julilili42/papers huggingface dataset:
NovoLign: metaproteomics by sequence alignment
2024-01-01

Abstract Tremendous advances in mass spectrometric and bioinformatic approaches have expanded proteomics into the field of microbial ecology. The commonly used spectral annotation method for metaproteomics data relies on database searching, which requires sample-specific databases obtained from whole metagenome sequencing experiments. However, creating these databases is complex, time-consuming, and prone to errors, potentially biasing experimental outcomes and conclusions. This asks for alternative approaches that can provide rapid and orthogonal insights into metaproteomics data. Here, we present NovoLign, a de novo metaproteomics pipeline that performs sequence alignment of de novo sequences from complete metaproteomics experiments. The pipeline enables rapid taxonomic profiling of complex communities and evaluates the taxonomic coverage of metaproteomics outcomes obtained from database searches. Furthermore, the NovoLign pipeline supports the creation of reference sequence databases for database searching to ensure comprehensive coverage. We assessed the NovoLign pipeline for taxonomic coverage and false positive annotations using a wide range of in silico and experimental data, including pure reference strains, laboratory enrichment cultures, synthetic communities, and environmental microbial communities. In summary, we present NovoLign, a de novo metaproteomics pipeline that employs large-scale sequence alignment to enable rapid taxonomic profiling, evaluation of database searching outcomes, and the creation of reference sequence databases. The NovoLign pipeline is publicly available via: https://github.com/hbckleikamp/NovoLign.
Exploring the Perceived Barriers of Effective Communication Within the Coach–Athlete Relationship: A Sample of Scandinavian Coaches and Athletes
2024-01-01

Coaching is a process that guides development and is shaped by sound relationships between athletes and coaches. Interpersonal communication represents a mechanism for developing functional relationships. However, not all interactions between coaches and athletes are optimal, and limited research has attempted to understand the factors that impede the ability to engage in effective communication. This study aimed to contribute to the literature by exploring the barriers experienced by high-performance coaches and athletes that hinder interpersonal communication within the coach–athlete relationship. A qualitative design grounded in a pragmatic philosophical position was utilised, and 20 semistructured interviews with 12 coaches and eight athletes participating in elite team sports were carried out. Interviews were conducted either in person or digitally via an online platform and analysed through content analysis. Barriers were identified for either coaches, athletes, or both and categorised as follows: (a) intrapersonal (e.g., lack of skills and negative experiences), (b) interpersonal (e.g., lack of concern/interest and power imbalance), and (c) environmental factors (e.g., hierarchy and toxic culture). These results suggest efforts should be focused on equipping coaches and athletes with intra- and interpersonal skills and empowering them to co-create a safe and united culture for themselves and their sport.
Role of AMPK and Sirtuins in Aging Heart: Basic and Translational Aspects
2024-01-01

Aging is a key risk factor for numerous diseases, including cardiac diseases. High energy demands of the heart require precise cellular energy sensing to prevent metabolic stress. AMPK and sirtuins are key intracellular metabolic sensors regulating numerous cell functions, like mitochondrial function and biogenesis, autophagy, and redox balance. However, their function is impaired during the aging process leading to mitochondrial dysfunction, oxidative stress, and inflammation culminating in cardiovascular diseases. The underlying molecular mechanisms leading to dysfunction of metabolic sensing in the aging heart are complex and comprise both intracellular and systemic age-related alterations. In this study, we overview the current knowledge on the impact of aging on cardiac metabolic sensing, with a focus on AMPK and sirtuins, while mTOR pathway was only marginally considered. A particular focus was given to systemic factors, e.g., inflammation, vascular diseases, and microbiome.
Wild and captive immature orangutans differ in their non-vocal communication with others, but not with their mothers
2024-01-01

