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.

Systematic identification of anticancer drug targets reveals a nucleus-to-mitochondria ROS-sensing pathway.

Multiple anticancer drugs have been proposed to cause cell death, in part, by increasing the steady-state levels of cellular reactive oxygen species (ROS). However, for most of these drugs, exactly how the resultant ROS function and are sensed is poorly understood. It remains unclear which proteins the ROS modify and their roles in drug sensitivity/resistance. To answer these questions, we examined 11 anticancer drugs with an integrated proteogenomic approach identifying not only many unique targets but also shared ones-including ribosomal components, suggesting common mechanisms by which drugs regulate translation. We focus on CHK1 that we find is a nuclear H2O2 sensor that launches a cellular program to dampen ROS. CHK1 phosphorylates the mitochondrial DNA-binding protein SSBP1 to prevent its mitochondrial localization, which in turn decreases nuclear H2O2. Our results reveal a druggable nucleus-to-mitochondria ROS-sensing pathway-required to resolve nuclear H2O2 accumulation and mediate resistance to platinum-based agents in ovarian cancers.

Life detection in a universe of false positives: Can the Fatal Flaws of Exoplanet Biosignatures be Overcome Absent a Theory of Life?

Astrobiology aims to determine the distribution and diversity of life in the universe. But as the word "biosignature" suggests, what will be detected is not life itself, but an observation implicating living systems. Our limited access to other worlds suggests this observation is more likely to reflect out-of-equilibrium gasses than a writhing octopus. Yet, anything short of a writhing octopus will raise skepticism about what has been detected. Resolving that skepticism requires a theory to delineate processes due to life and those due to abiotic mechanisms. This poses an existential question for life detection: How do astrobiologists plan to detect life on exoplanets via features shared between non-living and living systems? We argue that you cannot without an underlying theory of life. We illustrate this by analyzing the hypothetical detection of an "Earth 2.0" exoplanet. Without a theory of life, we argue the community should focus on identifying unambiguous features of life via four areas: examining life on Earth, building life in the lab, probing the solar system, and searching for technosignatures. Ultimately, we ask, what exactly do astrobiologists hope to learn by searching for life?

The Spatial Extracellular Proteomic Tumor Microenvironment Distinguishes Molecular Subtypes of Hepatocellular Carcinoma.

Hepatocellular carcinoma (HCC) mortality rates continue to increase faster than those of other cancer types due to high heterogeneity, which limits diagnosis and treatment. Pathological and molecular subtyping have identified that HCC tumors with poor outcomes are characterized by intratumoral collagenous accumulation. However, the translational and post-translational regulation of tumor collagen, which is critical to the outcome, remains largely unknown. Here, we investigate the spatial extracellular proteome to understand the differences associated with HCC tumors defined by Hoshida transcriptomic subtypes of poor outcome (Subtype 1; S1; n = 12) and better outcome (Subtype 3; S3; n = 24) that show differential stroma-regulated pathways. Collagen-targeted mass spectrometry imaging (MSI) with the same-tissue reference libraries, built from untargeted and targeted LC-MS/MS was used to spatially define the extracellular microenvironment from clinically-characterized, formalin-fixed, paraffin-embedded tissue sections. Collagen α-1(I) chain domains for discoidin-domain receptor and integrin binding showed distinctive spatial distribution within the tumor microenvironment. Hydroxylated proline (HYP)-containing peptides from the triple helical regions of fibrillar collagens distinguished S1 from S3 tumors. Exploratory machine learning on multiple peptides extracted from the tumor regions could distinguish S1 and S3 tumors (with an area under the receiver operating curve of ≥0.98; 95% confidence intervals between 0.976 and 1.00; and accuracies above 94%). An overall finding was that the extracellular microenvironment has a high potential to predict clinically relevant outcomes in HCC.

Inhibiting N-glycan processing increases the antibody binding affinity and effector function of human natural killer cells.

