julilili42/papers huggingface dataset:
Selection of Indicator Bird Species as a Baseline for Knowledge Assessment in Biodiversity Survey Studies
2023-07-06

The loss of Earth’s biodiversity is accompanied by a loss of public knowledge about species. Many scientists are convinced that knowledge about species is an important prerequisite to interest and investment in species conservation. In the past, knowledge about species has mostly been assessed using birds, but there is no consensus on which birds could serve as a baseline for knowledge about species in the general public. The aim of this study is to provide a list of the ‘golden 50′ bird species in Germany that can be used by educational institutions, as well as studies about species knowledge to make them more comparable. The list can also serve as a basis for the selection of so-called flagship species, which are used for the protection of habitats and other species due to their high likeability. To achieve this, three consecutive steps were conducted: an analysis of bird-related databases to determine which species might be common and known and two expert panel studies. The data analysis included several factors: species characteristics, Citizen Science data, public value and importance, and scientific studies. In both the first and second rounds, experts were asked for their opinion on which species should be known by the general public in Germany. The first expert panel, which consisted of only a small group of experts (n = 6), was mainly used to reduce the number of species for the second panel. In the second expert panel, 197 ornithologically qualified experts from all over Germany were asked for their assessment. The correlations between the expert assessments and the different variables were all significant (except for the species trait “colourfulness”), which validates the selection process used here and consequently the species list that has been compiled. The selection process can also be applied to other biogeographical regions or taxa.
Stuck With the Algorithm: Algorithmic Consciousness and Repertoire in Fridays for Future’s Data Contention
2023-07-06

By focusing on the transnational youth climate movement Fridays for Future, this article explores how activists understand algorithms and how they try to use them in their digital campaigns. A qualitative case study, this article provides insights from nine virtual in-depth semi-structured interviews with organizers in social media roles from Fridays for Future country collectives across the globe, giving youth activists the opportunity to tell stories about their understandings and experiences in working in datafied spaces. Four central themes emerge via a three-step qualitative data analysis: algorithmic consciousness (understanding, functions, issues, pitfalls, and misinterpretations), algorithm as stake (contentious importance, tactical politics), algorithm as repertoire (role in activism, algorithmic campaigning), and data contention&lt;em&gt; &lt;/em&gt;(data analysis, digital contentious tactics, uncritical uses). The interviews show that activists are stuck with the algorithm in two ways: They have to engage with them but are often unsure how. In that sense, activists frame algorithms as a stakeholder in their campaign but are often unclear on how they work. While organizers recognize algorithmic dependency on campaign success, they lack specific mobilization strategies, which prevents them from leveraging algorithms as a contentious tactic. Data contention includes conducting analytics and tailoring strategies to platforms; yet, datafied spaces are used largely uncritically. This article prompts scholars to go beyond textual analyses of digital activism and conduct research that centers on the experiences and practices of activists in dealing with algorithms and data as structural conditions for digital activism.
Dual-Time-Point Posttherapy177Lu-PSMA-617 SPECT/CT Describes the Uptake Kinetics of mCRPC Lesions and Prognosticates Patients’ Outcome
2023-07-06

