julilili42/papers huggingface dataset:
Odevixibat and partial external biliary diversion showed equal improvement of cholestasis in a patient with progressive familial intrahepatic cholestasis
2020-06-01

Untreated progressive familial intrahepatic cholestasis (PFIC) type 2, or bile salt exporter protein deficiency, frequently leads to severe pruritus, impaired growth and progressive liver fibrosis with risk of organ failure. We describe a 15-month-old male patient with severe pruritus diagnosed with PFIC type 2 enrolled in an open-label phase 2 study who received 4 weeks of treatment with odevixibat, an ileal bile acid transporter inhibitor under development for cholestatic liver disease treatment. The patient experienced reductions in serum bile acids and improvement in itching and sleep scores, and odevixibat was well tolerated. After the odevixibat study, symptoms returned and the patient underwent partial external biliary diversion (PEBD). Odevixibat treatment and PEBD produced similar normalisation of serum bile acid levels and improvements in pruritus and sleep disruptions. Thus, odevixibat appeared to be as effective as invasive PEBD in treating serum bile acids and cholestatic pruritus in this patient.
The role of feedback and instruction on the cross-situational learning of vocabulary and morphosyntax: Mixed effects models reveal local and global effects on acquisition
2020-06-01

First language acquisition is implicit, in that explicit information about the language structure to be learned is not provided to children. Instead, they must acquire both vocabulary and grammar incrementally, by generalizing across multiple situations that eventually enable links between words in utterances and referents in the environment to be established. However, this raises a problem of how vocabulary can be acquired without first knowing the role of the word within the syntax of a sentence. It also raises practical issues about the extent to which different instructional conditions – about grammar in advance of learning or feedback about correct decisions during learning – might influence second language acquisition of implicitly experienced information about the language. In an artificial language learning study, we studied participants learning language from inductive exposure, but under different instructional conditions. Language learners were exposed to complex utterances and complex scenes and had to determine the meaning and the grammar of the language from these co-occurrences with environmental scenes. We found that learning was boosted by explicit feedback, but not by explicit instruction about the grammar of the language, compared to an implicit learning condition. However, the effect of feedback was not general across all aspects of the language. Feedback improved vocabulary, but did not affect syntax learning. We further investigated the local, contextual effects on learning, and found that previous knowledge of vocabulary within an utterance improved learning but that this was driven only by certain grammatical categories in the language. The results have implications for theories of second language learning informed by our understanding of first language acquisition as well as practical implications for learning instruction and optimal, contingent adjustment of learners’ environment during their learning.
LNAPL Recovery Endpoints: Lessons Learnt Through Modeling, Experiments, and Field Trials
2020-06-01

Abstract It is important to estimate what light nonaqueous phase liquid (LNAPL) recovery can be practicably achieved from subsurface environments. Over the last decade, research to address this included a broad field program, laboratory measurements and experimentation, and modeling approaches. Here, we consolidate key findings from the research in the context of current literature and understanding, with a focus on a well‐validated, multiphase multicomponent modeling approach to achieve estimates of reasonable endpoints for LNAPL recovery. Simple analytical models can provide approximate saturation distributions and estimates of LNAPL recoverability via transmissivity approximation, but are insufficient to predict LNAPL saturation‐ and composition‐based recovery endpoints for various recovery technologies. This is because they cannot account for multiphase, multicomponent fate and transport and key processes such as hysteresis. Recent advances to improve estimates of the fraction of recoverable LNAPL and its transmissivity are summarized. These advances include further development and application of a well‐validated model to characterize active LNAPL recovery endpoints. We present key factors that affect the determination of LNAPL recovery endpoints, and outline how recovery endpoints are affected by natural source zone depletion (NSZD—currently gaining acceptance as a LNAPL remediation option). Major factors include geo‐physical characteristics of the formation, magnitude of an LNAPL release and partitioning properties of the key LNAPL constituents of concern. Based on the capabilities of the validated model, the paper also provides a basis to optimize LNAPL recovery efforts.
Multi‐parametric artificial neural network fitting of phase‐cycled balanced steady‐state free precession data
2020-06-01

