Scaling up analogical innovation with crowds and AI.

Analogy-the ability to find and apply deep structural patterns across domains-has been fundamental to human innovation in science and technology. Today there is a growing opportunity to accelerate innovation by moving analogy out of a single person's mind and distributing it across many information processors, both human and machine. Doing so has the potential to overcome cognitive fixation, scale to large idea repositories, and support complex problems with multiple constraints. Here we lay out a perspective on the future of scalable analogical innovation and first steps using crowds and artificial intelligence (AI) to augment creativity that quantitatively demonstrate the promise of the approach, as well as core challenges critical to realizing this vision.

Retrospective analysis of Schlafen11 (SLFN11) to predict the outcomes to therapies affecting the DNA damage response.

BACKGROUND: The absence of the putative DNA/RNA helicase Schlafen11 (SLFN11) is thought to cause resistance to DNA-damaging agents (DDAs) and PARP inhibitors. METHODS: We developed and validated a clinically applicable SLFN11 immunohistochemistry assay and retrospectively correlated SLFN11 tumour levels to patient outcome to the standard of care therapies and olaparib maintenance. RESULTS: High SLFN11 associated with improved prognosis to the first-line treatment with DDAs platinum-plus-etoposide in SCLC patients, but was not strongly linked to paclitaxel-platinum response in ovarian cancer patients. Multivariate analysis of patients with relapsed platinum-sensitive ovarian cancer from the randomised, placebo-controlled Phase II olaparib maintenance Study19 showed SLFN11 tumour levels associated with sensitivity to olaparib. Study19 patients with high SLFN11 had a lower progression-free survival (PFS) hazard ratio compared to patients with low SLFN11, although both groups had the benefit of olaparib over placebo. Whilst caveated by small sample size, this trend was maintained for PFS, but not overall survival, when adjusting for BRCA status across the olaparib and placebo treatment groups, a key driver of PARP inhibitor sensitivity. CONCLUSION: We provide clinical evidence supporting the role of SLFN11 as a DDA therapy selection biomarker in SCLC and highlight the need for further clinical investigation into SLFN11 as a PARP inhibitor predictive biomarker.

Sustained PU.1 levels balance cell-cycle regulators to prevent exhaustion of adult hematopoietic stem cells.

To provide a lifelong supply of blood cells, hematopoietic stem cells (HSCs) need to carefully balance both self-renewing cell divisions and quiescence. Although several regulators that control this mechanism have been identified, we demonstrate that the transcription factor PU.1 acts upstream of these regulators. So far, attempts to uncover PU.1's role in HSC biology have failed because of the technical limitations of complete loss-of-function models. With the use of hypomorphic mice with decreased PU.1 levels specifically in phenotypic HSCs, we found reduced HSC long-term repopulation potential that could be rescued completely by restoring PU.1 levels. PU.1 prevented excessive HSC division and exhaustion by controlling the transcription of multiple cell-cycle regulators. Levels of PU.1 were sustained through autoregulatory PU.1 binding to an upstream enhancer that formed an active looped chromosome architecture in HSCs. These results establish that PU.1 mediates chromosome looping and functions as a master regulator of HSC proliferation.

A graphical model approach visualizes regulatory relationships between genome-wide transcription factor binding profiles.

Integrated analysis of multiple genome-wide transcription factor (TF)-binding profiles will be vital to advance our understanding of the global impact of TF binding. However, existing methods for measuring similarity in large numbers of chromatin immunoprecipitation assays with sequencing (ChIP-seq), such as correlation, mutual information or enrichment analysis, are limited in their ability to display functionally relevant TF relationships. In this study, we propose the use of graphical models to determine conditional independence between TFs and showed that network visualization provides a promising alternative to distinguish 'direct' versus 'indirect' TF interactions. We applied four algorithms to measure 'direct' dependence to a compendium of 367 mouse haematopoietic TF ChIP-seq samples and obtained a consensus network known as a 'TF association network' where edges in the network corresponded to likely causal pairwise relationships between TFs. The 'TF association network' illustrates the role of TFs in developmental pathways, is reminiscent of combinatorial TF regulation, corresponds to known protein-protein interactions and indicates substantial TF-binding reorganization in leukemic cell types. With the rapid increase in TF ChIP-Seq data sets, the approach presented here will be a powerful tool to study transcriptional programmes across a wide range of biological systems.

