julilili42/papers huggingface dataset:
A (Dis-)information Theory of Revealed and Unrevealed Preferences: Emerging Deception and Skepticism via Theory of Mind
2023-01-01

Abstract In complex situations involving communication, agents might attempt to mask their intentions, exploiting Shannon’s theory of information as a theory of misinformation. Here, we introduce and analyze a simple multiagent reinforcement learning task where a buyer sends signals to a seller via its actions, and in which both agents are endowed with a recursive theory of mind. We show that this theory of mind, coupled with pure reward-maximization, gives rise to agents that selectively distort messages and become skeptical towards one another. Using information theory to analyze these interactions, we show how savvy buyers reduce mutual information between their preferences and actions, and how suspicious sellers learn to reinterpret or discard buyers’ signals in a strategic manner.
SIMSUM: Document-level Text Simplification via Simultaneous Summarization
2023-01-01

Document-level text simplification is a specific type of simplification which involves simplifying documents consisting of several sentences by rewriting them into fewer or more sentences. In this paper, we propose a new two-stage framework SIMSUM for automated document-level text simplification. Our model is designed with explicit summarization and simplification models and guides the generation using the main keywords of a source text. In order to evaluate our new model, we use two existing benchmark datasets for simplification, namely D-Wikipedia and Wiki-Doc. We compare our model's performance with state of the art and show that SIMSUM achieves top results on the D-Wikipedia dataset SARI (+1.20), D-SARI (+1.64), and FKGL (-0.35) scores, improving over the best baseline models. In order to evaluate the quality of the generated text, we analyze the outputs from different models qualitatively and demonstrate the merit of our new model. Our code and datasets are available (1).
Structured Reporting of Head and Neck Sonography Achieves Substantial Interrater Reliability
2023-01-01

Abstract Purpose Ultrasound examinations are often criticized for having higher examiner dependency compared to other imaging techniques. Compared to free-text reporting, structured reporting (SR) of head and neck sonography (HNS) achieves superior time efficiency as well as report quality. However, there are no findings concerning the influence of SR on the interrater reliability (IRR) of HNS. Materials and Methods Typical pathologies (n=4) in HNS were documented by video/images by two certified head and neck ultrasound instructors. Consequently, structured reports of these videos/images were created by n=9 senior physicians at departments of otolaryngology or maxillofacial surgery with DEGUM instructors on staff. Reports (n=36) were evaluated regarding overall completeness and IRR. Additionally, user satisfaction was assessed by a visual analog scale (VAS). Results SR yielded very high report completeness (91.8%) in all four cases with a substantial IRR (Fleiss‘ κ 0.73). Interrater agreement was high at 87.2% with very good user satisfaction (VAS 8.6). Conclusion SR has the potential to ensure high-quality examination reports with substantial comparability and very high user satisfaction. Furthermore, big data collection and analysis are facilitated by SR. Therefore, process quality, workflow, and scientific output are potentially enhanced by SR.
A new cryptodire from the Eocene of the Na Duong Basin (northern Vietnam) sheds new light on Pan-Trionychidae from Southeast Asia
2023-01-01

Striatochelys baba gen. et sp. nov. is a new pan-trionychid from the middle–upper Eocene (late Bartonian–Priabonian, 39–35 Ma) of the Na Duong Basin in northern Vietnam. It represents one of the best documented and most completely known Palaeogene pan-trionychid species from Asia. Striatochelys baba can be diagnosed by: (1) its relatively small size; (2) the absence of a preneural; (3) the presence of well-developed straight ridges on the costals and neurals in adults; (4) ridges more strongly developed posteriorly than anteriorly; and (5) entoplastron callosity in the shape of a bulge. A phylogenetic analysis recovers S. baba within Pan-Trionychinae in an unresolved polytomy with species of the genus Nilssonia. In addition, comparisons of the new taxon with plastomenids, pan-trionychids from the Palaeogene and extant trionychids from Asia demonstrate a particularly close resemblance to Nilssonia spp. Based on the close resemblance between S. baba and ‘Trionyx’ impressus (a pan-trionychid from the Maoming Basin of southern China), we here assign the latter species to the new genus Striatochelys. The close relationship between S. baba gen. et sp. nov. from the Na Duong Basin and S. impressa comb. nov. from the Maoming Basin further supports the hypothesis that a close connection between both localities existed, as already exemplified by other faunal elements such as pan-geoemydids and crocodylians.http://zoobank.org/urn:lsid:zoobank.org:pub:E8E5C4DE-E52A-43FB-B9C1-CE3ED2ED66C1
Accelerating Transformer Inference for Translation via Parallel Decoding
2023-01-01

