Phylogenomic analyses and comparative genomics of Pseudomonas syringae associated with almond (Prunus dulcis) in California.

We sequenced and comprehensively analysed the genomic architecture of 98 fluorescent pseudomonads isolated from different symptomatic and asymptomatic tissues of almond and a few other Prunus spp. Phylogenomic analyses, genome mining, field pathogenicity tests, and in vitro ice nucleation and antibiotic sensitivity tests were integrated to improve knowledge of the biology and management of bacterial blast and bacterial canker of almond. We identified Pseudomonas syringae pv. syringae, P. cerasi, and P. viridiflava as almond canker pathogens. P. syringae pv. syringae caused both canker and foliar (blast) symptoms. In contrast, P. cerasi and P. viridiflava only caused cankers, and P. viridiflava appeared to be a weak pathogen of almond. Isolates belonging to P. syringae pv. syringae were the most frequently isolated among the pathogenic species/pathovars, composing 75% of all pathogenic isolates. P. cerasi and P. viridiflava isolates composed 8.3 and 16.7% of the pathogenic isolates, respectively. Laboratory leaf infiltration bioassays produced results distinct from experiments in the field with both P. cerasi and P. syringae pv. syringae, causing significant necrosis and browning of detached leaves, whereas P. viridiflava conferred moderate effects. Genome mining revealed the absence of key epiphytic fitness-related genes in P. cerasi and P. viridiflava genomic sequences, which could explain the contrasting field and laboratory bioassay results. P. syringae pv. syringae and P. cerasi isolates harboured the ice nucleation protein, which correlated with the ice nucleation phenotype. Results of sensitivity tests to copper and kasugamycin showed a strong linkage to putative resistance genes. Isolates harbouring the ctpV gene showed resistance to copper up to 600 µg/ml. In contrast, isolates without the ctpV gene could not grow on nutrient agar amended with 200 µg/ml copper, suggesting ctpV can be used to phenotype copper resistance. All isolates were sensitive to kasugamycin at the label-recommended rate of 100µg/ml.

Clinicopathologic and Genomic Factors Impacting Efficacy of First-Line Chemoimmunotherapy in Advanced NSCLC.

INTRODUCTION: Although programmed cell death protein 1 and programmed death-ligand 1 (PD-L1) blockade in combination with platinum-doublet chemotherapy has become a mainstay of first-line treatment for advanced NSCLC, factors associated with efficacy of chemoimmunotherapy (CIT) are not well characterized. METHODS: In this multicenter retrospective analysis, clinicopathologic and genomic data were collected from patients with advanced NSCLC (lacking sensitizing genomic alterations in EGFR and ALK) and evaluated with clinical outcomes to first-line CIT. RESULTS: Among 1285 patients treated with CIT, a worsening performance status and increasing derived neutrophil-to-lymphocyte ratio in the blood were associated with a significantly reduced objective response rate (ORR), median progression-free survival (mPFS), and median overall survival (mOS). With increasing PD-L1 tumor proportion scores of less than 1%, 1% to 49%, 50% to 89%, and greater than or equal to 90%, there was a progressive improvement in ORR (32.7% versus 37.5% versus 51.6% versus 61.7%, p < 0.001), mPFS (5.0 versus 6.1 versus 6.8 versus 13.0 mo, p < 0.001), and generally mOS (12.9 versus 14.6 versus 34.7 versus 23.1 mo, p = 0.009), respectively. Of 789 NSCLCs with comprehensive genomic data, NSCLCs with a tumor mutational burden (TMB) greater than or equal to the 90th percentile had an improved ORR (53.5% versus 36.4%, p = 0.004), mPFS (10.8 versus 5.5 mo, p < 0.001), and mOS (29.2 versus 13.1 mo, p < 0.001), compared with those with a TMB less than the 90th percentile. In all-comers with nonsquamous NSCLC, the presence of an STK11, KEAP1, or SMARCA4 mutation was associated with significantly worse ORR, mPFS, and mOS to CIT (all p < 0.05); this was also observed in the KRAS-mutant subgroup of NSCLCs with co-occurring mutations in STK11, KEAP1, or SMARCA4 (all p < 0.05). In KRAS wild-type NSCLC, KEAP1 and SMARCA4 mutations were associated with a significantly shorter mPFS and mOS to CIT (all p < 0.05), but STK11 mutation status had no significant impact on mPFS (p = 0.16) or mOS (p = 0.38). CONCLUSIONS: In advanced NSCLC, better patient performance status, low derived neutrophil-to-lymphocyte ratio, increasing PD-L1 expression, a very high TMB, and STK11/KEAP1/SMARCA4 wild-type status are associated with improved clinical outcomes to first-line CIT.