Purpose Standard relaxation time quantification using phase‐cycled balanced steady‐state free precession (bSSFP), eg, motion‐insensitive rapid configuration relaxometry (MIRACLE), is subject to a considerable underestimation of tissue T 1 and T 2 due to asymmetric intra‐voxel frequency distributions. In this work, an artificial neural network (ANN) fitting approach is proposed to simultaneously extract accurate reference relaxation times (T 1 , T 2 ) and robust field map estimates ( , ΔB 0 ) from the bSSFP profile. Methods Whole‐brain bSSFP data acquired at 3T were used for the training of a feedforward ANN with N = 12, 6, and 4 phase‐cycles. The magnitude and phase of the Fourier transformed complex bSSFP frequency response served as input and the multi‐parametric reference set [T 1 , T 2 , , ∆B 0 ] as target. The ANN predicted relaxation times were validated against the target and MIRACLE. Results The ANN prediction of T 1 and T 2 for trained and untrained data agreed well with the reference, even for only four acquired phase‐cycles. In contrast, relaxometry based on 4‐point MIRACLE was prone to severe off‐resonance‐related artifacts. ANN predicted and ∆B 0 maps showed the expected spatial inhomogeneity patterns in high agreement with the reference measurements for 12‐point, 6‐point, and 4‐point bSSFP phase‐cycling schemes. Conclusion ANNs show promise to provide accurate brain tissue T 1 and T 2 values as well as reliable field map estimates. Moreover, the bSSFP acquisition can be accelerated by reducing the number of phase‐cycles while still delivering robust T 1 , T 2 , , and ∆B 0 estimates.
Predicting survival in melanoma patients treated with concurrent targeted- or immunotherapy and stereotactic radiotherapy
2020-06-01

Abstract Background Melanoma patients frequently develop brain metastases. The most widely used score to predict survival is the molGPA based on a mixed treatment of stereotactic radiotherapy (SRT) and whole brain radiotherapy (WBRT). In addition, systemic therapy was not considered. We therefore aimed to evaluate the performance of the molGPA score in patients homogeneously treated with SRT and concurrent targeted therapy or immunotherapy (TT/IT). Methods This retrospective analysis is based on an international multicenter database (TOaSTT) of melanoma patients treated with TT/IT and concurrent (≤30 days) SRT for brain metastases between May 2011 and May 2018. Overall survival (OS) was studied using Kaplan-Meier survival curves and log-rank testing. Uni- and multivariate analysis was performed to analyze prognostic factors for OS. Results One hundred ten patients were analyzed. 61, 31 and 8% were treated with IT, TT and with a simultaneous combination, respectively. A median of two brain metastases were treated per patient. After a median follow-up of 8 months, median OS was 8.4 months (0–40 months). The molGPA score was not associated with OS. Instead, cumulative brain metastases volume, timing of metastases (syn- vs. metachronous) and systemic therapy with concurrent IT vs. TT influenced OS significantly. Based on these parameters, the VTS score (volume-timing-systemic therapy) was established that stratified patients into three groups with a median OS of 5.1, 18.9 and 34.5 months, respectively ( p = 0.001 and 0.03). Conclusion The molGPA score was not useful for this cohort of melanoma patients undergoing local therapy for brain metastases taking into account systemic TT/IT. For these patients, we propose a prognostic VTS score, which needs to be validated prospectively.
Learning Unsupervised Hierarchical Part Decomposition of 3D Objects From a Single RGB Image
2020-06-01

