Abstract: Cancers exhibit extensive mutational heterogeneity, and the resulting long-tail phenomenon complicates the discovery of genes and pathways that are significantly mutated in cancer. We perform a pan-cancer analysis of mutated networks in 3,281 samples from 12 cancer types from The Cancer Genome Atlas (TCGA) using HotNet2, a new algorithm to find mutated subnetworks that overcomes the limitations of existing single-gene, pathway and network approaches. We identify 16 significantly mutated subnetworks that comprise well-known cancer signaling pathways as well as subnetworks with less characterized roles in cancer, including cohesin, condensin and others. Many of these subnetworks exhibit co-occurring mutations across samples. These subnetworks contain dozens of genes with rare somatic mutations across multiple cancers; many of these genes have additional evidence supporting a role in cancer. By illuminating these rare combinations of mutations, pan-cancer network analyses provide a roadmap to investigate new diagnostic and therapeutic opportunities across cancer types.

Abstract: Environmental pollution has been on the rise in the past few decades owing to increased human activities on energy reservoirs, unsafe agricultural practices and rapid industrialization. Amongst the pollutants that are of environmental and public health concerns due to their toxicities are: heavy metals, nuclear wastes, pesticides, green house gases, and hydrocarbons. Remediation of polluted sites using microbial process (bioremediation) has proven effective and reliable due to its eco-friendly features. Bioremediation can either be carried out ex situ or in situ, depending on several factors, which include but not limited to cost, site characteristics, type and concentration of pollutants. Generally, ex situ techniques apparently are more expensive compared to in situ techniques as a result of additional cost attributable to excavation. However, cost of on-site installation of equipment, and inability to effectively visualize and control the subsurface of polluted sites are of major concerns when carrying out in situ bioremediation. Therefore, choosing appropriate bioremediation technique, which will effectively reduce pollutant concentrations to an innocuous state, is crucial for a successful bioremediation project. Furthermore, the two major approaches to enhance bioremediation are biostimulation and bioaugmentation provided that environmental factors, which determine the success of bioremediation, are maintained at optimal range. This review provides more insight into the two major bioremediation techniques, their principles, advantages, limitations and prospects.

Abstract: The current study aims at characterizing the mechanisms that allow humans to entrain the mind and body to incoming rhythmic sensory inputs in real time. We addressed this unresolved issue by examining the relationship between covert neural processes and overt behavior in the context of musical rhythm. We measured temporal prediction abilities, sensorimotor synchronization accuracy and neural entrainment to auditory rhythms as captured using an EEG frequency-tagging approach. Importantly, movement synchronization accuracy with a rhythmic beat could be explained by the amplitude of neural activity selectively locked with the beat period when listening to the rhythmic inputs. Furthermore, stronger endogenous neural entrainment at the beat frequency was associated with superior temporal prediction abilities. Together, these results reveal a direct link between cortical and behavioral measures of rhythmic entrainment, thus providing evidence that frequency-tagged brain activity has functional relevance for beat perception and synchronization.

Abstract: To elucidate the genetic bases of mycorrhizal lifestyle evolution, we sequenced new fungal genomes, including 13 ectomycorrhizal (ECM), orchid (ORM) and ericoid (ERM) species, and five saprotrophs, which we analyzed along with other fungal genomes. Ectomycorrhizal fungi have a reduced complement of genes encoding plant cell wall-degrading enzymes (PCWDEs), as compared to their ancestral wood decayers. Nevertheless, they have retained a unique array of PCWDEs, thus suggesting that they possess diverse abilities to decompose lignocellulose. Similar functional categories of nonorthologous genes are induced in symbiosis. Of induced genes, 7-38% are orphan genes, including genes that encode secreted effector-like proteins. Convergent evolution of the mycorrhizal habit in fungi occurred via the repeated evolution of a 'symbiosis toolkit', with reduced numbers of PCWDEs and lineage-specific suites of mycorrhiza-induced genes.