¿Qué transmiten las memorias públicas oficiales sobre la actividad pediátrica? / What do official public reports convey about paediatric activity?

Introducción: la Pediatría es una especialidad médica que se desarrolla en Atención Primaria y hospitalaria. Saber cómo se exponen de manera oficial los resultados de la actividad asistencial de esta especialidad puede ser el primer paso para comparar los mismos y establecer un clima de transparencia y confianza en el sistema, así como para establecer y priorizar acciones de mejora. Material y métodos: estudio observacional descriptivo. Se localizaron sitios web institucionales (Ministerio de Sanidad, consejerías de sanidad). Se analizó la información de la actividad pediátrica, su accesibilidad, nivel de agregación, actualización, formato y visión de género y edad. Se valoró la concordancia interobservadores. Resultados: 17 instituciones aportaron indicadores. Los más utilizados fueron: consultas atendidas, presión asistencial y frecuentación. El acceso a la información fue libre, complejo y actualizado a dos años (2019). Los datos estaban en su mayoría desagregados (15) y expuestos en formato PDF. N.º de indicadores: entre 1 y 38 (media, 9). Solo cuatro regiones mostraron una visión de género y de edad. Índice de acuerdo Kappa (κ): 0,89. Conclusiones: la información ofrecida por las instituciones sanitarias relacionada con los indicadores y resultados de actividad pediátrica es heterogénea. Para ganar transparencia y confianza, y para mejorar la comparación entre organizaciones, su obtención debería ser más sencilla, homogénea y clara (AU)

Introduction: paediatrics is a medical specialty that unfolds in the primary care and hospital settings. Knowing how the outcomes of paediatric practice are officially reported may be the first step to compare them and establish a culture of transparency and trust in the system, and to establish and prioritise improvement actions.Material and methods: descriptive observational study. We identified institutional websites (Ministry of Health, regional health authorities) and analysed the information on paediatric care delivery, its accessibility, level of aggregation, recency, formatting and analysis of sex and age. We assessed inter-observer agreement.Results: 17 institutions provided information on indicators. The most used were the visits managed, caseloads and frequency of health care utilization. The information is free, difficult to access, and updated within the past 2 years (2019). Most of the data were disaggregated (15) and in PDF format. The number of indicators ranged from 1 to 38 (mean, 9). Only 4 regions presented information based on sex and age. We found a Cohen kappa coefficient (κ) of 0.89.Conclusions: the information on health care indicators and outcomes of paediatric care provided by healthcare institutions is heterogeneous. To gain transparency and trust, and to facilitate the comparison between organizations, it should be easier to obtain, homogeneous and clearer. (AU)

Development of PCR-Based Assays for Rapid and Reliable Detection and Identification of Canker-Causing Pathogens from Symptomatic Almond Trees.