Abstract In many group-living species, individuals are required to flexibly modify their communicative behaviour in response to current social challenges. To unravel whether sociality and communication systems co-evolve, research efforts have often targeted the links between social organisation and communicative repertoires. However, it is still unclear which social or interactional factors directly predict communicative complexity. To address this issue, we studied wild and zoo-housed immature orangutans of two species to assess the impact of the socio-ecological setting on the production of non-vocal signal repertoires. Specifically, we compared repertoire size, dyadic repertoire similarity, and number of social goals (i.e. observer’s estimate of the signaller’s intended interaction outcome) for communicative interactions with mothers versus other conspecifics, controlling for critical individual and environmental factors. In this small sample of immature orangutans, wild-captive contrasts were statistically significant only for other-directed repertoires, but not for mother-directed repertoires, and not for the number of social goals that immatures communicated towards. While the repertoires of individuals living in the same research setting were more similar than those living in contrasting settings, this difference was most pronounced for other-directed repertoires of the less socially tolerant orangutan species. These results suggest that the boosted interactional opportunities in captivity rather than mere differences in environmental affordances or communicative needs drive the wild-captive contrast in orangutan communicative repertoires. Overall, this fine-grained analysis of repertoires further underscores that not only a species’ social organisation but also the targeted audience may have a profound impact on communicative behaviour. Significance statement Navigating a dynamic social environment often requires flexible signal use. While it has repeatedly been shown that the social organisation and structure of species predict the complexity of their communication systems, the mechanisms underlying these relationships are largely unknown. Because targeted studies to assess this issue in great apes are difficult, we take an alternative approach here: we compare the same species living in the wild and in artificial habitats in captivity. This contrast allows a direct test of how repertoires respond to the relevant difference in socio-ecological conditions. Our results show that the diversity of interaction partners (i.e. social opportunities), but not the diversity of social goals (i.e. possible interaction outcomes) or the broader physical opportunities (i.e. safe ground use), predict the size and consistency of wild and captive signalling repertoires.
Multiple Dimensions of Gender Ideologies: How They Relate to Normative Judgments of the Gender Division of Parental Leave
2024-01-01

Abstract Previous research has found that gender ideologies are multidimensional. Additionally, their influence on work–care practices depends on the context, including the life stage, presence of children, and partners’ resources, which has received less attention. This study contributes to the understanding of the conditionality of gender ideologies by examining how dimensions of gender ideologies relate to more specific normative judgments regarding the division of parental leave and testing whether the association depends on partners’ relative earnings. I draw on data from a vignette experiment implemented in the representative German GESIS Panel and apply ordinary least squares (OLS) regression models with cluster-robust standard errors to 8,185 vignette evaluations of 2,249 respondents. More egalitarian ideologies regarding the division of employment and housework and less essentialist ideologies are associated with less traditional judgments of the division of parental leave. Support for individual choice is only associated with less traditional judgments on the condition that the mother earns more.
In-depth cross-validation of human and mouse CD4-specific minibodies for noninvasive PET imaging of CD4+ cells and response prediction to cancer immunotherapy
2024-01-01

