Laparoscopic vs robotic inguinal hernia repair: a comparison of learning curves and skill transference in general surgery residents.

BACKGROUND: There is no consensus on whether laparoscopic experience should be a prerequisite for robotic training. Further, there is limited information on skill transference between laparoscopic and robotic techniques. This study focused on the general surgery residents' learning curve and skill transference within the two minimally invasive platforms. METHODS: General surgery residents were observed during the performance of laparoscopic and robotic inguinal hernia repairs. The recorded data included objective measures (operative time, resident participation indicated by percent active time on console or laparoscopy relative to total case time, number of handoffs between the resident and attending), and subjective evaluations (preceptor and trainee assessments of operative performance) while controlling for case complexity, patient comorbidities, and residents' prior operative experience. Wilcoxon two-sample tests and Pearson Correlation coefficients were used for analysis. RESULTS: Twenty laparoscopic and forty-four robotic cases were observed. Mean operative times were 90 min for robotic and 95 min for laparoscopic cases (P = 0.4590). Residents' active participation time was 66% on the robotic platform and 37% for laparoscopic (P = < 0.0001). On average, hand-offs occurred 9.7 times during robotic cases and 6.3 times during laparoscopic cases (P = 0.0131). The mean number of cases per resident was 5.86 robotic and 1.67 laparoscopic (P = 0.0312). For robotic cases, there was a strong correlation between percent active resident participation and their prior robotic experience (r = 0.78) while there was a weaker correlation with prior laparoscopic experience (r = 0.47). On the other hand, prior robotic experience had minimal correlation with the percent active resident participation in laparoscopic cases (r = 0.12) and a weak correlation with prior laparoscopic experience (r = 0.37). CONCLUSION: The robotic platform may be a more effective teaching tool with a higher degree of entrustability indicated by the higher mean resident participation. We observed a greater degree of skill transference from laparoscopy to the robot, indicated by a higher degree of correlation between the resident's prior laparoscopic experience and the percent console time in robotic cases. There was minimal correlation between residents' prior robotic experience and their participation in laparoscopic cases. Our findings suggest that the learning curve for the robot may be shorter as prior robotic experience had a much stronger association with future robotic performance compared to the association observed in laparoscopy.

Mechanistic drivers of chromatin organization into compartments.

The human genome is not just a simple string of DNA, it is a complex and dynamic entity intricately folded within the cell's nucleus. This three-dimensional organization of chromatin, the combination of DNA and proteins in the nucleus, is crucial for many biological processes and has been prominently studied for its intricate relationship to gene expression. Indeed, the transcriptional machinery does not operate in isolation but interacts intimately with the folded chromatin structure. Techniques for chromatin conformation capture, including genome-wide sequencing approaches, have revealed key organizational features of chromatin, such as the formation of loops by CCCTC-binding factor (CTCF) and the division of loci into chromatin compartments. While much of the recent research and reviews have focused on CTCF loops, we discuss several new revelations that have emerged concerning chromatin compartments, with a particular focus on what is known about mechanistic drivers of compartmentalization. These insights challenge the traditional views of chromatin organization and reveal the complexity behind the formation and maintenance of chromatin compartments.

Predicting A/B compartments from histone modifications using deep learning.

The three-dimensional organization of genomes plays a crucial role in essential biological processes. The segregation of chromatin into A and B compartments highlights regions of activity and inactivity, providing a window into the genomic activities specific to each cell type. Yet, the steep costs associated with acquiring Hi-C data, necessary for studying this compartmentalization across various cell types, pose a significant barrier in studying cell type specific genome organization. To address this, we present a prediction tool called compartment prediction using recurrent neural networks (CoRNN), which predicts compartmentalization of 3D genome using histone modification enrichment. CoRNN demonstrates robust cross-cell-type prediction of A/B compartments with an average AuROC of 90.9%. Cell-type-specific predictions align well with known functional elements, with H3K27ac and H3K36me3 identified as highly predictive histone marks. We further investigate our mispredictions and found that they are located in regions with ambiguous compartmental status. Furthermore, our model's generalizability is validated by predicting compartments in independent tissue samples, which underscores its broad applicability.

