Miracle-dz/UniFAR-FTUs huggingface dataset:
Decoding Heterogeneity in Data-Driven Self-Monitoring Adherence Trajectories in Digital Lifestyle Interventions for Weight Loss: A Qualitative Study

Background: Data-driven trajectory modeling is a promising approach for identifying meaningful participant subgroups with various self-monitoring (SM) responses in digital lifestyle interventions. However, there is limited research investigating factors that underlie different subgroups. This qualitative study aimed to investigate factors contributing to participant subgroups with distinct SM trajectory in a digital lifestyle intervention over 6 months. Methods: Data were collected from a subset of participants (n = 20) in a 6-month digital lifestyle intervention. Participants were classified into Lower SM Group (n = 10) or a Higher SM (n = 10) subgroup based on their SM adherence trajectories over 6 months. Qualitative data were obtained from semi-structured interviews conducted at 3 months. Data were thematically analyzed using a constant comparative approach. Results: Participants were middle-aged (52.9 ± 10.2 years), mostly female (65%), and of Hispanic ethnicity (55%). Four major themes with emerged from the thematic analysis: Acceptance towards SM Technologies, Perceived SM Benefits, Perceived SM Barriers, and Responses When Facing SM Barriers. Participants across both subgroups perceived SM as positive feedback, aiding in diet and physical activity behavior changes. Both groups cited individual and technical barriers to SM, including forgetfulness, the burdensome SM process, and inaccuracy. The Higher SM Group displayed positive problem-solving skills that helped them overcome the SM barriers. In contrast, some in the Lower SM Group felt discouraged from SM. Both subgroups found diet SM particularly challenging, especially due to technical issues such as the inaccurate food database, the time-consuming food entry process in the Fitbit app. Conclusions: This study complements findings from our previous quantitative research, which used data-drive trajectory modeling approach to identify distinct participant subgroups in a digital lifestyle based on individuals’ 6-month SM adherence trajectories. Our results highlight the potential of enhancing action planning problem solving skills to improve SM adherence in the Lower SM Group. Our findings also emphasize the necessity of addressing the technical issues associated with current diet SM approaches. Overall, findings from our study may inform the development of practical SM improvement strategies in future digital lifestyle interventions. Trial registration: The study was pre-registered at ClinicalTrials.gov (NCT05071287) on April 30, 2022.
Semantic representations in inferior frontal and lateral temporal cortex during picture naming, reading, and repetition

Abstract Reading, naming, and repetition are classical neuropsychological tasks widely used in the clinic and psycholinguistic research. While reading and repetition can be accomplished by following a direct or an indirect route, pictures can be named only by means of semantic mediation. By means of fMRI multivariate pattern analysis, we evaluated whether this well‐established fundamental difference at the cognitive level is associated at the brain level with a difference in the degree to which semantic representations are activated during these tasks. Semantic similarity between words was estimated based on a word association model. Twenty subjects participated in an event‐related fMRI study where the three tasks were presented in pseudo‐random order. Linear discriminant analysis of fMRI patterns identified a set of regions that allow to discriminate between words at a high level of word‐specificity across tasks. Representational similarity analysis was used to determine whether semantic similarity was represented in these regions and whether this depended on the task performed. The similarity between neural patterns of the left Brodmann area 45 (BA45) and of the superior portion of the left supramarginal gyrus correlated with the similarity in meaning between entities during picture naming. In both regions, no significant effects were seen for repetition or reading. The semantic similarity effect during picture naming was significantly larger than the similarity effect during the two other tasks. In contrast, several regions including left anterior superior temporal gyrus and left ventral BA44/frontal operculum, among others, coded for semantic similarity in a task‐independent manner. These findings provide new evidence for the dynamic, task‐dependent nature of semantic representations in the left BA45 and a more task‐independent nature of the representational activation in the lateral temporal cortex and ventral BA44/frontal operculum.
Association of asthma and lung cancer risk: A pool of cohort studies and Mendelian randomization analysis