Abstract: Extensive cooperation among unrelated individuals is unique to humans, who often sacrifice personal benefits for the common good and work together to achieve what they are unable to execute alone. The evolutionary success of our species is indeed due, to a large degree, to our unparalleled other-regarding abilities. Yet, a comprehensive understanding of human cooperation remains a formidable challenge. Recent research in social science indicates that it is important to focus on the collective behavior that emerges as the result of the interactions among individuals, groups, and even societies. Non-equilibrium statistical physics, in particular Monte Carlo methods and the theory of collective behavior of interacting particles near phase transition points, has proven to be very valuable for understanding counterintuitive evolutionary outcomes. By studying models of human cooperation as classical spin models, a physicist can draw on familiar settings from statistical physics. However, unlike pairwise interactions among particles that typically govern solid-state physics systems, interactions among humans often involve group interactions, and they also involve a larger number of possible states even for the most simplified description of reality. The complexity of solutions therefore often surpasses that observed in physical systems. Here we review experimental and theoretical research that advances our understanding of human cooperation, focusing on spatial pattern formation, on the spatiotemporal dynamics of observed solutions, and on self-organization that may either promote or hinder socially favorable states.

Abstract: Background Patients with metastatic colorectal cancer with the BRAF V600E mutation have a poor prognosis, with a median overall survival of 4 to 6 months after failure of initial therapy. ...

Abstract: Multiple sclerosis (MS) is the commonest non-traumatic disabling disease to affect young adults. The incidence of MS is increasing worldwide, together with the socioeconomic impact of the disease. The underlying cause of MS and mechanisms behind this increase remain opaque, although complex gene-environment interactions almost certainly play a significant role. The epidemiology of MS indicates that low serum levels of vitamin D, smoking, childhood obesity and infection with the Epstein-Barr virus are likely to play a role in disease development. Changes in diagnostic methods and criteria mean that people with MS can be diagnosed increasingly early in their disease trajectory. Alongside this, treatments for MS have increased exponentially in number, efficacy and risk. There is now the possibility of a diagnosis of 'pre-symptomatic MS' being made; as a result potentially preventive strategies could be studied. In this comprehensive review, MS epidemiology, potential aetiological factors and pathology are discussed, before moving on to clinical aspects of MS diagnosis and management.

Abstract: We are living in an era of unprecedented rapid change for gastric cancer. For a long time it was the commonest cancer, but its occurrence started to decline suddenly in the 1950s. The reason was unknown at first, but in any case the sharp decrease in mortality without any active measures was welcomed in the USA as ‘‘an unplanned triumph’’ [1]. It is now clear that the decreasing trend in gastric cancer occurrence paralleled the decrease of Helicobacter pylori infection. This bacterium has inhabited the human stomach since humans left Africa 58,000 years ago [2], but its existence was revealed only recently. Its carcinogenic mechanism has been rigorously investigated in the past 20 years, and as if it were a criminal whose crime had been uncovered, it started to leave the human stomach before an eradication policy was launched. After an interval following the decline in the occurrence of of H. pylori-related gastric cancer, a new disease entity, lower esophageal adenocarcinoma, appeared and has rapidly increased in frequency together with esophagogastric junction cancer in Western countries. Most Eastern countries still seem to be in the final phase of the interval before the increase in the frequency of these troublesome diseases, and today the difference between East and West in clinical approaches to esophagogastric junction cancer seems to be the largest in history. Asian gastroenterologists and surgeons detect and treat early disease, mostly in the distal part of the stomach, by developing new diagnostic devices and function-preserving treatments. Their Western counterparts, on the other hand, desperately struggle against advanced tumors in the proximal part of the stomach, making full use of a multimodal, multidisciplinary approach. Bridging these two groups is worthwhile and beneficial, especially for the minority populations of patients in each group, but needs mutual understanding based on common points of view. Researchers and pathologists are highly expected to play a role in establishing a common language for these differing practices. Face-to-face meetings and discussions in recognition of the other’s standpoint would be particularly profitable. We organized the 88th Annual Meeting of the Japanese Gastric Cancer Association in March 2016, setting the congress theme as ‘‘Gastric cancer: Asia and the world.’’ Although this was essentially a domestic meeting, 70% of the sessions were conducted in English, and were attended by more than 2000 physicians and pathologists, including those from 14 countries. This special issue of Gastric Congress President of the 88th Annual Meeting of the Japanese Gastric Cancer Association.

