julilili42/papers huggingface dataset:
The Impact of Enzalutamide on the Prostate Cancer Patient Experience: A Summary Review of Health-Related Quality of Life across Pivotal Clinical Trials
2021-11-23

This review examines the impact of treatment with enzalutamide on health-related quality of life (HRQoL) in prostate cancer patients across the disease continuum based on pivotal clinical trials. We assessed the effect of enzalutamide on pain, symptom burden and overall HRQoL from randomized controlled trials. Patient experience was evaluated in men with metastatic hormone-sensitive prostate cancer (mHSPC), non-metastatic castration-resistant prostate cancer (nmCRPC) and metastatic castration-resistant prostate cancer (mCRPC) (pre-chemotherapy and post-chemotherapy). Patients across the disease continuum reported a generally positive status at baseline, with relatively low levels of pain and impairment due to cancer-related symptoms and high HRQoL. For patients with earlier-state prostate cancer, pain and symptom-related burden were low at study entry and remained so, regardless of whether patients received enzalutamide or control treatment. Patients with more advanced disease reported mitigation in pain and symptom burden while receiving treatment with enzalutamide. Enzalutamide was observed to slow deterioration of overall HRQoL most for patients with nmCRPC or mCRPC (statistical significance for between-group difference in median time to deterioration: mHSPC (confirmed) p = 0.2998; nmCRPC (confirmed) p = 0.0044; mCRPC (unconfirmed) p &lt; 0.0001). Across the prostate cancer continuum, enzalutamide is well-tolerated and delays the negative impact that disease progression has on quality of life.
Arabidopsis PII Proteins Form Characteristic Foci in Chloroplasts Indicating Novel Properties in Protein Interaction and Degradation
2021-11-23

The PII protein is an evolutionary, highly conserved regulatory protein found in both bacteria and higher plants. In bacteria, it modulates the activity of several enzymes, transporters, and regulatory factors by interacting with them and thereby regulating important metabolic hubs, such as carbon/nitrogen homeostasis. More than two decades ago, the PII protein was characterized for the first time in plants, but its physiological role is still not sufficiently resolved. To gain more insights into the function of this protein, we investigated the interaction behavior of AtPII with candidate proteins by BiFC and FRET/FLIM in planta and with GFP/RFP traps in vitro. In the course of these studies, we found that AtPII interacts in chloroplasts with itself as well as with known interactors such as N-acetyl-L-glutamate kinase (NAGK) in dot-like aggregates, which we named PII foci. In these novel protein aggregates, AtPII also interacts with yet unknown partners, which are known to be involved in plastidic protein degradation. Further studies revealed that the C-terminal component of AtPII is crucial for the formation of PII foci. Altogether, the discovery and description of PII foci indicate a novel mode of interaction between PII proteins and other proteins in plants. These findings may represent a new starting point for the elucidation of physiological functions of PII proteins in plants.
Giant Quartz Veins of the Pyrenees Database - Vein Width Dataset (MSEcxel Spreadsheet)
2021-11-23

&lt;p&gt;The &lt;strong&gt;GIVEPY Database&lt;/strong&gt; (GIant quartz VEins of the PYrenees) is an interactive tool that incorporates information of the geometry, distribution, statistics, and host rock types of 741 giant quartz veins that crop out in the fold and thrust belt of the Pyrenees. The GIVEPY Database follows the &lt;strong&gt;FAIR &lt;/strong&gt;principles of data management (Findable, Accessible, Interoperable and Reusable) and is available at:&nbsp;&lt;a href="https://givepy.info/"&gt;https://givepy.info/&lt;/a&gt;.&lt;/p&gt; &lt;p&gt;The Full Dataset consists of a ESRI Shapefile where the giant quartz veins of the Pyrenees are mapped following polygon superposition rules. The &lt;em&gt;.shp&lt;/em&gt;&nbsp;file can be opened in any Geographic Information System (GIS) environment. We recommend the use of the&nbsp;&lt;strong&gt;QGIS&lt;/strong&gt; software since it is open access and continuously updated.&lt;/p&gt; &lt;p&gt;The original CRS is:&lt;/p&gt; &lt;p&gt;EPSG: 32631 / WGS1984 - UTM Z31N&lt;/p&gt; &lt;p&gt;Do not hesitate to contact Eloi Gonz&aacute;lez-Esvertit if you have any questions:&nbsp;e.gonzalez-esvertit@ub.edu&lt;/p&gt;
Giant Quartz Veins of the Pyrenees Database - Full Dataset (MSExcel Spreadsheet)
2021-11-23

