Considerations for health care institutions training large language models on electronic health records

Large language models (LLMs) like ChatGPT have excited scientists across fields; in medicine, one source of excitement is the potential applications of LLMs trained on electronic health record (EHR) data. But there are tough questions we must first answer if health care institutions are interested in having LLMs trained on their own data; should they train an LLM from scratch or fine-tune it from an open-source model? For healthcare institutions with a predefined budget, what are the biggest LLMs they can afford? In this study, we take steps towards answering these questions with an analysis on dataset sizes, model sizes, and costs for LLM training using EHR data. This analysis provides a framework for thinking about these questions in terms of data scale, compute scale, and training budgets

The growth and form of knowledge networks by kinesthetic curiosity

Throughout life, we might seek a calling, companions, skills, entertainment, truth, self-knowledge, beauty, and edification. The practice of curiosity can be viewed as an extended and open-ended search for valuable information with hidden identity and location in a complex space of interconnected information. Despite its importance, curiosity has been challenging to computationally model because the practice of curiosity often flourishes without specific goals, external reward, or immediate feedback. Here, we show how network science, statistical physics, and philosophy can be integrated into an approach that coheres with and expands the psychological taxonomies of specific-diversive and perceptual-epistemic curiosity. Using this interdisciplinary approach, we distill functional modes of curious information seeking as searching movements in information space. The kinesthetic model of curiosity offers a vibrant counterpart to the deliberative predictions of model-based reinforcement learning. In doing so, this model unearths new computational opportunities for identifying what makes curiosity curious

Enhanced carbon uptake and reduced methane emissions in a newly restored wetland

Author Posting. © American Geophysical Union, 2020. This article is posted here by permission of American Geophysical Union for personal use, not for redistribution. The definitive version was published in Journal of Geophysical Research: Biogeosciences 125(1), (2020): e2019JG005222, doi:10.1029/2019JG005222.Wetlands play an important role in reducing global warming potential in response to global climate change. Unfortunately, due to the effects of human disturbance and natural erosion, wetlands are facing global extinction. It is essential to implement engineering measures to restore damaged wetlands. However, the carbon sink capacity of restored wetlands is unclear. We examined the seasonal change of greenhouse gas emissions in both restored wetland and natural wetland and then evaluated the carbon sequestration capacity of the restored wetland. We found that (1) the carbon sink capacity of the restored wetland showed clear daily and seasonal change, which was affected by light intensity, air temperature, and vegetation growth, and (2) the annual daytime (8–18 hr) sustained‐flux global warming potential was −11.23 ± 4.34 kg CO2 m−2 y−1, representing a much larger carbon sink than natural wetland (−5.04 ± 3.73 kg CO2 m−2 y−1) from April to December. In addition, the results showed that appropriate tidal flow management may help to reduce CH4 emission in wetland restoration. Thus, we proposed that the restored coastal wetland, via effective engineering measures, reliably acted as a large net carbon sink and has the potential to help mitigate climate change.We would like to thank Yangtze Delta Estuarine Wetland Ecosystem Ministry of Education & Shanghai Observation and Research Station for providing sites during our research. This research was supported by the National Key Research and Development Program of China (Grant 2017YFC0506002), the National Natural Science Foundation of China Overseas and Hong Kong‐Macao Scholars Collaborative Research Fund (Grant 31728003), the China Postdoctoral Science Foundation (Grant 2018M640362), the Shanghai University Distinguished Professor (Oriental Scholars) Program (Grant JZ2016006), the Open Fund of Shanghai Key Lab for Urban Ecological Processes and Eco‐Restoration (Grant SHUES2018B06), and the Scientific Projects of Shanghai Municipal Oceanic Bureau (Grant 2018‐03). The complete data set is available at https://data.4tu.nl/repository/uuid:536b2614‐c4ca‐43d2‐84dd‐6180fd859544

The effects of daily chlorhexidine bathing on cutaneous bacterial isolates: a pilot study

