julilili42/papers huggingface dataset:
Role of immunohistochemistry for interobserver agreement of Peritoneal Regression Grading Score in peritoneal metastasis
2021-12-23

Pressurized intraperitoneal aerosol chemotherapy (PIPAC)-directed therapy is a new treatment option for peritoneal metastasis (PM). The 4-tiered Peritoneal Regression Grading Score (PRGS) has been proposed for assessment of histological treatment response. We aimed to evaluate the effect of immunohistochemistry (IHC) on interobserver agreement of the PRGS. Hematoxylin and eosin (H&E)-stained and IHC-stained slides (n = 662) from 331 peritoneal quadrant biopsies (QBs) taken prior to 99 PIPAC procedures performed on 33 patients were digitalized and uploaded to a web library. Eight raters (five consultants and three residents) assessed the PRGS, and Krippendorff's alpha coefficients (α) were calculated. Results (IHC-PRGS) were compared with data published in 2019, using H&E-stained slides only (H&E-PRGS). Overall, agreement for IHC-PRGS was substantial to almost perfect. Agreement (all raters) regarding single QBs after treatment was substantial for IHC-PRGS (α = 0.69, 95% confidence interval [CI] = 0.66-0.72) and moderate for H&E-PRGS (α = 0.60, 95% CI = 0.56-0.64). Agreement (all raters) regarding the mean PRGS per QB set after treatment was higher for IHC-PRGS (α = 0.78, 95% CI = 0.73-0.83) than for H&E-PRGS (α = 0.71, 95% CI = 0.64-0.78). Among residents, agreement was almost perfect for IHC-PRGS and substantial for H&E-PRGS. Agreement (all raters) regarding maximum PRGS per QB set after treatment was substantial for IHC-PRGS (α = 0.61, 95% CI = 0.54-0.68) and moderate for H&E-PRGS (α = 0.60, 95% CI = 0.53-0.66). Among residents, agreement was substantial for IHC-PRGS (α = 0.66, 95% CI = 0.57-0.75) and moderate for H&E-PRGS (α = 0.55, 95% CI = 0.45-0.64). Additional IHC seems to improve the interobserver agreement of PRGS, particularly between less experienced raters.
On black hole area quantization and echoes
2021-12-23

Abstract In this work we argue that black hole (BH) area quantization of Bekenstein and Mukhanov should not give rise to measurable effects in terms of so-called gravitational wave echoes during BH mergers. We outline that the quantum spectrum of a BH should be washed out during and after BH mergers, and hence one should not expect echoes in this scenario. The extreme broadening of the spectrum is due to the large particle emission rate during ringdown. Our results question key assumptions being made in recent literature on this topic.
Real-World Data on the Use of Nivolumab Monotherapy in the Treatment of Advanced Renal Cell Carcinoma after Prior Therapy: Interim Results from the Noninterventional NORA Study
2021-12-23

Nivolumab is an antibody treatment approved for patients with advanced kidney cancer who have already received systemic therapy. Its approval was based on results from a clinical trial. Our study demonstrates its effectiveness and safety in "real-world" patients.
Classification of static asymptotically flat spacetimes with a photon sphere in Einstein-multiple-scalar field theory
2021-12-23

In the present paper we consider the Einstein-multiple-scalar field theory.\\nWhen the target space of the scalar fields is a complete, simply connected\\nRiemannian manifold with non-positive sectional curvature we prove that the\\nstatic and asymptotically flat solutions which posses a photon sphere are\\nuniquely specified by their asymptotic data, i.e. by their mass, scalar charges\\nand asymptotic values of the scalar fields. The unique solution with a photon\\nsphere and prescribed asymptotic data is explicitly constructed.\\n
Long-Term Patterns of Noise From Underwater Explosions and Their Relation to Fisheries in Southern California
2021-12-23