The <strong>GIVEPY Database</strong> (GIant quartz VEins of the PYrenees) is an interactive tool that incorporates information of the geometry, distribution, statistics, and host rock types of 741 giant quartz veins that crop out in the fold and thrust belt of the Pyrenees. The GIVEPY Database follows the <strong>FAIR </strong>principles of data management (Findable, Accessible, Interoperable and Reusable) and is available at: https://givepy.info/. The Full Dataset consists of a ESRI Shapefile where the giant quartz veins of the Pyrenees are mapped following polygon superposition rules. The <em>.shp</em> file can be opened in any Geographic Information System (GIS) environment. We recommend the use of the <strong>QGIS</strong> software since it is open access and continuously updated. The original CRS is: EPSG: 32631 / WGS1984 - UTM Z31N Do not hesitate to contact Eloi González-Esvertit if you have any questions: e.gonzalez-esvertit@ub.edu
Giant Quartz Veins of the Pyrenees Database - Full Dataset (ESRI Shapefile)
2021-11-23

&lt;p&gt;The &lt;strong&gt;GIVEPY Database&lt;/strong&gt; (GIant quartz VEins of the PYrenees) is an interactive tool that incorporates information of the geometry, distribution, statistics, and host rock types of 741 giant quartz veins that crop out in the fold and thrust belt of the Pyrenees. The GIVEPY Database follows the &lt;strong&gt;FAIR &lt;/strong&gt;principles of data management (Findable, Accessible, Interoperable and Reusable) and is available at:&nbsp;&lt;a href="https://givepy.info/"&gt;https://givepy.info/&lt;/a&gt;.&lt;/p&gt; &lt;p&gt;The Full Dataset consists of a ESRI Shapefile where the giant quartz veins of the Pyrenees are mapped following polygon superposition rules. The &lt;em&gt;.shp&lt;/em&gt;&nbsp;file can be opened in any Geographic Information System (GIS) environment. We recommend the use of the&nbsp;&lt;strong&gt;QGIS&lt;/strong&gt; software since it is open access and continuously updated.&lt;/p&gt; &lt;p&gt;The original CRS is:&lt;/p&gt; &lt;p&gt;EPSG: 32631 / WGS1984 - UTM Z31N&lt;/p&gt; &lt;p&gt;Do not hesitate to contact Eloi Gonz&aacute;lez-Esvertit if you have any questions:&nbsp;e.gonzalez-esvertit@ub.edu&lt;/p&gt;
Giant Quartz Veins of the Pyrenees Database - Vein Width Dataset (MSEcxel Spreadsheet)
2021-11-23

The <strong>GIVEPY Database</strong> (GIant quartz VEins of the PYrenees) is an interactive tool that incorporates information of the geometry, distribution, statistics, and host rock types of 741 giant quartz veins that crop out in the fold and thrust belt of the Pyrenees. The GIVEPY Database follows the <strong>FAIR </strong>principles of data management (Findable, Accessible, Interoperable and Reusable) and is available at: https://givepy.info/. The Full Dataset consists of a ESRI Shapefile where the giant quartz veins of the Pyrenees are mapped following polygon superposition rules. The <em>.shp</em> file can be opened in any Geographic Information System (GIS) environment. We recommend the use of the <strong>QGIS</strong> software since it is open access and continuously updated. The original CRS is: EPSG: 32631 / WGS1984 - UTM Z31N Do not hesitate to contact Eloi González-Esvertit if you have any questions: e.gonzalez-esvertit@ub.edu
Giant Quartz Veins of the Pyrenees Database - Full Dataset (MSExcel Spreadsheet)
2021-11-23

