julilili42/papers huggingface dataset:
Are Deep Neural Networks Adequate Behavioral Models of Human Visual Perception?
2023-03-31

Deep neural networks (DNNs) are machine learning algorithms that have revolutionized computer vision due to their remarkable successes in tasks like object classification and segmentation. The success of DNNs as computer vision algorithms has led to the suggestion that DNNs may also be good models of human visual perception. In this article, we review evidence regarding current DNNs as adequate behavioral models of human core object recognition. To this end, we argue that it is important to distinguish between statistical tools and computational models and to understand model quality as a multidimensional concept in which clarity about modeling goals is key. Reviewing a large number of psychophysical and computational explorations of core object recognition performance in humans and DNNs, we argue that DNNs are highly valuable scientific tools but that, as of today, DNNs should only be regarded as promising—but not yet adequate—computational models of human core object recognition behavior. On the way, we dispel several myths surrounding DNNs in vision science.
Cutaneous squamous cell carcinoma: state of the art, perspectives and unmet needs
2023-03-31

Summary Squamous cell carcinoma of the skin (cSCC) is one of the most common cancers of the Caucasian population and accounts for 20% of all cutaneous tumors. An S3 guideline from the German Guideline Program in Oncology has been available since 2019 and was updated in 2022. The diagnosis of cSCC is based on clinical examination. Excision and histological confirmation are required for clinically suspicious lesions to allow for prognostic assessment and correct treatment. The treatment of first choice is excision with complete histological assessment of the surgical margins. Adjuvant radiation therapy may be considered if there is a high risk of recurrence. The immune checkpoint inhibitor cemiplimab is approved and recommended as the treatment of first choice for locally advanced or metastatic cSCC in Europe. If contraindications are present, chemotherapy, EGFR inhibitors, or palliative radiation therapy may be used. Surveillance should be performed in a risk‐stratified manner and includes a dermatological control supplemented by sonography examinations in high‐risk patients. Much research is still needed for solid organ transplant patients, concomitant hematologic diseases, and cSCC showing primary or acquired resistance to immunotherapies. Current developments include new drug combinations, intralesional therapies alone or in combination with immune checkpoint inhibitors, and neoadjuvant approaches.
How to foster STEM learning during Covid-19 remote schooling: Combining virtual and video experiments
2023-03-31

Understanding scientific concepts is a fundamental aim of science education. Conceptual understanding can be fostered through inquiry learning with experiments. However, during the Covid-19 pandemic school closures hands-on experiments could hardly be realized. Fortunately, digital technologies allow for conducting experiments virtually by using interactive simulations or observing video recordings of hands-on experiments. In the present study, 154 seventh graders in remote schooling were involved in inquiry learning using either a combination of virtual and video experiments in two different orders or only virtual experiments. We hypothesized that in general inquiry learning fosters students' conceptual understanding in physics, which could be confirmed. Moreover, we expected the combinations to be more effective than learning with virtual experiments only due to the complementary roles of the prior, which was, however, not the case. We conclude that virtual and video experiments can be recommended to teachers if hands-on experimentation is not possible.
S1‐guideline cutaneous and subcutaneous leiomyosarcoma
2023-03-31

Summary Superficial leiomyosarcomas (LMS) are rare skin cancers (2–3% of cutaneous sarcomas) that originate from dermally located hair follicle muscles, dartos or areolar muscles (cutaneous/dermal LMS), or from vascular muscle cells of the subcutaneous adipose tissue (subcutaneous LMS). These superficial LMS are distinct from LMS of the deep soft tissues. Leiomyosarcomas are typically localized at the lower extremities, trunk or capillitium, and present as painful, erythematous to brownish nodules. Diagnosis is made by histopathology. The treatment of choice for primary LMS is complete (R0) microscopically controlled excision, with safety margins of 1 cm in dermal LMS, and 2 cm in subcutaneous LMS, if possible. Non‐resectable or metastatic LMS require individual treatment decisions. After R0 resection with 1 cm safety margins, the local recurrence rate of dermal LMS is very low, and metastasis is very rare. Subcutaneous LMS, very large, or incompletely excised LMS recur and metastasize more frequently. For this reason, clinical follow‐up examinations are recommended every six months for cutaneous LMS, and every three months for subcutaneous LMS within the first two years (in subcutaneous LMS including locoregional lymph node sonography). Imaging such as CT/MRI is indicated only in primary tumors with special features, recurrences, or already metastasized tumors.
Geographic variation of litter chemistry and palatability in an invasive plant versus its native competitor
2023-03-31