Autoregressive decoding limits the efficiency of transformers for Machine Translation (MT). The community proposed specific network architectures and learning-based methods to solve this issue, which are expensive and require changes to the MT model, trading inference speed at the cost of the translation quality. In this paper, we propose to address the problem from the point of view of decoding algorithms, as a less explored but rather compelling direction. We propose to reframe the standard greedy autoregressive decoding of MT with a parallel formulation leveraging Jacobi and Gauss-Seidel fixed-point iteration methods for fast inference. This formulation allows to speed up existing models without training or modifications while retaining translation quality. We present three parallel decoding algorithms and test them on different languages and models showing how the parallelization introduces a speedup up to 38% w.r.t. the standard autoregressive decoding and nearly 2x when scaling the method on parallel resources. Finally, we introduce a decoding dependency graph visualizer (DDGviz) that let us see how the model has learned the conditional dependence between tokens and inspect the decoding procedure.
In vivo imaging of CD8+ T cells in metastatic cancer patients: first clinical experience with simultaneous [89Zr]Zr-Df-IAB22M2C PET/MRI
2023-01-01

<b>Aim/Introduction:</b> Despite the spectacular success of immune checkpoint inhibitor therapy (ICT) in patients with metastatic cancer, only a limited proportion of patients benefit from ICT. CD8<sup>+</sup> cytotoxic T cells are important gatekeepers for the therapeutic response to ICT and are able to recognize MHC class I-dependent tumor antigens and destroy tumor cells. The radiolabeled minibody [<sup>89</sup>Zr]Zr-Df-IAB22M2C has a high affinity for human CD8<sup>+</sup> T cells and was successfully tested in a phase I study. Here, we aimed to gain the first clinical PET/MRI experience with the noninvasive assessment of the CD8<sup>+</sup> T-cell distribution in cancer patients by <i>in vivo</i> [<sup>89</sup>Zr]Zr-Df-IAB22M2C with a distinct focus of identifying potential signatures of successful ICT. <b>Material and Methods:</b> We investigated 8 patients with metastasized cancers undergoing ICT. Radiolabeling of Df-IAB22M2C with Zr-89 was performed according to Good Manufacturing Practice. Multiparametric PET/MRI was acquired 24 h after injection of 74.2±17.9 MBq [<sup>89</sup>Zr]Zr-Df-IAB22M2C. We analyzed [<sup>89</sup>Zr]Zr-Df-IAB22M2C uptake within the metastases and within primary and secondary lymphatic organs. <b>Results:</b> [<sup>89</sup>Zr]Zr-Df-IAB22M2C injection was tolerated well without noticeable side effects. The CD8 PET/MRI data acquisitions 24 hours post-administration of [<sup>89</sup>Zr]Zr-Df-IAB22M2C revealed good image quality with a relatively low background signal due to only low unspecific tissue uptake and marginal blood pool retention. Only two metastatic lesions showed markedly increased tracer uptake in our cohort of patients. Furthermore, we observed high interpatient variability in [<sup>89</sup>Zr]Zr-Df-IAB22M2C uptake within the primary and secondary lymphoid organs. Four out of five ICT patients exhibited rather high [<sup>89</sup>Zr]Zr-Df-IAB22M2C uptake in the bone marrow. Two of these four patients as well as two other patients yielded pronounced [<sup>89</sup>Zr]Zr-Df-IAB22M2C uptake within nonmetastatic lymph nodes. Interestingly, cancer progression in ICT patients was associated with a relatively low [<sup>89</sup>Zr]Zr-Df-IAB22M2C uptake in the spleen compared to the liver in 4 out of the 6 patients. Lymph nodes with enhanced [<sup>89</sup>Zr]Zr-Df-IAB22M2C uptake revealed significantly reduced apparent diffusion coefficient (ADC) values in diffusion weighted MRI. <b>Conclusion:</b> Our first clinical experiences revealed the feasibility of [<sup>89</sup>Zr]Zr-Df-IAB22M2C PET/MRI in assessing potential immune-related changes in metastases and primary and secondary lymphatic organs. According to our results, we hypothesize that alterations in [<sup>89</sup>Zr]Zr-Df-IAB22M2C uptake in primary and secondary lymphoid organs might be associated with the response to ICT.
Untangling the intertwined: metallic to semiconducting phase transition of colloidal MoS2 nanoplatelets and nanosheets
2023-01-01

