Combinatorial Blood Platelets-Derived circRNA and mRNA Signature for Early-Stage Lung Cancer Detection.

Despite the diversity of liquid biopsy transcriptomic repertoire, numerous studies often exploit only a single RNA type signature for diagnostic biomarker potential. This frequently results in insufficient sensitivity and specificity necessary to reach diagnostic utility. Combinatorial biomarker approaches may offer a more reliable diagnosis. Here, we investigated the synergistic contributions of circRNA and mRNA signatures derived from blood platelets as biomarkers for lung cancer detection. We developed a comprehensive bioinformatics pipeline permitting an analysis of platelet-circRNA and mRNA derived from non-cancer individuals and lung cancer patients. An optimal selected signature is then used to generate the predictive classification model using machine learning algorithm. Using an individual signature of 21 circRNA and 28 mRNA, the predictive models reached an area under the curve (AUC) of 0.88 and 0.81, respectively. Importantly, combinatorial analysis including both types of RNAs resulted in an 8-target signature (6 mRNA and 2 circRNA), enhancing the differentiation of lung cancer from controls (AUC of 0.92). Additionally, we identified five biomarkers potentially specific for early-stage detection of lung cancer. Our proof-of-concept study presents the first multi-analyte-based approach for the analysis of platelets-derived biomarkers, providing a potential combinatorial diagnostic signature for lung cancer detection.

The Legacy of Recurrent Introgression during the Radiation of Hares.

Hybridization may often be an important source of adaptive variation, but the extent and long-term impacts of introgression have seldom been evaluated in the phylogenetic context of a radiation. Hares (Lepus) represent a widespread mammalian radiation of 32 extant species characterized by striking ecological adaptations and recurrent admixture. To understand the relevance of introgressive hybridization during the diversification of Lepus, we analyzed whole exome sequences (61.7 Mb) from 15 species of hares (1-4 individuals per species), spanning the global distribution of the genus, and two outgroups. We used a coalescent framework to infer species relationships and divergence times, despite extensive genealogical discordance. We found high levels of allele sharing among species and show that this reflects extensive incomplete lineage sorting and temporally layered hybridization. Our results revealed recurrent introgression at all stages along the Lepus radiation, including recent gene flow between extant species since the last glacial maximum but also pervasive ancient introgression occurring since near the origin of the hare lineages. We show that ancient hybridization between northern hemisphere species has resulted in shared variation of potential adaptive relevance to highly seasonal environments, including genes involved in circadian rhythm regulation, pigmentation, and thermoregulation. Our results illustrate how the genetic legacy of ancestral hybridization may persist across a radiation, leaving a long-lasting signature of shared genetic variation that may contribute to adaptation. [Adaptation; ancient introgression; hybridization; Lepus; phylogenomics.].

Introgression drives repeated evolution of winter coat color polymorphism in hares.

Changing from summer-brown to winter-white pelage or plumage is a crucial adaptation to seasonal snow in more than 20 mammal and bird species. Many of these species maintain nonwhite winter morphs, locally adapted to less snowy conditions, which may have evolved independently. Mountain hares (Lepus timidus) from Fennoscandia were introduced into the Faroe Islands in 1855. While they were initially winter-white, within ∼65 y all Faroese hares became winter-gray, a morph that occurs in the source population at low frequency. The documented population history makes this a valuable model for understanding the genetic basis and evolution of the seasonal trait polymorphism. Through whole-genome scans of differentiation and single-nucleotide polymorphism (SNP) genotyping, we associated winter coat color polymorphism to the genomic region of the pigmentation gene Agouti, previously linked to introgression-driven winter coat color variation in the snowshoe hare (Lepus americanus). Lower Agouti expression in the skin of winter-gray individuals during the autumn molt suggests that regulatory changes may underlie the color polymorphism. Variation in the associated genomic region shows signatures of a selective sweep in the Faroese population, suggesting that positive selection drove the fixation of the variant after the introduction. Whole-genome analyses of several hare species revealed that the winter-gray variant originated through introgression from a noncolor changing species, in keeping with the history of ancient hybridization between the species. Our findings show the recurrent role of introgression in generating winter coat color variation by repeatedly recruiting the regulatory region of Agouti to modulate seasonal coat color change.

