julilili42/papers huggingface dataset:
AI Denoising Improves Image Quality and Radiological Workflows in Pediatric Ultra-Low-Dose Thorax Computed Tomography Scans
2022-06-24

(1) This study evaluates the impact of an AI denoising algorithm on image quality, diagnostic accuracy, and radiological workflows in pediatric chest ultra-low-dose CT (ULDCT). (2) Methods: 100 consecutive pediatric thorax ULDCT were included and reconstructed using weighted filtered back projection (wFBP), iterative reconstruction (ADMIRE 2), and AI denoising (PixelShine). Place-consistent noise measurements were used to compare objective image quality. Eight blinded readers independently rated the subjective image quality on a Likert scale (1 = worst to 5 = best). Each reader wrote a semiquantitative report to evaluate disease severity using a severity score with six common pathologies. The time to diagnosis was measured for each reader to compare the possible workflow benefits. Properly corrected mixed-effects analysis with post-hoc subgroup tests were used. Spearman’s correlation coefficient measured inter-reader agreement for the subjective image quality analysis and the severity score sheets. (3) Results: The highest noise was measured for wFBP, followed by ADMIRE 2, and PixelShine (76.9 ± 9.62 vs. 43.4 ± 4.45 vs. 34.8 ± 3.27 HU; each p &lt; 0.001). The highest subjective image quality was measured for PixelShine, followed by ADMIRE 2, and wFBP (4 (4–5) vs. 3 (4–5) vs. 3 (2–4), each p &lt; 0.001) with good inter-rater agreement (r ≥ 0.790; p ≤ 0.001). In diagnostic accuracy analysis, there was a good inter-rater agreement between the severity scores (r ≥ 0.764; p &lt; 0.001) without significant differences between severity score items per reconstruction mode (F (5.71; 566) = 0.792; p = 0.570). The shortest time to diagnosis was measured for the PixelShine datasets, followed by ADMIRE 2, and wFBP (2.28 ± 1.56 vs. 2.45 ± 1.90 vs. 2.66 ± 2.31 min; F (1.000; 99.00) = 268.1; p &lt; 0.001). (4) Conclusions: AI denoising significantly improves image quality in pediatric thorax ULDCT without compromising the diagnostic confidence and reduces the time to diagnosis substantially.
Kirkwood-Dirac quasiprobability approach to the statistics of incompatible observables
2022-06-24

Recent work has revealed the central role played by the Kirkwood-Dirac quasiprobability (KDQ) as a tool to properly account for non-classical features in the context of condensed matter physics (scrambling, dynamical phase transitions) metrology (standard and post-selected), thermodynamics (power output and fluctuation theorems), foundations (contextuality, anomalous weak values) and more. Given the growing relevance of the KDQ across the quantum sciences, our aim is two-fold: First, we highlight the role played by quasiprobabilities in characterizing the statistics of quantum observables and processes in the presence of measurement incompatibility. In this way, we show how the KDQ naturally underpins and unifies quantum correlators, quantum currents, Loschmidt echoes, and weak values. Second, we provide novel theoretical and experimental perspectives by discussing a wide variety of schemes to access the KDQ and its non-classicality features.
Glacier melt-down changes habitat characteristics and unique microbial community composition and physiology in alpine lake sediments
2022-06-24

Abstract Glacial melt-down alters hydrological and physico-chemical conditions in downstream aquatic habitats. In this study, we tested if sediment-associated microbial communities respond to the decrease of glaciers and associated meltwater flows in high-alpine lakes. We analyzed 16 lakes in forefield catchments of three glaciers in the Eastern Swiss Alps on physico-chemical and biological parameters. We compared lakes fed by glacier meltwater with hydrologically disconnected lakes, as well as “mixed” lakes that received water from both other lake types. Glacier-fed lakes had a higher turbidity (94 NTU) and conductivity (47 μS/cm), but were up to 5.2°C colder than disconnected lakes (1.5 NTU, 26 μS/cm). Nutrient concentration was low in all lakes (TN &amp;lt; 0.05 mg/l, TP &amp;lt; 0.02 mg/l). Bacterial diversity in the sediments decreased significantly with altitude. Bacterial community composition correlated with turbidity, temperature, conductivity, nitrate, and lake age and was distinctly different between glacier-fed compared to disconnected and mixed water lakes, but not between catchments. Chemoheterotrophic processes were more abundant in glacier-fed compared to disconnected and mixed water lakes where photoautotrophic processes dominated. Our study suggests that the loss of glaciers will change sediment bacterial community composition and physiology that are unique for glacier-fed lakes in mountain and polar regions.
A Comparison of Germany and the United Kingdom Indicates That More SARS-CoV-2 Circulation and Less Restrictions in the Warm Season Might Reduce Overall COVID-19 Burden
2022-06-24

