julilili42/papers huggingface dataset:
Changes in stiffness of the extracellular and pericellular matrix in the anulus fibrosus of lumbar intervertebral discs over the course of degeneration
2022-12-23

Analogous to articular cartilage, changes in spatial chondrocyte organisation have been proposed to be a strong indicator for local tissue degeneration in the intervertebral disc (IVD). While a progressive structural and functional degradation of the extracellular (ECM) and pericellular (PCM) matrix occurs in osteoarthritic cartilage, these processes have not yet been biomechanically elucidated in the IVD. We aimed to evaluate the local stiffness of the ECM and PCM in the anulus fibrosus of the IVD on the basis of local chondrocyte spatial organisation. Using atomic force microscopy, we measured the Young’s modulus of the local ECM and PCM in human and bovine disc samples using the spatial chondrocyte patterns as an image-based biomarker. By measuring tissue from 31 patients and six bovine samples, we found a significant difference in the elastic moduli (E) of the PCM in clusters when compared to the healthy patterns single cells ( p = 0.029), pairs ( p = 0.016), and string-formations ( p = 0.010). The ECM/PCM ratio ranged from 0.62–0.89. Interestingly, in the bovine IVD, the ECM/PCM ratio of the E significantly varied ( p = 0.002) depending on the tissue origin. Overall the reduced E in clusters demonstrates that cluster formation is not only a morphological phenomenon describing disc degeneration, but it marks a compromised biomechanical functioning. Immunohistochemical analyses indicate that collagen type III degradation might be involved. This study is the first to describe and quantify the differences in the E of the ECM in relation to the PCM in the anulus fibrosus of the IVD by means of atomic force microscopy on the basis of spatial chondrocyte organisation.
Broader functions of TIR domains in Arabidopsis immunity
2022-12-23

Abstract TIR domains are NAD-degrading enzymes that function during immune signaling in prokaryotes, plants, and animals. In plants, most TIR domains are incorporated into intracellular immune receptors. In Arabidopsis, TIR-derived small molecules bind and activate EDS1 heterodimers, which in turn activate RNLs, a class of cation channel-forming immune receptors. RNL activation drives cytoplasmic Ca 2+ influx, transcriptional reprogramming, pathogen resistance and host cell death. We screened for mutants that suppress an RNL activation mimic allele and identified a TIR-containing immune receptor, SADR1. Despite functioning downstream of an auto-activated RNL, SADR1 is not required for defense signaling triggered by other tested TIR-containing immune receptors. SADR1 is required for defense signaling initiated by some trans-membrane pattern recognition receptors and contributes to the unbridled spread of cell death in lesion simulating disease 1 . Together with RNLs, SADR1 regulates defense gene expression at infection site borders, likely in a non-autonomous manner. RNL mutants that cannot sustain this pattern of gene expression are unable to prevent disease spread beyond localized infection sites, suggesting that this pattern corresponds to a pathogen containment mechanism. SADR1 potentiates RNL-driven immune signaling partially through the activation of EDS1, but also partially independently of EDS1. We studied EDS1-independent TIR function using nicotinamide, an NADase inhibitor. We observed decreased defense induction from trans-membrane pattern recognition receptors and decreased calcium influx, pathogen growth restriction and host cell death following intracellular immune receptor activation. We demonstrate that TIR domains can potentiate calcium influx and defense and are thus broadly required for Arabidopsis immunity.
Curiosity-Motivated Incidental Learning With And Without Incentives: Early Consolidation And Midbrain-Hippocampal Resting-State Functional Connectivity
2022-12-23

