DrugMap: A quantitative pan-cancer analysis of cysteine ligandability.

Cysteine-focused chemical proteomic platforms have accelerated the clinical development of covalent inhibitors for a wide range of targets in cancer. However, how different oncogenic contexts influence cysteine targeting remains unknown. To address this question, we have developed "DrugMap," an atlas of cysteine ligandability compiled across 416 cancer cell lines. We unexpectedly find that cysteine ligandability varies across cancer cell lines, and we attribute this to differences in cellular redox states, protein conformational changes, and genetic mutations. Leveraging these findings, we identify actionable cysteines in NF-κB1 and SOX10 and develop corresponding covalent ligands that block the activity of these transcription factors. We demonstrate that the NF-κB1 probe blocks DNA binding, whereas the SOX10 ligand increases SOX10-SOX10 interactions and disrupts melanoma transcriptional signaling. Our findings reveal heterogeneity in cysteine ligandability across cancers, pinpoint cell-intrinsic features driving cysteine targeting, and illustrate the use of covalent probes to disrupt oncogenic transcription-factor activity.

Common and rare variant associations with clonal haematopoiesis phenotypes.

Clonal haematopoiesis involves the expansion of certain blood cell lineages and has been associated with ageing and adverse health outcomes1-5. Here we use exome sequence data on 628,388 individuals to identify 40,208 carriers of clonal haematopoiesis of indeterminate potential (CHIP). Using genome-wide and exome-wide association analyses, we identify 24 loci (21 of which are novel) where germline genetic variation influences predisposition to CHIP, including missense variants in the lymphocytic antigen coding gene LY75, which are associated with reduced incidence of CHIP. We also identify novel rare variant associations with clonal haematopoiesis and telomere length. Analysis of 5,041 health traits from the UK Biobank (UKB) found relationships between CHIP and severe COVID-19 outcomes, cardiovascular disease, haematologic traits, malignancy, smoking, obesity, infection and all-cause mortality. Longitudinal and Mendelian randomization analyses revealed that CHIP is associated with solid cancers, including non-melanoma skin cancer and lung cancer, and that CHIP linked to DNMT3A is associated with the subsequent development of myeloid but not lymphoid leukaemias. Additionally, contrary to previous findings from the initial 50,000 UKB exomes6, our results in the full sample do not support a role for IL-6 inhibition in reducing the risk of cardiovascular disease among CHIP carriers. Our findings demonstrate that CHIP represents a complex set of heterogeneous phenotypes with shared and unique germline genetic causes and varied clinical implications.

Genomic signature of Fanconi anaemia DNA repair pathway deficiency in cancer.

Fanconi anaemia (FA), a model syndrome of genome instability, is caused by a deficiency in DNA interstrand crosslink repair resulting in chromosome breakage1-3. The FA repair pathway protects against endogenous and exogenous carcinogenic aldehydes4-7. Individuals with FA are hundreds to thousands fold more likely to develop head and neck (HNSCC), oesophageal and anogenital squamous cell carcinomas8 (SCCs). Molecular studies of SCCs from individuals with FA (FA SCCs) are limited, and it is unclear how FA SCCs relate to sporadic HNSCCs primarily driven by tobacco and alcohol exposure or infection with human papillomavirus9 (HPV). Here, by sequencing genomes and exomes of FA SCCs, we demonstrate that the primary genomic signature of FA repair deficiency is the presence of high numbers of structural variants. Structural variants are enriched for small deletions, unbalanced translocations and fold-back inversions, and are often connected, thereby forming complex rearrangements. They arise in the context of TP53 loss, but not in the context of HPV infection, and lead to somatic copy-number alterations of HNSCC driver genes. We further show that FA pathway deficiency may lead to epithelial-to-mesenchymal transition and enhanced keratinocyte-intrinsic inflammatory signalling, which would contribute to the aggressive nature of FA SCCs. We propose that the genomic instability in sporadic HPV-negative HNSCC may arise as a result of the FA repair pathway being overwhelmed by DNA interstrand crosslink damage caused by alcohol and tobacco-derived aldehydes, making FA SCC a powerful model to study tumorigenesis resulting from DNA-crosslinking damage.

