julilili42/papers huggingface dataset:
Thin-Slice Prostate MRI Enabled by Deep Learning Image Reconstruction
2023-01-18

Objectives: Thin-slice prostate MRI might be beneficial for prostate cancer diagnostics. However, prolongation of acquisition time is a major drawback of thin-slice imaging. Therefore, the purpose of this study was to investigate the impact of a thin-slice deep learning accelerated T2-weighted (w) TSE imaging sequence (T2DLR) of the prostate as compared to conventional T2w TSE imaging (T2S). Materials and Methods: Thirty patients were included in this prospective study at one university center after obtaining written informed consent. T2S (3 mm slice thickness) was acquired first in three orthogonal planes followed by thin-slice T2DLR (2 mm slice thickness) in axial plane. Acquisition time of axial conventional T2S was 4:12 min compared to 4:37 min for T2DLR. Imaging datasets were evaluated by two radiologists using a Likert-scale ranging from 1–4, with 4 being the best regarding the following parameters: sharpness, lesion detectability, artifacts, overall image quality, and diagnostic confidence. Furthermore, preference of T2S versus T2DLR was evaluated. Results: The mean patient age was 68 ± 8 years. Sharpness of images and lesion detectability were rated better in T2DLR with a median of 4 versus a median of 3 in T2S (p &lt; 0.001 for both readers). Image noise was evaluated to be significantly worse in T2DLR as compared to T2S (p &lt; 0.001 and p = 0.021, respectively). Overall image quality was also evaluated to be superior in T2DLR versus T2S with a median of 4 versus 3 (p &lt; 0.001 for both readers). Both readers chose T2DLR in 29 cases as their preference. Conclusions: Thin-slice T2DLR of the prostate provides a significant improvement of image quality without significant prolongation of acquisition time.
On the Stability of Robust Dynamical Low-Rank Approximations for Hyperbolic Problems
2023-01-18

.The dynamical low-rank approximation (DLRA) is used to treat high-dimensional problems that arise in such diverse fields as kinetic transport and uncertainty quantification. Even though it is well known that certain spatial and temporal discretizations when combined with the DLRA approach can result in numerical instability, this phenomenon is poorly understood. In this paper we perform an stability analysis for the corresponding nonlinear equations of motion. This reveals the source of the instability for the projector-splitting integrator [C. Lubich and I. V. Oseledets, BIT, 54 (2014), pp. 171–188] when first discretizing the equations and then applying the DLRA. Based on this we propose a projector-splitting integrator, based on applying DLRA to the continuous system before performing the discretization, that recovers the classic CFL condition. We also show that the unconventional integrator [G. Ceruti and C. Lubich, BIT, 62 (2021), pp. 23–44] has more favorable stability properties. Moreover, we explain why the projector-splitting integrator performs better when approximating higher moments, while the unconventional integrator is generally superior for first order moments. Furthermore, an efficient and stable dynamical low-rank update for the scattering term in kinetic transport is proposed. Numerical experiments for kinetic transport and uncertainty quantification, which confirm the results of the stability analysis, are presented.Keywordsdynamical low-rank approximationnumerical stabilitykinetic equationsuncertainty quantificationprojector-splitting integratorunconventional integratorMSC codes35L6537M1565C2065P4065M12
Profile of the Multicenter Cohort of the German Cancer Consortium’s Clinical Communication Platform
2023-01-18