Background: Over the past 2 decades, population-based studies have shown an increased association between asthma and the risk of lung cancer. However, the causal links between these 2 conditions remain poorly understood. Methods: We conducted a comprehensive search of various databases, including PubMed, Embase, Web of Science, and Cochrane Library, up until May 04, 2023. Only articles published in English were included in our study. We performed a meta-analysis using random-effects models to calculate the odds ratio (OR) and corresponding 95% confidence interval (CI). Subgroup analyses were conducted based on study design, gender, and histologic types. We also conducted a 2-sample Mendelian randomization (MR) using the genome-wide association study pooled data (408,422 people) published by the UK Biobank to explore further the potential causal relationship between asthma and lung cancer. Results: Our meta-analysis reviewed 24 population-based cohort studies involving 1072,502 patients, revealing that asthma is significantly associated with an increased risk of lung cancer (OR = 1.29, 95% CI 1.19–1.38) in all individuals. Subgroup analysis showed a significantly higher risk of lung cancer in females with asthma (OR = 1.23, 95% CI 1.01–1.49). We found no significant association between asthma and lung adenocarcinoma (LUAD) (OR = 0.76, 95% CI 0.54–1.05), lung squamous carcinomas (LUSC) (OR = 1.09, 95% CI 0.79–1.50), or small-cell lung cancer (SCLC) (OR = 1.00, 95% CI 0.68–1.49). Interestingly, our MR analysis supported an increasing causality between asthma and lung cancer (OR = 1.11, 95% CI 1.04–1.17, P = .0008), specifically in those who ever smoker (OR = 1.09, 95% CI 1.01–1.16, P = .0173) and LUSC pathological type (OR = 1.15, 95% CI 1.05–1.26, P = .0038). Conclusion: Through meta-analysis, our study confirms that patients with asthma have a higher risk of developing lung cancer. Our MR study further support an increasing causal relationship between asthma and the risk of lung cancer, particularly in smokers and LUSC. Future studies examining the link between asthma and the risk of developing lung cancer should consider the bias of controlled and uncontrolled asthma.
The reproductive microbiome and maternal transmission of microbiota via eggs in Sceloporus virgatus

Abstract Maternal transmission of microbes occurs across the animal kingdom and is vital for offspring development and long-term health. The mechanisms of this transfer are most well-studied in humans and other mammals but are less well-understood in egg-laying animals, especially those with no parental care. Here, we investigate the transfer of maternal microbes in the oviparous phrynosomatid lizard, Sceloporus virgatus. We compared the microbiota of three maternal tissues—oviduct, cloaca, and intestine—to three offspring sample types: egg contents and eggshells on the day of oviposition, and hatchling intestinal tissue on the day of hatching. We found that maternal identity is an important factor in hatchling microbiome composition, indicating that maternal transmission is occurring. The maternal cloacal and oviductal communities contribute to offspring microbiota in all three sample types, with minimal microbes sourced from maternal intestines. This indicates that the maternal reproductive microbiome is more important for microbial inheritance than the gut microbiome, and the tissue-level variation of the adult S. virgatus microbiota must develop as the hatchling matures. Despite differences between adult and hatchling communities, offspring microbiota were primarily members of the Enterobacteriaceae and Yersiniaceae families (Phylum Proteobacteria), consistent with this and past studies of adult S. virgatus microbiomes.
Surface versus volume synthesis governs growth-dependent efficacy of a β-lactam antibiotic

The efficacy of β-lactam antibiotics depends strongly on bacterial growth rate. This can lead to poor correlation between in vivo action and in vitro assays, hindering effective prescribing – yet the mechanisms underlying growth-rate dependent β-lactam action remain unclear. Here, we investigate growth-rate dependent action of mecillinam, a β-lactam that targets the elongation-mediating PBP2 peptidoglycan transpeptidase enzyme, on Escherichia coli cells. We show that mecillinam alters the balance between the rates of cell surface area and volume synthesis in a growth-rate dependent manner. Under mecillinam treatment, cell volume increases exponentially at a rate ﬁxed by the growth medium, but the cell’s ability to produce new surface area is compromised by the antibiotic. On rich medium, this imbalance leads to lysis, but on poor medium, slow-growing cells reach a new balance between surface area and volume synthesis, allowing sustained growth even at concentrations of mecillinam far above the EUCAST MIC value. A mathematical model based on surface area vs volume synthesis can quantitatively explain growth-medium dependent differences in mecillinam killing, as well as rescue from killing when cell morphology is perturbed in a microfluidic device. β-lactam antibiotic action is mechanistically complex, yet our work suggests that simple conceptual principles can help understand the interplay between molecular mechanism and cell physiology, potentially contributing to more effective use of these drugs.
3D-ARM-Gaze: a public dataset of 3D Arm Reaching Movements with Gaze information in virtual reality

3D-ARM-Gaze is a public dataset designed to provide natural arm movements together with visual and gaze information when reaching objects in a wide reachable space from a precisely controlled, comfortably seated posture. Participants were involved in picking and placing objects in various positions and orientations in a virtual environment, whereby a specific procedure maximized the workspace explored while ensuring a consistent seated posture. The dataset regroups more than 2.5 million samples recorded from 20 healthy participants performing 14 000 single pick-and-place movements (700 per participant). While initially designed to explore novel prosthesis control strategies based on natural eye-hand and arm coordination, this dataset will also be useful to researchers interested in core sensorimotor control, humanoid robotics, human-robot interactions, as well as for the development and testing of associated solutions in gaze-guided computer vision.
Aggregating Residue-Level Protein Language Model Embeddings with Optimal Transport