Abstract: We propose a family of exactly solvable toy models for the AdS/CFT correspondence based on a novel construction of quantum error-correcting codes with a tensor network structure. Our building block is a special type of tensor with maximal entanglement along any bipartition, which gives rise to an isometry from the bulk Hilbert space to the boundary Hilbert space. The entire tensor network is an encoder for a quantum error-correcting code, where the bulk and boundary degrees of freedom may be identified as logical and physical degrees of freedom respectively. These models capture key features of entanglement in the AdS/CFT correspondence; in particular, the Ryu-Takayanagi formula and the negativity of tripartite information are obeyed exactly in many cases. That bulk logical operators can be represented on multiple boundary regions mimics the Rindlerwedge reconstruction of boundary operators from bulk operators, realizing explicitly the quantum error-correcting features of AdS/CFT recently proposed in [1].

Abstract: Recent studies reveal that circular RNAs (circRNAs) are a novel class of abundant, stable and ubiquitous noncoding RNA molecules in animals. Comprehensive detection of circRNAs from high-throughput transcriptome data is an initial and crucial step to study their biogenesis and function. Here, we present a novel chiastic clipping signal-based algorithm, CIRI, to unbiasedly and accurately detect circRNAs from transcriptome data by employing multiple filtration strategies. By applying CIRI to ENCODE RNA-seq data, we for the first time identify and experimentally validate the prevalence of intronic/intergenic circRNAs as well as fragments specific to them in the human transcriptome.

Abstract: Background: Coronavirus disease 2019 (COVID-19) is associated with diffuse lung damage Corticosteroids may modulate immune-mediated lung injury and reducing progression to respiratory failure and death Methods: The Randomised Evaluation of COVID-19 therapy (RECOVERY) trial is a randomized, controlled, open-label, adaptive, platform trial comparing a range of possible treatments with usual care in patients hospitalized with COVID-19 We report the preliminary results for the comparison of dexamethasone 6 mg given once daily for up to ten days vs usual care alone The primary outcome was 28-day mortality Results: 2104 patients randomly allocated to receive dexamethasone were compared with 4321 patients concurrently allocated to usual care Overall, 454 (216%) patients allocated dexamethasone and 1065 (246%) patients allocated usual care died within 28 days (age-adjusted rate ratio [RR] 083; 95% confidence interval [CI] 074 to 092; P<0001) The proportional and absolute mortality rate reductions varied significantly depending on level of respiratory support at randomization (test for trend p<0001): Dexamethasone reduced deaths by one-third in patients receiving invasive mechanical ventilation (290% vs 407%, RR 065 [95% CI 051 to 082]; p<0001), by one-fifth in patients receiving oxygen without invasive mechanical ventilation (215% vs 250%, RR 080 [95% CI 070 to 092]; p=0002), but did not reduce mortality in patients not receiving respiratory support at randomization (170% vs 132%, RR 122 [95% CI 093 to 161]; p=014) Conclusions: In patients hospitalized with COVID-19, dexamethasone reduced 28-day mortality among those receiving invasive mechanical ventilation or oxygen at randomization, but not among patients not receiving respiratory support

Abstract: Understanding and controlling charge and energy flow in state-of-the-art semiconductor quantum wells has enabled high-efficiency optoelectronic devices. Two-dimensional (2D) Ruddlesden-Popper perovskites are solution-processed quantum wells wherein the band gap can be tuned by varying the perovskite-layer thickness, which modulates the effective electron-hole confinement. We report that, counterintuitive to classical quantum-confined systems where photogenerated electrons and holes are strongly bound by Coulomb interactions or excitons, the photophysics of thin films made of Ruddlesden-Popper perovskites with a thickness exceeding two perovskite-crystal units (>1.3 nanometers) is dominated by lower-energy states associated with the local intrinsic electronic structure of the edges of the perovskite layers. These states provide a direct pathway for dissociating excitons into longer-lived free carriers that substantially improve the performance of optoelectronic devices.

