julilili42/papers huggingface dataset:
Comparison of aortic remodelling after conservative treatment or thoracic endovascular repair in type B dissections
2019-11-09

Abstract OBJECTIVES Our aim was to compare aortic remodelling in type B dissections after thoracic endovascular aortic repair (TEVAR) or conservative treatment. METHODS We conducted a retrospective analysis of computed tomography (CT) data sets at dissection onset and at the last follow-up in a group with conservative (group A) and TEVAR treatment (group B). An additional analysis of the preoperative CT images was performed in patients from group A, who were converted to TEVAR during follow-up. Diameters and lengths of all aortic segments were measured and growth rates were calculated. RESULTS We included 74 patients: 50 patients in group A (follow-up time: 1625 ± 209 days) and 24 patients in group B (follow-up time: 554 ± 129 days). The mean aortic diameter growth rate was significantly higher in group A than in group B in the mid-descending aorta (A: +7 mm/year; B: −4 mm/year; P = 0.003). Length growth difference was only present in the abdominal aortic segment and was more pronounced in group A (+2 vs ±0 mm/year; P = 0.009). The conversion rate from conservative treatment to TEVAR was 36% (n = 18). A false lumen diameter of &amp;gt;22 mm at baseline was associated with a higher rate of conversion (P = 0.036). After conversion, the mean growth rate in the proximal descending and mid-descending aorta decreased from preoperative +11 and +18 mm/year to postoperative −9 and −14 mm/year, respectively (P &amp;lt; 0.001). CONCLUSIONS In acute type B dissections, TEVAR stops aortic enlargement in the thoracic aorta, but promotes distal dilatation compared to the conservative treatment group. After conversion to TEVAR in conservatively pretreated chronic type B dissections, a more pronounced diameter decrease in the descending aorta was observed than in patients treated in the acute phase.
Antitumor Reactive T-Cell Responses Are Enhanced In Vivo by DAMP Prothymosin Alpha and Its C-Terminal Decapeptide
2019-11-09

Prothymosin α (proTα) and its C-terminal decapeptide proTα(100–109) were shown to pleiotropically enhance innate and adaptive immune responses. Their activities have been broadly studied in vitro, focusing primarily on the restoration of the deficient immunoreactivity of cancer patients’ leukocytes. Previously, we showed that proTα and proTα(100–109) act as danger-associated molecular patterns (DAMPs), ligate Toll-like receptor-4, signal through TRIF- and MyD88-dependent pathways, promote the maturation of dendritic cells and elicit T-helper type 1 (Th1) immune responses in vitro, leading to the optimal priming of tumor antigen-reactive T-cell functions. Herein, we assessed their activity in a preclinical melanoma model. Immunocompetent mice bearing B16.F1 tumors were treated with two cycles of proTα or proTα(100–109) together with a B16.F1-derived peptide vaccine. Coadministration of proTα or proTα(100–109) and the peptide vaccine suppressed melanoma-cell proliferation, as evidenced by reduced tumor-growth rates. Higher melanoma infiltration by CD3+ T cells was observed, whereas ex vivo analysis of mouse total spleen cells verified the in vivo induction of melanoma-reactive cytotoxic responses. Additionally, increased levels of proinflammatory and Th1-type cytokines were detected in mouse serum. We propose that, in the presence of tumor antigens, DAMPs proTα and proTα(100–109) induce Th1-biased immune responses in vivo. Their adjuvant ability to orchestrate antitumor immunoreactivities can eventually be exploited therapeutically in humans.
The most cosmopolitan European city: situating narratives and practices of cultural and social relations in Marseille
2019-11-10

Marseille’s identity as a cosmopolitan place was a key element in the city’s application to be European Capital of Culture (ECOC) in 2013, where the city was represented as ‘the most cosmopolitan’ in Europe. The language of cosmopolitanism enabled city leaders to align Marseille with ‘European’ values of cultural diversity and to highlight the city as a place of diverse cultural production. Such claims have incited interest in a country where cultural and ethnic differences are often considered a challenge to the ideals of French Republicanism. Narratives of social and cultural relations in Marseille are in fact highly variable. This article uses a neighbourhood arts project as a case study through which to explore and situate understandings, representations and experiences of cultural and social relations in the city.
Blood donor‐derived buffy coat to produce platelets in vitro
2019-11-10

