KaMRaT: a C++ toolkit for k-mer count matrix dimension reduction.

MOTIVATION: KaMRaT is designed for processing large k-mer count tables derived from multi-sample, RNA-seq data. Its primary objective is to identify condition-specific or differentially expressed sequences, regardless of gene or transcript annotation. RESULTS: KaMRaT is implemented in C++. Major functions include scoring k-mers based on count statistics, merging overlapping k-mers into contigs and selecting k-mers based on their occurrence across specific samples. AVAILABILITY AND IMPLEMENTATION: Source code and documentation are available via https://github.com/Transipedia/KaMRaT.

Primary hypocholesterolemia is associated with an increased risk of hepatic complications in the general population.

BACKGROUND & AIMS: Beyond cardiovascular disease protection, the health consequences of very low concentrations of low-density lipoprotein-cholesterol (LDL-C) remain a matter of debate. In primary hypobetalipoproteinemia (HBL), liver steatosis and cirrhosis have occasionally been reported. Here, we aimed to investigate the association between HBL and the risk of hepatic complications (cirrhosis complications and/or primary liver cancer) in the general population. METHODS: A cohort study was conducted in the French population-based cohort CONSTANCES. Participants with primary HBL (LDL-C <5th percentile for age and sex, [HBL]) were compared with those with normal LDL-C concentrations (40th-60th percentile, [Control]). Participants on lipid-lowering therapies were excluded. For hepatic complications, follow-up events were compared by calculating the incidence density ratio (IDR). The same analyses were replicated in the UK Biobank (UKBB) cohort. RESULTS: In the CONSTANCES and UKBB cohorts, 34,653 and 94,666 patients were analyzed, with median ages of 45 and 56 years, mean LDL-C concentrations (HBL vs. control) of 71 vs. 128 mg/dl and 86 vs. 142 mg/dl, and mean follow-up durations of 5.0 and 11.5 years, respectively. The HBL group presented a higher incidence of hepatic complications than the control group: 0.32/ vs. 0.07/1,000 person-years (IDR = 4.50, 95% CI 1.91-10.6) in CONSTANCES, and 0.69/ vs. 0.21/1,000 person-years (IDR = 3.27, 95% CI 2.63-4.06) in the UKBB. This risk proved to be independent of classic risk factors for liver disease (obesity, alcohol consumption, diabetes, viral hepatitis), including in a 5-year landmark analysis excluding early events. Sensitivity analyses based on apoliprotein-B levels (instead of LDL-C levels) or genetically defined HBL showed similar results. CONCLUSIONS: HBL is associated with a markedly increased risk of hepatic complications. HBL must be considered as a substantial independent risk factor for liver diseases which justifies specific prevention and screening. IMPACT AND IMPLICATIONS: Hypobetalipoproteinemia (HBL) is a lipid disorder characterized by permanent, inherited low levels (below the 5th percentile) of low-density lipoprotein-cholesterol. While HBL is associated with a lower risk of cardiovascular events, some studies suggest that it may be associated with a potential risk of hepatic steatosis and hepatic complications. Here, we studied the association between HBL and hepatic complications (defined as cirrhosis complications and/or primary liver cancer) in two populations of several hundred thousand people, both in France (CONSTANCES cohort) and the United Kingdom (UKBB). The results show that HBL is associated with a significant and independent excess risk of hepatic complications, including primary liver cancer. Thus, in people with HBL, the value of regular liver monitoring must be studied.

Integrative Pan-Cancer Genomic and Transcriptomic Analyses of Refractory Metastatic Cancer.

Metastatic relapse after treatment is the leading cause of cancer mortality, and known resistance mechanisms are missing for most treatments administered to patients. To bridge this gap, we analyze a pan-cancer cohort (META-PRISM) of 1,031 refractory metastatic tumors profiled via whole-exome and transcriptome sequencing. META-PRISM tumors, particularly prostate, bladder, and pancreatic types, displayed the most transformed genomes compared with primary untreated tumors. Standard-of-care resistance biomarkers were identified only in lung and colon cancers-9.6% of META-PRISM tumors, indicating that too few resistance mechanisms have received clinical validation. In contrast, we verified the enrichment of multiple investigational and hypothetical resistance mechanisms in treated compared with nontreated patients, thereby confirming their putative role in treatment resistance. Additionally, we demonstrated that molecular markers improve 6-month survival prediction, particularly in patients with advanced breast cancer. Our analysis establishes the utility of the META-PRISM cohort for investigating resistance mechanisms and performing predictive analyses in cancer. SIGNIFICANCE: This study highlights the paucity of standard-of-care markers that explain treatment resistance and the promise of investigational and hypothetical markers awaiting further validation. It also demonstrates the utility of molecular profiling in advanced-stage cancers, particularly breast cancer, to improve the survival prediction and assess eligibility to phase I clinical trials. This article is highlighted in the In This Issue feature, p. 1027.

Understanding the rheology of nanocontacts.