Abstract: Summary Background Expression of PD-L1 has been shown to be upregulated in some patients with gastric cancer. As part of the phase 1b KEYNOTE-012 study, we aimed to assess the safety and activity of the anti-PD-1 antibody pembrolizumab in patients with PD-L1-positive recurrent or metastatic adenocarcinoma of the stomach or gastro-oesophageal junction. Methods This study was a multicentre, open-label, phase 1b trial done at 13 cancer research centres in the USA, Israel, Japan, South Korea, and Taiwan. We enrolled patients with PD-L1-positive recurrent or metastatic adenocarcinoma of the stomach or gastro-oesophageal junction. Patients received intravenous pembrolizumab at 10 mg/kg once every 2 weeks for 24 months or until progression or unacceptable toxic effects occurred. Response was assessed every 8 weeks in accordance with Response Evaluation Criteria in Solid Tumors version 1.1. The primary objectives were safety in patients who received at least one dose of pembrolizumab and the proportion of patients achieving overall responses in patients who received at least one pembrolizumab dose and who either had a post-baseline scan or who discontinued therapy because of clinical disease progression or a treatment-related adverse event before the first post-baseline scan. The study is registered with ClinicalTrials.gov, number NCT01848834, and is ongoing but no longer enrolling patients. Findings From Oct 23, 2013, to May 5, 2014, 39 patients were enrolled. 36 were evaluable for response by central assessment. Eight (22%, 95% CI 10–39) patients were judged to have had an overall response at central review; all responses were partial. All 39 patients were included in the safety analyses. Five (13%) patients had a total of six grade 3 or 4 treatment-related adverse events, consisting of two cases of grade 3 fatigue, one case each of grade 3 pemphigoid, grade 3 hypothyroidism, and grade 3 peripheral sensory neuropathy, and one case of grade 4 pneumonitis. No treatment-related deaths occurred. Interpretation In this population of patients with recurrent or metastatic PD-L1-positive gastric cancer, pembrolizumab had a manageable toxicity profile and promising antitumour activity, warranting further study in phase 2 and 3 trials. Funding Merck & Co.

Abstract: Objective To assess the efficacy and safety of hydroxychloroquine plus standard of care compared with standard of care alone in adults with coronavirus disease 2019 (covid-19). Design Multicentre, open label, randomised controlled trial. Setting 16 government designated covid-19 treatment centres in China, 11 to 29 February 2020. Participants 150 patients admitted to hospital with laboratory confirmed covid-19 were included in the intention to treat analysis (75 patients assigned to hydroxychloroquine plus standard of care, 75 to standard of care alone). Interventions Hydroxychloroquine administrated at a loading dose of 1200 mg daily for three days followed by a maintenance dose of 800 mg daily (total treatment duration: two or three weeks for patients with mild to moderate or severe disease, respectively). Main outcome measure Negative conversion of severe acute respiratory syndrome coronavirus 2 by 28 days, analysed according to the intention to treat principle. Adverse events were analysed in the safety population in which hydroxychloroquine recipients were participants who received at least one dose of hydroxychloroquine and hydroxychloroquine non-recipients were those managed with standard of care alone. Results Of 150 patients, 148 had mild to moderate disease and two had severe disease. The mean duration from symptom onset to randomisation was 16.6 (SD 10.5; range 3-41) days. A total of 109 (73%) patients (56 standard of care; 53 standard of care plus hydroxychloroquine) had negative conversion well before 28 days, and the remaining 41 (27%) patients (19 standard of care; 22 standard of care plus hydroxychloroquine) were censored as they did not reach negative conversion of virus. The probability of negative conversion by 28 days in the standard of care plus hydroxychloroquine group was 85.4% (95% confidence interval 73.8% to 93.8%), similar to that in the standard of care group (81.3%, 71.2% to 89.6%). The difference between groups was 4.1% (95% confidence interval –10.3% to 18.5%). In the safety population, adverse events were recorded in 7/80 (9%) hydroxychloroquine non-recipients and in 21/70 (30%) hydroxychloroquine recipients. The most common adverse event in the hydroxychloroquine recipients was diarrhoea, reported in 7/70 (10%) patients. Two hydroxychloroquine recipients reported serious adverse events. Conclusions Administration of hydroxychloroquine did not result in a significantly higher probability of negative conversion than standard of care alone in patients admitted to hospital with mainly persistent mild to moderate covid-19. Adverse events were higher in hydroxychloroquine recipients than in non-recipients. Trial registration ChiCTR2000029868.

