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MotivationGraph representation learning is a family of related approaches that learn low-dimensional vector representations of nodes and other graph elements called embeddings. Embeddings approximate characteristics of the graph and can be used for a variety of machine-learning tasks such as novel edge prediction. For many biomedical applications, partial knowledge exists about positive edges that represent relationships between pairs of entities, but little to no knowledge is available about negative edges that represent the explicit lack of a relationship between two nodes. For this reason, classification procedures are forced to assume that the vast majority of unlabeled edges are negative. Existing approaches to sampling negative edges for training and evaluating classifiers do so by uniformly sampling pairs of nodes.ResultsWe show here that this sampling strategy typically leads to sets of positive and negative examples with imbalanced node degree distributions. Using representative heterogeneous biomedical knowledge graph and random walk-based graph machine learning, we show that this strategy substantially impacts classification performance. If users of graph machine-learning models apply the models to prioritize examples that are drawn from approximately the same distribution as the positive examples are, then performance of models as estimated in the validation phase may be artificially inflated. We present a degree-aware node sampling approach that mitigates this effect and is simple to implement.Availability and implementationOur code and data are publicly available at https://github.com/monarch-initiative/negativeExampleSelection.

Abstract The generation of antibody-drug conjugates with optimal functionality depends on many parameters. These include binder epitope, antibody format, linker composition, conjugation site(s), drug-to-antibody ratio, and conjugation method. The production of matrices that cover all possible parameters is a major challenge in identifying optimal antibody-drug conjugates. To address this bottleneck, we adapted our Format Chain Exchange technology (FORCE), originally established for bispecific antibodies, toward the generation of binder-format-payload matrices (pair-FORCE). Antibody derivatives with exchange-enabled Fc-heterodimers are combined with payload-conjugated Fc donors, and subsequent chain-exchange transfers payloads to antibody derivatives in different formats. The resulting binder-format-conjugate matrices can be generated with cytotoxic payloads, dyes, haptens, and large molecules, resulting in versatile tools for ADC screening campaigns. We show the relevance of pair-FORCE for identifying optimal HER2-targeting antibody-drug conjugates. Analysis of this matrix reveals that the notion of format-defines-function applies not only to bispecific antibodies, but also to antibody-drug conjugates.

Abstract Background Health-related quality of life (HRQL) has become an important outcome parameter in cardiology. The MOS 36-ltem Short-Form Health Survey (SF-36) and the PROMIS-29 are two widely used generic measures providing composite HRQL scores. The domains of the SF-36, a well-established instrument utilized for several decades, can be aggregated to physical (PCS) and mental (MCS) component summary scores. Alternative scoring algorithms for correlated component scores (PCSc and MCSc) have also been suggested. The PROMIS-29 is a newer but increasingly used HRQL measure. Analogous to the SF-36, physical and mental health summary scores can be derived from PROMIS-29 domain scores, based on a correlated factor solution. So far, scores from the PROMIS-29 are not directly comparable to SF-36 results, complicating the aggregation of research findings. Thus, our aim was to provide algorithms to convert PROMIS-29 data to well-established SF-36 component summary scores. Methods Data from n = 662 participants of the Berlin Long-term Observation of Vascular Events (BeLOVE) study were used to estimate linear regression models with either PROMIS-29 domain scores or aggregated PROMIS-29 physical/mental health summary scores as predictors and SF-36 physical/mental component summary scores as outcomes. Data from a subsequent assessment point (n = 259) were used to evaluate the agreement between empirical and predicted SF-36 scores. Results PROMIS-29 domain scores as well as PROMIS-29 health summary scores showed high predictive value for PCS, PCSc, and MCSc (R2 ≥ 70%), and moderate predictive value for MCS (R2 = 57% and R2 = 40%, respectively). After applying the regression coefficients to new data, empirical and predicted SF-36 component summary scores were highly correlated (r > 0.8) for most models. Mean differences between empirical and predicted scores were negligible (|SMD|

