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Regularization methods for high-dimensional data as a tool for seafood traceability
Get PDFFunding: This work is funded by national funds through the FCT - Fundação para a Ciência e a Tecnologia, I.P., under the scope of the projects UIDB/00297/2020 and UIDP/00297/2020 (Center for Mathematics and Applications).Seafood traceability, needed to regulate food safety, control fisheries, combat fraud, and prevent jeopardizing public health from harvesting in polluted locations, depends heavily on the prediction of the geographic origin of seafood. When the available datasets to study traceability are high-dimensional, standard classic statistical models fail. Under these circumstances, proper alternative methods are needed to predict accurately the geographic origin of seafood. In this study, we propose an analytical approach combining the use of regularization methods and resampling techniques to overcome the high-dimensionality problem. In particular, we analyze comparatively the Ridge regression, LASSO and Elastic net penalty-based approaches. These methods were applied to predict the origin of the saltwater clam Ruditapes philippinarum, a non-indigenous and commercially very relevant marine bivalve species that occurs commonly in European estuaries. Further, the resampling method of Monte Carlo Cross-Validation was implemented to overcome challenges related to the small sample size. The results of the three methods were compared. For fully reproducibility, an R Markdown file and the used dataset are provided. We conclude highlighting the insights that this methodology may bring to model a multi-categorical response based on high-dimensional dataset, with highly correlated explanatory variables, and combat the mislabeling of geographic origin of seafood.Peer reviewe
Numerical insights into the origin and nature of the ionized interstellar medium
No full textThis thesis investigates the origin and nature of diffuse ionized gas (DIG) in the Milky Way and other similar galaxies.
I have been developing the 3D radiation-hydrodynamics code, CMacIonize, to include the effect of supernova feedback, an IMF based star formation algorithm, non-equilibrium heating and cooling, and a time-dependent calculation of ionization state. The time-dependent ionization calculation was found to be crucial in reliably simulating the high altitude DIG, with recombination timescales in the low-density gas often exceeding 10~Myr, longer than the time variability of the available ionizing luminosity.
The time-dependent ionization state calculations are extended to include various ionized species of helium, carbon, nitrogen, oxygen, neon and sulphur, necessary for simulating collisionally excited emission from the DIG. Synthetic observations of edge on emission line ratios are found to match well to high-altitude observations from Milky Way analogue NGC 891, and inspire novel explanations for hardened line ratios which don't rely on secondary populations of spectrally hard sources.
I perform static photoionization simulations through observationally derived 3D density structures using known O stars as the source of ionizing luminosity. I generate a synthetic Hα sky including the effects of dust scattering and absorption. The synthetic sky bears excellent morphological resemblance to the observed Hα sky from surveys such as the Wisconsin H-Alpha Mapper (WHAM). Synthetic skies of other optical and infrared lines are also generated, standing as predictions for future all-sky spectroscopic surveys.
Using zoom-in radiation-hydrodynamics simulations, I investigate the effects of the missing temporal dimension in the static simulations. The static simulations assume ionization equilibrium and do not include the effects of supernova feedback. It is found that the equilibrium assumption is likely reliable for this region of higher density material close to the midplane, however some notable effects of supernova feedback are highlighted in the full time-dependent simulations
Integration of multi-omics data for the classification of glioma types and identification of novel biomarkers
Get PDFFunding: This work was funded by national funds through the FCT—Fundação para a Ciência e a Tecnologia, I.P., with references CEECINST/00042/2021, UIDB/00297/2020, and UIDP/00297/2020 (NOVA Math), UIDB/00667/2020 and UIDP/00667/2020 (UNIDEMI), and under the scope of the research project “MONET—Multi-omic networks in gliomas” (PTDC/CCI-BIO/4180/2020).Glioma is currently one of the most prevalent types of primary brain cancer. Given its high level of heterogeneity along with the complex biological molecular markers, many efforts have been made to accurately classify the type of glioma in each patient, which, in turn, is critical to improve early diagnosis and increase survival. Nonetheless, as a result of the fast-growing technological advances in high-throughput sequencing and evolving molecular understanding of glioma biology, its classification has been recently subject to significant alterations. In this study, we integrate multiple glioma omics modalities (including mRNA, DNA methylation, and miRNA) from The Cancer Genome Atlas (TCGA), while using the revised glioma reclassified labels, with a supervised method based on sparse canonical correlation analysis (DIABLO) to discriminate between glioma types. We were able to find a set of highly correlated features distinguishing glioblastoma from lower-grade gliomas (LGGs) that were mainly associated with the disruption of receptor tyrosine kinases signaling pathways and extracellular matrix organization and remodeling. Concurrently, the discrimination of the LGG types was characterized primarily by features involved in ubiquitination and DNA transcription processes. Furthermore, we could identify several novel glioma biomarkers likely helpful in both diagnosis and prognosis of the patients, including the genes PPP1R8, GPBP1L1, KIAA1614, C14orf23, CCDC77, BVES, EXD3, CD300A, and HEPN1. Collectively, this comprehensive approach not only allowed a highly accurate discrimination of the different TCGA glioma patients but also presented a step forward in advancing our comprehension of the underlying molecular mechanisms driving glioma heterogeneity. Ultimately, our study also revealed novel candidate biomarkers that might constitute potential therapeutic targets, marking a significant stride toward personalized and more effective treatment strategies for patients with glioma.Peer reviewe