Abstract: Many chameleons, and panther chameleons in particular, have the remarkable ability to exhibit complex and rapid colour changes during social interactions such as male contests or courtship. It is generally interpreted that these changes are due to dispersion/aggregation of pigment-containing organelles within dermal chromatophores. Here, combining microscopy, photometric videography and photonic band-gap modelling, we show that chameleons shift colour through active tuning of a lattice of guanine nanocrystals within a superficial thick layer of dermal iridophores. In addition, we show that a deeper population of iridophores with larger crystals reflects a substantial proportion of sunlight especially in the near-infrared range. The organization of iridophores into two superposed layers constitutes an evolutionary novelty for chameleons, which allows some species to combine efficient camouflage with spectacular display, while potentially providing passive thermal protection.

Abstract: Attention mechanisms have seen wide adoption in neural NLP models. In addition to improving predictive performance, these are often touted as affording transparency: models equipped with attention provide a distribution over attended-to input units, and this is often presented (at least implicitly) as communicating the relative importance of inputs. However, it is unclear what relationship exists between attention weights and model outputs. In this work we perform extensive experiments across a variety of NLP tasks that aim to assess the degree to which attention weights provide meaningful “explanations” for predictions. We find that they largely do not. For example, learned attention weights are frequently uncorrelated with gradient-based measures of feature importance, and one can identify very different attention distributions that nonetheless yield equivalent predictions. Our findings show that standard attention modules do not provide meaningful explanations and should not be treated as though they do.

Abstract: Abstract DAVID is a popular bioinformatics resource system including a web server and web service for functional annotation and enrichment analyses of gene lists. It consists of a comprehensive knowledgebase and a set of functional analysis tools. Here, we report all updates made in 2021. The DAVID Gene system was rebuilt to gain coverage of more organisms, which increased the taxonomy coverage from 17 399 to 55 464. All existing annotation types have been updated, if available, based on the new DAVID Gene system. Compared with the last version, the number of gene-term records for most annotation types within the updated Knowledgebase have significantly increased. Moreover, we have incorporated new annotations in the Knowledgebase including small molecule-gene interactions from PubChem, drug-gene interactions from DrugBank, tissue expression information from the Human Protein Atlas, disease information from DisGeNET, and pathways from WikiPathways and PathBank. Eight of ten subgroups split from Uniprot Keyword annotation were assigned to specific types. Finally, we added a species parameter for uploading a list of gene symbols to minimize the ambiguity between species, which increases the efficiency of the list upload and eliminates confusion for users. These current updates have significantly expanded the Knowledgebase and enhanced the discovery power of DAVID.

Abstract: Neural network pruning techniques can reduce the parameter counts of trained networks by over 90%, decreasing storage requirements and improving computational performance of inference without compromising accuracy. However, contemporary experience is that the sparse architectures produced by pruning are difficult to train from the start, which would similarly improve training performance. We find that a standard pruning technique naturally uncovers subnetworks whose initializations made them capable of training effectively. Based on these results, we articulate the "lottery ticket hypothesis:" dense, randomly-initialized, feed-forward networks contain subnetworks ("winning tickets") that - when trained in isolation - reach test accuracy comparable to the original network in a similar number of iterations. The winning tickets we find have won the initialization lottery: their connections have initial weights that make training particularly effective. We present an algorithm to identify winning tickets and a series of experiments that support the lottery ticket hypothesis and the importance of these fortuitous initializations. We consistently find winning tickets that are less than 10-20% of the size of several fully-connected and convolutional feed-forward architectures for MNIST and CIFAR10. Above this size, the winning tickets that we find learn faster than the original network and reach higher test accuracy.