(1) Background: Between March 2020 and January 2022 severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2) caused five infection waves in Europe. The first and the second wave was caused by wildtype SARS-CoV-2, while the following waves were caused by the variants of concern Alpha, Delta, and Omicron respectively. (2) Methods: In the present analysis, the first four waves were compared in Germany and the UK, in order to examine the COVID-19 epidemiology and its modulation by non-pharmaceutical interventions (NPI). (3) Results: The number of COVID-19 patients on intensive care units and the case fatality rate were used to estimate disease burden, the excess mortality to assess the net effect of NPI and other measures on the population. The UK was more severely affected by the first and the third wave while Germany was more affected by the second wave. The UK had a higher excess mortality during the first wave, afterwards the excess mortality in both countries was nearly identical. While most NPI were lifted in the UK in July 2021, the measures were kept and even aggravated in Germany. Nevertheless, in autumn 2021 Germany was much more affected, nearly resulting in a balanced sum of infections and deaths compared to the UK. Within the whole observation period, in Germany the number of COVID-19 patients on ICUs was up to four times higher than in the UK. Our results show that NPI have a limited effect on COVID-19 burden, seasonality plays a crucial role, and a higher virus circulation in a pre-wave situation could be beneficial. (4) Conclusions: Although Germany put much more effort and resources to fight the pandemic, the net balance of both countries was nearly identical, questioning the benefit of excessive ICU treatments and of the implementation of NPI, especially during the warm season.
A Novel PNGase Rc for Improved Protein N-Deglycosylation in Bioanalytics and Hydrogen–Deuterium Exchange Coupled With Mass Spectrometry Epitope Mapping under Challenging Conditions
2022-06-24

N-linked glycosylation is a ubiquitous posttranslational modification of proteins. While it plays an important role in the biological function of proteins, it often poses a major challenge for their analytical characterization. Currently available peptide <i>N</i>-glycanases (PNGases) are often inefficient at deglycosylating proteins due to sterically inaccessible N-glycosylation sites. This usually leads to poor sequence coverage in bottom-up analysis using liquid chromatography with tandem mass spectrometry and makes it impossible to obtain an intact mass signal in top-down MS analysis. In addition, most PNGases operate optimally only in the neutral to slightly acidic pH range and are severely compromised in the presence of reducing and denaturing substances, which limits their use for advanced bioanalysis based on hydrogen-deuterium exchange in combination with mass spectrometry (HDX-MS). Here, we present a novel peptide <i>N</i>-glycanase from <i>Rudaea cellulosilytica</i> (PNGase Rc) for which we demonstrate broad substrate specificity for <i>N</i>-glycan hydrolysis from multiply occupied and natively folded proteins. Our results show that PNGase Rc is functional even under challenging, HDX quenching conditions (pH 2.5, 0 °C) and in the presence of 0.4 M tris(2-carboxyethyl)phosphine, 4 M urea, and 1 M guanidinium chloride. Most importantly, we successfully applied the PNGase Rc in an HDX-MS workflow to determine the epitope of a nanobody targeting the extracellular domain of human signal-regulating protein alpha (SIRPα).
Cognitive control mechanisms in language processing: are there both within- and across-task conflict adaptation effects?
2022-06-24