<sup>177</sup>Lu-PSMA-617 is an effective therapeutic option in metastasized castration-resistant prostate cancer (mCRPC). However, some patients progress under treatment. We hypothesized that the tracer kinetics within the metastases may influence the therapy effectiveness and tested this hypothesis by analyzing uptake parameters on 2 consecutive posttherapy SPECT/CT scans. <b>Methods:</b> mCRPC patients treated with <sup>177</sup>Lu-PSMA-617 and with available posttherapy SPECT/CT imaging (24 and 48 h after the first treatment) were enrolled retrospectively. Volumes of interest were defined on lymph node metastasis (LNM) and bone metastasis (BM) on both SPECT/CT scans. The reduction of the percentage injected dose (%IDred) between the 2 SPECT/CT scans was computed. We compared %IDred of responders (prostate-specific antigen drop ≥ 50% after 2 cycles of <sup>177</sup>Lu-PSMA-617) and nonresponders. We tested the association of %IDred with progression-free survival and overall survival (OS) using a univariate Kaplan-Meier (KM) analysis and a multivariate Cox regression model. <b>Results:</b> Fifty-five patients (median age, 73 y; range, 54-87 y) were included. %IDred in LNM and BM was greater in nonresponders than in responders (for LNM, 36% in nonresponders [interquartile range (IQR), 26%-47%] vs. 24% in responders [IQR, 12%-33%] [<i>P</i> = 0.003]; for BM, 35% in nonresponders [IQR, 27%-52%] vs. 18% in responders [IQR, 15%-29%] [<i>P</i> = 0.002]). For progression-free survival, in KM analysis, greater %IDred in LNM (<i>P</i> = 0.008) and BM (<i>P</i> = 0.001) was associated with shorter survival, whereas in multivariate analysis, only %IDred in LNM was retained (<i>P</i> = 0.03). In univariate KM analysis of OS, greater %IDred in BM was associated with shorter survival (<i>P</i> = 0.002). In multivariate OS analysis, BM %IDred (<i>P</i> = 0.009) was retained. <b>Conclusion:</b> The <sup>177</sup>Lu-PSMA-617 clearance rate from mCRPC metastases appears to be a relevant prognosticator of response and survival, with faster clearing possibly signaling a shorter radiopharmaceutical residence time and absorbed dose. Dual-time-point analysis appears to be a feasible and readily available approach to estimate the likelihood of response and patients' survival.
Detection of IgE-autoantibodies to nuclear antigens in patients with systemic sclerosis and analysis of their clinical relevance
2023-07-06

IgE-autoantibodies against CENP-A/B and topo-I occur in SSc underlining the concept that SSc may be a T helper cell type 2 mediated disease. IgE-anti-CENP-A-antibodies correlated with disease activity, but this has to be confirmed in larger studies.
Filling the blank space: Branched 4-nonylphenols isomers are responsible for robust constitutive androstane receptor (CAR) activation by nonylphenol
2023-07-06

4-Nonylphenol (4-NP), a para-substituted phenolic compound mixture comprising a straight or branched carbon chain, is a widespread ubiquitous environmental pollutant and food contaminant. 4-NP, particularly the branched form, has been identified as an endocrine disruptor with potent activities on estrogen nuclear receptors. Constitutive Androstane Receptor (CAR, NR1I3) is another crucial nuclear receptor that regulates hepatic lipid, glucose, and steroid metabolism and is involved in endocrine disruption mechanism. The nonylphenol mixture has been described as an extremely potent activator of both human and rodent CAR. However, detailed mechanistic aspects of CAR activation by NP are enigmatic and it is not known if 4-NP can directly interact with the CAR ligand binding domain (LBD). Here we examined interactions of individual branched (22NP, 33NP, and 353NP) and linear 4-NPs with CAR and its variants using molecular dynamics (MD) simulations, cellular experiments with various CAR constructs or CAR ligand binding domain (LBD) mutants, or in differentiated HepaRG hepatocyte cellular model. Our results demonstrate that branched 4-NPs display more stable poses to activate both wild-type (wt)CAR1 as well as CAR3 variant LBDs in MD simulations. Consistently, branched 4-NP activated CAR3 and wtCAR1 LBD more efficiently than linear 4-NP or tert-nonylphenol (22NP). Furthermore, in HepaRG cells, we observed that all NP significantly up-regulated CYP2B6, a relevant hallmark for CAR activation. This is the first study to provide detailed insights into the direct interaction between individual 4-NPs and the human CAR-LBD, as well as its dominant variant CAR3 The work could contribute to the safer use of individual NPs in many areas of industry.
Extracellular Matrix Expression in Human Pancreatic Fat Cells of Patients with Normal Glucose Regulation, Prediabetes and Type 2 Diabetes
2023-07-06