Humans perceive the 3D world as a set of distinct objects that are characterized by various low-level (geometry, reflectance) and high-level (connectivity, adjacency, symmetry) properties. Recent methods based on convolutional neural networks (CNNs) demonstrated impressive progress in 3D reconstruction, even when using a single 2D image as input. However, the majority of these methods focuses on recovering the local 3D geometry of an object without considering its part-based decomposition or relations between parts. We address this challenging problem by proposing a novel formulation that allows to jointly recover the geometry of a 3D object as a set of primitives as well as their latent hierarchical structure without part-level supervision. Our model recovers the higher level structural decomposition of various objects in the form of a binary tree of primitives, where simple parts are represented with fewer primitives and more complex parts are modeled with more components. Our experiments on the ShapeNet and D-FAUST datasets demonstrate that considering the organization of parts indeed facilitates reasoning about 3D geometry.
Trigeminal endonasal perception – an outcome predictor for septoplasty
2020-06-01

The preoperative evaluation of the trigeminal sensitivity could improve patientsâ€TM selection for septoplasty with a higher rate of satisfaction. Endonasal trigeminal sensitivity is directly linked with subjective outcome. Therefore, patients with low trigeminal sensitivity should undergo septoplasty only after thorough counselling.
Distribution of the 21-Gene Breast Recurrence Score in Patients with Primary Breast Cancer in Germany
2020-06-01

Abstract Background Multigene assays are being used increasingly to aid in decision-making about chemotherapy in breast cancer. Here, we present the 21-gene recurrence score (RS) of patients tested in routine clinical practice in Germany. Patients and Methods In a retrospective analysis, 4695 patients with hormone receptor-positive and HER2-negative early breast cancer (pT1 – 3, pN0 – 1, M0) were included in whom RS testing was conducted in Germany between November 2015 and July 2018. RS groups as defined in the TAILORx trial (RS result 0 – 10; 11 – 25; 26 – 100) were used. Results Of these patients, 21% were assigned to the low RS group, 63% to the midrange RS group, and 15% to the high RS group. 1772 (81%) of 2175 node-negative patients over 50 years of age were grouped either into the low RS group or the midrange RS group. The portion of patients with a low or midrange RS was 90% among node-positive patients (1284 of 1432 patients), 79% among patients with Ki-67-high (≥ 20%) tumors (1829 of 2310 patients), 86% vs. 70% among patients with G2 and G3 tumors (3244 of 3762 patients and 368 of 522 patients), respectively, 88% among patients with a tumor size of &gt; 5 cm (140 of 159 patients), and 82% among node-negative patients at high clinical risk (1110 of 1352). Conclusions The distribution of the 21-gene RS in German patients that were tested in routine clinical practice indicates that, according to the results of the TAILORx trial, chemotherapy may not be beneficial in most of these.
Optimizing Rank-Based Metrics With Blackbox Differentiation
2020-06-01

Rank-based metrics are some of the most widely used criteria for performance evaluation of computer vision models. Despite years of effort, direct optimization for these metrics remains a challenge due to their non-differentiable and non-decomposable nature. We present an efficient, theoretically sound, and general method for differentiating rank-based metrics with mini-batch gradient descent. In addition, we address optimization instability and sparsity of the supervision signal that both arise from using rank-based metrics as optimization targets. Resulting losses based on recall and Average Precision are applied to image retrieval and object detection tasks. We obtain performance that is competitive with state-of-the-art on standard image retrieval datasets and consistently improve performance of near state-of-the-art object detectors. The code is available at https://github.com/martius-lab/blackbox-backprop
Systems biology markup language (SBML) level 3 package: multistate, multicomponent and multicompartment species, version 1, release 2
2020-06-01