Controlling the Collision Type and Frequency of Single Pt Nanoparticles at Chemically Modified Gold Electrodes.

Studying the electrochemical response of single nanoparticles at an electrode surface gives insight into the dynamic and stochastic processes that occur at the electrode interface. Herein, we investigated single platinum nanoparticle collision dynamics and type (elastic vs inelastic) at gold electrode surfaces modified with self-assembled monolayers (SAMs) of varying terminal chemistries. Collision events are measured via the faradaic current from catalytic reactions at the Pt surface. By changing the terminal, solution-facing group of a thiolate monolayer, we observed the effect of hydrophobicity at the solution-electrode interface on single-particle collisions by employing either a hydrophobic -CH3 terminal group (1-hexanethiol), a hydrophilic -OH terminal group (6-mercaptohexanol), or an equimolar mixture of the two. Changes in the terminal group lead to alterations in collision-induced current magnitude, collisional frequency, and the distinct shape of the collision event current transient. The effects of the terminal group of the SAM were probed by measuring quantitative differences in the events monitored through both the hydrogen evolution reaction (HER) and hydrazine oxidation. In both cases, a platinum nanoparticle (PtNP) favors adsorption to bare and hydrophilic surfaces but demonstrates elastic collision behavior when it collides with a hydrophobic surface. In the case of a mixed monolayer, distinct characteristics of hydrophobic and hydrophilic surfaces are observed. We report how single nanoparticle collisions can reveal nanoscale surface heterogeneity and can be used to manipulate the nature of single-particle interactions on an electrode surface by functionalized self-assembled monolayers.

Single Voltammetric Sweep Calibration-Free Interrogation of Electrochemical Aptamer-Based Sensors Employing Continuous Square Wave Voltammetry.

Continuous square wave voltammetry (cSWV) is a technique that enables the continuous collection of current data (at 100 kHz) to maximize the information content obtainable from a single voltammetric sweep. This data collection procedure results in the generation of multiple voltammograms corresponding to different effective square wave frequencies. The application of cSWV brings significant benefits to electrochemical aptamer-based (E-AB) sensors. The E-AB sensor platform permits continuous real-time monitoring of small biological molecules. Traditionally, E-AB sensors report only on changes in analyte concentration rather than absolute quantification in matrices when basal concentrations are not known a priori. This is because they exhibit a voltammetric peak current even in the absence of a target. However, using a dual-frequency approach, calibration-free sensing can be performed effectively, eliminating the sensor-to-sensor variation by taking ratiometric current responses obtained at two different frequencies from two different voltammetric sweeps. In employing our approach, cSWV provides a great advantage over the conventionally used square wave voltammetry since the required voltammograms are collected with a single sweep, which improves the temporal resolution of the measurement when considering the current at multiple frequencies for improved accuracy and reduced surface interrogation. Moreover, we show here that using cSWV provides significantly improved concentration predictions. E-AB sensors sensitive to ATP and tobramycin were interrogated across a wide range of concentrations. With this approach, cSWV allowed us to estimate the target concentration, retaining up to an ±5% error of the expected concentration when tested in buffer and complex media.

Utilization of Spontaneous Alkyne-Gold Self-Assembly Chemistry as an Alternative Method for Fabricating Electrochemical Aptamer-Based Sensors.