Cognitive conflict is regarded as a crucial factor in triggering subsequent adjustments in cognitive control. Recent studies have suggested that the implementation of control following conflict detection might be domain-general in that conflict experienced in the language domain recruits control processes that deal with conflict experienced in non-linguistic domains. During language comprehension, humans often have to recover from conflicting interpretations as quickly and accurately as possible. In this study, we investigate how people adapt to conflict experienced during processing semantically ambiguous sentences. Experiments 1 to 3 investigated whether such semantic conflict produces the congruency sequence effect (CSE) within a subsequent manual Stroop task and whether Stroop conflict leads to adjustments in semantic processing. Experiments 4 to 6 investigated whether semantic conflict results in conflict adaptation in subsequent sentence processing. Although processing conflict was consistently experienced during sentence reading and in the Stroop task, we did not observe any within-task or cross-task adaptation effects. Specifically, there were no cross-task CSEs from the linguistic task to the Stroop task and vice versa (experiments 1–3)—speaking against the assumption of domain-general control mechanisms. Moreover, experiencing conflict within a semantically ambiguous sentence did not ease the processing of a subsequent ambiguous sentence (experiments 4–6). Implications of these findings will be discussed.
Multiparametric dual-time-point [18F]FDG-PET/MRI for lymph node staging in patients with untreated FIGO I/II cervical carcinoma
2022-06-24

<title>Abstract</title> <bold>Purpose:</bold>[<sup>18</sup>F]FDG PET/MRI comes with limited sensitivity for initial detection of lymph node metastases (LNM) in early stage cervical carcinoma. Therefore, the aim of this prospective study was to investigate the additional value of multiparametric dual-time-point PET/MRI and to asses potential influencing factors for LNM detection.<bold>Methods: </bold>63 patients underwent whole-body dual-time-point [<sup>18</sup>F]FDG-PET/MRI ≈60+90min p.i. (Biograph mMR®, Siemens Healthineers). 251 LN were evaluated visually by nuclear medicine and radiology expert, quantified multiparametrically and were correlated with histology. Multiparametric analysis was performed using a logistic regression-based malignancy score (MS).<bold>Results:</bold>Overall prevalence of LNM was 17.1% and dependent on tumor grade (Gx 1/6, G1:0/19, G2:18/106, G3:24/120). Grading of the primary tumor (G2/G3) had a significant impact on visual detection (sens: 8.3%/31%).Best single parameter for LNM detection was SUVavg, however with a significant loss of discriminatory power in G2 vs. G3 tumors (AUC: 0.673/ 0.901). For multiparametric analysis, the independent predictors “SUVavg, ∆SUVpeak (60 to 90 min p.i.), LN sphericity, ADC and histologic grade” were included in the MS. Application of the MS enhanced AUCs especially in G2 tumors (AUC: G2:0.769; G3:0.877) and improved accuracy for single LNM from 34.5% to 55.5% compared to the best univariate parameter SUVavg.Equated to the expert consensus, use of the malignancy score increased overall sensitivity from 31.0% to 79.3% (Youden optimum) with a moderate decrease in specificity from 98.3% to 75.6%.<bold>Conclusion:</bold>Low histologic grad (G2 vs. G3) hampers visual detectability of LNM in [<sup>18</sup>F]FDG-PET/MRI.<bold> </bold>Multiparametric evaluation of dual-time-point PET/MRI has the potential to improve accuracy compared to visual interpretation and enables sufficient N-staging also in G2 tumors.<bold>Trial registration:</bold>DRKS00014346. Registered April 4, 2018 - retrospectively registered,https://www.drks.de/drks_web/navigate.do?navigationId=trial.HTML&amp;TRIAL_ID=DRKS00014346
Fostering Pre-Service Physics Teachers’ Pedagogical Content Knowledge Regarding Digital Media
2022-06-25

Since the use of digital media opens new possibilities in physics education, pre-service teachers should develop pedagogical content knowledge (PCK) regarding digital media during teacher education. In the joint project DiKoLeP (German for: digital competencies of pre-service teachers in physics) of RWTH Aachen University, the University of Graz and the University of Tübingen, we therefore developed and implemented a university teaching concept with certain core elements to foster this digital-media PCK of pre-service physics teachers. The teaching concept was implemented as a university seminar at the three universities, considering the common core elements as well as individual curricular requirements. We evaluated the teaching concept in a pre-post-design with a recently developed knowledge test to measure digital-media PCK. Our findings indicated that the developed knowledge test is suitable to validly measure the digital-media PCK of pre-service physics teachers. Furthermore, first results of the empirical evaluation at the three participating universities showed a significant increase in students’ digital-media PCK with a small-to-medium effect for students who attended the theoretical as well as the practical sessions of the seminar.
Effects of selective attention on the C1 ERP component: A systematic review and meta‐analysis
2022-06-25

