julilili42/papers huggingface dataset:
Pediatric Cancer Data Commons: Federating and Democratizing Data for Childhood Cancer Research
2021-10-18

The international pediatric oncology community has a long history of research collaboration. In the United States, the 2019 launch of the Children's Cancer Data Initiative puts the focus on developing a rich and robust data ecosystem for pediatric oncology. In this spirit, we present here our experience in constructing the Pediatric Cancer Data Commons (PCDC) to highlight the significance of this effort in fighting pediatric cancer and improving outcomes and to provide essential information to those creating resources in other disease areas. The University of Chicago's PCDC team has worked with the international research community since 2015 to build data commons for children's cancers. We identified six critical features of successful data commons design and implementation: (1) establish the need for a data commons, (2) develop and deploy the technical infrastructure, (3) establish and implement governance, (4) make the data commons platform easy and intuitive for researchers, (5) socialize the data commons and create working knowledge and expertise in the research community, and (6) plan for longevity and sustainability. Data commons are critical to conducting research on large patient cohorts that will ultimately lead to improved outcomes for children with cancer. There is value in connecting high-quality clinical and phenotype data to external sources of data such as genomic, proteomics, and imaging data. Next steps for the PCDC include creating an informed and invested data-sharing culture, developing sustainable methods of data collection and sharing, standardizing genetic biomarker reporting, incorporating radiologic and molecular analysis data, and building models for electronic patient consent. The methods and processes described here can be extended to any clinical area and provide a blueprint for others wishing to develop similar resources.
Psychosocial demands and resources for working time organization in GP practices. Results from a team-based ethnographic study in Germany
2021-10-18

Abstract Background General practitioners (GPs) are challenged, e.g. by long working hours, and as employers they are responsible for the creation of working conditions that prevent work-related psychosocial risks. Leadership behaviour plays an important role within the working conditions of employees, thus we focused on two research questions: To what extent and how do GPs fulfil their role as entrepreneurs and leaders responsible for occupational safety and health of the team members in the organization of working time of the employees? What psychosocial factors result from the way of organization of working time for the practice team? Methods Data was collected by participant observations, individual interviews with six GPs, and five focus group discussions with 19 members of the practice staff in total. We gained access to five general practices through a teaching network associated with the Institute for General Medicine, University Hospital Essen (Germany). The analysis was carried out according to the Grounded Theory approach. Results GPs have several roles and related tasks to fulfil in the organization of working time. This can lead to perceived psychological stress. With regard to the organization of predictable working hours, vacations and sickness absence, the GPs determined the scope of action of the practice assistants. The delegation of these tasks took place to varying degrees and resulted in different work-related resources and stressors. Conclusion We described transactional and transformational leadership behaviours which are all related to specific psychosocial demands and resources and may overlap on site. Leadership training seems recommendable as part of the training of GPs and other future leaders of micro-enterprises to promote self-reflection by the entrepreneurs and leaders and strengthen occupational health of leaders and staff.
ViSpa (Vision Spaces): A computer-vision-based representation system for individual images and concept prototypes, with large-scale evaluation
2021-10-18

Quantitative, data-driven models for mental representations have long enjoyed popularity and success in psychology (for example, distributional semantic models in the language domain), but have largely been missing for the visual domain. To overcome this, we present ViSpa (Vision Spaces), high-dimensional vector spaces that include vision-based representation for naturalistic images as well as concept prototypes. These vectors are derived directly from visual stimuli through a deep convolutional neural network (DCNN) trained to classify images, and allow us to compute vision-based similarity scores between any pair of images and/or concept prototypes. We successfully evaluate these similarities against human behavioral data in a series of large-scale studies, including off-line judgments – visual similarity judgments for the referents of word pairs (Study 1) and for image pairs (Study 2), and typicality judgments for images given a label (Study 3) – as well as on-line processing times and error rates in a discrimination (Study 4) and priming task (Study 5) with naturalistic image material. ViSpa similarities predict behavioral data across all tasks, which renders ViSpa a theoretically appealing model for vision-based representations and a valuable research tool for data analysis and the construction of experimental material: ViSpa allows for precise control over experimental material consisting of images (also in combination with words), and introduces a specifically vision-based similarity for word pairs. To make ViSpa available to a wide audience, this article a) includes (video) tutorials on how to use ViSpa in R, and b) presents a user-friendly web interface at http://vispa.fritzguenther.de.
Differentiating Surgeons’ Expertise solely by Eye Movement Features
2021-10-18

Medical schools are increasingly seeking to use objective measures to assess surgical skills. This extends even to perceptual skills, which are particularly important in minimally invasive surgery. Eye tracking provides a promising approach to obtaining such objective metrics of visual perception. In this work, we report on results of a cadaveric study of visual perception during shoulder arthroscopy. We present a model for classifying surgeons into three levels of expertise using only eye movements. The model achieves a classification accuracy of 84.44% using only a small set of selected features. We also examine and characterize the changes in visual perception metrics between the different levels of expertise, forming a basis for development of a system for objective assessment.
The Na+-activated K+ channel Slack contributes to synaptic development and plasticity
2021-10-18

