 cm depth) from two soil orders (Inceptisols and Entisols). The soil properties measured were: pH, soil texture, organic carbon (OC), cation exchange capacity (CEC), electrical conductivity (EC), soil microbial respiration (SMR), carbonate calcium equivalent (CCE), soil porosity (SP), bulk density (BD), exchangeable sodium percentage (ESP), mean weight diameter (MWD), available potassium (AK), total nitrogen (TN), available phosphorus (AP), available Fe (AFe), available Zn (AZn), available Mn (AMn), and available Cu (ACu). Mean wheat grain yield for the two years for all of the 100 sampling sites was also gathered. The SQIw was calculated using two weighting methods (FA and MLR) and maps were created using a digital soil mapping framework. The soil indicators taken in the minimum data set (MDS) were AK, clay, CEC, AP, SMR, and sand. The correlation between the MLR weighting technique (SQI-M) and the rainfed wheat yield (r=0.62) was slightly larger than that the correlation of yield with the FA weighted technique (SQI-F) (r=0.58). Results showed that the means of both SQI-M and SQI-F and rainfed wheat yield for Inceptisols were higher than for Entisols although these differences were not statistically significant. Both SQI-M and SQI-F showed that areas with Entisols had lower proportions of good soil quality grades (Grade I and II), and higher proportions of poor soil quality grades (Grade IV and V) compared to Inceptisols. Based on these results, soil type must be considered for soil quality assessment in future studies to maintain and enhance soil quality and sustainable production. The overall soil quality of the study region was of poor and moderate grades. To improve soil quality, it is therefore recommended that effective practices such as the implementation of scientific integrated nutrient management involving the combined use of organic and inorganic fertilizers in rainfed wheat fields be promoted.
Seven-day Fasting as a multimodal complex interventionfor Adults with Type 1 Diabetes –&nbsp;Feasibility, Benefit and Safety in a Controlled Pilot StudyFeasibility of Fasting for Adults with Type 1 Diabetes&nbsp;
2020-09-28

Abstract Aims/Hypothesis: Intermittent as well as prolonged fasting are receiving considerable attention and appear favorable in conditions like the metabolic syndrome, type 2 diabetes, rheumatic diseases and others. Fasting for people with type 1 diabetes is generally considered too risky. However, the ability and possibility to change from carbohydrate to ketone-based fuel supply might also be relevant for people with type 1 diabetes. The aim of this patient-led research was to investigate the feasibility, benefit and safety of a seven-day multimodal fasting intervention in people with type 1 diabetes. Methods: A non-randomized controlled pilot study, with 20 participants with and 10 without type 1 diabetes. Data acquisition took place prior, post and four months after the intervention and daily during intervention. Results: 29 of 30 participants finished the intervention. Mean ß-hydroxybutyrate as representative ketone body increased to 2.8 ± 1.9 mmol/L on day 7 while average glucose remained between 4.9 ± 1.5 to 7.5 ± 2.3 mmol/L [89 ± 27 and 136 ± 40 mg/dL]. Fasting-related side effects were all temporary, and slightly more prevalent in those with type 1 diabetes. Mean daily insulin dose was adjusted from 24.4 (3-50) IU on the day before fasting to 7.6 (0-26.7) IU on day 7. Quality of life (WHO-5) normalized from 54.0 ± 4.4 to 68.8 ± 15.0 (p = 0.01) after fasting. There was a decrease from before until the follow-up four month later of weight from 77.6 ± 20.4 kg to 76.6 ± 20.9 kg (p = 0.023) and for the BMI from (27.68 ± 7.04) to (26.74 ± 7.15) kg/m 2 (p = 0.008). Diastolic blood pressure increased from 69.75 ± 11.41 mmHg to 75.74 ± 8.42 mmHg (p = 0.028) and stayed in a healthy range on average. Conclusions/Interpretation: This study demonstrates the feasibility, benefits and safety aspects of a 7-day fast in adults with type 1 diabetes.
Role of SGK1 in the Osteogenic Transdifferentiation and Calcification of Vascular Smooth Muscle Cells Promoted by Hyperglycemic Conditions
2020-09-29