Motivation Protein language models (PLMs) have emerged as powerful approaches for mapping protein sequences into informative embeddings suitable for a range of applications. PLMs, as well as many other protein representation schemes, generate per-token (i.e., per-residue) representations, leading to variable-sized outputs based on protein length. This variability presents a challenge for protein-level prediction tasks, which require uniform-sized embeddings for consistent analysis across different proteins. Prior work has typically resorted to average pooling to summarize token-level PLM outputs. It is, however, unclear if such an aggregation operation effectively prioritizes the relevant information across token-level representations. Results Addressing this, we introduce a novel method utilizing sliced-Wasserstein embeddings to convert variable-length PLM outputs into fixed-length protein-level representations. Inspired by the success of optimal transport techniques in representation learning, we first conceptualize per-token PLM outputs as samples from a probabilistic distribution. We then employ sliced-Wasserstein distances to map these samples against a learnable reference set, creating a Euclidean embedding in the output space. The resulting embedding is agnostic to the length of the input and represents the entire protein. Across a range of state-of-the-art pre-trained ESM-2 PLMs, with varying model sizes, we show the superiority of our method over average pooling for protein-drug and protein-protein interaction. Our aggregation scheme is especially effective when model size is constrained, enabling smaller-scale PLMs to match or exceed the performance of average-pooled larger-scale PLMs. Since using smaller models reduces computational resource requirements, our approach not only promises more accurate inference but can also help democratize access to foundation models. Availability and implementation The implementation code can be found at https://github.com/navid-naderi/PLM_SWE.
The proteome is a terminal electron acceptor

Microbial metabolism is impressively flexible, enabling growth even when available nutrients differ greatly from biomass in redox state. E. coli, for example, rearranges its physiology to grow on reduced and oxidized carbon sources through several forms of fermentation and respiration. To understand the limits on and evolutionary consequences of metabolic flexibility, we developed a mathematical model coupling redox chemistry with principles of cellular resource allocation. Our integrated model clarifies key phenomena, including demonstrating that autotrophs grow slower than heterotrophs because of constraints imposed by intracellular production of reduced carbon. Our model further indicates that growth is improved by adapting the redox state of biomass to nutrients, revealing an unexpected mode of evolution where proteins accumulate mutations benefiting organismal redox balance. One sentence summary Microbial proteins adapt their composition on physiological and evolutionary timescales to ensure organismal redox balance.
Efficient CRISPR genome editing and integrative genomic analyses reveal the mosaicism of Cas-induced mutations and pleiotropic effects of scarlet gene in an emerging model system

Despite the revolutionary impacts of CRISPR-Cas gene editing systems, the effective and widespread use of CRISPR technologies in emerging model organisms still faces significant challenges. These include the inefficiency in generating heritable mutations at the organismal level, limited knowledge about the genomic consequences of gene editing, and an inadequate understanding of the inheritance patterns of CRISPR-Cas-induced mutations. This study addresses these issues by 1) developing an efficient microinjection delivery method for CRISPR editing in the microcrustacean Daphnia pulex; 2) assessing the editing efficiency of Cas9 and Cas12a nucleases, examining mutation inheritance patterns, and analyzing the local and global mutation spectrum in the scarlet mutants; and 3) investigating the transcriptomes of scarlet mutants to understand the pleiotropic effects of scarlet underlying their swimming behavior changes. Our reengineered CRISPR microinjection method results in efficient biallelic editing with both nucleases. While indels are dominant in Cas-induced mutations, a few on-site large deletions (>1kb) are observed, most likely caused by microhomology-mediated end joining repair. Knock-in of a stop codon cassette to the scarlet locus was successful, despite complex induced mutations surrounding the target site. Moreover, extensive germline mosaicism exists in some mutants, which unexpectedly produce different phenotypes/genotypes in their asexual progenies. Lastly, our transcriptomic analyses unveil significant gene expression changes associated with scarlet knock-out and altered swimming behavior in mutants, including several genes (e.g., NMDA1, ABAT, CNTNAP2) involved in human neurodegenerative diseases. This study expands our understanding of the dynamics of gene editing in the tractable model organism Daphnia and highlights its promising potential as a neurological disease model.
popDMS infers mutation effects from deep mutational scanning data

Deep mutational scanning (DMS) experiments provide a powerful method to measure the functional effects of genetic mutations at massive scales. However, the data generated from these experiments can be difficult to analyze, with significant variation between experimental replicates. To overcome this challenge, we developed popDMS, a computational method based on population genetics theory, to infer the functional effects of mutations from DMS data. Through extensive tests, we found that the functional effects of single mutations and epistasis inferred by popDMS are highly consistent across replicates, comparing favorably with existing methods. Our approach is flexible and can be widely applied to DMS data that includes multiple time points, multiple replicates, and different experimental conditions.
Impact of inter-species hybridisation on antifungal drug response in the Saccharomyces genus