Mechanical stiffness, as opposed to softness, is a fundamental property of solids. Its persistence or rheological evolution in vibrating solid-solid nanocontacts is important in physics, materials science and technology. A puzzling apparent liquefaction under oscillatory strain, totally unexpected at room temperature, was suggested by recent experiments on solid gold nano-junctions. Here we show theoretically that realistically simulated nanocontacts actually remain crystalline even under large oscillatory strains. Tensile and compressive slips, respectively of "necking" and "bellying" types, do take place, but recover reversibly even during fast oscillatory cycles. We also show that, counterintuitively, the residual stress remains tensile after both slips, driving the averaged stiffness from positive to negative, thus superficially mimicking a liquid's. Unlike a liquid, however, rheological softening occurs by stick-slip, predicting largely frequency independent stiffness with violent noise in stress and conductance, properties compatible with experiments. The baffling large amplitude rheology of gold nanocontacts and its consequences should apply, with different parameters, to many other metals.

Multiscale Characterization of the Influence of the Organic-Inorganic Interface on the Dielectric Breakdown of Nanocomposites.

Nanoscale engineered materials such as nanocomposites can display or be designed to enhance their material properties through control of the internal interfaces. Here, we unveil the nanoscale origin and important characteristics of the enhanced dielectric breakdown capabilities of gold nanoparticle/polymer nanocomposites. Our multiscale approach spans from the study of a single chemically designed organic/inorganic interface to micrometer-thick films. At the nanoscale, we relate the improved breakdown strength to the interfacial charge retention capability by combining scanning probe measurements and density functional theory calculations. At the meso- and macroscales, our findings highlight the relevance of the nanoparticle concentration and distribution in determining and enhancing the dielectric properties, as well as identifying this as a crucial limiting factor for the achievable sample size.

The contribution of uncharted RNA sequences to tumor identity in lung adenocarcinoma.

The identity of cancer cells is defined by the interplay between genetic, epigenetic transcriptional and post-transcriptional variation. A lot of this variation is present in RNA-seq data and can be captured at once using reference-free, k-mer analysis. An important issue with k-mer analysis, however, is the difficulty of distinguishing signal from noise. Here, we use two independent lung adenocarcinoma datasets to identify all reproducible events at the k-mer level, in a tumor versus normal setting. We find reproducible events in many different locations (introns, intergenic, repeats) and forms (spliced, polyadenylated, chimeric etc.). We systematically analyze events that are ignored in conventional transcriptomics and assess their value as biomarkers and for tumor classification, survival prediction, neoantigen prediction and correlation with the immune microenvironment. We find that unannotated lincRNAs, novel splice variants, endogenous HERV, Line1 and Alu repeats and bacterial RNAs each contribute to different, important aspects of tumor identity. We argue that differential RNA-seq analysis of tumor/normal sample collections would benefit from this type k-mer analysis to cast a wider net on important cancer-related events. The code is available at https://github.com/Transipedia/dekupl-lung-cancer-inter-cohort.

Amplitude nanofriction spectroscopy.

Atomic scale friction, an indispensable element of nanotechnology, requires a direct access to, under actual growing shear stress, its successive live phases: from static pinning, to depinning and transient evolution, eventually ushering in steady state kinetic friction. Standard tip-based atomic force microscopy generally addresses the steady state, but the prior intermediate steps are much less explored. Here we present an experimental and simulation approach, where an oscillatory shear force of increasing amplitude leads to a one-shot investigation of all these successive aspects. Demonstration with controlled gold nanocontacts sliding on graphite uncovers phenomena that bridge the gap between initial depinning and large speed sliding, of potential relevance for atomic scale time and magnitude dependent rheology.

Atomic rheology of gold nanojunctions.

Despite extensive investigations of dissipation and deformation processes in micro- and nano-sized metallic samples1-7, the mechanisms at play during the deformation of systems with ultimate (molecular) size remain unknown. Although metallic nanojunctions, which are obtained by stretching metallic wires down to the atomic level, are typically used to explore atomic-scale contacts5,8-11, it has not been possible until now to determine the full equilibrium and non-equilibrium rheological flow properties of matter at such scales. Here, by using an atomic-force microscope equipped with a quartz tuning fork, we combine electrical and rheological measurements on ångström-size gold junctions to study the non-linear rheology of this model atomic system. By subjecting the junction to increasing subnanometric deformations we observe a transition from a purely elastic regime to a plastic one, and eventually to a viscous-like fluidized regime, similar to the rheology of soft yielding materials12-14, although orders of magnitude different in length scale. The fluidized state furthermore exhibits capillary attraction, as expected for liquid capillary bridges. This shear fluidization cannot be captured by classical models of friction between atomic planes15,16 and points to an unexpected dissipative behaviour of defect-free metallic junctions at ultimate scales. Atomic rheology is therefore a powerful tool that can be used to probe the structural reorganization of atomic contacts.

MicroMegascope based dynamic surface force apparatus.

Surface force apparatus (SFA) allows accurate resolving of the interfacial properties of fluids confined between extended surfaces. The accuracy of the SFA makes it an ubiquitous tool for the nanoscale mechanical characterization of soft matter systems. The SFA traditionally measures force-distance profiles through interferometry with subnanometric distance precision. However, these techniques often require a dedicated and technically demanding experimental setup, and there remains a need for versatile and simple force-distance measurement tools. Here we present a MicroMegascope based dynamic SFA capable of accurate measurement of the dynamic force profile of a liquid confined between a millimetric sphere and a planar substrate. Normal and shear mechanical impedance is measured within the classical frequency modulation framework. We measure rheological and frictional properties from micrometric to molecular confinement. We also highlight the resolution of small interfacial features such as ionic liquid layering. This apparatus shows promise as a versatile force-distance measurement device for exotic surfaces or extreme environments.