Abstract: Misinformation about COVID-19 is a major threat to public health. Using five national samples from the UK (n = 1050 and n = 1150), Ireland (n = 700), the USA (n = 700), Spain (n = 700) and Mexico (n = 700), we examine predictors of belief in the most common statements about the virus that contain misinformation. We also investigate the prevalence of belief in COVID-19 misinformation across different countries and the role of belief in such misinformation in predicting relevant health behaviours. We find that while public belief in misinformation about COVID-19 is not particularly common, a substantial proportion views this type of misinformation as highly reliable in each country surveyed. In addition, a small group of participants find common factual information about the virus highly unreliable. We also find that increased susceptibility to misinformation negatively affects people's self-reported compliance with public health guidance about COVID-19, as well as people's willingness to get vaccinated against the virus and to recommend the vaccine to vulnerable friends and family. Across all countries surveyed, we find that higher trust in scientists and having higher numeracy skills were associated with lower susceptibility to coronavirus-related misinformation. Taken together, these results demonstrate a clear link between susceptibility to misinformation and both vaccine hesitancy and a reduced likelihood to comply with health guidance measures, and suggest that interventions which aim to improve critical thinking and trust in science may be a promising avenue for future research.

Abstract: Genome sequencing has become a powerful tool for studying emerging infectious diseases; however, genome sequencing directly from clinical samples (ie, without isolation and culture) remains challenging for viruses such as Zika, for which metagenomic sequencing methods may generate insufficient numbers of viral reads Here we present a protocol for generating coding-sequence-complete genomes, comprising an online primer design tool, a novel multiplex PCR enrichment protocol, optimized library preparation methods for the portable MinION sequencer (Oxford Nanopore Technologies) and the Illumina range of instruments, and a bioinformatics pipeline for generating consensus sequences The MinION protocol does not require an Internet connection for analysis, making it suitable for field applications with limited connectivity Our method relies on multiplex PCR for targeted enrichment of viral genomes from samples containing as few as 50 genome copies per reaction Viral consensus sequences can be achieved in 1-2 d by starting with clinical samples and following a simple laboratory workflow This method has been successfully used by several groups studying Zika virus evolution and is facilitating an understanding of the spread of the virus in the Americas The protocol can be used to sequence other viral genomes using the online Primal Scheme primer designer software It is suitable for sequencing either RNA or DNA viruses in the field during outbreaks or as an inexpensive, convenient method for use in the lab

Abstract: Large wild herbivores are crucial to ecosystems and human societies. We highlight the 74 largest terrestrial herbivore species on Earth (body mass ≥100 kg), the threats they face, their important and often overlooked ecosystem effects, and the conservation efforts needed to save them and their predators from extinction. Large herbivores are generally facing dramatic population declines and range contractions, such that ~60% are threatened with extinction. Nearly all threatened species are in developing countries, where major threats include hunting, land-use change, and resource depression by livestock. Loss of large herbivores can have cascading effects on other species including large carnivores, scavengers, mesoherbivores, small mammals, and ecological processes involving vegetation, hydrology, nutrient cycling, and fire regimes. The rate of large herbivore decline suggests that ever-larger swaths of the world will soon lack many of the vital ecological services these animals provide, resulting in enormous ecological and social costs.

Abstract: Immune systems distinguish “self” from “nonself” to maintain homeostasis and must differentially gate access to allow colonization by potentially beneficial, nonpathogenic microbes. Plant roots grow within extremely diverse soil microbial communities but assemble a taxonomically limited root-associated microbiome. We grew isogenic Arabidopsis thaliana mutants with altered immune systems in a wild soil and also in recolonization experiments with a synthetic bacterial community. We established that biosynthesis of, and signaling dependent on, the foliar defense phytohormone salicylic acid is required to assemble a normal root microbiome. Salicylic acid modulates colonization of the root by specific bacterial families. Thus, plant immune signaling drives selection from the available microbial communities to sculpt the root microbiome.

Abstract: Cerebral organoids—3D cultures of human cerebral tissue derived from pluripotent stem cells—have emerged as models of human cortical development. However, the extent to which in vitro organoid systems recapitulate neural progenitor cell proliferation and neuronal differentiation programs observed in vivo remains unclear. Here we use single-cell RNA sequencing (scRNA-seq) to dissect and compare cell composition and progenitor-to-neuron lineage relationships in human cerebral organoids and fetal neocortex. Covariation network analysis using the fetal neocortex data reveals known and previously unidentified interactions among genes central to neural progenitor proliferation and neuronal differentiation. In the organoid, we detect diverse progenitors and differentiated cell types of neuronal and mesenchymal lineages and identify cells that derived from regions resembling the fetal neocortex. We find that these organoid cortical cells use gene expression programs remarkably similar to those of the fetal tissue to organize into cerebral cortex-like regions. Our comparison of in vivo and in vitro cortical single-cell transcriptomes illuminates the genetic features underlying human cortical development that can be studied in organoid cultures.