Abstract Human memory is selective and not all experiences are remembered. Both monetary rewards/incentives and curiosity have been found to motivate and facilitate learning by dopaminergic midbrain projections to the hippocampus during encoding. In this study, we examined potential brain mechanisms during early consolidation period that jointly or independently contribute to these facilitating effects. Participants (N = 50) watched 36 videos of magic tricks and rated their “subjective feelings of curiosity” while the availability of extrinsic incentives was manipulated between groups. Functional magnetic resonance imaging (fMRI) data were acquired before, during, and after learning, and memory for magic tricks was assessed one week after. Our analysis focused on the change in resting-state functional connectivity (RSFC) between the dopaminergic midbrain and the anterior hippocampus, a dopaminergic consolidation mechanism previously reported in the context of extrinsically motivated learning. Changes in RSFC were correlated with behavioural measures of learning, i.e., the total number of items encoded and the curiosity-driven memory benefit. We found that brain-behaviour correlations differed depending on the availability of extrinsic incentives. More specifically, the correlation between the total number of items encoded and RSFC change was significantly different in the incentivised compared to the control group. The curiosity-driven memory benefit, however, did not correlate with changes in RSFC in either of the groups. In sum, this suggests that curiosity-motivated learning might be supported by different consolidation mechanisms compared to extrinsically motivated learning and that extrinsic incentives influence consolidation mechanisms supporting learning. Key points A new curiosity-motivated incidental encoding paradigm was used to investigate how dopaminergic consolidation mechanisms support learning and whether this is further influenced by the availability of monetary incentives. Changes in resting-state functional connectivity between the dopaminergic midbrain and the anterior hippocampus, a dopaminergic consolidation mechanism, predicted learning outcomes significantly differently if monetary incentives were available. These results might suggest that learning motivated by curiosity might rely on different neural mechanisms during early consolidation than learning motivated by monetary incentives.
Engineered Agrobacterium improves transformation by mitigating plant immunity detection
2022-12-24

Summary Agrobacterium tumefaciens microbe‐associated molecular pattern elongation factor Tu (EF‐Tu) is perceived by orthologs of the Arabidopsis immune receptor EFR activating pattern‐triggered immunity (PTI) that causes reduced T‐DNA‐mediated transient expression. We altered EF‐Tu in A. tumefaciens to reduce PTI and improved transformation efficiency. A robust computational pipeline was established to detect EF‐Tu protein variation in a large set of plant bacterial species and identified EF‐Tu variants from bacterial pathogen Pseudomonas syringae pv. tomato DC3000 that allow the pathogen to escape EFR perception. Agrobacterium tumefaciens strains were engineered to substitute EF‐Tu with DC3000 variants and examined their transformation efficiency in plants. Elongation factor Tu variants with rarely occurred amino acid residues were identified within DC3000 EF‐Tu that mitigates recognition by EFR. Agrobacterium tumefaciens strains were engineered by expressing DC3000 EF‐Tu instead of native agrobacterial EF‐Tu and resulted in decreased plant immunity detection. These engineered A. tumefaciens strains displayed an increased efficiency in transient expression in both Arabidopsis thaliana and Camelina sativa . The results support the potential application of these strains as improved vehicles to introduce transgenic alleles into members of the Brassicaceae family.
From school strikes to webinars: Mapping the forced digitalization of Fridays for Future’s activism during the COVID-19 pandemic
2022-12-24

This paper discusses the forced digitalization of activism brought about by the COVID-19 pandemic in the case of the transnational environmental youth movement Fridays for Future (FFF). Theoretically, we engage with social movement action repertoires to study the shifts in protest tactics associated with the social restrictions during the early stages of the pandemic. A qualitative content analysis of 781 posts across all 27 national FFF Facebook pages in the European Union reveals four clusters of digital action types: digital contentious actions; online information and education; digital community engagement and online partnership development. While digital media were part of FFF’s action repertoire in pre-pandemic times, our findings yield that the shift from the movement’s iconic street protests to exclusively digital tactics privileges community-building and education over contentious actions, potentially softening the political impact of the movement’s landmark ‘school strike’. Furthermore, although timely tactical flexibility kept the movement going during country lockdowns, the forced digitalization in the early stages of the pandemic primarily recombined existing action tactics rather than innovating them.
Randomized Controlled Evaluation of a Group-Based Training for Parents of Adolescents with Gaming Disorder or Social Network Use Disorder
2022-12-24