<title>Abstract</title> Treatment concepts in oncology are becoming increasingly personalized and diverse. Successively, changes in standards of care mandate continuous monitoring of patient pathways and clinical outcomes based on large, representative real-world data. The German Cancer Consortium’s (DKTK) Clinical Communication Platform (CCP) provides such opportunity. Connecting fourteen university hospital-based cancer centers, the CCP relies on a federated IT-infrastructure sourcing data from facility-based cancer registry units and biobanks. Federated analyses resulted in a cohort of 600,915 patients, out of which 232,991 were incident since 2013 and for which a comprehensive documentation is available. Next to demographic data (i.e., age at diagnosis: 2.0% 0–20 years, 8.3% 21–40 years, 30.9% 41–60 years, 50.1% 61–80 years, 8.8% 81 + years; and gender: 45.2% female, 54.7% male, 0.1% other) and diagnoses (five most frequent tumor origins: 22,523 prostate, 18,409 breast, 15,575 lung, 13,964 skin/malignant melanoma, 9,005 brain), the cohort dataset contains information about therapeutic interventions and response assessments and is connected to 287,883 liquid and tissue biosamples. Focusing on diagnoses and therapy-sequences, showcase analyses of diagnosis-specific sub-cohorts (pancreas, larynx, kidney, thyroid gland) demonstrate the analytical opportunities offered by the cohort’s data. Due to its data granularity and size, the cohort is a potential catalyst for translational cancer research. It provides rapid access to comprehensive patient groups and may improve the understanding of the clinical course of various (even rare) malignancies. Therefore, the cohort may serve as a decisions-making tool for clinical trial design and contributes to the evaluation of scientific findings under real-world conditions.
Dense Nuclear Matter Equation of State from Heavy-Ion Collisions
2023-01-18

The nuclear equation of state (EOS) is at the center of numerous theoretical and experimental efforts in nuclear physics, motivated by its crucial role in our understanding of the properties of nuclear matter found on Earth, in neutron stars, and in neutron-star mergers. With advances in microscopic theories for nuclear interactions, the availability of experiments probing nuclear matter under conditions not reached before, and the advent of multi-messenger astronomy, the next decade will bring new opportunities for determining the nuclear matter EOS.
Probing the sub-cellular mechanisms of LCA5-Leber Congenital Amaurosis and associated gene therapy with expansion microscopy
2023-01-18

Abstract Leber Congenital Amaurosis (LCA) is a group of Inherited Retinal Diseases (IRDs) characterized by the early onset and rapid loss of photoreceptor cells. Despite the discovery of a growing number of genes associated with this disease, the molecular mechanisms of photoreceptor cell degeneration of most LCA subtypes remain poorly understood. Here, using retina-specific affinity proteomics combined with Ultrastructure Expansion Microscopy (U-ExM), we revealed the structural and molecular defects underlying LCA type 5 (LCA5) with unprecedented resolution. We showed that LCA5 -encoded lebercilin, together with Retinitis Pigmentosa 1 protein (RP1) and the intraflagellar transport (IFT) proteins IFT81 and IFT88, localize at the bulge region of the photoreceptor outer segment (OS), a region crucial for OS membrane disc formation. Next, we demonstrated that mutant mice deficient for lebercilin exhibit early axonemal defects at the bulge region and the distal OS, accompanied by reduced level of RP1 and IFT proteins, affecting membrane disc formation and presumably leading to photoreceptor death. Finally, we probed the LCA5 gene augmentation therapy strategy using U-ExM by monitoring its subcellular outcome. We found that, expression of LCA5 partially restores the bulge region, preserves OS axoneme structure and membrane disc formation, as well as photoreceptor survival.
Video Data: Spatiotemporal visual statistics of aquatic environments in the natural habitats of zebrafish
2023-01-18

Video dataset accompanying " Spatiotemporal visual statistics of aquatic environments in the natural habitats of zebrafish." See accompanying Github repository for more documentation and analysis code.
Video Data: Spatiotemporal visual statistics of aquatic environments in the natural habitats of zebrafish
2023-01-18

&lt;p&gt;Video dataset accompanying &quot;&nbsp;Spatiotemporal visual statistics of aquatic environments in the natural habitats of zebrafish.&quot; See accompanying &lt;a href="https://github.com/eacooper/ZebrafishAquaticVisualStatsCode"&gt;Github repository&lt;/a&gt; for more documentation and analysis code.&lt;/p&gt;
Closing the Gap between the Auditory Nerve and Cochlear Implant Electrodes: Which Neurotrophin Cocktail Performs Best for Axonal Outgrowth and Is Electrical Stimulation Beneficial?
2023-01-19

