14 examples of how LLMs can transform materials science and chemistry: a reflection on a large language model hackathon.

Large-language models (LLMs) such as GPT-4 caught the interest of many scientists. Recent studies suggested that these models could be useful in chemistry and materials science. To explore these possibilities, we organized a hackathon. This article chronicles the projects built as part of this hackathon. Participants employed LLMs for various applications, including predicting properties of molecules and materials, designing novel interfaces for tools, extracting knowledge from unstructured data, and developing new educational applications. The diverse topics and the fact that working prototypes could be generated in less than two days highlight that LLMs will profoundly impact the future of our fields. The rich collection of ideas and projects also indicates that the applications of LLMs are not limited to materials science and chemistry but offer potential benefits to a wide range of scientific disciplines.

Biomimetic Extracellular Scaffolds by Microfluidic Superstructuring of Nanofibers.

The extracellular matrix is a dynamic framework bearing chemical and morphological cues that support many cellular functions, and artificial analogs with well-defined chemistry are of great interest for biomedical applications. Herein, we describe hierarchical, extracellular-matrix-mimetic microgels, termed "superbundles" (SBs) composed of peptide amphiphile (PA) supramolecular nanofiber networks created using flow-focusing microfluidic devices. We explore the effects of altered flow rate ratio and PA concentration on the ability to create SBs and develop design rules for producing SBs with both cationic and anionic PA nanofibers and gelators. We demonstrate the morphological similarities of SBs to decellularized extracellular matrices and showcase their ability to encapsulate and retain proteinaceous cargos with a wide variety of isoelectric points. Finally, we demonstrate that the novel SB morphology does not affect the well-established biocompatibility of PA gels.

Diagnostic thresholds and optimal collection protocol of salivary pepsin for gastroesophageal reflux disease.

Gastroesophageal reflux disease (GERD) is primarily diagnosed based on symptoms and response to a proton-pump inhibitor (PPI) trial. Gold standard testing requires an invasive endoscopic procedure, often with ambulatory pH monitoring. Salivary pepsin is a potential noninvasive modality for GERD diagnosis. This study aimed to assess diagnostic performance of salivary pepsin thresholds for GERD and determine optimal collection protocol of saliva in an external validation cohort. Over 10 months, adults with symptoms of GERD undergoing esophagogastroduodenoscopy with wireless pH-monitoring off PPI were enrolled. Saliva was self-collected by participants over 4 days across three different time points: fasting ante meridiem (AM), post-prandial, and bedtime (PM). Pepsin levels were calculated via Peptest. Pepsin variability and agreement were determined using linear mixed effects models and intraclass correlation. Validation of diagnostic threshold and performance characteristics were evaluated by receiver-operator curve analysis. Twenty participants enrolled in the study; 50% with physiologic acid exposure (acid exposure time < 4% no GERD) and 50% with elevated acid exposure (GERD). Mean pepsin concentrations were significantly lower in the AM (22.6 ± 25.2 ng/mL) compared to post-prandial (44.5 ± 36.7 ng/mL) and PM (55.4 ± 47.0 ng/mL). Agreement between pepsin concentrations across 3 days was substantial for AM samples (kappa 0.61), with lower agreement for post-prandial and PM samples. A single AM pepsin concentration of 25 ng/mL was 67% accurate for GERD with 56% sensitivity and 78% specificity. This validation study highlights fair accuracy and performance characteristics of a single fasting AM salivary pepsin concentration for the diagnosis of GERD.

Salivary biomarkers and esophageal disorders.

Saliva is a complex physiologic fluid that contains an abundance of biological analytes, or biomarkers. Recent research has shown that these biomarkers may be able to convey the physiologic health of a person. Work has been done linking derangements in these salivary biomarkers to a wide variety of pathologic disorders ranging from oncologic diseases to atopic conditions. The specific area of interest for this review paper is esophageal disorders. Particularly because the diagnosis and management of esophageal disorders often includes invasive testing such as esophagogastroduodenoscopy, prolonged pH monitoring, and biopsy. The aim of this review will be to explore salivary biomarkers (pepsin, bile, epidermal growth factor, and micro-RNA) that are being studied as they relate specifically to esophageal disorders. Finally, it will explore the benefits of salivary testing and identify areas of possible future research.

Factors that Impact Day-to-Day Esophageal Acid Reflux Variability and Its Diagnostic Significance for Gastroesophageal Reflux Disease.