Impaired Handgrip Strength Does Not Predict Postoperative Morbidity in Major Hepatobiliary Surgery.

BACKGROUND: Assessment of preoperative handgrip strength (HGS) is an objective and inexpensive bedside tool, which has been investigated to predict morbidity risk in elective surgery. However, its use is not validated in patients undergoing major elective hepatobiliary surgery (MEHS). The aim of this study is to investigate the use of HGS to predict morbidity in patients undergoing MEHS. METHODS: This is a single-center prospective study involving 81 patients who underwent MEHS over 21 mo from July 2014 to March 2016. MEHS was defined as any hepatobiliary surgery expected to last more than 2 h and/or with an anticipated blood loss of ≥500 mL. HGS was assessed in both dominant and nondominant hands with standardization and subsequently recorded and expressed as a percentage of a general, age- and gender-matched normative values. RESULTS: The mean age was 65.2 ± 9.5 y with male predominance (n = 52, 64.2%). Approximately, half of the patients underwent liver resection (n = 43, 53.1%). There was no difference in the incidence of Clavien-Dindo ≥ grade IIIA in both dominant HGS (impaired HGS 8/33 [24.2%], normal HGS 6/48 [12.5%]; P = 0.170) and nondominant HGS (impaired HGS 8/33 [21.1%], normal HGS 6/43 [14%]; P = 0.399). Dominant and nondominant HGS showed poor discriminatory ability in the prediction of Clavien-Dindo ≥ grade IIIA complications (dominant HGS area under the curve [AUC] = 0.572; nondominant HGS AUC 0.545). However, the use of dominant HGS showed moderate discriminatory ability to predict the length of hospital stay ≥21 d (AUC = 0.759). CONCLUSIONS: The use of HGS may not predict Clavien-Dindo ≥ grade IIIA complications, but predicts a prolonged length of hospital stay ≥21 d.

Key regulators control distinct transcriptional programmes in blood progenitor and mast cells.

Despite major advances in the generation of genome-wide binding maps, the mechanisms by which transcription factors (TFs) regulate cell type identity have remained largely obscure. Through comparative analysis of 10 key haematopoietic TFs in both mast cells and blood progenitors, we demonstrate that the largely cell type-specific binding profiles are not opportunistic, but instead contribute to cell type-specific transcriptional control, because (i) mathematical modelling of differential binding of shared TFs can explain differential gene expression, (ii) consensus binding sites are important for cell type-specific binding and (iii) knock-down of blood stem cell regulators in mast cells reveals mast cell-specific genes as direct targets. Finally, we show that the known mast cell regulators Mitf and c-fos likely contribute to the global reorganisation of TF binding profiles. Taken together therefore, our study elucidates how key regulatory TFs contribute to transcriptional programmes in several distinct mammalian cell types.

CODEX: a next-generation sequencing experiment database for the haematopoietic and embryonic stem cell communities.

CODEX (http://codex.stemcells.cam.ac.uk/) is a user-friendly database for the direct access and interrogation of publicly available next-generation sequencing (NGS) data, specifically aimed at experimental biologists. In an era of multi-centre genomic dataset generation, CODEX provides a single database where these samples are collected, uniformly processed and vetted. The main drive of CODEX is to provide the wider scientific community with instant access to high-quality NGS data, which, irrespective of the publishing laboratory, is directly comparable. CODEX allows users to immediately visualize or download processed datasets, or compare user-generated data against the database's cumulative knowledge-base. CODEX contains four types of NGS experiments: transcription factor chromatin immunoprecipitation coupled to high-throughput sequencing (ChIP-Seq), histone modification ChIP-Seq, DNase-Seq and RNA-Seq. These are largely encompassed within two specialized repositories, HAEMCODE and ESCODE, which are focused on haematopoiesis and embryonic stem cell samples, respectively. To date, CODEX contains over 1000 samples, including 221 unique TFs and 93 unique cell types. CODEX therefore provides one of the most complete resources of publicly available NGS data for the direct interrogation of transcriptional programmes that regulate cellular identity and fate in the context of mammalian development, homeostasis and disease.

