Grounding Complex Natural Language Commands for Temporal Tasks in Unseen Environments

Grounding navigational commands to linear temporal logic (LTL) leverages its unambiguous semantics for reasoning about long-horizon tasks and verifying the satisfaction of temporal constraints. Existing approaches require training data from the specific environment and landmarks that will be used in natural language to understand commands in those environments. We propose Lang2LTL, a modular system and a software package that leverages large language models (LLMs) to ground temporal navigational commands to LTL specifications in environments without prior language data. We comprehensively evaluate Lang2LTL for five well-defined generalization behaviors. Lang2LTL demonstrates the state-of-the-art ability of a single model to ground navigational commands to diverse temporal specifications in 21 city-scaled environments. Finally, we demonstrate a physical robot using Lang2LTL can follow 52 semantically diverse navigational commands in two indoor environments.Comment: Conference on Robot Learning 202

Evaluating the Potential of Leading Large Language Models in Reasoning Biology Questions

Recent advances in Large Language Models (LLMs) have presented new opportunities for integrating Artificial General Intelligence (AGI) into biological research and education. This study evaluated the capabilities of leading LLMs, including GPT-4, GPT-3.5, PaLM2, Claude2, and SenseNova, in answering conceptual biology questions. The models were tested on a 108-question multiple-choice exam covering biology topics in molecular biology, biological techniques, metabolic engineering, and synthetic biology. Among the models, GPT-4 achieved the highest average score of 90 and demonstrated the greatest consistency across trials with different prompts. The results indicated GPT-4's proficiency in logical reasoning and its potential to aid biology research through capabilities like data analysis, hypothesis generation, and knowledge integration. However, further development and validation are still required before the promise of LLMs in accelerating biological discovery can be realized

Robust estimation of bacterial cell count from optical density

Optical density (OD) is widely used to estimate the density of cells in liquid culture, but cannot be compared between instruments without a standardized calibration protocol and is challenging to relate to actual cell count. We address this with an interlaboratory study comparing three simple, low-cost, and highly accessible OD calibration protocols across 244 laboratories, applied to eight strains of constitutive GFP-expressing E. coli. Based on our results, we recommend calibrating OD to estimated cell count using serial dilution of silica microspheres, which produces highly precise calibration (95.5% of residuals <1.2-fold), is easily assessed for quality control, also assesses instrument effective linear range, and can be combined with fluorescence calibration to obtain units of Molecules of Equivalent Fluorescein (MEFL) per cell, allowing direct comparison and data fusion with flow cytometry measurements: in our study, fluorescence per cell measurements showed only a 1.07-fold mean difference between plate reader and flow cytometry data

Finishing the euchromatic sequence of the human genome

The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers ∼99% of the euchromatic genome and is accurate to an error rate of ∼1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human enome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead

Hyperoxemia and excess oxygen use in early acute respiratory distress syndrome : Insights from the LUNG SAFE study

Publisher Copyright: © 2020 The Author(s). Copyright: Copyright 2020 Elsevier B.V., All rights reserved.Background: Concerns exist regarding the prevalence and impact of unnecessary oxygen use in patients with acute respiratory distress syndrome (ARDS). We examined this issue in patients with ARDS enrolled in the Large observational study to UNderstand the Global impact of Severe Acute respiratory FailurE (LUNG SAFE) study. Methods: In this secondary analysis of the LUNG SAFE study, we wished to determine the prevalence and the outcomes associated with hyperoxemia on day 1, sustained hyperoxemia, and excessive oxygen use in patients with early ARDS. Patients who fulfilled criteria of ARDS on day 1 and day 2 of acute hypoxemic respiratory failure were categorized based on the presence of hyperoxemia (PaO2 > 100 mmHg) on day 1, sustained (i.e., present on day 1 and day 2) hyperoxemia, or excessive oxygen use (FIO2 ≥ 0.60 during hyperoxemia). Results: Of 2005 patients that met the inclusion criteria, 131 (6.5%) were hypoxemic (PaO2 < 55 mmHg), 607 (30%) had hyperoxemia on day 1, and 250 (12%) had sustained hyperoxemia. Excess FIO2 use occurred in 400 (66%) out of 607 patients with hyperoxemia. Excess FIO2 use decreased from day 1 to day 2 of ARDS, with most hyperoxemic patients on day 2 receiving relatively low FIO2. Multivariate analyses found no independent relationship between day 1 hyperoxemia, sustained hyperoxemia, or excess FIO2 use and adverse clinical outcomes. Mortality was 42% in patients with excess FIO2 use, compared to 39% in a propensity-matched sample of normoxemic (PaO2 55-100 mmHg) patients (P = 0.47). Conclusions: Hyperoxemia and excess oxygen use are both prevalent in early ARDS but are most often non-sustained. No relationship was found between hyperoxemia or excessive oxygen use and patient outcome in this cohort. Trial registration: LUNG-SAFE is registered with ClinicalTrials.gov, NCT02010073publishersversionPeer reviewe