Electrochemical aptamer-based (E-AB) sensors are a promising class of biosensors which use structure-switching redox-labeled oligonucleotides (aptamers) codeposited with passivating alkanethiol monolayers on electrode surfaces to specifically bind and detect target analytes. Signaling in E-AB sensors is an outcome of aptamer conformational changes upon target binding, with the sequence of the aptamer imparting specificity toward the analyte of interest. The change in conformation translates to a change in electron transfer between the redox label attached to the aptamer and the underlying electrode and is related to analyte concentration, allowing specific electrochemical detection of nonelectroactive analytes. E-AB sensor measurements are reagentless with time resolutions of seconds or less and may be miniaturized into the submicron range. Traditionally these sensors are fabricated using thiol-on-gold chemistry. Here we present an alternate immobilization chemistry, gold-alkyne binding, which results in an increase in sensor lifetimes under ideal conditions by up to ∼100%. We find that gold-alkyne binding is spontaneous and supports efficient E-AB sensor signaling with analytical performance characteristics similar to those of thiol generated monolayers. The surface modification differs from gold-thiol binding only in the time and aptamer concentration required to achieve similar aptamer surface coverages. In addition, alkynated aptamers differ from their thiolated analogues only by their chemical handle for surface attachment, so any existing aptamers can be easily adapted to utilize this attachment strategy.

Tuning the Probe-Bilayer Architecture of Silver Nanoneedle-based Ion Channel Probes.

Ion channel probes, as one of the ion channel platforms, provide an appealing opportunity to perform localized detection with a high precision level. These probes come basically in two classes: glass and metal. While the glass-based probes showed the potential to be employed for molecular sensing and chemical imaging, these probes still suffer from limited resolution and lack of control over protein insertion. On the other hand, metal-based nanoneedle probes (gold and silver) have been recently developed to allow reducing probe dimensions to the nanoscale geometry. More specifically, silver probes are preferable owing to their ability to mitigate the channel current decay observed with gold probes and provide a stable DC channel current. However, there are still some challenges related to the probe design and bilayer curvature that render such probes insensitive to small changes in the tip-substrate distance. Herein, we introduce two main pathways to control the probe-bilayer architecture; the first is by altering the probe shape and geometry during the fabrication process of silver probes. The second pathway is by altering the surface characteristics of the silver probe via an electrophoretic deposition process. Our findings reveal that varying the electrochemical etching parameters results in different probe geometries and producing sharper tips with a 2-fold diameter reduction. In addition, the electrophoretic deposition of a cathodic paint on the silver nanoneedle surface led to a miniaturized exposed silver tip that enables the formation of a confined bilayer. We further investigated the characteristics of bilayers supported on both the sharper nanoneedles and the HSR-coated silver probes produced by controlling the etching conditions and electrodeposition process, respectively. We believe this work paves the way to rationally design silver nanoneedle ion channel probes, which are well suited for localized molecular sensing and chemical imaging.

Do DNA Double-Strand Breaks Drive Aging?

DNA double-strand breaks (DSBs) are rare, but highly toxic, lesions requiring orchestrated and conserved machinery to prevent adverse consequences, such as cell death and cancer-causing genome structural mutations. DSBs trigger the DNA damage response (DDR) that directs a cell to repair the break, undergo apoptosis, or become senescent. There is increasing evidence that the various endpoints of DSB processing by different cells and tissues are part of the aging phenotype, with each stage of the DDR associated with specific aging pathologies. In this Perspective, we discuss the possibility that DSBs are major drivers of intrinsic aging, highlighting the dynamics of spontaneous DSBs in relation to aging, the distinct age-related pathologies induced by DSBs, and the segmental progeroid phenotypes in humans and mice with genetic defects in DSB repair. A model is presented as to how DSBs could drive some of the basic mechanisms underlying age-related functional decline and death.

CENP-A chromatin prevents replication stress at centromeres to avoid structural aneuploidy.

Chromosome segregation relies on centromeres, yet their repetitive DNA is often prone to aberrant rearrangements under pathological conditions. Factors that maintain centromere integrity to prevent centromere-associated chromosome translocations are unknown. Here, we demonstrate the importance of the centromere-specific histone H3 variant CENP-A in safeguarding DNA replication of alpha-satellite repeats to prevent structural aneuploidy. Rapid removal of CENP-A in S phase, but not other cell-cycle stages, caused accumulation of R loops with increased centromeric transcripts, and interfered with replication fork progression. Replication without CENP-A causes recombination at alpha-satellites in an R loop-dependent manner, unfinished replication, and anaphase bridges. In turn, chromosome breakage and translocations arise specifically at centromeric regions. Our findings provide insights into how specialized centromeric chromatin maintains the integrity of transcribed noncoding repetitive DNA during S phase.