Abstract: Reactive astrocytes are astrocytes undergoing morphological, molecular, and functional remodeling in response to injury, disease, or infection of the CNS. Although this remodeling was first described over a century ago, uncertainties and controversies remain regarding the contribution of reactive astrocytes to CNS diseases, repair, and aging. It is also unclear whether fixed categories of reactive astrocytes exist and, if so, how to identify them. We point out the shortcomings of binary divisions of reactive astrocytes into good-vs-bad, neurotoxic-vs-neuroprotective or A1-vs-A2. We advocate, instead, that research on reactive astrocytes include assessment of multiple molecular and functional parameters-preferably in vivo-plus multivariate statistics and determination of impact on pathological hallmarks in relevant models. These guidelines may spur the discovery of astrocyte-based biomarkers as well as astrocyte-targeting therapies that abrogate detrimental actions of reactive astrocytes, potentiate their neuro- and glioprotective actions, and restore or augment their homeostatic, modulatory, and defensive functions.

Abstract: Summary Background In the TRIBE study, FOLFOXIRI (fluorouracil, leucovorin, oxaliplatin, and irinotecan) plus bevacizumab significantly improved progression-free survival of patients with metastatic colorectal cancer compared with FOLFIRI (fluorouracil, leucovorin, and irinotecan) plus bevacizumab. In this updated analysis, we aimed to provide mature results for overall survival—a secondary endpoint—and report treatment efficacy in RAS and BRAF molecular subgroups. Methods TRIBE was an open-label, multicentre, phase 3 randomised study of patients (aged 18–70 years with Eastern Cooperative Oncology Group [ECOG] performance status of 2 or less and aged 71–75 years with an ECOG performance status of 0) with unresectable metastatic colorectal cancer who were recruited from 34 Italian oncology units. Patients were randomly assigned (1:1) via a web-based procedure to receive FOLFIRI plus bevacizumab or FOLFOXIRI plus bevacizumab. Bevacizumab was given as a 5 mg/kg intravenous dose. FOLFIRI consisted of a 180 mg/m 2 intravenous infusion of irinotecan for 60 min followed by a 200 mg/m 2 intravenous infusion of leucovorin for 120 min, a 400 mg/m 2 intravenous bolus of fluorouracil, and a 2400 mg/m 2 continuous infusion of fluorouracil for 46 h. FOLFOXIRI consisted of a 165 mg/m 2 intravenous infusion of irinotecan for 60 min, followed by an 85 mg/m 2 intravenous infusion of oxaliplatin given concurrently with 200 mg/m 2 leucovorin for 120 min, followed by a 3200 mg/m 2 continuous infusion of fluorouracil for 48 h. Tissue samples for RAS and BRAF mutational status analyses were centrally collected. In this updated analysis, we assessed the secondary endpoint of overall survival in the main cohort and treatment efficacy in RAS and BRAF molecular subgroups. All analyses were by intention to treat. TRIBE was concluded on Nov 30, 2014. The trial is registered with ClinicalTrials.gov, number NCT00719797. Findings Between July 17, 2008, and May 31, 2011, 508 patients were randomly assigned. At a median follow-up of 48·1 months (IQR 41·7–55·6), median overall survival was 29·8 months (95% CI 26·0–34·3) in the FOLFOXIRI plus bevacizumab group compared with 25·8 months (22·5–29·1) in the FOLFIRI plus bevacizumab group (hazard ratio [HR] 0·80, 95% CI 0·65–0·98; p=0·03). Median overall survival was 37·1 months (95% CI 29·7–42·7) in the RAS and BRAF wild-type subgroup compared with 25·6 months (22·4–28·6) in the RAS -mutation-positive subgroup (HR 1·49, 95% CI 1·11–1·99) and 13·4 months (8·2–24·1) in the BRAF -mutation-positive subgroup (HR 2·79, 95% CI 1·75–4·46; likelihood-ratio test p interaction =0·52). Interpretation FOLFOXIRI plus bevacizumab is a feasible treatment option for those patients who meet the inclusion criteria of the present study, irrespective of baseline clinical characteristics and RAS or BRAF mutational status. Funding GONO (Gruppo Oncologico del Nord Ovest) Cooperative Group and ARCO Foundation.