Trunk and scaffold canker diseases (TSCDs) of almond cause significant yield and tree losses and reduce the lifespan of orchards. In California, several pathogens cause TSCDs, including Botryosphaeriaceae, Ceratocystis destructans, Eutypa lata, Collophorina hispanica, Pallidophorina paarla, Cytospora, Diaporthe, and Phytophthora spp. Field diagnosis of TSCDs is challenging because symptom delineation among the diseases is not clear. Accurate diagnosis of the causal species requires detailed examination of symptoms and subsequent isolation on medium and identification using morphological criteria and subsequent confirmation using molecular tools. The process is time-consuming and difficult, particularly as morphological characteristics are variable and overlap among species. To facilitate diagnosis of TSCD, we developed PCR assays using 23 species-specific primers designed by exploiting sequence differences in the translation elongation factor, ß-tubulin, or internal transcribed spacer gene. Using genomic DNA from pure cultures of each fungal and oomycete species, each primer pair successfully amplified a single DNA fragment from the target pathogen but not from selected nontarget pathogens or common endophytes. Although 10-fold serial dilution of fungal DNA extracted from either pure cultures or infected wood samples detected as little as 0.1 pg of DNA sample, consistent detection required 10 ng of pathogen DNA from mycelial samples or from wood chips or drill shavings from artificially or naturally infected almond wood samples with visible symptoms. The new PCR assay represents an improved tool for diagnostic laboratories and will be critical to implement effective disease surveillance and control measures.

[Descriptive analysis of hospital activity indicators published by the Autonomous Regional Governments in the Spanish National Health System.] / Análisis descriptivo de los indicadores de actividad hospitalaria publicados por las consejerías de salud.

OBJECTIVE: The supply of health activity data by health regional governments does not have a current study of the issue. The aim of this study was to analyze and describe the indicators of hospital activity related to public health organizations (health departments in the Spanish National Health System) showing the most notable experiences in this regard. METHODS: Observational study. General Internet search engines were used to find and evaluate institutional web portals (Ministry of Health, regional health governments) detailing existence, availability, accessibility and quality of information (aggregation, update, format, gender and age vision) of hospital management activity offered between 2015-2019. Descriptive statistics were used with estimation of inter-observer concordance. RESULTS: Generation of a list of 22 web portals for public health services. All the institutions evaluated had information on hospital activity. It is complex to find, freely available, disaggregated (14), updated (2018), in PDF format (15), gender vision: 2 (Catalonia and Madrid). No. of indicators per region: between 10 and 99 (average=54). Kappa agreement index (κ)=0.84. Notable contributions: Catalonia and Madrid, with other practices to highlight (Castilla y León, Murcia). CONCLUSIONS: The analysis of the management information offered by health regional governments shows a generic pattern of information that is difficult to access, disaggregated and updated at least two years from the time of the study, with a wide range of indicators, reduced contribution of the gender vision and in PDF format, which makes research and teaching difficult.

OBJETIVO: La oferta de datos de actividad sanitaria por las consejerías de salud no dispone de un estudio actual de la cuestión. El objetivo de este trabajo fue analizar y describir los indicadores de actividad hospitalaria relacionada con las organizaciones sanitarias públicas (consejerías de salud/sanidad en el Sistema Nacional de Salud español) mostrando las experiencias más notables en este sentido. METODOS: Estudio observacional. Se utilizaron buscadores generales de Internet para encontrar y valorar portales web institucionales (Ministerio de Sanidad, consejerías de sanidad/salud autonómicas) detallando existencia, disponibilidad, accesibilidad y calidad de la información (agregación, actualización, formato, visión de género y edad) de actividad de gestión hospitalaria ofrecida entre 2015-2019. Se usó estadística descriptiva con la estimación de la concordancia interobservadores. RESULTADOS: Se generó un listado de 22 webs de servicios públicos de salud. Todas las instituciones valoradas disponían de información sobre actividad hospitalaria. Es compleja de encontrar, de libre acceso, desagregada (14), actualizada (2018), en formato PDF (15), visión de género: 2 (Catalunya y Madrid). Nº de indicadores por región: entre 10 y 99 (promedio=54). Índice de acuerdo Kappa (κ)=0,84. Aportaciones notables: Cataluña y Madrid, con otras prácticas a resaltar (Castilla y León, Murcia). CONCLUSIONES: El análisis de la información de gestión ofrecida por las consejerías de salud muestra un patrón genérico de información de difícil acceso, desagregada y actualizada como mínimo a dos años vista desde el momento del estudio, con un rango amplio de indicadores, reducida aportación de la visión de género y en formato PDF que dificulta la investigación y docencia.