Abstract Human mutations of the Na + -activated K + channel Slack ( KCNT1 ) are associated with epilepsy and intellectual disability. Accordingly, Slack knockout mice ( Slack −/− ) exhibit cognitive flexibility deficits in distinct behavioral tasks. So far, however, the underlying causes as well as the role of Slack in hippocampus-dependent memory functions remain enigmatic. We now report that infant (P6–P14) Slack −/− lack both hippocampal LTD and LTP, likely due to impaired NMDA receptor (NMDAR) signaling. Postsynaptic GluN2B levels are reduced in infant Slack −/− , evidenced by lower amplitudes of NMDAR-meditated excitatory postsynaptic potentials. Low GluN2B affected NMDAR-mediated Ca 2+ -influx, rendering cultured hippocampal Slack −/− neurons highly insensitive to the GluN2B-specific inhibitor Ro 25-6981. Furthermore, dephosphorylation of the AMPA receptor (AMPAR) subunit GluA1 at S845, which is involved in AMPAR endocytosis during homeostatic and neuromodulator-regulated plasticity, is reduced after chemical LTD (cLTD) in infant Slack −/− . We additionally detect a lack of mGluR-induced LTD in infant Slack −/− , possibly caused by upregulation of the recycling endosome-associated small GTPase Rab4 which might accelerate AMPAR recycling from early endosomes. Interestingly, LTP and mGluR LTD, but not LTD and S845 dephosphorylation after cLTD are restored in adult Slack −/− . This together with normalized expression levels of GluN2B and Rab4 hints to developmental “restoration” of LTP expression despite Slack ablation, whereas in infant and adult brain, NMDAR-dependent LTD induction depends on this channel. Based on the present findings, NMDAR and vesicular transport might represent novel targets for the therapy of intellectual disability associated with Slack mutations. Consequently, careful modulation of hippocampal Slack activity should also improve learning abilities.
Neanderthals of Porto Selvaggio in southern Italy: lithic industry of Grotta Torre dell'Alto (Nardò, Lecce)
2021-10-18

ABSTRACT Porto Selvaggio in southern Italy is where the Uluzzian culture was first identified and documented, providing key insights into the transition from the Middle to the Upper Paleolithic. The area has also yielded evidence for continuous occupations by Neanderthals spanning between Marine Isotope Stage (MIS) 5 and 3. Situated in the Natural Regional Park of Porto Selvaggio, different sites were excavated by Borzatti von Löwenstern in the 1960 and 1970s. As one of the initiatives in the research program of the Museo della Preistoria di Nardò, we have revisited the artifact assemblages from these caves. Based on the lithic analysis of production sequences, we document the development of Levallois and laminar methods before MIS 3 when this form of reduction sequence presumably dominated in the region according to the previous research. The review of the lithic assemblages is combined with the contextualization of chronostratigraphy and paleoenvironmental study in the region to consider the possible role that this region had for Neanderthals during unfavorable climatic conditions.
The "Situative Nature" of Competence and Value Beliefs and the Predictive Power of Autonomy Support: A Multilevel Investigation of Repeated Observations
2021-10-18

These are the supplemental materials for the following paper: Parrisius, C., Gaspard, H., Zitzmann, S., Trautwein, U., &amp; Nagengast, B. (2021). The "situative nature" of competence and value beliefs and the predictive power of autonomy support: A multilevel investigation of repeated observations. Journal of Educational Psychology, Advance online publication. http://dx.doi.org/10.1037/edu0000680
Establishing and Boosting Communication in The European Reference Network For Rare Neurological Diseases (ERN-RND): The Impact of Offering Free Educational Webinars
2021-10-18