Constrained transcription factor spacing is prevalent and important for transcriptional control of mouse blood cells.

Combinatorial transcription factor (TF) binding is essential for cell-type-specific gene regulation. However, much remains to be learned about the mechanisms of TF interactions, including to what extent constrained spacing and orientation of interacting TFs are critical for regulatory element activity. To examine the relative prevalence of the 'enhanceosome' versus the 'TF collective' model of combinatorial TF binding, a comprehensive analysis of TF binding site sequences in large scale datasets is necessary. We developed a motif-pair discovery pipeline to identify motif co-occurrences with preferential distance(s) between motifs in TF-bound regions. Utilizing a compendium of 289 mouse haematopoietic TF ChIP-seq datasets, we demonstrate that haematopoietic-related motif-pairs commonly occur with highly conserved constrained spacing and orientation between motifs. Furthermore, motif clustering revealed specific associations for both heterotypic and homotypic motif-pairs with particular haematopoietic cell types. We also showed that disrupting the spacing between motif-pairs significantly affects transcriptional activity in a well-known motif-pair-E-box and GATA, and in two previously unknown motif-pairs with constrained spacing-Ets and Homeobox as well as Ets and E-box. In this study, we provide evidence for widespread sequence-specific TF pair interaction with DNA that conforms to the 'enhanceosome' model, and furthermore identify associations between specific haematopoietic cell-types and motif-pairs.

Immune Cell Abundance and T-cell Receptor Landscapes Suggest New Patient Stratification Strategies in Head and Neck Squamous Cell Carcinoma.

Head and neck squamous cell carcinoma (HNSCC) is a molecularly and spatially heterogeneous disease frequently characterized by impairment of immunosurveillance mechanisms. Despite recent success with immunotherapy treatment, disease progression still occurs quickly after treatment in the majority of cases, suggesting the need to improve patient selection strategies. In the quest for biomarkers that may help inform response to checkpoint blockade, we characterized the tumor microenvironment (TME) of 162 HNSCC primary tumors of diverse etiologic and spatial origin, through gene expression and IHC profiling of relevant immune proteins, T-cell receptor (TCR) repertoire analysis, and whole-exome sequencing. We identified five HNSCC TME categories based on immune/stromal composition: (i) cytotoxic, (ii) plasma cell rich, (iii) dendritic cell rich, (iv) macrophage rich, and (v) immune-excluded. Remarkably, the cytotoxic and plasma cell rich subgroups exhibited a phenotype similar to tertiary lymphoid structures (TLS), which have been previously linked to immunotherapy response. We also found an increased richness of the TCR repertoire in these two subgroups and in never smokers. Mutational patterns evidencing APOBEC activity were enriched in the plasma cell high subgroup. Furthermore, specific signal propagation patterns within the Ras/ERK and PI3K/AKT pathways associated with distinct immune phenotypes. While traditionally CD8/CD3 T-cell infiltration and immune checkpoint expression (e.g., PD-L1) have been used in the patient selection process for checkpoint blockade treatment, we suggest that additional biomarkers, such as TCR productive clonality, smoking history, and TLS index, may have the ability to pull out potential responders to benefit from immunotherapeutic agents. SIGNIFICANCE: Here we present our findings on the genomic and immune landscape of primary disease in a cohort of 162 patients with HNSCC, benefitting from detailed molecular and clinical characterization. By employing whole-exome sequencing and gene expression analysis of relevant immune markers, TCR profiling, and staining of relevant proteins involved in immune response, we highlight how distinct etiologies, cell intrinsic, and environmental factors combine to shape the landscape of HNSCC primary disease.

Profiling of Aroma-Active Compounds in Ylang-Ylang Essential Oils by Aroma Extract Dilution Analysis (AEDA) and Chemometric Methods.