Using autoencoders as a weight initialization method on deep neural networks for disease detection.

BACKGROUND: As of today, cancer is still one of the most prevalent and high-mortality diseases, summing more than 9 million deaths in 2018. This has motivated researchers to study the application of machine learning-based solutions for cancer detection to accelerate its diagnosis and help its prevention. Among several approaches, one is to automatically classify tumor samples through their gene expression analysis. METHODS: In this work, we aim to distinguish five different types of cancer through RNA-Seq datasets: thyroid, skin, stomach, breast, and lung. To do so, we have adopted a previously described methodology, with which we compare the performance of 3 different autoencoders (AEs) used as a deep neural network weight initialization technique. Our experiments consist in assessing two different approaches when training the classification model - fixing the weights after pre-training the AEs, or allowing fine-tuning of the entire network - and two different strategies for embedding the AEs into the classification network, namely by only importing the encoding layers, or by inserting the complete AE. We then study how varying the number of layers in the first strategy, the AEs latent vector dimension, and the imputation technique in the data preprocessing step impacts the network's overall classification performance. Finally, with the goal of assessing how well does this pipeline generalize, we apply the same methodology to two additional datasets that include features extracted from images of malaria thin blood smears, and breast masses cell nuclei. We also discard the possibility of overfitting by using held-out test sets in the images datasets. RESULTS: The methodology attained good overall results for both RNA-Seq and image extracted data. We outperformed the established baseline for all the considered datasets, achieving an average F1 score of 99.03, 89.95, and 98.84 and an MCC of 0.99, 0.84, and 0.98, for the RNA-Seq (when detecting thyroid cancer), the Malaria, and the Wisconsin Breast Cancer data, respectively. CONCLUSIONS: We observed that the approach of fine-tuning the weights of the top layers imported from the AE reached higher results, for all the presented experiences, and all the considered datasets. We outperformed all the previous reported results when comparing to the established baselines.

The transcriptional landscape of seasonal coat colour moult in the snowshoe hare.

Seasonal coat colour change is an important adaptation to seasonally changing environments but the evolution of this and other circannual traits remains poorly understood. In this study, we use gene expression to understand seasonal coat colour moulting in wild snowshoe hares (Lepus americanus). We used hair colour to follow the progression of the moult, simultaneously sampling skin from three moulting stages in hares collected during the peak of the spring moult from white winter to brown summer pelage. Using RNA sequencing, we tested whether patterns of expression were consistent with predictions based on the established phases of the hair growth cycle. We found functionally consistent clustering across skin types, with 766 genes differentially expressed between moult stages. "White" pelage showed more differentially expressed genes that were upregulated relative to other skin types, involved in the transition between late telogen (quiescent stage) and the onset of anagen (proliferative stage). Skin samples from transitional "intermediate" and "brown" pelage were transcriptionally similar and resembled the regressive transition to catagen (regressive stage). We also detected differential expression of several key circadian clock and pigmentation genes, providing important means to dissect the bases of alternate seasonal colour morphs. Our results reveal that pelage colour is a useful biomarker for seasonal change but that there is a consistent lag between the main gene expression waves and change in visible coat colour. These experiments establish that developmental sampling from natural populations of nonmodel organisms can provide a crucial resource to dissect the genetic basis and evolution of complex seasonally changing traits.

Decreases in adolescent weekly alcohol use in Europe and North America: evidence from 28 countries from 2002 to 2010.