Increasing evidence emphasizes the pivotal role of CD4<sup>+</sup> T cells in orchestrating cancer immunity. Noninvasive <i>in vivo</i> imaging of the temporal dynamics of CD4<sup>+</sup> T cells and their distribution patterns might provide novel insights into their effector and regulator cell functions during cancer immunotherapy (CIT). <b>Methods:</b> We conducted a comparative analysis of <sup>89</sup>Zr-labeled anti-mouse (m) and anti-human (h) CD4-targeting minibodies (Mbs) for <i>in vivo</i> positron emission tomography (PET)/magnetic resonance imaging (MRI) of CD4<sup>+</sup> T cells in human xenografts, syngeneic tumor-bearing wild-type (WT), and human CD4<sup>+</sup> knock-in (hCD4-KI) mouse models. <b>Results:</b> Both <sup>89</sup>Zr-CD4-Mbs yielded high radiolabeling efficiencies of >90%, immunoreactivities of >70%, and specific <i>in vitro</i> binding to their target antigens. The specificity of <i>in vivo</i> targeting of <sup>89</sup>Zr-hCD4-Mb was confirmed by PET/MRI, revealing ~4-fold greater <sup>89</sup>Zr-hCD4-Mb uptake in subcutaneous hCD4<sup>+</sup> hematopoietic peripheral blood acute lymphoblastic leukemia tumors (HPB-ALL) than in solid hCD4<sup>-</sup> diffuse histiocytic lymphomas (DHL) and <sup>89</sup>Zr-mCD4-Mb uptake in hCD4<sup>+</sup> HPB-ALL tumors. In a comparative cross-validation study in anti-programmed death ligand (αPD-L1)/anti-4-1BB-treated orthotopic PyMT mammary carcinoma-bearing hCD4-KI and WT mice, we detected 2- to 3-fold enhanced species-specific <sup>89</sup>Zr-hCD4-Mb or <sup>89</sup>Zr-mCD4-Mb uptake within CD4<sup>+</sup> cell-enriched secondary lymphatic organs (lymph nodes and spleens). The <sup>89</sup>Zr-hCD4-Mb uptake in the PyMT tumors was more pronounced in hCD4-KI mice compared to the WT control littermates. Most importantly, MC38 adenocarcinoma-bearing mice treated with a combination of αPD-L1 and anti-lymphocyte-activation gene 3 (αLag-3) antibodies exhibited ~1.4-fold higher <sup>89</sup>Zr-mCD4-Mb uptake than mice that were not responsive to therapy or sham-treated mice. <b>Conclusion:</b> CD4 PET/MRI enabled monitoring of the CD4<sup>+</sup> cell distribution in secondary lymphatic organs and the tumor microenvironment, capable of predicting sensitivity to CIT. Our imaging approach will provide deeper insights into the underlying molecular mechanisms of CD4-directed cancer immunotherapies in preclinical mouse models and is applicable for clinical translation.
A Virtual Reality Anatomy Model of the Temporal Bone in ORL Residency Training—Gain or Gadget?
2024-01-01

OBJECTIVES Virtual reality (VR) appears to be a promising educational tool for otorhinolaryngology (ORL) residency training, as it allows for safe and effective practice immediate feedback and potential improvements in patient outcomes. Despite these advantages, VR has not yet been incorporated into residency training in ORL, which may be due to limited availability or validation and skepticism toward incorporation of new training methods. This study investigates whether a VR model of the temporal bone improves learning success for ORL residents in comparison to standard plastic models and whether it depends on surgeon's experience. We also included a subjective evaluation of the learning experience with both models. METHODS ORL residents and specialists at 2 German university hospitals were tested on their knowledge of temporal bone anatomy after training with either VR or standard plastic models. In addition, we compared knowledge of the temporal bone anatomy before- and after-VR training. Lastly, a subjective survey on the benefits and limitations of VR was conducted to assess participants’ views on this new technology. RESULTS About 85% of the participants considered VR to be better than conventional models and agreed that VR was a useful tool for teaching complex anatomy. Objective evaluation showed significant improvement in knowledge after using VR (before/after comparison), especially in participants with a higher level of preexisting knowledge. Direct comparison to conventional plastic models showed no superiority of the VR model. CONCLUSION VR models in ORL are not only appealing and motivating for residents, but also objectively improve their anatomical knowledge, especially in advanced residency. In addition, VR—in contrast to the plastic model—offers opportunities for further development and optimization.
Data protection concerns are a statistically significant reason for refusal: Exploratory study of the patient perspective on telemedicine services based on 735 gynecological surgery patients
2024-01-01

