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We report on a cross-disciplinary collaboration between sociology and mathematics education to more effectively cultivate quantitative literacy (QL) in the introductory sociology course. Focusing on an instructional unit presenting the Gini coefficient (the most commonly used summary measure of income inequality), we engaged in iterative cycles of presentation, assessment, and redesign across four semester-long courses. Assessments were guided by insights from mathematics education--such as the procedural/conceptual distinction, student misconceptions, and student noticing--and characterized by extensive informal discussion and analysis of patterns in student exam responses. Assessments were formalized via coding of specific response elements and used to identify strategic foci for revision and redesign (including creating a brief instructional video series and an active learning exercise). In this article, we highlight the value of cross-disciplinary collaboration in QL pedagogy, demonstrate the effectiveness of analyzing specific elements and patterns of student comprehension to revise pedagogical presentation, and advocate for the strategic utility of the Gini coefficient for cultivating QL in introductory sociology.

In recent years, computing education researchers have investigated the impact of problem context on students' learning and programming performance. This work continues the investigation motivated, in part, by cognitive load theory and educational research in computer science and other disciplines. The results of this study could help inform computing assessment design. If the context and authenticity of a programming problem aid student performance then, instructors' time in creating appropriately contextualized programming problem descriptions is time well-spent. On the other hand, if the context of a programming problem hinders performance, then instructors should leave it out of programming problems. Recent studies investigating the impact of programming problem context on student success have arrived at different conclusions. Presented here is a series of experiments, conducted over 3 years, investigating the impact of context on novice programmers' success in algorithmic programming assignments using three contextualized tasks and their generic counterparts. This experiment series also looked into the possibility of "authenticity" as a factor affecting performance. Common sense would suggest that a student would perform better on a problem if they understood or cared about it. Contextualization could provide authenticity and authenticity could provide interest. Research suggests that perceiving a problem as authentic has a positive effect on engagement and learning. Alternatively, if a problem is "just an abstract set of numbers", it may be harder to make sense of the details and the lack of context could consequently contribute additional cognitive load to an already challenging assignment. The results of this study show that assignment context and problem context authenticity have no effect on the performance of novice programmers. We think, however, that contextualization could be worth investing in to support students' interest in computing. Additional implications of the results suggest that instructors can assign equivalent versions of the same problem in varied contexts to suit their students' interests without worrying if the context will hinder performance.

Abstract The Gram-negative bacterium Klebsiella pneumoniae is an important human pathogen. Its treatment has been complicated by the emergence of multi-drug resistant strains. The human complement system is an important part of our innate immune response that can directly kill Gram-negative bacteria by assembling membrane attack complex (MAC) pores into the bacterial outer membrane. To resist this attack, Gram-negative bacteria can modify their lipopolysaccharide (LPS). Especially the decoration of the LPS outer core with the O-antigen polysaccharide has been linked to increased bacterial survival in serum, but not studied in detail. In this study, we characterized various clinical Klebsiella pneumoniae isolates and show that expression of the LPS O1-antigen correlates with resistance to complement-mediated killing. Mechanistic data reveal that the O1-antigen does not inhibit C3b deposition and C5 conversion. In contrast, we see more efficient formation of C5a, and deposition of C6 and C9 when an O-antigen is present. Further downstream analyses revealed that the O1-antigen prevents correct insertion and polymerization of the final MAC component C9 into the bacterial membrane. Altogether, we show that the LPS O1-antigen is a key determining factor for complement resistance by K. pneumoniae and provide insights into the molecular basis of O1-mediated MAC evasion.