Acoustic deterrents can reduce marine mammal interactions with fisheries and aquacultures, but they contribute to an increasing level of underwater noise. In Southern California, commercially produced explosive deterrents, commonly known as “seal bombs,” are used to protect fishing gear and catch from pinniped predation, which can cause extensive economic losses for the fishing community. Passive acoustic monitoring data collected between 2005 and 2016 at multiple sites within the Southern California Bight and near Monterey Bay revealed high numbers of these small-charge underwater explosions, long-term, spatio-temporal patterns in their occurrence, and their relation to different commercial purse-seine fishing sectors. The vast majority of explosions occurred at nighttime and at many nearshore sites high explosion counts were detected, up to 2,800/day. Received sound exposure levels of up to 189 dB re 1 μPa 2 -s indicate the potential for negative effects on marine life, especially in combination with the persistence of recurring explosions during periods of peak occurrence. Due to the highly significant correlation and similar spatio-temporal patterns of market squid landings and explosion occurrence at many sites, we conclude that the majority of the recorded explosions come from seal bombs being used by the California market squid purse-seine fishery. Additionally, seal bomb use declined over the years of the study, potentially due to a combination of reduced availability of market squid driven by warm water events in California and regulation enforcement. This study is the first to provide results on the distribution and origin of underwater explosions off Southern California, but there is a substantial need for further research on seal bomb use in more recent years and their effects on marine life, as well as for establishing environmental regulations on their use as a deterrent.
Quantum router: Storing and redirecting light at the photon level
2021-12-23

We propose a method for spatially re-routing single photons or light in a\\ncoherent state with small average photon number by purely electronic means,\\ni.e. without using mechanical devices such as micro-mirror arrays. The method\\nis based on mapping the quantum state of the incoming light onto a spin-wave in\\nan atomic ensemble as is done in quantum memories of light. Then the wavevector\\nof the spin-wave is modified in a controlled way by an applied magnetic field\\ngradient. Finally, by re-applying the same control beam as for storing, the\\nsignal pulse is released in a new direction that depends on the deflected\\nwavevector of the spin-wave. We show by numerical simulation that efficiencies\\ncan be achieved for arbitrary deflection angles in the plane that are\\ncomparable with simple photon storage and re-emission in forward direction, and\\npropose a new method for eliminating the stored momentum as source of\\ndecoherence in the quantum memory. In a reasonable parameter regime, the\\nre-routing should be achievable on a time-scale on the order of few to\\n microseconds, depending on the deflection angle. The shifts in the\\nwavevector that can be achieved using the Zeeman-effect, with otherwise minimal\\nchanges to the spin-wave, can also be used to complement existing ac-Stark\\nspin-wave manipulation methods.\\n
AI Lung Segmentation and Perfusion Analysis of Dual-Energy CT Can Help to Distinguish COVID-19 Infiltrates from Visually Similar Immunotherapy-Related Pneumonitis Findings and Can Optimize Radiological Workflows
2021-12-23

(1) To explore the potential impact of an AI dual-energy CT (DECT) prototype on decision making and workflows by investigating its capabilities to differentiate COVID-19 from immunotherapy-related pneumonitis. (2) Methods: From 3 April 2020 to 12 February 2021, DECT from biometrically matching patients with COVID-19, pneumonitis, and inconspicuous findings were selected from our clinical routine. Three blinded readers independently scored each pulmonary lobe analogous to CO-RADS. Inter-rater agreement was determined with an intraclass correlation coefficient (ICC). Averaged perfusion metrics per lobe (iodine uptake in mg, volume without vessels in ml, iodine concentration in mg/mL) were extracted using manual segmentation and an AI DECT prototype. A generalized linear mixed model was used to investigate metric validity and potential distinctions at equal CO-RADS scores. Multinomial regression measured the contribution “Reader”, “CO-RADS score”, and “perfusion metrics” to diagnosis. The time to diagnosis was measured for manual vs. AI segmentation. (3) Results: We included 105 patients (62 ± 13 years, mean BMI 27 ± 2). There were no significant differences between manually and AI-extracted perfusion metrics (p = 0.999). Regardless of the CO-RADS score, iodine uptake and concentration per lobe were significantly higher in COVID-19 than in pneumonitis (p &lt; 0.001). In regression, iodine uptake had a greater contribution to diagnosis than CO-RADS scoring (Odds Ratio (OR) = 1.82 [95%CI 1.10–2.99] vs. OR = 0.20 [95%CI 0.14–0.29]). The AI prototype extracted the relevant perfusion metrics significantly faster than radiologists (10 ± 1 vs. 15 ± 2 min, p &lt; 0.001). (4) Conclusions: The investigated AI prototype positively impacts decision making and workflows by extracting perfusion metrics that differentiate COVID-19 from visually similar pneumonitis significantly faster than radiologists.
Flexible and efficient simulation-based inference for models of decision-making
2021-12-23