Risk Factors for Trochanteric Bursitis Following Total Hip Arthroplasty: A Radiographic Analysis.

BACKGROUND: Trochanteric bursitis (TB) is a prevalent complication following total hip arthroplasty (THA), with increased offset hypothesized as a potential risk factor. This study investigated potential TB predictors in THA patients, including radiographic measurements of offset and leg length, comorbidities, and patient characteristics. METHODS: In this retrospective cohort study, all THA patients from a single academic tertiary care center between 2005 and 2021 were reviewed. Exclusion criteria included less than one-year follow-up, osteonecrosis, or fracture. Manual radiographic measurements of offset (acetabular, femoral, and total) and leg length from preoperative and postoperative antero-posterior pelvis X-rays were taken, with scaling using femoral cortical diameter. Univariable and multivariable Cox proportional hazard models were employed to estimate TB risk. RESULTS: Of 1,094 patients, 103 (9.4%) developed TB, with a median (Q1, Q3) time to presentation of 41.8 weeks (25.5, 66.9). In univariable models, only sex was associated with increased TB risk, with women exhibiting a 1.79 times increased risk (hazard ratio: 1.79 (1.16, 2.76), P = .009). Changes in acetabular offset, femoral offset, total offset, and leg length between preoperative and postoperative radiographs were not associated with an increased risk of developing TB in the univariate or multivariate models. Furthermore, various offset thresholds were evaluated, with no amount of increased offset showing increased TB risk. CONCLUSIONS: This study found no relationship between femoral, acetabular, or total offset and TB following THA. These findings suggest that surgeons may consider adding offset for increased prosthetic stability in high-risk cases. However, given that this is a retrospective study, the authors are not advocating for the routine use of increased offset. The study identified women as a risk factor with a 1.79 times higher TB risk, highlighting the importance of counseling women patients on this heightened risk.

Older adults' perceptions of ageism, discrimination, and racism.

Older adults often experience different forms of discrimination, whether it be on the basis of their age, gender, race, or ethnicity (Rochon et al. 2021). Many older adults have stated they have experienced the health care system differently because of their race or ethnicity . Understanding older adults' experiences and their perceptions of ageism and racism can guide future work. This observational cross-sectional study captured community-dwelling older adults' perceptions about their experiences with ageism and racism. A few opened-ended questions were included in the cross-sectional survey. While results did not yield differences with respect to perceptions of ageism by race; there were statistically significant results in regard to perceived racism, with higher scores on the racism scales for individuals who self-identified as Black. Discussion and implications for practice, policy and research are explored.

Dependent Competing Failure Processes in Reliability Systems.

This paper deals with a reliability system hit by three types of shocks ranked as harmless, critical, or extreme, depending on their magnitudes, being below H1, between H1 and H2, and above H2, respectively. The system's failure is caused by a single extreme shock or by a total of N critical shocks. In addition, the system fails under occurrences of M pairs of shocks with lags less than some δ (δ-shocks) in any order. Thus, the system fails when one of the three named cumulative damages occurs first. Thus, it fails due to the competition of the three associated shock processes. We obtain a closed-form joint distribution of the time-to-failure, shock count upon failure, δ-shock count, and cumulative damage to the system on failure, to name a few. In particular, the reliability function directly follows from the marginal distribution of the failure time. In a modified system, we restrict δ-shocks to those with small lags between consecutive harmful shocks. We treat the system as a generalized random walk process and use an embellished variant of discrete operational calculus developed in our earlier work. We demonstrate analytical tractability of our formulas which are also validated, through Monte Carlo simulation.

Effects of Nucleic Acid Structural Heterogeneity on the Electrochemistry of Tethered Redox Molecules.