Minimum Information about a Biosynthetic Gene cluster

A wide variety of enzymatic pathways that produce specialized metabolites in bacteria, fungi and plants are known to be encoded in biosynthetic gene clusters. Information about these clusters, pathways and metabolites is currently dispersed throughout the literature, making it difficult to exploit. To facilitate consistent and systematic deposition and retrieval of data on biosynthetic gene clusters, we propose the Minimum Information about a Biosynthetic Gene cluster (MIBiG) data standard.Chemistry and Chemical Biolog

Exploring the nonlinear effects of built environment characteristics on customized bus service

The high failure rate of demand-responsive transit (DRT) systems suggests that DRT services are viable only in selected areas. However, few studies have quantitatively examined how built environment characteristics affect DRT use. Applying gradient boosting decision trees to the data of customized bus service (CBS, a type of DRT) in Dalian, we investigate the nonlinear association between the built environment and CBS use, controlling for demographics and service features. Local accessibility at the residence and workplace are the most important correlates of CBS use, followed by the proximity of workplace to bus stop. Some built environment variables (including distance from workplace to transit stops, distance from residence to business centers, and population density) influence CBS use differently from traditional transit use observed in the literature. Furthermore, built environment variables show salient threshold associations with CBS use, guiding planners to design the CBS system efficiently

Skill Transfer for Temporally-Extended Task Specifications

Deploying robots in real-world domains, such as households and flexible manufacturing lines, requires the robots to be taskable on demand. Linear temporal logic (LTL) is a widely-used specification language with a compositional grammar that naturally induces commonalities across tasks. However, the majority of prior research on reinforcement learning with LTL specifications treats every new formula independently. We propose LTL-Transfer, a novel algorithm that enables subpolicy reuse across tasks by segmenting policies for training tasks into portable transition-centric skills capable of satisfying a wide array of unseen LTL specifications while respecting safety-critical constraints. Our experiments in a Minecraft-inspired domain demonstrate the capability of LTL-Transfer to satisfy over 90% of 500 unseen tasks while training on only 50 task specifications and never violating a safety constraint. We also deployed LTL-Transfer on a quadruped mobile manipulator in a household environment to show its ability to transfer to many fetch and delivery tasks in a zero-shot fashion

CD151 Represses Mammary Gland Development by Maintaining the Niches of Progenitor Cells

Tetraspanin CD151 interacts with laminin-binding integrins (i.e., α3β1, α6β1 and α6β4) and other cell surface molecules to control diverse cellular and physiological processes, ranging from cell adhesion, migration and survival to tissue architecture and homeostasis. Here, we report a novel role of CD151 in maintaining the branching morphogenesis and activity of progenitor cells during the pubertal development of mammary glands. In contrast to the disruption of laminin-binding integrins, CD151 removal in mice enhanced the tertiary branching in mammary glands by 2.4-fold and the number of terminal end buds (TEBs) by 30%, while having minimal influence on either primary or secondary ductal branching. Consistent with these morphological changes are the skewed distribution of basal/myoepithelial cells and a 3.2-fold increase in proliferating Ki67-positive cells. These novel observations suggest that CD151 impacts the branching morphogenesis of mammary glands by upregulating the activities of bipotent progenitor cells. Indeed, our subsequent analyses indicate that upon CD151 removal the proportion of CD24HiCD49fLowprogenitor cells in the mammary gland increased by 34%, and their proliferating and differentiating activities were significantly upregulated. Importantly, fibronectin, a pro-branching extracellular matrix (ECM) protein deposited underlying mammary epithelial or progenitor cells, increased by \u3e7.2-fold. Moreover, there was a concomitant increase in the expression and nuclear distribution of Slug, a transcription factor implicated in the maintenance of mammary progenitor cell activities. Taken together, our studies demonstrate that integrin-associated CD151 represses mammary branching morphogenesis by controlling progenitor cell activities, ECM integrity and transcription program