Background and objectives Platelet transfusion is a standard medical therapy used to treat several bleeding disorders. However, a critical drawback is the dependency on donor‐derived platelets, which leads to concerns like insufficient availability and immunological complications. In vitro platelet production from hematopoietic progenitor cells (CD34) may represent a reasonable solution. Materials and methods CD34+ cells were isolated from either buffy coat or peripheral blood and compared in terms of platelet production in vitro. The number and the quality of magnetically isolated CD34+ cells and their capability to differentiate into mature megakaryocytes were investigated using flow cytometry. Additionally, the functionality of megakaryocytes in term of in vitro platelet production was tested. Results Similar purity and quantity of CD34+ cells was found after their isolation from both cell sources. In contrast, after 6 days of culture, enhanced number of CD34+ cells isolated from buffy coat compared with peripheral blood was observed (5·3 x 106 vs. 3·0 x 106, respectively). Interestingly, despite a comparable nuclear maturation phenotype, the yield of platelets released from buffy coat‐derived megakaryocytes was significantly higher than from peripheral blood cells (platelet yield pro MK: 7·2 vs. 2·7, respectively). Importantly, platelets produced from buffy coat‐derived cells could be activated by agonists. Conclusion Haematopoietic progenitor cells isolated from buffy coat have increased yield of platelets released from mature megakaryocytes and enhanced in vitro functionality, compared with peripheral blood‐derived cells. Our study, suggests that buffy coat, obtained during blood donation processing, might be a promising source of megakaryocytes for in vitro platelet production.
Technological and behavioural complexity in expedient industries: The importance of use-wear analysis for understanding flake assemblages
2019-11-11

Expedient lithic technology has been described as unchanging and without or very limited presence of formal tool types. However, this premise seems to limit the discussion on technological and behavioural complexity when studying amorphous flake industries. To address this issue, we employed multi-stage use-wear analysis to identify features that are not detectable through macroscopic approach. Our analysis of chert tools from Leang Sarru, North Sulawesi indicated the use of both unmodified flakes and retouched tools for plant processing, and we detected evidence for the manufacture of composite tools. Microscopic wear traces on unretouched flakes show that these were attached to shafts for possible use as hafted tools, but not necessarily as projectiles. Our results suggest that simple flake assemblages can be part of complex tool production and present an alternative view on the seemingly unchanging lithic technology from the Late Pleistocene to the Holocene. Furthermore, our current understanding of expedient lithic technology should be reassessed as features that are not observable with standard morphological and technological analyses may be detected through use-wear analysis. Overall, the applied methodology and results of this study are relevant to Pleistocene and Early Holocene archaeological sites and assemblages that exhibit the dilemma of inferring technological and behavioural complexity through the analysis of simple stone tools.
Children’s conversion of cultural capital into educational success: the symbolic and skill-generating functions of cultural capital
2019-11-11

A prominent explanation of intergenerational educational inequality is Bourdieu's cultural reproduction theory. Indeed, previous studies have frequently shown that children's cultural capital relates to academic outcomes. However, it remains unclear how children convert their cultural capital into achievement. While Bourdieu argued that cultural capital influences academic outcomes primarily by biasing teachers' grades, other researchers have proposed the alternative explanation that children's cultural capital absorption directly translates into academic skills. Using survey data on 2975 fifth graders from the German National Educational Panel Study, we disentangle these two mechanisms of children's cultural capital conversion; and argue that the main conversion mechanism depends on the cultural capital dimension examined. The results of our structural equation model suggest that both mechanisms are at work and that the main conversion mechanism depends on the dimension of cultural capital examined.
Systematic spatiotemporal mapping reveals divergent cell death pathways in three mouse models of hereditary retinal degeneration
2019-11-11