The aroma-active compounds in the extra, first, and third grades of ylang-ylang essential oils (YYEO) from Comoros and Madagascar were identified by gas chromatography-mass spectrometry with olfactometry (GC-MS/O) using an aroma extract dilution analysis (AEDA) technique. In the previous study, the authors investigated differences in volatile compound profiles between YYEO of different grades and regions using GC coupled with a flame ionization detector (FID) and GC-MS. This study follows up with identification of the aroma-active compounds present in YYEO of various grades from both origins and to profile the aroma of those oils. For the first time, principal component analysis (PCA) on AEDA logarithmic flavor dilution (LFD) data was performed, in comparison with the corresponding PCA on GC-FID-MS data. Based on AEDA data, 21 aroma-active compounds were found across all samples and grades of YYEO, with 8 common ones previously identified by GC-FID. Linalool had the highest odor activity and is the major component of YYEO, followed by geraniol, although the latter only appeared as a much smaller peak in the chromatogram. Other trace compounds such as eugenol and vanillin were also found to be significant to the aroma of YYEO. Using PCA on resulting LFD data, YYEO from Comoros were found to have spicier odor qualities as compared to those from Madagascar. The main contributors that determine the difference in a spicy aroma profile of Comoros and Madagascar oils are vanillin, methyl eugenol, and trans-cinnamyl acetate.

Anti-PD-L1 and anti-CD73 combination therapy promotes T cell response to EGFR-mutated NSCLC.

Treatment with anti-PD-1 and anti-PD-L1 therapies has shown durable clinical benefit in non-small cell lung cancer (NSCLC). However, patients with NSCLC with epidermal growth factor receptor (EGFR) mutations do not respond as well to treatment as patients without an EGFR mutation. We show that EGFR-mutated NSCLC expressed higher levels of CD73 compared with EGFR WT tumors and that CD73 expression was regulated by EGFR signaling. EGFR-mutated cell lines were significantly more resistant to T cell killing compared with WT cell lines through suppression of T cell proliferation and function. In a xenograft mouse model of EGFR-mutated NSCLC, neither anti-PD-L1 nor anti-CD73 antibody alone inhibited tumor growth compared with the isotype control. In contrast, the combination of both antibodies significantly inhibited tumor growth, increased the number of tumor-infiltrating CD8+ T cells, and enhanced IFN-γ and TNF-α production of these T cells. Consistently, there were increases in gene expression that corresponded to inflammation and T cell function in tumors treated with the combination of anti-PD-L1 and anti-CD73. Together, these results further support the combination of anti-CD73 and anti-PD-L1 therapies in treating EGFR-mutated NSCLC, while suggesting that increased T cell activity may play a role in response to therapy.

PDGF, TGF-beta, and FGF signaling is important for differentiation and growth of mesenchymal stem cells (MSCs): transcriptional profiling can identify markers and signaling pathways important in differentiation of MSCs into adipogenic, chondrogenic, and osteogenic lineages.

We compared the transcriptomes of marrow-derived mesenchymal stem cells (MSCs) with differentiated adipocytes, osteocytes, and chondrocytes derived from these MSCs. Using global gene-expression profiling arrays to detect RNA transcripts, we have identified markers that are specific for MSCs and their differentiated progeny. Further, we have also identified pathways that MSCs use to differentiate into adipogenic, chondrogenic, and osteogenic lineages. We identified activin-mediated transforming growth factor (TGF)-beta signaling, platelet-derived growth factor (PDGF) signaling and fibroblast growth factor (FGF) signaling as the key pathways involved in MSC differentiation. The differentiation of MSCs into these lineages is affected when these pathways are perturbed by inhibitors of cell surface receptor function. Since growth and differentiation are tightly linked processes, we also examined the importance of these 3 pathways in MSC growth. These 3 pathways were necessary and sufficient for MSC growth. Inhibiting any of these pathways slowed MSC growth, whereas a combination of TGF-beta, PDGF, and beta-FGF was sufficient to grow MSCs in a serum-free medium up to 5 passages. Thus, this study illustrates it is possible to predict signaling pathways active in cellular differentiation and growth using microarray data and experimentally verify these predictions.

Human thrust in aquatic environment: The effect of post-activation potentiation on flutter kick.