BACKGROUND: This study examined trends in adolescent weekly alcohol use between 2002 and 2010 in 28 European and North American countries. METHODS: Analyses were based on data from 11-, 13- and 15-year-old adolescents who participated in the Health Behaviour in School-Aged Children (HBSC) study in 2002, 2006 and 2010. RESULTS: Weekly alcohol use declined in 20 of 28 countries and in all geographic regions, from 12.1 to 6.1% in Anglo-Saxon countries, 11.4 to 7.8% in Western Europe, 9.3 to 4.1% in Northern Europe and 16.3 to 9.9% in Southern Europe. Even in Eastern Europe, where a stable trend was observed between 2002 and 2006, weekly alcohol use declined between 2006 and 2010 from 12.3 to 10.1%. The decline was evident in all gender and age subgroups. CONCLUSIONS: These consistent trends may be attributable to increased awareness of the harmful effects of alcohol for adolescent development and the implementation of associated prevention efforts, or changes in social norms and conditions. Although the declining trend was remarkably similar across countries, prevalence rates still differed considerably across countries.

Immunoassay interferences: laboratory pitfall in the diagnosis of adrenocortical carcinoma.

A woman in her late 50s with recent onset of hypertension, diabetes, lumbar pain and unintentional weight loss was diagnosed with a cortisol and androgen-producing adrenal mass. Despite this, serum adrenocorticotropic hormone (ACTH) concentration was inappropriately elevated, which was investigated thoroughly. Investigations included a brain magnetic resonance imaging to exclude concomitant pituitary adenoma, a corticotropin-releasing hormone stimulation test and a gallium-68 DOTATATE and 18F-FDOPA PET scan, both excluding ectopic ACTH production. Considering the disparity between clinical presentation and biochemical results, the ACTH was reanalysed using the Cobas immunoassay (Roche, Switzerland), ultimately unveiling the cause for ACTH elevation. ACTH levels had previously been measured with ACTH Immulite (Siemens, Germany), a two-site immunoassay which is prone to interferences causing falsely elevated ACTH concentrations. Inaccurate laboratory levels can lead to diagnosis delay and unnecessary diagnostic procedures and a close communication between the physicians and laboratorians is of utmost importance.

How Fish Population Genomics Can Promote Sustainable Fisheries: A Road Map.

Maintenance of genetic diversity in marine fishes targeted by commercial fishing is a grand challenge for the future. Most of these species are abundant and therefore important for marine ecosystems and food security. Here, we present a road map of how population genomics can promote sustainable fisheries. In these species, the development of reference genomes and whole genome sequencing is key, because genetic differentiation at neutral loci is usually low due to large population sizes and gene flow. First, baseline allele frequencies representing genetically differentiated populations within species must be established. These can then be used to accurately determine the composition of mixed samples, forming the basis for population demographic analysis to inform sustainably set fish quotas. SNP-chip analysis is a cost-effective method for determining baseline allele frequencies and for population identification in mixed samples. Finally, we describe how genetic marker analysis can transform stock identification and management.

Tumor-secreted extracellular vesicles counteract therapy response by triggering inflammatory mesenchymal stem cell development.

PURPOSE: Therapy resistance is a major clinical hurdle in bone cancer treatment and seems to be largely driven by poorly understood microenvironmental factors. Recent evidence suggests a critical role for a unique subpopulation of mesenchymal stem cells with inflammatory features (iMSCs), though their origin and function remained unexplored. We demonstrate that cancer-secreted extracellular vesicles (EVs) trigger the development of iMSCs, which hinder therapy response in vivo, and set out to identify strategies to counteract their function. EXPERIMENTAL DESIGN: The role of iMSCs in therapy resistance was evaluated in an orthotopic xenograft mouse model of osteosarcoma. EV-induced alterations of the MSC transcriptome were analyzed and compared with scRNA-seq data of osteosarcoma and multiple myeloma patient biopsies. Functional assays identified EV components driving iMSC development. We assessed the efficacy of clinical drugs in blocking iMSC-induced resistance in vivo. RESULTS: We found that iMSCs are induced by interaction with cancer EVs and completely abrogate the antimetastatic effect of TGFb signaling inhibition. Importantly, EV-induced iMSCs faithfully recapitulate the inflammatory single-cell RNA signature of stromal cells enriched in multiple myeloma and osteosarcoma patient biopsies. Mechanistically, cancer EVs act through two distinct mechanisms. EV-associated TGFb induces IL6 production, while the EV-RNA cargo enhances TLR3-mediated chemokine production. We reveal that simultaneous blockade of downstream EV-activated pathways with ladarixin and tocilizumab disrupts metastasis formation and overcomes iMSC-induced resistance. CONCLUSIONS: Our observations establish iMSCs as major contributors to drug resistance, reveal EVs as physiological triggers of iMSC development and highlight a promising combination strategy to improve therapy response in bone cancer patients.

