Culture and amplification-free nanopore sequencing for rapid detection of pathogens and antimicrobial resistance genes from urine.

PURPOSE: Urinary Tract Infections (UTIs) are among the most prevalent infections globally. Every year, approximately 150 million people are diagnosed with UTIs worldwide. The current state-of-the-art diagnostic methods are culture-based and have a turnaround time of 2-4 days for pathogen identification and susceptibility testing. METHODS: This study first establishes an optical density culture-based method for spiking healthy urine samples with the six most prevalent uropathogens. Urine samples were spiked at clinically significant concentrations of 103-105 CFU/ml. Three DNA extraction kits (BioStic, PowerFood, and Blood and Tissue) were investigated based on the DNA yield, average processing time, elution volume, and the average cost incurred per extraction. After DNA extraction, the samples were sequenced using MinION and Flongle flow cells. RESULTS: The Blood and Tissue kit outperformed the other kits based on the investigated parameters. Using nanopore sequencing, all the pathogens and corresponding genes were only identified at a spike concentration of 105 CFU/ml, achieved after 10 min and 3 hours of sequencing, respectively. However, some pathogens and antibiotic-resistance genes (ARG) could be identified from spikes at 103 colony formation units (CFU/mL). The overall turnaround time was five hours, from sample preparation to sequencing-based identification of pathogen ID and antimicrobial resistance genes. CONCLUSION: This study demonstrates excellent promise in reducing the time required for informed antibiotic administration from 48 to 72 h to five hours, thereby reducing the number of empirical doses and increasing the chance of saving lives.

Phishing vulnerability compounded by older age, apolipoprotein E e4 genotype, and lower cognition.

With technological advancements, financial exploitation tactics have expanded into the online realm. Older adults may be particularly susceptible to online scams due to age- and Alzheimer's disease-related changes in cognition. In this study, 182 adults ranging from 18 to 90 years underwent cognitive assessment, genotyping for apolipoprotein E e4 (APOE4), and completed the lab-based Short Phishing Email Suspicion Test (S-PEST) as well as the real-life PHishing Internet Task (PHIT). Across both paradigms, older age predicted heightened susceptibility to phishing, with this enhanced susceptibility pronounced among older APOE4 allele carriers with lower working memory. Additionally, performance in both phishing tasks was correlated in that reduced ability to discriminate between phishing and safe emails in S-PEST predicted greater phishing susceptibility in PHIT. The current study identifies older age, APOE4, and lower cognition as risk factors for phishing vulnerability and introduces S-PEST as an easy-to-administer, ecologically valid tool for assessing phishing susceptibility.

Directed exploration is elevated in affective disorders but reduced by an aversive interoceptive state induction.

Elevated anxiety and uncertainty avoidance are known to exacerbate maladaptive choice in individuals with affective disorders. However, the differential roles of state vs. trait anxiety remain unclear, and underlying computational mechanisms have not been thoroughly characterized. In the present study, we investigated how a somatic (interoceptive) state anxiety induction influences learning and decision-making under uncertainty in individuals with clinically significant levels of trait anxiety. A sample of 58 healthy comparisons (HCs) and 61 individuals with affective disorders (iADs; i.e., depression and/or anxiety) completed a previously validated explore-exploit decision task, with and without an added breathing resistance manipulation designed to induce state anxiety. Computational modeling revealed a pattern in which iADs showed greater information-seeking (i.e., directed exploration; Cohen's d=.39, p=.039) in resting conditions, but that this was reduced by the anxiety induction. The affective disorders group also showed slower learning rates across conditions (Cohen's d=.52, p=.003), suggesting more persistent uncertainty. These findings highlight a complex interplay between trait anxiety and state anxiety. Specifically, while elevated trait anxiety is associated with persistent uncertainty, acute somatic anxiety can paradoxically curtail exploratory behaviors, potentially reinforcing maladaptive decision-making patterns in affective disorders.

Individuals with Methamphetamine Use Disorder Show Reduced Directed Exploration and Learning Rates Independent of an Aversive Interoceptive State Induction.

Methamphetamine Use Disorder (MUD) is associated with substantially reduced quality of life. Yet, decisions to use persist, due in part to avoidance of anticipated withdrawal states. However, the specific cognitive mechanisms underlying this decision process, and possible modulatory effects of aversive states, remain unclear. Here, 56 individuals with MUD and 58 healthy comparisons (HCs) performed a decision task, both with and without an aversive interoceptive state induction. Computational modeling measured the tendency to test beliefs about uncertain outcomes (directed exploration) and the ability to update beliefs in response to outcomes (learning rates). Compared to HCs, those with MUD exhibited less directed exploration and slower learning rates, but these differences were not affected by aversive state induction. These results suggest novel, state-independent computational mechanisms whereby individuals with MUD may have difficulties in testing beliefs about the tolerability of abstinence and in adjusting behavior in response to consequences of continued use.