Novel approaches are required to improve the efficacy of immunotherapies and increase the proportion of patients who experience a benefit. Antibody-dependent cell-mediated cytotoxicity (ADCC) contributes to the efficacy of many monoclonal antibodies therapies. Natural killer (NK) cells mediate ADCC, though responses are highly variable and depend on prior treatment as well as other factors. Thus, strategies to increase NK cell activity are expected to improve multiple therapies. Both cytokine treatment and NK cell receptor engineering are being explored to increase ADCC. Post-translational modifications, including glycosylation, are widely recognized as mediators of cellular processes but minimally explored as an alternative strategy to increase ADCC. We evaluated the impact of treatment with kifunensine, an inhibitor of asparagine-linked (N-)glycan processing, on ADCC using primary and cultured human NK cells. We also probed affinity using binding assays and CD16a structure with nuclear magnetic resonance spectroscopy. Treating primary human NK cells and cultured YTS-CD16a cells with kifunensine doubled ADCC in a CD16a-dependent manner. Kifunensine treatment also increased the antibody-binding affinity of CD16a on the NK cell surface. Structural interrogation identified a single CD16a region, proximal to the N162 glycan and the antibody-binding interface, perturbed by the N-glycan composition. The observed increase in NK cell activity following kifunensine treatment synergized with afucosylated antibodies, further increasing ADCC by an additional 33%. These results demonstrate native N-glycan processing is an important factor that limits NK cell ADCC. Furthermore, optimal antibody and CD16a glycoforms are defined that provide the greatest ADCC activity.

Identifying robust adaptive irrigation operating policies to balance deeply uncertain economic food production and groundwater sustainability trade-offs.

Increasing irrigation demand has heavily relied on groundwater use, especially in places with highly variable water supplies that are vulnerable to drought. Groundwater management in agriculture is becoming increasingly challenging given the growing effects from overdraft and groundwater depletion worldwide. However, multiple challenges emerge when seeking to develop sustainable groundwater management in irrigated systems, such as trade-offs between the economic revenues from food production and groundwater resources, as well as the broad array of uncertainties in food-water systems. In this study we explore the applicability of Evolutionary Multi-Objective Direct Policy Search (EMODPS) to identify adaptive irrigation policies that water agencies and farmers can implement including operational decisions related to land use and groundwater use controls as well as groundwater pumping fees. The EMODPS framework yields state-aware, adaptive policies that respond dynamically as system state conditions change, for example with variable surface water (e.g., shifting management strategies across wet versus dry years). For this study, we focus on the Semitropic Water Storage district located in the San Joaquin Valley, California to provide broader insights relevant to ongoing efforts to improve groundwater sustainability in the state. Our findings demonstrate that adaptive irrigation policies can achieve sufficiently flexible groundwater management to acceptably balance revenue and sustainability goals across a wide range of uncertain future scenarios. Among the evaluated policy decisions, pumping restrictions and reductions in inflexible irrigation demands from tree crops are actions that can support dry-year pumping while maximizing groundwater storage recovery during wet years. Policies suggest that an adaptive pumping fee is the most flexible decision to control groundwater pumping and land use.

Endovascular Release of a 50-Year-Old Adams-Deweese IVC Clip to Facilitate Percutaneous Repair of Mitral Valve Regurgitation.

Percutaneous mitral valve (MV) repair using MitraClip requires large-caliber venous access. We describe a patient with a ligated inferior vena cava due to an Adams-DeWeese clip placed 50 years prior, who had progressive shortness of breath and lower extremity symptoms secondary to severe mitral regurgitation and chronic iliocaval deep venous thrombosis. Due to comorbidities, MitraClip was recommended over surgery for MV repair. Caval luminal gain was required to facilitate endovascular access for the MitraClip system. Stent-mediated release of the inferior vena cava clip allowed successful passage of the delivery sheath from the common femoral vein to MV and subsequent valve repair.

"We have to clean ourselves to ensure that our children are healthy and beautiful": findings from a qualitative assessment of a hand hygiene poster in rural Uganda.