Abstract Aim Latitudinal variation in biotic interactions is recognized as a driver underlying variation in plant invasion success and therefore an important issue in conservation biogeography. However, previous studies have mainly focused on interactions between living plants and herbivores, whereas litter traits and detritivory have been hardly studied along latitude or compared between native and invasive plants. Our aim was to compare latitudinal variation in leaf litter chemistry and palatability to detritivores between invasive and native plants, and investigate which chemical traits determine detritivory and whether they are climate‐driven. Location China. Taxa Spartina alterniflora , Phragmites australis , Porcellio laevis , Chiromantes dehaani . Methods We combined field surveys with laboratory experiments to compare latitudinal variation in litter chemistry between the widespread invasive Spartina alterniflora and its native competitor Phragmites australis across their co‐occurring range (20.9–40.7° N, ~2200 km). For both species, we examined litter palatability to two common detritivores ( Porcellio laevis and Chiromantes dehaani ) along the same latitude. We also analysed relationships among climate, litter traits and detritivory. Results In five of nine litter traits, we found latitudinal clines, with little difference between the two plant species in how they responded across the gradient. Litter palatability decreased with increasing latitude, but was generally higher in Spartina than Phragmites . Two key litter traits (C:P ratio and flavonoid content) were significantly associated with temperature of origin and with detritivory. Main Conclusions There were geographic clines in litter traits and palatability, with strong links between climate, litter chemistry and detritivory, in both Spartina and Phragmites . Spartina litter, however, was more rapidly decomposed by detritivores, which could create positive feedbacks, and contributes to the successful Spartina invasion along China's coast. Future ecological restoration projects should therefore dispose Spartina plant tissue or litter off‐site, to reduce the competitiveness of Spartina and support the conservation of native Phragmites .
No evidence of oligoclonal bands, intrathecal immunoglobulin synthesis and B cell recruitment in acute ischemic stroke
2023-03-31

Background Within the past 10 years, immune mechanisms associated with acute ischemic stroke (AIS) have been brought into focus, but data on B cell activation and intrathecal Ig production is still scarce. In this study, we determined the prevalence of an elevated IgG index, positive oligoclonal bands (OCBs) and chemokine C-X-C motif ligand 13 (CXCL13) levels in the cerebrospinal fluid (CSF) as markers of intrathecal IgG synthesis and B cell activation in patients with AIS. Methods In a retrospective study we analyzed the cerebrospinal fluid (CSF) from 212 patients with AIS from December 2013 to May 2018 assessing intrathecal Ig synthesis, OCBs and CXCL13 concentrations. Results Overall, 5.7% (12/212) of AIS patients showed an intrathecal IgG synthesis, 0.5% (1/212) with isolated elevated IgG index, 5.2% (7/136) isolated positive OCBs and 2.9% (4/136) both elevated IgG index and positive OCBs. CXCL13 levels were elevated in 3.6% (3/83) of the patients. Approximately one third of these patients had simultaneously chronic inflammatory CNS disease (multiple sclerosis, neuromyelitis optica spectrum disorder, neurosarcoidosis). There was no significant association between CSF findings and stroke characteristics including vascular territory, localization, volume, etiology, acute treatment, or blood-brain barrier dysfunction. Intrathecal IgG synthesis was more common in patients with prior stroke. Longitudinal CSF analysis did not reveal any newly-occurring, but instead mostly persistent or even disappearing intrathecal IgG synthesis after AIS. Conclusions We found no evidence of a relevant B cell recruitment and intrathecal IgG synthesis in patients with AIS. In fact, the occurrence of intrathecal IgG synthesis was associated with concurrent chronic inflammatory CNS disease or previous stroke. Consequently, in patients with first-ever AIS and intrathecal IgG synthesis, physicians should search for concomitant inflammatory CNS disease.
A Metastable Ketenyl Radical–Water Complex from UV Photolysis of the Carboxymethyl Radical
2023-03-31