Colonic in vitro fermentation of mycoprotein promotes shifts in gut microbiota, with enrichment of Bacteroides species.

Mycoprotein is a fungal-derived ingredient used for meat alternative products whose fungal cell walls are rich in dietary fibre (ß-glucans and chitin) and defines its structure. Several health benefits have been reported after mycoprotein consumption, however, little is known about the impact of mycoprotein fermentation on the gut microbiota. This study aims to identify changes in microbiome composition and microbial metabolites during colonic fermentation of mycoprotein following simulated upper gastrointestinal digestion. Changes in microbial populations and metabolites produced by the fermentation of mycoprotein fibre were investigated and compared to a plant (oat bran) and an animal (chicken) comparator. In this model fermentation system, mycoprotein and oat showed different but marked changes in the microbial population compared to chicken, which showed minimal differentiation. In particular, Bacteroides species known for degrading ß-glucans were found in abundance following fermentation of mycoprotein fibre. Mycoprotein fermentation resulted in short-chain fatty acid production comparable with oat and chicken at 72 h. Significantly higher branched-chain amino acids were observed following chicken fermentation. This study suggests that the colonic fermentation of mycoprotein can promote changes in the colonic microbial profile. These results highlight the impact that the unique structure of mycoprotein can have on digestive processes and the gut microbiota.

HiCrayon reveals distinct layers of multi-state 3D chromatin organization.

The co-visualization of chromatin conformation with 1D 'omics data is key to the multi-omics driven data analysis of 3D genome organization. Chromatin contact maps are often shown as 2D heatmaps and visually compared to 1D genomic data by simple juxtaposition. While common, this strategy is imprecise, placing the onus on the reader to align features with each other. To remedy this, we developed HiCrayon, an interactive tool that facilitates the integration of 3D chromatin organization maps and 1D datasets. This visualization method integrates data from genomic assays directly into the chromatin contact map by coloring interactions according to 1D signal. HiCrayon is implemented using R shiny and python to create a graphical user interface (GUI) application, available in both web or containerized format to promote accessibility. HiCrayon is implemented in R, and includes a graphical user interface (GUI), as well as a slimmed-down web-based version that lets users quickly produce publication-ready images. We demonstrate the utility of HiCrayon in visualizing the effectiveness of compartment calling and the relationship between ChIP-seq and various features of chromatin organization. We also demonstrate the improved visualization of other 3D genomic phenomena, such as differences between loops associated with CTCF/cohesin vs. those associated with H3K27ac. We then demonstrate HiCrayon's visualization of organizational changes that occur during differentiation and use HiCrayon to detect compartment patterns that cannot be assigned to either A or B compartments, revealing a distinct 3rd chromatin compartment. Overall, we demonstrate the utility of co-visualizing 2D chromatin conformation with 1D genomic signals within the same matrix to reveal fundamental aspects of genome organization. Local version: https://github.com/JRowleyLab/HiCrayon Web version: https://jrowleylab.com/HiCrayon.

Comparisons between atypical anorexia nervosa and anorexia nervosa: Psychological and comorbidity patterns.