The cation condensation-induced collapse of electrode-bound nucleic acids and the resulting change in the electrochemical signal is a useful tool to predict the structure and redox probe location of heterogeneous structures of surface-tethered DNA probes─a common architecture employed in the development of electrochemical sensors. In this paper, we measure the faradaic current of an appended redox molecule at the 3' position of the nucleic acid using cyclic voltammetry before and after nucleic acid collapse for various nucleic acid architectures and heterogeneous mixtures on the same electrode surface. The voltammetric peak current change with collapse correlates with the proximity of the redox molecules from the surface. For stem-loop probes, the terminal methylene blue is initially held closer to the surface, such that inducing collapse, by reducing the dielectric permittivity of the interrogation solution, results in a ∼30% increase in current. However, when incorporating pseudoknot probes that hold methylene blue further away from the electrode surface, the current change is much larger (∼120%), indicating a larger conformation change. Upon a 50:50 ratio of the two, we observe a change in current that relates to the ratiometric distribution of the probe used to make the surfaces. Additionally, using cyclic voltammetry, we find that the change between diffusion-limited and diffusion-independent peak currents is dependent upon the distinct structural characteristics of DNA probes on the surface (stem-loop or pseudoknot), as well as the ratios of different DNA probes on the surface. Thus, we demonstrate that the heterogeneous nature of DNA probes governs the corresponding electrochemical signals, which can lead to a better understanding on how to predict the structures of functional nucleic acids on electrode surfaces and how this affects surface-to-surface variability and electrochemical response.

Observing Real-Time Formation of Self-Assembled Monolayers on Polycrystalline Gold Surfaces with Scanning Electrochemical Cell Microscopy.

Self-assembled monolayers (SAMs) of alkanethiols on gold have become a central focus of controllable surface chemistry because they can be easily formed from the solution phase and characterized using various techniques. Understanding the formation processes occurring at a nanoscale level is crucial to form defect-free SAMs for tailored applications in bio- and nanotechnology. Although many reports study and characterize SAMs after they are formed on gold surfaces, typical methods have not extensively studied the SAM formation process at the nanoscale. This paper focuses on the formation of defect-free SAMs and elucidates the formation mechanism occurring at the nanoscale level during the formation process. Exploiting the strength of scanning electrochemical cell microscopy, we monitored SAM formation via a soluble redox reporter on a polycrystalline gold foil using voltammetric and amperometric techniques. We formed SAMs by varying the concentration of 3-mercapto-1-propanol [HS(CH2)3OH], 6-mercapto-1-hexanol [HS(CH2)6OH], and 9-mercapto-1-nonanol [HS(CH2)9OH] to determine the effects of the thiol chain length, concentration, and location on the substrate (grain boundaries) on monolayer formation. We observed real-time changes in the quasisteady-state current of our redox reporter during the self-assembly process. Importantly, we formed defect-free SAMs at the nanoscale level using different concentrations of HS(CH2)6OH and HS(CH2)9OH and found that SAM formation at the nanoscale is concentration-dependent and varies when at a boundary between two crystal grains.

Sequential movement pattern-mining (SMP) in field-based team-sport: A framework for quantifying spatiotemporal data and improve training specificity?

Athlete external load is typically quantified as volumes or discretised threshold values using distance, speed and time. A framework accounting for the movement sequences of athletes has previously been proposed using radio frequency data. This study developed a framework to identify sequential movement sequences using GPS-derived spatiotemporal data in team-sports and establish its stability. Thirteen rugby league players during one match were analysed to demonstrate the application of the framework. The framework (Sequential Movement Pattern-mining [SMP]) applies techniques to analyse i) geospatial data (i.e., decimal degree latitude and longitude), ii) determine players turning angles, iii) improve movement descriptor assignment, thus improving movement unit formation and iv) improve the classification and identification of players' frequent SMP. The SMP framework allows for sub-sequences of movement units to be condensed, removing repeated elements, which offers a novel technique for the quantification of similarities or dis-similarities between players and playing positions. The SMP framework provides a robust and stable method that allows, for the first time the analysis of GPS-derived data and identifies the frequent SMP of field-based team-sport athletes. The application of the SMP framework in practice could optimise the outcomes of training of field-based team-sport athletes by improving training specificity.

