julilili42/papers huggingface dataset:
Low‐grade fibromyxoid sarcoma: A report of the Cooperative Weichteilsarkom Studiengruppe (CWS)
2019-11-17

ABSTRACT Background Low‐grade fibromyxoid sarcoma (LGFMS) is a rare soft‐tissue tumor with benign histologic appearance, though fully malignant behavior is possible. Methods Patients with LGFMS &lt;21 years registered in Cooperative Weichteilsarkom Studiengruppe trials until 2017 were analyzed. Firstline treatment consisted of complete surgical resection whenever possible. Results Median age of 31 patients was 10.9 years (first month to 17.1 years). Twenty‐six tumors were confirmed to the tissue of origin (T1), four invaded contiguous structures (T2), one was TX. Eight were &gt;5 cm. The best surgical result was resection with free margins (R0) in 24 and microscopic residuals (R1) in seven. Five‐year event‐free (EFS), 5‐year local‐relapse‐free (LRFS), and 5‐year overall‐survival were 71 ± 18.6% confidence interval (CI) 95%, 76 ± 17.6% CI 95%, and 100%, respectively. Six patients suffered local relapse in a median of 1 year, one combined within 1.3 year and one metastatic relapse with lesions in the lung, back muscles, and thigh discovered in whole‐body imaging 6 years after the first diagnosis. In univariate analysis, T status correlated with EFS (T1 79.6 ± 18.6%, T2 50.0 ± 49.0%, P = .038). Resection with free margins tends to be associated with better LRFS (R0 82.4 ± 18.6%, R1 53.6 ± 39.4%, P = .053). Among 24 patients with R0 resection, five (21%) suffered relapse, thereof three local, one metastatic, and one combined. Among seven patients with R1‐resection, three (43%) suffered local relapse. Conclusion Special caution is advisable in T2 tumors. The metastatic potential with lesions in unusual sites indicates that affected patients need to be informed. If long‐term follow‐up with whole‐body imaging is beneficial, it may be addressed in larger intergroup analyses. Further research in disease biology is essential for optimal treatment and follow‐up care.
A metamodel for competence assessment
2019-11-17

Purpose This paper aims to propose an explorative metamodel of the key organizational competences management and presents a Web-based tool (Co.S.M.O. © Competences Software Management for Organizations) for all-around assessment of the identified competences. Design/methodology/approach Building on the Great Eight Competencies Model- GEC, the European Qualifications Framework-EQF and focus group feedback, an online questionnaire was developed to manage the key organizational competences and to adapt the competence metamodel to the Italian context. Findings The competence metamodel described in this study and its newly designed tool (software with online questionnaire) could be used at the organizational level to improve productivity and efficiency by allowing an easy identification of key organizational competences and facilitating their acquisition and sharing. Research limitations/implications Currently, the metamodel is mainly theoretical and the software sustained only a partial validation. Practical implications The developed tool is a dynamic, easy to use and interactive Web-based software useful for managing the competences in both for-profit and not-for-profit organizations. Social implications European official documents invite companies and institutions to work together and share human capital: the European Qualifications Framework-EQF, at the base of this model, facilitates a common organizational language for human resources management. Originality/value Managerial competence literature indicates that a comprehensive model capturing a link between the EQF and a managerial competence model has not yet been considered in the literature.
The neurobiology of innate, volitional and learned vocalizations in mammals and birds
2019-11-18

Vocalization is an ancient vertebrate trait essential to many forms of communication, ranging from courtship calls to free verse. Vocalizations may be entirely innate and evoked by sexual cues or emotional state, as with many types of calls made in primates, rodents and birds; volitional, as with innate calls that, following extensive training, can be evoked by arbitrary sensory cues in non-human primates and corvid songbirds; or learned, acoustically flexible and complex, as with human speech and the courtship songs of oscine songbirds. This review compares and contrasts the neural mechanisms underlying innate, volitional and learned vocalizations, with an emphasis on functional studies in primates, rodents and songbirds. This comparison reveals both highly conserved and convergent mechanisms of vocal production in these different groups, despite their often vast phylogenetic separation. This similarity of central mechanisms for different forms of vocal production presents experimentalists with useful avenues for gaining detailed mechanistic insight into how vocalizations are employed for social and sexual signalling, and how they can be modified through experience to yield new vocal repertoires customized to the individual's social group. This article is part of the theme issue ‘What can animal communication teach us about human language?’
Gas Sensing of NiO‐SCCNT Core–Shell Heterostructures: Optimization by Radial Modulation of the Hole‐Accumulation Layer
2019-11-18