Epigenetic-related transcriptional reprogramming elucidated by identification and validation of a novel reference gene combination for RT-qPCR studies in porcine oocytes of contrasting quality.

BACKGROUND: Reliable RT-qPCR results are dependent on appropriate normalisation. Oocyte maturation studies can be challenging in this respect, as the stage of development can distinctively affect reference gene transcript abundance. The aim of this study was to validate the use of reference genes in oocyte in vitro maturation RT-qPCR studies, and thereafter, examine the abundance of transcripts supporting histone modification during oocyte and early embryo development in oocytes of contrasting quality. METHODS AND RESULTS: Total RNA from oocytes from prepubertal gilts and sows was extracted either directly succeeding follicle aspiration or after 44 h in vitro maturation, followed by RT-qPCR. The stability of YWHAG, HPRT1, ACTB, GAPDH, HMBS and PFKP, was analysed by NormFinder and further cross-validated by assessing results generated following application of different combinations of potential reference genes for normalisation of the RT-qPCR data. Combining ACTB and PFKP generated high stability according to NormFinder and concordant results. Applying this normalisation, gilt derived oocytes displayed significantly higher abundance than oocytes from sows of almost all the epigenetic-related transcripts studied (HDAC2, SIRT1, SALL4, KDM1A, KDM1B, KDM5A), both before and after maturation. CONCLUSIONS: This study identified the combined use of ACTB and PFKP as the optimal normalisation for porcine oocyte RT-qPCR data. In oocytes collected from prepubertal gilts, transcription did not appear to be silenced at the time of aspiration, and accumulation of transcripts supporting histone modification facilitating proper fertilization and further embryo development seemed delayed. The results imply the epigenetic-related transcripts may have potential as markers of oocyte quality.

Differential impacts of healthy cognitive aging on directed and random exploration.

Deciding whether to explore unknown opportunities or exploit well-known options is a ubiquitous part of our everyday lives. Extensive work in college students suggests that young people make explore-exploit decisions using a mixture of information seeking and random behavioral variability. Whether, and to what extent, older adults use the same strategies is unknown. To address this question, 51 older adults (ages 65-74) and 32 younger adults (ages 18-25) completed the Horizon Task, a gambling task that quantifies information seeking and behavioral variability as well as how these strategies are controlled for the purposes of exploration. Qualitatively, we found that older adults performed similar to younger adults on this task, increasing both their information seeking and behavioral variability when it was adaptive to explore. Quantitively, however, there were substantial differences between the age groups, with older adults showing less information seeking overall and less reliance on variability as a means to explore. In addition, we found a subset of approximately 26% of older adults whose information seeking was close to zero, avoiding informative options even when they were clearly the better choice. Unsurprisingly, these "information avoiders" performed worse on the task. In contrast, task performance in the remaining "information seeking" older adults was comparable to that of younger adults suggesting that age-related differences in explore-exploit decision making may be adaptive except when they are taken to extremes. (PsycInfo Database Record (c) 2024 APA, all rights reserved).

Age-group differences in trust-related decision-making and learning.

Facial impressions contribute to evaluations of trustworthiness. Older adults are especially vulnerable to trust violations, incurring risks for deception and exploitation. Using the newly developed social Iowa Gambling Task (S-IGT), we examined age-group differences in the impact of facial trustworthiness on decision-making and learning. In the congruent condition (CS-IGT), advantageous decks were paired with trustworthy faces and disadvantageous decks with untrustworthy faces. In the incongruent condition (IS-IGT), this pairing was reversed. Younger (n = 143) and older (n = 129) participants completed either the standard Iowa Gambling Task (IGT), CS-IGT, or IS-IGT. Both age groups preferred trustworthy faces in their initial choices. Older adults performed worse than younger adults across all tasks over time. Further, compared to younger adults, older adults performed worse on the IS-IGT, suggesting that incongruent facial cues interfered with older adults' performance, which aligns with reduced sensitivity to negative social reputations in aging. Multilevel modeling also indicated that age-group differences were most pronounced across all tasks in the last 40 trials. Together these findings suggest that differences between younger and older adults in experience-dependent decision-making are magnified in social contexts that involve a "wolf in sheep's clothing," which may reflect age-related difficulties in integrating incongruent information.

