Autonomous Acquisition of Natural Language

An important part of human intelligence is the ability to use language. Humans learn how to use language in a society of language users, which is probably the most effective way to learn a language from the ground up. Principles that might allow an artificial agents to learn language this way are not known at present. Here we present a framework which begins to address this challenge. Our auto-catalytic, endogenous, reflective architecture (AERA) supports the creation of agents that can learn natural language by observation. We present results from two experiments where our S1 agent learns human communication by observing two humans interacting in a realtime mock television interview, using gesture and situated language. Results show that S1 can learn multimodal complex language and multimodal communicative acts, using a vocabulary of 100 words with numerous sentence formats, by observing unscripted interaction between the humans, with no grammar being provided to it a priori, and only high-level information about the format of the human interaction in the form of high-level goals of the interviewer and interviewee and a small ontology. The agent learns both the pragmatics, semantics, and syntax of complex sentences spoken by the human subjects on the topic of recycling of objects such as aluminum cans, glass bottles, plastic, and wood, as well as use of manual deictic reference and anaphora

Autonomous Acquisition of Natural Situated Communication

An important part of human intelligence, both historically and operationally, is our ability to communicate. We learn how to communicate, and maintain our communicative skills, in a society of communicators – a highly effective way to reach and maintain proficiency in this complex skill. Principles that might allow artificial agents to learn language this way are in completely known at present – the multi-dimensional nature of socio-communicative skills are beyond every machine learning framework so far proposed. Our work begins to address the challenge of proposing a way for observation-based machine learning of natural language and communication. Our framework can learn complex communicative skills with minimal up-front knowledge. The system learns by incrementally producing predictive models of causal relationships in observed data, guided by goal-inference and reasoning using forward-inverse models. We present results from two experiments where our S1 agent learns human communication by observing two humans interacting in a realtime TV-style interview, using multimodal communicative gesture and situated language to talk about recycling of various materials and objects. S1 can learn multimodal complex language and multimodal communicative acts, a vocabulary of 100 words forming natural sentences with relatively complex sentence structure, including manual deictic reference and anaphora. S1 is seeded only with high-level information about goals of the interviewer and interviewee, and a small ontology; no grammar or other information is provided to S1 a priori. The agent learns the pragmatics, semantics, and syntax of complex utterances spoken and gestures from scratch, by observing the humans compare and contrast the cost and pollution related to recycling aluminum cans, glass bottles, newspaper, plastic, and wood. After 20 hours of observation S1 can perform an unscripted TV interview with a human, in the same style, without making mistakes

The BARD1 Cys557Ser Variant and Breast Cancer Risk in Iceland

BACKGROUND: Most, if not all, of the cellular functions of the BRCA1 protein are mediated through heterodimeric complexes composed of BRCA1 and a related protein, BARD1. Some breast-cancer-associated BRCA1 missense mutations disrupt the function of the BRCA1/BARD1 complex. It is therefore pertinent to determine whether variants of BARD1 confer susceptibility to breast cancer. Recently, a missense BARD1 variant, Cys557Ser, was reported to be at increased frequencies in breast cancer families. We investigated the role of the BARD1 Cys557Ser variant in a population-based cohort of 1,090 Icelandic patients with invasive breast cancer and 703 controls. We then used a computerized genealogy of the Icelandic population to study the relationships between the Cys557Ser variant and familial clustering of breast cancer. METHODS AND FINDINGS: The Cys557Ser allele was present at a frequency of 0.028 in patients with invasive breast cancer and 0.016 in controls (odds ratio [OR] = 1.82, 95% confidence interval [CI] 1.11–3.01, p = 0.014). The alleleic frequency was 0.037 in a high-predisposition group of cases defined by having a family history of breast cancer, early onset of breast cancer, or multiple primary breast cancers (OR = 2.41, 95% CI 1.22–4.75, p = 0.015). Carriers of the common Icelandic BRCA2 999del5 mutation were found to have their risk of breast cancer further increased if they also carried the BARD1 variant: the frequency of the BARD1 variant allele was 0.047 (OR = 3.11, 95% CI 1.16–8.40, p = 0.046) in 999del5 carriers with breast cancer. This suggests that the lifetime probability of a BARD1 Cys557Ser/BRCA2 999del5 double carrier developing breast cancer could approach certainty. Cys557Ser carriers, with or without the BRCA2 mutation, had an increased risk of subsequent primary breast tumors after the first breast cancer diagnosis compared to non-carriers. Lobular and medullary breast carcinomas were overrepresented amongst Cys557Ser carriers. We found that an excess of ancestors of contemporary carriers lived in a single county in the southeast of Iceland and that all carriers shared a SNP haplotype, which is suggestive of a founder event. Cys557Ser was found on the same SNP haplotype background in the HapMap Project CEPH sample of Utah residents. CONCLUSIONS: Our findings suggest that BARD1 Cys557Ser is an ancient variant that confers risk of single and multiple primary breast cancers, and this risk extends to carriers of the BRCA2 999del5 mutation