Abstract Biocrusts represent associations of lichens, green algae, cyanobacteria, fungi and other microorganisms, colonizing soils in varying proportions of principally arid biomes. The so-called grit crust represents a recently discovered type of biocrust situated in the Coastal Range of the Atacama Desert (Chile) made of microorganisms growing on and in granitoid pebbles, resulting in a checkerboard pattern visible to the naked eye on the landscape scale. This specific microbiome fulfills a broad range of ecosystem services, all probably driven by fog and dew-induced photosynthetic activity of mainly micro-lichens. To understand its biodiversity and impact, we applied a polyphasic approach on the phototrophic microbiome of this biocrust, combining isolation and characterization of the lichen photobionts, multi-gene phylogeny of the photobionts and mycobionts based on a direct sequencing and microphotography approach, metabarcoding and determination of chlorophylla+b contents. Metabarcoding showed that yet undescribed lichens within the Caliciaceae dominated the biocrust together with Trebouxia as the most abundant eukaryote in all plots. Together with high mean chlorophylla+b contents exceeding 410 mg m−2, this distinguished the symbiotic algae Trebouxia as the main driver of the grit crust ecosystem. The trebouxioid photobionts could be assigned to the I (T. impressa/gelatinosa) and A (T. arboricola) clades and represented several lineages containing five potential species candidates, which were identified based on the unique phylogenetic position, morphological features, and developmental cycles of the corresponding isolates. These results designate the grit crust as the only known coherent soil layer with significant landscape covering impact of at least 440 km2, predominantly ruled by a single symbiotic algal genus.

Abstract Collagen is the most abundant protein in mammals and a major structural component of the extracellular matrix (ECM). Changes to ECM composition occur as a result of numerous physiological and pathophysiological causes, and a common means to evaluate these changes is the collagen 3 (Col3) to collagen 1 (Col1) ratio. Current methods to measure the Col3/1 ratio suffer from a lack of specificity and often under- or over-estimate collagen composition and quantity. This manuscript presents a targeted liquid chromatography tandem mass spectrometry (LC–MS/MS) method for quantification of Col3 and Col1 in FFPE tissues. Using surrogate peptides to generate calibration curves, Col3 and Col1 are readily quantified in FFPE tissue sections with high accuracy and precision. The method is applied to several tissue types from both human and reindeer sources, demonstrating its generalizability. In addition, the targeted LC–MS/MS method permits quantitation of the hydroxyprolinated form of Col3, which has significant implications for understanding not only the quantity of Col3 in tissue, but also understanding of the pathophysiology underlying many causes of ECM changes. This manuscript presents a straightforward, accurate, precise, and generalizable method for quantifying the Col3/1 ratio in a variety of tissue types and organisms.

Abstract Intrinsic breast cancer molecular subtyping (IBCMS) provides significant prognostic information for patients with breast cancer and helps determine treatment. This study compared IBCMS methods on various gene-expression platforms in PALOMA-2 and PALLET trials. PALOMA-2 tumor samples were profiled using EdgeSeq and nanostring and subtyped with AIMS, PAM50, and research-use-only (ruo)Prosigna. PALLET tumor biopsies were profiled using mRNA sequencing and subtyped with AIMS and PAM50. In PALOMA-2 (n = 222), a 54% agreement was observed between results from AIMS and gold-standard ruoProsigna, with AIMS assigning 67% basal-like to HER2-enriched. In PALLET (n = 224), a 69% agreement was observed between results from PAM50 and AIMS. Different IBCMS methods may lead to different results and could misguide treatment selection; hence, a standardized clinical PAM50 assay and computational approach should be used. Trial number: NCT01740427

Introduction Delirium, a clinical manifestation of acute encephalopathy, is associated with extended hospitalisation, long-term cognitive dysfunction, increased mortality and high healthcare costs. Despite intensive research, there is still no targeted treatment. Delirium is characterised by electroencephalography (EEG) slowing, increased relative delta power and decreased functional connectivity. Recent studies suggest that transcranial alternating current stimulation (tACS) can entrain EEG activity, strengthen connectivity and improve cognitive functioning. Hence, tACS offers a potential treatment for augmenting EEG activity and reducing the duration of delirium. This study aims to evaluate the feasibility and assess the efficacy of tACS in reducing relative delta power.Methods and analysis A randomised, double-blind, sham-controlled trial will be conducted across three medical centres in the Netherlands. The study comprises two phases: a pilot phase (n=30) and a main study phase (n=129). Participants are patients aged 50 years and older who are diagnosed with delirium using the Diagnostic and Statistical Manual of Mental Disorders, Fifth Edition, Text Revision criteria (DSM-5-TR), that persists despite treatment of underlying causes. During the pilot phase, participants will be randomised (1:1) to receive either standardised (10 Hz) tACS or sham tACS. In the main study phase, participants will be randomised to standardised tACS, sham tACS or personalised tACS, in which tACS settings are tailored to the participant. All participants will undergo daily 30 min of (sham) stimulation for up to 14 days or until delirium resolution or hospital discharge. Sixty-four-channel resting-state EEG will be recorded pre- and post the first tACS session, and following the final tACS session. Daily delirium assessments will be acquired using the Intensive Care Delirium Screening Checklist and Delirium Observation Screening Scale. The pilot phase will assess the percentage of completed tACS sessions and increased care requirements post-tACS. The primary outcome variable is change in relative delta EEG power. Secondary outcomes include (1) delirium duration and severity, (2) quantitative EEG measurements, (3) length of hospital stay, (4) cognitive functioning at 3 months post-tACS and (5) tACS treatment burden. Study recruitment started in April 2024 and is ongoing.Ethics and dissemination The study has been approved by the Medical Ethics Committee of the Utrecht University Medical Center and the Institutional Review Boards of all participating centres. Trial results will be disseminated via peer-reviewed publications and conference presentations.Trial registration number NCT06285721.