Background: Internet Use Disorder (IUD), Gaming Disorder (GD), and Social Network Use Disorder (SNUD) are common phenomena among adolescents and young adults. Negative consequences of such disorders can be observed in the individuals themselves and in the family system. Although parents can influence their children in many ways, they are rarely considered in interventions. The present study examines the effectiveness of a group-based training for parents of adolescents with IUD, GD, or SNUD. Methods: A total of 76 parents of adolescents (12 to 20 years) were randomly assigned to the intervention group (IG) or the waiting list control group. Parents in the IG participated over eight weeks in six sessions of training (topics: psychoeducation, parenting behaviour, parent-child relationships, parent-child communication, and stress and relaxation). Questionnaires on adolescent symptomatology, parent-child relationships, and parental burden were collected before and after the intervention/waiting period. Results: The training reduced the IUD symptomatology of adolescents from the parents’ perspective. GD symptomatology improved for at-risk users, though not for pathological users. Some aspects of the parent-child relationships improved in the mothers’ judgment. Parental stress was already low before the training. Conclusions: The presented parent group training can be used to improve IUD symptomatology in adolescents and is effective in the context of early intervention for at-risk computer gamers.
Hydrodynamics of Non‐Equilibrium Soil Water Retention
2022-12-24

Abstract Water retention in soil exhibits diverse phenomena, including suction‐saturation hysteresis, non‐unique air entrapment at zero suction and negative suction under partial saturations. The constancy of suction after a long rest can be broken by relatively minor mechanical or hydraulic agitations such as low‐amplitude wetting cycles—this fact is here being related to metastable states that differ from the true equilibrium. The complete suction‐saturation relationships are thus being recovered using non‐equilibrium Landau's hydrodynamic theory and Onsager's reciprocity principles. Equilibrium suction does not pertain to hysteresis, yet can be approached through small amplitude agitations over long duration. Conditions for rate independence are being described, while rate‐dependency are also accommodated and illustrated. Finally, it is shown that the new non‐equilibrium theory retains the rigorously derived equilibrium result of the effective stress of partially saturated soils.
Sleep and neurocognitive outcome in primary school children with Robin Sequence
2022-12-25

Abstract Study objectives To investigate neurocognitive and behavioral outcomes at primary school age in relation to obstructive sleep apnea (OSA) in children with Robin sequence (RS) treated with the Tuebingen palatal plate in infancy and to assess the impact of OSA in these patients. Methods Forty-two primary school-aged children (n = 21 with RS, n = 21 age- and sex-matched controls) underwent polysomnography, intelligence testing (“Wechsler Intelligence Scale for Children—Fifth Edition” [WISC-V]), and anthropometrics. Families completed a 7-day sleep diary and questionnaires on sleep and behavior (Children’s Sleep Habits Questionnaire [CSHQ] and the Child Behavior Checklist [CBCL]). Results In children with RS (17 non-syndromic, four syndromic; median age 9.7 [8.5–10.8] years), the obstructive apnea-hypopnea index (OAHI) was significantly higher than in controls (1.3 [0.4–2.7]/h vs. 0.4 [0.1–0.6]/h). Two syndromic children with RS were already on nocturnal respiratory support for OSA prior to our study, and one non-syndromic child was diagnosed with severe OSA (OAHI 57/h) despite an unremarkable medical history and questionnaire. The overall intelligence quotient in children with RS was within the normal range and did not differ between children with RS and healthy peers (102 vs. 108, p = .05). However, children with RS had values in the at-risk clinical range for externalizing behavior. Conclusions These children with RS showed an increased risk of OSA and behavioral problems, suggesting regular screening for OSA throughout childhood. Neurocognitive scores in children with RS were within the normal range after adequate treatment of OSA during infancy.
Vaccine Side Effects in Health Care Workers after Vaccination against SARS-CoV-2: Data from TüSeRe:exact Study
2022-12-25

As the Corona Disease 2019 (COVID-19) caused by SARS-CoV-2 persists, vaccination is one of the key measures to contain the spread. Side effects (SE) from vaccination are one of the reasons for reluctance to vaccinate. We systematically investigated self-reported SE after the first, second, and booster vaccinations. The data were collected during the TüSeRe: exact study (Tübinger Monitoring Studie zur exakten Analyse der Immunantwort nach Vakzinierung). Employees of health and research institutions were invited to participate. Study participants were asked to fill out an online questionnaire and report their SE after each dose of SARS-CoV-2 vaccination. A total of 1046 participants (mean age: 44 ± 12.9 years; female, n = 815 (78%); male, n = 231 (22%)) were included in the analysis. Local and systemic SE were more frequent after receiving the vector-based vaccine ChAdOx1 nCoV-19 in the first vaccination. However, local and systemic SE were more common after receiving mRNA vaccines (BNT162b2, mRNA-1273) in the second vaccination. Compared to the BNT162b2 vaccine, more SE have been observed after receiving the mRNA-1273 vaccine in the booster vaccination. In multivariate analysis, local and systemic side effects were associated with vaccine type, age and gender. Local and systemic SE are common after SARS-CoV-2 vaccines. The frequency of self-reported local and systemic SE differ significantly between mRNA and vector-based vaccines.
Data on common carotid artery occlusion inducing focalized stroke lesions after Pertussis toxin injection
2022-12-25

