julilili42/papers huggingface dataset:
The Density of Fan-Planar Graphs
2022-02-11

A topological drawing of a graph is fan-planar if for each edge the edges crossing form a star and no endpoint of is enclosed by and its crossing edges. A fan-planar graph is a graph admitting such a drawing. Equivalently, this can be formulated by three forbidden patterns, one of which is the configuration where is crossed by two independent edges and the other two where is crossed by two incident edges in a way that encloses some endpoint of . A topological drawing is simple if any two edges have at most one point in common. Fan-planar graphs are a new member in the ever-growing list of topological graphs defined by forbidden intersection patterns, such as planar graphs and their generalizations, Turán-graphs and Conway's thrackle conjecture. Hence fan-planar graphs fall into an important field in combinatorial geometry with applications in various areas of discrete mathematics. As every -planar graph is fan-planar and every fan-planar graph is -quasiplanar, they also fit perfectly in a recent series of works on nearly-planar graphs from the areas of graph drawing and combinatorial embeddings. In this paper we show that every fan-planar graph on vertices has at most edges, even though a fan-planar drawing may have a quadratic number of crossings. Our bound, which is tight for every , indicates how nicely fan-planar graphs fit in the row with planar graphs ( edges) and -planar graphs ( edges). With this, fan-planar graphs form an inclusion-wise largest non-trivial class of topological graphs defined by forbidden patterns, for which the maximum number of edges on vertices is known exactly. We demonstrate that maximum fan-planar graphs carry a rich structure, which makes this class attractive for many algorithms commonly used in graph drawing. Finally, we discuss possible extensions and generalizations of these new concepts.
Prospective validation of a new imaging scorecard to assess leptomeningeal metastasis: A joint EORTC BTG and RANO effort
2022-02-11

Abstract Background Validation of the 2016 RANO MRI scorecard for leptomeningeal metastasis failed for multiple reasons. Accordingly, this joint EORTC Brain Tumor Group and RANO effort sought to prospectively validate a revised MRI scorecard for response assessment in leptomeningeal metastasis. Methods Coded paired cerebrospinal MRI of 20 patients with leptomeningeal metastases from solid cancers at baseline and follow-up after treatment and instructions for assessment were provided via the EORTC imaging platform. The Kappa coefficient was used to evaluate the interobserver pairwise agreement. Results Thirty-five raters participated, including 9 neuroradiologists, 17 neurologists, 4 radiation oncologists, 3 neurosurgeons, and 2 medical oncologists. Among single leptomeningeal metastases-related imaging findings at baseline, the best median concordance was noted for hydrocephalus (Kappa = 0.63), and the worst median concordance for spinal linear enhancing disease (Kappa = 0.46). The median concordance of raters for the overall response assessment was moderate (Kappa = 0.44). Notably, the interobserver agreement for the presence of parenchymal brain metastases at baseline was fair (Kappa = 0.29) and virtually absent for their response to treatment. 394 of 700 ratings (20 patients x 35 raters, 56%) were fully completed. In 308 of 394 fully completed ratings (78%), the overall response assessment perfectly matched the summary interpretation of the single ratings as proposed in the scorecard instructions. Conclusion This study confirms the principle utility of the new scorecard, but also indicates the need for training of MRI assessment with a dedicated reviewer panel in clinical trials. Electronic case report forms with “blocking options” may be required to enforce completeness and quality of scoring.
Long-Term Clinical Outcome and Prognostic Factors of Children and Adolescents with Localized Rhabdomyosarcoma Treated on the CWS-2002P Protocol
2022-02-11

