14 Examples of How LLMs Can Transform Materials Science and Chemistry: A Reflection on a Large Language Model Hackathon

Large-language models (LLMs) such as GPT-4 caught the interest of many scientists. Recent studies suggested that these models could be useful in chemistry and materials science. To explore these possibilities, we organized a hackathon. This article chronicles the projects built as part of this hackathon. Participants employed LLMs for various applications, including predicting properties of molecules and materials, designing novel interfaces for tools, extracting knowledge from unstructured data, and developing new educational applications. The diverse topics and the fact that working prototypes could be generated in less than two days highlight that LLMs will profoundly impact the future of our fields. The rich collection of ideas and projects also indicates that the applications of LLMs are not limited to materials science and chemistry but offer potential benefits to a wide range of scientific disciplines

The fascial connections of the pectineal ligament

In clinical settings, the pectineal ligament forms a basic landmark for surgical approaches. However, to date, the detailed fascial topography of this ligament is not well understood. The aim of this study was to describe the morphology of the pectineal ligament including its fascial connections to surrounding structures. The spatial–topographical relations of 10 fresh and embalmed specimens were dissected, stained, slice plastinated, and analyzed macroscopically, and in three cases histological approaches were also used. The pectineal ligament is attached ventrally and superiorly to the pectineus muscle, connected to the inguinal ligament by the lacunar ligament and to the tendinous origin of rectus abdominis muscle and the iliopubic tract. It forms a site of origin for the internal obturator muscle, and throughout its curved course, the ligament attaches to both the fasciae of iliopsoas and the internal obturator muscle. However, dorsally, these fasciae pass free from the bone, while the pectineal ligament itself is adhered to it. The organ fasciae are seen apart from the pectineal ligament and its connections. The pectineal ligament seems to form a connective tissue junction between the anterior and medial compartment of the thigh. This ligament, however, is free to other compartments arisen from the embryonal gut and to the urogenital ridge. These features of the pectineal ligament are important to consider during orthopedic and trauma surgical approaches, in gynecology, hernia and incontinence surgery, and in operations for pelvic floor and neovaginal reconstruction

The protein inhibitor of neuronal nitric oxide synthase (PIN): characterization of its action on pure nitric oxide synthases

AbstractNeuronal NO synthase (nNOS) was discovered recently to interact specifically with the protein PIN (protein inhibitor of nNOS) [Jaffrey, S.R. and Snyder, S.H. (1996) Science 274, 774–777]. We have studied the effects on pure NOS enzymes of the same GST-tagged PIN used in the original paper. Unexpectedly, all NOS isoenzymes were inhibited. The IC50 for nNOS was 18±6 μM GST-PIN with 63 nM nNOS after 30 min at 37°C. Uncoupled NADPH oxidation was inhibited similarly, whereas cytochrome c reductase activity, the KM for l-arginine, and dimerization were unaffected. We reconsider the physiological role of PIN in the light of these results

On the interplay between microstructure, residual stress and fracture toughness of (Hf-Nb-Ta-Zr)C multi-metal carbide hard coatings

The development of sputtered coatings with improved hardness-toughness property combination is widely sought after. Multi-element ceramic carbide (Hf-Nb-Ta-Zr)C coatings with excess carbon, synthesized by DC co-sputtering is presented in this study as a promising candidate to achieve this objective. The specific roles of microstructure and residual stress are decoupled in order to understand their influence on the mechanical properties. Extensive mechanical characterization through in situ testing of focused ion beam fabricated microcantilevers and nanoindentation based approaches are adopted to quantitatively separate the effect of residual stresses on the fracture toughness of the (Hf-Nb-Ta-Zr)C coatings. Residual stress free, microcantilever testing in notched and unnotched conditions, in combination with microstructural characterization unambiguously reveals the intrinsic mechanical behavior of coatings, which solely depend on the microstructure. On the other hand, nanoindentation based testing techniques probe the influence of residual stress and microstructure on the measured mechanical properties. The segregation and thickening of carbon-rich clusters, especially to the grain boundaries with increasing deposition temperatures is speculated to lead to substantial degradation in all mechanical properties measured. An easier fracture path through grain boundaries leads to a reduction in fracture resistance, which is possibly related to carbon enrichment