Objective Internet-based healthcare is a crucial facet of telemedicine. Here, we examine telemedicine methods in perioperative care for gynecological surgery from a patient's perspective. We aim to understand the patients’ needs during perioperative gynecological care and suggest how to optimize telemedicine services based on these insights. Methods The data were gathered via self-report questionnaires from patients who came in for preparatory consultations for gynecological surgery from May to November 2022. This process involved questioning 735 women about their past usage of internet-based services, personal information, and their views on telemedicine services. The study, which assured full anonymity, had voluntary participation. Results This participant pool consisted of 735 females. Around half ( n = 365, 49.66%) were preparing for outpatient surgery, while a significant number ( n = 322, 43.81%) were slated for inpatient surgery. Statistically, data protection concerns were the only significant factor influencing consent to telemedicine. While nonsignificant results were found for individuals with minimal concerns ( b = 0.08; odds ratio [OR] = 1.09, p = 0.791), markedly significant results ( p &lt; 0.001) emerged for those expressing more concerns with b = 1.45 and OR = 4.28. This suggests that the likelihood of refusing consent to telemedicine is 4.28 times higher for those with significant data protection concerns compared with those with no concerns. Conclusion The patient's perspective on telemedicine services for gynecological surgery is influenced by several factors. These include the patient's age, computer skills, travel distance, occupation, education level, severity of the disease, satisfaction with previous treatments, treatment location, and referral method. Of these, concerns about data security significantly impact patient satisfaction. Hence, it is critical to prioritize this factor when offering telemedical services to meet patients’ needs.
Cover crop monocultures and mixtures enhance bacterial abundance and functionality in the maize root zone
2024-01-01

Abstract Cover cropping is an effective method to protect agricultural soils from erosion, promote nutrient and moisture retention, encourage beneficial microbial activity, and maintain soil structure. Re-utilization of winter cover crop root channels by maize roots during summer allows the cash crop to extract resources from distal regions in the soil horizon. In this study, we investigated how cover cropping during winter followed by maize (Zea mays L.) during summer affects the spatiotemporal composition and function of the bacterial communities in the maize rhizosphere and surrounding soil samples using quantitative polymerase chain reaction (PCR), 16S ribosomal ribonucleic acid (rRNA) gene amplicon sequencing, and metaproteomics. We found that the bacterial community differed significantly among cover crop species, soil depths, and maize growth stages. Bacterial abundance increased in reused root channels, and it continued to increase as cover crop diversity changed from monocultures to mixtures. Mixing Fabaceae with Brassicaceae or Poaceae enhanced the overall contributions of several steps of the bacterial carbon and nitrogen cycles, especially glycolysis and the pentose phosphate pathway. The deeper root channels of Fabaceae and Brassicaceae as compared to Poaceae corresponded to higher bacterial 16S rRNA gene copy numbers and improved community presence in the subsoil regimes, likely due to the increased availability of root exudates secreted by maize roots. In conclusion, root channel reuse improved the expression of metabolic pathways of the carbon and nitrogen cycles and the bacterial communities, which is beneficial to the soil and to the growing crops.
The international HAE guideline under real-life conditions: From possibilities to limits in daily life – current real-world data of 8 German angioedema centers
2024-01-01

The current guideline serves as the foundation for daily practice in treating HAE at specialized centers. Thus, for rare conditions like HAE, an exchange among the treating centers is essential to adequately address specific issues and rare subgroups.
Association of latent factors of neuroinflammation with Alzheimer's disease pathology and longitudinal cognitive decline
2024-01-01

Abstract INTRODUCTION We investigated the association of inflammatory mechanisms with markers of Alzheimer's disease (AD) pathology and rates of cognitive decline in the AD spectrum. METHODS We studied 296 cases from the Deutsches Zentrum für Neurodegenerative Erkrankungen Longitudinal Cognitive Impairment and Dementia Study (DELCODE) cohort, and an extension cohort of 276 cases of the Alzheimer's Disease Neuroimaging Initiative study. Using Bayesian confirmatory factor analysis, we constructed latent factors for synaptic integrity, microglia, cerebrovascular endothelial function, cytokine/chemokine, and complement components of the inflammatory response using a set of inflammatory markers in cerebrospinal fluid. RESULTS We found strong evidence for an association of synaptic integrity, microglia response, and cerebrovascular endothelial function with a latent factor of AD pathology and with rates of cognitive decline. We found evidence against an association of complement and cytokine/chemokine factors with AD pathology and rates of cognitive decline. DISCUSSION Latent factors provided access to directly unobservable components of the neuroinflammatory response and their association with AD pathology and cognitive decline.
A microphysiological system for parallelized morphological and electrophysiological read-out of 3D neuronal cell culture
2024-01-01