Chlorhexidine gluconate (CHG) is a topical antiseptic used in a myriad of clinical settings. Recently, CHG baths have been shown to decrease multidrug-resistant organism acquisition and infections and catheter-associated bloodstream infections. The present study examined the effects of daily bathing with CHG on the recovery and antimicrobial susceptibility of cultivable cutaneous bacteria. The objectives of this study were to (1) explore the effects of clinical CHG bathing on cultivable cutaneous bacteria, (2) study the relationship between CHG minimum inhibitory concentration and antimicrobial susceptibility of coagulase-negative staphylococci, and (3) demonstrate the feasibility of the approach so a more definitive study may be performed. Significant decreases in bacterial colony counts and phenotypic diversity occurred with greater CHG exposure. The findings also suggest an inverse relationship between CHG minimum inhibitory concentration and antimicrobial susceptibility. Larger prospective studies are necessary to fully investigate the clinical impact of CHG usage

Validation of Reference Housekeeping Genes for Gene Expression Studies in Western Corn Rootworm (\u3cem\u3eDiabrotica virgifera virgifera\u3c/em\u3e)

Quantitative Real-time PCR (qRT-PCR) is a powerful technique to investigate comparative gene expression. In general, normalization of results using a highly stable housekeeping gene (HKG) as an internal control is recommended and necessary. However, there are several reports suggesting that regulation of some HKGs is affected by different conditions. The western corn rootworm (WCR), Diabrotica virgifera virgifera LeConte (Coleoptera: Chrysomelidae), is a serious pest of corn in the United States and Europe. The expression profile of target genes related to insecticide exposure, resistance, and RNA interference has become an important experimental technique for study of western corn rootworms; however, lack of information on reliable HKGs under different conditions makes the interpretation of qRT-PCR results difficult. In this study, four distinct algorithms (Genorm, NormFinder, BestKeeper and delta-CT) and five candidate HKGs to genes of reference (β-actin; GAPDH, glyceraldehyde-3-phosphate dehydrogenase; β-tubulin; RPS9, ribosomal protein S9; EF1a, elongation factor-1α) were evaluated to determine the most reliable HKG under different experimental conditions including exposure to dsRNA and Bt toxins and among different tissues and developmental stages. Although all the HKGs tested exhibited relatively stable expression among the different treatments, some differences were noted. Among the five candidate reference genes evaluated, β-actin exhibited highly stable expression among different life stages. RPS9 exhibited the most similar pattern of expression among dsRNA treatments, and both experiments indicated that EF1a was the second most stable gene. EF1a was also the most stable for Bt exposure and among different tissues. These results will enable researchers to use more accurate and reliable normalization of qRT-PCR data in WCR experiments

Placenta Growth Factor-1 antagonizes VEGF-induced angiogenesis and tumor growth by the formation of functionally inactive PlGF-1/VEGF heterodimers

AbstractTumor growth and metastasis require concomitant growth of new blood vessels, which are stimulated by angiogenic factors, including vascular endothelial growth factor (VEGF), secreted by most tumors. Whereas the angiogenic property and molecular mechanisms of VEGF have been well studied, the biological function of its related homolog, placenta growth factor (PlGF), is poorly understood. Here we demonstrate that PlGF-1, an alternatively spliced isoform of the PlGF gene, antagonizes VEGF-induced angiogenesis when both factors are coexpressed in murine fibrosarcoma cells. Overexpression of PlGF-1 in VEGF-producing tumor cells results in the formation of PlGF-1/VEGF heterodimers and depletion of the majority of mouse VEGF homodimers. The heterodimeric form of PlGF-1/VEGF lacks the ability to induce angiogenesis in vitro and in vivo. Similarly, PlGF-1/VEGF fails to activate the VEGFR-2-mediated signaling pathways. Further, PlGF-1 inhibits the growth of a murine fibrosarcoma by approximately 90% when PlGF-1-expressing tumor cells are implanted in syngeneic mice. In contrast, overexpression of human VEGF in murine tumor cells causes accelerated and exponential growth of primary fibrosarcomas and early hepatic metastases. Our data demonstrate that PlGF-1, a member of the VEGF family, acts as a natural antagonist of VEGF when both factors are synthesized in the same population of cells. The underlying mechanism is due to the formation of functionally inactive heterodimers