We report here the results of the prospective, non-randomized, historically controlled CWS-2002P study in patients ≤ 21 years with localized RMS developed with the aim to improve the long-term outcome by adapting the burden of therapy to risk profile and to investigate the feasibility and relation to the outcome of maintenance therapy (MT) in the high-risk groups. Patients were allocated into low-risk (LR), standard-risk (SR), high-risk (HR), and very high-risk (VHR) groups. Chemotherapy consisted of vincristine (VCR) and dactinomycin (ACTO-D) for all patients with the addition of ifosfamide (IFO) in the SR, HR, and VHR and doxorubicin (DOX) in the HR and VHR groups. Low-dose cyclophosphamide and vinblastine maintenance therapy (MT) over 6 months was recommended in the HR and VHR groups. A total of 444 patients have been included in this analysis. With a median follow-up of 9·6 years (IQR 7·6–10·9) for patients alive, the 5-year EFS and OS for the whole group was 73% (95% CI 69–77) and 80% (95% CI 76–84), respectively. The 5-year EFS by risk group was 100% in the LR, 79% (95% CI 72–84) in the SR, 69% (95% CI 63–75) in the HR, and 42% (95% CI 23–61) in the VHR (log-rank p = 0.000). The 5-year EFS was 77% (95% CI 70–84) for 155 patients in the HR group who received MT as compared to 63% (95% CI 50–76) for 49 patients who did not (log-rank p = 0.015). Neither the reduction in the IFO dose in the SR nor the increased dose intensity of DOX in HR groups influenced the outcome when compared to the previous CWS and other European studies. MT was feasible, seemed to have an impact on prognosis, and should be studied in a well-controlled prospective trial in this patient population. The weighting of risk factors used for therapy stratification needs to be reevaluated.
Does Playing Apart Really Bring Us Together? Investigating the Link Between Perceived Loneliness and the Use of Video Games During a Period of Social Distancing
2022-02-11

During the COVID-19 pandemic, several countries implemented social distancing measures to contain virus transmission. However, these vital safety measures have the potential to impair mental health or wellbeing, for instance, from increased perceived loneliness. Playing social video games may offer a way to continue to socialize while adhering to social distancing measures. To examine this issue further, the present online survey investigated social gaming during the pandemic and its association to perceived loneliness within a German-speaking sample. Results indicated a small positive correlation between general gaming frequency and perceived loneliness. Detailed analysis revealed a negative association between perceived loneliness and increased social forms of video gaming. Specifically, gamers with a higher social motive for gaming perceived less loneliness, but gamers with a dominant escape motive demonstrated a positive link to perceived loneliness. The use of social gaming in times of social distancing seems to play a small but significant factor in perceived loneliness compared to other demographical data. The findings are discussed with respect to methodological limitations, effect sizes, and sample characteristics. The results enrich the current knowledge on video gaming and its link to social wellbeing and provide a more nuanced picture than simplistic investigations of screen time.
A Three-Dimensional Organoid Model of Primary Breast Cancer to Investigate the Effects of Oncolytic Virotherapy
2022-02-11

Background: Although several oncolytic viruses have already been tested in early-stage clinical studies of breast cancer, there is still an urgent need to develop patient-derived experimental systems that mimic the response of breast cancer to oncolytic agents in preparation of testing different oncolytic viruses in clinical trials. We addressed this need by developing a protocol to study the effects of oncolytic viruses in stable organoid cell cultures derived from breast cancer tissue. Methods: We used an established three-dimensional organoid model derived from tissue of 10 patients with primary breast cancer. We developed an experimental protocol for infecting organoid cultures with oncolytic viruses and compared the oncolytic effects of a measles vaccine virus (MeV) and a vaccinia virus (GLV) genetically engineered to express either green fluorescent protein (MeV-GFP) and red fluorescent protein (GLV-0b347), respectively, or a suicide gene encoding a fusion of cytosine deaminase with uracil phosphoribosyltransferase (MeV-SCD and GLV-1h94, respectively), thereby enabling enzymatic conversion of the prodrug 5-fluorocytosine (5-FC) into cytotoxic compounds 5-fluorouracil (5-FU) and 5-fluorouridine monophosphate (5-FUMP). Results: The method demonstrated that all oncolytic viruses significantly inhibited cell viability in organoid cultures derived from breast cancer tissue. The oncolytic effects of the oncolytic viruses expressing suicide genes (MeV-SCD and GLV-1h94) were further enhanced by virus-triggered conversion of the prodrug 5-FC to toxic 5-FU and toxic 5-FUMP. Conclusions: We were able to develop a protocol to assess the effects of two different types of oncolytic viruses in stable organoid cell cultures derived from breast cancer tissue. The greatest oncolytic effects were observed when the oncolytic viruses were engineered to express a suicide gene (MeV-SCD and GLV-1h94) in the presence of the prodrug 5-FC. The model therefore provides a promising in vitro method to help further testing and engineering of new generations of virotherapeutic vectors for in vivo use.
Quality of Life After Vestibular Schwannoma Surgery: A Question of Perspective
2022-02-11