The psychophysiology of Mastermind: Characterizing response times and blinking in a high-stakes television game show.

Television game shows have proven to be a valuable resource for studying human behavior under conditions of high stress and high stakes. However, previous work has focused mostly on choices-ignoring much of the rich visual information that is available on screen. Here, we take a first step to extracting more of this information by investigating the response times and blinking of contestants in the BBC show Mastermind. In Mastermind, contestants answer rapid-fire quiz questions while a camera slowly zooms in on their faces. By labeling contestants' behavior and blinks from 25 episodes, we asked how accuracy, response times, and blinking varied over the course of the game. For accuracy and response times, we tested whether contestants responded more accurately and more slowly after an error-exhibiting the "post-error increase in accuracy" and "post-error slowing" which has been repeatedly observed in the lab. For blinking, we tested whether blink rates varied according to the cognitive demands of the game-decreasing during periods of cognitive load, such as when pondering a response, and increasing at event boundaries in the task, such as the start of a question. In contrast to the lab, evidence for post-error changes in accuracy and response time was weak, with only marginal effects observed. In line with the lab, blinking varied over the course of the game much as we predicted. Overall, our findings demonstrate the potential of extracting dynamic signals from game shows to study the psychophysiology of behavior in the real world.

Cumulus Cell and Oocyte Gene Expression in Prepubertal Gilts and Sows Identifies Cumulus Cells as a Prime Informative Parameter of Oocyte Quality.

Cumulus cells (CCs) are pivotal during oocyte development. This study aimed to identify novel marker genes for porcine oocyte quality by examining the expression of selected genes in CCs and oocytes, employing the model of oocytes from prepubertal animals being of reduced quality compared to those from adult animals. Total RNA was extracted either directly after follicle aspiration or after in vitro maturation, followed by RT-qPCR. Immature gilt CCs accumulated BBOX1 transcripts, involved in L-carnitine biosynthesis, to a 14.8-fold higher level (p < 0.05) relative to sows, while for CPT2, participating in fatty acid oxidation, the level was 0.48 (p < 0.05). While showing no differences between gilt and sow CCs after maturation, CPT2 and BBOX1 levels in oocytes were higher in gilts at both time points. The apparent delayed lipid metabolism and reduced accumulation of ALDOA and G6PD transcripts in gilt CCs after maturation, implying downregulation of glycolysis and the pentose phosphate pathway, suggest gilt cumulus-oocyte complexes have inadequate ATP stores and oxidative stress balance compared to sows at the end of maturation. Reduced expression of BBOX1 and higher expression of CPT2 in CCs before maturation and higher expression of G6PD and ALDOA after maturation are new potential markers of oocyte quality.

Childhood unpredictability and the development of exploration.

Early in development, the process of exploration helps children gather new information that fosters learning about the world. Yet, it is unclear how childhood experiences may influence the way humans approach new learning. What influences decisions to exploit known, familiar options versus trying a novel alternative? We found that childhood unpredictability, characterized by unpredictable caregiving and unstable living environments, was associated with reduced exploratory behavior. This effect holds while controlling for individual differences, including anxiety and stress. Individuals who perceived their childhoods as unpredictable explored less and were instead more likely to repeat previous choices (habitual responding). They were also more sensitive to uncertainty than to potential rewards, even when the familiar options yielded lower rewards. We examined these effects across multiple task contexts and via both in-person (N = 78) and online replication (N = 84) studies among 10- to 13-y-olds. Results are discussed in terms of the potential cascading effects of unpredictable environments on the development of decision-making and the effects of early experience on subsequent learning.

Frontal-midline theta and posterior alpha oscillations index early processing of spatial representations during active navigation.

Previous research has demonstrated that humans combine multiple sources of spatial information such as self-motion and landmark cues while navigating through an environment. However, it is unclear whether this involves comparing multiple representations obtained from different sources during navigation (parallel hypothesis) or building a representation first based on self-motion cues and then combining with landmarks later (serial hypothesis). We tested these two hypotheses (parallel vs serial) in an active navigation task using wireless mobile scalp EEG recordings. Participants walked through an immersive virtual hallway with or without conflicts between self-motion and landmarks (i.e., intersections) and pointed toward the starting position of the hallway. We employed the oscillatory signals recorded during mobile wireless scalp EEG as a means of identifying when participant representations based on self-motion versus landmark cues might have first emerged. We found that path segments, including intersections present early during navigation, were more strongly associated with later pointing error, regardless of when they appeared during encoding. We also found that there was sufficient information contained within the frontal-midline theta and posterior alpha oscillatory signals in the earliest segments of navigation involving intersections to decode condition (i.e., conflicting vs not conflicting). Together, these findings suggest that intersections play a pivotal role in the early development of spatial representations, suggesting that memory representations for the geometry of walked paths likely develop early during navigation, in support of the parallel hypothesis.