Abstract Background Cancer predisposition syndromes (CPS) impact about 10% of patients with pediatric cancer. Genetic testing (CPS‐GT) has multiple benefits, but few studies have described parent and child knowledge and attitudes regarding CPS‐GT decision‐making. This study examined parent and patient CPS‐GT decision‐making knowledge and attitudes. Procedure English‐ or Spanish‐speaking parents of children with pediatric cancer and patients with pediatric cancer ages 15–18 within 12 months of diagnosis or relapse were eligible to participate. Seventy‐five parents and 19 parent‐patient dyads (N = 94 parents, 77.7% female, 43.6% Latino/a/Hispanic; 19 patients, 31.6% female) completed surveys measuring CPS‐GT‐related beliefs. Independent samples t‐tests compared parent responses across sociodemographic characteristics and parent‐patient responses within dyads. Results Spanish‐speaking parents were significantly more likely than English‐speaking parents to believe that CPS‐GT not being helpful (p

IntroductionSome cyanobacteria can use far-red light (FRL) to drive oxygenic photosynthesis, a phenomenon known as Far-Red Light Photoacclimation (FaRLiP). It can expand photosynthetically active radiation beyond the visible light (VL) range. Therefore, it holds promise for biotechnological applications and may prove useful for the future human exploration of outer space. Typically, FaRLiP relies on a cluster of ~20 genes, encoding paralogs of the standard photosynthetic machinery. One of them, a highly divergent D1 gene known as chlF (or psbA4), is the synthase responsible for the formation of the FRL-absorbing chlorophyll f (Chl f) that is essential for FaRLiP. The minimum gene set required for this phenotype is unclear. The desert cyanobacterium Chroococcidiopsis sp. CCMEE 010 is unusual in being capable of FaRLiP with a reduced gene cluster (15 genes), and it lacks most of the genes encoding FR-Photosystem I.MethodsHere we investigated whether the reduced gene cluster of Chroococcidiopsis sp. CCMEE 010 is transcriptionally regulated by FRL and characterized the spectral changes that occur during the FaRLiP response of Chroococcidiopsis sp. CCMEE 010. In addition, the heterologous expression of the Chl f synthase from CCMEE 010 was attempted in three closely related desert strains of Chroococcidiopsis.ResultsAll 15 genes of the FaRLiP cluster were preferentially expressed under FRL, accompanied by a progressive red-shift of the photosynthetic absorption spectrum. The Chl f synthase from CCMEE 010 was successfully expressed in two desert strains of Chroococcidiopsis and transformants could be selected in both VL and FRL.DiscussionIn Chroococcidiopsis sp. CCME 010, all the far-red genes of the unusually reduced FaRLiP cluster, are transcriptionally regulated by FRL and two closely related desert strains heterologously expressing the chlF010 gene could grow in FRL. Since the transformation hosts had been reported to survive outer space conditions, such an achievement lays the foundation toward novel cyanobacteria-based technologies to support human space exploration.