Abstract Rule-based modeling is an approach that permits constructing reaction networks based on the specification of rules for molecular interactions and transformations. These rules can encompass details such as the interacting sub-molecular domains and the states and binding status of the involved components. Conceptually, fine-grained spatial information such as locations can also be provided. Through “wildcards” representing component states, entire families of molecule complexes sharing certain properties can be specified as patterns. This can significantly simplify the definition of models involving species with multiple components, multiple states, and multiple compartments. The systems biology markup language (SBML) Level 3 Multi Package Version 1 extends the SBML Level 3 Version 1 core with the “type” concept in the Species and Compartment classes. Therefore, reaction rules may contain species that can be patterns and exist in multiple locations. Multiple software tools such as Simmune and BioNetGen support this standard that thus also becomes a medium for exchanging rule-based models. This document provides the specification for Release 2 of Version 1 of the SBML Level 3 Multi package. No design changes have been made to the description of models between Release 1 and Release 2; changes are restricted to the correction of errata and the addition of clarifications.
Nonlinear reflection as a cause of the short-latency component in stimulus-frequency otoacoustic emissions simulated by the methods of compression and suppression
2020-06-01

Stimulus-frequency otoacoustic emissions (SFOAEs) are generated by coherent reflection of forward traveling waves by perturbations along the basilar membrane. The strongest wavelets are backscattered near the place where the traveling wave reaches its maximal amplitude (tonotopic place). Therefore, the SFOAE group delay might be expected to be twice the group delay estimated in the cochlear filters. However, experimental data have yielded steady-state SFOAE components with near-zero latency. A cochlear model is used to show that short-latency SFOAE components can be generated due to nonlinear reflection of the compressor or suppressor tones used in SFOAE measurements. The simulations indicate that suppressors produce more pronounced short-latency components than compressors. The existence of nonlinear reflection components due to suppressors can also explain why SFOAEs can still be detected when suppressors are presented more than half an octave above the probe-tone frequency. Simulations of the SFOAE suppression tuning curves showed that phase changes in the SFOAE residual as the suppressor frequency increases are mostly determined by phase changes of the nonlinear reflection component.
The impact of event type and geographical proximity on threat appraisal and emotional reactions to Wikipedia articles
2020-06-01

The online encyclopedia Wikipedia strives for objectivity and neutrality. However, Wikipedia also provides articles about negative events (e.g., earthquakes, terrorist attacks) that likely elicit strong, negative emotions. These emotions might slip into Wikipedia articles. Previous research has demonstrated that Wikipedia articles on terrorist attacks contained more anger-related content than Wikipedia articles on earthquakes. This previous research focused on the expression of emotional reactions in existing Wikipedia articles and used an automatic linguistic analysis tool that counted the number of emotion-related words. In order to extend this approach, the first aim of the present research was to replicate these findings by focusing on the emotional reactions during and after reading the articles. Second, previous research did not look at the geographical location of the negative events, which may be a relevant, influential factor. Emotional reactions may be stronger for geographically closer events (i.e., Europe for Europeans) than for geographically more distant events (i.e., Asia). Two studies, one with few raters rating their emotional reactions to many Wikipedia articles (S1 Study) and another with many raters rating their emotional reactions to few Wikipedia articles (S1 Study), demonstrated that Wikipedia articles on terrorist attacks elicited more threat, anger, sadness, and anxiety than Wikipedia articles on earthquakes. These effects occurred for negative events in Europe but were absent for events in Asia, with one exception. The anger effect was the same across Europe and Asia. Thus, event type and geographical proximity are relevant factors for explaining threat and emotional reactions to Wikipedia articles.
[Effective factors in multifamily therapy in patients with eating disorders : Critical appraisal and implications for practice].
2020-06-01

Multifamily therapy (MFT), the treatment of several families simultaneously, is an established method of psychotherapy used in a wide range of diagnoses. However, there is limited knowledge about the exact factors of action of this treatment method. The development of MFT as a separate form of therapy is presented, as are its previous applications in the treatment of patients with eating disorders. Known factors of change are critically evaluated, new factors of change are discussed and the practical application in MFT in the context of inpatient treatment of adolescents with eating disorders is demonstrated.Processes in the large group that have not yet been considered, such as emotional contagion, exaltation of emotion and subgroup formation and work with the meta-family, are described for the first time in the context of MFT and possibly represent mediators in the therapeutic process.The model of affect and process resonance in Plassmann's individual therapy can be applied well to the processes in the MFT and possibly represents its own effect factor through the production of episodes of secure attachment. Further research on the factors of change in the MFT is of practical relevance.
The rotation–activity relation of M dwarfs: From K2 to TESS and PLATO
2020-06-01