Previous antibiotic exposure increases risk of infection with extended-spectrum-β-lactamase- and AmpC-producing Escherichia coli and Klebsiella pneumoniae in pediatric patients

The objective of this study was to determine whether antibiotic exposure is associated with extended-spectrum-beta-lactamase- or AmpC-producing Escherichia coli or Klebsiella pneumoniae infections in children. We collected extended-spectrum-beta-lactamase- or AmpC-producing E. coli or K. pneumoniae isolates and same-species susceptible controls from normally sterile sites of patients aged ≤21 years, along with associated clinical data, at four free-standing pediatric centers. After controlling for potential confounders, the relative risk of having an extended-spectrum-beta-lactamase-producing isolate rather than a susceptible isolate was 2.2 times higher (95% confidence interval [CI], 1.49 to 3.35) among those with antibiotic exposure in the 30 days prior to infection than in those with no antibiotic exposure. The results were similar when analyses were limited to exposure to third-generation cephalosporins, other broad-spectrum beta-lactams, or trimethoprim-sulfamethoxazole. Conversely, the relative risk of having an AmpC-producing versus a susceptible isolate was not significantly elevated with any antibiotic exposure in the 30 days prior to infection (adjusted relative risk ratio, 1.12; 95% CI, 0.65 to 1.91). However, when examining subgroups of antibiotics, the relative risk of having an AmpC-producing isolate was higher for patients with exposure to third-generation cephalosporins (adjusted relative risk ratio, 4.48; 95% CI, 1.75 to 11.43). Dose-response relationships between antibiotic exposure and extended-spectrum-beta-lactamase-producing or AmpC-producing isolates were not demonstrated. These results reinforce the need to study and implement pediatric antimicrobial stewardship strategies, and they indicate that epidemiological studies of third-generation cephalosporin-resistant E. coli and K. pneumoniae isolates should include resistance mechanisms when possible

Rydberg-atom-based single-photon detection for haloscope axion searches

We propose a Rydberg-atom-based single-photon detector for signal readout in dark matter haloscope experiments between 40 ${\mu}$eV and 200 ${\mu}$eV (10 GHz and 50 GHz). At these frequencies, standard haloscope readout using linear amplifiers is limited by quantum measurement noise, which can be avoided by using a single-photon detector. Our single-photon detection scheme can offer scan rate enhancements up to a factor of $10^4$ over traditional linear amplifier readout, and is compatible with many different haloscope cavities. We identify multiple haloscope designs that could use our Rydberg-atom-based single-photon detector to search for QCD axions with masses above 40 ${\mu}$eV (10 GHz), currently a minimally explored parameter space.Comment: 15 pages, 8 figure

The role of prenatal violence exposure in the development of disparities in childrens adiposity from birth to middle childhood.

OBJECTIVE: This study examined whether womens exposure to multiple types of violence during childhood and pregnancy was associated with childrens BMI trajectories and whether parenting quality moderated those associations. METHODS: A cohort of 1288 women who gave birth between 2006 and 2011 self-reported their exposure to childhood traumatic events, intimate partner violence (IPV), and residential address (linked to geocoded index of violent crime) during pregnancy. Childrens length/height and weight at birth and at age 1, 2, 3, 4 to 6, and 8 years were converted to BMI z scores. Observed mother-child interactions were behaviorally coded during a dyadic teaching task. RESULTS: Covariate-adjusted growth mixture models identified three trajectories of childrens BMI from birth to 8 years old: Low-Stable (17%), Moderate-Stable (59%), and High-Rising (22%). Children whose mothers experienced more types of IPV during pregnancy were more likely to be in the High-Rising than the Low-Stable (odds ratio [OR] = 2.62; 95% CI: 1.27-5.41) trajectory. Children whose mothers lived in higher crime neighborhoods were more likely to be in the High-Rising than the Low-Stable (OR = 1.11; 95% CI:1.03-1.17) or Moderate-Stable trajectories (OR = 1.08; CI: 1.03-1.13). Main effects of childhood traumatic events and moderation by parenting were not detected. CONCLUSIONS: Maternal experiences of violence during pregnancy increase childrens risk for developing overweight, highlighting intergenerational transmission of social adversity in childrens health