Previously, we found that human pancreatic preadipocytes (PPAs) and islets influence each other and that the crosstalk with the fatty liver via the hepatokine fetuin-A/palmitate induces inflammatory responses. Here, we examined whether the mRNA-expression of pancreatic extracellular matrix (ECM)-forming and -degrading components differ in PPAs from individuals with normal glucose regulation (PPAs-NGR), prediabetes (PPAs-PD), and type 2 diabetes (PPAs-T2D), and whether fetuin-A/palmitate impacts ECM-formation/degradation and associated monocyte invasion. Human pancreatic resections were analyzed (immuno)histologically. PPAs were studied for mRNA expression by real-time PCR and protein secretion by Luminex analysis. Furthermore, co-cultures with human islets and monocyte migration assays in Transwell plates were conducted. We found that in comparison with NGR-PPAs, TIMP-2 mRNA levels were lower in PPAs-PD, and TGF-β1 mRNA levels were higher in PPAs-T2D. Fetuin-A/palmitate reduced fibronectin, decorin, TIMP-1/-2 and TGF-ß1 mRNA levels. Only fibronectin was strongly downregulated by fetuin-A/palmitate independently of the glycemic status. Co-culturing of PPAs with islets increased TIMP-1 mRNA expression in islets. Fetuin-A/palmitate increased MMP-1, usherin and dermatopontin mRNA-levels in co-cultured islets. A transmigration assay showed increased monocyte migration towards PPAs, which was enhanced by fetuin-A/palmitate. This was more pronounced in PPAs-T2D. The expression of distinct ECM components differs in PPAs-PD and PPAs-T2D compared to PPAs-NGR, suggesting that ECM alterations can occur even in mild hyperglycemia. Fetuin-A/palmitate impacts on ECM formation/degradation in PPAs and co-cultured islets. Fetuin-A/palmitate also enhances monocyte migration, a process which might impact on matrix turnover.
Non-decameric NLRP3 forms an MTOC-independent inflammasome
2023-07-07

Summary NLRP3 is an inflammasome-forming protein that plays a key role in conditions ranging from infections to Alzheimer’s disease. NLRP3 is activated by many potassium (K + )-dependent or - independent stimuli related to pathogens or sterile insults. Molecularly, human NLRP3 assembles into a decameric ‘cage’ and its interaction with both the trans-Golgi network (TGN) and the microtubule organization centre (MTOC) has been proposed as critical for NLRP3 activation. However, the relative mechanistic requirement for K + -dependent versus - independent stimuli is unclear. Using spatially and dynamically high-resolution microscopy in human macrophages, we found that K + -dependent NLRP3 stimulation triggers two distinct activation pathways: ( i ) the decameric cage-dependent pathway, which was also exclusively required for the K + -independent stimulus, imiquimod; and ( ii ) a cage- and TGN/MTOC-independent pathway that was fully functional in an NLRP3 protein engineered to form monomers and unable to interact with membrane lipids. Collectively, our results delineate two parallel yet biologically distinct NLRP3 activation pathways.
Predicting Visual Fixations
2023-07-07

As we navigate and behave in the world, we are constantly deciding, a few times per second, where to look next. The outcomes of these decisions in response to visual input are comparatively easy to measure as trajectories of eye movements, offering insight into many unconscious and conscious visual and cognitive processes. In this article, we review recent advances in predicting where we look. We focus on evaluating and comparing models: How can we consistently measure how well models predict eye movements, and how can we judge the contribution of different mechanisms? Probabilistic models facilitate a unified approach to fixation prediction that allows us to use explainable information explained to compare different models across different settings, such as static and video saliency, as well as scanpath prediction. We review how the large variety of saliency maps and scanpath models can be translated into this unifying framework, how much different factors contribute, and how we can select the most informative examples for model comparison. We conclude that the universal scale of information gain offers a powerful tool for the inspection of candidate mechanisms and experimental design that helps us understand the continual decision-making process that determines where we look.
Single‐Cell Integration of BMD GWAS Results Prioritize Candidate Genes Influencing Age‐Related Bone Loss
2023-07-07

The regulation of bone mineral density (BMD) is highly influenced by genetics and age. Although genome‐wide association studies (GWAS) for BMD have uncovered many genes through their proximity to associated variants (variant nearest‐neighbor [VNN] genes), the cell‐specific mechanisms of each VNN gene remain unclear. This is primarily due to the inability to prioritize these genes by cell type and age‐related expression. Using age‐related transcriptomics, we found that the expression of many VNN genes was upregulated in the bone and marrow from aged mice. Candidate genes from GWAS were investigated using single‐cell RNA‐sequencing (scRNA‐seq) datasets to enrich for cell‐specific expression signatures. VNN candidate genes are highly enriched in osteo‐lineage cells, osteocytes, hypertrophic chondrocytes, and Lepr+ mesenchymal stem cells. These data were used to generate a “blueprint” for Cre‐loxp mouse line selection for functional validation of candidate genes and further investigation of their role in BMD maintenance throughout aging. In VNN‐gene‐enriched cells, Sparc , encoding the extracellular matrix (ECM) protein osteonectin, was robustly expressed. This, along with expression of numerous other ECM genes, indicates that many VNN genes likely have roles in ECM deposition by osteoblasts. Overall, we provide data supporting streamlined translation of GWAS candidate genes to potential novel therapeutic targets for the treatment of osteoporosis. © 2023 The Authors. JBMR Plus published by Wiley Periodicals LLC on behalf of American Society for Bone and Mineral Research.
Critical nanomaterial attributes of iron-carbohydrate nanoparticles: Leveraging orthogonal methods to resolve the 3-dimensional structure
2023-07-07