Abstract Hierarchical core–shell (C–S) heterostructures composed of a NiO shell deposited onto stacked‐cup carbon nanotubes (SCCNTs) are synthesized by atomic layer deposition (ALD). A film of NiO particles (0.80–21.8 nm in thickness) is uniformly deposited onto the inner and outer walls of the SCCNTs. The electrical resistance of the samples is found to increase of many orders of magnitude with the increasing of the NiO thickness. The response of NiO–SCCNT sensors toward low concentrations of acetone and ethanol at 200 °C is studied. The sensing mechanism is based on the modulation of the hole‐accumulation region in the NiO shell layer upon chemisorption of the reducing gas molecules. The electrical conduction mechanism is further studied by the incorporation of an Al 2 O 3 dielectric layer at NiO and SCCNT interfaces. The investigations on NiO–Al 2 O 3 –SCCNT, Al 2 O 3 –SCCNT, and NiO–SCCNT coaxial heterostructures reveal that the sensing mechanism is strictly related to the NiO shell layer. The remarkable performance of the NiO–SCCNT sensors toward acetone and ethanol benefits from the conformal coating by ALD, large surface area of the SCCNTs, and the optimized p‐NiO shell layer thickness followed by the radial modulation of the space‐charge region.
Association of longitudinal risk profile trajectory clusters with adipose tissue depots measured by magnetic resonance imaging
2019-11-18

Abstract The objective of the study was to identify associations of longitudinal trajectories of traditional cardiometabolic risk factors with abdominal and ectopic adipose tissue depots measured by magnetic resonance imaging (MRI). We measured total abdominal, visceral, and subcutaneous adipose tissue in liter and intrahepatic, intrapancreatic and renal sinus fat as fat fractions by MRI in 325 individuals free of cardiovascular disease at Exam 3 of a population-based cohort. We related these MRI measurements at Exam 3 to longitudinal risk profile trajectory clusters, based on risk factor measurements from Exam 3, Exam 2 (seven years prior to MRI) and Exam 1 (14 years prior to MRI). Based on the levels and longitudinal trajectories of several risk factors (blood pressure, lipid profile, anthropometric measurements, HbA1c), we identified three different trajectory clusters. These clusters displayed a graded association with all adipose tissue traits after adjustment for potential confounders (e.g. visceral adipose tissue: β ClusterII = 1.30 l, 95%-CI:[0.84 l;1.75 l], β ClusterIII = 3.32 l[2.74 l;3.90 l]; intrahepatic: Estimate ClusterII = 1.54[1.27,1.86], Estimate ClusterIII = 2.48[1.93,3.16]. Associations remained statistically significant after additional adjustment for the risk factor levels at Exam 1 or Exam 3, respectively. Trajectory clusters provided additional information in explaining variation in the different fat compartments beyond risk factor profiles obtained at individual exams. In conclusion, sustained high risk factor levels and unfavorable trajectories are associated with high levels of adipose tissue; however, the association with cardiometabolic risk factors varies substantially between different ectopic adipose tissues. Trajectory clusters, covering longitudinal risk profiles, provide additional information beyond single-point risk profiles. This emphasizes the need to incorporate longitudinal information in cardiometabolic risk estimation.
Detailed seismic bathymetry beneath Ekstroem Ice Shelf, Antarctica: Implications for glacial history and ice-ocean interaction
2019-11-18