&lt;p&gt;The &lt;strong&gt;GIVEPY Database&lt;/strong&gt; (GIant quartz VEins of the PYrenees) is an interactive tool that incorporates information of the geometry, distribution, statistics, and host rock types of 741 giant quartz veins that crop out in the fold and thrust belt of the Pyrenees. The GIVEPY Database follows the &lt;strong&gt;FAIR &lt;/strong&gt;principles of data management (Findable, Accessible, Interoperable and Reusable) and is available at:&nbsp;&lt;a href="https://givepy.info/"&gt;https://givepy.info/&lt;/a&gt;.&lt;/p&gt; &lt;p&gt;The Full Dataset consists of a ESRI Shapefile where the giant quartz veins of the Pyrenees are mapped following polygon superposition rules. The &lt;em&gt;.shp&lt;/em&gt;&nbsp;file can be opened in any Geographic Information System (GIS) environment. We recommend the use of the&nbsp;&lt;strong&gt;QGIS&lt;/strong&gt; software since it is open access and continuously updated.&lt;/p&gt; &lt;p&gt;The original CRS is:&lt;/p&gt; &lt;p&gt;EPSG: 32631 / WGS1984 - UTM Z31N&lt;/p&gt; &lt;p&gt;Do not hesitate to contact Eloi Gonz&aacute;lez-Esvertit if you have any questions:&nbsp;e.gonzalez-esvertit@ub.edu&lt;/p&gt;
Giant Quartz Veins of the Pyrenees Database - Full Dataset (ESRI Shapefile)
2021-11-23

The <strong>GIVEPY Database</strong> (GIant quartz VEins of the PYrenees) is an interactive tool that incorporates information of the geometry, distribution, statistics, and host rock types of 741 giant quartz veins that crop out in the fold and thrust belt of the Pyrenees. The GIVEPY Database follows the <strong>FAIR </strong>principles of data management (Findable, Accessible, Interoperable and Reusable) and is available at: https://givepy.info/. The Full Dataset consists of a ESRI Shapefile where the giant quartz veins of the Pyrenees are mapped following polygon superposition rules. The <em>.shp</em> file can be opened in any Geographic Information System (GIS) environment. We recommend the use of the <strong>QGIS</strong> software since it is open access and continuously updated. The original CRS is: EPSG: 32631 / WGS1984 - UTM Z31N Do not hesitate to contact Eloi González-Esvertit if you have any questions: e.gonzalez-esvertit@ub.edu
Deep Learning Applications in Magnetic Resonance Imaging: Has the Future Become Present?
2021-11-24

Deep learning technologies and applications demonstrate one of the most important upcoming developments in radiology. The impact and influence of these technologies on image acquisition and reporting might change daily clinical practice. The aim of this review was to present current deep learning technologies, with a focus on magnetic resonance image reconstruction. The first part of this manuscript concentrates on the basic technical principles that are necessary for deep learning image reconstruction. The second part highlights the translation of these techniques into clinical practice. The third part outlines the different aspects of image reconstruction techniques, and presents a review of the current literature regarding image reconstruction and image post-processing in MRI. The promising results of the most recent studies indicate that deep learning will be a major player in radiology in the upcoming years. Apart from decision and diagnosis support, the major advantages of deep learning magnetic resonance imaging reconstruction techniques are related to acquisition time reduction and the improvement of image quality. The implementation of these techniques may be the solution for the alleviation of limited scanner availability via workflow acceleration. It can be assumed that this disruptive technology will change daily routines and workflows permanently.
Pregnancy and brain architecture: Associations with hormones, cognition and affect
2021-11-24

Abstract Sex hormones such as estradiol (E2) have long‐lasting influence on brain architecture. Recent studies indicate further structural changes during hormonal transition periods including pregnancy, when women experience the greatest increase in sex hormone levels across their life span. In the present study, three groups of women ( n = 44) with different levels of E2 underwent structural magnetic resonance imaging: (1) first‐time pregnant women ( n = 13, ‘extreme E2 group’); (2), nulliparous, naturally cycling women who received 12 mg of E2 valerate ( n = 16, ‘high E2 group’); and (3) nulliparous, naturally cycling women receiving a placebo and hence low E2 ( n = 15, ‘low E2 group’). Blood samples were taken to assess hormonal levels. Moreover, parameters for cognition, emotion regulation and affect were assessed. On the neuronal level, the extreme E2 compared to the high E2 group showed a reduced gray matter volume in the left putamen. However, no significant differences were found between the low vs. high E2 groups, nor between the low E2 and extreme E2 groups. Cognitive performance was reduced in the extreme E2 group, although a positive affect was increased compared to the high E2 and low E2 groups. Furthermore, regression analyses revealed several associations between cognition, subjective measures of affect, emotion regulation and gray matter volume. A volume reduction of the left putamen during pregnancy further supports the notion that the female brain is shaped by hormonal transition phases, possibly preparing women for their future roles (e.g., pregnant women for their role as mothers).
Toward explainable and advisable model for self‐driving cars
2021-11-24