Colloidal ultrathin 2D MoS 2 nanoplatelets and nanosheets provide a toolbox for future spin- and valleytronic applications. Colloidal chemistry offers innovative strategies to tune the materials' optoelectronic properties from metallic to semiconducting.
Parameter-efficient Modularised Bias Mitigation via AdapterFusion
2023-01-01

Deepak Kumar, Oleg Lesota, George Zerveas, Daniel Cohen, Carsten Eickhoff, Markus Schedl, Navid Rekabsaz. Proceedings of the 17th Conference of the European Chapter of the Association for Computational Linguistics. 2023.
Characterizing the marine mammal exposome by iceberg modeling, linking chemical analysis and in vitro bioassays
2023-01-01

The analysis of mixtures of environmental contaminants from marine mammal organs revealed distinct distribution patterns for single compounds. The combination of chemical analysis and bioassays can comprehensively characterize the mixture exposome.
Edge contacts accelerate the response of MoS2 photodetectors
2023-01-01

Edge contacts are compared to top contacts in terms of the photocurrent response of MoS 2 multilayers. The faster response of the edge contacts is attributed to the predominantly in-plane direction of charge carrier diffusion.
Emukit: A Python toolkit for decision making under uncertainty
2023-01-01

Emukit is a highly flexible Python toolkit for enriching decision making under uncertainty with statistical emulation. It is particularly pertinent to complex processes and simulations where data are scarce or difficult to acquire. Emukit provides a common framework for a range of iterative methods that propagate well-calibrated uncertainty estimates within a design loop, such as Bayesian optimisation, Bayesian quadrature and experimental design. It also provides multi-fidelity modelling capabilities. We describe the software design of the package, illustrate usage of the main APIs, and showcase the breadth of use cases in which the library already has been used by the research community.
Accessing three-branched high-affinity cereblon ligands for molecular glue and protein degrader design
2023-01-01

The Petasis borono-Mannich reaction was employed for an entry towards three-branched cereblon ligands. The high-affinity ligands were used to assemble molecular glues and proteolysis targeting chimeras (PROTACs) targeting BRD4 for degradation.
Prevalence of Pathogenic Germline Variants in Women with Non-Familial Unilateral Triple-Negative Breast Cancer
2023-01-01

Introduction: International guidelines recommend genetic testing for women with familial breast cancer at an expected prevalence of pathogenic germline variants (PVs) of at least 10%. In a study sample of the German Consortium for Hereditary Breast and Ovarian Cancer (GC-HBOC), we have previously shown that women with TNBC diagnosed before the age of 50 years but without a family history of breast or ovarian cancer (sTNBC) meet this criterion. The present study investigates the PV prevalence in BRCA1, BRCA2, and nine additional cancer predisposition genes in an extended sTNBC study sample including a cohort of women with a later age at sTNBC diagnosis. Patients and Methods: In 1,600 women with sTNBC (median age at diagnosis: 41 years, range 19–78 years), we investigated the association between age at diagnosis and PV occurrence in cancer predisposition genes using logistic regression. Results: 260 sTNBC patients (16.2%) were found to have a PV in cancer predisposition genes (BRCA1: n = 170 [10.6%]; BRCA2: n = 46 [2.9%], other: n = 44 [2.8%]). The PV prevalence in women diagnosed between 50 and 59 years (n = 194) was 11.3% (22/194). Logistic regression showed a significant increase in PV prevalence with decreasing age at diagnosis (OR 1.41 per 10 years younger age at diagnosis; 95% confidence interval: 1.21–1.65; p &lt; 0.001). The PV prevalence predicted by the model was above 10% for diagnoses before the age of 56.8 years. Conclusion: Based on the data presented, we recommend genetic testing by gene panel analysis for sTNBC patients diagnosed before the age of 60 years. Due to the still uncertain estimate for women with sTNBC diagnosed above the age of 60 years, further studies are needed.
Mental Number Representations Are Spatially Mapped Both by Their Magnitudes and Ordinal Positions
2023-01-01