The shape of ice-shelf cavities are a major source of uncertainty in understanding ice-ocean interactions. This limits assessments of the response of the Antarctic ice sheets to climate change. Here we use vibroseis seismic reflection surveys to map the bathymetry beneath the Ekström Ice Shelf, Dronning Maud Land. The new bathymetry reveals an inland-sloping trough, reaching depths of 1100 m below sea level, near the current grounding line, which we attribute to erosion by palaeo-ice streams. The trough does not cross-cut the outer parts of the continental shelf. Conductivity-temperature-depth profiles within the ice-shelf cavity reveal the presence of cold water at shallower depths and tidal mixing at the ice-shelf margins. It is unknown if warm water can access the trough. The new bathymetry is thought to be representative of many ice shelves in Dronning Maud Land, which together regulate the ice loss from a substantial area of East Antarctica.
In Staphylococcus aureus, the Particulate State of the Cell Envelope Is Required for the Efficient Induction of Host Defense Responses
2019-11-18

Upon microbial infection, host immune cells recognize bacterial cell envelope components through cognate receptors. Although bacterial cell envelope components function as innate immune molecules, the role of the physical state of the bacterial cell envelope (i.e., particulate versus soluble) in host immune activation has not been clearly defined. Here, using two different forms of the staphylococcal cell envelope of Staphylococcus aureus RN4220 and USA300 LAC strains, we provide biochemical and immunological evidence that the particulate state is required for the effective activation of host innate immune responses. In a murine model of peritoneal infection, the particulate form of the staphylococcal cell envelope (PCE) induced the production of chemokine (CX-C motif) ligand 1 (CXCL1) and CC chemokine ligand 2 (CCL2), the chemotactic cytokines for neutrophils and monocytes, respectively, resulting in a strong influx of the phagocytes into the peritoneal cavity. In contrast, compared with PCE, the soluble form of cell envelope (SCE), which was derived from PCE by treatment with cell wallhydrolyzing enzymes, showed minimal activity. PCE also induced the secretion of calprotectin (myeloid-related protein 8/14 [MRP8/14] complex), a phagocyte-derived antimicrobial protein, into the peritoneal cavity at a much higher level than did SCE. The injected PCE particles were phagocytosed by the infiltrated neutrophils and monocytes and then delivered to mediastinal draining lymph nodes. More importantly, intraperitoneally (i.p.) injected PCE efficiently protected mice from S. aureus infection, which was abolished by the depletion of either monocytes/macrophages or neutrophils. This study demonstrated that the physical state of bacterial cells is a critical factor for efficient host immune activation and the protection of hosts from staphylococcal infections.
A high-resolution gene expression atlas links dedicated meristem genes to key architectural traits
2019-11-19

The shoot apical meristem (SAM) orchestrates the balance between stem cell proliferation and organ initiation essential for postembryonic shoot growth. Meristems show a striking diversity in shape and size. How this morphological diversity relates to variation in plant architecture and the molecular circuitries driving it are unclear. By generating a high-resolution gene expression atlas of the vegetative maize shoot apex, we show here that distinct sets of genes govern the regulation and identity of stem cells in maize versus Arabidopsis. Cell identities in the maize SAM reflect the combinatorial activity of transcription factors (TFs) that drive the preferential, differential expression of individual members within gene families functioning in a plethora of cellular processes. Subfunctionalization thus emerges as a fundamental feature underlying cell identity. Moreover, we show that adult plant characters are, to a significant degree, regulated by gene circuitries acting in the SAM, with natural variation modulating agronomically important architectural traits enriched specifically near dynamically expressed SAM genes and the TFs that regulate them. Besides unique mechanisms of maize stem cell regulation, our atlas thus identifies key new targets for crop improvement.
Effects of Sorption on Redox Properties of Natural Organic Matter
2019-11-19