Rationale and ethical assessment of an oropharyngeal gonorrhoea controlled human infection model
Get PDFFunding: This work was supported by a Clinician Researchers: Applied Research in Health Grant from the Medical Research Future Fund (MRFAR000354); a postgraduate scholarship from the National Health and Medical Research Council (GNT2005380 to E. W.); Investigator Grants from the National Health and Medical Research Council (GNT2025960 to J. S. H., GNT2025840 to M. Y. C., GNT1174555 to D. A. W.); and Leadership Investigator Grants from the National Health and Medical Research Council (GNT1172900 to C. K. F., GNT2016396 to J. S. M.).Infection with Neisseria gonorrhoeae, the causative agent of gonorrhoea, causes significant morbidity worldwide and can have long-term impacts on reproductive health. The greatest global burden of gonorrhoea occurs in low- and middle-income settings. Global public health significance is increasing due to rising antimicrobial resistance (AMR), which threatens future gonorrhoea management. The oropharynx is an important asymptomatic reservoir for gonorrhoea transmission and a high-risk site for development of AMR and treatment failure. Controlled human infection model (CHIM) studies using N. gonorrhoeae may provide a means to accelerate the development of urgently needed therapeutics, vaccines and other biomedical prevention strategies. A gonorrhoea urethritis CHIM has been used since the 1980s with no reported serious adverse events. Here, we describe the rationale for an oropharyngeal gonorrhoea CHIM, including analysis of potential ethical issues that should inform the development of this novel study design.Peer reviewe
Vocal accommodation in bonobos
Get PDFFunding: Funding was provided by the French Ministère de l’Enseignement Supérieur et de la Recherche (Ph.D. grant to S.K.), the university of Saint-Etienne (visiting professorship to K.Z. and research funding to F.L.), the European Research Council (K.Z. grant PRILANG 283871), the CNRS and the Institut Universitaire de France (F.L. & N.M.).Dialects and accents in human speech have a demonstrated social function as markers of group identity and often serve as psychological foundations of trust and cooperation. The extent to which this phenomenon is a feature of primate communication more generally is still debated. Here, we show that the vocal signatures of bonobos, Pan paniscus, belonging to three social groups show group-specific acoustic features independent of genetic relatedness. We compared the barks of 22 adults from the three groups and found that individuals currently living together had more similar barks than individuals that had never met or had lost touch with each other, regardless of their degree of genetic relatedness. We concluded that group-specific vocal accommodation is present in bonobos, suggesting an early evolutionary emergence of vocal plasticity in apes, which could be a means to signal social closeness between individuals.Peer reviewe
Social and individual factors mediate chimpanzee vocal ontogeny
Get PDFThis work was supported by the Swiss National Science Foundation grant (501100001711-166458) awarded to K.Z., the St Leonard College Inter-University scholarship awarded to J.C. and K.Z., and individual mobility grants from Swiss universities and St Leonard College awarded to A.S.Human language develops in social interactions. In other ape species, the role of social learning in vocal ontogeny can be typically underappreciated, mainly because it has received little empirical attention. Here, we examine the development of pant hoot vocalisations during vocal exchanges in immature wild chimpanzees (Pan troglodytes schweinfurthii) of the Sonso community of the Budongo Forest, Uganda. We investigated how maternal gregariousness, age, sex, and social context are associated with behavioural and vocal responses to other group members’ calls. We show that the older sons of gregarious mothers are more likely to orient their attention, respond vocally to the calls of others, and are overall more exposed to others’ calls compared to other immature individuals. This effect is strongest in the presence of adult males and when their mothers also respond vocally, suggesting that chimpanzee vocal development is enhanced by social and vocal exposure. Our findings are consistent with a more flexible and socially mediated chimpanzee vocal ontogeny than previously assumed and show some parallels with animal vocal learners and children language acquisition.Peer reviewe
Customer orientation and stock resilience during adversity periods
Get PDFCustomer orientation reflects the organizational culture and climate that promote behaviors enabling the firm to create superior value for its customers. Using a textual measure of customer orientation ( ) constructed from 10-K filings, we document a positive and economically significant relation between and stock returns in the financial crisis of 2008–2009 and the COVID-19 pandemic. High- firms outperform low- firms by 1.5% per month during the financial crisis and by 4.7% per month during the COVID-19 crisis. This positive -returns relation is robust to different treatments and persists after accounting for factors that contribute to corporate resilience, such as activities. Our findings lend credence to the notion that customer orientation enhances a firm’s social capital, leading to improved operational performance during adverse periods, whilst our empirical evidence further supports that and represent distinct pathways for building trust. Consequently, firms that prioritize customer orientation experience greater resilience to negative shocks, especially during periods of low market confidence.Peer reviewe
Not loud, but detailed : an exploration of intimacy through amplification, recording, and production techniques
Get PDFThis commentary accompanies six new compositions written between 2019 and 2023, presented through audio recordings and musical scores. There are also accompanying photos, video and audio clips that provide insights into my working process during the creation of these pieces.