Análisis descriptivo de los indicadores de actividad hospitalaria publicados por las consejerías de salud / Descriptive analysis of hospital activity indicators published by the Autonomous Regional Governments in the Spanish National Health System

Fundamentos: La oferta de datos de actividad sanitaria por las consejerías de salud no dispone de un estudio actual de la cuestión. El objetivo de este trabajo fue analizar y describir los indicadores de actividad hospitalaria relacionada con las organizaciones sanitarias públicas (consejerías de salud/sanidad en el Sistema Nacional de Salud español) mostrando las experiencias más notables en este sentido. Métodos: Estudio observacional. Se utilizaron buscadores generales de Internet para encontrar y valorar portales web institucionales (Ministerio de Sanidad, consejerías de sanidad/salud autonómicas) detallando existencia, disponibilidad, accesibilidad y calidad de la información (agregación, actualización, formato, visión de género y edad) de actividad de gestión hospitalaria ofrecida entre 2015-2019. Se usó estadística descriptiva con la estimación de la concordancia interobservadores. Resultados: Se generó un listado de 22 webs de servicios públicos de salud. Todas las instituciones valoradas disponían de información sobre actividad hospitalaria. Es compleja de encontrar, de libre acceso, desagregada (14), actualizada (2018), en formato PDF (15), visión de género: 2 (Catalunya y Madrid). Nº de indicadores por región: entre 10 y 99 (promedio=54). Índice de acuerdo Kappa (κ)=0,84. Aportaciones notables: Cataluña y Madrid, con otras prácticas a resaltar (Castilla y León, Murcia). Conclusiones: El análisis de la información de gestión ofrecida por las consejerías de salud muestra un patrón genérico de información de difícil acceso, desagregada y actualizada como mínimo a dos años vista desde el momento del estudio, con un rango amplio de indicadores, reducida aportación de la visión de género y en formato PDF que dificulta la investigación y docencia.(AU)

Background: The supply of health activity data by health regional governments does not have a current study of the issue. The aim of this study was to analyze and describe the indicators of hospital activity related to public health organizations (health departments in the Spanish National Health System) showing the most notable experiences in this regard. Methods: Observational study. General Internet search engines were used to find and evaluate institutional web portals (Ministry of Health, regional health governments) detailing existence, availability, accessibility and quality of information (aggregation, update, format, gender and age vision) of hospital management activity offered between 2015-2019. Descriptive statistics were used with estimation of interobserver concordance. Results: Generation of a list of 22 web portals for public health services. All the institutions evaluated had information on hospital activity. It is complex to find, freely available, disaggregated (14), updated (2018), in PDF format (15), gender vision: 2 (Catalonia and Madrid). No. of indicators per region: between 10 and 99 (average=54). Kappa agreement index (κ)=0.84. Notable contributions: Catalonia and Madrid, with other practices to highlight (Castilla y León, Murcia). Conclusions: The analysis of the management information offered by health regional governments shows a generic pattern of information that is difficult to access, disaggregated and updated at least two years from the time of the study, with a wide range of indicators, reduced contribution of the gender vision and in PDF format, which makes research and teaching difficult.(AU)

Feasibility and first reports of the MATCH-R repeated biopsy trial at Gustave Roussy.