Abstract The C1 event‐related potential (ERP) captures the earliest stage of feedforward processing in the primary visual cortex (V1). An ongoing debate is whether top‐down selective attention can modulate the C1. One side of the debate pointed out that null findings appear to outnumber positive findings; thus, selective attention does not seem to influence the C1. However, this suggestion is not based on a valid approach to summarizing evidence across studies. Therefore, we conducted a systematic review and meta‐analysis investigating the effects of selective attention on the C1, involving 47 experiments and 794 subjects in total. Despite heterogeneity across studies, results suggested that attention has a moderate effect on the C1 (Cohen's = 0.33, p &lt; .0001); that is, C1 amplitude is larger for visual stimuli that are attended than unattended. These results suggest that C1 is affected by top‐down selective attention.
Associations of Different Emotion Regulation Strategies with Coping-Efficacy, Rumination and Stress
2022-06-25

Abstract Background In order to investigate the relationship between stress-reactive rumination and the implementation of different emotion-regulation strategies (ERS), the pilot study at hand assessed ecological momentary assessment data twice per day from currently depressed patients (n = 21) and healthy controls (n = 23). Methods We analyzed differences in the implementation of ERS (body-based, behavioral, cognitive, social and multiple) and the occurrence of stress, rumination and self-efficacy between the groups as well as associations of ERS implementation at a given time-point and later levels of stress and rumination. Results Overall, patients reported higher subjective stress levels as well as increased ruminative thinking as a response to life stress and, in addition, a more frequent implementation of ERS. Comparing the implementation of ERS, cognitive ERS were implemented most often in the clinical group in comparison to healthy controls. All ERS were associated with increased self-efficacy at the time-point they were implemented. The implementation of cognitive ERS (e.g., reframing) at a given time-point significantly predicted reduced rumination and stress at later time-points. Conclusions Clinical and non-clinical groups seem to differ in their implementation of ERS. While the implementation of all investigated ERS is related to increased coping-efficacy, ERS on a cognitive level seem to be advantageous in reducing stress as well as rumination.
Tropical Mirror Symmetry in Dimension One
2022-06-25

We prove a tropical mirror symmetry theorem for descendant Gromov-Witten\\ninvariants of the elliptic curve, generalizing the tropical mirror symmetry\\ntheorem for Hurwitz numbers of the elliptic curve, Theorem 2.20 in [B\\\\"ohm J.,\\nBringmann K., Buchholz A., Markwig H., J. Reine Angew. Math. 732 (2017),\\n211-246, arXiv:1309.5893]. For the case of the elliptic curve, the tropical\\nversion of mirror symmetry holds on a fine level and easily implies the\\nequality of the generating series of descendant Gromov-Witten invariants of the\\nelliptic curve to Feynman integrals. To prove tropical mirror symmetry for\\nelliptic curves, we investigate the bijection between graph covers and sets of\\nmonomials contributing to a coefficient in a Feynman integral. We also soup up\\nthe traditional approach in mathematical physics to mirror symmetry for the\\nelliptic curve, involving operators on a Fock space, to give a proof of\\ntropical mirror symmetry for Hurwitz numbers of the elliptic curve. In this\\nway, we shed light on the intimate relation between the operator approach on a\\nbosonic Fock space and the tropical approach.\\n
Rethinking Guo Xiang’s Concept of “Nothing” in the Perspective of His Reception of Laozi and Zhuangzi
2022-06-25

Since Feng Youlan and Tang Yongtong, scholars have mostly understood Guo Xiang’s “supreme nothing” (至無, zhi wu) as “non-existence”, arguing that by denying Dao as the origin of the universe, the philosophical tradition of Laozi, Zhuangzi, and Wang Bi, he strives to prove “self-generation” (自生, zi sheng) of all things. This way of interpretation not only leads to various dilemmas from the perspective of intellectual history, but also diverges from Guo Xiang’s own account of Dao. The purpose of this paper is to argue that Guo Xiang, instead of dismissing it, solidifies the opinion of Laozi and Zhuangzi on the transcendence of Dao through the concept of “supreme nothing”, and that the self-generation of all things is the logical endpoint of this reinforcement. The seemingly opposite viewpoints of transcendence and immanence, “Dao generates all things” and “All things are self-generated”, merge with each other in the context of the proposition “Dao follows nature” (道法自然, dao fa zi ran) in Laozi.
Developer’s Guide to an Organ-on-Chip Model
2022-06-27