Neurotrophins promote neurite outgrowth of auditory neurons and may help closing the gap to cochlear implant (CI) electrodes to enhance electrical hearing. The best concentrations and mix of neurotrophins for this nerve regrowth are unknown. Whether electrical stimulation (ES) during outgrowth is beneficial or may direct axons is another open question. Auditory neuron explant cultures of distinct cochlear turns of 6–7 days old mice were cultured for four days. We tested different concentrations and combinations of BDNF and NT-3 and quantified the numbers and lengths of neurites with an advanced automated analysis. A custom-made 24-well electrical stimulator based on two bulk CIs served to test different ES strategies. Quantification of receptors trkB, trkC, p75NTR, and histological analysis helped to analyze effects. We found 25 ng/mL BDNF to perform best, especially in basal neurons, a negative influence of NT-3 in combined BDNF/NT-3 scenarios, and tonotopic changes in trk and p75NTR receptor stainings. ES largely impeded neurite outgrowth and glia ensheathment in an amplitude-dependent way. Apical neurons showed slight benefits in neurite numbers and length with ES at 10 and 500 μA. We recommend BDNF as a potent drug to enhance the man-machine interface, but CIs should be better activated after nerve regrowth.
Pregnancy-related hypophysitis revisited
2023-01-19

Abstract Objective The aim of the study is to assess the distinguishing features of pregnancy-related hypophysitis (PR-Hy) compared to non-pregnancy autoimmune hypophysitis and to evaluate the changing therapeutic approaches and outcomes in PR-Hy over time. Design Retrospective analysis of all published cases with PR-Hy and 6 own cases. Methods A PubMed search was performed and abstracts screened for publications with information on cases with PR-Hy from which full-text review was performed. Clinical features, diagnostic findings, and outcome in relation to treatment modalities in PR-Hy were assessed. Results One hundred and forty-eight cases with PR-Hy were identified. PR-Hy was significantly delimited from non-PR-Hy by the frequent occurrence of the chiasmal syndrome (50% vs 13%, P &amp;lt; .0001), higher rate of intrasellar origin (94% vs 74%, P = .0005), lower rate of pituitary stalk involvement (39% vs 86%, P &amp;lt; .0001), and low rate of diabetes insipidus (12% vs 54%, P &amp;lt; .0001). The role of surgery in PR-Hy decreased over time while noninvasive treatment modalities increased. The recurrence rate after high-dose glucocorticoid therapy (33%) was high and exceeded that of surgery (2%) and conservative management (2%). In contrast to initial reports on PR-Hy, recent literature regarding outcome of mother's and child's health was positive. The frequency of spontaneous preterm delivery was not increased. Recurrent PR-Hy in a subsequent pregnancy was reported in only two females. Conclusion PR-Hy has distinct features that delineate the disorder from non-PR-Hy. With increasing experience in diagnosis, availability of adequate replacement therapy, and improved treatment modalities, PR-Hy has lost its threat and the outcome is encouraging.
The effect of Kuntai capsule on ovarian function in cisplatin-induced premature ovarian insufficiency rats
2023-01-19

Objective This study aims to evaluate the effect of Kuntai capsule on ovarian function in cisplatin-induced premature ovarian insufficiency rats and to explore the mechanism of Kuntai capsule on the ovarian function of rats. Methods Seventy-four female Sprague-Dawley rats were used for this study. Eight of the rats were randomly assigned to the Control group. The remaining sixty-six rats were utilized to establish the POI model via Cisplatin and then randomly divided into four groups: the model Control group, the Estradiol group, and groups treated with low and high doses of Kuntai capsule. For the 28-day administration, the Control and model Control groups were intragastrically administered with 2.0 mL of 0.9% sodium chloride daily, the Estradiol group with 2.0 mL of Estradiol suspension (0.2mg/kg/d), and the low dose Kuntai capsule group and the high dose Kuntai capsule group with 2.0 mL of Kuntai capsule suspension (0.6g/kg/d, 1.8g/kg/d, respectively). Sex hormone levels, estrous cycle, and ovarian coefficient of the five groups were compared, histological sections analyzed follicle counts, and the protein expressions of growth differentiation factor 9, light chain 3 A-II, and Beclin 1 in the ovarian tissue were detected by Western blotting. Results After the 28-day administration, the serum Estradiol and Follicle-Stimulating Hormone levels of the group treated with low dose of Kuntai capsule were not significantly different from the Control group, the serum anti-Müllerian Hormone level of the group treated with high dose of Kuntai capsule was significantly higher than the Estradiol group. The estrous cycle of the group treated with low dose of Kuntai capsule was significantly lower than the model Control group. Regarding ovarian coefficient, resting and growing follicles, growth differentiation factor 9, light chain 3 A-II, and Beclin 1 expression, both Kuntai capsule groups outperformed the model Control group with the statistical difference ( P &amp;lt;0.05). Conclusion Kuntai capsule can improve the estrous cycle and ovarian coefficient of rats with premature ovarian insufficiency, maintain the number of resting and growing follicles, and up-regulate the protein expression of growth differentiation factor 9, light chain 3 A-II, and Beclin 1 of rats’ ovaries.
A Peritoneal Purse-String Suture Prevents Symptomatic Lymphoceles in Retzius-Sparing Robot-Assisted Radical Prostatectomy
2023-01-19