Unravelling the biological processes driving tumour resistance is necessary to support the development of innovative treatment strategies. We report the design and feasibility of the MATCH-R prospective trial led by Gustave Roussy with the primary objective of characterizing the molecular mechanisms of resistance to cancer treatments. The primary clinical endpoints consist of analyzing the type and frequency of molecular alterations in resistant tumours and compare these to samples prior to treatment. Patients experiencing disease progression after an initial partial response or stable disease for at least 24 weeks underwent a tumour biopsy guided by CT or ultrasound. Molecular profiling of tumours was performed using whole exome sequencing, RNA sequencing and panel sequencing. At data cut-off for feasibility analysis, out of 333 inclusions, tumour biopsies were obtained in 303 cases (91%). From these biopsies, 278 (83%) had sufficient quality for analysis by high-throughput next generation sequencing (NGS). All 278 samples underwent targeted NGS, 215 (70.9%) RNA sequencing and 222 (73.2%) whole exome sequencing. In total, 163 tumours were implanted in NOD scid gamma (NSG) or nude mice and 54 patient-derived xenograft (PDX) models were established, with a success rate of 33%. Adverse events secondary to invasive tumour sampling occurred in 24 patients (7.6%). Study recruitment is still ongoing. Systematic molecular profiling of tumours and the development of patient-derived models of acquired resistance to targeted agents and immunotherapy is feasible and can drive the selection of the next therapeutic strategy.

The Correlation of English Language Proficiency and Indices of Stress and Anxiety in Migrants from Puerto Rico after Hurricane Maria: A Preliminary Study.

OBJECTIVE: Using validated psychological assessment instruments, this study examined the psychological distress associated with potential language barriers experienced by over 135 000 Puerto Rican residents who either temporarily or permanently migrated to the continental United States with the landfall of Hurricane Maria in 2017. METHODS: Participants were Puerto Rican residents (n = 107) who remained in Puerto Rico (control) or left the island for at least 3 months because of Hurricane Maria (migrants). Participants completed an online survey in their preferred language (Spanish or English), which assessed self-reported English language proficiency, Kessler Psychological Distress Scale (K6), Posttraumatic Stress Disorder Checklist for DSM 5, Patient Health Questionnaire 9-item depression scale, and the Generalized Anxiety Disorder 7-item scale. It was hypothesized that migrants with lower self-reported English proficiency would have comparatively higher indices of post-disaster distress than those with a higher proficiency. RESULTS: Dividing the migrant group by preferred language for questionnaire completion, the Fisher's exact test showed significant differences in prevalence of severe mental distress, as defined by K6 scores above 13, between the Spanish-preferring migrants (30.4%), English-preferring migrants (0%), and controls (9.6%). CONCLUSION: Our results support a possible correlation between decreased language proficiency in post-disaster migrants and a higher risk factor for severe mental distress.

Diverse Resistance Mechanisms to the Third-Generation ALK Inhibitor Lorlatinib in ALK-Rearranged Lung Cancer.

PURPOSE: Lorlatinib is a third-generation anaplastic lymphoma kinase (ALK) tyrosine kinase inhibitor with proven efficacy in patients with ALK-rearranged lung cancer previously treated with first- and second-generation ALK inhibitors. Beside compound mutations in the ALK kinase domain, other resistance mechanisms driving lorlatinib resistance remain unknown. We aimed to characterize the mechanisms of resistance to lorlatinib occurring in patients with ALK-rearranged lung cancer and design new therapeutic strategies in this setting. EXPERIMENTAL DESIGN: Resistance mechanisms were investigated in 5 patients resistant to lorlatinib. Longitudinal tumor biopsies were studied using high-throughput next-generation sequencing. Patient-derived models were developed to characterize the acquired resistance mechanisms, and Ba/F3 cell mutants were generated to study the effect of novel ALK compound mutations. Drug combinatory strategies were evaluated in vitro and in vivo to overcome lorlatinib resistance. RESULTS: Diverse biological mechanisms leading to lorlatinib resistance were identified. Epithelial-mesenchymal transition (EMT) mediated resistance in two patient-derived cell lines and was susceptible to dual SRC and ALK inhibition. We characterized three ALK kinase domain compound mutations occurring in patients, L1196M/D1203N, F1174L/G1202R, and C1156Y/G1269A, with differential susceptibility to ALK inhibition by lorlatinib. We identified a novel bypass mechanism of resistance caused by NF2 loss-of-function mutations, conferring sensitivity to treatment with mTOR inhibitors. CONCLUSIONS: This study shows that mechanisms of resistance to lorlatinib are diverse and complex, requiring new therapeutic strategies to tailor treatment upon disease progression.