Abstract: BackgroundRomosozumab is a monoclonal antibody that binds to and inhibits sclerostin, increases bone formation, and decreases bone resorption. MethodsWe enrolled 4093 postmenopausal women with osteoporosis and a fragility fracture and randomly assigned them in a 1:1 ratio to receive monthly subcutaneous romosozumab (210 mg) or weekly oral alendronate (70 mg) in a blinded fashion for 12 months, followed by open-label alendronate in both groups. The primary end points were the cumulative incidence of new vertebral fracture at 24 months and the cumulative incidence of clinical fracture (nonvertebral and symptomatic vertebral fracture) at the time of the primary analysis (after clinical fractures had been confirmed in ≥330 patients). Secondary end points included the incidences of nonvertebral and hip fracture at the time of the primary analysis. Serious cardiovascular adverse events, osteonecrosis of the jaw, and atypical femoral fractures were adjudicated. ResultsOver a period of 24 months, a 48% lower risk...

Abstract: Across scientific disciplines, there is a rapidly growing recognition of the need for more statistically robust, transparent approaches to data visualization. Complementary to this, many scientists have called for plotting tools that accurately and transparently convey key aspects of statistical effects and raw data with minimal distortion. Previously common approaches, such as plotting conditional mean or median barplots together with error-bars have been criticized for distorting effect size, hiding underlying patterns in the raw data, and obscuring the assumptions upon which the most commonly used statistical tests are based. Here we describe a data visualization approach which overcomes these issues, providing maximal statistical information while preserving the desired 'inference at a glance' nature of barplots and other similar visualization devices. These "raincloud plots" can visualize raw data, probability density, and key summary statistics such as median, mean, and relevant confidence intervals in an appealing and flexible format with minimal redundancy. In this tutorial paper, we provide basic demonstrations of the strength of raincloud plots and similar approaches, outline potential modifications for their optimal use, and provide open-source code for their streamlined implementation in R, Python and Matlab ( https://github.com/RainCloudPlots/RainCloudPlots). Readers can investigate the R and Python tutorials interactively in the browser using Binder by Project Jupyter.

Abstract: High-quality materials are critical for advances in plasmonics, especially as researchers now investigate quantum effects at the limit of single surface plasmons or exploit ultraviolet- or CMOS-compatible metals such as aluminum or copper. Unfortunately, due to inexperience with deposition methods, many plasmonics researchers deposit metals under the wrong conditions, severely limiting performance unnecessarily. This is then compounded as others follow their published procedures. In this perspective, we describe simple rules collected from the surface-science literature that allow high-quality plasmonic films of aluminum, copper, gold, and silver to be easily deposited with commonly available equipment (a thermal evaporator). Recipes are also provided so that films with optimal optical properties can be routinely obtained.

Abstract: Learning a similarity function between pairs of objects is at the core of learning to rank approaches In information retrieval tasks we typically deal with query-document pairs, in question answering -- question-answer pairs However, before learning can take place, such pairs needs to be mapped from the original space of symbolic words into some feature space encoding various aspects of their relatedness, eg lexical, syntactic and semantic Feature engineering is often a laborious task and may require external knowledge sources that are not always available or difficult to obtain Recently, deep learning approaches have gained a lot of attention from the research community and industry for their ability to automatically learn optimal feature representation for a given task, while claiming state-of-the-art performance in many tasks in computer vision, speech recognition and natural language processing In this paper, we present a convolutional neural network architecture for reranking pairs of short texts, where we learn the optimal representation of text pairs and a similarity function to relate them in a supervised way from the available training data Our network takes only words in the input, thus requiring minimal preprocessing In particular, we consider the task of reranking short text pairs where elements of the pair are sentences We test our deep learning system on two popular retrieval tasks from TREC: Question Answering and Microblog Retrieval Our model demonstrates strong performance on the first task beating previous state-of-the-art systems by about 3\% absolute points in both MAP and MRR and shows comparable results on tweet reranking, while enjoying the benefits of no manual feature engineering and no additional syntactic parsers