Beyond generative models: superfast traversal, optimization, novelty, exploration and discovery (STONED) algorithm for molecules using SELFIES

Inverse design allows the generation of molecules with desirable physical quantities using property optimization. Deep generative models have recently been applied to tackle inverse design, as they possess the ability to optimize molecular properties directly through structure modification using gradients. While the ability to carry out direct property optimizations is promising, the use of generative deep learning models to solve practical problems requires large amounts of data and is very time-consuming. In this work, we propose STONED - a simple and efficient algorithm to perform interpolation and exploration in the chemical space, comparable to deep generative models. STONED bypasses the need for large amounts of data and training times by using string modifications in the SELFIES molecular representation. First, we achieve non-trivial performance on typical benchmarks for generative models without any training. Additionally, we demonstrate applications in high-throughput virtual screening for the design of drugs, photovoltaics, and the construction of chemical paths, allowing for both property and structure-based interpolation in the chemical space. Overall, we anticipate our results to be a stepping stone for developing more sophisticated inverse design models and benchmarking tools, ultimately helping generative models achieve wider adoption

Growth curves of sorghum roots via quantile regression with P-splines

Plant roots are a major pool of total carbon in the planet and their dynamics are directly relevant to greenhouse gas balance. Composted wastes are increasingly used in agriculture for environmental and economic reasons and their role as a substitute for traditional fertilizers needs to be tested on all plant components. Here we propose a regression quantile approach based on P-splines to assess, quantify and compare the root growth patterns in two treatment groups respectively undergoing compost and traditional fertilization

Revealing the coral habitat effect on benthopelagic fauna diversity in the Santa Maria di Leuca cold-water coral province using different devices and Bayesian hierarchical modelling

Data from two experimental longline surveys and two video inspections carried out in Santa Maria di Leuca cold-water coral province (Mediterranean Sea) during spring-autumn 2010 were used in order to compare the benthopelagic abundance and diversity between coral and non-coral habitats and between different devices. The sampling was carried out in two types of habitat: a coral habitat with carbonate mounds and a non-coral habitat characterized by intermound sea floor. A Bayesian hierarchical modelling approach to accommodate factors influencing community assemblages was used considering the number of species, the Shannon-Wiener diversity index and the two most abundant species represented by the European conger (Conger conger) and blackbelly rosefish (Helicolenus dactylopterus). A relevant effect of the habitat factor was observed for both the number of species and the diversity index, showing a higher species number and diversity index in the coral habitat than in the non-coral habitat. Concerning the relevance of fixed effects from the model on the probability of observing non-zero (positive) abundances, the devices considered, longline and baited lander, did not show different influence for either C. conger or H. dactylopterus. In the case of positive abundance, a relevant device effect was only observed for H. dactylopterus, showing higher abundances for longline than for baited lander. A habitat effect was detected, with positive abundances for both species in the coral habitat. This study proves that structurally complex habitats generated by cold-water corals influence the distribution and diversity of the benthopelagic fauna, and that the use of different devices can provide complementary useful results. Increased knowledge about the role of cold-water corals in the associated benthopelagic fauna could lead to better conservation of one of the most important hot spots of biodiversity in the Mediterranean Sea

The Hay Wells Syndrome-Derived TAp63aQ540L Mutant has Impaired Transcriptional and Cell Growth Regulatory Activity

p63 mutations have been associated with several human hereditary disorders characterized by ectodermal dysplasia such as EEC (ectrodactyly, ectodermal dysplasia, clefting) syndrome, ADULT (acro, dermato, ungual, lacrimal, tooth) syndrome and AEC (ankyloblepharon, ectodermal dysplasia, clefting) syndrome (also called Hay-Wells syndrome). The location and functional effects of the mutations that underlie these syndromes reveal a striking genotype-phenotype correlation. Unlike EEC and ADULT that result from missense mutations in the DNA-binding domain of p63, AEC is solely caused by missense mutations in the SAM domain of p63. In this paper we report a study on the TAp63alpha isoform, the first to be expressed during development of the embryonic epithelia, and on its naturally occurring Q540L mutant derived from an AEC patient. To assess the effects of the Q540L mutation, we generated stable cell lines expressing TAp63alpha wt, DeltaNp63alpha or the TAp63alpha-Q540L mutant protein and used them to systematically compare the cell growth regulatory activity of the mutant and wt p63 proteins and to generate, by microarray analysis, a comprehensive profile of differential gene expression. We found that the Q540L substitution impairs thetranscriptional activity of TAp63alpha and causes misregulation of genes involved in the control of cell growth and epidermal differentiation