Six pelagic seabird species of the North Atlantic engage in a fly-and-forage strategy during their migratory movements

Bird migration is commonly defined as a seasonal movement between breeding and non-breeding grounds. It generally involves relatively straight and directed large-scale movements, with a latitudinal change, and specific daily activity patterns comprising less or no foraging and more traveling time. Our main objective was to describe how this general definition applies to seabirds. We investigated migration characteristics of 6 pelagic seabird species (little auk Alle alle, Atlantic puffin Fratercula arctica, common guillemot Uria aalge, Brünnich’s guillemot U. lomvia, black-legged kittiwake Rissa tridactyla and northern fulmars Fulmarus glacialis). We analysed an extensive geolocator positional and saltwater immersion dataset from 29 colonies in the North-East Atlantic and across several years (2008-2019). We used a novel method to identify active migration periods based on segmentation of time series of track characteristics (latitude, longitude, net-squared displacement). Additionally, we used the saltwater immersion data of geolocators to infer bird activity. We found that the 6 species had, on average, 3 to 4 migration periods and 2 to 3 distinct stationary areas during the non-breeding season. On average, seabirds spent the winter at lower latitudes than their breeding colonies and followed specific migration routes rather than non-directionally dispersing from their colonies. Differences in daily activity patterns were small between migratory and stationary periods, suggesting that all species continued to forage and rest while migrating, engaging in a ‘fly-and-forage’ migratory strategy. We thereby demonstrate the importance of habitats visited during seabird migrations as those that are not just flown over, but which may be important for re-fuelling.publishedVersio

The sequences of 150,119 genomes in the UK Biobank

Detailed knowledge of how diversity in the sequence of the human genome affects phenotypic diversity depends on a comprehensive and reliable characterization of both sequences and phenotypic variation. Over the past decade, insights into this relationship have been obtained from whole-exome sequencing or whole-genome sequencing of large cohorts with rich phenotypic data(1,2). Here we describe the analysis of whole-genome sequencing of 150,119 individuals from the UK Biobank(3). This constitutes a set of high-quality variants, including 585,040,410 single-nucleotide polymorphisms, representing 7.0% of all possible human single-nucleotide polymorphisms, and 58,707,036 indels. This large set of variants allows us to characterize selection based on sequence variation within a population through a depletion rank score of windows along the genome. Depletion rank analysis shows that coding exons represent a small fraction of regions in the genome subject to strong sequence conservation. We define three cohorts within the UK Biobank: a large British Irish cohort, a smaller African cohort and a South Asian cohort. A haplotype reference panel is provided that allows reliable imputation of most variants carried by three or more sequenced individuals. We identified 895,055 structural variants and 2,536,688 microsatellites, groups of variants typically excluded from large-scale whole-genome sequencing studies. Using this formidable new resource, we provide several examples of trait associations for rare variants with large effects not found previously through studies based on whole-exome sequencing and/or imputation

The Prospective Dutch Colorectal Cancer (PLCRC) cohort: real-world data facilitating research and clinical care

Real-world data (RWD) sources are important to advance clinical oncology research and evaluate treatments in daily practice. Since 2013, the Prospective Dutch Colorectal Cancer (PLCRC) cohort, linked to the Netherlands Cancer Registry, serves as an infrastructure for scientific research collecting additional patient-reported outcomes (PRO) and biospecimens. Here we report on cohort developments and investigate to what extent PLCRC reflects the “real-world”. Clinical and demographic characteristics of PLCRC participants were compared with the general Dutch CRC population (n = 74,692, Dutch-ref). To study representativeness, standardized differences between PLCRC and Dutch-ref were calculated, and logistic regression models were evaluated on their ability to distinguish cohort participants from the Dutch-ref (AU-ROC 0.5 = preferred, implying participation independent of patient characteristics). Stratified analyses by stage and time-period (2013–2016 and 2017–Aug 2019) were performed to study the evolution towards RWD. In August 2019, 5744 patients were enrolled. Enrollment increased steeply, from 129 participants (1 hospital) in 2013 to 2136 (50 of 75 Dutch hospitals) in 2018. Low AU-ROC (0.65, 95% CI: 0.64–0.65) indicates limited ability to distinguish cohort participants from the Dutch-ref. Characteristics that remained imbalanced in the period 2017–Aug’19 compared with the Dutch-ref were age (65.0 years in PLCRC, 69.3 in the Dutch-ref) and tumor stage (40% stage-III in PLCRC, 30% in the Dutch-ref). PLCRC approaches to represent the Dutch CRC population and will ultimately meet the current demand for high-quality RWD. Efforts are ongoing to improve multidisciplinary recruitment which will further enhance PLCRC’s representativeness and its contribution to a learning healthcare system