OBJECTIVE: Literature comparing "atypical" anorexia nervosa (atypical AN) and anorexia nervosa (AN) suggests these diagnoses share significant similarities in eating disorder (ED) pathology and psychiatric comorbidities. This study evaluated potential differences in ED pathology, psychiatric comorbidity, associated mechanisms (i.e., ED fears and perfectionism), and demographic factors (i.e., ethnicity and age) between individuals with atypical AN and AN. METHOD: Data from seven protocols were combined for a total 464 individuals diagnosed with atypical AN (n = 215) or AN (n = 249). Between-group differences in ED severity and behaviors, psychiatric comorbidities, ED fears, perfectionism, and demographic factors were assessed using t-tests, Wilcoxon rank-sum tests, and Fisher's exact test. RESULTS: Participants with atypical AN reported higher levels of overvaluation of weight and shape than those with AN. Participants with AN scored higher on food-related fears (anxiety about eating, food avoidance behaviors, and feared concerns) and fears of social eating, as well as obsessive-compulsive symptoms. Participants with AN were more likely to identify as Asian or Pacific Islander. No other statistically significant differences were found between groups for overall ED severity, ED behaviors, psychiatric comorbidities, general ED fears, perfectionism, or demographic factors. DISCUSSION: Overall, results support previous literature indicating limited differences between individuals with atypical AN and AN, though individuals with atypical AN reported more overvaluation of weight and shape and those with AN reported higher food and social eating fears and obsessive-compulsive symptoms. Relatively few overall differences between atypical AN and AN highlight the importance of exploring dimensional conceptualizations of AN as an alternative to the current categorical conceptualization. PUBLIC SIGNIFICANCE: This study assessed differences among individuals with atypical anorexia nervosa and anorexia nervosa in eating disorder severity and behaviors, comorbid psychiatric diagnoses, associated mechanisms, and demographic factors. Few differences emerged, though participants with atypical anorexia nervosa reported more overvaluation of weight and shape, while those with anorexia nervosa reported more food and social eating fears and higher obsessive-compulsive symptoms. Results support exploration of these diagnoses as a spectrum disorder.

Clinical Implications of the Relationship Between Naltrexone Plasma Levels and the Subjective Effects of Heroin in Humans.

BACKGROUND: Extended-release naltrexone (NTX) is an opioid antagonist approved for relapse prevention after medical withdrawal. Its therapeutic effect is dependent on the NTX plasma level, and as it decreases, patients may lack protection against relapse and overdose. Therefore, identifying the minimally effective NTX level needed to block opioid-induced subjective effects has important clinical implications. METHODS: This secondary, individual-level analysis of data collected in a human laboratory study was conducted to evaluate the relationship between NTX levels and subjective effects of an intravenously administered 25-mg challenge dose of heroin in non-treatment-seeking participants with opioid use disorder (N = 12). Subjective ratings of drug liking using a 100-mm visual analog scale (VAS) and NTX levels were measured across 6 weeks after participants received a single injection of either extended-release NTX 192 mg (N = 6) or 384 mg (N = 6). Cubic spline mixed-effects models were used to provide 95% prediction intervals for individual changes in liking scores as a function of NTX levels. RESULTS: Naltrexone levels above 2 ng/mL blocked nearly all VAS ratings of drug liking after intravenous heroin administration. Participants with NTX levels ≥ 2 ng/mL had minimal (≤20 mm) changes from placebo in VAS ratings of drug liking based on 95% prediction intervals. In contrast, NTX levels < 2 ng/mL were associated with greater variability in individual-level subjective responses. CONCLUSIONS: In clinical practice, a plasma level range of 1 to 2 ng/mL is considered to be therapeutic in providing heroin blockade. The current findings suggest that a higher level (>2 ng/mL) may be needed to produce a consistent blockade.

Grow up, be persistent, and stay focused: keys for solving foraging problems by free-ranging possums.

Individuals within a species often vary in both their problem-solving approach and ability, affecting their capacity to access novel food resources. Testing problem-solving in free-ranging individuals is crucial for understanding the fundamental ecological implications of problem-solving capacity. To examine the factors affecting problem-solving in free-ranging animals, we presented three food-extraction tasks of increasing difficulty to urban common brushtail possums (Trichosurus vulpecula). We quantified two measures of problem-solving performance: trial outcome (success/failure) and time to solve and tested the influence of a range of potential drivers, including individual traits (personality, body weight, sex, and age), mechanistic behaviors that quantify problem-solving approach (work time, functional behavior time, behavioral diversity, and flexibility), and prior experience with the puzzles. We found that mechanistic behaviors were key drivers of performance. Individuals displaying greater persistence (higher work and functional behavior time) were more likely to solve a food-extraction task on their first attempt. Individuals also solved problems faster if they were more persistent and had lower behavioral flexibility. Personality indirectly affected time to solve one of the three problems by influencing time allocated to functional behaviors. Finally, adults solved the most difficult problem faster than juveniles. Overall, our study provides rare insight into the drivers underlying the problem-solving performance of wild animals. Such insight could be used to improve management strategies and conservation efforts, such as food or bait deployment, tailored to suit the innovative foraging abilities of target individuals in new and changing environments.

