HESI workshop summary: Interpretation of developmental and reproductive toxicity endpoints and the impact on data interpretation of adverse events.

The Health and Environmental Sciences Institute Developmental and Reproductive Toxicology (HESI-DART) group held a hybrid in-person and virtual workshop in Washington, DC, in 2022. The workshop was entitled, "Interpretation of DART in Regulatory Contexts and Frameworks." There were 154 participants (37 in person and 117 virtual) across 9 countries. The purpose of the workshop was to capture key consensus approaches used to assess DART risks associated with chemical product exposure when a nonclinical finding is identified. The decision-making process for determining whether a DART endpoint is considered adverse is critical because the outcome may have downstream implications (e.g., increased animal usage, modifications to reproductive classification and pregnancy labeling, impact on enrollment in clinical trials and value chains). The workshop included a series of webinar modules to train and engage in discussions with federal and international regulators, clinicians, academic investigators, nongovernmental organizations, contract research organization scientists, and private sector scientists on the best practices and principles of interpreting DART and new approach methodologies in the context of regulatory requirements and processes. Despite the differences in regulatory frameworks between the chemical and pharmaceutical sectors, the same foundational principles for data interpretation should be applied. The discussions led to the categorization of principles, which offer guidance for the systematic interpretation of data. Step 1 entails identifying any hazard by closely analyzing the data at the study endpoint level, while Step 2 involves assessing risk using weight of evidence. These guiding principles were derived from the collective outcomes of the workshop deliberations.

Scientific AI in Materials Science: a Path to a Sustainable and Scalable Paradigm.

Recently there has been an ever-increasing trend in the use of machine learning (ML) and artificial intelligence (AI) methods by the materials science, condensed matter physics, and chemistry communities. This perspective article identifies key scientific, technical, and social opportunities that the materials community must prioritize to consistently develop and leverage Scientific AI (SciAI) to provide a credible path towards the advancement of current materials-limited technologies. Here we highlight the intersections of these opportunities with a series of proposed paths forward. The opportunities are roughly sorted from scientific/technical (e.g. development of robust, physically meaningful multiscale material representations) to social (e.g. promoting an AI-ready workforce). The proposed paths forward range from developing new infrastructure and capabilities to deploying them in industry and academia. We provide a brief introduction to AI in materials science and engineering, followed by detailed discussions of each of the opportunities and paths forward.

Simultaneous atomic-resolution electron ptychography and Z-contrast imaging of light and heavy elements in complex nanostructures.

The aberration-corrected scanning transmission electron microscope (STEM) has emerged as a key tool for atomic resolution characterization of materials, allowing the use of imaging modes such as Z-contrast and spectroscopic mapping. The STEM has not been regarded as optimal for the phase-contrast imaging necessary for efficient imaging of light materials. Here, recent developments in fast electron detectors and data processing capability is shown to enable electron ptychography, to extend the capability of the STEM by allowing quantitative phase images to be formed simultaneously with incoherent signals. We demonstrate this capability as a practical tool for imaging complex structures containing light and heavy elements, and use it to solve the structure of a beam-sensitive carbon nanostructure. The contrast of the phase image contrast is maximized through the post-acquisition correction of lens aberrations. The compensation of defocus aberrations is also used for the measurement of three-dimensional sample information through post-acquisition optical sectioning.

An apparatus for spatially resolved, temperature dependent reflectance measurements for identifying thermochromism in combinatorial thin film libraries.

A metrology and data analysis protocol is described for high throughput determination of thermochromic metal-insulator phase diagrams for lightly substituted VO2 thin films. The technique exploits the abrupt change in near infrared optical properties, measured in reflection, as an indicator of the temperature- or impurity-driven metal-insulator transition. Transition metal impurities were introduced in a complementary combinatorial synthesis process for producing thin film libraries with the general composition space V(1-x-y)M(x)M'(y)O2, with M and M' being transition metals and x and y varying continuously across the library. The measurement apparatus acquires reflectance spectra in the visible or near infrared at arbitrarily many library locations, each with a unique film composition, at temperatures of 1 °C-85 °C. Data collection is rapid and automated; the measurement protocol is computer controlled to automate the collection of thousands of reflectance spectra, representing hundreds of film compositions at tens of different temperatures. A straightforward analysis algorithm is implemented to extract key information from the thousands of spectra such as near infrared thermochromic transition temperatures and regions of no thermochromic transition; similarly, reflectance to the visible spectrum generates key information for materials selection of smart window materials. The thermochromic transition for 160 unique compositions on a thin film library with the general formula V(1-x-y)M(x)M'(y)O2 can be measured and described in a single 20 h experiment. The resulting impurity composition-temperature phase diagrams will contribute to the understanding of metal-insulator transitions in doped VO2 systems and to the development of thermochromic smart windows.