Gastroesophageal reflux disease (GERD) is a common disease affecting a significant number of adults both globally and in the USA. GERD is clinically diagnosed based on patient-reported symptoms, and the gold standard for diagnosis is ambulatory reflux monitoring, a tool particularly utilized in the common scenario of non-response to therapy or atypical features. Over the past 20 years, there has been a shift toward extending the duration of reflux monitoring, initially from 24 to 48 h and more recently to 96 h, primarily based on a demonstrated increase in diagnostic yield. Further, multiple studies demonstrate clinically relevant variability in day-to-day acid exposure levels in nearly 30% of ambulatory reflux monitoring studies. For these reasons, an ongoing clinical dilemma relates to the optimal activities patients should engage in during prolonged reflux monitoring. Thus, the aims of this review are to detail what is known about variability in daily acid exposure, discuss factors that are known to influence this day-to-day variability (i.e., sleep patterns, dietary/eating habits, stress, exercise, and medications), and finally provide suggestions for patient education and general GERD management to reduce variation in esophageal acid exposure levels.

Resilience in the Face of Adversity: Family Processes and the Immigrant Paradox in Youth Externalizing Problems.

BACKGROUND: Despite increased exposure to social adversity, immigrant youth have fewer externalizing problems compared to non-immigrants. Explanations for this apparent advantage remain unclear. This study examined the extent to which socio-economic characteristics and family processes account for group differences in externalizing problems between immigrant and non-immigrant youth. METHODS: Data come from a population-based cross-sectional study of 1,449 youth and their primary caregiver in Hamilton, Ontario. Computer-assisted structured interviews were administered separately to primary caregivers and youth, which included assessments of externalizing problems and measures of family obligation, parental monitoring, value of education and socio-economic characteristics. RESULTS: First- and second-generation immigrant youth had lower levels of externalizing problems compared to non-immigrants. The magnitude of group differences was larger for parent (d = 0.37-0.55) versus youth reports of externalizing behaviours (d = 0.15-0.29). Family socio-economic and process characteristics partially accounted for group differences, which remained significant in the parent-reported model but rendered non-significant in the youth-reported model. CONCLUSION: Results suggesting the potential protective effects of positive family processes for immigrant youth could be extended to non-immigrant youth to inform the development of parenting and family skills interventions. Promoting familial sources of resilience is a potential avenue for reversing downward trends in mental health seen across successive generations of immigrant youth, while also reducing risk of behavioural difficulties among non-immigrant youth.

Recombinant MVA-prime elicits neutralizing antibody responses by inducing antigen-specific B cells in the germinal center.

The RV144 HIV-1 vaccine trial has been the only clinical trial to date that has shown any degree of efficacy and associated with the presence of vaccine-elicited HIV-1 envelope-specific binding antibody and CD4+ T-cell responses. This trial also showed that a vector-prime protein boost combined vaccine strategy was better than when used alone. Here we have studied three different priming vectors-plasmid DNA, recombinant MVA, and recombinant VSV, all encoding clade C transmitted/founder Env 1086 C gp140, for priming three groups of six non-human primates each, followed by a protein boost with adjuvanted 1086 C gp120 protein. Our data showed that MVA-priming favors the development of higher antibody binding titers and neutralizing activity compared with other vectors. Analyses of the draining lymph nodes revealed that MVA-prime induced increased germinal center reactivity characterized by higher frequencies of germinal center (PNAhi) B cells, higher frequencies of antigen-specific B-cell responses as well as an increased frequency of the highly differentiated (ICOShiCD150lo) Tfh-cell subset.

Platelet-rich plasma in noninvasive procedures for atrophic acne scars: A systematic review and meta-analysis.

BACKGROUND: The use of platelet-rich plasma (PRP) combined with noninvasive, nonenergy procedures for atrophic acne scars has shown promise. To date, there has not been a systematic review or meta-analysis of the effectiveness of this therapy. AIMS: To use meta-analysis to compare Goodman and Baron qualitative scores, patient satisfaction outcomes, and adverse effects in patients undergoing combination procedures with PRP, combination procedures without PRP, and noninvasive monotherapy without PRP in the treatment of patients with atrophic acne scars. PATIENTS/METHODS: The Pubmed and Cochrane library databases were searched for relevant studies published before May 1, 2019. PRISMA guidelines were utilized. Studies that compared the use of PRP in combination with a noninvasive procedure and therapies without PRP for the treatment of atrophic acne scars were included. Cochrane's handbook was utilized to assess the individual biases of the included studies. Publication bias was assessed. RESULTS: A total of 311 participants (153 whole-face participants and 158 split-face participants) were reviewed across eight included studies. Quantitative analysis of 241 participants across six included studies showed a statistically significant reduction in scar severity scores in favor of microneedling or subcision with PRP (P < .001). Combination therapy with intradermal or topical PRP was significantly more effective than monotherapy alone and combination therapy with an adjunct other than PRP (P < .001 and .001, respectively). CONCLUSION: This systematic review and meta-analysis demonstrated that microneedling or subcision with PRP produced statistically significant improvement in validated outcomes over microneedling or subcision alone.

