Knowledge graphs have become a common approach for knowledge representation. Yet, the application of graph methodology is elusive due to the sheer number and complexity of knowledge sources. In addition, semantic incompatibilities hinder efforts to harmonize and integrate across these diverse sources. As part of The Biomedical Translator Consortium, we have developed a knowledge graph–based question-answering system designed to augment human reasoning and accelerate translational scientific discovery: the Translator system. We have applied the Translator system to answer biomedical questions in the context of a broad array of diseases and syndromes, including Fanconi anemia, primary ciliary dyskinesia, multiple sclerosis, and others. A variety of collaborative approaches have been used to research and develop the Translator system. One recent approach involved the establishment of a monthly “Question-of-the-Month (QotM) Challenge” series. Herein, we describe the structure of the QotM Challenge; the six challenges that have been conducted to date on drug-induced liver injury, cannabidiol toxicity, coronavirus infection, diabetes, psoriatic arthritis, and ATP1A3-related phenotypes; the scientific insights that have been gleaned during the challenges; and the technical issues that were identified over the course of the challenges and that can now be addressed to foster further development of the prototype Translator system. We close with a discussion on Large Language Models such as ChatGPT and highlight differences between those models and the Translator system.

Early in the COVID-19 pandemic, the World Health Organization stressed the importance of daily clinical assessments of infected patients, yet current approaches frequently consider cross-sectional timepoints, cumulative summary measures, or time-to-event analyses. Statistical methods are available that make use of the rich information content of longitudinal assessments. We demonstrate the use of a multistate transition model to assess the dynamic nature of COVID-19-associated critical illness using daily evaluations of COVID-19 patients from 9 academic hospitals. We describe the accessibility and utility of methods that consider the clinical trajectory of critically ill COVID-19 patients.

OBJECTIVES/GOALS: Osteoarthritis (OA) is a cartilage destroying disease. We are investigating abaloparatide (ABL) activation of parathyroid hormone receptor type 1 (PTH1R), which is expressed by articular chondrocytes in OA. We propose ABL treatment is chondroprotective in murine PTOA via stimulation of matrix production and inhibition of chondrocyte maturation. METHODS/STUDY POPULATION: 16-week-old C57BL/6 male mice received destabilization of the medial meniscus (DMM) surgery to induce knee PTOA. Beginning 2 weeks post-DMM, 40 μg/kg of ABL (or saline) was administered daily via subcutaneous injection and tissues were harvested after 6 weeks of daily injections and 8 weeks after DMM surgery. Harvested joint tissues were used for histological and molecular assessment of OA using three 5 μm thick sagittal sections from each joint, 50 μm apart, cut from the medial compartment of injured knees. Safranin O/Fast Green tissue staining and immunohistochemistry-based detection of type 10 collagen (Col10) and lubricin (Prg4) was performed using standard methods. Histomorphometric quantification of tibial cartilage area and larger hypertrophic-like cells was performed using the Osteomeasure system. RESULTS/ANTICIPATED RESULTS: Safranin O/Fast Green stained sections showed a decreased cartilage loss in DMM joints from ABL-treated versus saline-treated mice. Histomorphometric analysis of total tibial cartilage area revealed preservation of cartilage tissue on the tibial surface. Immunohistochemical analyses showed that upregulation of Col10 in DMM joints was mitigated in the cartilage of ABL-treated mice, and chondrocyte expression of Prg4 was increased in uncalcified cartilage areas in ABL-treated group. The Prg4 finding suggests a matrix anabolic effect that may counter OA cartilage loss. Quantification of chondrocytes in uncalcified and calcified tibial cartilage areas revealed a reduction in the number of larger hypertrophic-like cells in ABL treated mice, suggesting deceleration of hypertrophic differentiation. DISCUSSION/SIGNIFICANCE: Cartilage preservation/regeneration therapies would fill a critical unmet need. We demonstrate that an osteoporosis drug targeting PTH1R decelerates PTOA in mice. ABL treatment was associated with preservation of cartilage, decreased Col10, increased Prg4, and decreased number of large hypertrophic-like chondrocytes in the tibial cartilage.

We apply two methods to estimate the 21-cm bispectrum from data taken within the Epoch of Reionisation (EoR) project of the Murchison Widefield Array (MWA). Using data acquired with the Phase II compact array allows a direct bispectrum estimate to be undertaken on the multiple redundantly spaced triangles of antenna tiles, as well as an estimate based on data gridded to the uv-plane. The direct and gridded bispectrum estimators are applied to 21 h of high-band (167–197 MHz; z = 6.2–7.5) data from the 2016 and 2017 observing seasons. Analytic predictions for the bispectrum bias and variance for point-source foregrounds are derived. We compare the output of these approaches, the foreground contribution to the signal, and future prospects for measuring the bispectra with redundant and non-redundant arrays. We find that some triangle configurations yield bispectrum estimates that are consistent with the expected noise level after 10 h, while equilateral configurations are strongly foreground-dominated. Careful choice of triangle configurations may be made to reduce foreground bias that hinders power spectrum estimators, and the 21-cm bispectrum may be accessible in less time than the 21-cm power spectrum for some wave modes, with detections in hundreds of hours.