High-throughput measurements of thermochromic behavior in V(1-x)Nb(x)O(2) combinatorial thin film libraries.

We describe a high-throughput characterization of near-infrared thermochromism in V1-xNbxO2 combinatorial thin film libraries. The oxide thin film library was prepared with a VO2 crystal structure and a continuous gradient in composition with Nb concentrations in the range of less than 1% to 45%. The thermochromic phase transition from monoclinic to tetragonal was characterized by the accompanying change in near-infrared reflectance. With increasing Nb substitution, the transition temperature was depressed from 65 to 35 °C, as desirable for smart window applications. However, the magnitude of the reflectance change across the thermochromic transition was also reduced with increasing Nb film content. Data collection, handling, and analysis supporting thermochromic characterization were fully automated to achieve high throughput. Using this system, in 14 h, temperature-dependent infrared reflectances were measured at 165 arbitrary locations on a thin film combinatorial library; these measurements were analyzed for thermochromic transitions in minutes.

Release of targeted p53 from the mitochondrion as an early signal during mitochondrial dysfunction.

Increased accumulation of p53 tumor suppressor protein is an early response to low-level stressors. To investigate the fate of mitochondrial-sequestered p53, mouse embryonic fibroblast cells (MEFs) on a p53-deficient genetic background were transfected with p53-EGFP fusion protein led by a sense (m53-EGFP) or antisense (c53-EGFP) mitochondrial import signal. Rotenone exposure (100nM, 1h) triggered the translocation of m53-EGFP from the mitochondrion to the nucleus, thus shifting the transfected cells from a mitochondrial p53 to a nuclear p53 state. Antibodies for p53 serine phosphorylation or lysine acetylation indicated a different post-translational status of recombinant p53 in the nucleus and mitochondrion, respectively. These data suggest that cycling of p53 through the mitochondria may establish a direct pathway for p53 signaling from the mitochondria to the nucleus during mitochondrial dysfunction. PK11195, a pharmacological ligand of mitochondrial TSPO (formerly known as the peripheral-type benzodiazepine receptor), partially suppressed the release of mitochondria-sequestered p53. These findings support the notion that p53 function mediates a direct signaling pathway from the mitochondria to nucleus during mitochondrial dysfunction.

Differential programming of p53-deficient embryonic cells during rotenone block.

Mitochondrial dysfunction has been implicated in chemical toxicities. The present study used an in vitro model to investigate the differential expression of metabolic pathways during cellular stress in p53-efficient embryonic fibroblasts compared to p53-deficient cells. These cell lines differed with respect to NADH/NAD(+) balance. This ratio constitutes a driving force for NAD- and NADH-dependent reactions and is inversed upon exposure to Rotenone (complex I inhibitor). Rotenone perturbed the structure of the elongated fibrillar tubulin network and decreased mRNA expression of tubulin genes both suggesting reprogramming and reorganization of the cytoskeleton in both cell lines. These changes were reflected in the abundance of specific mRNA and microRNA (miRNA) species as determined from genome-based analysis. Changes in mRNA and miRNA expression profiles reflected differences in energy utilizing pathways, consistent with the notion that the p53 pathway influences the cellular response to mitochondrial dysfunction and that at least some control may be embedded within specific mRNA/miRNA networks in embryonic cells.

Statistical Analysis of a Round-Robin Measurement Survey of Two Candidate Materials for a Seebeck Coefficient Standard Reference Material.

In an effort to develop a Standard Reference Material (SRM™) for Seebeck coefficient, we have conducted a round-robin measurement survey of two candidate materials-undoped Bi2Te3 and Constantan (55 % Cu and 45 % Ni alloy). Measurements were performed in two rounds by twelve laboratories involved in active thermoelectric research using a number of different commercial and custom-built measurement systems and techniques. In this paper we report the detailed statistical analyses on the interlaboratory measurement results and the statistical methodology for analysis of irregularly sampled measurement curves in the interlaboratory study setting. Based on these results, we have selected Bi2Te3 as the prototype standard material. Once available, this SRM will be useful for future interlaboratory data comparison and instrument calibrations.

MCM-41 supported Cu-Mn catalysts for catalytic oxidation of toluene at low temperatures.