BACKGROUND: Neonatal sepsis is a major cause of mortality worldwide, with most deaths occurring in low-income countries. The World Health Organisation (WHO) '5 Moments for Hand Hygiene' poster has been used to reduce hospital-acquired infections, but there is no similar tool to prevent community-acquired newborn infections in low-resource settings. This assessment, part of the BabyGel Pilot study, evaluated the acceptability of the 'Newborn Moments for Hand Hygiene in the Home' poster. This was an educational tool which aimed to remind mothers in rural Uganda to clean their hands to prevent neonatal infection. METHODS: The BabyGel pilot was a cluster randomised trial that assessed the post-partum use of alcohol-based hand rub (ABHR) to prevent neonatal infections in Mbale, Uganda. Fifty-five women in 5 village clusters received the ABHR and used it from birth to 3 months postnatally, with use guided by the new poster. Following the study, 5 focus group discussions (FGDs) were conducted consisting of 6-8 purposively sampled participants from intervention villages. FGDs were audio-recorded, transcribed then translated into English. Transcripts were inductively coded using ATLAS.ti® and qualitatively analysed using thematic content analysis. RESULTS: Most mothers reported that they understood the message in the poster ("The picture shows me you must use these drugs to keep your baby healthy") and that they could adhere to the moments from the poster. Some participants used the information from the poster to encourage other caregivers to use the ABHR ("after explaining to them, they liked it"). Other potential moments for hand hygiene were introduced by participants, such as after tending to domestic animals and gardening. CONCLUSION: The poster was well-received, and participants reported compliance with the moments for hand hygiene (although the full body wipe of the baby has since been removed). The poster will be adapted into a sticker format on the ABHR bottle. More focus could be put into an education tool for other caregivers who wish to hold the baby. Overall, the study demonstrated the acceptability of an adapted version of the WHO Moments for Hand Hygiene poster in the introduction of an intervention in the community. TRIAL REGISTRATION: ISRCTN67852437 , registered 02/03/2015. TRIAL FUNDING: Medical Research Council/ Wellcome Trust/ DfID (Global Health Trials Scheme).

Criticality Distinguishes the Ensemble of Biological Regulatory Networks.

The hypothesis that many living systems should exhibit near-critical behavior is well motivated theoretically, and an increasing number of cases have been demonstrated empirically. However, a systematic analysis across biological networks, which would enable identification of the network properties that drive criticality, has not yet been realized. Here, we provide a first comprehensive survey of criticality across a diverse sample of biological networks, leveraging a publicly available database of 67 Boolean models of regulatory circuits. We find all 67 networks to be near critical. By comparing to ensembles of random networks with similar topological and logical properties, we show that criticality in biological networks is not predictable solely from macroscale properties such as mean degree ⟨K⟩ and mean bias in the logic functions ⟨p⟩, as previously emphasized in theories of random Boolean networks. Instead, the ensemble of real biological circuits is jointly constrained by the local causal structure and logic of each node. In this way, biological regulatory networks are more distinguished from random networks by their criticality than by other macroscale network properties such as degree distribution, edge density, or fraction of activating conditions.

Ventromedial prefrontal cortex activity and pathological worry in generalised anxiety disorder.

BACKGROUND: Pathological worry is a hallmark feature of generalised anxiety disorder (GAD), associated with dysfunctional emotional processing. The ventromedial prefrontal cortex (vmPFC) is involved in the regulation of such processes, but the link between vmPFC emotional responses and pathological v. adaptive worry has not yet been examined.AimsTo study the association between worry and vmPFC activity evoked by the processing of learned safety and threat signals. METHOD: In total, 27 unmedicated patients with GAD and 56 healthy controls (HC) underwent a differential fear conditioning paradigm during functional magnetic resonance imaging. RESULTS: Compared to HC, the GAD group demonstrated reduced vmPFC activation to safety signals and no safety-threat processing differentiation. This response was positively correlated with worry severity in GAD, whereas the same variables showed a negative and weak correlation in HC. CONCLUSIONS: Poor vmPFC safety-threat differentiation might characterise GAD, and its distinctive association with GAD worries suggests a neural-based qualitative difference between healthy and pathological worries.Declaration of interestNone.

A high-throughput pH-based colorimetric assay: application focus on alpha/beta hydrolases.