The unpaired electron impacts the binding between radicals and ordinary closed-shell molecules in noncovalent complexes. Conversely, the complexation partner can enhance, decrease, or even control the reactivity of the interacting radical. Previously, such radical-molecule (and especially radical-water) complexes were studied by controlled assembly of the interacting partners which mostly leads to formation of the thermodynamically most stable species. Here, we show that UV photolysis of the resonance-stabilized carboxymethyl radical isolated in a cryogenic argon matrix at 4 K leads to the intermediary formation of a metastable, noncovalent complex of the ketenyl radical with a water molecule. In this complex, the ketenyl radical binds water at its terminal carbon atom, although a more stable isomer exists in which water interacts with the C-H bond of the radical. Rigorous W1 theory computations confirm that the ketenyl radical is a stronger donor in C-H···O interactions than ketene itself, while it performs comparably well as an acceptor. We propose that complex formation proceeds <i>via</i> an initial excited-state C-O bond breaking reaction in carboxymethyl under release of an OH radical, which is supported by multireference QD-NEVPT2 computations.
SCAview: an Intuitive Visual Approach to the Integrative Analysis of Clinical Data in Spinocerebellar Ataxias
2023-03-31

Abstract With SCAview, we present a prompt and comprehensive tool that enables scientists to browse large datasets of the most common spinocerebellar ataxias intuitively and without technical effort. Basic concept is a visualization of data, with a graphical handling and filtering to select and define subgroups and their comparison. Several plot types to visualize all data points resulting from the selected attributes are provided. The underlying synthetic cohort is based on clinical data from five different European and US longitudinal multicenter cohorts in spinocerebellar ataxia type 1, 2, 3, and 6 (SCA1, 2, 3, and 6) comprising &gt; 1400 patients with overall &gt; 5500 visits. First, we developed a common data model to integrate the clinical, demographic, and characterizing data of each source cohort. Second, the available datasets from each cohort were mapped onto the data model. Third, we created a synthetic cohort based on the cleaned dataset. With SCAview, we demonstrate the feasibility of mapping cohort data from different sources onto a common data model. The resulting browser-based visualization tool with a thoroughly graphical handling of the data offers researchers the unique possibility to visualize relationships and distributions of clinical data, to define subgroups and to further investigate them without any technical effort. Access to SCAview can be requested via the Ataxia Global Initiative and is free of charge.
Fornix fractional anisotropy mediates the association between Mediterranean diet adherence and memory four years later in older adults without dementia
2023-03-31

ABSTRACT Here, we investigated whether fractional anisotropy (FA) of hippocampus-relevant white-matter tracts mediates the association between baseline Mediterranean diet adherence (MeDiAd) and verbal episodic memory over four years. Participants were healthy older adults with and without subjective cognitive decline and patients with amnestic mild cognitive impairment from the DELCODE cohort study ( n = 376; age: 71.47 ± 6.09 years; 48.7% female). MeDiAd and diffusion data were obtained at baseline. Verbal episodic memory was assessed at baseline and four yearly follow-ups. The associations between baseline MeDiAd and white matter, and verbal episodic memory’s mean and rate of change over four years were tested with latent growth curve modeling. Baseline MeDiAd was associated with verbal episodic memory four years later (95% confidence interval, CI [0.01, 0.32]) but not with its rate of change over this period. Baseline Fornix FA mediated – and, thus, explained – that association (95% CI [0.002, 0.09]). Fornix FA may be an appropriate response biomarker of Mediterranean diet interventions on verbal memory in older adults.
Delineating disorder-general and disorder-specific dimensions of psychopathology from functional brain networks in a developmental clinical sample
2023-03-31