Abstract Calcium (Ca 2+ ) dysregulation has been linked to neuronal cell death, including in hereditary retinal degeneration. Ca 2+ dysregulation is thought to cause rod and cone photoreceptor cell death. Spatial and temporal heterogeneities in retinal disease models have hampered validation of this hypothesis. We examined the role of Ca 2+ in photoreceptor degeneration, assessing the activation pattern of Ca 2+ ‐dependent calpain proteases, generating spatiotemporal maps of the entire retina in the cpfl1 mouse model for primary cone degeneration, and in the rd1 and rd10 models for primary rod degeneration. We used Gaussian process models to distinguish the temporal sequences of degenerative molecular processes from other variability sources.In the rd1 and rd10 models, spatiotemporal pattern of increased calpain activity matched the progression of primary rod degeneration. High calpain activity coincided with activation of the calpain‐2 isoform but not with calpain‐1, suggesting differential roles for both calpain isoforms. Primary rod loss was linked to upregulation of apoptosis‐inducing factor, although only a minute fraction of cells showed activity of the apoptotic marker caspase‐3. After primary rod degeneration concluded, caspase‐3 activation appeared in cones, suggesting apoptosis as the dominant mechanism for secondary cone loss. Gaussian process models highlighted calpain activity as a key event during primary rod photoreceptor cell death. Our data suggest a causal link between Ca 2+ dysregulation and primary, nonapoptotic degeneration of photoreceptors and a role for apoptosis in secondary degeneration of cones, highlighting the importance of the spatial and temporal location of key molecular events, which may guide the evaluation of new therapies.
ClinCNV: novel method for allele-specific somatic copy-number alterations detection
2019-11-11

Abstract Motivation Large somatic copy number alterations (CNA), short indels and single nucleotide variants (SNVs) are playing important role in cancer development and can serve as a predictor for targeted therapy selection as well as prognostic factor. Genomic microarrays, FISH, MLPA and many other technologies are widely used for detection of CNAs. Whole-genome sequencing (WGS), whole-exome sequencing (WES) and targeted panel sequencing (TPS) are well established, highly accurate tools for detection of SNVs and small indels, but detection of larger structural variants using WGS, WES and TPS data remains challenging. We developed a tool for high-resolution allele-specific detection of somatic CNAs in NGS data using statistical approach. Results We have developed a new method for read-depth and B-allele frequency (BAF) based multi-sample detection of copy-number changes in paired normal-tumor NGS data and showed its performance using large cohorts of WES and TPS sequenced samples. Availability ClinCNV is freely available on https://github.com/imgag/ClinCNV .
The impact of physicians’ recommendations on treatment preference and attitudes: a randomized controlled experiment on shared decision-making
2019-11-11

Making decisions based on their own evaluation of relevant information and beliefs is very challenging for patients. Many patients feel that they lack the knowledge to make a decision and expect a recommendation by their physician. We conducted an experimental study to examine the impact of physicians' recommendations on the decision-making process. N = 194 medical laypeople were placed in a hypothetical scenario where they suffered from a cruciate ligament rupture and were faced with the decision about a treatment (surgery or physiotherapy). In a 3 × 2 between-group design we investigated the impact of physicians' recommendations (for surgery, for physiotherapy, no recommendation) and reasoning style (scientific, narrative) on treatment preference, certainty and satisfaction regarding treatment preference, and attitudes. We found that the recommendation had a significant influence on treatment preference and attitudes toward both treatments. Additionally, we found a significant increase in certainty and satisfaction after the intervention, independently of whether they received a recommendation. This finding suggested that a recommendation was not required to strengthen participants' confidence in their decision. There were no effects of reasoning style. We discuss the implications and suggest that physicians should be careful with recommendations in situations in which patients' preferences are important.
Comment on “Zamariola et al., (2018), Interoceptive Accuracy Scores are Problematic: Evidence from Simple Bivariate Correlations” - The Empirical Data Base, the Conceptual Reasoning and the Analysis behind this Statement are Misconceived and do not Support the Authors’ Conclusions
2019-11-11