Electrophysiology of 3D neural cultures: our multilayer microfluidics on glass microelectrode arrays enable parallel analysis of compartmentalized 3D neural models, with applications in neurology, pharmacology research and substance testing.
Religious coping or coping with religion? Religious belief and practice during incarceration in German youth prisons
2024-01-01

Prisoners' religiosity can be a helpful resource for a successful reintegration into society. Yet, the Christian-focused institutional concepts do not meet the religious needs of Muslims. We assumed that Muslim inmates would find strategies to deal with this lack of religious opportunity structure and postulated that the association between religious practice and belief would change over time. We chose a multi-method approach and collected data of 766 Christian and Muslim inmates from four different youth prisons on religious belief and practice via questionnaires and interviews. Qualitative data illustrates how Muslim inmates experience inequality when it comes to practicing their religion. Religious practice and time served was found to predict religious belief. Time served moderated the association between religious belief and practice. Steeper slopes for Muslims with longer time spent in prison indicated two different coping styles: 'engage' and 'retreat'. However, inmates favored 'retreat' over 'engage'. Further research on Muslims' religious coping mechanisms is needed to build an understanding of religiosity as a resource during and after incarceration.
Management of Patients Undergoing CAR-T Cell Therapy in Germany
2024-01-01

&lt;b&gt;&lt;i&gt;Introduction:&lt;/i&gt;&lt;/b&gt; Chimeric antigen receptor positive T cell (CAR-T cell) treatment became standard therapy for relapsed or refractory hematologic malignancies, such as non-Hodgkin’s lymphoma and multiple myeloma. Owing to the rapidly progressing field of CAR-T cell therapy and the lack of generally accepted treatment guidelines, we hypothesized significant differences between centers in the prevention, diagnosis, and management of short- and long-term complications. &lt;b&gt;&lt;i&gt;Methods:&lt;/i&gt;&lt;/b&gt; To capture the current CAR-T cell management among German centers to determine the medical need and specific areas for future clinical research, the DAG-HSZT (Deutsche Arbeitsgemeinschaft für Hämatopoetische Stammzelltransplantation und Zelluläre Therapie; German Working Group for Hematopoietic Stem Cell Transplantation and Cellular Therapy) performed a survey among 26 German CAR-T cell centers. &lt;b&gt;&lt;i&gt;Results:&lt;/i&gt;&lt;/b&gt; We received answers from 17 centers (65%). The survey documents the relevance of evidence in the CAR-T cell field with a homogeneity of practice in areas with existing clinical evidence. In contrast, in areas with no – or low quality – clinical evidence, we identified significant variety in management in between the centers: management of cytokine release syndrome, immune effector cell-related neurotoxicity syndrome, IgG substitution, autologous stem cell backups, anti-infective prophylaxis, and vaccinations. &lt;b&gt;&lt;i&gt;Conclusion:&lt;/i&gt;&lt;/b&gt; The results indicate the urgent need for better harmonization of supportive care in CAR-T cell therapies including clinical research to improve clinical outcome.
Dispersive liquid–liquid microextraction as a novel enrichment approach for compound-specific carbon isotope analysis of chlorinated phenols
2024-01-01

Dispersive liquid–liquid microextraction (DLLME) is a promising approach to enrich (semi-)volatile organics from aqueous samples prior to compound-specific stable isotope analysis (CSIA) by gas chromatography-isotope ratio mass spectrometry (GC-IRMS).
Proof-Theoretic Semantics: An Autobiographical Survey
2024-01-01

In this autobiographical sketch, which is followed by a bibliography of my writings, I try to relate my intellectual development to problems, ideas and results in proof-theoretic semantics on which I have worked and to which I have contributed.
Creativity is motivated by novelty. Curiosity is triggered by uncertainty
2024-01-01

Abstract Although creativity and curiosity can be similarly construed as knowledge-building processes, their underlying motivation is fundamentally different. Specifically, curiosity drives organisms to seek information that reduces uncertainty so that they can make a better prediction about the world. On the contrary, creative processes aim to connect distant pieces of information, maximizing novelty and utility.