<title>Abstract</title> <bold>Background:</bold> Since it first started operating in 2017, the European Reference Network for Rare Neurological Diseases (ERN-RND) implemented a multi-channel communication strategy to effectively reach its target audience: healthcare professionals, patients, researchers, industry representatives and the general public. It first created a website containing useful and up to date information followed by social media accounts. We compared the analytical data collected about the ERN-RND website and social media channels (Twitter, Facebook, YouTube) during two periods: October 2018 to September 2019 and the year after the ERN-RND free educational webinars were launched, from October 2019 to September 2020. This allowed us to quantify the impact of offering a tangible product (webinars) on the communication strategy. <bold>Results: </bold>The analytical data obtained from October 2018 to September 2019 and from October 2019 to September 2020 clearly shows a significant increase in traffic and followers since the launch of the ERN-RND webinars in November 2019. We also created a communication survey which was disseminated between February and June 2021. We collected responses from 61 people: 38 healthcare professionals, 11 scientists, 10 patients (advocates), 2 industry representatives, 1 patient association, 1 charity representative, 1 resident and 1 master student. Most respondents answered ”webinars” as the number one reason when asked about which content they look for on the ERN-RND website. <bold>Conclusions: </bold>Offering a tangible product - such as the webinars presented in this report - to a specific target group (healthcare professionals) supported our communication strategy by driving traffic to ERN-RND communication channels. It has also successfully tackled ERN-RND’s general aim: by enabling the flow of knowledge on rare neurological and movement disorders reach the medical community in hospitals treating patients with these rare and complex conditions, patients ultimately benefit from improved and faster diagnosis, care, and treatment. We aim to set up similar strategies to effectively reach other or the same target groups. For healthcare professionals, organising eConsultations via the Clinical Patient Management System (CPMS) or disseminating standards of care such as diagnostic and therapeutic algorithms as well as clinical practice guidelines might offer potential. For the patient community, organising customised and multilingual webinars could also work.
Influence of Pharyngeal Anaesthesia on Post-Bronchoscopic Coughing: A Prospective, Single Blinded, Multicentre Trial
2021-10-18

Background: Local anaesthesia of the pharynx (LAP) was introduced in the era of rigid bronchoscopy (which was initially a conscious procedure under local anaesthetic), and continued into the era of flexible bronchoscopy (FB) in order to facilitate introduction of the FB. LAP reduces cough and gagging reflex, but its post-procedural effect is unclear. This prospective multicentre trial evaluated the effect of LAP on coughing intensity/time and patient comfort after FB, and the feasibility of FB under propofol sedation alone, without LAP. Material and methods: FB was performed in 74 consecutive patients under sedation with propofol, either alone (35 patients, 47.3%) or with additional LAP (39 patients, 52.7%). A primary endpoint of post-procedural coughing duration in the first 10 min after awakening was evaluated. A secondary endpoint was the cough frequency, quality and development of coughing in the same period during the 10 min post-procedure. Finally, the ease of undertaking the FB and the patient’s tolerance and safety were evaluated from the point of view of the investigator, the assistant technician and the patient. Results: We observed a trend to a shorter cumulative coughing time of 48.6 s in the group without LAP compared to 82.8 s in the group receiving LAP within the first 10 min after the procedure, although this difference was not significant (p = 0.24). There was no significant difference in the cough frequency, quality, peri-procedural complication rate, nor patient tolerance or safety. FB, including any additional procedure, could be performed equally well with or without LAP in both groups. Conclusions: Our study suggests that undertaking FB under deep sedation without LAP does to affect post-procedural cough duration and frequency. However, further prospective randomised controlled trials are needed to further support this finding.
Statistical bias control in typology
2021-10-18

&lt;p&gt;These are the code and data files for the paper &lt;em&gt;Statistical bias control in typology&lt;/em&gt; which will appear in Linguistic Typology.&lt;/p&gt; &lt;p&gt;Please cite the paper: https://www.degruyter.com/document/doi/10.1515/lingty-2021-0002/html&lt;/p&gt;
Peptide conjugates of 18β-glycyrrhetinic acid as potent inhibitors of α-glucosidase and AGEs-induced oxidation
2021-10-19

18β-Glycyrrhetinic acid (18β-GA) is known for several biological activities, and has been the focus of extensive research for the development of therapeutic agents. In the current study, 18β-GA-peptide conjugates 2-11 were evaluated for their in vitro α-glucosidase inhibitory and antiglycation activities. Structure-activity relationship (SAR) established and molecular interactions of active bioconjugates with the enzyme's binding sites were predicted through molecular modeling approach. In tripeptide moiety of conjugates 2-11, peptide residue at position 1 was found to have a significant role on α-glucosidase inhibition. The most active 18β-GA-peptide conjugates 5 (18β-GA-Cys<sup>1</sup>-Tyr<sup>2</sup>-Gly<sup>3</sup>), and 8 (18β-GA-Pro<sup>1</sup>-Tyr<sup>2</sup>-Gly<sup>3</sup>) exhibited several-fold potent α-glucosidase inhibition (IC<sub>50</sub> values 20-28 μM), as compared to standard drug acarbose (IC<sub>50</sub> = 875.8 ± 2.10 μM). Kinetic studies of potent compounds, 4-8 revealed that conjugate 5 exhibits competitive-type of inhibition, while conjugates 6-8 showed a non-competitive type of inhibition. The simulation studies also supported the kinetic results that conjugate 5 (18β-GA-Cys<sup>1</sup>-Tyr<sup>2</sup>-Gly<sup>3</sup>) inhibits the α-glucosidase enzyme by blocking its substrate binding site. AGEs-induced NO<sup>•</sup> inhibitors play an important role in controlling the inflammation associated with diabetes mellitus. The peptide conjugates 2-11 were also evaluated in vitro for AGEs-induced NO<sup>•</sup> inhibition using RAW 264.7 macrophage cell line. Our data revealed that conjugates 7-10 were the more potent AGEs-induced NO<sup>•</sup> inhibitors, comparable to standards rutin, and PDTC. The peptide conjugate 5 (a competitive inhibitor of α-glucosidase) also exhibited a strong inhibitory activity against AGEs-induced NO<sup>•</sup> production. Furthermore, peptide conjugates 2-11 were found non-cytotoxic to mouse fibroblast NIH-3T3, and murine macrophages RAW 264.7 cell lines. In conclusion, our data demonstrates that besides possessing strong α-glucosidase inhibition, the newly synthesized peptide conjugates also alleviated the AGEs-induced NO<sup>•</sup> production in RAW macrophages. Dual inhibition of α-glucosidase enzyme, and AGEs-induced NO<sup>•</sup> production by 18β-GA-peptide conjugates qualify them for further research in anti-diabetic drug discovery.
Motivations for birdwatching: Support for a three-dimensional model
2021-10-19