Abstract Inferring parameters of computational models that capture experimental data is a central task in cognitive neuroscience. Bayesian statistical inference methods usually require the ability to evaluate the likelihood of the model—however, for many models of interest in cognitive neuroscience, the associated likelihoods cannot be computed effciently. Simulation-based inference (SBI) offers a solution to this problem by only requiring access to simulations produced by the model. Here, we provide an effcient SBI method for models of decision-making. Our approach, Mixed Neural Likelihood Estimation (MNLE), trains neural density estimators on model simulations to emulate the simulator, and is designed to capture both the continuous (e.g., reaction times) and discrete (choices) data of decision-making models. The likelihoods of the emulator can then be used to perform Bayesian parameter inference on experimental data using standard approximate inference methods like Markov Chain Monte Carlo sampling. We demonstrate MNLE on two variants of the drift-diffusion model (DDM) and compare its performance to a recently proposed method for SBI on DDMs, called Likelihood Approximation Networks (LANs, Fengler et al. 2021). We show that MNLE is substantially more effcient than LANs: it achieves similar likelihood accuracy with six orders of magnitude fewer training simulations, and is substantially more accurate than LANs when both are trained with the same budget. This enables researchers to train MNLE on custom-tailored models of decision-making, leading to fast iteration of model design for scientific discovery.
Mechanical properties of lithic raw materials from Kazakhstan: comparing chert, shale, and porphyry
2021-12-23

The study of lithic raw material quality has become one of the major interpretive tools to investigate the raw material selection behaviour and its influence to the knapping technology. In order to make objective assessments of raw material quality, their mechanical properties (e.g., fracture resistance, hardness, modulus of elasticity) should be measured. However, such comprehensive investigations are lacking for the Palaeolithic of Kazakhstan. In this work, we investigate geological and archaeological lithic raw material samples of chert, porphyry, and shale collected from the Inner Asian Mountain Corridor (henceforth IAMC). Selected samples of aforementioned rocks were tested by means of Vickers and Knoop indentation methods to determine one aspect of their mechanical properties: their indentation fracture resistance (a value closely related to fracture toughness). These tests were complemented by traditional petrographic studies to characterise the mineralogical composition and evaluate the level of impurities that could have potentially affected the mechanical properties. The results show that materials, such as porphyry, previously thought to be of lower quality due to the anisotropic composition and coarse feldspar and quartz phenocrysts embedded in a silica rich matrix, possess fracture toughness values that can be compared to those of chert. Thus, it appears that different raw materials cannot be distinguished from the point of view of indentation fracture resistance, calling for detailed supplementary analyses of different fracture properties. This work also offers first insight into the quality of archaeological porphyry that was utilised as a primary raw material at various Middle and Upper Palaeolithic sites in the IAMC.
Accreting protoplanets: Spectral signatures and magnitude of gas and dust extinction at Hα
2021-12-24