Natural organic matter (NOM) is an important redox-active component of natural porous media and predominantly occurs in the sorbed state. Nevertheless, the effects of NOM sorption at minerals on its redox properties are unknown and thus are the major objective of this study. We report how adsorption of three different humic acids (HAs) to redox-inert sorbents (polar Al<sub>2</sub>O<sub>3</sub> and nonpolar DAX-8 resin) affects their electron-exchange capacities (EEC) and redox states. The electron-donating capacity of HAs sorbed at Al<sub>2</sub>O<sub>3</sub> increased by up to 200%, whereas the EEC of the remaining dissolved HA fractions decreased compared with their initial properties. Sorption at DAX-8, however, did not affect significantly the EEC of HAs. We rationalize these results by (i) preferential sorption of NOM components rich in redox-active groups (e.g., quinone, polyphenols) and (ii) surface-catalyzed polymerization of polyphenolic compounds. Our results demonstrate that even in the absence of electron exchange with the sorbent, adsorption to polar mineral surfaces considerably affects the redox properties of NOM. Quantification of the redox state and EEC of adsorbed NOM is thus crucial for assessing electron-transfer processes as well as organic carbon stabilization and sequestration in soils and sediments.
A Non-interventional Clinical Trial Assessing Immune Responses After Radiofrequency Ablation of Liver Metastases From Colorectal Cancer
2019-11-19

<b>Background:</b> Radiofrequency ablation (RFA) is an established treatment option for malignancies located in the liver. RFA-induced irreversible coagulation necrosis leads to the release of danger signals and cellular content. Hence, RFA may constitute an endogenous <i>in situ</i> tumor vaccination, stimulating innate and adaptive immune responses, including tumor-antigen specific T cells. This may explain a phenomenon termed abscopal effect, namely tumor regression in untreated lesions evidenced after distant thermal ablation or irradiation. In this study, we therefore assessed systemic and local immune responses in individual patients treated with RFA. <b>Methods:</b> For this prospective clinical trial, patients with liver metastasis from colorectal carcinoma (mCRC) receiving RFA and undergoing metachronous liver surgery for another lesion were recruited (<i>n</i> = 9) during a 5-year period. Tumor and non-malignant liver tissue samples from six patients were investigated by whole transcriptome sequencing and tandem-mass spectrometry, characterizing naturally presented HLA ligands. Tumor antigen-derived HLA-restricted peptides were selected by different predefined approaches. Further, candidate HLA ligands were manually curated. Peripheral blood mononuclear cells were stimulated <i>in vitro</i> with epitope candidate peptides, and functional T cell responses were assessed by intracellular cytokine staining. Immunohistochemical markers were additionally investigated in surgically resected mCRC from patients treated with (<i>n</i> = 9) or without RFA (<i>n</i> = 7). <b>Results:</b> In all six investigated patients, either induced immune responses and/or pre-existing T cell immunity against the selected targets were observed. Multi-cytokine responses were <i>inter alia</i> directed against known tumor antigens such as cyclin D1 but also against a (predicted) mutation contained in ERBB3. Immunohistochemistry did not show a relevant influx of immune cells into distant malignant lesions after RFA treatment (<i>n</i> = 9) as compared to the surgery only mCRC group (<i>n</i> = 7). <b>Conclusions:</b> Using an individualized approach for target selection, RFA induced and/or boosted T cell responses specific for individual tumor antigens were more frequently detectable as compared to previously published observations with well-characterized tumor antigens. However, the witnessed modest RFA-induced immunological effects alone may not be sufficient for the rejection of established tumors. Therefore, these findings warrant further clinical investigation including the assessment of RFA combination therapies e.g., with immune stimulatory agents, cancer vaccination, and/or immune checkpoint inhibitors.
Language technology for digital humanities: introduction to the special issue
2019-11-19

The use of digital resources and tools across humanities disciplines is steadily increasing, giving rise to new research paradigms and associated methods that are commonly subsumed under the term digital humanities.Digital humanities does not constitute a new discipline in itself, but rather a new approach to humanities research that cuts across different existing humanities disciplines.While digital humanities extends well beyond language-based research, textual resources and spoken language materials play a central role in most humanities disciplines.In order to showcase the use of language tools and resources in digital humanities research, the LT4DH (Language Technology for Digital Humanities) workshop was held at COLING 2016 in Osaka, Japan.Discussions focused mainly on the following topics:-Case studies of using language technology and/or language resources with the goal of finding new answers to existing research questions in a particular humanities discipline or addressing entirely new research questions.
Cognitive-Emotional Involvement During Mirror Exposure Is Not Accompanied by Physiological Activation in Binge Eating Disorder
2019-11-19