There are many potential approaches to marine carbon dioxide removal (mCDR), of which ocean iron fertilization (OIF) has the longest history of study. However, OIF studies to date were not primarily designed to quantify the durability of carbon (C) storage, nor how wise OIF might be as an mCDR approach. To quantify C sequestration, we introduce a metric called the “centennial tonne,” defined as 1,000 kg of C isolated from atmospheric contact for on average at least 100 years. We present the activities needed to assess OIF from a scientific and technological perspective, and additionally, how it might be responsibly studied and potentially deployed. The five activities include: field studies in the Northeast Pacific; improved modeling for field studies, data assimilation and predictions at larger scales; improvements in monitoring, reporting and verification (MRV) for C, and also MRV for tracking ecological and environmental impacts; and developing new iron sources and their delivery, to increase efficiencies and reduce costs. The fifth activity is to understand whether public and community support exists for OIF, and what governance structures might support further research and possible deployment of OIF. This article is written by a multidisciplinary experts group called Exploring Ocean Iron Solutions (ExOIS) that is organized around a responsible code of conduct. Of the mCDR approaches, OIF has the potential to be low cost, scalable, and rapidly deployable. Reducing CO2 emissions must lead the way, but there is also an urgency to decide under what conditions and whether OIF might be deployed or not.

Abstract Alpha-synuclein (αS)-rich Lewy bodies and neurites in the cerebral cortex correlate with the presence of dementia in Parkinson disease (PD) and Dementia with Lewy bodies (DLB), but whether αS influences synaptic vesicle dynamics in human cortical neurons is unknown. Using a new iPSC-based assay platform for measuring synaptic vesicle cycling, we found that in human cortical glutamatergic neurons, increased αS from either transgenic expression or triplication of the endogenous locus in patient-derived neurons reduced synaptic vesicle cycling under both stimulated and spontaneous conditions. Thus, using a robust, easily adopted assay platform, we show for the first time αS-induced synaptic dysfunction in human cortical neurons, a key cellular substrate for PD dementia and DLB.

Preventing the introduction of Listeria monocytogenes, subsequent biofilm formation, and persistence in food processing environments is important for reducing the risk of cross-contamination of ready-to-eat foods. This study determined the effect of Ɛ-poly-lysine (EPL), hydrogen peroxide (HP), and lauric arginate (LAE) on L. monocytogenes biofilm formation and the inactivation of mature biofilms. For inhibition studies, biofilms of L. monocytogenes Scott A (serotype 4b) and 2014L-6025 (serotype 1/2b) were developed separately at 37 °C for 48 h in the presence of sub-inhibitory concentrations (SIC) of either EPL (10 ppm), HP (2 ppm), or LAE (1.5 ppm) on polystyrene plates and stainless-steel rounds. Inactivation was determined by exposing mature biofilms on each surface to each antimicrobial at their minimum bactericidal concentration (MBC), 10xMBC, or 100xMBC for 24 h at 37 °C. The presence of these antimicrobials at SIC did not inhibit biofilm formation on either surface and their effect on mature biofilms varied by strain and surface. Application of EPL at 1xMBC (100 ppm) for 24 h resulted in greater reductions in counts of both strains on polystyrene than HP (40 ppm) and LAE (5 ppm) under the same conditions at 1xMBC (P ≤ 0.0243). Exposure of mature biofilms to LAE at 10xMBC (50 ppm) for 1 h was more effective in reducing counts on polystyrene than HP at 10xMBC (400 ppm) for the same duration (P ≤ 0.0136), and both HP and LAE applied at 100xMBC (4,000 and 500 ppm, respectively) for 24 h more effectively inactivated mature biofilms of L. monocytogenes Scott A on polystyrene compared to EPL (10,000 ppm) (P ≤ 0.0307). Application of LAE at 10xMBC for 24 h was more effective at inactivating strain Scott A on stainless steel compared to 10xMBC of EPL (1,000 ppm) or HP (P ≤ 0.0430). Future studies are needed to determine the efficacy of these and other antimicrobials on additional strains and serotypes of L. monocytogenes at temperatures relevant to food production and storage.