Antifungal drug resistance across fungal and yeast pathogens presents one of the major concerns for global public health. Understanding the interactions between genetic background and environment is important for the development of new, effective treatments of infections. Allelic variation within populations of Ascomycota as well as hybridisation impacts the phenotype in response to stressful conditions, including to antifungal drugs. We exploited recent advances in multigenerational breeding of Saccharomyces interspecies hybrids to study the impact of hybridisation on antifungal resistance and identify quantitative trait loci (QTL) responsible for the phenotypes observed. A library of Saccharomyces cerevisiae x S. kudriavzevii hybrid offspring was screened in the presence of sub-lethal concentrations of six antifungal drugs and revealed a broad phenotypic diversity across the progeny. QTL analysis was carried out comparing alleles between the pools of high and low fitness offspring, identifying hybrid-specific genetic regions involved in resistance to fluconazole, micafungin and flucytosine. We found both drug specific and pleiotropic regions, and through gene ontology and SIFT analysis we identify potential causal genes, such as BCK2 and DNF1 that were validated via reciprocal hemizygosity analysis. We highlight 41 regions that contain genes not previously associated with resistance phenotypes in the literature. The results of this screening will help identify new pathways contributing to drug resistance, and lead to greater understanding of how allelic variation, hybridisation and evolution affect antifungal drug resistance in yeast and fungi.
Les rayonnements UV-C : un moyen de lutte pour stimuler les défenses du fraisier et de la tomate en cours de culture et améliorer la qualité / conservation des fruits après récolte

Certains champignons sont tres dommageables pour les plantes mais aussi pour la conservation apres recolte des produits vegetaux. Les restrictions reglementaires concernant l’utilisation des fongicides necessitent de trouver des solutions alternatives. L'amelioration de la resistance des plantes en utilisant des methodes physiques, comme les rayonnements UV, peut presenter une alternative prometteuse en association avec d’autres methodes dans le cadre d’une protection integree des cultures. L'objectif de cette these a ete d’etudier l’effet des rayonnements UV-C sur la sensibilite des plantes aux agents pathogenes. Les rayonnements UV-C ont ete appliques durant la culture, seuls ou en combinaison a des agents de biocontrole, ou en post-recolte. Les experimentations ont ete menees sur deux especes vegetales : le fraisier et la tomate.Sur fraisier, des traitements UV-C a une dose de 1,70 kJ/m² entrainent une diminution systematique d'environ 20 % de la sensibilite des feuilles a Botrytis cinerea et diminuent jusqu’a 50 % le nombre de feuilles attaquees par Podosphaera aphanis, l’agent causal de l’oidium. Chez la tomate, la protection des feuilles contre B. cinerea atteint 43 % avec une dose d’UV-C cumulee de 4,0 kJ/m². Ces memes traitements UV-C appliques sur fruits reduisent la sensibilite des fraises vis-a-vis de Rhizopus de 75 % mais aucun effet n’est observe vis-a-vis de B. cinerea. Au contraire, sur fruits de tomate, la sensibilite est diminuee d'environ 63 % contre cet agent pathogene. Parallelement, des tests biochimiques et gustatifs suggerent que la qualite des fruits n’est pas significativement amelioree ni alteree par les expositions UV-C. Malgre un effet germicide marque des rayonnements UV-C sur feuilles de fraisiers, aucun effet benefique de l’application de ces rayonnements sur le niveau d’efficacite d’agents de lutte biologique n’a ete mis en evidence.Nos observations sont encourageantes pour envisager une utilisation de cette methode dans un schema de protection integree des cultures. Cependant, une comprehension claire de la facon dont les rayonnements UV-C sont percus par les plantes et traduits en mecanismes de defense est necessaire avant que leur utilisation ne soit recommandee sur le terrain.
In vitro Study of Topical Antiseptics Used to Treat Mycological Gill Rot Disease in Cyprinus carpio

Antiseptics are widely used in fish diseases to control the growth of fungal on living tissues (External body surface and Gills). The current study included the antifungal effects of antiseptics (Malachite green 5mg/l, Methylene blue 10mg /l, Potassium permanganate 20 ppm, NaCl 5% , Quaternary ammonium 0.5 ml/l, Copper sulfate 0. 5 mg/l, Formalin 250 ppm and Povidone iodine 100mg/l) against Branchiomyces sanguinis, where several laboratory tests were used to evaluated the antifungal activity of antiseptics that used in the this study include Minimum inhibitory concentration, Spore growth test, Radial growth assay, Agar-well diffusion method of sensitive test. The results showed that Malachite green, Copper sulfate , Quaternary ammonium and Formalin were highly effectiveness against Branchiomyces sanguinis, while the Methylene blue, Potassium permanganate, NaCl and Povidone iodine were least effective in comparison with other antiseptics used in this study.