This article contains raw and processed data related to research published by Vega et al. (2022). This complementary dataset provides further insight into the experimental validation of a single common carotid artery occlusion (CCAO) model upon pretreatment with pertussis toxin (PTX). We present data showing the extent of different PTX concentrations on neurological severity measured by Bederson score following CCAO. In addition, data indicate a protective effect of isoflurane on cerebral infarction and neurological deficits, as well as the consequences of PTX pretreatment on reperfusion after occlusion using time-of-flight magnetic resonance angiography. With these data, we aim to provide detailed experimental settings of this newly described model.
CCNE1 and survival of patients with tubo‐ovarian high‐grade serous carcinoma: An Ovarian Tumor Tissue Analysis consortium study
2022-12-26

Abstract Background Cyclin E1 (CCNE1) is a potential predictive marker and therapeutic target in tubo‐ovarian high‐grade serous carcinoma (HGSC). Smaller studies have revealed unfavorable associations for CCNE1 amplification and CCNE1 overexpression with survival, but to date no large‐scale, histotype‐specific validation has been performed. The hypothesis was that high‐level amplification of CCNE1 and CCNE1 overexpression, as well as a combination of the two, are linked to shorter overall survival in HGSC. Methods Within the Ovarian Tumor Tissue Analysis consortium, amplification status and protein level in 3029 HGSC cases and mRNA expression in 2419 samples were investigated. Results High‐level amplification (&gt;8 copies by chromogenic in situ hybridization) was found in 8.6% of HGSC and overexpression (&gt;60% with at least 5% demonstrating strong intensity by immunohistochemistry) was found in 22.4%. CCNE1 high‐level amplification and overexpression both were linked to shorter overall survival in multivariate survival analysis adjusted for age and stage, with hazard stratification by study (hazard ratio [HR], 1.26; 95% CI, 1.08‐1.47, p = .034, and HR, 1.18; 95% CI, 1.05‐1.32, p = .015, respectively). This was also true for cases with combined high‐level amplification/overexpression (HR, 1.26; 95% CI, 1.09‐1.47, p = .033). CCNE1 mRNA expression was not associated with overall survival (HR, 1.00 per 1‐SD increase; 95% CI, 0.94‐1.06; p = .58). CCNE1 high‐level amplification is mutually exclusive with the presence of germline BRCA1/2 pathogenic variants and shows an inverse association to RB1 loss. Conclusion This study provides large‐scale validation that CCNE1 high‐level amplification is associated with shorter survival, supporting its utility as a prognostic biomarker in HGSC.
Statistical protocol for analyzing 3D muscle attachment sites based on the “Validated Entheses‐based Reconstruction of Activity” (VERA) approach
2022-12-26

Abstract In anthropological sciences, the areas of the bones where muscles or ligaments attach (“entheses” or “muscle attachments”) are routinely used for reconstructing habitual physical activity based on skeletal remains. However, several previous studies have argued against this practice, considering the low measuring repeatability of most traditional evaluation techniques and the former lack of supportive experimental evidence for an actual effect of physical activity on entheseal morphology. In 2016, I proposed a repeatable virtual approach for reconstructing habitual physical activity using entheseal morphology, which has been validated based on several experimental studies on laboratory animal species and human skeletons with uniquely detailed and longitudinal occupational documentation. This method, which was later named the “Validated Entheses‐based Reconstruction of Activity” (VERA) method, relies on a precise protocol for virtually delineating and quantifying entheseal areas on three‐dimensional bone models. The obtained area measurements are then subjected to size adjustment and multivariate statistical analyses, which have been experimentally shown to reveal group correlations among entheses that reflect habitual coordination among muscle groups. This paper presents the first critical review of all the various statistical approaches previously employed for analyzing entheses using VERA (so far), providing the first coherent step‐by‐step protocol for the complete univariate and multivariate analysis of entheseal three‐dimensional data. These include the introduction of a new, simple, and fast plotting technique for the initial screening of group entheseal patterns prior to multivariate analysis (i.e., the “VERA Bar‐Chart”), followed by the calculation of the “group entheseal patterning index” (hereafter GEPI%).
Implementation of a Full Digital Workflow by 3D Printing Intraoral Splints Used in Dental Education: An Exploratory Observational Study with Respect to Students’ Experiences
2022-12-26