First-line systemic treatment strategies in patients with initially unresectable colorectal cancer liver metastases (CAIRO5):an open-label, multicentre, randomised, controlled, phase 3 study from the Dutch Colorectal Cancer Group

Background: Patients with initially unresectable colorectal cancer liver metastases might qualify for local treatment with curative intent after reducing the tumour size by induction systemic treatment. We aimed to compare the currently most active induction regimens. Methods: In this open-label, multicentre, randomised, phase 3 study (CAIRO5), patients aged 18 years or older with histologically confirmed colorectal cancer, known RAS/BRAFV600E mutation status, WHO performance status of 0–1, and initially unresectable colorectal cancer liver metastases were enrolled at 46 Dutch and one Belgian secondary and tertiary centres. Resectability or unresectability of colorectal cancer liver metastases was assessed centrally by an expert panel of liver surgeons and radiologists, at baseline and every 2 months thereafter by predefined criteria. Randomisation was done centrally with the minimisation technique via a masked web-based allocation procedure. Patients with right-sided primary tumour site or RAS or BRAFV600E mutated tumours were randomly assigned (1:1) to receive FOLFOX or FOLFIRI plus bevacizumab (group A) or FOLFOXIRI plus bevacizumab (group B). Patients with left-sided and RAS and BRAFV600E wild-type tumours were randomly assigned (1:1) to receive FOLFOX or FOLFIRI plus bevacizumab (group C) or FOLFOX or FOLFIRI plus panitumumab (group D), every 14 days for up to 12 cycles. Patients were stratified by resectability of colorectal cancer liver metastases, serum lactate dehydrogenase concentration, choice of irinotecan versus oxaliplatin, and BRAFV600E mutation status (for groups A and B). Bevacizumab was administered intravenously at 5 mg/kg. Panitumumab was administered intravenously at 6 mg/kg. FOLFIRI consisted of intravenous infusion of irinotecan at 180 mg/m2 with folinic acid at 400 mg/m2, followed by bolus fluorouracil at 400 mg/m2 intravenously, followed by continuous infusion of fluorouracil at 2400 mg/m2. FOLFOX consisted of oxaliplatin at 85 mg/m2 intravenously together with the same schedule of folinic acid and fluorouracil as in FOLFIRI. FOLFOXIRI consisted of irinotecan at 165 mg/m2 intravenously, followed by intravenous infusion of oxaliplatin at 85 mg/m2 with folinic acid at 400 mg/m2, followed by continuous infusion of fluorouracil at 3200 mg/m2. Patients and investigators were not masked to treatment allocation. The primary outcome was progression-free survival, analysed on a modified intention-to-treat basis, excluding patients who withdrew consent before starting study treatment or violated major entry criteria (no metastatic colorectal cancer, or previous liver surgery for colorectal cancer liver metastases). The study is registered with ClinicalTrials.gov, NCT02162563, and accrual is complete. Findings: Between Nov 13, 2014, and Jan 31, 2022, 530 patients (327 [62%] male and 203 [38%] female; median age 62 years [IQR 54–69]) were randomly assigned: 148 (28%) patients to group A, 146 (28%) patients to group B, 118 (22%) patients to group C, and 118 (22%) patients to group D. Groups C and D were prematurely closed for futility. 521 patients were included in the modified intention-to-treat population (147 in group A, 144 in group B, 114 in group C, and 116 in group D). The median follow-up at the time of this analysis was 51·1 months (95% CI 47·7–53·1) in groups A and B and 49·9 months (44·5–52·5) in in groups C and D. Median progression-free survival was 9·0 months (95% CI 7·7–10·5) in group A versus 10·6 months (9·9–12·1) in group B (stratified hazard ratio [HR] 0·76 [95% CI 0·60–0·98]; p=0·032), and 10·8 months (95% CI 9·9–12·6) in group C versus 10·4 months (9·8–13·0) in group D (stratified HR 1·11 [95% CI 0·84–1·48]; p=0·46). The most frequent grade 3–4 events in groups A and B were neutropenia (19 [13%] patients in group A vs 57 [40%] in group B; p&lt;0·0001), hypertension (21 [14%] vs 20 [14%]; p=1·00), and diarrhoea (five [3%] vs 28 [19%]; p&lt;0·0001), and in groups C and D were neutropenia (29 [25%] vs 24 [21%]; p=0·44), skin toxicity (one [1%] vs 29 [25%]; p&lt;0·0001), hypertension (20 [18%] vs eight [7%]; p=0·016), and diarrhoea (five [4%] vs 18 [16%]; p=0·0072). Serious adverse events occurred in 46 (31%) patients in group A, 75 (52%) patients in group B, 41 (36%) patients in group C, and 49 (42%) patients in group D. Seven treatment-related deaths were reported in group B (two due to multiorgan failure, and one each due to sepsis, pneumonia, portal vein thrombosis, septic shock and liver failure, and sudden death), one in group C (multiorgan failure), and three in group D (cardiac arrest, pulmonary embolism, and abdominal sepsis). Interpretation: In patients with initially unresectable colorectal cancer liver metastases, FOLFOXIRI-bevacizumab was the preferred treatment in patients with a right-sided or RAS or BRAFV600E mutated primary tumour. In patients with a left-sided and RAS and BRAFV600E wild-type tumour, the addition of panitumumab to FOLFOX or FOLFIRI showed no clinical benefit over bevacizumab, but was associated with more toxicity. Funding: Roche and Amgen.</p