Abstract Humans learn to drive through both practice and theory, for example, by studying the rules, while most self‐driving systems are limited to the former. Being able to incorporate human knowledge of typical causal driving behavior should benefit autonomous systems. We propose a new approach that learns vehicle control with the help of human advice. Specifically, our system learns to summarize its visual observations in natural language, predict an appropriate action response (eg, “I see a pedestrian crossing, so I stop”), and predict the controls, accordingly. Moreover, to enhance the interpretability of our system, we introduce a fine‐grained attention mechanism that relies on semantic segmentation and object‐centric RoI pooling. We show that our approach of training the autonomous system with human advice, grounded in a rich semantic representation, matches or outperforms prior work in terms of control prediction and explanation generation. Our approach also results in more interpretable visual explanations by visualizing object‐centric attention maps. We evaluate our approach on a novel driving dataset with ground‐truth human explanations, the Berkeley DeepDrive eXplanation (BDD‐X) dataset.
Temperature dependence of nitrate-reducing Fe(II) oxidation by Acidovorax strain BoFeN1 – evaluating the role of enzymatic vs. abiotic Fe(II) oxidation by nitrite
2021-11-24

ABSTRACT Fe(II) oxidation coupled to nitrate reduction is a widely observed metabolism. However, to what extent the observed Fe(II) oxidation is driven enzymatically or abiotically by metabolically produced nitrite remains puzzling. To distinguish between biotic and abiotic reactions, we cultivated the mixotrophic nitrate-reducing Fe(II)-oxidizing Acidovorax strain BoFeN1 over a wide range of temperatures and compared it to abiotic Fe(II) oxidation by nitrite at temperatures up to 60°C. The collected experimental data were subsequently analyzed through biogeochemical modeling. At 5°C, BoFeN1 cultures consumed acetate and reduced nitrate but did not significantly oxidize Fe(II). Abiotic Fe(II) oxidation by nitrite at different temperatures showed an Arrhenius-type behavior with an activation energy of 80±7 kJ/mol. Above 40°C, the kinetics of Fe(II) oxidation were abiotically driven, whereas at 30°C, where BoFeN1 can actively metabolize, the model-based interpretation strongly suggested that an enzymatic pathway was responsible for a large fraction (ca. 62%) of the oxidation. This result was reproduced even when no additional carbon source was present. Our results show that at below 30°C, i.e. at temperatures representing most natural environments, biological Fe(II) oxidation was largely responsible for overall Fe(II) oxidation, while abiotic Fe(II) oxidation by nitrite played a less important role.
Effective transfer entropy to measure information flows in credit markets
2021-11-24

Abstract In this paper we propose to study the dynamics of financial contagion between the credit default swap (CDS) and the sovereign bond markets through effective transfer entropy, a model-free methodology which enables to overcome the required hypotheses of classical price discovery measures in the statistical and econometric literature, without being restricted to linear dynamics. By means of effective transfer entropy we correct for small sample biases which affect the traditional Shannon transfer entropy, as well as we are able to conduct inference on the estimated directional information flows. In our empirical application, we analyze the CDS and bond market data for eight countries of the European Union, and aim to discover which of the two assets is faster at incorporating the information on the credit risk of the underlying sovereign. Our results show a clear and statistically significant prominence of the bond market for pricing the sovereign credit risk, especially during the crisis period. During the post-crisis period, instead, a few countries behave dissimilarly from the others, in particular Spain and the Netherlands.
Oscillatory Potentials in Achromatopsia as a Tool for Understanding Cone Retinal Functions
2021-11-24

Achromatopsia (ACHM) is an inherited autosomal recessive disease lacking cone photoreceptors functions. In this study, we characterize the time-frequency representation of the full-field electroretinogram (ffERG) component oscillatory potentials (OPs), to investigate the connections between photoreceptors and the inner retinal network using ACHM as a model. Time-frequency characterization of OPs was extracted from 52 controls and 41 achromat individuals. The stimulation via ffERG was delivered under dark-adaptation (DA, 3.0 and 10.0 cd·s·m−2) to assess mixed rod-cone responses. The ffERG signal was subsequently analyzed using a continuous complex Morlet transform. Time-frequency maps of both DA conditions show the characterization of OPs, disclosing in both groups two distinct time-frequency windows (~70–100 Hz and &gt;100 Hz) within 50 ms. Our main result indicates a significant cluster (p &lt; 0.05) in both conditions of reduced relative power (dB) in ACHM people compared to controls, mainly at the time-frequency window &gt;100 Hz. These results suggest that the strongly reduced but not absent activity of OPs above 100 Hz is mostly driven by cones and only in small part by rods. Thus, the lack of cone modulation of OPs gives important insights into interactions between photoreceptors and the inner retinal network and can be used as a biomarker for monitoring cone connection to the inner retina.
High-Throughput Screening Platform in Postnatal Heart Cells and Chemical Probe Toolbox to Assess Cardiomyocyte Proliferation
2021-11-24