Complete catalytic oxidation of toluene was investigated on Cu-Mn doped mesoporous and microporous catalysts, i.e., Cu-Mn/MCM-41, Cu-Mn/beta-zeolite, Cu-Mn/ZSM-5 (where SiO2/Al2O3 is either 25 or 38), and Cu-Mn/porous silica, in the presence of excess oxygen. The result shows that mesoporous catalysts have exhibited the highest catalytic activity among these catalysts above. The less amount of coke formation due to the unique mesoporous structures could play a key role in the high activity on the mesoporous catalyst. In addition, the bimetallic Cu-Mn-MCM-41 supported catalyst shows higher oxidation activity than either single metal catalyst, i.e., Cu-MCM-41 and Mn-MCM-41. The highly dispersed Cu-Mn mixed oxides on mesoporous structures probably provide active sites for the complete oxidation of toluene on these mesoporous catalysts.

The outcomes of pathway database computations depend on pathway ontology.

Different biological notions of pathways are used in different pathway databases. Those pathway ontologies significantly impact pathway computations. Computational users of pathway databases will obtain different results depending on the pathway ontology used by the databases they employ, and different pathway ontologies are preferable for different end uses. We explore differences in pathway ontologies by comparing the BioCyc and KEGG ontologies. The BioCyc ontology defines a pathway as a conserved, atomic module of the metabolic network of a single organism, i.e. often regulated as a unit, whose boundaries are defined at high-connectivity stable metabolites. KEGG pathways are on average 4.2 times larger than BioCyc pathways, and combine multiple biological processes from different organisms to produce a substrate-centered reaction mosaic. We compared KEGG and BioCyc pathways using genome context methods, which determine the functional relatedness of pairs of genes. For each method we employed, a pair of genes randomly selected from a BioCyc pathway is more likely to be related by that method than is a pair of genes randomly selected from a KEGG pathway, supporting the conclusion that the BioCyc pathway conceptualization is closer to a single conserved biological process than is that of KEGG.

Effects of KI encapsulation in single-walled carbon nanotubes by Raman and optical absorption spectroscopy.

The effect of KI encapsulation in narrow (HiPCO) single-walled carbon nanotubes is studied via Raman spectroscopy and optical absorption. The analysis of the data explores the interplay between strain and structural modifications, bond-length changes, charge transfer, and electronic density of states. KI encapsulation appears to be consistent with both charge transfer and strain that shrink both the C-C bonds and the overall nanotube along the axial direction. The charge transfer in larger semiconducting nanotubes is low and comparable with some cases of electrochemical doping, while optical transitions between pairs of singularities of the density of states are quenched for narrow metallic nanotubes. Stronger changes in the density of states occur in some energy ranges and are attributed to polarization van der Waals interactions caused by the ionic encapsulate. Unlike doping with other species, such as atoms and small molecules, encapsulation of inorganic compounds via the molten-phase route provides stable effects due to maximal occupation of the nanotube inner space.

Thermal stability and reactivity of metal halide filled single-walled carbon nanotubes.

Thermal stability and reactivity to oxidation of several nanocomposite systems obtained by encapsulation of metal halides in single-walled carbon nanotubes are studied. Thermogravimetric analysis coupled with Raman spectroscopy allows insight into the various contributing factors, such as charge transfer, strain, and defect formation, and establishing a hierarchy of reactivity for the systems studied (AgX@SWCNTs, with X = Br, I; SWCNTs = arc discharge and HiPCO). The activation energy for oxidation decreases considerably after filling, indicating that filled nanotubes are more amenable to controlled modifications based on chemical reactivity than the originating empty nanotubes. The complete removal of the carbon shell at high temperatures does not preserve the nanowire morphology of the encapsulated halides; these are freed on surfaces in the form of nanoparticles arranged in 1D patterns. Metallic nanoparticles were obtained after hydrogen reduction of the halides, and growth of silicon nanowires in the footprint of the originating nanocomposites was demonstrated from such Co seeds. MX@SWCNTs (M = Ag, Co) can thus be used as environmentally stable nanoscale containers that allow the deliverance of catalytic nanoparticles in a prepatterned and aligned way.

Genome annotation errors in pathway databases due to semantic ambiguity in partial EC numbers.