In this commentary, I discuss how I have explored intimacy in my compositions through technical means, both acoustic (sustain, resonance, microtonality) and electronic (close-miking, time-stretching, and other production techniques), and through nostalgia, by which I mean a perceived emotional relationship between the music and the listener. My use of the term ‘intimacy’ refers to a musical aesthetic that is characterised not only by a perceived sonic closeness between sound source and listener, but also by a perceived emotional relationship between the listener and performer(s). This intimacy in my music can be afforded to quiet and delicate sounds through sonic magnification, in which the detail of each sound is focused on and thoroughly examined in various ways, resulting in often imperfect, highly detailed, and almost tactile sounds.
For the creation of this compositional body of work, I have developed an approach that integrates a considerable number of disparate musical frameworks and that encompasses several techniques and compositional tools, which have grown out of my experience as an experimental electric guitarist fused with my practice as a contemporary classical composer. These techniques include instrument manipulation, object amplification, improvisation and production techniques, as well as my attempts to translate these ideas into purely acoustic composition. I have synthesised these elements into a personal and unified compositional whole, which has defined both my compositional process and the resulting compositional work
Potential evidence of reengagement attempts following interruptions of a triadic social game in bonobos and chimpanzees
Get PDFFunding: The present research was supported by the Swiss National Science Foundation (Grant No. CR31I3_166331 awarded to AB and KZ). RH thanks K\u00F6lner Gymnasial- und Stiftungsfonds and EG thanks the Service de l\u2019Egalit\u00E9 des Chances of the University of Neuch\u00E2tel for supporting their field stay in DRC. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. We thank La Vall\u00E9e des Singes and its former director Emmanuel Le Grelle as well as Le Conservatoire pour la Conservation des Primates and ABC Congo, particularly Fanny Minesi, Rapha\u00EBl Belais and Claudine Andr\u00E9, for allowing access to the study sites and subjects. We are particularly thankful for the support of the animal keepers at La Vall\u00E9e des Singes and at Lola Ya Bonobo who acted as experimenters and helped us implement the trials, and to H\u00E9ritier Izansone, for his invaluable assistance throughout the study.When humans engage in joint action, they seem to so with an underlying sense of joint commitment, a feeling of mutual obligation towards their partner and a shared goal. Whether our closest living relatives, bonobos and chimpanzees, experience and understand joint commitment in the same way is subject to debate. Crucial evidence concerns how participants respond to interruptions of joint actions, particularly if they protest or attempt to reengage their reluctant or distracted partners. During dyadic interactions, bonobos and chimpanzees exhibit evidence of reengagement following interruptions of naturalistic joint activities with conspecifics, according to recent studies. Yet, data are still inconsistent for triadic games, where two social partners engage with each other socially by focusing on a common object. We addressed this issue by engaging N=23 apes (5 adult chimpanzees, 5 infant bonobos, 13 adult bonobos) in a “tug-of-war” game with a human experimenter who abruptly stopped playing. Following interruptions, adult apes readily produced communicative signals towards the experimenter (>60% of subjects on first trial), which we interpreted as reengagement attempts of their passive social partner, with no group differences in this respect. Infant bonobos, by contrast, communicated rarely with the experimenters compared to adult bonobos, and never during their first trial. Crucially, when infant bonobos signaled to passive partners, they predominantly used tactile signals, but rarely exhibited behaviors related to the game, which were instead commonly seen in adults. It is thus possible that bonobos and chimpanzees share some of the basic motivational foundations for joint commitment, yet that this capacity is subject to developmental effects.Peer reviewe
The changing nature of foundation work : advancing the field by understanding the foundation professional experience
Get PDFFunding: The Diana, Princess of Wales Memorial Fund and the University of St. Andrews School of Management supported this research with funding.The nature of foundation work is underexplored with little attention to the internal dynamics of foundations. Focus has been on the organizational level describing foundations’ societal roles, but understanding the individual experiences of those working within foundations would remove much of the mystery of these institutions. This article focuses on the experiences of the individual foundation professional, by exploring the entry-to-exit of UK family foundation CEOs. This study demonstrates inherent tensions between amateur and emerging professional influences in foundation roles. In asking about the changing nature of foundation work, this article highlights three underexplored elements: competing expertise, inconsistent field formalization, and a professionalizing context. Understanding these elements are crucial for implementing effective and equitable field-level initiatives. Focusing on foundation professional experiences challenges the “black box” narrative by providing a greater understanding of foundation work and its evolution.Peer reviewe
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