In diabetes mellitus, hyperglycemia promotes the osteogenic transdifferentiation of vascular smooth muscle cells (VSMCs) to enhance medial vascular calcification, a common complication strongly associated with cardiovascular disease and mortality. The mechanisms involved are, however, still poorly understood. Therefore, the present study explored the potential role of serum- and glucocorticoid-inducible kinase 1 (SGK1) during vascular calcification promoted by hyperglycemic conditions. Exposure to high-glucose conditions up-regulated the SGK1 expression in primary human aortic VSMCs. High glucose increased osteogenic marker expression and activity and, thus, promoted the osteogenic transdifferentiation of VSMCs, effects significantly suppressed by additional treatment with the SGK1 inhibitor EMD638683. Moreover, high glucose augmented the mineralization of VSMCs in the presence of calcification medium, effects again significantly reduced by SGK1 inhibition. Similarly, SGK1 knockdown blunted the high glucose-induced osteogenic transdifferentiation of VSMCs. The osteoinductive signaling promoted by high glucose required SGK1-dependent NF-κB activation. In addition, advanced glycation end products (AGEs) increased the SGK1 expression in VSMCs, and SGK1 inhibition was able to interfere with AGEs-induced osteogenic signaling. In conclusion, SGK1 is up-regulated and mediates, at least partly, the osteogenic transdifferentiation and calcification of VSMCs during hyperglycemic conditions. Thus, SGK1 inhibition may reduce the development of vascular calcification promoted by hyperglycemia in diabetes.
Blocking Y-Box Binding Protein-1 through Simultaneous Targeting of PI3K and MAPK in Triple Negative Breast Cancers
2020-09-29

The multifunctional protein Y-box binding protein-1 (YB-1) regulates all the so far described cancer hallmarks including cell proliferation and survival. The MAPK/ERK and PI3K/Akt pathways are also the major pathways involved in cell growth, proliferation, and survival, and are the frequently hyperactivated pathways in human cancers. A gain of function mutation in KRAS mainly leads to the constitutive activation of the MAPK pathway, while the activation of the PI3K/Akt pathway occurs either through the loss of PTEN or a gain of function mutation of the catalytic subunit alpha of PI3K (PIK3CA). In this study, we investigated the underlying signaling pathway involved in YB-1 phosphorylation at serine 102 (S102) in KRAS(G13D)-mutated triple-negative breast cancer (TNBC) MDA-MB-231 cells versus PIK3CA(H1047R)/PTEN(E307K) mutated TNBC MDA-MB-453 cells. Our data demonstrate that S102 phosphorylation of YB-1 in KRAS-mutated cells is mainly dependent on the MAPK/ERK pathway, while in PIK3CA/PTEN-mutated cells, YB-1 S102 phosphorylation is entirely dependent on the PI3K/Akt pathway. Independent of the individual dominant pathway regulating YB-1 phosphorylation, dual targeting of MEK and PI3K efficiently inhibited YB-1 phosphorylation and blocked cell proliferation. This represents functional crosstalk between the two pathways. Our data obtained from the experiments, applying pharmacological inhibitors and genetic approaches, shows that YB-1 is a key player in cell proliferation, clonogenic activity, and tumor growth of TNBC cells through the MAPK and PI3K pathways. Therefore, dual inhibition of these two pathways or single targeting of YB-1 may be an effective strategy to treat TNBC.
Entanglement statistics in Markovian open quantum systems: A matter of mutation and selection
2020-09-29

Controlling dynamical fluctuations in open quantum systems is essential both for our comprehension of quantum nonequilibrium behavior and for its possible application in near-term quantum technologies. However, understanding these fluctuations is extremely challenging due, to a large extent, to a lack of efficient important sampling methods for quantum systems. Here, we devise a unified framework-based on population-dynamics methods-for the evaluation of the full probability distribution of generic time-integrated observables in Markovian quantum jump processes. These include quantities carrying information about genuine quantum features, such as quantum superposition or entanglement, not accessible with existing numerical techniques. The algorithm we propose provides dynamical free-energy and entropy functionals which, akin to their equilibrium counterpart, permit one to unveil intriguing phase-transition behavior in quantum trajectories. We discuss some applications and further disclose coexistence and hysteresis, between a highly entangled phase and a low entangled one, in large fluctuations of a strongly interacting few-body system.
Global Analysis of the Mammalian MHC class I Immunopeptidome at the Organism-Wide Scale
2020-09-29