Background Intratumoral heterogeneity (ITH) and subclonal antigen expression blunt antitumor immunity and are associated with poor responses to immune-checkpoint blockade immunotherapy (ICB) in patients with cancer. The underlying mechanisms however thus far remained elusive, preventing the design of novel treatment approaches for patients with high ITH tumors.Methods We developed a mouse model of lung adenocarcinoma with defined expression of different neoantigens (NeoAg), enabling us to analyze how these impact antitumor T-cell immunity and to study underlying mechanisms. Data from a large cancer patient cohort was used to study whether NeoAg architecture characteristics found to define tumor immunogenicity in our mouse models are linked to ICB responses in patients with cancer.Results We demonstrate that concurrent expression and clonality define NeoAg architectures which determine the immunogenicity of individual NeoAg and drive immune evasion of tumors with heterogenous NeoAg expression. Mechanistically, we identified concerted interplays between concurrent T-cell responses induced by cross-presenting dendritic cells (cDC1) mirroring the tumor NeoAg architecture during T-cell priming in the lymph node. Depending on the characteristics and clonality of respective NeoAg, this interplay mutually benefited concurrent T-cell responses or led to competition between T-cell responses to different NeoAg. In tumors with heterogenous NeoAg expression, NeoAg architecture-induced suppression of T-cell responses against branches of the tumor drove immune evasion and caused resistance to ICB. Therapeutic RNA-based vaccination targeting immune-suppressed T-cell responses synergized with ICB to enable control of tumors with subclonal NeoAg expression. A pan-cancer clinical data analysis indicated that competition and synergy between T-cell responses define responsiveness to ICB in patients with cancer.Conclusions NeoAg architectures modulate the immunogenicity of NeoAg and tumors by dictating the interplay between concurrent T-cell responses mediated by cDC1. Impaired induction of T-cell responses supports immune evasion in tumors with heterogenous NeoAg expression but is amenable to NeoAg architecture-informed vaccination, which in combination with ICB portrays a promising treatment approach for patients with tumors exhibiting high ITH.

O Governo angolano está a desenvolver mecanismos para a redução das desigualdades de género no mundo do trabalho, quebrando barreiras culturais e tradicionais, tais como a natureza da mulher de ser esposa, mãe, cuidadora e doméstica. Assim, o objetivo desse trabalho foi compreender o impacto do efeito teto de vidro no contexto laboral de mulheres angolanas. Pretendeu-se também identificar se as mulheres angolanas percebem discriminação no ambiente de trabalho, se há diferença salarial entre géneros, se há equilíbrio entre vida privada e trabalho e se há divergências entre organizações públicas e privadas. Foi realizado um estudo qualitativo básico ou genérico, que inclui descrição, interpretação e entendimentos de padrões recorrentes. Participaram do estudo onze mulheres e como critério de inserção foram escolhidas mulheres angolanas exercendo funções em empresas públicas ou privadas. Como técnica de recolha foram realizadas entrevistas individuais semiestruturadas, que duraram cerca de 30 a 40 minutos. As entrevistas foram gravadas com a anuência das entrevistadas. Os dados recolhidos foram analisados de acordo com as técnicas de análise de conteúdo. Os resultados mostraram que a maioria das entrevistadas teve dificuldades em situar-se na pergunta, tendo em conta aquilo que percebem como discriminação, ou seja, não tem como ser discriminação uma situação já naturalizada; foram identificadas divergências entre organizações públicas e privadas e notou-se que existe uma maior segregação das mulheres, o que as remete na condição de terem de optar por umas das duas esferas (família ou trabalho). Todas as entrevistadas afirmaram ter igualdade salarial entre géneros. Pode-se concluir que, o efeito teto de vidro impacta de maneira pouco hostil o contexto laboral de mulheres angolanas, sendo considerado mais como proteção e não como fator discriminatório.

BackgroundCaloric restriction can delay the development of metabolic diseases ranging from insulin resistance to type 2 diabetes and is linked to both changes in the composition and metabolic function of the gut microbiota and immunological consequences. However, the interaction between dietary intake, the microbiome, and the immune system remains poorly described.ResultsWe transplanted the gut microbiota from an obese female before (AdLib) and after (CalRes) an 8-week very-low-calorie diet (800 kcal/day) into germ-free mice. We used 16S rRNA sequencing to evaluate taxa with differential abundance between the AdLib- and CalRes-microbiota recipients and single-cell multidimensional mass cytometry to define immune signatures in murine colon, liver, and spleen. Recipients of the CalRes sample exhibited overall higher alpha diversity and restructuring of the gut microbiota with decreased abundance of several microbial taxa (e.g., Clostridium ramosum, Hungatella hathewayi, Alistipi obesi). Transplantation of CalRes-microbiota into mice decreased their body fat accumulation and improved glucose tolerance compared to AdLib-microbiota recipients. Finally, the CalRes-associated microbiota reduced the levels of intestinal effector memory CD8+ T cells, intestinal memory B cells, and hepatic effector memory CD4+ and CD8+ T cells.ConclusionCaloric restriction shapes the gut microbiome which can improve metabolic health and may induce a shift towards the naïve T and B cell compartment and, thus, delay immune senescence. Understanding the role of the gut microbiome as mediator of beneficial effects of low calorie diets on inflammation and metabolism may enhance the development of new therapeutic treatment options for metabolic diseases.Trial registrationNCT01105143 , "Effects of negative energy balance on muscle mass regulation," registered 16 April 2010. Video Abstract.