A recent paper by Zamariola and colleagues is widely cited as an authority on the invalidity of the Heartbeat Counting Task as a measure of interoceptive accuracy. Given the widespread interest in this field, it is essential that papers about methods are conceptually and empirically sound. However, only one of the authors’ four criticisms appears to be substantiated, i.e. that people count too few heartbeats. Their main arguments about “simple bivariate correlations”, as well as their finding that interoceptive accuracy and heart rate correlate, depend on wholly ‘spurious correlations’ arising from the apparently overlooked point that interoceptive accuracy is a ratio. Moreover, scrutiny of the authors’ data suggests that their fourth criticism (that interoceptive accuracy is lower on longer trials) is an order effect. We present data from our own labs to refute it. We draw the authors’ and editors’ attention to these issues and trust that they will reconsider these erroneous conclusions.
Dynamic B0 shimming of the motor cortex and cerebellum with a multicoil shim setup for BOLD fMRI at 9.4T
2019-11-11

Purpose We assessed how improved static magnetic field (B 0 ) homogeneity with a dynamic multicoil shimming can influence the blood oxygen level dependent (BOLD) contrast to noise when echo planar imaging (EPI) sequence is used for a motor task functional MRI study. We showed that a multicoil shim setup can be a proper choice for dynamic shimming of 2 spatially distant areas with different inhomogeneity distributions. Methods A 16‐channel multicoil shim setup is used to provide improved B 0 homogeneity by dynamic slice‐wise shimming. The performance of dynamic B 0 shimming was investigated in 2 distinct brain regions, the motor cortex and the cerebellum, in the same experiment during a finger‐tapping task. Temporal SNR (tSNR), geometric distortion of the EPIs, and results of an analysis with a general linear model before and after shimming with the multicoil were compared. Results Reduced B 0 deviation by 30% and 52% in the cerebellum and motor cortex, respectively, resulted in higher tSNR and a reduction of distortions in the EPI. Statistical analysis applied to the EPIs showed higher t values and increased number of voxels above significance threshold when shimming with the multicoil setup. Conclusions Improved B 0 homogeneity leads to higher tSNR and enhances the detection of BOLD signal.
Experimental proof that multivariate patterns among muscle attachments (entheses) can reflect repetitive muscle use
2019-11-12

Abstract Reconstructions of habitual activity in past populations and extinct human groups is a primary goal of paleoanthropological research. Muscle attachment scars (entheses) are widely considered as indicators of habitual activity and many attempts have been made to use them for this purpose. However, their interpretation remains equivocal due to methodological limitations and a paucity of empirical data supporting an interaction between systematic muscle forces and entheseal morphology. We have recently addressed the first issue with precise three-dimensional measuring protocols and rigorous multivariate analysis focusing on the patterns among different entheses rather than comparing each entheseal structure separately. In a previous study, the resulting entheseal correlations reflected synergistic muscle groups that separated individuals according to their lifelong occupational activities. Here we address the second issue by applying this methodology to existing micro-computed tomography data from rats that have undergone muscle stimulation under experimental conditions. In contrast to previous animal studies, we relied on blind analytical procedures across two research institutions and controlled for most factors of interindividual variability. Results demonstrated that the multivariate associations among different entheseal surfaces can directly reflect repetitive muscle recruitment and provide essential information on muscle use.
Auto-regulation of Rab5 GEF activity in Rabex5 by allosteric structural changes, catalytic core dynamics and ubiquitin binding
2019-11-12