Inherited thrombophilia and portal vein thrombosis in cirrhosis: A systematic review and meta-analysis.

BACKGROUND: Portal vein thrombosis (PVT) is common in cirrhosis. PVT is associated with high morbidity and mortality. Individual reports suggest that PVT occurs more frequently in patients with cirrhosis and inherited thrombophilia. The relationship between cirrhosis, PVT development, and inherited thrombophilia was explored in this study. The aim of the study was to determine whether cirrhotic patients with nontumoral PVT have an increased rate of inherited thrombophilia. METHODS: Studies were identified by searching electronic databases up to October 2017 with English language and human subject restrictions. Two independent reviewers screened citations and extracted data. Magnitude of effect was calculated to obtain aggregate estimates of effect size and 95% confidence intervals (CIs). Between-study variability and heterogeneity were assessed. RESULTS: Of 2893 citations identified, 9 studies composed of 1929 subjects with cirrhosis were included. The overall prevalence of PVT was 6.5% (n = 125). Both prothrombin G20210A mutation (odds ratio [OR], 2.43; 95% CI, 1.07-5.53; P = 0.03) and factor V Leiden (FVL) (OR, 1.98; 95% CI, 1.06-3.68; P = 0.03) were significantly associated with PVT risk. Methyltetrahydrofolate reductase C677T mutation was not associated with increased PVT risk. No heterogeneity or publication bias was observed. One important study with opposite findings could not be included due to lack of primary data. CONCLUSIONS: FVL and PTG20210A mutation were associated with increased PVT risk in patients with cirrhosis. This finding reframes the role of inherited thrombophilia in PVT development in patients with cirrhosis. Future prospective studies investigating screening for inherited thrombophilia in all cirrhosis patients with PVT seem warranted.

H5N1 Vaccine-Elicited Memory B Cells Are Genetically Constrained by the IGHV Locus in the Recognition of a Neutralizing Epitope in the Hemagglutinin Stem.

Because of significant viral diversity, vaccines that elicit durable and broad protection against influenza have been elusive. Recent research has focused on the potential of highly conserved regions of the viral hemagglutinin (HA) as targets for broadly neutralizing Ab responses. Abs that bind the highly conserved stem or stalk of HA can be elicited by vaccination in humans and animal models and neutralize diverse influenza strains. However, the frequency and phenotype of HA stem-specific B cells in vivo remain unclear. In this article, we characterize HA stem-specific B cell responses following H5N1 vaccination and describe the re-expansion of a pre-existing population of memory B cells specific for stem epitopes. This population uses primarily, but not exclusively, IGHV1-69-based Igs for HA recognition. However, within some subjects, allelic polymorphism at the ighv1-69 locus can limit IGHV1-69 immunodominance and may reduce circulating frequencies of stem-reactive B cells in vivo. The accurate definition of allelic selection, recombination requirements, and ontogeny of neutralizing Ab responses to influenza will aid rational influenza vaccine design.

Yersinia enterocolitica Septicemia After Chitterling Ingestion in a Pediatric Patient With Iron Overload Disease: A Case Report.

Yersinia enterocolitica is a gram-negative cocobacillus causing a range of illness from self-limited enteritis to invasive disease, including septicemia. It is a particularly virulent pathogen in patients with underlying hemoglobinopathies who are predisposed to iron overload. A substantial risk factor for disease in children and infants is exposure to the household preparation of chitterlings. Early identification of these patients is critical in the pediatric intensive care unit as this cause of septicemia can be missed with the potential for significant morbidity. We report an interesting case of Yersinia septicemia in a patient with iron overload disease from chitterling ingestion managed in the pediatric intensive care unit.