The Spatial-Numerical Association of Response Codes (SNARC) effect – i.e., faster responses to small numbers with the left compared to the right side and to large numbers with the right compared to the left side – suggests that numbers are associated with space. However, it remains unclear whether the SNARC effect evolves from a number’s magnitude or the ordinal position of a number in working memory. One problem is that, in different paradigms, the task demands influence the role of ordinality and magnitude. While single-task setups in which participants judge the parity of a displayed number indicate the importance of magnitude for the SNARC effect, evidence for ordinal influences usually comes from experiments where ordinal sequences have to be memorized or setups in which participants possess pre-existing knowledge of the ordinality of stimuli. Therefore, in this preregistered study, we employed a SNARC task without secondary ordinal sequence memorization. We dissociate ordinal and magnitude accounts by carefully manipulating experimental stimulus sets. The results indicate that even though the magnitude model better accounts for the observed data, the ordinal position seems to matter as well. Hence, numbers are associated with space in both a magnitude- and an order-respective manner, yielding a mixture of both compatibility effects. Moreover, a multiple coding framework may most accurately explain the roots of the SNARC effect.
Retrospective cohort study to devise a treatment decision score predicting adverse 24-month radiological activity in early multiple sclerosis
2023-01-01

Background: Multiple sclerosis (MS) is a chronic neuroinflammatory disease affecting about 2.8 million people worldwide. Disease course after the most common diagnoses of relapsing-remitting multiple sclerosis (RRMS) and clinically isolated syndrome (CIS) is highly variable and cannot be reliably predicted. This impairs early personalized treatment decisions. Objectives: The main objective of this study was to algorithmically support clinical decision-making regarding the options of early platform medication or no immediate treatment of patients with early RRMS and CIS. Design: Retrospective monocentric cohort study within the Data Integration for Future Medicine (DIFUTURE) Consortium. Methods: Multiple data sources of routine clinical, imaging and laboratory data derived from a large and deeply characterized cohort of patients with MS were integrated to conduct a retrospective study to create and internally validate a treatment decision score [Multiple Sclerosis Treatment Decision Score (MS-TDS)] through model-based random forests (RFs). The MS-TDS predicts the probability of no new or enlarging lesions in cerebral magnetic resonance images (cMRIs) between 6 and 24 months after the first cMRI. Results: Data from 65 predictors collected for 475 patients between 2008 and 2017 were included. No medication and platform medication were administered to 277 (58.3%) and 198 (41.7%) patients. The MS-TDS predicted individual outcomes with a cross-validated area under the receiver operating characteristics curve (AUROC) of 0.624. The respective RF prediction model provides patient-specific MS-TDS and probabilities of treatment success. The latter may increase by 5–20% for half of the patients if the treatment considered superior by the MS-TDS is used. Conclusion: Routine clinical data from multiple sources can be successfully integrated to build prediction models to support treatment decision-making. In this study, the resulting MS-TDS estimates individualized treatment success probabilities that can identify patients who benefit from early platform medication. External validation of the MS-TDS is required, and a prospective study is currently being conducted. In addition, the clinical relevance of the MS-TDS needs to be established.
Intravenous thrombolysis in acute ischemic stroke after antagonization of unfractionated heparin with protamine: case series and systematic review of literature
2023-01-01

