ARIES: A Corpus of Scientific Paper Edits Made in Response to Peer Reviews

Revising scientific papers based on peer feedback is a challenging task that requires not only deep scientific knowledge and reasoning, but also the ability to recognize the implicit requests in high-level feedback and to choose the best of many possible ways to update the manuscript in response. We introduce this task for large language models and release ARIES, a dataset of review comments and their corresponding paper edits, to enable training and evaluating models. We study two versions of the task: comment-edit alignment and edit generation, and evaluate several baselines, including GPT-4. We find that models struggle even to identify the edits that correspond to a comment, especially in cases where the comment is phrased in an indirect way or where the edit addresses the spirit of a comment but not the precise request. When tasked with generating edits, GPT-4 often succeeds in addressing comments on a surface level, but it rigidly follows the wording of the feedback rather than the underlying intent, and includes fewer technical details than human-written edits. We hope that our formalization, dataset, and analysis will form a foundation for future work in this area.Comment: 11 pages, 2 figure

Pulmonary delivery of vancomycin dry powder aerosol to intubated rabbits

TGX-221 is a potent, selective, and cell membrane permeable inhibitor of the PI3K p110β catalytic subunit. Recent studies showed that TGX-221 has anti-proliferative activity against PTEN-deficient tumor cell lines including prostate cancers. The objective of this study was to develop an encapsulation system for parenterally delivering TGX-221 to the target tissue through a prostate-specific membrane aptamer (PSMAa10) with little or no side effects. In this study, PEG-PCL micelles were formulated to encapsulate the drug, and a prodrug strategy was pursued to improve the stability of the carrier system. Fluorescence imaging studies demonstrated that the cellular uptake of both drug and nanoparticles were significantly improved by targeted micelles in a PSMA positive cell line. The area under the plasma concentration time curve of the micelle formulation in nude mice was 2.27-fold greater than the naked drug, and the drug clearance rate was 17.5-fold slower. These findings suggest a novel formulation approach for improving site-specific drug delivery of a molecular-targeted prostate cancer treatment

Concordant Gene Expression in Leukemia Cells and Normal Leukocytes Is Associated with Germline cis-SNPs

The degree to which gene expression covaries between different primary tissues within an individual is not well defined. We hypothesized that expression that is concordant across tissues is more likely influenced by genetic variability than gene expression which is discordant between tissues. We quantified expression of 11,873 genes in paired samples of primary leukemia cells and normal leukocytes from 92 patients with acute lymphoblastic leukemia (ALL). Genetic variation at >500,000 single nucleotide polymorphisms (SNPs) was also assessed. The expression of only 176/11,783 (1.5%) genes was correlated (p<0.008, FDR = 25%) in the two tissue types, but expression of a high proportion (20 of these 176 genes) was significantly related to cis-SNP genotypes (adjusted p<0.05). In an independent set of 134 patients with ALL, 14 of these 20 genes were validated as having expression related to cis-SNPs, as were 9 of 20 genes in a second validation set of HapMap cell lines. Genes whose expression was concordant among tissue types were more likely to be associated with germline cis-SNPs than genes with discordant expression in these tissues; genes affected were involved in housekeeping functions (GSTM2, GAPDH and NCOR1) and purine metabolism

The Semantic Reader Project: Augmenting Scholarly Documents through AI-Powered Interactive Reading Interfaces

Scholarly publications are key to the transfer of knowledge from scholars to others. However, research papers are information-dense, and as the volume of the scientific literature grows, the need for new technology to support the reading process grows. In contrast to the process of finding papers, which has been transformed by Internet technology, the experience of reading research papers has changed little in decades. The PDF format for sharing research papers is widely used due to its portability, but it has significant downsides including: static content, poor accessibility for low-vision readers, and difficulty reading on mobile devices. This paper explores the question "Can recent advances in AI and HCI power intelligent, interactive, and accessible reading interfaces -- even for legacy PDFs?" We describe the Semantic Reader Project, a collaborative effort across multiple institutions to explore automatic creation of dynamic reading interfaces for research papers. Through this project, we've developed ten research prototype interfaces and conducted usability studies with more than 300 participants and real-world users showing improved reading experiences for scholars. We've also released a production reading interface for research papers that will incorporate the best features as they mature. We structure this paper around challenges scholars and the public face when reading research papers -- Discovery, Efficiency, Comprehension, Synthesis, and Accessibility -- and present an overview of our progress and remaining open challenges

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

N-Acylethanolamines in human reproductive fluids

N-Acylethanolamines (NAEs) are an important family of lipid-signaling molecules. Arachidonylethanolamide (anandamide) (AEA), palmitoylethanolamide (PEA), and oleoylethanolamide (OEA) are co-produced from similar phospholipid precursors when neurons are stimulated. AEA is an endogenous agonist (endocannabinoid) for cannabinoid receptors. It binds with higher affinity to type CB1 than to type CB2 cannabinoid receptors. PEA does not bind to CB1, while the hypothesis that it reacts with putative CB2-like receptors has been questioned. OEA does not activate currently known cannabinoid receptors, but it mimics the effects of AEA and cannabinoids in reducing the fertilizing capacity of sea urchin sperm. OEA and PEA also act as entourage compounds by inhibiting the hydrolysis of AEA by fatty acid amide hydrolase. Cannabinoid receptors and/or AEA are present in mammalian reproductive organs including the testis, epididymis, prostate, ovary, uterus, sperm, preimplantation embryo and placenta, as well as prostatic and mammary carcinomas. We now report that analysis by high-performance liquid chromatography/mass spectrometry (HPLC/MS) shows the presence of AEA, PEA, and OEA in human seminal plasma, mid-cycle oviductal fluid, follicular fluid, amniotic fluid, milk, and fluids from malignant ovarian cysts. Previous studies showed that AEA-signaling via cannabinoid receptors regulates capacitation and fertilizing potential of human sperm, early embryonic development and blastocyst implantation into the uterine mucosa of rodents, as well as proliferation of human mammary and prostatic carcinomas. Current results imply that NAEs also may modulate follicular maturation and ovulation, normal and pathological ovarian function, placental and fetal physiology, lactation, infant physiology, and behavior. Collectively, these findings suggest that NAEs in human reproductive fluids may help regulate multiple physiological and pathological processes in the reproductive system, and imply that exogenous cannabinoids delivered by marijuana smoke might impact these processes. This study has potential medical and public policy ramifications because of the incidence of marijuana abuse by adolescents and adults in our society, previously documented reproductive effects of marijuana, and the ongoing debate about medicinal use of marijuana and cannabinoids

ACCoRD: A Multi-Document Approach to Generating Diverse Descriptions of Scientific Concepts

Systems that can automatically define unfamiliar terms hold the promise of improving the accessibility of scientific texts, especially for readers who may lack prerequisite background knowledge. However, current systems assume a single "best" description per concept, which fails to account for the many potentially useful ways a concept can be described. We present ACCoRD, an end-to-end system tackling the novel task of generating sets of descriptions of scientific concepts. Our system takes advantage of the myriad ways a concept is mentioned across the scientific literature to produce distinct, diverse descriptions of target scientific concepts in terms of different reference concepts. To support research on the task, we release an expert-annotated resource, the ACCoRD corpus, which includes 1,275 labeled contexts and 1,787 hand-authored concept descriptions. We conduct a user study demonstrating that (1) users prefer descriptions produced by our end-to-end system, and (2) users prefer multiple descriptions to a single "best" description