Energy Metabolites as Biomarkers in Ischemic and Dilated Cardiomyopathy

With more than 25 million people affected, heart failure (HF) is a global threat. As energy production pathways are known to play a pivotal role in HF, we sought here to identify key metabolic changes in ischemic- and non-ischemic HF by using a multi-OMICS approach. Serum metabolites and mRNAseq and epigenetic DNA methylation profiles were analyzed from blood and left ventricular heart biopsy specimens of the same individuals. In total we collected serum from n = 82 patients with Dilated Cardiomyopathy (DCM) and n = 51 controls in the screening stage. We identified several metabolites involved in glycolysis and citric acid cycle to be elevated up to 5.7-fold in DCM (p = 1.7 × 10−6 ). Interestingly, cardiac mRNA and epigenetic changes of genes encoding rate-limiting enzymes of these pathways could also be found and validated in our second stage of metabolite assessment in n = 52 DCM, n = 39 ischemic HF and n = 57 controls. In conclusion, we identified a new set of metabolomic biomarkers for HF. We were able to identify underlying biological cascades that potentially represent suitable intervention targets

Polygenic architecture of human neuroanatomical diversity

International audienceWe analyzed the genomic architecture of neuroanatomical diversity using magnetic resonance imaging and single nucleotide polymorphism (SNP) data from >26 000 individuals from the UK Biobank project and 5 other projects that had previously participated in the ENIGMA (Enhancing NeuroImaging Genetics through Meta-Analysis) consortium. Our results confirm the polygenic architecture of neuroanatomical diversity, with SNPs capturing from 40% to 54% of regional brain volume variance. Chromosomal length correlated with the amount of phenotypic variance captured, r ~ 0.64 on average, suggesting that at a global scale causal variants are homogeneously distributed across the genome. At a local scale, SNPs within genes (~51%) captured ~1.5 times more genetic variance than the rest, and SNPs with low minor allele frequency (MAF) captured less variance than the rest: the 40% of SNPs with MAF <5% captured <one fourth of the genetic variance. We also observed extensive pleiotropy across regions, with an average genetic correlation of rG ~ 0.45. Genetic correlations were similar to phenotypic and environmental correlations; however, genetic correlations were often larger than phenotypic correlations for the left/right volumes of the same region. The heritability of differences in left/right volumes was generally not statistically significant, suggesting an important influence of environmental causes in the variability of brain asymmetry. Our code is available at https://github.com/neuroanatomy/genomic-architecture

A whole-blood transcriptome meta-analysis identifies gene expression signatures of cigarette smoking

Cigarette smoking is a leading modifiable cause of death worldwide. We hypothesized that cigarette smoking induces extensive transcriptomic changes that lead to target-organ damage and smoking-related diseases. We performed a metaanalysis of transcriptome-wide gene expression using whole blood-derived RNA from 10,233 participants of European ancestry in six cohorts (including 1421 current and 3955 former smokers) to identify associations between smoking and altered gene expression levels. At a false discovery rate (FDR) < 0.1, we identified 1270 differentially expressed genes in current vs. never smokers, and 39 genes in former vs. never smokers. Expression levels of 12 genes remained elevated up to 30 years after smoking cessation, suggesting that the molecular consequence of smoking may persist for decades. Gene ontology analysis revealed enrichment of smoking-related genes for activation of platelets and lymphocytes, immune response, and apoptosis. Many of the top smoking-related differentially expressed genes, including LRRN3 and GPR15, have DNA methylation loci in promoter regions that were recently reported to be hypomethylated among smokers. By linking differential gene expression with smoking-related disease phenotypes, we demonstrated that stroke and pulmonary function show enrichment for smoking-related gene expression signatures. Mediation analysis revealed the expression of several genes (e.g. ALAS2) to be putative mediators of the associations between smoking and inflammatory biomarkers (IL6 and C-re