Background and aims: Intravenous thrombolysis (IVT) is standard of care for disabling acute ischemic stroke (AIS) within a time window of ⩽ 4.5 h. Some AIS patients cannot be treated with IVT due to limiting contraindications, including heparin usage in an anticoagulating dose within the past 24 h or an elevated activated prothrombin time (aPTT) &gt; 15 s. Protamine is a potent antidote to unfractionated heparin. Objectives: The objective of this study was to investigate the safety and efficacy of IVT in AIS patients after antagonization of unfractionated heparin with protamine. Methods: Patients from our stroke center (between January 2015 and September 2021) treated with IVT after heparin antagonization with protamine were analyzed. National Institutes of Health Stroke Scale (NIHSS) was used for stroke severity and modified Rankin Scale (mRS) for outcome assessment. Substantial neurological improvement was defined as the difference between admission and discharge NIHSS of ⩾8 or discharge NIHSS of ⩽1. Good outcome at follow-up after 3 months was defined as mRS 0–2. Safety data were obtained for mortality, symptomatic intracerebral hemorrhage (sICH), and for adverse events due to protamine. Second, a systematic review was performed searching PubMed and Scopus for studies and case reviews presenting AIS patients treated with IVT after heparin antagonization with protamine. The search was limited from January 1, 2011 to September 29, 2021. Furthermore, we conducted a propensity score matching comparing protamine-treated patients to a control IVT group without protamine (ratio 2:1, match tolerance 0.2). Results: A total of 16 patients, 5 treated in our hospital and 11 from literature, [65.2 ± 13.1 years, 37.5% female, median premorbid mRS (pmRS) 1 (IQR 1, 4)] treated with IVT after heparin antagonization using protamine were included and compared to 31 IVT patients [76.2 ± 10.9 years, 45% female, median pmRS 1 (IQR 0, 2)]. Substantial neurological improvement was evident in 68.8% of protamine-treated patients versus 38.7% of control patients ( p = 0.028). Good clinical outcome at follow-up was observed in 56.3% versus 58.1% of patients ( p = 0.576). No adverse events due to protamine were reported, one patient suffered sICH after secondary endovascular thrombectomy of large vessel occlusion. Mortality was 6.3% versus 22.6% ( p = 0.236). Conclusion: IVT after heparin antagonization with protamine seems to be safe and, prospectively, may extend the number of AIS patients who can benefit from reperfusion treatment using IVT. Further prospective registry trials would be helpful to further investigate the clinical applicability of heparin antagonization.
In situ fNIRS measurements during cognitive behavioral emotion regulation training in rumination-focused therapy: A randomized-controlled trial
2023-01-01

Repetitive negative thinking (RNT), including rumination, plays a key role in various psychopathologies. Although several psychotherapeutic treatments have been developed to reduce RNT, the neural correlates of those specific treatments and of psychotherapy in general are largely unknown. Functional near-infrared spectroscopy (fNIRS) offers the potential to investigate the neural correlates of psychotherapeutic techniques in situ. Therefore, in this study we investigated the efficacy and neural correlates of a fNIRS adapted Mindfulness-based Emotion Regulation Training (MBERT) for the treatment of depressive rumination in 42 subjects with major depressive disorder (MDD) in a cross-over designed randomized controlled trial. Using psychometric measures, subjective ratings and fNIRS, we analyzed in situ changes in depressive symptom severity, ruminative thoughts and cortical activity in the Cognitive Control Network (CCN). Our results show that MBERT is effective in treating depressive symptoms and rumination. On a neural level, we found consistently higher cortical activation during emotion regulation training compared to control trials in the bilateral inferior frontal gyrus (IFG) and dorsolateral prefrontal cortex (DLPFC). Furthermore, cortical oxygenation decreased from session to session in the bilateral DLPFC. The relevance of the results for the psychotherapeutic treatment of MDD as well as further necessary investigations are discussed.
Patterns, predictors and prognostic relevance of high-grade hematotoxicity after temozolomide or temozolomide-lomustine in the CeTeG/NOA-09 trial
2023-01-01

Abstract Purpose In the randomized phase III trial CeTeG/NOA-09, temozolomide (TMZ)/lomustine (CCNU) combination therapy was superior to TMZ in newly diagnosed MGMT methylated glioblastoma, albeit reporting more frequent hematotoxicity. Here, we analyze high grade hematotoxicity and its prognostic relevance in the trial population. Methods Descriptive and comparative analysis of hematotoxicity adverse events ≥ grade 3 (HAE) according to the Common Terminology of Clinical Adverse Events, version 4.0 was performed. The association of HAE with survival was assessed in a landmark analysis. Logistic regression analysis was performed to predict HAE during the concomitant phase of chemotherapy. Results HAE occurred in 36.4% and 28.6% of patients under CCNU/TMZ and TMZ treatment, respectively. The median onset of the first HAE was during concomitant chemotherapy (i.e. first CCNU/TMZ course or daily TMZ therapy), and 42.9% of patients with HAE receiving further courses experienced repeat HAE. Median HAE duration was similar between treatment arms (CCNU/TMZ 11.5; TMZ 13 days). Chemotherapy was more often discontinued due to HAE in CCNU/TMZ than in TMZ (19.7 vs. 6.3%, p = 0.036). The occurrence of HAE was not associated with survival differences (p = 0.76). Regression analysis confirmed older age (OR 1.08) and female sex (OR 2.47), but not treatment arm, as predictors of HAE. Conclusion Older age and female sex are associated with higher incidence of HAE. Although occurrence of HAE was not associated with shorter survival, reliable prediction of patients at risk might be beneficial to allow optimal management of therapy and allocation of supportive measures. Trial registration NCT01149109.