Research involving α/ß hydrolases, including α-amino acid ester hydrolase and cocaine esterase, has been limited by the lack of an online high throughput screening assay. The development of a high throughput screening assay capable of detecting α/ß hydrolase activity toward specific substrates and/or chemical reactions (e.g., hydrolysis in lieu of amidase activity and/or synthesis instead of thioesterase activity) is of interest in a broad set of scientific questions and applications. Here we present a general framework for pH-based colorimetric assays, as well as the mathematical considerations necessary to estimate de novo the experimental response required to assign a 'hit' or a 'miss,' in the absence of experimental standard curves. This combination is valuable for screening the hydrolysis and synthesis activity of α/ß hydrolases on a variety of substrates, and produces data comparable to the current standard technique involving High Performance Liquid Chromatography (HPLC). In contrast to HPLC, this assay enables screening experiments to be performed with greater efficiency.

Predictors and consequences of health anxiety symptoms: a novel twin modeling study.

OBJECTIVE: The question of how to best conceptualize health anxiety (HA) from a diagnostic and etiological perspective remains debated. The aim was to examine the relationship between HA and the symptoms of anxiety and obsessive-compulsive-related disorders in a normative twin population. METHOD: Four hundred and ninety-six monozygotic adult twin pairs from the Australian Twin Registry participated in the study (age, 34.4 ± 7.72 years; 59% females). Validated scales were used to assess each domain. We applied a twin regression methodology-ICE FALCON-to determine whether there was evidence consistent with 'causal' relationships between HA and other symptoms by fitting and comparing model estimates. RESULTS: Estimates were consistent with higher levels of obsessing ('unwanted thoughts') (P = 0.008), social anxiety (P = 0.03), and body dysmorphic symptoms (P = 0.008) causing higher levels of HA symptoms, and with higher levels of HA symptoms causing higher levels of physical/somatic anxiety symptoms (P = 0.001). CONCLUSION: Obsessional thoughts, body dysmorphic concerns, and social anxiety symptoms may have a causal influence on HA. To report physical/somatic anxiety appears to be a consequence of the underlying presence of HA-related fears. Should our results be confirmed by longitudinal studies, the evaluation and treatment of HA may benefit from the consideration of these identified risk factors.

Towards fully commercial, UV-compatible fiber patch cords.

We present and analyze two pathways to produce commercial optical-fiber patch cords with stable long-term transmission in the ultraviolet (UV) at powers up to ~ 200 mW, and typical bulk transmission between 66-75 %. Commercial fiber patch cords in the UV are of great interest across a wide variety of scientific applications ranging from biology to metrology, and the lack of availability has yet to be suitably addressed. We provide a guide to producing such solarization-resistant, hydrogen-passivated, polarization-maintaining, connectorized and jacketed optical fibers compatible with demanding scientific and industrial applications. Our presentation describes the fabrication and hydrogen loading procedure in detail and presents a high-pressure vessel design, calculations of required H2 loading times, and information on patch cord handling and the mitigation of bending sensitivities. Transmission at 313 nm is measured over many months for cumulative energy on the fiber output of > 10 kJ with no demonstrable degradation due to UV solarization, in contrast to standard uncured fibers. Polarization sensitivity and stability are characterized yielding polarization extinction ratios between 15 dB and 25 dB at 313 nm, where we find patch cords become linearly polarizing. We observe that particle deposition at the fiber facet induced by high-intensity UV exposure can (reversibly) deteriorate patch cord performance and describe a technique for nitrogen purging of fiber collimators which mitigates this phenomenon.

Neural signatures of human fear conditioning: an updated and extended meta-analysis of fMRI studies.