Herein, we analyse by experimental techniques the human kicking thrust and measure the effect of a warm-up routine that includes post-activation potentiation (PAP) sets on front-crawl flutter kick thrust, kinematics, and performance. Sixteen male competitive swimmers with 22.13 ±â€¯3.84 years of age were randomly assigned in a crossover manner to undergo a standard warm-up (non-PAP; control condition) and a warm-up that included PAP sets (PAP; experimental condition) consisting in 2 × 5 repetitions of unloaded countermovement jump. Participants performed a 25 m all-out trial in front-crawl with only flutter kicks eight min after each warm-up. Kinetics (i.e., peak thrust, mean thrust, and thrust-time integral) and kinematics (i.e., speed, speed fluctuation and kicking frequency) were experimentally collected by an in-house customized system composed of differential pressure sensors, speedo-meter, and underwater camera. Peak thrust (P = 0.02, d = 0.66) and mean thrust (P = 0.10, d = 0.40) were increased by 15% in PAP compared to non-PAP. Large and significant differences were noted in speed (P = 0.01, d = 0.54) and speed fluctuation (P = 0.02, d = 0.58), which improved by 10% in PAP compared with non-PAP. In conclusion, a warm-up that includes PAP sets improves kicking thrust, kinematics and performance.

Fungal Isolates in Peritoneal Fluid Culture Do Not Impact Peri-Operative Outcomes of Peptic Ulcer Perforation.

Background: Fungal isolates from peritoneal fluid sampling in patients with perforated peptic ulcer (PPU) is not uncommon and its management unclear. This study aims to evaluate whether the presence of fungus in peritoneal fluid cultures is a predictor of morbidity and mortality after laparotomy for PPU. Method: This is a single-center retrospective study including adult patients with perforated gastric and duodenal ulcers over a 10-year period (January 2004 to January 2014). Evaluation of predictors contributing to fungal growth was conducted using multiple logistic regression analysis. Operative factors and 30-day mortality and morbidity outcomes were compared against fungal growth using a multivariable generalized linear mixed model analysis. Results: The median age was 58 (interquartile range [IQR] 44-70) years with 110 (20.3%) females. In addition to hypertension and hyperlipidemia, diabetes mellitus (13.5%), ischemic heart disease (2.6%), and heart failure (2.4%) were common. Fungus was cultured from peritoneal fluid in 209 (38.6%) patients. Median American Society of Anesthesiology (ASA) score was 2 (IQR 2-3) and median Mannheim peritonitis index (MPI) score was 15 (IQR 10-20). Free air was detected in 323 (59.6%) patients and 52 (9.6%) patients had gastrectomy. Median length of stay was 7 (IQR 6-11) days. All-cause complications were seen in 53 (9.8%) patients, of whom 37 patients (6.8%) developed intra-abdominal collection, 20 patients (3.7%) had anastomotic leakage, and 12 patients (2.2%) required repeat operation. Thirty-day mortality was seen in 47 (8.7%) patients. Multivariable analysis showed age (median age, 64; IQR 53-74) as a predictor of fungal growth (p < 0.001) but fungal growth not a predictor of adverse peri-operative outcomes. Conclusion: Fungal isolates in peritoneal fluid cultures are more likely to occur in older patients who have PPU. Presence of fungal isolates does not impact peri-operative outcomes.

Linking pattern completion in the hippocampus to predictive coding in visual cortex.

Models of predictive coding frame perception as a generative process in which expectations constrain sensory representations. These models account for expectations about how a stimulus will move or change from moment to moment, but do not address expectations about what other, distinct stimuli are likely to appear based on prior experience. We show that such memory-based expectations in human visual cortex are related to the hippocampal mechanism of pattern completion.

Shared transcription factors contribute to distinct cell fates.

Genome-wide transcription factor (TF) binding profiles differ dramatically between cell types. However, not much is known about the relationship between cell-type-specific binding patterns and gene expression. A recent study demonstrated how the same TFs can have functional roles when binding to largely non-overlapping genomic regions in hematopoietic progenitor and mast cells. Cell-type specific binding profiles of shared TFs are therefore not merely the consequence of opportunistic and functionally irrelevant binding to accessible chromatin, but instead have the potential to make meaningful contributions to cell-type specific transcriptional programs.

The epidermis comprises autonomous compartments maintained by distinct stem cell populations.