Recent studies on the use of plant-derived and other bioactive compounds and antimicrobials in food have challenged the idea that exposure to antimicrobials at sublethal or subinhibitory concentrations (SICs) increases the virulence potential of bacterial pathogens including Listeria monocytogenes. The objective of this study was to determine the effect of exposure to SICs of Ɛ-polylysine (EPL), hydrogen peroxide (HP), and lauric arginate (LAE) on L. monocytogenes virulence. For all assays, L. monocytogenes strains Scott A and 2014L-6025 were grown to mid-log phase in the presence of SICs of EPL, HP, or LAE. Motility was determined by spot inoculating cultures on soft brain heart infusion agar (0.3% agar). Cultures grown in SICs of antimicrobials were also inoculated onto Caco-2 cells (10:1 MOI) to determine the effects on subsequent adhesion and invasion. Last, the relative expression of key virulence genes (prfA, plcB, hlyA, actA, inlA, inlB, sigB, and virR) following growth in SICs was determined by RT-qPCR. Results indicate that L. monocytogenes growth in the presence of SICs of EPL, HP, or LAE did not affect the motility, adhesion, or invasion capacity of either strain. Changes in gene expression were observed for both L. monocytogenes strains. More specifically, SICs of EPL and LAE reduced hlyA expression in Scott A, whereas SICs of EPL and HP increased the expression of virR. The upregulation of sigB and actA in the presence of EPL and LAE, respectively, was observed in strain 2014L-6025. These findings indicate that exposure to SICs of these antimicrobials has varying effects on L. monocytogenes that differ by strain. Although no phenotypic effects were observed in terms of motility, adhesion, and invasion, the observed changes in virulence gene expression warrant further investigation.

Microalgae, known for their land-sparing cultivation and remarkable photosynthetic efficiency, play a crucial role in advancing sustainable development goals. This study explored the use of cost-effective inorganic carbon (the ionic form of CO2) and organic carbon sources (lactose, a primary sugar in whey wastewater) to support the growth of Chlorella sorokiniana UTEX 1230, and improved protein content through nitrogen supply optimization. NaHCO3 proved to be more effective than Na2CO3, resulting in a 3.4-fold increase in biomass concentration, with an initial 5 mM HCO3‾ concentration compared to the basal medium. Further addition of 0.75 % lactose led to a 4.05-fold increase in biomass concentration, with the maximum specific growth rate at 1.28/d, maximum biomass concentration at 695.88 mg/L, and maximum biomass productivity at 250.91 mg/L/d. Nitrogen supplementation greatly increased protein concentration from 16.41 % (250 mg/L NaNO3) to 52.95 % (1000 mg/L NaNO3). These results support the potential for utilizing whey wastewater bioremediation to produce high-value protein via microalgal cultivation.

Lysosomal function is impaired in Niemann-Pick disease type C1 (NPC1), a rare and inherited neurodegenerative disorder, resulting in late endosomal/lysosomal accumulation of unesterified cholesterol. The precise pathogenic mechanism of NPC1 remains incompletely understood. In this study, we employed metabolomics to uncover secondary accumulated substances in NPC1. Our findings unveiled a substantial elevation in the levels of three alkyl-lysophosphatidylcholine [alkyl-LPC, also known as lyso-platelet activating factor (PAF)] species in NPC1 compared to controls across various tissues, including brain tissue from individuals with NPC1, liver, spleen, cerebrum, cerebellum, and brain stem from NPC1 mice, as well as in both brain and liver tissue from NPC1 cats. The three elevated alkyl-LPC species were as follows: LPC O-16:0, LPC O-18:1, and LPC O-18:0. However, the levels of PAF 16:0, PAF 18:1, and PAF 18:0 were not altered in NPC1. In the NPC1 feline model, the brain and liver alkyl-LPC levels were reduced following 2-hydroxypropyl-β-cyclodextrin (HPβCD) treatment, suggesting that alkyl-LPCs are secondary storage metabolites in NPC1 disease. Unexpectedly, cerebrospinal fluid (CSF) levels of LPC O-16:0 and LPC O-18:1 were decreased in individuals with NPC1 compared to age-appropriate comparison samples, and their levels were increased in 80% of participants 2 years after intrathecal HPβCD treatment. The fold increases in CSF LPC O-16:0 and LPC O-18:1 levels were more pronounced in responders compared to nonresponders. This study identified alkyl-LPC species as secondary storage metabolites in NPC1 and indicates that LPC O-16:0 and LPC O-18:1, in particular, could serve as potential biomarkers for tracking treatment response in NPC1 patients.