Domestic Violence against LGBTI People: Perspectives of Portuguese Education Professionals.

Lesbian, gay, bisexual, trans and intersex (LGBTI) people are more likely to be exposed to domestic violence than the rest of the population. Using a descriptive qualitative methodology, 28 professionals from the educational sector, aged between 28 and 64 years old (M = 44.5), were interviewed to describe and understand their perspectives on the sector's ability to support, intervene and get involved with LGBTI people and, particularly, with victims or former victims of domestic violence. Through a thematic content analysis, three main themes emerged: (i) life trajectories of LGBTI people; (ii) domestic violence perpetrated against LGBTI people; and (iii) training of the educational sector to intervene with LGBTI people. The results show that Portuguese education professionals are not trained to recognize and intervene with LGBTI people and, in particular, with those who are victims of domestic violence, since they are unaware of the existence of protocols and/or guidelines for detecting and preventing risk situations among students. Furthermore, the curricular plan fails in the coverage of domestic violence and LGBTI-related topics, although the National Strategy for Citizenship Education has been implemented in Portugal since 2017. Findings suggest the need to invest in education professionals' training.

The evolution of white-tailed jackrabbit camouflage in response to past and future seasonal climates.

The genetic basis of adaptive traits has rarely been used to predict future vulnerability of populations to climate change. We show that light versus dark seasonal pelage in white-tailed jackrabbits (Lepus townsendii) tracks snow cover and is primarily determined by genetic variation at endothelin receptor type B (EDNRB), corin serine peptidase (CORIN), and agouti signaling protein (ASIP). Winter color variation was associated with deeply divergent alleles at these genes, reflecting selection on both ancestral and introgressed variation. Forecasted reductions in snow cover are likely to induce widespread camouflage mismatch. However, simulated populations with variation for darker winter pelage are predicted to adapt rapidly, providing a trait-based genetic framework to facilitate evolutionary rescue. These discoveries demonstrate how the genetic basis of climate change adaptation can inform conservation.

Fill in the blank for fashion complementary outfit product Retrieval: VISUM summer school competition.

Every year, the VISion Understanding and Machine intelligence (VISUM) summer school runs a competition where participants can learn and share knowledge about Computer Vision and Machine Learning in a vibrant environment. 2021 VISUM's focused on applying those methodologies in fashion. Recently, there has been an increase of interest within the scientific community in applying computer vision methodologies to the fashion domain. That is highly motivated by fashion being one of the world's largest industries presenting a rapid development in e-commerce mainly since the COVID-19 pandemic. Computer Vision for Fashion enables a wide range of innovations, from personalized recommendations to outfit matching. The competition enabled students to apply the knowledge acquired in the summer school to a real-world problem. The ambition was to foster research and development in fashion outfit complementary product retrieval by leveraging vast visual and textual data with domain knowledge. For this, a new fashion outfit dataset (acquired and curated by FARFETCH) for research and benchmark purposes is introduced. Additionally, a competitive baseline with an original negative sampling process for triplet mining was implemented and served as a starting point for participants. The top 3 performing methods are described in this paper since they constitute the reference state-of-the-art for this particular problem. To our knowledge, this is the first challenge in fashion outfit complementary product retrieval. Moreover, this joint project between academia and industry brings several relevant contributions to disseminating science and technology, promoting economic and social development, and helping to connect early-career researchers to real-world industry challenges.

In vitro cross-talk between metastasis-competent circulating tumor cells and platelets in colon cancer: a malicious association during the harsh journey in the blood.