Objective Health-related quality of life (HRQoL) and self-reported outcome measures have a relevant impact on the medical decision-making process. They capture either the current status and allow for multiple prospective evaluations in the course of a treatment or rely on the retrospective comparison of health of patients before and after an intervention to assess its benefit. Importantly, these patient-assessed measures may be influenced by psychological factors. We compared HRQoL and perceived benefit in the course of surgical vestibular schwannoma (VS) treatment, as assessed by the patients from a prospective and retrospective point-of-view, and evaluated the influence of co-morbid depression. Methods Within a prospective observational single-center study, forty-three patients with VS were investigated before and after retrosigmoid tumor resection. SF-36, Beck Depression Inventory and patient-assessed clinical symptoms were acquired before surgery and at follow-up. At follow-up, the Glasgow Benefit Inventory (GBI) was acquired as well. Results SF-36 scores were significantly lower than the age and sex matched normative data in six and three out of eight categories before and after surgery, respectively. Three categories improved significantly after vs. before surgery; one of them (global health) reached a minimal clinical important difference. In contrast, patients reported predominantly a deterioration, when asked for a retrospective evaluation of the benefit (i.e., GBI). Depression correlated with both SF-36 and GBI, determined dissatisfaction, improved significantly after surgery and was the measure that had the largest impact on HRQoL. Conclusion Prospective and retrospective HRQoL measures may lead to different findings and can be confounded by psychological factors.
Phase diagram of quantum generalized Potts-Hopfield neural networks
2022-02-11

Abstract We introduce and analyze an open quantum generalization of the q-state Potts-Hopfield neural network (NN), which is an associative memory model based on multi-level classical spins. The dynamics of this many-body system is formulated in terms of a Markovian master equation of Lindblad type, which allows to incorporate both probabilistic classical and coherent quantum processes on an equal footing. By employing a mean field description we investigate how classical fluctuations due to temperature and quantum fluctuations effectuated by coherent spin rotations affect the ability of the network to retrieve stored memory patterns. We construct the corresponding phase diagram, which in the low temperature regime displays pattern retrieval in analogy to the classical Potts-Hopfield NN. When increasing quantum fluctuations, however, a limit cycle phase emerges, which has no classical counterpart. This shows that quantum effects can qualitatively alter the structure of the stationary state manifold with respect to the classical model, and potentially allow one to encode and retrieve novel types of patterns.
Divergence Between Informant and Self-Ratings of Activities of Daily Living Impairments in Parkinson’s Disease
2022-02-11