Context. Accreting planetary-mass objects have been detected at H α , but targeted searches have mainly resulted in non-detections. Accretion tracers in the planetary-mass regime could originate from the shock itself, making them particularly susceptible to extinction by the accreting material. High-resolution ( R &gt; 50 000) spectrographs operating at H α should soon enable one to study how the incoming material shapes the line profile. Aims. We calculate how much the gas and dust accreting onto a planet reduce the H α flux from the shock at the planetary surface and how they affect the line shape. We also study the absorption-modified relationship between the H α luminosity and accretion rate. Methods. We computed the high-resolution radiative transfer of the H α line using a one-dimensional velocity–density–temperature structure for the inflowing matter in three representative accretion geometries: spherical symmetry, polar inflow, and magnetospheric accretion. For each, we explored the wide relevant ranges of the accretion rate and planet mass. We used detailed gas opacities and carefully estimated possible dust opacities. Results. At accretion rates of Ṁ ≲ 3 × 10 −6 M J yr −1 , gas extinction is negligible for spherical or polar inflow and at most A H α ≲ 0.5 mag for magnetospheric accretion. Up to Ṁ ≈ 3 × 10 −4 M J yr −1 , the gas contributes A H α ≲ 4 mag. This contribution decreases with mass. We estimate realistic dust opacities at H α to be κ ~ 0.01–10 cm 2 g −1 , which is 10–10 4 times lower than in the interstellar medium. Extinction flattens the L H α – Ṁ relationship, which becomes non-monotonic with a maximum luminosity L H α ~ 10 −4 L ⊙ towards Ṁ ≈ 10 −4 M J yr −1 for a planet mass ~10 M J . In magnetospheric accretion, the gas can introduce features in the line profile, while the velocity gradient smears them out in other geometries. Conclusions. For a wide part of parameter space, extinction by the accreting matter should be negligible, simplifying the interpretation of observations, especially for planets in gaps. At high Ṁ , strong absorption reduces the H α flux, and some measurements can be interpreted as two Ṁ values. Highly resolved line profiles ( R ~ 10 5 ) can provide (complex) constraints on the thermal and dynamical structure of the accretion flow.
Artifacts in EEG-Based BCI Therapies: Friend or Foe?
2021-12-24

EEG-based brain–computer interfaces (BCI) have promising therapeutic potential beyond traditional neurofeedback training, such as enabling personalized and optimized virtual reality (VR) neurorehabilitation paradigms where the timing and parameters of the visual experience is synchronized with specific brain states. While BCI algorithms are often designed to focus on whichever portion of a signal is most informative, in these brain-state-synchronized applications, it is of critical importance that the resulting decoder is sensitive to physiological brain activity representative of various mental states, and not to artifacts, such as those arising from naturalistic movements. In this study, we compare the relative classification accuracy with which different motor tasks can be decoded from both extracted brain activity and artifacts contained in the EEG signal. EEG data were collected from 17 chronic stroke patients while performing six different head, hand, and arm movements in a realistic VR-based neurorehabilitation paradigm. Results show that the artifactual component of the EEG signal is significantly more informative than brain activity with respect to classification accuracy. This finding is consistent across different feature extraction methods and classification pipelines. While informative brain signals can be recovered with suitable cleaning procedures, we recommend that features should not be designed solely to maximize classification accuracy, as this could select for remaining artifactual components. We also propose the use of machine learning approaches that are interpretable to verify that classification is driven by physiological brain states. In summary, whereas informative artifacts are a helpful friend in BCI-based communication applications, they can be a problematic foe in the estimation of physiological brain states.
Associations do not energize behavior: on the forgotten legacy of Kurt Lewin
2021-12-24

Abstract Hundred years ago, Kurt Lewin published a series of articles in which he vehemently argued against the idea that associations between stimuli and responses motivate behavior. This article reviews his empirical work and theory and the cogency of Lewin’s conclusion according to modern standards. We conclude that Lewin’s criticism of the contiguity principle of associationism is still valid, and is now supported by a broad range of theories on learning, motivation, and action control. Implications for modern dual-system theory and modern theories on motivated action and (instructed) task sets are discussed.
Accreting protoplanets: Spectral signatures and magnitude of gas and dust extinction at H
2021-12-24