Circulating inflammation signature predicts overall survival and relapse-free survival in metastatic colorectal cancer.

BACKGROUND: Metastatic colorectal cancer (mCRC) is a highly heterogeneous disease from a clinical, molecular, and immunological perspective. Current predictive models rely primarily in tissue based genetic analysis, which not always correlate with inflammatory response. Here we evaluated the role of a circulating inflammatory signature as a prognostic marker in mCRC. METHODS: Two hundred eleven newly diagnosed patients with mCRC were enrolled in the study. One hundred twenty-one patients had unresectable metastases, whereas ninety patients had potentially resectable liver metastases at presentation. Analysis of miR-21, IL-6, and IL-8 in the plasma of peripheral blood was performed at baseline. Patients with high circulating levels of ≥2 of the three inflammation markers (miR-21, IL-6, and IL-8) were considered to have the "Inflammation phenotype-positive CISIG". RESULTS: Positive CISIG was found in 39/90 (43%) and 50/121 (45%) patients in the resectable and unresectable cohort, respectively. In the resectable population the median relapse-free survival was 18.4 compared to 31.4 months (p = 0.001 HR 2.09, 95% CI 1.2-3.67) for positive vs. negative CISIG. In contrast, the individual components were not significant. In the same population the median overall survival was 46.2 compared to 66.0 months (p = 0.0003, HR 2.57, 95% CI 1.26-5.27) for positive vs. negative CISIG, but not significant for the individual components. In the unresectable population, the median overall survival was 13.5 compared to 25.0 months (p = 0.0008, HR 2.49, 95% CI 1.46-4.22) for positive vs. negative CISIG. IL-6 was independently prognostic with overall survival of 16.2 compared to 27.0 months (p = 0.004, HR 1.96, 95% CI 1.24-3.11) for high vs. low IL-6, but not the other components. Using a Cox regression model, we demonstrated that CISIG is an independent predictive marker of survival in patients with unresectable disease (HR 1.8, 95% CI 1.2, 2.8, p < 0.01). CONCLUSION: In two different cohorts, we demonstrated that CISIG is a strong prognostic factor of relapse-free and overall survival of patients with mCRC. Based on these data, analysis of circulating inflammatory signaling can be complimentary to traditional molecular testing.

Valproic acid disrupts the oscillatory expression of core circadian rhythm transcription factors.

Valproic acid (VPA) is a well-established therapeutic used in treatment of seizure and mood disorders as well as migraines and a known hepatotoxicant. About 50% of VPA users experience metabolic disruptions, including weight gain, hyperlipidemia, and hyperinsulinemia, among others. Several of these metabolic abnormalities are similar to the effects of circadian rhythm disruption. In the current study, we examine the effect of VPA exposure on the expression of core circadian transcription factors that drive the circadian clock via a transcription-translation feedback loop. In cells with an unsynchronized clock, VPA simultaneously upregulated the expression of genes encoding core circadian transcription factors that regulate the positive and negative limbs of the feedback loop. Using low dose glucocorticoid, we synchronized cultured fibroblast cells to a circadian oscillatory pattern. Whether VPA was added at the time of synchronization or 12h later at CT12, we found that VPA disrupted the oscillatory expression of multiple genes encoding essential transcription factors that regulate circadian rhythm. Therefore, we conclude that VPA has a potent effect on the circadian rhythm transcription-translation feedback loop that may be linked to negative VPA side effects in humans. Furthermore, our study suggests potential chronopharmacology implications of VPA usage.

Class I lysine deacetylases promote glucocorticoid-induced transcriptional repression through functional interaction with LSD1.