Intracellular trafficking depends on the function of Rab GTPases, whose activation is regulated by guanine exchange factors (GEFs). The Rab5 GEF, Rabex5, was previously proposed to be auto-inhibited by its C-terminus. Here, we studied full-length Rabex5 and Rabaptin5 proteins as well as domain deletion Rabex5 mutants using hydrogen deuterium exchange mass spectrometry. We generated a structural model of Rabex5, using chemical cross-linking mass spectrometry and integrative modeling techniques. By correlating structural changes with nucleotide exchange activity for each construct, we uncovered new auto-regulatory roles for the ubiquitin binding domains and the Linker connecting those domains to the catalytic core of Rabex5. We further provide evidence that enhanced dynamics in the catalytic core are linked to catalysis. Our results suggest a more complex auto-regulation mechanism than previously thought and imply that ubiquitin binding serves not only to position Rabex5 but to also control its Rab5 GEF activity through allosteric structural alterations.
Delirium Screening in Aphasic Patients With the Intensive Care Delirium Screening Checklist (ICDSC): A Prospective Cohort Study
2019-11-12

<b>Background:</b> Ten to thirty percent of stroke patients suffer from post-stroke delirium. This leads to a longer hospital stay and increased mortality. Therefore, early detection and treatment are needed. All established delirium screening tools require some degree of language function. We sought to investigate whether the Intensive Care Delirium Screening Checklist (ICDSC) is suitable for delirium screening in patients with post-stroke aphasia. <b>Methods:</b> A prospective cohort study was carried out in adult patients consecutively admitted to the Stroke Unit of University Hospital Tuebingen, between July 2017 and December 2018. The index test, ICDSC, was compared with the DSM-V diagnostic criteria as reference standard. Measures of diagnostic precision and the degree of agreement were obtained. <b>Results:</b> Three hundred and forty six patients were included in the analysis. Aphasia was present in 231 (66.8%) and absent in 115 (33.2%) patients. Delirium was present in 83 out of 231 (36%) patients with aphasia and 32 out of 115 (27.8%) patients without aphasia (<i>p</i> = 0.132). For patients without aphasia, sensitivity and specificity at the established cut-off value of ≥ 4 points were 100% and 78%, respectively. For patients with aphasia, the test demonstrated inferior performance, with a sensitivity and specificity of 98% and 55%, respectively. It was necessary to increase the cut-off value to ≥ 5 points. Through this, sensitivity was 90% (95% CI, 81.9-95.8%) and specificity was 75% (95% CI, 67.2-81.8%). The degree of agreement to the DSM-V criteria was "substantial" (Cohen's κ = 0.61). <b>Conclusion:</b> For the purpose of delirium screening in patients with aphasia, increasing the ICDSC cut-off value to ≥ 5 points enables effective screening. Further studies are necessary to characterize post-stroke delirium.
Physiological Responses During Hybrid BNCI Control of an Upper-Limb Exoskeleton
2019-11-12

When combined with assistive robotic devices, such as wearable robotics, brain/neural-computer interfaces (BNCI) have the potential to restore the capabilities of handicapped people to carry out activities of daily living. To improve applicability of such systems, workload and stress should be reduced to a minimal level. Here, we investigated the user’s physiological reactions during the exhaustive use of the interfaces of a hybrid control interface. Eleven BNCI-naive healthy volunteers participated in the experiments. All participants sat in a comfortable chair in front of a desk and wore a whole-arm exoskeleton as well as wearable devices for monitoring physiological, electroencephalographic (EEG) and electrooculographic (EoG) signals. The experimental protocol consisted of three phases: (i) Set-up, calibration and BNCI training; (ii) Familiarization phase; and (iii) Experimental phase during which each subject had to perform EEG and EoG tasks. After completing each task, the NASA-TLX questionnaire and self-assessment manikin (SAM) were completed by the user. We found significant differences (p-value &lt; 0.05) in heart rate variability (HRV) and skin conductance level (SCL) between participants during the use of the two different biosignal modalities (EEG, EoG) of the BNCI. This indicates that EEG control is associated with a higher level of stress (associated with a decrease in HRV) and mental work load (associated with a higher level of SCL) when compared to EoG control. In addition, HRV and SCL modulations correlated with the subject’s workload perception and emotional responses assessed through NASA-TLX questionnaires and SAM.