Studying wildlife-oriented motivations is important for park design, citizen science projects, and avitourism. In previous work, motivations were modeled as social, achievement, and appreciation oriented components of wildlife-related motivations. The aims of this study were to test the components of this model with birdwatchers and to study any variation in motivations to participate in birdwatching in a European context. Data from birdwatchers were collected in German speaking countries and a total of 2,743 birdwatchers participated in this study (1,285 female, 1,446 male, 12 diverse). Exploratory factor analysis revealed a three-factor final solution with social, achievement, and enjoyment of nature factors as primary motivations, which supported the three-factor model of recreation motivations and can help to tailor programs, exhibitions, or guided tours according to birdwatcher motivations, and recruit people for conservation actions and citizen science programs.
Tricopper Melaminate, a Metal–Organic Framework Containing Dehydrogenated Melamine and Cu–Cu Bonding
2021-10-19

Crystals of Cu<sub>3</sub>(C<sub>3</sub>N<sub>6</sub>H<sub>3</sub>) are formed by a solid-state reaction of CuCl with melamine to form a layered framework structure with open pores running along the hexagonal axis direction of the <i>P</i>6/<i>mcc</i> structure. The compound contains the hitherto unknown (C<sub>3</sub>N<sub>6</sub>H<sub>3</sub>)<sup>3-</sup> ion, assigned as melaminate. Bonding interactions within and between Cu-Cu dumbbells, which connect melaminate ions into layers, are analyzed by density functional theory calculations of the electron localization function and directional Young's modulus. Band structure calculations reveal the material to be a semiconductor with a band gap on the order of 2 eV.
Tumor DNA‐methylome derived epigenetic fingerprint identifies HPV‐negative head and neck patients at risk for locoregional recurrence after postoperative radiochemotherapy
2021-10-19

Abstract Biomarkers with relevance for loco‐regional therapy are needed in human papillomavirus negative aka HPV(−) head and neck squamous cell carcinoma (HNSCC). Based on the premise that DNA methylation pattern is highly conserved, we sought to develop a reliable and robust methylome‐based classifier identifying HPV(−) HNSCC patients at risk for loco‐regional recurrence (LR) and all‐event progression after postoperative radiochemotherapy (PORT‐C). The training cohort consisted of HPV‐DNA negative HNSCC patients (n = 128) homogeneously treated with PORT‐C in frame of the German Cancer Consortium—Radiation Oncology Group (DKTK‐ROG) multicenter biomarker trial. DNA Methylation analysis was performed using Illumina 450 K and 850 K‐EPIC microarray technology. The performance of the classifier was integrated with a series of biomarkers studied in the training set namely hypoxia‐, 5‐microRNA (5‐miR), stem‐cell gene‐expression signatures and immunohistochemistry (IHC)‐based immunological characterization of tumors (CD3/CD8/PD‐L1/PD1). Validation occurred in an independent cohort of HPV(−) HNSCC patients, pooled from two German centers (n = 125). We identified a 38‐methylation probe‐based HPV(−) Independent Classifier of disease Recurrence (HICR) with high prognostic value for LR, distant metastasis and overall survival ( P &lt; 10 −9 ). HICR remained significant after multivariate analysis adjusting for anatomical site, lymph node extracapsular extension (ECE) and size (T‐stage). HICR high‐risk tumors were enriched for younger patients with hypoxic tumors (15‐gene signature) and elevated 5‐miR score. After adjustment for hypoxia and 5‐miR covariates, HICR maintained predicting all endpoints. HICR provides a novel mean for assessing the risk of LR in HPV(−) HNSCC patients treated with PORT‐C and opens a new opportunity for biomarker‐assisted stratification and therapy adaptation in these patients.