Small molecule inhibitors of lysine deacetylases (KDACs) are approved for clinical use in treatment of several diseases. Nuclear receptors, such as the glucocorticoid receptor (GR) use lysine acetyltransferases (KATs or HATs) and KDACs to regulate transcription through acetylation and deacetylation of protein targets such as histones. Previously we have shown that KDAC1 activity facilitates GR-activated transcription at about half of all cellular target genes. In the current study we examine the role of Class I KDACs in glucocorticoid-mediated repression of gene expression. Inhibition of KDACs through two structurally distinct Class I-selective inhibitors prevented dexamethasone (Dex)-mediated transcriptional repression in a gene-selective fashion. In addition, KDAC activity is also necessary to maintain repression. Steroid receptor coactivator 2 (SRC2), which is known to play a vital role in GR-mediated repression of pro-inflammatory genes, was found to be dispensable for repression of glucocorticoid target genes sensitive to KDAC inhibition. At the promoters of these genes, KDAC inhibition did not result in altered nucleosome occupancy or histone H3 acetylation. Surprisingly, KDAC inhibition rapidly induced a significant decrease in H3K4Me2 at promoter nucleosomes with no corresponding change in H3K4Me3, suggesting the activation of the lysine demethylase, LSD1/KDM1A. Depletion of LSD1 expression via siRNA restored Dex-mediated repression in the presence of KDAC inhibitors, suggesting that LSD1 activation at these gene promoters is incompatible with transcriptional repression. Treatment with KDAC inhibitors does not alter cellular levels of LSD1 or its association with Dex-repressed gene promoters. Therefore, we conclude that Class I KDACs facilitate Dex-induced transcriptional repression by suppressing LSD1 complex activity at selected target gene promoters. Rather than facilitating repression of transcription, LSD1 opposes it in these gene contexts.

Predicting episodic memory formation for movie events.

Episodic memories are long lasting and full of detail, yet imperfect and malleable. We quantitatively evaluated recollection of short audiovisual segments from movies as a proxy to real-life memory formation in 161 subjects at 15 minutes up to a year after encoding. Memories were reproducible within and across individuals, showed the typical decay with time elapsed between encoding and testing, were fallible yet accurate, and were insensitive to low-level stimulus manipulations but sensitive to high-level stimulus properties. Remarkably, memorability was also high for single movie frames, even one year post-encoding. To evaluate what determines the efficacy of long-term memory formation, we developed an extensive set of content annotations that included actions, emotional valence, visual cues and auditory cues. These annotations enabled us to document the content properties that showed a stronger correlation with recognition memory and to build a machine-learning computational model that accounted for episodic memory formation in single events for group averages and individual subjects with an accuracy of up to 80%. These results provide initial steps towards the development of a quantitative computational theory capable of explaining the subjective filtering steps that lead to how humans learn and consolidate memories.

Resensitization to Crizotinib by the Lorlatinib ALK Resistance Mutation L1198F.

In a patient who had metastatic anaplastic lymphoma kinase (ALK)-rearranged lung cancer, resistance to crizotinib developed because of a mutation in the ALK kinase domain. This mutation is predicted to result in a substitution of cysteine by tyrosine at amino acid residue 1156 (C1156Y). Her tumor did not respond to a second-generation ALK inhibitor, but it did respond to lorlatinib (PF-06463922), a third-generation inhibitor. When her tumor relapsed, sequencing of the resistant tumor revealed an ALK L1198F mutation in addition to the C1156Y mutation. The L1198F substitution confers resistance to lorlatinib through steric interference with drug binding. However, L1198F paradoxically enhances binding to crizotinib, negating the effect of C1156Y and resensitizing resistant cancers to crizotinib. The patient received crizotinib again, and her cancer-related symptoms and liver failure resolved. (Funded by Pfizer and others; ClinicalTrials.gov number, NCT01970865.).

PF-06463922, an ALK/ROS1 Inhibitor, Overcomes Resistance to First and Second Generation ALK Inhibitors in Preclinical Models.

We report the preclinical evaluation of PF-06463922, a potent and brain-penetrant ALK/ROS1 inhibitor. Compared with other clinically available ALK inhibitors, PF-06463922 displayed superior potency against all known clinically acquired ALK mutations, including the highly resistant G1202R mutant. Furthermore, PF-06463922 treatment led to regression of EML4-ALK-driven brain metastases, leading to prolonged mouse survival, in a superior manner. Finally, PF-06463922 demonstrated high selectivity and safety margins in a variety of preclinical studies. These results suggest that PF-06463922 will be highly effective for the treatment of patients with ALK-driven lung cancers, including those who relapsed on clinically available ALK inhibitors because of secondary ALK kinase domain mutations and/or brain metastases.