Context. Accreting planetary-mass objects have been detected at H α, but targeted searches have mainly resulted in non-detections. Accretion tracers in the planetary-mass regime could originate from the shock itself, making them particularly susceptible to extinction by the accreting material. High-resolution (R > 50 000) spectrographs operating at H α should soon enable one to study how the incoming material shapes the line profile. Aims. We calculate how much the gas and dust accreting onto a planet reduce the H α flux from the shock at the planetary surface and how they affect the line shape. We also study the absorption-modified relationship between the H α luminosity and accretion rate. Methods. We computed the high-resolution radiative transfer of the H α line using a one-dimensional velocity–density–temperature structure for the inflowing matter in three representative accretion geometries: spherical symmetry, polar inflow, and magnetospheric accretion. For each, we explored the wide relevant ranges of the accretion rate and planet mass. We used detailed gas opacities and carefully estimated possible dust opacities. Results. At accretion rates of Ṁ ≲ 3 × 10−6 MJ yr−1, gas extinction is negligible for spherical or polar inflow and at most AH α ≲ 0.5 mag for magnetospheric accretion. Up to Ṁ ≈ 3 × 10−4 MJ yr−1, the gas contributes AH α ≲ 4 mag. This contribution decreases with mass. We estimate realistic dust opacities at H α to be κ ~ 0.01–10 cm2 g−1, which is 10–104 times lower than in the interstellar medium. Extinction flattens the LH α –Ṁ relationship, which becomes non-monotonic with a maximum luminosity LH α ~ 10−4 L⊙ towards Ṁ ≈ 10−4 MJ yr−1 for a planet mass ~10 MJ. In magnetospheric accretion, the gas can introduce features in the line profile, while the velocity gradient smears them out in other geometries. Conclusions. For a wide part of parameter space, extinction by the accreting matter should be negligible, simplifying the interpretation of observations, especially for planets in gaps. At high Ṁ, strong absorption reduces the H α flux, and some measurements can be interpreted as two Ṁ values. Highly resolved line profiles (R ~ 105) can provide (complex) constraints on the thermal and dynamical structure of the accretion flow.
Apolipoprotein E derived from CD11c+ cells ameliorates atherosclerosis
2021-12-25

Atherosclerosis is studied in models with dysfunctional lipid homeostasis-predominantly the ApoE<sup>-/-</sup> mouse. The role of antigen-presenting cells (APCs) for lipid homeostasis is not clear. Using a LacZ reporter mouse, we showed that CD11c<sup>+</sup> cells were enriched in aortae of ApoE<sup>-/-</sup> mice. Systemic long-term depletion of CD11c<sup>+</sup> cells in ApoE<sup>-/-</sup> mice resulted in significantly increased plaque formation associated with reduced serum ApoE levels. In CD11c<sup>cre+</sup>ApoE<sup>fl/fl</sup> and Albumin<sup>cre+</sup>ApoE<sup>fl/fl</sup> mice, we could show that ≈70% of ApoE is liver-derived and ≈25% originates from CD11c<sup>+</sup> cells associated with significantly increased atherosclerotic plaque burden in both strains. Exposure to acLDL promoted cholesterol efflux from CD11c<sup>+</sup> cells and cell-specific deletion of ApoE resulted in increased inflammation reflected by increased IL-1β serum levels. Our results determined for the first time the level of ApoE originating from CD11c<sup>+</sup> cells and demonstrated that CD11c<sup>+</sup> cells ameliorate atherosclerosis by the secretion of ApoE.
Using Teacher Dashboards to Assess Group Collaboration in Problem-based Learning
2021-12-26

Assessing group collaboration is a critical element in Problem-based Learning (PBL). In asynchronous online PBL settings, facilitators encounter challenges to assess group collaboration because of delayed responses, lack of social cues, and the orchestration load. Teacher dashboards have the potential to support facilitators to assess collaboration by providing synthesized and visualized information about student learning. Previous studies have explored facilitators’ user experience of teacher dashboards. However, little is known about how facilitators with different levels of PBL expertise interpret dashboard information differently. In this study, we analyzed ten PBL facilitators’ utterance moves while interacting with an online teacher dashboard to examine the difference between expert and novice facilitators as they used each visualization. This study can inform the design of teacher dashboards on collaboration assessment.
Microstratigraphic preservation of ancient faunal and hominin DNA in Pleistocene cave sediments
2021-12-27

Significance DNA preserved in sediments has emerged as an important source of information about past ecosystems, independent of the discovery of skeletal remains. However, little is known about the sources of sediment DNA, the factors affecting its long-term preservation, and the extent to which it may be translocated after deposition. Here, we show that impregnated blocks of intact sediment are excellent archives of DNA. DNA distribution is highly heterogeneous at the microscale in the cave sediment we studied, suggesting that postdepositional movement of DNA is unlikely to be a common phenomenon in cases where the stratigraphy is undisturbed. Combining micromorphological analysis with microstratigraphic retrieval of ancient DNA therefore allows genetic information to be associated with the detailed archaeological and ecological record preserved in sediments.