Sperm quality parameters, fertilizing potential, metabolites, and DNA methylation in cold-stored and cryopreserved milt from Atlantic salmon (Salmo salar L.).

Cold storage and freezing/thawing of milt may affect sperm functionality and the subsequent fertilization ability of milt. This study aimed to investigate sperm quality parameters and fertilization potential of Atlantic salmon milt, stored cold and subsequently cryopreserved, using different storage conditions. The objective was also to assess if analysis of milt metabolites and sperm DNA methylation signatures could be applicable to further elucidate sperm quality and fertilization following preservation. Milt samples were collected from eight mature Atlantic salmon males and stored for 4 days at 2°C and 8°C. Samples were taken on day one of storage at 2°C and on day four of storage at 2°C and 8°C. Storage for 4 days at 8°C is expected to be detrimental to sperm quality, and was included to create contrasts. Correspondingly, aliquots of cold-stored milt were prepared for cryopreservation, resulting in a total of six experimental conditions. Samples from all six experimental conditions were used in fertilization trials and analyzed for sperm viability, motility, ATP content, DNA fragmentation index, and High DNA stainability. In addition, milt samples from four of the males were analyzed for targeted metabolites and DNA methylation signatures by reduced representation bisulfite sequencing. The fertilization trials were performed using sperm:egg ratios of 75 × 103 and 500 × 103, respectively. Storage duration, temperature, and cryopreservation of cold-stored milt influenced several sperm quality parameters, metabolites, and DNA methylation signatures. The total motility, progressive motility, ATP, and velocity parameters were the sperm parameters with the strongest correlation to fertilization rates (p < 0.01). Several metabolites were correlated with fertility rates in both cold-stored and cryopreserved samples (p < 0.05). The fertilizing capacity of cold-stored milt was significantly reduced after 4 days of storage at 8°C, while corresponding cryopreserved milt showed reduced fertilization at both storage temperatures (2°C and 8°C) (p < 0.05). The results indicate that cryopreservation of milt stored for 1 day does not compromise either fertilization ability or DNA methylation signatures.

Frontal-midline theta and posterior alpha oscillations index early processing of spatial representations during active navigation.

Previous research has demonstrated that humans combine multiple sources of spatial information such as self-motion and landmark cues, while navigating through an environment. However, it is unclear whether this involves comparing multiple representations obtained from different sources during navigation (parallel hypothesis) or building a representation first based on self-motion cues and then combining with landmarks later (serial hypothesis). We tested these two hypotheses (parallel vs. serial) in an active navigation task using wireless mobile scalp EEG recordings. Participants walked through an immersive virtual hallway with or without conflicts between self-motion and landmarks (i.e., intersections) and pointed toward the starting position of the hallway. We employed the oscillatory signals recorded during mobile wireless scalp EEG as means of identifying when participant representations based on self-motion vs. landmark cues might have first emerged. We found that path segments, including intersections present early during navigation, were more strongly associated with later pointing error, regardless of when they appeared during encoding. We also found that there was sufficient information contained within the frontal-midline theta and posterior alpha oscillatory signals in the earliest segments of navigation involving intersections to decode condition (i.e., conflicting vs. not conflicting). Together, these findings suggest that intersections play a pivotal role in the early development of spatial representations, suggesting that memory representations for the geometry of walked paths likely develop early during navigation, in support of the parallel hypothesis.

Distinct genome-wide DNA methylation and gene expression signatures in classical monocytes from African American patients with systemic sclerosis.