Background: Platelets are active players in hemostasis, coagulation and also tumorigenesis. The cross-talk between platelets and circulating tumor cells (CTCs) may have various pro-cancer effects, including promoting tumor growth, epithelial-mesenchymal transition (EMT), metastatic cell survival, adhesion, arrest and also pre-metastatic niche and metastasis formation. Interaction with CTCs might alter the platelet transcriptome. However, as CTCs are rare events, the cross-talk between CTCs and platelets is poorly understood. Here, we used our established colon CTC lines to investigate the colon CTC-platelet cross-talk in vitro and its impact on the behavior/phenotype of both cell types. Methods: We exposed platelets isolated from healthy donors to thrombin (positive control) or to conditioned medium from three CTC lines from one patient with colon cancer and then we monitored the morphological and protein expression changes by microscopy and flow cytometry. We then analyzed the transcriptome by RNA-sequencing of platelets indirectly (presence of a Transwell insert) co-cultured with the three CTC lines. We also quantified by reverse transcription-quantitative PCR the expression of genes related to EMT and cancer development in CTCs after direct co-culture (no Transwell insert) with platelets. Results: We observed morphological and transcriptomic changes in platelets upon exposure to CTC conditioned medium and indirect co-culture (secretome). Moreover, the expression levels of genes involved in EMT (p < 0.05) were decreased in CTCs co-cultured with platelets, but not of genes encoding mesenchymal markers (FN1 and SNAI2). The expression levels of genes involved in cancer invasiveness (MYC, VEGFB, IL33, PTGS2, and PTGER2) were increased. Conclusion: For the first time, we studied the CTC-platelet cross-talk using our unique colon CTC lines. Incubation with CTC conditioned medium led to platelet aggregation and activation, supporting the hypothesis that their interaction may contribute to preserve CTC integrity during their journey in the bloodstream. Moreover, co-culture with platelets influenced the expression of several genes involved in invasiveness and EMT maintenance in CTCs.

Tumor-educated platelet blood tests for Non-Small Cell Lung Cancer detection and management.

Liquid biopsy approaches offer a promising technology for early and minimally invasive cancer detection. Tumor-educated platelets (TEPs) have emerged as a promising liquid biopsy biosource for the detection of various cancer types. In this study, we processed and analyzed the TEPs collected from 466 Non-small Cell Lung Carcinoma (NSCLC) patients and 410 asymptomatic individuals (controls) using the previously established thromboSeq protocol. We developed a novel particle-swarm optimization machine learning algorithm which enabled the selection of an 881 RNA biomarker panel (AUC 0.88). Herein we propose and validate in an independent cohort of samples (n = 558) two approaches for blood samples testing: one with high sensitivity (95% NSCLC detected) and another with high specificity (94% controls detected). Our data explain how TEP-derived spliced RNAs may serve as a biomarker for minimally-invasive clinical blood tests, complement existing imaging tests, and assist the detection and management of lung cancer patients.

Dance is the new metal: adolescent music preferences and substance use across Europe.

This study examined relationships between music preferences and substance use (tobacco, alcohol, cannabis) among 18,103 fifteen-year-olds from 10 European countries. In 2005-2006, across Europe, preferences for mainstream Pop (pop chart music) and Highbrow (classical music and jazz) were negatively associated with substance use, while preferences for Dance (house/trance and techno/hardhouse) were associated positively with substance use. In three countries, links were identified between liking Rock (rock, heavy metal punk/hardcore, and gothic) and substance use; associations between Urban (hip-hop and R&B) and substance use were mixed. No substantial gender differences emerged in these patterns, and controlling for relevant covariates did not attenuate the predictive value of substance use. The findings are consistent with the conclusion that music is a robust marker of adolescent substance use.

Attitudes of Portuguese Judges and Victim Support Professionals Toward Intimate Partner Homicide Committed by Women.