Abstract The interplay between functional brain network maturation and psychopathology during development remains elusive. To establish the structure of psychopathology and its neurobiological mechanisms, mapping of both shared and unique functional connectivity patterns across developmental clinical populations is needed. We investigated shared associations between resting-state functional connectivity and psychopathology in children and adolescents aged 5-21 (n=1689). Specifically, we used partial least squares (PLS) to identify latent variables (LV) between connectivity and both symptom scores and diagnostic information. We also investigated associations between connectivity and each diagnosis specifically, controlling for other diagnosis categories. PLS identified five significant LVs between connectivity and symptoms, mapping onto the psychopathology hierarchy. The first LV resembled a general psychopathology factor, followed by dimensions of internalising-externalising, neurodevelopment, somatic complaints, and thought problems. Another PLS with diagnostic data revealed one significant LV, resembling a cross-diagnostic case-control pattern. The diagnosis-specific PLS identified a unique connectivity pattern for autism spectrum disorder (ASD). All LVs were associated with distinct patterns of functional connectivity. These dimensions largely replicated in an independent sample (n=420) from the same dataset, as well as to an independent cohort (n = 3504). This suggests that covariance in developmental functional brain networks supports transdiagnostic dimensions of psychopathology.
Data from A Pro-Regenerative Environment Triggers Premalignant to Malignant Transformation of Senescent Hepatocytes
2023-03-31

&lt;div&gt;Abstract&lt;p&gt;Unfortunately, available liver cancer treatments are associated with modest survival advantage. The biggest factor improving survival is early detection, but the current understanding of early transformation events is limited. Therefore, we set up a model to study these early events and investigated the relationship of premalignant, senescent hepatocytes, a regenerative environment, and the influence of secreted factors on liver tumorigenesis. Oncogene-induced senescence (OIS) was triggered in a subset of mouse hepatocytes, which under normal conditions, are eliminated by immunosurveillance. Inducing liver damage and regeneration was sufficient to trigger immunosurveillance escape of OIS hepatocytes, resulting in premalignant to malignant transformation and hepatocellular tumor development. Trefoil factor 3 (TFF3) was found to be overexpressed in OIS hepatocytes and in hepatocellular carcinoma. TFF3 deficiency strongly attenuated malignant transformation by increasing insulin-like growth factor binding protein 5 (IGFBP5) expression, which consequently dampened IGF receptor signaling. Furthermore, analysis of precancerous liver tissue validated TFF3 as an early liver cancer biomarker. Altogether, these findings provide mechanistic insights into early transformation and immunosurveillance escape in liver cancer, revealing TFF3 and IGFBP5 to be important players with opposite roles in tumorigenesis.&lt;/p&gt;Significance:&lt;p&gt;Liver damage induces a compensatory regenerative response that can drive premalignant to malignant transformation of senescent hepatocytes.&lt;/p&gt;&lt;/div&gt;
Data from SC68896, a Novel Small Molecule Proteasome Inhibitor, Exerts Antiglioma Activity <i>In vitro</i> and <i>In vivo</i>
2023-03-31

&lt;div&gt;Abstract&lt;p&gt;&lt;b&gt;Purpose:&lt;/b&gt; Glioblastomas are among the most lethal neoplasms, with a median survival of &lt;1 year. Modulation of the proteasome function has emerged as a novel approach to cancer pharmacotherapy. Here, we characterized the antitumor properties of SC68896, a novel small molecule proteasome inhibitor.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Experimental Design:&lt;/b&gt; Different tumor cell lines were tested by crystal violet staining for sensitivity to SC68896, given alone or in combination with death ligands. The molecular mechanisms mediating SC68896-induced cell death and changes in cell cycle progression were assessed by immunoblot and flow cytometry. An orthotopic human glioma xenograft model in nude mice was used to examine the &lt;i&gt;in vivo&lt;/i&gt; activity of SC68896.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Results:&lt;/b&gt; SC68896 inhibits the proliferation of cell lines of different types of cancer, including malignant glioma. Exposure of LNT-229 glioma cells to SC68896 results in a concentration- and time-dependent inhibition of the proteasome, with a consequent accumulation of p21 and p27 proteins, cell cycle arrest, caspase cleavage, and induction of apoptosis. Using RNA interference, we show that the effect of SC68896 on glioma cells is facilitated by wild-type p53. SC68896 sensitizes glioma cells to tumor necrosis factor–related apoptosis–inducing ligand and CD95 ligand and up-regulates the cell surface expression of the tumor necrosis factor–related apoptosis–inducing ligand receptor cell death receptors 4 and 5, which may contribute to this sensitization. Intracerebral glioma–bearing nude mice treated either i.p. or intratumorally with SC68896 experience prolonged survival.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Conclusions:&lt;/b&gt; SC68896 is the first proteasome inhibitor that exerts antiglioma activity &lt;i&gt;in vivo&lt;/i&gt;. It may represent a novel prototype agent for the treatment of malignant gliomas and warrants clinical evaluation. (Clin Cancer Res 2009;15(21):6609–18)&lt;/p&gt;&lt;/div&gt;
Data from Unexpected Abundance of HLA Class II Presented Peptides in Primary Renal Cell Carcinomas
2023-03-31