ABSTRACT Understanding the molecular principles that govern the composition of the mammalian MHC-I immunopeptidome (MHC-Ii) across different primary tissues is fundamentally important to predict how T cell respond in different contexts in vivo . Here, we performed a global analysis of the mammalian MHC-Ii from 29 and 19 primary human and mouse tissues, respectively. First, we observed that different HLA-A, -B and -C allotypes do not contribute evenly to the global composition of the MHC-Ii across multiple human tissues. Second, we found that peptides that are presented in a tissue-dependent and -independent manner share very distinct properties. Third, we discovered that proteins that are evolutionarily hyperconserved represent the primary source of the MHC-Ii at the organism-wide scale. Finally, we uncovered new components of the antigen processing and presentation network that may drive the high level of heterogeneity of the MHC-Ii across different tissues in mammals. This study opens up new avenues toward a system-wide understanding of antigen presentation in vivo and may serve as ground work to understand tissue-dependent T cell responses in autoimmunity, infectious diseases and cancer.
Staphylococcus aureus Releases Proinflammatory Membrane Vesicles To Resist Antimicrobial Fatty Acids
2020-09-30

The nares of one in three humans are colonized by Staphylococcus aureus . In these environments, and arguably on all mucosal surfaces, bacteria encounter fatty acids with antimicrobial properties. Our study uncovers that S. aureus releases membrane vesicles (MVs) that act as decoys to protect the bacterium against antimicrobial fatty acids (AFAs). The AFA-neutralizing effects of MVs were neither strain specific nor restricted to one particular AFA. Hence, MVs may represent “public goods” playing an overlooked role in shaping bacterial communities in AFA-rich environments such as the skin and nose. Intriguingly, in addition to MV biogenesis, S. aureus modulates MV composition in response to exposure to AFAs, including an increased release of lipoproteins. These MVs strongly stimulate the innate immunity via Toll-like receptor 2 (TLR2). TLR2-mediated inflammation, which helps to fight infections, may exacerbate inflammatory disorders like atopic dermatitis. Our study highlights intricate immune responses preventing infections from colonizing bacteria.
ipA-MedGAN: Inpainting of Arbitrary Regions in Medical Imaging
2020-09-30

Local deformations in medical modalities are common phenomena due to a multitude of factors such as metallic implants or limited field of views in magnetic resonance imaging (MRI). Completion of the missing or distorted regions is of special interest for automatic image analysis frameworks to enhance post-processing tasks such as segmentation or classification. In this work, we propose a new generative framework for medical image inpainting, titled ipA-MedGAN. It bypasses the limitations of previous frameworks by enabling inpainting of arbitrary shaped regions without a prior localization of the regions of interest. Thorough qualitative and quantitative comparisons with other inpainting and translational approaches have illustrated the superior performance of the proposed framework for the task of brain MR inpainting.
The electrophysiological underpinnings of variation in verbal working memory capacity
2020-09-30

Abstract Working memory (WM) consists of short-term storage and executive components. We studied cortical oscillatory correlates of these two components in a large sample of 156 participants to assess separately the contribution of them to individual differences in WM. The participants were presented with WM tasks of above-average complexity. Some of the tasks required only storage in WM, others required storage and mental manipulations. Our data indicate a close relationship between frontal midline theta, central beta activity and the executive components of WM. The oscillatory counterparts of the executive components were associated with individual differences in verbal WM performance. In contrast, alpha activity was not related to the individual differences. The results demonstrate that executive components of WM, rather than short-term storage capacity, play the decisive role in individual WM capacity limits.
Advanced Fusion Imaging and Contrast-Enhanced Imaging (CT/MRI–CEUS) in Oncology
2020-09-30

Fusion imaging depicts an innovative technique that facilitates combining assets and reducing restrictions of advanced ultrasound and cross-sectional imaging. The purpose of the present retrospective study was to evaluate the role of fusion imaging for assessing hepatic and renal lesions. Between 02/2011–08/2020, 92 patients in total were included in the study, of which 32 patients had hepatic lesions, 60 patients had renal lesions. Fusion imaging was technically successful in all patients. No adverse side effects upon intravenous (i.v.) application of SonoVue® (Bracco, Milan, Italy) were registered. Fusion imaging could clarify all 11 (100%) initially as indeterminate described hepatic lesions by computed tomography/magnetic resonance imaging (CT/MRI). Moreover, 5/14 (36%) initially suspicious hepatic lesions could be validated by fusion imaging, whereas in 8/14 (57%), malignant morphology was disproved. Moreover, fusion imaging allowed for the clarification of 29/30 (97%) renal lesions initially characterized as suspicious by CT/MRI, of which 19/30 (63%) underwent renal surgery, histopathology revealed malignancy in 16/19 (84%), and benignity in 3/19 (16%). Indeterminate findings could be elucidated by fusion imaging in 20/20 (100%) renal lesions. Its accessibility and repeatability, even during pregnancy and in childhood, its cost-effectiveness, and its excellent safety profile, make fusion imaging a promising instrument for the thorough evaluation of hepatic and renal lesions in the future.