Body image interventions have been shown to reduce self-reported cognitive-emotional facets of body image disturbance in binge eating disorder (BED). However, more objective assessment methods are required to evaluate the effects of these interventions. Therefore, the present study aimed at investigating the usefulness of vocally encoded emotional arousal as physiological correlate of body dissatisfaction during mirror exposure in women with BED. Women with BED (n = 60) and weight-matched controls (CG; n = 60) participated in an experimental thought-sampling procedure including a mirror exposure and a control condition in a repeated-measures design. Fundamental frequency as a vocal correlate of emotional arousal as well as negative, neutral, and positive body-related cognitions during both conditions were analyzed. In line with our hypotheses, the BED group verbalized more negative, and less positive and neutral body-related cognitions during the mirror exposure condition compared to the CG. Contrary to our hypotheses, though, there was a stronger increase in physiological arousal between the control and the mirror exposure condition in the CG relative to the BED group. Furthermore, a significant negative correlation between fundamental frequency and the severity of cognitive-emotional body image disturbances emerged. The findings indicate a cognitive-emotional over-involvement with physical appearance during mirror exposure in women with BED compared to weight-matched controls in the absence of a corresponding physiological pattern. Results are discussed in terms of an impaired ability of women with BED to show adequate physiological responses to body-related stress. In addition, methodological recommendations for future research are presented.
The kinesin-8 Kip3 depolymerizes microtubules with a collective force-dependent mechanism
2019-11-19

ABSTRACT Microtubules are highly dynamic filaments with dramatic structural rearrangements and length changes during the cell cycle. An accurate control of the microtubule length is essential for many cellular processes in particular, during cell division. Motor proteins from the kinesin-8 family depolymerize microtubules by interacting with their ends in a collective and length-dependent manner. However, it is still unclear how kinesin-8 depolymerizes microtubules. Here, we tracked the microtubule end-binding activity of yeast kinesin-8, Kip3, under varying loads and nucleotide conditions using high-precision optical tweezers. We found that single Kip3 motors spent up to 200 s at the microtubule end and were not stationary there but took several 8-nm forward and backward steps that were suppressed by loads. Interestingly, increased loads, similar to increased motor concentrations, also exponentially decreased the motors’ residence time at the microtubule end. On the microtubule lattice, loads also exponentially decreased the run length and time. However, for the same load, lattice run times were significantly longer compared to end residence times suggesting the presence of a distinct force-dependent detachment mechanism at the microtubule end. The force dependence of the end residence time enabled us to estimate what force must act on a single motor to achieve the microtubule depolymerization speed of a motor ensemble. This force is higher than the stall force of a single Kip3 motor, supporting a collective force-dependent depolymerization mechanism that unifies the so-called “bump-off” and “switching” models. Understanding the mechanics of kinesin-8’s microtubule end activity will provide important insights into cell division with implications for cancer research. STATEMENT OF SIGNIFICANCE Kinesin-8 motors are important for microtubule length regulation and are over-expressed in different types of cancer. Yet, on the molecular level, it is unclear how these motors depolymerize microtubules. Using high-precision optical tweezers, we measured how single yeast kinesin-8 motors, Kip3, interacted with the microtubule end. Interestingly, we found that single Kip3 motors were still motile at the microtubule end. The force dependence of how long single motors were associated with the microtubule end enabled us to estimate what force motors must exert onto each other to achieve the collective microtubule depolymerization speed of many motors. Our data support a collective force-dependent depolymerization mechanism. A better understanding of Kip3’s microtubule end activity has implications for cell division and associated diseases.
On the Aperture Problem of Binocular 3D Motion Perception
2019-11-19

Like many predators, humans have forward-facing eyes that are set a short distance apart so that an extensive region of the visual field is seen from two different points of view. The human visual system can establish a three-dimensional (3D) percept from the projection of images into the left and right eye. How the visual system integrates local motion and binocular depth in order to accomplish 3D motion perception is still under investigation. Here, we propose a geometric-statistical model that combines noisy velocity constraints with a spherical motion prior to solve the aperture problem in 3D. In two psychophysical experiments, it is shown that instantiations of this model can explain how human observers disambiguate 3D line motion direction behind a circular aperture. We discuss the implications of our results for the processing of motion and dynamic depth in the visual system.