Restoring lost heart muscle is an attractive goal for cardiovascular regenerative medicine. One appealing strategy is the therapeutic stimulation of cardiomyocyte proliferation, which <i>inter alia</i> remains challenging due to available assay technologies capturing the complex biology. Here, a high-throughput-formatted phenotypic assay platform was established using rodent whole heart-derived cells to preserve the cellular environment of cardiomyocytes. Several readouts allowed the quantification of cycling cardiomyocytes, including a transgenic H2B-mCherry system for unequivocal, automated detection of cardiomyocyte nuclei. A chemical genetics approach revealed pronounced species differences and furnished pan-kinase inhibitors <b>5</b> and <b>36</b> as potent and robust inducers of endoreplication and acytokinetic mitosis. Combined profiling of the commonly used p38 MAPK inhibitors SB203580 (<b>1</b>), SB239063 (<b>2</b>) and a novel set of skepinone-L (<b>6</b>) derivatives pointed to off-target effects beyond p38 that might be critical for effective cardiomyocyte cytokinesis. Kinome-focused screening eventually furnished TG003 (<b>38</b>) as a novel candidate for stimulating cardiomyocyte proliferation.
Development of a Questionnaire to Measure the Perceived Injustice of People Who Have Experienced Violence in War and Conflict Areas: Perceived Injustice Questionnaire (PIQ)
2021-11-24

Objectives: The primary aim of this research was to develop a questionnaire that assesses perceived injustice among survivors of war and trauma in conflict areas and to evaluate its psychometric properties. This paper presents the first preliminary validation. Furthermore, the assumption that the general perception of injustice correlates with one’s own experiences of injustice and violence was tested. Methods: The 24-item Perceived Injustice Questionnaire (PIQ) was administered partly online and partly in a paper–pencil version to 89 students of the University of Dohuk in Northern Iraq, an area that has been affected by crisis and war for many years. Principal component analysis was used for factor extraction and internal consistency was determined. The Mann–Whitney-U test was used to calculate the group differences between people with and without experience of physical violence and strong experiences of injustice because Kolmogorov–Smirnov tests showed that the data are not normally distributed. Results: Principal component analysis yielded a four-component solution with eigenvalues being the greater one. Cronbach’s alpha for each scale was acceptable to satisfactory. Significant results of the Mann–Whitney U tests supported our assumptions of between-group differences on each of the subscales (emotional and cognitive consequences, injustice perception, injustice experience, revenge, and forgiveness). Discussion: The findings of this study support the construct validity and the reliability of the PIQ. For this reason, it can be seen as a useful addition to the psychological assessment in psychotherapeutic settings of survivors of war and violence. In conclusion, and based on the PIQ, we suggest the development of a new set of therapy modules with worksheets, focusing on the perception, dealing, and understanding of feeling of injustice as an addition to the existing trauma therapy manual for therapy in war and conflict areas.
Using AnnoTree to get more assignments, faster, in DIAMOND+MEGAN microbiome analysis
2021-11-24

ABSTRACT In microbiome analysis, one main approach is to align metagenomic sequencing reads against a protein-reference database such as NCBI-nr, and then to perform taxonomic and functional binning based on the alignments. This approach is embodied, for example, in the standard DIAMOND+MEGAN analysis pipeline, which first aligns reads against NCBI-nr using DIAMOND and then performs taxonomic and functional binning using MEGAN. Here we propose the use of the AnnoTree protein database, rather than NCBI-nr, in such alignment-based analyses to determine the prokaryotic content of metagenomic samples. We demonstrate a 2-fold speedup over the usage of the prokaryotic part of NCBI-nr, and increased assignment rates, in particular, assigning twice as many reads to KEGG. In addition to binning to the NCBI taxonomy, MEGAN now also bins to the GTDB taxonomy. IMPORTANCE The NCBI-nr database is not explicitly designed for the purpose of microbiome analysis and its increasing size makes its unwieldy and computationally expensive for this purpose. The AnnoTree protein database is only one quarter the size of the full NCBI-nr database and is explicitly designed for metagenomic analysis, and so should be supported by alignment-based pipelines.