mFast-SeqS-based aneuploidy score in circulating cell-free DNA is a prognostic biomarker in prostate cancer

Multiple prognostic biomarkers, including circulating tumor cell (CTC) counts, exist in metastatic castration-resistant prostate cancer (mCRPC) patients, but none of them have been implemented into daily clinical care. The modified fast aneuploidy screening test-sequencing system (mFast-SeqS), which yields a genome-wide aneuploidy score, is able to reflect the fraction of cell-free tumor DNA (ctDNA) within cell-free DNA (cfDNA) and may be a promising biomarker in mCRPC. In this study, we investigated the prognostic value of dichotomized aneuploidy scores (<5 vs ≥5) as well as CTC counts (<5 vs ≥5) in 131 mCRPC patients prior to treatment with cabazitaxel. We validated our findings in an independent cohort of 50 similarly treated mCRPC patients. We observed that, similar to the dichotomized CTC count [HR: 2.92; 95% confidence interval (CI);1.84-4.62], dichotomized aneuploidy scores (HR: 3.24; CI: 2.12-4.94) significantly correlated with overall survival in mCRPC patients. We conclude that a dichotomized aneuploidy score from cfDNA is a prognostic marker for survival in mCRPC patients within our discovery cohort and in an independent mCRPC validation cohort. Therefore, this easy and robust minimally-invasive assay can be readily implemented as a prognostic marker in mCRPC. Dichotomized aneuploidy score might also be used as a stratification factor in clinical studies to account for tumor load

Seasonal variation of mercury contamination in Arctic seabirds: A pan-Arctic assessment

Mercury (Hg) is a natural trace element found in high concentrations in top predators, including Arctic seabirds. Most current knowledge about Hg concentrations in Arctic seabirds relates to exposure during the summer breeding period when researchers can easily access seabirds at colonies. However, the few studies focused on winter have shown higher Hg concentrations during the non-breeding period than breeding period in several tissues. Hence, improving knowledge about Hg exposure during the non-breeding period is crucial to understanding the threats and risks encountered by these species year-round. We used feathers of nine migratory alcid species occurring at high latitudes to study bird Hg exposure during both the breeding and non-breeding periods. Overall, Hg concentrations during the non-breeding period were ~3 times higher than during the breeding period. In addition, spatial differences were apparent within and between the Atlantic and Pacific regions. While Hg concentrations during the non-breeding period were ~9 times and ~3 times higher than during the breeding period for the West and East Atlantic respectively, Hg concentrations in the Pacific during the non-breeding period were only ~1.7 times higher than during the breeding period. In addition, individual Hg concentrations during the non-breeding period for most of the seabird colonies were above 5 μg g−1 dry weight (dw), which is considered to be the threshold atwhich deleterious effects are observed, suggesting that some breeding populations might be vulnerable to non-breeding Hg exposure. Since wintering area locations, and migration routes may influence seasonal Hg concentrations, it is crucial to improve our knowledge about spatial ecotoxicology to fully understand the risks associated with Hg contamination in Arctic seabirds. Polar Top predators Metal Seasonal variation FeathersacceptedVersio