Clinfo.ai: An Open-Source Retrieval-Augmented Large Language Model System for Answering Medical Questions using Scientific Literature

The quickly-expanding nature of published medical literature makes it challenging for clinicians and researchers to keep up with and summarize recent, relevant findings in a timely manner. While several closed-source summarization tools based on large language models (LLMs) now exist, rigorous and systematic evaluations of their outputs are lacking. Furthermore, there is a paucity of high-quality datasets and appropriate benchmark tasks with which to evaluate these tools. We address these issues with four contributions: we release Clinfo.ai, an open-source WebApp that answers clinical questions based on dynamically retrieved scientific literature; we specify an information retrieval and abstractive summarization task to evaluate the performance of such retrieval-augmented LLM systems; we release a dataset of 200 questions and corresponding answers derived from published systematic reviews, which we name PubMed Retrieval and Synthesis (PubMedRS-200); and report benchmark results for Clinfo.ai and other publicly available OpenQA systems on PubMedRS-200.Comment: Preprint of an article published in Pacific Symposium on Biocomputing copyright 2024 World Scientific Publishing Co., Singapore, http://psb.stanford.edu

Spitzer and near-infrared observations of a new bi-polar protostellar outflow in the Rosette Molecular Cloud

We present and discuss \emph{Spitzer} and near-infrared H$_{2}$ observations of a new bi-polar protostellar outflow in the Rosette Molecular Cloud. The outflow is seen in all four IRAC bands and partially as diffuse emission in the MIPS 24 $\mu$m band. An embedded MIPS 24 $\mu$m source bisects the outflow and appears to be the driving source. This source is coincident with a dark patch seen in absorption in the 8 $\mu$m IRAC image. \emph{Spitzer} IRAC color analysis of the shocked emission was performed from which thermal and column density maps of the outflow were constructed. Narrow-band near-infrared (NIR) images of the flow reveal H$_2$ emission features coincident with the high temperature regions of the outflow. This outflow has now been given the designation MHO 1321 due to the detection of NIR H$_2$ features. We use these data and maps to probe the physical conditions and structure of the flow.Comment: Accepted for publication in The Astrophysical Journa

Regional-Specific Effects of Ovarian Hormone Loss on Synaptic Plasticity in Adult Human APOE Targeted Replacement Mice

The human apolipoprotein ε4 allele (APOE4) has been implicated as one of the strongest genetic risk factors associated with Alzheimer’s disease (AD) and in influencing normal cognitive functioning. Previous studies have demonstrated that mice expressing human apoE4 display deficits in behavioral and neurophysiological outcomes compared to those with apoE3. Ovarian hormones have also been shown to be important in modulating synaptic processes underlying cognitive function, yet little is known about how their effects are influenced by apoE. In the current study, female adult human APOE targeted replacement (TR) mice were utilized to examine the effects of human APOE genotype and long-term ovarian hormone loss on synaptic plasticity in limbic regions by measuring dendritic spine density and electrophysiological function. No significant genotype differences were observed on any outcomes within intact mice. However, there was a significant main effect of genotype on total spine density in apical dendrites in the hippocampus, with post-hoc t-tests revealing a significant reduction in spine density in apoE3 ovariectomized (OVX) mice compared to sham operated mice. There was also a significant main effect of OVX on the magnitude of LTP, with post-hoc t-tests revealing a decrease in apoE3 OVX mice relative to sham. In contrast, apoE4 OVX mice showed increased synaptic activity relative to sham. In the lateral amygdala, there was a significant increase in total spine density in apoE4 OVX mice relative to sham. This increase in spine density was consistent with a significant increase in spontaneous excitatory activity in apoE4 OVX mice. These findings suggest that ovarian hormones differentially modulate synaptic integrity in an apoE-dependent manner within brain regions that are susceptible to neurophysiological dysfunction associated with AD