IntroductionMaternal intervillous monocytes (MIMs) and fetal Hofbauer cells (HBCs) are myeloid-derived immune cells at the maternal-fetal interface. Maternal reproductive history is associated with differential risk of pregnancy complications. The molecular phenotypes and roles of these distinct monocyte/macrophage populations and the influence of gravidity on these phenotypes has not been systematically investigated.MethodsHere, we used RNA sequencing to study the transcriptional profiles of MIMs and HBCs in normal term pregnancies.ResultsOur analyses revealed distinct transcriptomes of MIMs and HBCs. Genes involved in differentiation and cell organization pathways were more highly expressed in MIMs vs. HBCs. In contrast, HBCs had higher expression of genes involved in inflammatory responses and cell surface receptor signaling. Maternal gravidity influenced monocyte programming, as expression of pro-inflammatory molecules was significantly higher in MIMs from multigravidae compared to primigravidae. In HBCs, multigravidae displayed enrichment of gene pathways involved in cell-cell signaling and differentiation.DiscussionOur results demonstrated that MIMs and HBCs have highly divergent transcriptional signatures, reflecting their distinct origins, locations, functions, and roles in inflammatory responses. Furthermore, maternal gravidity influences the gene signatures of MIMs and HBCs, potentially modulating the interplay between tolerance and trained immunity. The phenomenon of reproductive immune memory may play a novel role in the differential susceptibility of primigravidae to pregnancy complications.

Abstract Mutations in the α-Synuclein (αS) gene promote αS monomer aggregation that causes neurodegeneration in familial Parkinson’s disease (fPD). However, most mouse models expressing single-mutant αS transgenes develop neuronal aggregates very slowly, and few have dopaminergic cell loss, both key characteristics of PD. To accelerate neurotoxic aggregation, we previously generated fPD αS E46K mutant mice with rationally designed triple mutations based on the α-helical repeat motif structure of αS (fPD E46K→3 K). The 3 K variant increased αS membrane association and decreased the physiological tetramer:monomer ratio, causing lipid- and vesicle-rich inclusions and robust tremor-predominant, L-DOPA responsive PD-like phenotypes. Here, we applied an analogous approach to the G51D fPD mutation and its rational amplification (G51D → 3D) to generate mutant mice. In contrast to 3 K mice, G51D and 3D mice accumulate monomers almost exclusively in the cytosol while also showing decreased αS tetramer:monomer ratios. Both 1D and 3D mutant mice gradually accumulate insoluble, higher-molecular weight αS oligomers. Round αS neuronal deposits at 12 mos immunolabel for ubiquitin and pSer129 αS, with limited proteinase K resistance. Both 1D and 3D mice undergo loss of striatal TH+ fibers and midbrain dopaminergic neurons by 12 mos and a bradykinesia responsive to L-DOPA. The 3D αS mice have decreased tetramer:monomer equilibria and recapitulate major features of PD. These fPD G51D and 3D mutant mice should be useful models to study neuronal αS-toxicity associated with bradykinetic motor phenotypes.

Abstract Gene editing strategies for cystic fibrosis are challenged by the complex barrier properties of airway epithelia. We previously reported that the amphiphilic S10 shuttle peptide non-covalently combined with CRISPR-associated (Cas) ribonucleoprotein (RNP) enabled editing of human and mouse airway epithelial cells. Here, we derive the S315 peptide as an improvement over S10 in delivering base editor RNP. Following intratracheal aerosol delivery of Cy5-labeled peptide in rhesus macaques, we confirm delivery throughout the respiratory tract. Subsequently, we target CCR5 with co-administration of ABE8e-Cas9 RNP and S315. We achieve editing efficiencies of up-to 5.3% in rhesus airway epithelia. Moreover, we document persistence of edited epithelia for up to 12 months in mice. Finally, delivery of ABE8e-Cas9 targeting the CFTR R553X mutation restores anion channel function in cultured human airway epithelia. These results demonstrate the therapeutic potential of base editor delivery with S315 to functionally correct the CFTR R553X mutation in respiratory epithelia.