Flow cytometry reveals that H5N1 vaccination elicits cross-reactive stem-directed antibodies from multiple Ig heavy-chain lineages.

UNLABELLED: An understanding of the antigen-specific B-cell response to the influenza virus hemagglutinin (HA) is critical to the development of universal influenza vaccines, but it has not been possible to examine these cells directly because HA binds to sialic acid (SA) on most cell types. Here, we use structure-based modification of HA to isolate HA-specific B cells by flow cytometry and characterize the features of HA stem antibodies (Abs) required for their development. Incorporation of a previously described mutation (Y98F) to the receptor binding site (RBS) causes HA to bind only those B cells that express HA-specific Abs, but it does not bind nonspecifically to B cells, and this mutation has no effect on the binding of broadly neutralizing Abs to the RBS. To test the specificity of the Y98F mutation, we first demonstrated that previously described HA nanoparticles mediate hemagglutination and then determined that the Y98F mutation eliminates this activity. Cloning of immunoglobulin genes from HA-specific B cells isolated from a single human subject demonstrates that vaccination with H5N1 influenza virus can elicit B cells expressing stem monoclonal Abs (MAbs). Although these MAbs originated mostly from the IGHV1-69 germ line, a reasonable proportion derived from other genes. Analysis of stem Abs provides insight into the maturation pathways of IGVH1-69-derived stem Abs. Furthermore, this analysis shows that multiple non-IGHV1-69 stem Abs with a similar neutralizing breadth develop after vaccination in humans, suggesting that the HA stem response can be elicited in individuals with non-stem-reactive IGHV1-69 alleles. IMPORTANCE: Universal influenza vaccines would improve immune protection against infection and facilitate vaccine manufacturing and distribution. Flu vaccines stimulate B cells in the blood to produce antibodies that neutralize the virus. These antibodies target a protein on the surface of the virus called HA. Flu vaccines must be reformulated annually, because these antibodies are mostly specific to the viral strains used in the vaccine. But humans can produce broadly neutralizing antibodies. We sought to isolate B cells whose genes encode influenza virus antibodies from a patient vaccinated for avian influenza. To do so, we modified HA so it would bind only the desired cells. Sequencing the antibody genes of cells marked by this probe proved that the patient produced broadly neutralizing antibodies in response to the vaccine. Many sequences obtained had not been observed before. There are more ways to generate broadly neutralizing antibodies for influenza virus than previously thought.

Highly multiplexed quantitation of gene expression on single cells.

Highly multiplexed, single-cell technologies reveal important heterogeneity within cell populations. Recently, technologies to simultaneously measure expression of 96 (or more) genes from a single cell have been developed for immunologic monitoring. Here, we report a rigorous, optimized, quantitative methodology for using this technology. Specifically: we describe a unique primer/probe qualification method necessary for quantitative results; we show that primers do not compete in highly multiplexed amplifications; we define the limit of detection for this assay as a single mRNA transcript; and, we show that the technical reproducibility of the system is very high. We illustrate two disparate applications of the platform: a "bulk" approach that measures expression patterns from 100 cells at a time in high throughput to define gene signatures, and a single-cell approach to define the coordinate expression patterns of multiple genes and reveal unique subsets of cells.

Endothelin-1 is a transcriptional target of p53 in epidermal keratinocytes and regulates ultraviolet-induced melanocyte homeostasis.

Keratinocytes contribute to melanocyte activity by influencing their microenvironment, in part, through secretion of paracrine factors. Here, we discovered that p53 directly regulates Edn1 expression in epidermal keratinocytes and controls UV-induced melanocyte homeostasis. Selective ablation of endothelin-1 (EDN1) in murine epidermis (EDN1(ep-/-) ) does not alter melanocyte homeostasis in newborn skin but decreases dermal melanocytes in adult skin. Results showed that keratinocytic EDN1 in a non-cell autonomous manner controls melanocyte proliferation, migration, DNA damage, and apoptosis after ultraviolet B (UVB) irradiation. Expression of other keratinocyte-derived paracrine factors did not compensate for the loss of EDN1. Topical treatment with EDN1 receptor (EDNRB) antagonist BQ788 abrogated UV-induced melanocyte activation and recapitulated the phenotype seen in EDN1(ep-/-) mice. Altogether, the present studies establish an essential role of EDN1 in epidermal keratinocytes to mediate UV-induced melanocyte homeostasis in vivo.

Data exploration, quality control and testing in single-cell qPCR-based gene expression experiments.