Patient-derived models of acquired resistance can identify effective drug combinations for cancer.

Targeted cancer therapies have produced substantial clinical responses, but most tumors develop resistance to these drugs. Here, we describe a pharmacogenomic platform that facilitates rapid discovery of drug combinations that can overcome resistance. We established cell culture models derived from biopsy samples of lung cancer patients whose disease had progressed while on treatment with epidermal growth factor receptor (EGFR) or anaplastic lymphoma kinase (ALK) tyrosine kinase inhibitors and then subjected these cells to genetic analyses and a pharmacological screen. Multiple effective drug combinations were identified. For example, the combination of ALK and MAPK kinase (MEK) inhibitors was active in an ALK-positive resistant tumor that had developed a MAP2K1 activating mutation, and the combination of EGFR and fibroblast growth factor receptor (FGFR) inhibitors was active in an EGFR mutant resistant cancer with a mutation in FGFR3. Combined ALK and SRC (pp60c-src) inhibition was effective in several ALK-driven patient-derived models, a result not predicted by genetic analysis alone. With further refinements, this strategy could help direct therapeutic choices for individual patients.

Class I lysine deacetylases facilitate glucocorticoid-induced transcription.

Nuclear receptors use lysine acetyltransferases and lysine deacetylases (KDACs) in regulating transcription through histone acetylation. Lysine acetyltransferases interact with steroid receptors upon binding of an agonist and are recruited to target genes. KDACs have been shown to interact with steroid receptors upon binding to an antagonist. We have shown previously that KDAC inhibitors (KDACis) potently repress the mouse mammary tumor virus promoter through transcriptional mechanisms and impair the ability of the glucocorticoid receptor (GR) to activate it, suggesting that KDACs can play a positive role in GR transactivation. In the current study, we extended this analysis to the entire GR transcriptome and found that the KDACi valproic acid impairs the ability of agonist-bound GR to activate about 50% of its target genes. This inhibition is largely due to impaired transcription rather than defective GR processing and was also observed using a structurally distinct KDACi. Depletion of KDAC1 expression mimicked the effects of KDACi in over half of the genes found to be impaired in GR transactivation. Simultaneous depletion of KDACs 1 and 2 caused full or partial impairment of several more GR target genes. Altogether we found that Class I KDAC activity facilitates GR-mediated activation at a sizable fraction of GR-activated target genes and that KDAC1 alone or in coordination with KDAC2 is required for efficient GR transactivation at many of these target genes. Finally, our work demonstrates that KDACi exposure has a significant impact on GR signaling and thus has ramifications for the clinical use of these drugs.

A comparative study of six European databases of medically oriented Web resources.

OBJECTIVES: The paper describes six European medically oriented databases of Web resources, pertaining to five quality-controlled subject gateways, and compares their performance. METHOD: The characteristics, coverage, procedure for selecting Web resources, record structure, searching possibilities, and existence of user assistance were described for each database. Performance indicators for each database were obtained by means of searches carried out using the key words, "myocardial infarction." RESULTS: Most of the databases originated in the 1990s in an academic or library context and include all types of Web resources of an international nature. Five databases use Medical Subject Headings. The number of fields per record varies between three and nineteen. The language of the search interfaces is mostly English, and some of them allow searches in other languages. In some databases, the search can be extended to Pubmed. Organizing Medical Networked Information, Catalogue et Index des Sites Médicaux Francophones, and Diseases, Disorders and Related Topics produced the best results. CONCLUSIONS: The usefulness of these databases as quick reference resources is clear. In addition, their lack of content overlap means that, for the user, they complement each other. Their continued survival faces three challenges: the instability of the Internet, maintenance costs, and lack of use in spite of their potential usefulness.