Background: The retzius-sparing approach for robotic-assisted radical prostatectomy (RARP) has been increasingly adopted. Symptomatic lymphoceles are a widespread complication of RARP with pelvic lymph node dissection. Here, we present a new technique, the peritoneal purse-string suture (PPSS), that seems to reduce the rate of symptomatic lymphoceles following retzius-sparing RARP with extended pelvic lymph node dissection (ePLND). Methods: The radical prostatectomy and bilateral lymphadenectomy are performed through three separate peritoneal openings. The PPSS uses a single suture in a way similar to a purse-string suture; the openings of both lymphadenectomy fields are widened, and the rectovesical opening from the prostatectomy is simultaneously closed. This report retrospectively evaluates the perioperative and postoperative outcomes of two consecutive patient cohorts undergoing RARP with ePLND by a single surgeon between May 2015 and June 2019, one cohort prior to introducing PPSS as control (n = 145) and the other after introducing PPSS (n = 91). Results: The two study groups were comparable on baseline characteristics, except ASA. There were no Clavien–Dindo grade IV-V complications, and comparable rates of grade I-III complications. The difference in postoperative lymphocele formation was 22% in PPSS versus 27% in the control group (p = 0.33). The rate of symptomatic lymphoceles was significantly lower in the PPSS group (3% vs. 10%, p = 0.047). Conclusion: The PPSS is a feasible procedure that reduces symptomatic lymphoceles in patients undergoing RARP with a retzius-sparing approach.
Staining of activated ß2-integrins in combination with CD137 and CD154 for sensitive identification of functional antigen-specific CD4+ and CD8+ T cells
2023-01-19

Common flow cytometry-based methods used for functional assessment of antigen-specific T cells rely on de novo expression of intracellular cytokines or cell surface activation induced markers. They come with some limitations such as complex experimental setting, loss of cell viability and often high unspecific background which impairs assay sensitivity. We have previously shown that staining of activated ß 2 -integrins either with multimers of their ligand ICAM-1 or with a monoclonal antibody can serve as a functional marker detectable on T cells after minutes (CD8 + ) or few hours (CD4 + ) of activation. Here, we present a simple method for detection of activated ß 2 -integrins in combination with established cell surface activation induced markers. We observed that activated ß 2 -integrins were still detectable after 14 hours of stimulation, allowing their detection together with CD137 and CD154. Combinatorial gating of cells expressing activated ß 2 -integrins and CD137 or CD154 reduced background in unstimulated samples, increasing the signal-to-noise ratio and allowing improved assessment of low-frequency T cell responses. Extracellular staining of these markers highly correlated with production of intracellular cytokines IL-2, TNF or IFNγ in CD4 + and CD8 + T cells. As an exemplary application, SARS-CoV-2 spike-specific T cell responses were assessed in individuals after COVID-19 vaccination. This method should be useful for epitope discovery projects and for the simultaneous monitoring of low-frequency antigen-specific CD4 + and CD8 + T cell responses in various physiological situations.
Influences of cognitive control on number processing: New evidence from switching between two numerical tasks
2023-01-19