This investigation analyzed the attitudes of Portuguese judges and victim support professionals toward intimate partner homicide committed by women. By administering an online survey disseminated by the Portuguese Superior Council for the Magistracy and the Commission for Citizenship and Gender Equality, we found that both groups of professionals are not always aligned in their attitudes toward domestic violence and intimate partner homicide, which could jeopardize the articulation between both sectors needed for an effective preventive intervention. However, most professionals of both groups tend to disagree that women provoke their aggressors or lie about their condition as victims of domestic violence and agree that there is a need for increased security and prevention of intimate partner homicides against female and male victims when reporting domestic violence.

The Portuguese version of the visual vertigo analog scale.

OBJECTIVES: Visual vertigo occurs after a vestibular disorder compromising daily living. It can be assessed by "the Visual Vertigo Analogue Scale" (VVAS), a self-administered questionnaire without Portuguese version. To perform the translation, cross cultural adaptation, and validation of VVAS from English to Portuguese. METHODS: Prospective study involving the translation and cross-cultural adaptation of the VVAS into the Portuguese language, according to recognized guidelines. It was completed by 63 healthy controls and 198 participants with vestibulopathy who also completed the Dizziness Handicap Inventory (DHI) to further explore the link between DHI and VVAS. Groups were compared for severity of visual vertigo and VVAS reliability and internal consistency were tested. RESULTS: The VVAS score was significantly higher in vestibular group (p < 0.001). A Cronbach's α of 0.9 confirmed the valid internally consistent of the applied version. The severity score of VVAS showed a positive strong correlation with DHI (p < 0.0001). CONCLUSION: The present Portuguese translation of the scale showed satisfactory properties for the assessment of self-perceived and severity of visual vertigo in a significant group of vestibular Portuguese patients.

Detection and localization of early- and late-stage cancers using platelet RNA.

Cancer patients benefit from early tumor detection since treatment outcomes are more favorable for less advanced cancers. Platelets are involved in cancer progression and are considered a promising biosource for cancer detection, as they alter their RNA content upon local and systemic cues. We show that tumor-educated platelet (TEP) RNA-based blood tests enable the detection of 18 cancer types. With 99% specificity in asymptomatic controls, thromboSeq correctly detected the presence of cancer in two-thirds of 1,096 blood samples from stage I-IV cancer patients and in half of 352 stage I-III tumors. Symptomatic controls, including inflammatory and cardiovascular diseases, and benign tumors had increased false-positive test results with an average specificity of 78%. Moreover, thromboSeq determined the tumor site of origin in five different tumor types correctly in over 80% of the cancer patients. These results highlight the potential properties of TEP-derived RNA panels to supplement current approaches for blood-based cancer screening.

Individual Resilience Interventions: A Systematic Review in Adult Population Samples over the Last Decade.

Resilience interventions have been gaining importance among researchers due to their potential to provide well-being and reduce the prevalence of mental disorders that are becoming an increasing concern, especially in Western countries, because of the costs associated. The purpose of this systematic review is to identify the intervention studies carried out in the last decade in adult population samples, evaluate their methodological quality and highlight the trends of these types of interventions. This review was performed using systematic literature searches in the following electronic databases: B-on, PubMed, PsycNet and Science Direct. The application of eligibility criteria resulted in the inclusion of 38 articles, of which 33 were randomized controlled trials and the other five were nonrandomized controlled studies. Although most studies showed statistical significance for their results, these were constrained by the great heterogeneity of the studies, the lack of power of the samples and their fair methodological quality. Therefore, it is important to consolidate the theoretical basis and standardize certain methodologies so that the effects of the interventions can be compared through a meta-analysis.

Depression preceding the diagnosis of pancreatic cancer.

Pancreatic cancer is the tumour related to higher rates of depression. Several papers have validated the association between pancreatic cancer and depression. It was noticed that in some cases the psychiatric symptoms precede the somatic ones. We present a case of a progressive and incapacitating diffuse abdominal pain, initially attributed to psychosomatic disorder. This hindered a timely correct diagnosis leading to a poor outcome. A pancreatic adenocarcinoma in an unresectable stage was confirmed by histopathology. The patient underwent chemotherapy.