Abstract Studies of the rotation–activity relation of late‐type stars are essential to enhance our understanding of stellar dynamos and angular momentum evolution. We study the rotation–activity relation with K2 for M dwarfs, where it is especially poorly understood. We analyzed the light curves of all bright and nearby M dwarfs form the Superblink proper motion catalog that were in the K2 field of view. Using a sample of 430 M dwarfs observed in campaigns C0–C19 in long‐cadence mode, we determined the rotation period and a wealth of activity diagnostics. Our study of the rotation–activity relation based on photometric activity indicators confirmed the previously published abrupt change of the activity level at a rotation period of ∼10 days. Our sample, which is more than three times larger, increases the statistical significance of this finding.
Prediction of soil macronutrients using fractal parameters and artificial intelligence methods
2020-06-01

Aim of study: To evaluate artificial neural networks (ANN), and k-Nearest Neighbor (k-NN) to support vector regression (SVR) models for estimation of available soil nitrogen (N), phosphorous (P) and available potassium (K).Area of study: Two separate agricultural sites in Semnan and Gorgan, in Semnan and Golestan provinces of Iran, respectively.Material and methods: Complete data set of soil properties was used to evaluate the models’ performance using a k-fold test data set scanning procedures. Soil property measures including clay, sand and silt content, soil organic carbon (SOC), electrical conductivity (EC), lime content as well as fractal dimension (D) were used for the prediction of soil macronutrients. A Gamma test was utilized for defining the optimum combination of the input variables.Main results: The sensitivity analysis showed that OC, EC, and clay were the most significant variables in the prediction of soil macronutrients. The SVR model was more accurate compared to the ANN and k-NN models. N values were estimated more accurately than K and P nutrients, in all the applied models.Research highlights: The accuracy of models among the test stages illustrated that using a single data set for investigation of model performance could be misleading. Therefore, the complete data set would be necessary for suitable evaluation of the model.
University Foundations and Philanthropic Fundraising in Chinese Higher Education: a Promising Trend with Challenges
2020-06-01

This study overviews policies and practice of philanthropic fundraising in Chinese universities with a focus on university foundations. It briefly reviews the theoretical dimensions of philanthropic fundraising in higher education from a global perspective and university philanthropic fundraising models as well as their applications in Chinese universities. It shows the important role of university foundations in generating philanthropic revenue in Chinese universities. By identifying challenges and the general trends, it explores strategies for sustainable philanthropic fundraising for Chinese universities, which may provide stakeholders with a helpful and relevant reference to promote philanthropic fundraising of Chinese universities. It also gives a general guidance of philanthropic fundraising strategies for Chinese universities.
Importance of electron-positron pairs on the maximum possible luminosity of the accretion columns in ULXs
2020-06-01

Abstract One of the models explaining the high luminosity of pulsing ultra-luminous X-ray sources (pULXs) was suggested by Mushtukov et al. (2015). They showed that the accretion columns on the surfaces of highly magnetized neutron stars can be very luminous due to opacity reduction in the high magnetic field. However, a strong magnetic field leads also to amplification of the electron-positron pairs creation. Therefore, increasing of the electron and positron number densities compensates the cross-section reduction, and the electron scattering opacity does not decrease with the magnetic field magnification. As a result, the maximum possible luminosity of the accretion column does not increase with the magnetic field. It ranges between 10 40 − 10 41 erg s −1 depending only slightly on the magnetic field strength.