The complex anatomy of the epidermis contains multiple adult stem cell populations, but the extent to which they functionally overlap during homeostasis, wound healing, and tumor initiation remains poorly defined. Here, we demonstrate that Lrig1(+ve) cells are highly proliferative epidermal stem cells. Long-term clonal analysis reveals that Lrig1(+ve) cells maintain the upper pilosebaceous unit, containing the infundibulum and sebaceous gland as independent compartments, but contribute to neither the hair follicle nor the interfollicular epidermis, which are maintained by distinct stem cell populations. In contrast, upon wounding, stem cell progeny from multiple compartments acquire lineage plasticity and make permanent contributions to regenerating tissue. We further show that oncogene activation in Lrig1(+ve) cells drives hyperplasia but requires auxiliary stimuli for tumor formation. In summary, our data demonstrate that epidermal stem cells are lineage restricted during homeostasis and suggest that compartmentalization may constitute a conserved mechanism underlying epithelial tissue maintenance.

A distinct reactive oxygen species profile confers chemoresistance in glioma-propagating cells and associates with patient survival outcome.

AIMS: We explore the role of an elevated O2(-):H2O2 ratio as a prosurvival signal in glioma-propagating cells (GPCs). We hypothesize that depleting this ratio sensitizes GPCs to apoptotic triggers. RESULTS: We observed that an elevated O2(-):H2O2 ratio conferred enhanced resistance in GPCs, and depletion of this ratio by pharmacological and genetic methods sensitized cells to apoptotic triggers. We established the reactive oxygen species (ROS) Index as a quantitative measure of a normalized O2(-):H2O2 ratio and determined its utility in predicting chemosensitivity. Importantly, mice implanted with GPCs of a reduced ROS Index demonstrated extended survival. Analysis of tumor sections revealed effective targeting of complementarity determinant 133 (CD133)- and nestin-expressing neural precursors. Further, we established the Connectivity Map to interrogate a gene signature derived from a varied ROS Index for the patterns of association with individual patient gene expression in four clinical databases. We showed that patients with a reduced ROS Index demonstrate better survival. These data provide clinical evidence for the viability of our O2(-):H2O2-mediated chemosensitivity profiles. INNOVATION AND CONCLUSION: Gliomas are notoriously recurrent and highly infiltrative, and have been shown to arise from stem-like cells. We implicate an elevated O2(-):H2O2 ratio as a prosurvival signal in GPC self-renewal and proliferation. The ROS Index provides quantification of O2(-):H2O2-mediated chemosensitivity, an advancement in a previously qualitative field. Intriguingly, glioma patients with a reduced ROS Index correlate with longer survival and the Proneural molecular classification, a feature frequently associated with tumors of better prognosis. These data emphasize the feasibility of manipulating the O2(-):H2O2 ratio as a therapeutic strategy.

Progenitor-like traits contribute to patient survival and prognosis in oligodendroglial tumors.

PURPOSE: Patient-derived glioma-propagating cells (GPC) contain karyotypic and gene expression profiles that are found in the primary tumor. However, their clinical relevance is unclear. We ask whether GPCs contribute to disease progression and survival outcome in patients with glioma by analyzing gene expression profiles. EXPERIMENTAL DESIGN: We tapped into public sources of GPC gene expression data and derived a gene signature distinguishing oligodendroglial from glioblastoma multiforme (GBM) GPCs. By adapting a method in glioma biology, the Connectivity Map, we interrogated its strength of association in public clinical databases. We validated the top-ranking signaling pathways Wnt, Notch, and TGFß, in GPCs and primary tumor specimens. RESULTS: We observed that patients with better prognosis correlated with oligodendroglial GPC features and lower tumor grade, and this was independent of the current clinical indicator, 1p/19q status. Patients with better prognosis had proneural tumors whereas the poorly surviving cohort had mesenchymal tumors. In addition, oligodendroglial GPCs were more sensitive to Wnt and Notch inhibition whereas GBM GPCs responded to TGFßR1 inhibition. CONCLUSIONS: We provide evidence that GPCs are clinically relevant. In addition, the more favorable prognosis of oligodendroglial tumors over GBM could be recapitulated transcriptomically at the GPC level, underscoring the relevance of this cellular model. Our gene signature detects molecular heterogeneity in oligodendroglial tumors that cannot be accounted for by the 1p/19q status alone, indicating that stem-like traits contribute to clinical status. Collectively, these data highlight the limitation of morphology-based histologic analyses in tumor classification, consequently impacting on treatment decisions.