Abstract Background Anaplastic thyroid cancer (ATC) is a rare and aggressive neoplasm. We still lack effective treatment options, so survival rates remain very low. Here, we aimed to evaluate the activity of the combination of lenvatinib and pembrolizumab as systemic first-line therapy in ATC. Methods In a retrospective analysis, we investigated the activity and tolerability of combined lenvatinib (starting dose 14 to 24 mg daily) and pembrolizumab (200 mg every three weeks) as first-line therapy in an institutional cohort of ATC patients. Results Five patients with metastatic ATC received lenvatinib and pembrolizumab as systemic first-line therapy. The median progression-free survival was 4.7 (range 0.8–5.9) months, and the median overall survival was 6.3 (range 0.8-not reached) months. At the first follow-up, one patient had partial response, three patients had stable disease, and one patient was formally not evaluable due to interference of assessment by concomitant acute infectious thyroiditis. This patient was then stable for more than one year and was still on therapy at the data cutoff without disease progression. Further analyses revealed deficient DNA mismatch repair, high CD8+ lymphocyte infiltration, and low macrophage infiltration in this patient. Of the other patients, two had progressive disease after adverse drug reactions and therapy de-escalation, and two died after the first staging. For all patients, the PD-L1 combined positive score ranged from 12 to 100%. Conclusions The combination of lenvatinib and pembrolizumab was effective and moderately tolerated in treatment-naïve ATC patients with occasional long-lasting response. However, we could not confirm the exceptional responses for this combination therapy reported before in pretreated patients.

Despite beneficial cardiovascular effects, substantial long-term modulation of food pattern could only be achieved in a limited number of participants. The impact of attitude towards healthy nutrition (ATHN) on successful modulation of dietary behavior is unclear, especially in the elderly. We aimed to analyze whether the personal ATHN influences 12-month adherence to two different dietary intervention regimes within a 36-month randomized controlled trial. Methods: 502 subjects were randomized to an intervention group (IG; dietary pattern focused on high intake of unsaturated fatty acids (UFA), plant protein and fiber) or control group (CG; dietary recommendation in accordance with the German Society of Nutrition) within a 36-month dietary intervention trial. Sum scores for effectiveness, appreciation and practice of healthy nutrition were assessed using ATHN questionnaire during the trial (n = 344). Linear regression models were used to investigate associations between ATHN and dietary patterns at baseline and at month 12. Results: Retirement, higher education level, age and lower body mass index (BMI) were associated with higher ATHN sum scores. ATHN was similar in CG and IG. Higher baseline intake of polyunsaturated fatty acids (PUFA) and fiber as well as lower intake in saturated fatty acids (SFA) were associated with higher scores in practice in both groups. The intervention resulted in a stronger increase of UFA, protein and fiber in the IG after 12 months, while intake of SFA declined (p < 0.01). Higher scores in appreciation were significantly associated with higher intake of fiber and lower intake of SFA in the CG at month 12, whereas no associations between ATHN and macronutrient intake were observed in the IG after 12 months. Conclusions: While ATHN appeared to play a role in general dietary behavior, ATHN did not affect the success of the specific dietary intervention in the IG at month 12. Thus, the dietary intervention achieved a substantial modification of dietary pattern in the IG and was effective to override the impact of the individual ATHN on dietary behavior.