Classical Pavlovian fear conditioning remains the most widely employed experimental model of fear and anxiety, and continues to inform contemporary pathophysiological accounts of clinical anxiety disorders. Despite its widespread application in human and animal studies, the neurobiological basis of fear conditioning remains only partially understood. Here we provide a comprehensive meta-analysis of human fear-conditioning studies carried out with functional magnetic resonance imaging (fMRI), yielding a pooled sample of 677 participants from 27 independent studies. As a distinguishing feature of this meta-analysis, original statistical brain maps were obtained from the authors of 13 of these studies. Our primary analyses demonstrate that human fear conditioning is associated with a consistent and robust pattern of neural activation across a hypothesized genuine network of brain regions resembling existing anatomical descriptions of the 'central autonomic-interoceptive network'. This finding is discussed with a particular emphasis on the neural substrates of conscious fear processing. Our associated meta-analysis of functional deactivations-a scarcely addressed dynamic in fMRI fear-conditioning studies-also suggests the existence of a coordinated brain response potentially underlying the 'safety signal' (that is, non-threat) processing. We attempt to provide an integrated summary on these findings with the view that they may inform ongoing studies of fear-conditioning processes both in healthy and clinical populations, as investigated with neuroimaging and other experimental approaches.

Sex-based differences in skeletal muscle kinetics and fiber-type composition.

Previous studies have identified over 3,000 genes that are differentially expressed in male and female skeletal muscle. Here, we review the sex-based differences in skeletal muscle fiber composition, myosin heavy chain expression, contractile function, and the regulation of these physiological differences by thyroid hormone, estrogen, and testosterone. The findings presented lay the basis for the continued work needed to fully understand the skeletal muscle differences between males and females.

The effects of stress-tension on depression and anxiety symptoms: evidence from a novel twin modelling analysis.

BACKGROUND: Negative mood states are composed of symptoms of depression and anxiety, and by a third factor related to stress, tension and irritability. We sought to clarify the nature of the relationships between the factors by studying twin pairs. METHOD: A total of 503 monozygotic twin pairs completed the Depression Anxiety Stress Scales (DASS), an instrument that assesses symptoms of depression, anxiety and stress-tension. We applied a recently developed twin regression methodology - Inference about Causation from Examination of FAmiliaL CONfounding (ICE FALCON) - to test for evidence consistent with the existence of 'causal' influences between the DASS factors. RESULTS: There was evidence consistent with the stress-tension factor having a causal influence on both the depression (p < 0.0001) and anxiety factors (p = 0.001), and for the depression factor having a causal influence on the anxiety factor (p < 0.001). CONCLUSIONS: Our findings suggest a critical role for stress-tension in the structure of negative mood states, and that interventions that target it may be particularly effective in reducing depression and anxiety symptoms.

Functional brain-imaging correlates of negative affectivity and the onset of first-episode depression.

BACKGROUND: The amygdala and subgenual anterior cingulate cortex (sACC) are key brain regions for the generation of negative affect. In this longitudinal fMRI study of adolescents we investigated how amygdala-sACC connectivity was correlated with negative affectivity (NA) both cross-sectionally and longitudinally, and examined its relationship to the onset of first-episode depression. METHOD: Fifty-six adolescents who were part of a larger longitudinal study of adolescent development were included. They had no history of mental illness at the time of their baseline scan (mean age 16.5 years) and had a follow-up scan 2 years later (mean age 18.8 years). We used resting-state functional-connectivity MRI to investigate whether cross-sectional and change measures of amygdala-sACC connectivity were (i) correlated with NA and its change over time, and (ii) related to the onset of first-episode depression. RESULTS: The magnitude of amygdala connectivity with sACC showed significant positive correlation with NA at both time-points. Further analysis confirmed that change in amygdala-sACC connectivity between assessments was correlated with change in NA. Eight participants developed a first episode of depression between the baseline and follow-up assessments: they showed increased amygdala-sACC connectivity at follow-up. CONCLUSIONS: Amygdala-sACC connectivity is associated with NA in adolescence, with change in connectivity between these regions showing positive correlation with change in NA. Our observation that the onset of depression was associated with an increase in connectivity between the regions provides support for the neurobiological 'scar' hypothesis of depression.

Improving red cell transfusion in the elective surgical setting: an improvement collaborative with evaluation.