Objective To examine the agreement between self- and informant-reported activities of daily living (ADL) deficits in Parkinson’s Disease (PD) patients, and to examine factors influencing ADL ratings. Background In PD, the loss of functional independence is an important outcome of disease progression. The valid assessment of ADL function in PD is essential, but it is unclear to what extent informants’ and patients’ perceptions of their daily functions concur, and how other factors may influence both ratings. Methods Data of 150 PD patients who underwent cognitive and motor testing, as well as their informants were analyzed. The 10-item Functional Activities Questionnaire (FAQ), completed separately by patients (FAQ-S) and their informants (FAQ-I), assessed ADL function. Weighted κ statistics summarized level of agreement, and a discrepancy score (FAQ-I – FAQ-S) quantified agreement. Correlation analyses between FAQ total scores, patient and informant characteristics, and cognitive scores were conducted, with post hoc regressions to determine the associations between both FAQ scores and cognition, independent of patient characteristics. Results The sample included 87 patients with normal cognition, 50 with mild cognitive impairment, and 13 with dementia. Overall, there was fair to moderate agreement between patients and informants on individual FAQ items (0.27 ≤ κ ≤ 0.61, p &amp;lt; 0.004), with greater discrepancies with increasing cognitive impairment. Patients’ age, motor severity, non-motor burden, and depression also affected both ratings (0.27 ≤ r ≤ 0.50, p &amp;lt; 0.001), with motor severity showing the greatest influence on both ratings. Both the FAQ-I and FAQ-S were correlated with almost all cognitive domains. Post hoc regression analyses controlling for patient characteristics showed that the attention domain was a significant predictor of both the FAQ-S and FAQ-I scores, and memory was also a significant predictor of the FAQ-I score. Only 29.3% of patients agreed perfectly with informants on the FAQ total score, with informants most commonly rating ADL impairments as more severe than patients. Conclusions Patient and informant ratings of ADL function using FAQ items showed moderate agreement, with only few items reaching substantial agreement. Ratings of both were associated with patient cognitive status, but also other characteristics. In addition to patient and informant reports, objective measures are needed to accurately classify ADL deficits in PD.
Limited reciprocal surrogacy of bird and habitat diversity and inconsistencies in their representation in Romanian protected areas
2022-02-11

Because it is impossible to comprehensively characterize biodiversity at all levels of organization, conservation prioritization efforts need to rely on surrogates. As species distribution maps of relished groups as well as high-resolution remotely sensed data increasingly become available, both types of surrogates are commonly used. A good surrogate should represent as much of biodiversity as possible, but it often remains unclear to what extent this is the case. Here, we aimed to address this question by assessing how well bird species and habitat diversity represent one another. We conducted our study in Romania, a species-rich country with high landscape heterogeneity where bird species distribution data have only recently started to become available. First, we prioritized areas for conservation based on either 137 breeding bird species or 36 habitat classes, and then evaluated their reciprocal surrogacy performance. Second, we examined how well these features are represented in already existing protected areas. Finally, we identified target regions of high conservation value for the potential expansion of the current network of reserves (as planned under the new EU Biodiversity Strategy for 2030). We found a limited reciprocal surrogacy performance, with bird species performing slightly better as a conservation surrogate for habitat diversity than vice versa. We could also show that areas with a high conservation value based on habitat diversity were represented better in already existing protected areas than areas based on bird species, which varied considerably between species. Our results highlight that taxonomic and environmental (i.e., habitat types) data may perform rather poorly as reciprocal surrogates, and multiple sources of data are required for a full evaluation of protected areas expansion.
Serum/glucocorticoid‐regulated kinase 1‐targeted transient receptor potential oxalate subtype 1 regulates bladder smooth muscle cell proliferation due to bladder outlet obstruction in mice via activated T cell nuclear factor transcription factor 2
2022-02-11