The PuZZling Li-Rich Red Giant Associated With NGC 6819

A Li-rich red giant (RG) star (2M19411367+4003382) recently discovered in the direction of NGC 6819 belongs to the rare subset of Li-rich stars that have not yet evolved to the luminosity bump, an evolutionary stage where models predict Li can be replenished. The currently favored model to explain Li enhancement in first-ascent RGs like 2M19411367+4003382 requires deep mixing into the stellar interior. Testing this model requires a measurement of C-12/C-13, which is possible to obtain from Apache Point Observatory Galactic Evolution Experiment (APOGEE) spectra. However, the Li-rich star also has abnormal asteroseismic properties that call into question its membership in the cluster, even though its radial velocity and location on color-magnitude diagrams are consistent with membership. To address these puzzles, we have measured a wide array of abundances in the Li-rich star and three comparison stars using spectra taken as part of the APOGEE survey to determine the degree of stellar mixing, address the question of membership, and measure the surface gravity. We confirm that the Li-rich star is a RG with the same overall chemistry as the other cluster giants. However, its log g is significantly lower, consistent with the asteroseismology results and suggestive of a very low mass if the star is indeed a cluster member. Regardless of the cluster membership, the C-12/C-13 and C/N ratios of the Li-rich star are consistent with standard first dredge-up, indicating that Li dilution has already occurred, and inconsistent with internal Li enrichment scenarios that require deep mixing.National Science Foundation AST1109888NSF AST-1358862, AST 1109718, AST 1312863Alfred P. Sloan FoundationNational Science FoundationU.S. Department of Energy Office of ScienceUniversity of ArizonaBrazilian Participation GroupBrookhaven National LaboratoryCarnegie Mellon UniversityUniversity of FloridaFrench Participation GroupGerman Participation GroupHarvard UniversityInstituto de Astrofisica de CanariasMichigan State/NotreDame/JINA Participation GroupJohns Hopkins UniversityLawrence Berkeley National LaboratoryMax Planck Institute for AstrophysicsMax Planck Institute for Extraterrestrial PhysicsNew Mexico State UniversityNew York UniversityOhio State UniversityPennsylvania State UniversityUniversity of PortsmouthPrinceton UniversitySpanish Participation GroupUniversity of TokyoUniversity of UtahVanderbilt UniversityUniversity of VirginiaUniversity of WashingtonYale UniversityNational Aeronautics and Space AdministrationTwo Micron All Sky SurveyUniversity of MassachusettsInfrared Processing and Analysis Center/California Institute of TechnologyU.S. Government NAG W-2166Astronom

Targeted disruption of cubilin reveals essential developmental roles in the structure and function of endoderm and in somite formation

BACKGROUND: Cubilin is a peripheral membrane protein that interacts with the integral membrane proteins megalin and amnionless to mediate ligand endocytosis by absorptive epithelia such as the extraembryonic visceral endoderm (VE). RESULTS: Here we report the effects of the genetic deletion of cubilin on mouse embryonic development. Cubilin gene deletion is homozygous embryonic lethal with death occurring between 7.5–13.5 days post coitum (dpc). Cubilin-deficient embryos display developmental retardation and do not advance morphologically beyond the gross appearance of wild-type 8–8.5 dpc embryos. While mesodermal structures such as the allantois and the heart are formed in cubilin mutants, other mesoderm-derived tissues are anomalous or absent. Yolk sac blood islands are formed in cubilin mutants but are unusually large, and the yolk sac blood vessels fail to undergo remodeling. Furthermore, somite formation does not occur in cubilin mutants. Morphological abnormalities of endoderm occur in cubilin mutants and include a stratified epithelium in place of the normally simple columnar VE epithelium and a stratified cuboidal epithelium in place of the normally simple squamous epithelium of the definitive endoderm. Cubilin-deficient VE is also functionally defective, unable to mediate uptake of maternally derived high-density lipoprotein (HDL). CONCLUSION: In summary, cubilin is required for embryonic development and is essential for the formation of somites, definitive endoderm and VE and for the absorptive function of VE including the process of maternal-embryo transport of HDL