MOTIVATION: Cell populations are never truly homogeneous; individual cells exist in biochemical states that define functional differences between them. New technology based on microfluidic arrays combined with multiplexed quantitative polymerase chain reactions now enables high-throughput single-cell gene expression measurement, allowing assessment of cellular heterogeneity. However, few analytic tools have been developed specifically for the statistical and analytical challenges of single-cell quantitative polymerase chain reactions data. RESULTS: We present a statistical framework for the exploration, quality control and analysis of single-cell gene expression data from microfluidic arrays. We assess accuracy and within-sample heterogeneity of single-cell expression and develop quality control criteria to filter unreliable cell measurements. We propose a statistical model accounting for the fact that genes at the single-cell level can be on (and a continuous expression measure is recorded) or dichotomously off (and the recorded expression is zero). Based on this model, we derive a combined likelihood ratio test for differential expression that incorporates both the discrete and continuous components. Using an experiment that examines treatment-specific changes in expression, we show that this combined test is more powerful than either the continuous or dichotomous component in isolation, or a t-test on the zero-inflated data. Although developed for measurements from a specific platform (Fluidigm), these tools are generalizable to other multi-parametric measures over large numbers of events. AVAILABILITY: All results presented here were obtained using the SingleCellAssay R package available on GitHub (http://github.com/RGLab/SingleCellAssay).

Effects of the World Bank's maternal and child health intervention on Indonesia's poor: evaluating the safe motherhood project.

This article examines the impact of the World Bank's Safe Motherhood Project (SMP) on health outcomes for Indonesia's poor. Provincial data from 1990 to 2005 was analyzed combining a difference-in-differences approach in multivariate regression analysis with matching of intervention (SMP) and control group provinces and adjusting for possible confounders. Our results indicated that, after taking into account the impact of two other concurrent development projects, SMP was statistically significantly associated with a net beneficial change in under-five mortality, but not with infant mortality, total fertility rate, teenage pregnancy, unmet contraceptive need or percentage of deliveries overseen by trained health personnel. Unemployment and the pupil-teacher ratio were statistically significantly associated with infant mortality and percentage deliveries overseen by trained personnel, while pupil-teacher ratio and female education level were statistically significantly associated with under-five mortality. Clinically relevant changes (52-68% increase in the percentage of deliveries overseen by trained personnel, 25-33% decrease in infant mortality rate, and 8-14% decrease in under-five mortality rate) were found in both the intervention (SMP) and control groups.

Improving catalytic function by ProSAR-driven enzyme evolution.

We describe a directed evolution approach that should find broad application in generating enzymes that meet predefined process-design criteria. It augments recombination-based directed evolution by incorporating a strategy for statistical analysis of protein sequence activity relationships (ProSAR). This combination facilitates mutation-oriented enzyme optimization by permitting the capture of additional information contained in the sequence-activity data. The method thus enables identification of beneficial mutations even in variants with reduced function. We use this hybrid approach to evolve a bacterial halohydrin dehalogenase that improves the volumetric productivity of a cyanation process approximately 4,000-fold. This improvement was required to meet the practical design criteria for a commercially relevant biocatalytic process involved in the synthesis of a cholesterol-lowering drug, atorvastatin (Lipitor), and was obtained by variants that had at least 35 mutations.

A site-selective dual anchoring strategy for artificial metalloprotein design.

Introducing nonnative metal ions or metal-containing prosthetic groups into a protein can dramatically expand the repertoire of its functionalities and thus its range of applications. Particularly challenging is the control of substrate-binding and thus reaction selectivity such as enantioselectivity. To meet this challenge, both non-covalent and single-point attachments of metal complexes have been demonstrated previously. Since the protein template did not evolve to bind artificial metal complexes tightly in a single conformation, efforts to restrict conformational freedom by modifying the metal complexes and/or the protein are required to achieve high enantioselectivity using the above two strategies. Here we report a novel site-selective dual anchoring (two-point covalent attachment) strategy to introduce an achiral manganese salen complex (Mn(salen)), into apo sperm whale myoglobin (Mb) with bioconjugation yield close to 100%. The enantioselective excess increases from 0.3% for non-covalent, to 12.3% for single point, and to 51.3% for dual anchoring attachments. The dual anchoring method has the advantage of restricting the conformational freedom of the metal complex in the protein and can be generally applied to protein incorporation of other metal complexes with minimal structural modification to either the metal complex or the protein.