&lt;div&gt;Abstract&lt;p&gt;&lt;b&gt;Purpose:&lt;/b&gt; To elicit a long-lasting antitumor immune response, CD8&lt;sup&gt;+&lt;/sup&gt; and CD4&lt;sup&gt;+&lt;/sup&gt; T cells should be activated. We attempted to isolate HLA-DR–presented peptides directly from dissected solid tumors, in particular from renal cell carcinoma, to identify MHC class II ligands from tumor-associated antigens (TAA) for their use in peptide-based immunotherapy.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Experimental Design:&lt;/b&gt; Tumor specimens were analyzed by immunohistochemical staining for their HLA class II expression. HLA class II peptides were subsequently isolated and identified by mass spectrometry. Gene expression analysis was done to detect genes overexpressed in tumor tissue. Peptides from identified TAAs were used to induce peptide-specific CD4&lt;sup&gt;+&lt;/sup&gt; T-cell responses in healthy donors and in tumor patients.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Results:&lt;/b&gt; In the absence of inflammation, expression of MHC class II molecules is mainly restricted to cells of the immune system. To our surprise, we were able to isolate and characterize hundreds of class II peptides directly from primary dissected solid tumors, especially from renal cell carcinomas, and from colorectal carcinomas and transitional cell carcinomas. Infiltrating leukocytes expressed MHC class II molecules and tumor cells, very likely under the influence of IFNγ. Our list of identified peptides contains ligands from several TAAs, including insulin-like growth factor binding protein 3 and matrix metalloproteinase 7. The latter bound promiscuously to HLA-DR molecules and were able to elicit CD4&lt;sup&gt;+&lt;/sup&gt; T-cell responses.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Conclusions:&lt;/b&gt; Thus, our direct approach will rapidly expand the limited number of T-helper epitopes from TAAs for their use in clinical vaccination protocols.&lt;/p&gt;&lt;/div&gt;
Longitudinal clusters of long-term trajectories in patients with early-onset chronic depression: Two years of naturalistic follow-up after extensive psychological treatment
2023-03-31

Introduction: In clinical trials, mostly group-level treatment effects of repeated cross-sectional measures are analyzed. However, substantial heterogeneity regarding individual symptom profiles and the variability of treatment effects are often neglected, especially over the long-term course. To provide effective personalized treatments, investigations of these characteristics are urgently needed.Methods: Depression severity ratings over 104 weeks of follow-up after year-long treatment with the Cognitive Behavioral Analysis System of Psychotherapy (CBASP) or Supportive Psychotherapy (SP) were analyzed. Longitudinal cluster analysis and multinomial logistic regression analysis were conducted to investigate intraindividual trajectories from one of the largest psychotherapy trials in early-onset chronic depression.Results: Two-year post-study-treatment trajectories of N=188 patients with early-onset chronic depression were grouped into four prototypical clusters. Overall, 16.0% of patients remitted (cluster 1) and most of them did not receive any treatment during the two-year follow-up. However, 84.0% of patients continued to experience subthreshold (37.2% cluster 2) or major depressive symptoms (46.8% clusters 3-4) and spent on average more than half of the follow-up in pharmacological and psychological treatment. Hierarchical regression analysis indicated that previous study treatment with CBASP or SP did not significantly predict cluster allocation, while baseline variables accounted for a large proportion of explained variance (R2N=.64).Conclusion: While some patients experienced stable remission over two years of follow-up, the majority of patients experienced subthreshold or major depressive symptoms regardless of former study treatment with CBASP or SP. This calls for a long-term perspective implementing staging and innovative treatment approaches such as the sequential model or modular psychotherapy.