Surface chemistry in Ti-6Al-4V feedstock as influenced by powder reuse in electron beam additive manufacturing.

X-ray photoelectron spectroscopy (XPS) as well as scanning and transmission electron microscopy (SEM/TEM) analysis was carried out on four Ti-6Al-4V powders used in electron beam powder-bed fusion (PBF-EB) production environments: virgin low oxygen (0.080 wt% O), reused medium oxygen (0.140 wt% O), reused high oxygen (0.186 wt% O), and virgin high oxygen (0.180 wt% O). The two objectives of this comparative analyses were to (1) investigate high oxygen containing Grade 23 Ti-6Al-4V powders which were further oxidized as a function of reuse and (2) comparing the two virgin Grade 23 and Grade 5 powders of similar oxygen content. The microstructure of the low oxygen virgin Grade 23 powder was consistent with martensitic α' microstructure, whereas the reused powder displayed tempered α/ß Widmänstatten microstructure. XPS revealed a decrease in TiO2 at the surface of the reused powders with an increase in Al2O3. This trend is energetically favorable at the temperatures and pressures in PBF-EB machines, and it is consistent with the thermodynamics of Al2O3 vs. TiO2 reactions. An unexpected amount of nitrogen was measured on the titanium powder, with a general increase in nitride on the surface of the particles as a function of reuse in the Grade 23 powder.

The invisible gap: Older adults' communication with health care providers about concomitant use of alcohol and medications.

The purpose of this study was to assess the impact of a new educational intervention, Communicating with your Health Care Providers, which was designed to assist older adults in communicating with their physicians and other health care providers and improving their knowledge about concomitant alcohol and medication risks. A randomized control trial was conducted in older adult centers in an urban community. Participants were assigned to either the intervention group or a control group that received traditional services. The intervention group received educational material about health, physical and other aging changes, medication use and possible adverse interactions between alcohol and medications, as well as strategies to initiate communication with physicians and other health care providers. The outcomes measured were: (1) interest in communicating with physicians and health care providers; (2) perception of the importance of communication; and (3) knowledge about concomitant alcohol and medication use. MANCOVA tests indicated that the intervention group had greater knowledge about the risks of combining alcohol with prescription medications than the control group, as well as greater interest in having health care discussions with their physicians and other health care providers. These findings may be translated into future educational programming for community centers.

Silver Nanoneedle Probes Enable Sustained DC Current, Single-Channel Resistive Pulse Nanopore Sensing.

Resistive pulse sensing using ion channel proteins (biological nanopores) has been evolving as a single-molecule approach to detect small biomolecules owing to atomically precise pore size reproducibility, high signal-to-noise ratio, and molecular selectivity. The incorporation of biological nanopores in sensing platforms requires a stable lipid membrane that can be formed by a variety of methods such as the painting method and droplet-based techniques. However, these methods are limited by the fragility of the unsupported bilayer or the need for specific microdevices. Electrode-supported bilayers, in which a metal electrode is used as a support structure, have been recently developed using a fine gold nanoneedle. We previously described the utility of the gold nanoneedle-supported ion channel probe to detect small molecules with high spatial resolution; however, it exhibited a channel current decay over time, which affected the binding frequency of the target molecule to the protein pore as well. Here, we introduce a silver nanoneedle probe to support the lipid bilayer formation and ion channel measurements. The silver nanoneedle mitigates the current decay observed on gold electrodes and produces stable DC channel currents. Our findings propose the formation of a AgCl layer creating a nonpolarizable electrode. The new nanoneedle is successfully applied for single-molecule detection of sulfonated ß-cyclodextrin (S7ßCD) using αHL as a test bed protein. We believe that this new silver nanoneedle platform has great potential given the relative ease of lipid bilayer formation and stable open channel currents.