Intravenous iron-carbohydrate nanomedicines are widely used to treat iron deficiency and iron deficiency anemia across a wide breadth of patient populations. These colloidal solutions of nanoparticles are complex drugs which inherently makes physicochemical characterization more challenging than small molecule drugs. There have been advancements in physicochemical characterization techniques such as dynamic light scattering and zeta potential measurement, that have provided a better understanding of the physical structure of these drug products in vitro. However, establishment and validation of complementary and orthogonal approaches are necessary to better understand the 3-dimensional physical structure of the iron-carbohydrate complexes, particularly with regard to their physical state in the context of the nanoparticle interaction with biological components such as whole blood (i.e. the nano-bio interface).
Pro-Calcifying Role of Enzymatically Modified LDL (eLDL) in Aortic Valve Sclerosis via Induction of IL-6 and IL-33
2023-07-07

One of the contributors to atherogenesis is enzymatically modified LDL (eLDL). eLDL was detected in all stages of aortic valve sclerosis and was demonstrated to trigger the activation of p38 mitogen-activated protein kinase (p38 MAPK), which has been identified as a pro-inflammatory protein in atherosclerosis. In this study, we investigated the influence of eLDL on IL-6 and IL-33 induction, and also the impact of eLDL on calcification in aortic valve stenosis (AS). eLDL upregulated phosphate-induced calcification in valvular interstitial cells (VICs)/myofibroblasts isolated from diseased aortic valves, as demonstrated by alizarin red staining. Functional studies demonstrated activation of p38 MAPK as well as an altered gene expression of osteogenic genes known to be involved in vascular calcification. In parallel with the activation of p38 MAPK, eLDL also induced upregulation of the cytokines IL-6 and IL-33. The results suggest a pro-calcifying role of eLDL in AS via induction of IL-6 and IL-33.
Association of Estrogen Receptor 1 PvuII and XbaI Polymorphisms and Peripheral Estrogen Receptor 1 mRNA Levels with Alzheimer’s Disease in Turkish Patients
2023-07-07

Objective: Estrogen receptor 1 (ESR1) polymorphisms are associated with Alzheimer's disease (AD) and polymorphisms in the first intronic region of the gene are known to affect ESR1 mRNA transcription. The first intronic region of the ESR1 contains two polymorphisms that have received the most attention: PvuII rs2234693 (NM 000125.3: c.453-397T&gt;C) and XbaI rs9340799 (NM 000125.3: c.453-351A&gt;G). Both polymorphisms have been shown to be associated with AD, but consistent findings across populations have not been established. This study aimed to determine whether ESR1 PvuII and XbaI polymorphisms are associated with the disease in a cohort of Turkish AD patients. Whether PvuII and XbaI polymorphisms affect disease susceptibility by influencing ESR1 mRNA expression was also examined. Materials and Methods: Genotyping was performed in 424 patients with AD (mean age: 64.5 +- 11.1 yrs) and 302 controls (mean age: 56.4 +- 13.0 yrs). The polymerase chain reaction (PCR) and restriction enzyme digestion methods were used to determine the prevalence of the ESR1 PvuII and XbaI polymorphisms. The ESR1 mRNA expression was analyzed in the peripheral blood cells of 85 patients and 53 age-matched controls using quantitative real-time PCR. Results: No significant difference in genotype and allele frequencies of ESR1 PvuII and XbaI polymorphisms between the patients and controls was found. However, the frequencies of the PvuII C and XbaI G alleles were significantly higher in the patients with the apolipoprotein-E (APOE) &#949;4 allele. The ESR1 mRNA levels were significantly lower in the patients with AD compared with the controls (P = 0.001). The XbaI A allele was significantly associated with lower ESR1 mRNA levels (P = 0.044) and this association remained significant even after adjusting for confounders such as age, gender and APOE &#949;4 carrier status (P = 0.035). Conclusion: This study demonstrated that the distribution of PvuII and XbaI alleles is associated with the APOE &#949;4 allele. The XbaI polymorphism may be associated with a higher risk of AD by altering ESR1 mRNA levels.
Acylated- and unacylated ghrelin during an oral glucose tolerance test in humans at risk for type 2 diabetes mellitus
2023-07-07