We report on a new type of systematic annotation error in genome and pathway databases that results from the misinterpretation of partial Enzyme Commission (EC) numbers such as '1.1.1.-'. This error results in the assignment of genes annotated with a partial EC number to many or all biochemical reactions that are annotated with the same partial EC number. That inference is faulty because of the ambiguous nature of partial EC numbers. We have observed this type of error in multiple databases, including KEGG, VIMSS and IMG, all of which assign genes to KEGG pathways. The Escherichia coli subset of the KEGG database exhibits this error for 6.8% of its gene-reaction assignments. For example, KEGG contains 17 reactions that are annotated with EC 1.1.1.-. A group of three E.coli genes, b1580 [putative dehydrogenase, NAD(P)-binding, starvation-sensing protein], b3787 (UDP-N-acetyl-D-mannosaminuronic acid dehydrogenase) and b0207 (2,5-diketo-D-gluconate reductase B), is assigned to 15 of those reactions, despite experimental evidence indicating different single functions for two of the three genes. Furthermore, the databases (DBs) are internally inconsistent in that the description of gene functions for genes with partial EC numbers is inconsistent with the activities implied by reactions to which the genes were assigned. We infer that these inconsistencies result from the processing used to match gene products to reactions within KEGG's metabolic pathways. These errors affect scientists who use these DBs as online encyclopedias and they affect bioinformaticists who use these DBs to train and validate newly developed algorithms.

A composite method for the determination of the chirality of single walled carbon nanotubes.

An approach to the unambiguous determination of the conformation of individual single walled nanotubes utilizing high-resolution transmission electron microscopy and digital image processing is described. The exit plane wave of single walled nanotubes restored from a focal series of images is used in a stepwise characterization procedure utilizing both the phase of the real space restoration and its Fourier transform. A combination of these complementary characterization steps yields an accurate measurement of the chiral vector for an individual nanotube.

Identifying, appraising, and implementing medical education curricula: a guide for medical educators.

As physicians' requirements for knowledge and skills evolve, medical educators often encounter the need for new curricula. This article presents an approach to identifying, appraising, and adapt-ing an established curriculum as an alternative to developing a new one. A published managed care curriculum is reviewed as an educational case example.

Results from the Lake Michigan Mass Balance study: concentrations and fluxes of atmospheric polychlorinated biphenyls and trans-nonachlor.

In this paper, we summarize the data and methods used to estimate atmospheric exchange of polychlorinated biphenyls (PCBs) and trans-nonachlor with Lake Michigan. This work was conducted as part of the Lake Michigan Mass Balance (LMMB) study. For the atmospheric component of the LMMB, more than 400 gas- and particulate-phase samples were collected at eight sites on the shore around the lake (shoreline) and at 14 sites on the lake (over-water). We review the quality of the data set; describe the concentrations in atmospheric gas and particulate phases; report local, instantaneous, net gas fluxes; and estimate annual deposition of the particle-associated compounds. The quality of the data set is high except for a subset of over-water samples where PCB contamination is suspected. Gas-phase trans-nonachlor concentrations (although not the resulting gas fluxes) are inversely correlated with latitude and positively correlated with temperature. Gas-phase sigmaPCBs (sum of 98 congener groups) are highest in concentration at the Chicago site and lowest at the Sleeping Bear Dunes site. The resulting sigmaPCB gas fluxes exhibit a seasonality that reflects elevated summertime gas-phase concentrations not compensated by temperature-corrected Henry's law coefficients. Particulate-phase deposition is much smaller in magnitude than gas fluxes, for either compound. Gas and particulate fluxes are comparable only at the Chicago site and only when large (> 10 microm) particulates are considered.

Effects of a chewable sodium bicarbonate oral composition on plaque and gingivitis.

The purpose of this pilot study was to evaluate the effects of an effervescent sodium bicarbonate based oral composition on plaque and gingivitis. Subjects selected for this study presented at screening with moderate plaque and American Academy of Periodontology (AAP) Type I/II periodontal status. At baseline, subjects were allocated to one of two groups by simple randomization; placebo (n=16) and active (n=16). During the study two subjects withdrew due to non-compliance and one because of a death in the family. Data were collected at baseline, day 14, and day 28. The Plaque Index (PI) of Silness and Loe was used to quantify the amount of supragingival plaque surrounding six selected teeth (3,14,8,19,24,30), and the Gingival Index (GI) of Loe and Silness was used to assess bleeding tendencies and visual appearance on the same six teeth. A soft tissue oral assessment was completed at each visit. Subjects were asked to perform study treatment three times a day, after meals, and continue with normal oral hygiene procedures. Subjects were requested to complete a 28-day diary to assess compliance. Data were analyzed using repeated measures analysis of variance. There were no statistically significant differences between the placebo and the active product groups and no statistical significant interaction between product and location within the mouth or visit for either the plaque or gingival scores. Results reveal the product was safe to oral tissues and was well accepted by subjects.

Evidence-based medicine training in graduate medical education: past, present and future.