Over the past decade, organ-on-chip research has been one of the most prolific areas of the entire field of tissue engineering. The development of organ-on-chip models requires an integrated interdisciplinary approach merging technologies and concepts from several different disciplines, including microfabrication, microfluidics, biomaterials, stem cell science, pharma-/toxicology, and medicine. In this perspective, we follow the journey of an organ-on-chip through its many different stages, from (i) the initial idea/specific scientific question to (ii) the design/concept phase, (iii) the engineering (fabrication and materials, sensor/actuator integration) and (iv) biology considerations (cell sources, biomaterials/scaffold), (v) the cell injection and tissue assembly process, (vi) the assay development, and (vii) the functional validation, all the way to (viii) the final applications. By summarizing some of the key learnings and findings from a developer's perspective and identifying suitable introductory reviews, this perspective strives to provide a conceptual, stepwise guide for the holistic development of an organ-on-chip model.
Resting-state functional connectivity patterns associated with childhood maltreatment in a large bicentric cohort of adults with and without major depression
2022-06-27

Abstract Background Childhood maltreatment (CM) represents a potent risk factor for major depressive disorder (MDD), including poorer treatment response. Altered resting-state connectivity in the fronto-limbic system has been reported in maltreated individuals. However, previous results in smaller samples differ largely regarding localization and direction of effects. Methods We included healthy and depressed samples [ n = 624 participants with MDD; n = 701 healthy control (HC) participants] that underwent resting-state functional MRI measurements and provided retrospective self-reports of maltreatment using the Childhood Trauma Questionnaire. A-priori defined regions of interest [ROI; amygdala, hippocampus, anterior cingulate cortex (ACC)] were used to calculate seed-to-voxel connectivities. Results No significant associations between maltreatment and resting-state connectivity of any ROI were found across MDD and HC participants and no interaction effect with diagnosis became significant. Investigating MDD patients only yielded maltreatment-associated increased connectivity between the amygdala and dorsolateral frontal areas [ p FDR &lt; 0.001; η 2 partial = 0.050; 95%-CI (0.023–0.085)]. This effect was robust across various sensitivity analyses and was associated with concurrent and previous symptom severity. Particularly strong amygdala-frontal associations with maltreatment were observed in acutely depressed individuals [ n = 264; p FDR &lt; 0.001; η 2 partial = 0.091; 95%-CI (0.038–0.166)). Weaker evidence – not surviving correction for multiple ROI analyses – was found for altered supracallosal ACC connectivity in HC individuals associated with maltreatment. Conclusions The majority of previous resting-state connectivity correlates of CM could not be replicated in this large-scale study. The strongest evidence was found for clinically relevant maltreatment associations with altered adult amygdala-dorsolateral frontal connectivity in depression. Future studies should explore the relevance of this pathway for a maltreated subgroup of MDD patients.
A Targetable Myeloid Inflammatory State Governs Disease Recurrence in Clear-Cell Renal Cell Carcinoma
2022-06-27

Abstract It is poorly understood how the tumor immune microenvironment influences disease recurrence in localized clear-cell renal cell carcinoma (ccRCC). Here we performed whole-transcriptomic profiling of 236 tumors from patients assigned to the placebo-only arm of a randomized, adjuvant clinical trial for high-risk localized ccRCC. Unbiased pathway analysis identified myeloid-derived IL6 as a key mediator. Furthermore, a novel myeloid gene signature strongly correlated with disease recurrence and overall survival on uni- and multivariate analyses and is linked to TP53 inactivation across multiple data sets. Strikingly, effector T-cell gene signatures, infiltration patterns, and exhaustion markers were not associated with disease recurrence. Targeting immunosuppressive myeloid inflammation with an adenosine A2A receptor antagonist in a novel, immunocompetent, Tp53-inactivated mouse model significantly reduced metastatic development. Our findings suggest that myeloid inflammation promotes disease recurrence in ccRCC and is targetable as well as provide a potential biomarker-based framework for the design of future immuno-oncology trials in ccRCC. Significance: Improved understanding of factors that influence metastatic development in localized ccRCC is greatly needed to aid accurate prediction of disease recurrence, clinical decision-making, and future adjuvant clinical trial design. Our analysis implicates intratumoral myeloid inflammation as a key driver of metastasis in patients and a novel immunocompetent mouse model. This article is highlighted in the In This Issue feature, p. 2221