Long-Term Effects of Chronic Intermittent Ethanol Exposure in Adolescent and Adult Rats: Radial-Arm Maze Performance and Operant Food Reinforced Responding

Background: Adolescence is not only a critical period of late-stage neurological development in humans, but is also a period in which ethanol consumption is often at its highest. Given the prevalence of ethanol use during this vulnerable developmental period we assessed the long-term effects of chronic intermittent ethanol (CIE) exposure during adolescence, compared to adulthood, on performance in the radial-arm maze (RAM) and operant food-reinforced responding in male rats. Methodology/Principal Findings: Male Sprague Dawley rats were exposed to CIE (or saline) and then allowed to recover. Animals were then trained in either the RAM task or an operant task using fixed- and progressive- ratio schedules. After baseline testing was completed all animals received an acute ethanol challenge while blood ethanol levels (BECs) were monitored in a subset of animals. CIE exposure during adolescence, but not adulthood decreased the amount of time that animals spent in the open portions of the RAM arms (reminiscent of deficits in risk-reward ntegration) and rendered animals more susceptible to the acute effects of an ethanol challenge on working memory tasks. The operant food reinforced task showed that these effects were not due to altered food motivation or to differential sensitivity to the nonspecific performance-disrupting effects of ethanol. However, CIE pre-treated animals had lower BEC levels than controls during the acute ethanol challenges indicating persistent pharmacokinetic tolerance to ethanol after the CIE treatment. There was little evidence of enduring effects of CIE alone on traditional measures of spatial and working memory. Conclusions/Significance: These effects indicate that adolescence is a time of selective vulnerability to the long-term effects of repeated ethanol exposure on neurobehavioral function and acute ethanol sensitivity. The positive and negative findings reported here help to further define the nature and extent of the impairments observed after adolescent CIE and provide direction for future research

Thrombosis, major bleeding, and survival in COVID-19 supported by VV- ECMO in the first vs second wave- multicentre observational study in the UK

BACKGROUND: Bleeding and thrombosis are major complications of veno-venous extracorporeal membrane (VV-ECMO). OBJECTIVES: To assess thrombosis, major bleeding (MB) and 180-day in patients supported by VV-ECMO between first (1st March-31st May 2020) and second (1st June 2020-30th June 2021) waves of the COVID-19 pandemic. PATIENTS/METHODS: Observational study of 309 consecutive patients (≥18years) with severe COVID-19 supported by VV-ECMO in four nationally commissioned ECMO centres, UK. RESULTS: Median age was 48 (19-75)years and 70.6% were male. Probabilities of survival, thrombosis, and MB at 180 days in the overall cohort were 62.5% (193/309), 39.8%(123/309) and 30%(93/309). In multivariate analysis, age >55 years (HR 2.29 [1.33-3.93],p=0.003) and elevated creatinine (HR 1.91 [1.19-3.08],p=0.008) were associated with increased mortality. Corrected for duration of VV-ECMO support, arterial thrombosis alone (HR 3.0 [95% CI1.5-5.9], P= 0.002) or circuit thrombosis alone (HR 3.9 [95% 2.4-6.3], P<0.001), but not venous thrombosis, increased mortality. MB during ECMO had 3-fold risk (95% CI 2.6-5.8, P<0.001) of mortality. The first wave cohort had more males (76.7% vs 64%, p=0.014), higher 180-day survival (71.1% vs 53.3% p=0.003), more venous thrombosis alone (46.4% vs 29.2%, p=0.02) and lower circuit thrombosis (9.2% vs 28.1%, p<0.001). The second wave cohort received more steroids (121/150 [80.6%] vs 86/159 [54.1%], p<0.0001) and Tocilizumab (20/150 [13.3%] vs 4/159 [2.5%] p=0.005). CONCLUSIONS: MB and thrombosis are frequent complications in patients on VV-ECMO and significantly increase mortality. Arterial thrombosis alone or circuit thrombosis alone increased mortality whilst venous thrombosis alone had no effect. MB during ECMO support increased mortality 3.9-fold