Fully digital workflows gained acceptance in dental practice and thereby are of interest for undergraduate education. An exploratory clinical observation was designed to track the implementation of such a workflow with novice digital users in order to describe its feasibility, time investment, and pitfalls. Methods: Students were invited to provide feedback for their experiences with a training module that consisted of the following: intraoral scanning, computer-aided design (CAD), manual finishing, and insertion of a 3D-printed bite splint for the lower jaw. Results: A total of 82 fourth-year students participated in the module. The average time required to perform an intraoral scan was 17 m 5 s, and all students were able to design a splint with an average time of 2 h 38 m. Students who indicated prior experience with CAD seem to outperform inexperienced students in both CAD task completion and intraoral scanning. The initial fit was reported as clinically acceptable by 68.5% of the participants, while 79% rated the workflow as very good to satisfactory and indicated that the training was helpful for dental practice. Conclusions: The implementation of a digital workflow in undergraduate dental education is feasible and has acceptable clinical results. However, CAD is time-intensive, and the experience can be challenging.
Anticancer Drug Conjugates Incorporating Estrogen Receptor Ligands
2022-12-26

Hormone-dependent cancers, such as certain types of breast cancer are characterized by over-expression of estrogen receptors (ERs). Anticancer drug conjugates combining ER ligands with other classes of anticancer agents may not only benefit from dual action at both anti-cancer targets but also from selective delivery of cytotoxic agents to ER-positive tumor cells resulting in less toxicity and adverse effects. Moreover, they could also take advantage of overcoming resistance typical for anti-hormonal monotherapy such as tamoxifen. In this review, we discuss the design, structures and pharmacological effects of numerous series of drug conjugates containing ER ligands such as selective ER modulators (tamoxifen, 4-hydroxytamoxifen, endoxifen), selective ER degraders (ICI-164384) and ER agonists (estradiol) linked to diverse anti-cancer agents including histone-deacetylase inhibitors, DNA-alkylating agents, antimitotic agents and epidermal growth factor receptor inhibitors.
Testing the susceptibility of larval stages of Simulium to temephos and Bacillus thuringiensis var israelensis in Germany and Northern Cameroon
2022-12-26

Abstract Assays to evaluate the susceptibility of Simulium larvae to temephos and Bacillus thuringiensis var israelensis ( Bti ) were carried out by setting‐up an in vitro laboratory test (‘bio assay’) and a semi‐natural test (‘système de goutières’) to assess the LC50/LC90 values. Larvae of Simulium species in Cameroon ( S. damnosum s.l., S. hargreavesi , S. vorax and S. cervicornutum ) and ( S. ( Odagmia ) ornatum and S. latipes ) in Germany were identified and tested. In the bio‐assay, 50 larvae were exposed for 10 min to concentrations from 0.01 to 10 ppm. For the Simulium from Germany, the LC50 (LC90) values after 3 and 6 h were 3.1 (27.9) and 0.14 (1.26) ppm for temephos and for Bti 7.8 (70.2) and 1.7 (15.3) ppm, respectively. For Cameroonian species, the values of LC50 (LC90) were lower, that is, 0.42 (8.04), 0.14 (2.70) and 0.073 (1.38) ppm, respectively, after 3, 6 and 12 h for temephos. In a semi natural condition, the LC50 of 10 min of application of temephos was 0.84 ppm after 3 h and a working solution (2.6 L) of Bti killed 50% after 6 h. To detect an upcoming of any resistance as it happened in Ivory Coast, a study of the occurrence resistance genes should be implemented.