BACKGROUND: Systemic sclerosis (SSc) is a multisystem autoimmune disorder that has an unclear etiology and disproportionately affects women and African Americans. Despite this, African Americans are dramatically underrepresented in SSc research. Additionally, monocytes show heightened activation in SSc and in African Americans relative to European Americans. In this study, we sought to investigate DNA methylation and gene expression patterns in classical monocytes in a health disparity population. METHODS: Classical monocytes (CD14+ + CD16-) were FACS-isolated from 34 self-reported African American women. Samples from 12 SSc patients and 12 healthy controls were hybridized on MethylationEPIC BeadChip array, while RNA-seq was performed on 16 SSc patients and 18 healthy controls. Analyses were computed to identify differentially methylated CpGs (DMCs), differentially expressed genes (DEGs), and CpGs associated with changes in gene expression (eQTM analysis). RESULTS: We observed modest DNA methylation and gene expression differences between cases and controls. The genes harboring the top DMCs, the top DEGs, as well as the top eQTM loci were enriched for metabolic processes. Genes involved in immune processes and pathways showed a weak upregulation in the transcriptomic analysis. While many genes were newly identified, several other have been previously reported as differentially methylated or expressed in different blood cells from patients with SSc, supporting for their potential dysregulation in SSc. CONCLUSIONS: While contrasting with results found in other blood cell types in largely European-descent groups, the results of this study support that variation in DNA methylation and gene expression exists among different cell types and individuals of different genetic, clinical, social, and environmental backgrounds. This finding supports the importance of including diverse, well-characterized patients to understand the different roles of DNA methylation and gene expression variability in the dysregulation of classical monocytes in diverse populations, which might help explaining the health disparities.

The effects of time horizon and guided choices on explore-exploit decisions in rodents.

Humans and animals have to balance the need for exploring new options with exploiting known options that yield good outcomes. This tradeoff is known as the explore-exploit dilemma. To better understand the neural mechanisms underlying how humans and animals address the explore-exploit dilemma, a good animal behavioral model is critical. Most previous rodents explore-exploit studies used ethologically unrealistic operant boxes and reversal learning paradigms in which the decision to abandon a bad option is confounded by the need for exploring a novel option for information collection, making it difficult to separate different drives and heuristics for exploration. In this study, we investigated how rodents make explore-exploit decisions using a spatial navigation horizon task (Wilson et al., 2014) adapted to rats to address the above limitations. We compared the rats' performance to that of humans using identical measures. We showed that rats use prior information to effectively guide exploration. In addition, rats use information-driven directed exploration like humans, but the extent to which they explore has the opposite dependance on time horizon than humans. Moreover, we found that free choices and guided choices have different influences on exploration in rodents, a finding that has not yet been tested in humans. This study reveals that the explore-exploit spatial behavior of rats is more complex than previously thought. (PsycInfo Database Record (c) 2023 APA, all rights reserved).

Prediction of high fecal propionate-to-butyrate ratios using 16S rRNA-based detection of bacterial groups with liquid array diagnostics.

Butyrate and propionate represent two of three main short-chain fatty acids produced by the intestinal microbiota. In healthy populations, their levels are reportedly equimolar, whereas a deviation in their ratio has been observed in various diseased cohorts. Monitoring such a ratio represents a valuable metric; however, it remains a challenge to adopt short-chain fatty acid detection techniques in clinical settings because of the volatile nature of these acids. Here we aimed to estimate short-chain fatty acid information indirectly through a novel, simple quantitative PCR-compatible assay (liquid array diagnostics) targeting a limited number of microbiome 16S markers. Utilizing 15 liquid array diagnostics probes to target microbiome markers selected by a model that combines partial least squares and linear discriminant analysis, the classes (normal vs high propionate-to-butyrate ratio) separated at a threshold of 2.6 with a prediction accuracy of 96%.

Facial Trustworthiness Perception Across the Adult Life Span.

OBJECTIVES: Trust is crucial for successful social interaction across the life span. Perceiver age, facial age, and facial emotion have been shown to influence trustworthiness perception, but the complex interplay between these perceiver and facial characteristics has not been examined. METHOD: Adopting an adult life-span developmental approach, 199 adults (aged 22-78 years) rated the trustworthiness of faces that systematically varied in age (young, middle-aged, and older) and emotion (neutral, happy, sad, fearful, angry, and disgusted) from the FACES Lifespan Database. RESULTS: The study yielded three key results. First, on an aggregated level, facial trustworthiness perception did not differ by perceiver age. Second, all perceivers rated young faces as the most trustworthy, and middle-aged and older (but not young) perceivers rated older faces as least trustworthy. Third, facial emotions signaling threat (fear, anger, and disgust) relative to neutral, happy, and sad expressions moderated age effects on facial trustworthiness perception. DISCUSSION: Findings from this study highlight the impact of perceiver and facial characteristics on facial trustworthiness perception in adulthood and aging and have potential to inform first impression formation, with effects on trait attributions and behavior. This publication also provides normative data on perceived facial trustworthiness for the FACES Lifespan Database.