Abstract Background/Objectives The orexigenic peptide hormone ghrelin has been implicated in the pathophysiology of obesity and type 2 diabetes mellitus through its effects on nutrient homeostasis. Ghrelin is subject to a unique post-translational acyl modification regulating its biochemical activity. Subjects/Methods In this study we aimed to investigate the relation of acylated (AcG) as well as unacylated ghrelin (UnG) with body weight and insulin resistance in the fasting ( n = 545) and post-oral glucose tolerance test (oGTT) state ( n = 245) in a metabolically well characterized cohort covering a broad range of BMI (17.95 kg/m2–76.25 kg/m2). Results Fasting AcG (median 94.2 pg/ml) and UnG (median 175.3 pg/ml) were negatively and the AcG/UnG ratio was positively correlated with BMI (all p &lt; 0.0001). Insulin sensitivity (ISI) correlated positively with AcG ( p = 0.0014) and UnG ( p = 0.0004) but not with the AcG/UnG ratio. In a multivariate analysis, including ISI and BMI, only BMI, but not ISI was independently associated with AcG and UnG concentrations. Significant changes of AcG and UnG concentrations were detectable after oGTT stimulation, with slight decreases after 30 min and increases after 90–120 min. Subject stratification into BMI-divergent groups revealed more pronounced AcG increases in the two groups with BMI &lt; 40 kg/m2. Conclusion Our data demonstrate lower concentrations for both AcG and UnG with increasing BMI as well as an increased proportion of the biologically active, acylated form of ghrelin giving point to pharmacologic intervention in ghrelin acylation and/or increase in UnG for treatment of obesity despite decreased absolute AcG levels.
We see what we hear: dissonant music engages early visual processing
2023-07-07

Abstract The neuroscientific examination of music processing in audiovisual contexts offers a valuable framework to assess how auditory information influences the emotional encoding of visual information. Using fMRI during naturalistic film viewing, we investigated the neural mechanisms underlying music’s effect on valence inferences during mental state attribution. Thirty-eight participants watched the same short-film accompanied by systematically controlled consonant or dissonant music. Subjects were instructed to think about the main character’s intentions. The results revealed that increasing levels of dissonance led to more negatively-valenced inferences, displaying the profound emotional impact of musical dissonance. Crucially, at the neuroscientific level and despite music being the sole manipulation, dissonance evoked the response of the primary visual cortex response (V1). Functional/effective connectivity analysis showed a stronger coupling between the auditory ventral stream (AVS) and V1 in response to tonal dissonance, and demonstrated the modulation of early visual processing via top-down feedback inputs from the AVS to V1. These V1 signal changes indicate the influence of high-level contextual representations associated with tonal dissonance on early visual cortices, serving to facilitate the emotional interpretation of visual information. The findings substantiate the critical role of audio-visual integration in shaping higher-order functions such as social cognition. Significance statement The present study reveals responses in the primary visual cortex modulated by musical information: tonal dissonance recruits early visual processing via feedback interactions from the auditory ventral pathway to the primary visual cortex. We demonstrate that the auditory “what” ventral stream plays a role in assigning meaning to non-verbal sound cues, such as dissonant music conveying negative emotions, providing an interpretative framework that serves to process the audio-visual experience. Our results highlight the significance of employing systematically controlled music, which can isolate emotional valence from the arousal dimension, to elucidate the brain’s sound-to-meaning interface and its distributive crossmodal effects on early visual encoding during naturalistic film viewing. Data sharing All relevant data are available from the figshare database DOI: 10.6084/m9.figshare.21345240