Evidence-based medicine (EBM) training remains a challenge to educators, particularly in graduate medical education. In this article, I trace the history of EBM in American medical education, review traditional journal clubs and contrast them to free-standing EBM curricula, petition for the advancement of integrated EBM teaching and propose an agenda for future work. Traditional journal clubs are unsuitable to teach evidence-based decision making because of their exclusive focus on critical appraisal. In contrast, EBM curricula cover the identification, appraisal and application of evidence in the context of individual patient scenarios. The effectiveness of some recent efforts reflects increasing attention to curriculum development principles and scientific rigour. The integration of EBM training into residents' established clinical venues offers theoretical educational advantages and confronts the challenge of practising EBM under the imperatives of 'real time' patient care. Initial responses to this formidable challenge show promise, but their feasibility and effectiveness remain to be explored. A more complete understanding of the epidemiology of residents' emerging clinical questions will inform continued curriculum development in integrated EBM training.

Residents' medical information needs in clinic: are they being met?

PURPOSE: Little is known about how often residents encounter unanswered clinical questions in their training. This knowledge would facilitate the development of curricula to help residents practice evidence-based medicine. This study was conducted to determine the frequency, characteristics, and pursuit of residents' clinical questions. SUBJECTS AND METHODS: Residents in a university-based primary care internal medicine program were observed in two hospital-based teaching clinics. Residents were interviewed after each patient encounter to determine whether they had any remaining clinical questions. At the end of each clinic session, they recorded their level of agreement with a series of statements about factors that were expected to motivate residents to seek the answers to each question. One week later, residents were contacted to determine if they had pursued these questions. RESULTS: Sixty-four residents were interviewed after 401 (99%) of 404 patient encounters. They identified 280 new questions, approximately 2 questions for every 3 patients. The most common types of questions were related to therapy (38%) or diagnosis (27%). The residents were subsequently contacted about 277 (99%) of their questions. Of these, only 80 (29%) were pursued, most commonly by consulting textbooks (31%), original articles (21%), or attending physicians (17%). In a multivariable analysis, belief that the patient expected the answer (odds ratio [OR] = 2.3, 95% confidence interval [CI]: 1.3 to 4.0, P = 0.004) and fear of malpractice exposure (OR = 2.1, 95% CI: 1.0 to 4.3, P = 0.05) were associated with information pursuit. Lack of time (60%) and forgetting the question (29%) were the most frequent reasons for failing to pursue a question. CONCLUSION: Residents frequently encountered new clinical questions in the outpatient clinic, but infrequently answered them. Efforts to demonstrate the feasibility of timely searches, remind them of their questions, and reinforce the exigency (educational if not clinical) of all questions may reclaim missed opportunities for self-directed learning.

Pregnancy-dependent expression of leukaemia inhibitory factor (LIF), LIF receptor-beta and interleukin-6 (IL-6) messenger ribonucleic acids in the porcine female reproductive tract.

Leukaemia inhibitory factor (LIF) and interleukin-6 (IL-6) are candidate embryo-maternal signalling molecules which are present within the uterine luminal micro-environment. We examined the relative expression of the mRNAs encoding LIF and IL-6, as well as the LIF-binding subunit (LIFR-beta) of the LIF receptor and, as a potential downstream cytokine-responsive gene, beta(2)-microglobulin (beta(2)m), in porcine peri-implantation conceptuses, and in placenta and endometrium during early and mid-pregnancy. Peri-implantation spherical and filamentous conceptuses expressed LIFR-beta and beta(2)m mRNAs with no LIF mRNA present. Rapid development in days 11/12 spherical conceptuses to the filamentous stage was accompanied by transiently increased IL-6 gene expression. The corresponding endometrium, in contrast, expressed LIF in addition to these other mRNAs. LIFR-beta, IL-6 and beta(2)m, but not LIF mRNAs, were expressed in the Jag-1 cell line, an in vitro model for porcine day 14 trophoblast. The greatest steady-state amounts of LIF, LIFR-beta and IL-6 mRNAs in both the endometrium and placenta were evident at the post-implantation stages (days 30 and 60>day 18 of pregnancy). Treatment of porcine endometrial explants with human recombinant (hr)LIF or hrIL-6 resulted in no change in, or diminished, the presence of endometrial beta(2)m mRNA, respectively. Addition of LIF to peri-implantation conceptus explant cultures, in contrast, induced beta(2)m mRNA synthesis. These results highlight the potential importance of both the endometrium and placenta as sources, as well as targets, of these cytokines throughout pregnancy. Cytokine modulation of beta(2)m, a known in vitro mitogen, may constitute one mechanism for local control of trophoblast and endometrial proliferation.