We describe the motivation and design details of the ‘Phase II’ upgrade of the Murchison Widefield Array radio telescope. The expansion doubles to 256 the number of antenna tiles deployed in the array. The new antenna tiles enhance the capabilities of the Murchison Widefield Array in several key science areas. Seventy-two of the new tiles are deployed in a regular configuration near the existing array core. These new tiles enhance the surface brightness sensitivity of the array and will improve the ability of the Murchison Widefield Array to estimate the slope of the Epoch of Reionisation power spectrum by a factor of ∼3.5. The remaining 56 tiles are deployed on long baselines, doubling the maximum baseline of the array and improving the array u, v coverage. The improved imaging capabilities will provide an order of magnitude improvement in the noise floor of Murchison Widefield Array continuum images. The upgrade retains all of the features that have underpinned the Murchison Widefield Array’s success (large field of view, snapshot image quality, and pointing agility) and boosts the scientific potential with enhanced imaging capabilities and by enabling new calibration strategies.

Research was conducted to determine the utility of a single, temperature-independent Weibull function for describing cumulative seed germination under several temperature regimes with 14 sets of weed and crop seed germination data. A modified cumulative Weibull function was derived to distribute germination times for individuals within the population and distributed the occurrence of germination given ample sample size and appropriate sample interval. The descriptive and predictive attributes of the stochastic model component are well suited for incorporation into seed germination models and are likely applicable to models to predict distribution of times for other developmental processes of plants.

Long sediment cores (12.5 and 13.5 m) from two lakes in Yunnan Province were used to infer the paleoclimate of southwest China over the past 50,000 yr. During the Holocene and marine isotope stage (MIS 3), bio-induced carbonate precipitation and organic matter (OM) production was high, suggesting warm temperatures and high primary productivity. In contrast, sediment inorganic carbon (IC) and organic carbon (OC) concentrations were low in last glacial deposits from 38,000 to 12,000 cal yr B.P., indicating cool temperatures and low productivity. The 50,000-yr record has alternating peaks of carbonate and coarse-grain (>38 μm) quartz that reflect warm, moist interglacial or interstadial conditions alternating with cold, dry glacial or stadial conditions, respectively. Spectral analysis of the carbonate and quartz signals reveals power concentrated at periods of 7200 and 8900 cal yr, respectively, that may reflect a nonlinear climate response to precessional forcing at a time of reduced eccentricity modulation (McIntyre and Molfino, 1996). Oxygen isotope values of calcite from Yunnan lake cores indicate the summer monsoon was weak during the last glaciation from 50,000 to 12,000 cal yr B.P. The summer monsoon intensified between 12,000 and 8000 cal yr B.P., but weakened gradually in response to insolation forcing during the mid-to-late Holocene. Our results support the Overpeck et al. (1996) model that posits a weak summer monsoon during the last glaciation that responded nonlinearly to insolation forcing when its intensity was affected by Eurasian snow cover and ice-sheet extent. The summer monsoon intensified and responded linearly to seasonal insolation forcing in the Holocene when ice volume diminished.

Although extinction risk has been found to have a consistent negative relationship with geographic range across wide temporal and taxonomic scales, the effect has been difficult to disentangle from factors such as sampling, ecological niche, or clade. In addition, studies of extinction risk have focused on benthic invertebrates with less work on planktic taxa. We employed a global set of 1114 planktic graptolite species from the Ordovician to lower Devonian to analyze the predictive power of species’ traits and abiotic factors on extinction risk, combining general linear models (GLMs), partial least-squares regression (PLSR), and permutation tests. Factors included measures of geographic range, sampling, and graptolite-specific factors such as clade, biofacies affiliation, shallow water tolerance, and age cohorts split at the base of the Katian and Rhuddanian stages.

The percent variance in durations explained varied substantially between taxon subsets from 12% to 45%. Overall commonness, the correlated effects of geographic range and sampling, was the strongest, most consistent factor (12–30% variance explained), with clade and age cohort adding up to 18% and other factors <10%. Surprisingly, geographic range alone contributed little explanatory power (<5%). It is likely that this is a consequence of a nonlinear relationship between geographic range and extinction risk, wherein the largest reductions in extinction risk are gained from moderate expansion of small geographic ranges. Thus, even large differences in range size between graptolite species did not lead to a proportionate difference in extinction risk because of the large average ranges of these species. Finally, we emphasize that the common practice of determining the geographic range of taxa from the union of all occurrences over their duration poses a substantial risk of overestimating the geographic scope of the realized ecological niche and, thus, of further conflating sampling effects on observed duration with the biological effects of range size on extinction risk.

The reversible switching between the amorphous and crystalline phases of Ge2Sb2Te5 (GST) is investigated with ab initio molecular dynamics. We apply different quench rates (-16 K/ps, -5 K/ps, -2 K/ps, and -0.45 K/ps) and different annealing temperatures (500 K, 600 K, 700 K, and 800 K) to amorphize and crystallize GST respectively. Results show that the generated amorphous is strongly dependent on the quench rate. For -16 K/ps and -5 K/ps, generated amorphous samples have different density of crystal seeds, higher in the later. The amorphous structure formed at -2 K/ps contains a single crystalline cluster, while that formed at the quench rate of -0.45 K/ps had sufficient time to completely crystallize the amorphous phase. Annealing the amorphous systems formed at different rates shows that crystallization depends both on the annealing temperature and on the structure of the initial system (i.e., whether or not it contains crystalline clusters or crystal seeds). At 500 K, formation of crystalline clusters occurs readily within a few ps while the rate at which they grow is slow, taking 0.9 ns to complete the crystallization. In contrast, crystalline cluster formation is inhibited at 800 K. In the intermediate temperature range, both crystalline cluster formation and growth occur within a few hundred ps indicating that these temperatures leads to the fastest crystallization. The crystallization of a 63-atom at ∼900 K resulted in a highly relaxed crystal structure showing a clear tendency for separation of Ge and Sb species in layers. This model also indicates a tendency of segregation of vacancies, suggesting that vacancy layering may play a key role in the crystallization process.