A Regulatory Mechanism Involving TBP-1/Tat-Binding Protein 1 and Akt/PKB in the Control of Cell Proliferation

TBP-1 /Tat-Binding Protein 1 (also named Rpt-5, S6a or PSMC3) is a multifunctional protein, originally identified as a regulator of HIV-1-Tat mediated transcription. It is an AAA-ATPase component of the 19S regulative subunit of the proteasome and, as other members of this protein family, fulfils different cellular functions including proteolysis and transcriptional regulation. We and others reported that over expression of TBP-1 diminishes cell proliferation in different cellular contexts with mechanisms yet to be defined. Accordingly, we demonstrated that TBP-1 binds to and stabilizes the p14ARF oncosuppressor increasing its anti-oncogenic functions. However, TBP-1 restrains cell proliferation also in the absence of ARF, raising the question of what are the molecular pathways involved. Herein we demonstrate that stable knock-down of TBP-1 in human immortalized fibroblasts increases cell proliferation, migration and resistance to apoptosis induced by serum deprivation. We observe that TBP-1 silencing causes activation of the Akt/PKB kinase and that in turn TBP-1, itself, is a downstream target of Akt/PKB. Moreover, MDM2, a known Akt target, plays a major role in this regulation. Altogether, our data suggest the existence of a negative feedback loop involving Akt/PKB that might act as a sensor to modulate TBP-1 levels in proliferating cells

HER2 expression as a potential marker for response to therapy targeted to the EGFR

Since human epidermal growth factor receptor 2 (HER2) is known to participate with the epidermal growth factor receptor (EGFR) in mitogenic signalling, we hypothesised that HER2 overexpression might indicate responsiveness to EGFR targeted therapies. MCF7 breast cancer cells transfected with the HER2 gene were subcloned to establish a set of genetically related cell lines expressing graded levels of HER2 by immunoblot analysis. The subcloned cell lines and parental MCF7 cells were characterised by their growth characteristics, and cell by cell patterns of EGFR, HER2 and HER3 expression as well as levels of phosphorylated mitogen-activated protein kinase (MAPK) and AKT by laser scanning cytometry (LSC). Growth inhibition assays were used to characterise response to EGFR targeted therapy, and to determine the relationship between therapeutic response and levels of tyrosine kinase expression. The levels of growth inhibition of AG1478 and of the AG1478-trastuzumab combinations were correlated with levels of HER2 expression among the different cell lines. Among EGFR, HER2 and HER3, HER2 overexpression was the best single predictive marker, but combinations of two markers provided additional predictive information

Deficit of social cognition in subjects with surgically treated frontal lobe lesions and in subjects affected by schizophrenia

The ability of humans to predict and explain other people’s behaviour by attributing independent mental states such as desires and beliefs to them, is considered to be due to our ability to construct a “Theory of Mind”. Recently, several neuroimaging studies have implicated the medial frontal lobes as playing a critical role in a dedicated “mentalizing” or “Theory of Mind” network in the human brain. In this study we compare the performance of patients with right and left medial prefrontal lobe lesions in theory of mind and in social cognition tasks, with the performance of people with schizophrenia. We report a similar social cognitive profile between patients with prefrontal lobe lesions and schizophrenic subjects in terms of understanding of false beliefs, in understanding social situations and in using tactical strategies. These findings are relevant for the functional anatomy of “Theory of Mind”