Abstract Bladder outlet obstruction (BOO) is a type of chronic disease that is mainly caused by benign prostatic hyperplasia. Previous studies discovered the involvements of both serum/glucocorticoid‐regulated kinase 1 (SGK1) and activated T cell nuclear factor transcription factor 2 (NFAT2) in the proliferation of smooth muscle cells after BOO. However, the relationship between these two molecules is yet to be explored. Thus, this study explored the specific mechanism of the SGK1‐NFAT2 signaling pathway in mouse BOO‐mediated bladder smooth muscle cell proliferation in vivo and in vitro. In vivo experiments were performed by suturing 1/2 of the external urethra of female BALB/C mice to cause BOO for 2 weeks. In vitro, mouse bladder smooth muscle cells (MBSMCs) were treated with dexamethasone (Dex) or dexamethasone + SB705498 for 12 h and were transfected with SGK1 siRNA for 48 h. The expression and distribution of SGK1, transient receptor potential oxalate subtype 1 (TRPV1), NFAT2, and proliferating cell nuclear antigen (PCNA) were measured by Western blotting, polymerase chain reaction, and immunohistochemistry. The relationship between SGK1 and TRPV1 was analyzed by coimmunoprecipitation . The proliferation of MBSMCs was examined by 5‐ethynyl‐2′‐deoxyuridine and cell counting kit 8 assays. Bladder weight, smooth muscle thickness, and collagen deposition in mice after 2 weeks of BOO were examined. Bladder weight, smooth muscle thickness, the collagen deposition ratio, and the expression of SGK1, TRPV1, NFAT2, and PCNA were significantly increased in mice after 2 weeks of BOO. Compared with the control, 10 μM Dex promoted the expression of these four molecules and the proliferation of MBSMCs. After inhibiting TRPV1, only the expression of SGK1 was not affected, and the proliferation of MBSMCs was inhibited. After silencing SGK1, the expression of these four molecules and the proliferation of MBSMCs decreased. Coimmunoprecipitation suggested that SGK1 acted directly on TRPV1. In this study, SGK1 targeted TRPV1 to regulate the proliferation of MBSMCs mediated by BOO in mice through NFAT2 and then affected the process of bladder remodeling after BOO. This finding may provide a strategy for BOO drug target screening.
Data and code for "Sustainable Human Population Density in Western Europe between 560.000 and 360.000 years ago"
2022-02-11

This dataset contains the modeling results GIS data (maps) of the study “Sustainable Human Population Density in Western Europe between 560.000 and 360.000 years ago” by Rodríguez et al. (2022). The NPP data (npp.zip) was computed using an empirical formula (the Miami model) from palaeo temperature and palaeo precipitation data aggregated for each timeslice from the Oscillayers dataset (Gamisch, 2019), as defined in Rodríguez et al. (2022, in review). The Population densities file (pop_densities.zip) contains the computed minimum and maximum population densities rasters for each of the defined MIS timeslices. With the population density value Dc in logarithmic form log(Dc). The Species Distribution Model (sdm.7z) includes input data (folder /data), intermediate results (folder /work) and results and figures (folder /results). All modelling steps are included as an R project in the folder /scripts. The R project is subdivided into individual scripts for data preparation (1.x), sampling procedure (2.x), and model computation (3.x). The habitat range estimation (habitat_ranges.zip) includes the potential spatial boundaries of the hominin habitat as binary raster files with 1=presence and 0=absence. The ranges rely on a dichotomic classification of the habitat suitability with a threshold value inferred from the 5% quantile of the presence data. The habitat suitability (habitat_suitability.zip) is the result of the Species Distribution Modelling and describes the environmental suitability for hominin presence based on the sites considered in this study. The values range between 0=low and 1=high suitability. The dataset includes the mean (pred_mean) and standard deviation (pred_std) of multiple model runs.
BEAST begins: Sample characteristics and survey performance of the B-star Exoplanet Abundance Study
2022-02-12

While the occurrence rate of wide giant planets appears to increase with stellar mass at least up through the A-type regime, B-type stars have not been systematically studied in large-scale surveys so far. It therefore remains unclear up to what stellar mass this occurrence trend continues. The B-star Exoplanet Abundance Study (BEAST) is a direct imaging survey with the extreme adaptive optics instrument SPHERE, targeting 85 B-type stars in the young Scorpius-Centaurus (Sco-Cen) region with the aim to detect giant planets at wide separations and constrain their occurrence rate and physical properties. The statistical outcome of the survey will help determine if and where an upper stellar mass limit for planet formation occurs. In this work, we describe the selection and characterization of the BEAST target sample. Particular emphasis is placed on the age of each system, which is a central parameter in interpreting direct imaging observations. We implement a novel scheme for age dating based on kinematic sub-structures within Sco-Cen, which complements and expands upon previous age determinations in the literature. We also present initial results from the first epoch observations, including the detections of ten stellar companions, of which six were previously unknown. All planetary candidates in the survey will need follow up in second epoch observations, which are part of the allocated observational programme and will be executed in the near future.