A growing body of research suggests that basic numerical abilities such as number magnitude and number parity processing are influenced by cognitive control. So far, however, evidence for number processing being influenced by cognitive control came primarily from observed adaptations to stimulus set characteristics (e.g., ratio or order of specific stimulus types) and switches between a numerical and non-numerical task. Complementing this previous research, the present study employed a task switching paradigm exclusively involving numerical tasks (i.e., magnitude comparisons and parity judgements) to examine how cognitive control processes influence number processing. Participants were presented with a single-digit number and had to either judge its parity or compare its magnitude with a standard of 5, depending on a preceding cue. Based on previous results, we expected the numerical distance effect and the spatial–numerical association of response codes (SNARC) effect to be modulated in switch trials requiring the exertion of cognitive control. Partly in line with our expectations, the numerical distance effect was reduced in switch trials. However, no modulation of the SNARC effect was observed. The results pattern suggests that number processing is influenced by cognitive control, depending on task requirements and the type of numerical information (i.e., numerical magnitude vs spatial association of numbers) that is processed. To reconcile the present and previous results, we propose an information prioritisation account, suggesting that cognitive control primarily influences the processing of the information type that requires the most explicit processing.
Influence of reward and location on dogs’ behaviour toward an interactive artificial agent
2023-01-19

Abstract Animal–robot interaction studies provide outstanding opportunities to understand the principles of social interactions. Here we investigated whether dogs’ behaviour toward a cooperative artificial agent (Unidentified Moving Object (UMO)) is influenced by receiving a reward directly from the agent, and by variability in the UMO’s location. In a problem-solving task, the UMO either helped dogs to obtain food (Direct Reward Group, DRG) or to fetch an object followed by an indirect reward from the owner/experimenter (Indirect Reward Group, IRG). During the Familiarization, the UMO either started from the same location or changed its starting location in all trials. In the Test phase, dogs faced the same task, but additionally a second, unfamiliar UMO was present. We found that both reward groups gazed at the UMO with decreasing latency during the Familiarization, with the IRG showing more gaze alternations between UMO and hiding location. Dogs showed no preference for either UMO in the Test phase but looked at the familiar UMO sooner if it had changed its location during the Familiarization. Thus, direct reward is not necessary to elicit elements of socially competent behavior in dogs, but variability in its motion may be important to improve the UMO’s animacy and promote flexible learning.
From experiences to numbers: the production of international disability statistics
2023-01-19

The call for internationally comparable data on disability has been omnipresent in recent disability politics. Several attempts have been made to develop and implement a standardized approach toward disability statistics, with the Washington Group Short Census Questions (WGSQ) being the most prominent. How does this questionnaire 'measure' disability? How do disability statistics translate the diversity of lived experiences into 'objective' numbers? Combining a sociology of quantification and disability studies, this article focuses on the social practices of disability statistics that contribute to the generation of 'disability' as a social category. After contextualizing 'disability' in international organizations' discourses, it uses document analysis to empirically reconstruct statistical experts' recommendations regarding definition, operationalization, data collection, and processing. The analysis shows how binary categorical boundaries are (re)introduced and successively objectified during this process. It also unfolds a risk-based approach that underlies the WGSQ and deviates from a social model of disability.
Modelling German Word Stress
2023-01-19

Standard linguistic and psycholinguistic approaches to stress assignment argue that the position of word stress is determined on the basis of abstract information such as syllable weight and number of syllables in the word. In the present study, we contrasted this approach with a perspective based on learning analogies according to which speakers learn to associate basic word form cues to stress position. To do so, we use a simple two-layer neural network trained with an error-driven learning mechanism to predict stress position in German morphologically simple and complex words. We find that networks trained on word forms outperformed networks trained on cues that represent abstract information. Moreover, most standard approaches assign stress from right to left. We tested this proposal and found that in morphologically simple words, assignment from right yielded better results than assignment from left, supporting the standard approach. By contrast, in morphologically complex words assignment from left outperformed assignment from right. We discuss the implications of our results for psycholinguistic theories of stress assignment by taking into account word form cues, abstract cues, assigning direction, and the representation of stress in the mental lexicon.