BACKGROUND & OBJECTIVES: Significant research conducted in New South Wales (NSW) hospitals' indicated that about 30% of red cell transfusions in stable adult patients was inappropriate. Of the total Australian government blood product budget in 2009-2010 (i.e. $878·8 million dollars) was spent on fresh blood products and plasma collection. The Clinical Excellence Commission (CEC) launched a systematic intervention called Blood Watch (BW) aiming to reduce inappropriate red cell transfusions in all NSW hospitals. An evaluation of BW was undertaken to measure the effectiveness of the programme and to estimate the associated potential cost-saving. MATERIALS & METHODS: Through the deterministic linkage of the four population-based administrative databases, three outcome indicators and four process indicators were developed. The analyses were of five elective surgical groups as they were the focus of the interventions. Three-level logistic regression and three-level linear regression were used to explore the time trend of the study process and outcome indicators. Modelling of the possible avoided red cell transfusions was also undertaken using a quadratic regression technique. RESULTS: Overall, there was a 27·4% reduction of the blood usage after the introduction of the BW programme and the reductions were consistent across five elective surgical groups. Such a reduction was associated with annual cost-savings of over $8·5 million. CONCLUSIONS: The BW programme which was based on collaborative improvement methods and implemented at scale led to significant reduction of blood usage, consistently across five elective surgical groups and significant cost-saving.

Incidentalomas during imaging for primary hyperparathyroidism--incidence and clinical outcomes.

BACKGROUND: Imaging for pre-operative localisation of parathyroid glands in primary hyperparathyroidism is now routine. This has led to the detection of incidental lesions (incidentalomas) in other organs, the nature of which is not well characterised. The aim of this study was to determine the incidence, characteristics and outcomes in patients who had incidental findings on parathyroid imaging. METHODS: Records of patients who underwent imaging for primary hyperparathyroidism over 2 years were reviewed to identify incidental lesions detected on parathyroid imaging. Patients with persistent or renal hyperparathyroidism were excluded. Details on the management of detected incidentalomas were obtained from patient records. RESULTS: Incidentalomas were identified in 17 of 170 patients (10%) undergoing parathyroid imaging. Incidentalomas included thyroid (n = 11), breast (n = 3), lateral compartment of the neck (n = 1), lung (n = 1) and clavicle (n = 1). However, no disease of clinical significance needing treatment was detected on further investigation. CONCLUSIONS: Although a significant proportion of patients undergoing parathyroid imaging had incidental lesions detected, these seem to be of little clinical significance. The morbidity and cost of further interventions on these incidentalomas need to be weighed against the benefits of routine imaging in improving outcomes of first-time surgery in patients with primary hyperparathyroidism.

Application of a decision analytic framework for adoption of clinical trial results: are the data regarding TARGIT-A IORT ready for prime time?

The results from randomized clinical trials are often adopted slowly. This practice potentially prevents many people from benefiting from more effective care. Provide a framework for analyzing clinical trial results to determine whether and when early adoption of novel interventions is appropriate. The framework includes the evaluation of three components: confidence in trial results, impact of early, and late adoption if trial results are reversed or sustained. The adverse impact of early adoption, and the opportunity cost of late adoption are determined using Markov modeling to simulate the impact of early and late adoption in terms of quality of life years and resources gained or lost. We applied the framework to the TARGIT-A randomized clinical trial comparing intraoperative radiation (IORT) to standard external beam radiation (EBRT) and considered these results in the context of trials comparing endocrine therapy with and without radiation therapy in postmenopausal women. Confidence in the TARGIT-A trial 4 year results is high because the peak hazard for local recurrence in the trial is between 2 and 3 years. This is consistent with most trials, and no second peak has been observed in similar patient populations, suggesting that the TARGIT-A trial results are stable. The interventions offer approximately equivalent life expectancy. If IORT local recurrences rate were as high as 10 % at 10 years (which is higher than expected), we would project only 0.002 fewer expected life years (less than 1 day) compared to EBRT if IORT is adopted early. However, there is a $1.7 billion opportunity cost of waiting an additional 5 years to adopt IORT in low risk, hormone-receptor-positive, postmenopausal women. EBRT costs an additional $1467 in indirect costs per patient. Applying an evaluative framework for the adoption of clinical trial results to the TARGIT-A IORT therapy trial results in the assessment that the trial results are stable, early adoption would lead to minimal adverse impact, and substantially less resource use. Both IORT and no radiation are reasonable strategies to adopt.