Oral demonstration of knowledge is an effective learning and assessment strategy. It has been shown that generating explanations to oneself, or self-explaining, can improve student understanding of information. This can be achieved via student-generated videos. The quantitative effects of student-generated videos on learning and assessment in postsecondary education are unknown. To our knowledge, this is the first study to analyze the effects asynchronous student-generated videos have on student learning and assessment in a large-enrollment ([approximately] 400 students), undergraduate physiology course. Students were charged with making self-generated videos discussing major physiological concepts and uploading these videos to Flip for assessment. Flip is an online, social education platform for asynchronous video-based discussion. In the present study, we combined four semesters (n = 1,100 students) of Flip data and analyzed the effects it had on student examination performance. Specifically, we first analyzed how students performed on exam questions corresponding to their Flip prompts in comparison to students not assigned those prompts [25/44 (57%) were statistically significantly different]. Second, we analyzed the association between Flip prompt score and performance on corresponding exam questions [39/44 (89%) were statistically significantly different]. Third, we analyzed the association between cumulative Flip score and performance on all corresponding, and noncorresponding exam questions. Finally, we analyzed the association between cumulative Flip score and averaged exam performance. There was a positive association (r = 0.54). Taken together, our data suggest that asynchronous student-generated Flip videos can facilitate student learning and assessment in a large-enrollment, undergraduate physiology course.

Abstract Obesity is an enormous health problem, and many patients do not respond to any of the available therapies. Deep brain stimulation (DBS) is currently investigated as a potential treatment for morbid obesity. In this study, we tested the hypothesis that high-frequency DBS targeting the nucleus accumbens (NAc) shell region reduces food intake and weight gain in mice fed a high-fat diet. We implanted male C57BL/6J mice with bilateral electrodes and a head-mounted microstimulator enabling continuous stimulation for up to 5 weeks. In successfully operated animals (n = 9 per group, high-frequency vs. sham stimulation), we investigated immediate and long-term stimulation effects on metabolic and behavioral phenotypes. Here we show that stimulation acutely induced a transient reduction in energy expenditure and locomotor activity but did not significantly affect spontaneous food intake, social interaction, anxiety or exploratory behaviors. In contrast, continuous stimulation over 5 weeks led to a decrease in food intake and thigmotaxis (the tendency to stay near walls in an open lit arena). However, chronic stimulation did not substantially change weight gain in mice fed a high-fat diet. Our results do not support the use of continuous high-frequency NAc shell DBS as a treatment for obesity. However, DBS can alter obesity-related parameters with differing short and long-term effects. Therefore, future research should employ time and context-sensitive experimental designs to assess the potential of DBS for clinical translation in this area.

Abstract Background 5-Aminovaleric acid betaine (5-AVAB) has recently been identified as a diet and microbial-dependent factor inducing obesity and hepatic steatosis in mice fed a Western diet. Accumulating evidence suggests a role in metabolic dysfunction associated with obesity, diabetes, and fatty liver disease. However, whether 5-AVAB plays a role in human disease is unclear, and human data are sparse. Methods We measured circulating 5-AVAB serum levels in 143 individuals with overweight or obesity participating in a randomized intervention study (NCT00850629) investigating the long-term effect of a weight maintenance strategy after diet-induced weight reduction. Results Higher 5-AVAB serum levels correlate with worse estimates of obesity, glucose metabolism, and hepatic steatosis after weight loss. Furthermore, higher 5-AVAB levels after weight loss independently predict detrimental changes in glucose metabolism 18 months after the successful weight reduction. Conclusion Our human data supports previous findings in rodents indicating a relevant, potentially disadvantageous function of 5-AVAB in the context of metabolic dysbalance.

This classic essay by Eduard Spranger (1882-1963) is here published for the first time in English, in a translation by Stephanie Wilde. In this contribution Spranger discusses and advocates the need for a vocational school that addresses the civic and individual needs of students as well as the vocational requirements of the nation. He emphasises personal growth, the need for self-knowledge in making a vocational choice and makes a point about the importance of the social role of occupations and the role that being part of a community plays in developing citizenship. He identifies that tasks of the vocational school as both to develop greater self-awareness and to lead young people into civic and vocational engagement. In doing this he acknowledges the influence of Georg Kerschensteiner on his own thought. Much turns in the discussion on differences between German and English expressions, and these are discussed in the complementary essay, 'The Legitimation of School-based Bildung in the Context of Vocational Education and Training. The Legacy of Eduard Spranger', by Philipp Gonon. An introduction to the broader context is provided in 'Founding German Vocational Education: Kerschensteiner, Spranger and Fischer as key figures in the classical German VET Theory' '…' by Christian Steibe, Dina Kuhlee and Christopher Winch, the Editors of this Special Issue.