Chromatin alternates between A and B compartments at kilobase scale for subgenic organization.

Nuclear compartments are prominent features of 3D chromatin organization, but sequencing depth limitations have impeded investigation at ultra fine-scale. CTCF loops are generally studied at a finer scale, but the impact of looping on proximal interactions remains enigmatic. Here, we critically examine nuclear compartments and CTCF loop-proximal interactions using a combination of in situ Hi-C at unparalleled depth, algorithm development, and biophysical modeling. Producing a large Hi-C map with 33 billion contacts in conjunction with an algorithm for performing principal component analysis on sparse, super massive matrices (POSSUMM), we resolve compartments to 500 bp. Our results demonstrate that essentially all active promoters and distal enhancers localize in the A compartment, even when flanking sequences do not. Furthermore, we find that the TSS and TTS of paused genes are often segregated into separate compartments. We then identify diffuse interactions that radiate from CTCF loop anchors, which correlate with strong enhancer-promoter interactions and proximal transcription. We also find that these diffuse interactions depend on CTCF's RNA binding domains. In this work, we demonstrate features of fine-scale chromatin organization consistent with a revised model in which compartments are more precise than commonly thought while CTCF loops are more protracted.

Considerations and caveats for analyzing chromatin compartments.

Genomes are organized into nuclear compartments, separating active from inactive chromatin. Chromatin compartments are readily visible in a large number of species by experiments that map chromatin conformation genome-wide. When analyzing these maps, a common step is the identification of genomic intervals that interact within A (active) and B (inactive) compartments. It has also become increasingly common to identify and analyze subcompartments. We review different strategies to identify A/B and subcompartment intervals, including a discussion of various machine-learning approaches to predict these features. We then discuss the strengths and limitations of current strategies and examine how these aspects of analysis may have impacted our understanding of chromatin compartments.

The human inactive X chromosome modulates expression of the active X chromosome.

The "inactive" X chromosome (Xi) has been assumed to have little impact, in trans, on the "active" X (Xa). To test this, we quantified Xi and Xa gene expression in individuals with one Xa and zero to three Xis. Our linear modeling revealed modular Xi and Xa transcriptomes and significant Xi-driven expression changes for 38% (162/423) of expressed X chromosome genes. By integrating allele-specific analyses, we found that modulation of Xa transcript levels by Xi contributes to many of these Xi-driven changes (≥121 genes). By incorporating metrics of evolutionary constraint, we identified 10 X chromosome genes most likely to drive sex differences in common disease and sex chromosome aneuploidy syndromes. We conclude that human X chromosomes are regulated both in cis, through Xi-wide transcriptional attenuation, and in trans, through positive or negative modulation of individual Xa genes by Xi. The sum of these cis and trans effects differs widely among genes.

Defining a cohort of anemia-activated cis elements reveals a mechanism promoting erythroid precursor function.

Acute anemia elicits broad transcriptional changes in erythroid progenitors and precursors. We previously discovered a cis-regulatory transcriptional enhancer at the sterile alpha motif domain-14 enhancer locus (S14E), defined by a CANNTG-spacer-AGATAA composite motif and occupied by GATA1 and TAL1 transcription factors, is required for survival in severe anemia. However, S14E is only 1 of dozens of anemia-activated genes containing similar motifs. In a mouse model of acute anemia, we identified populations of expanding erythroid precursors, which increased expression of genes that contain S14E-like cis elements. We reveal that several S14E-like cis elements provide important transcriptional control of newly identified anemia-inducing genes, including the Ssx-2 interacting protein (Ssx2ip). Ssx2ip expression was determined to play an important role in erythroid progenitor/precursor cell activities, cell cycle regulation, and cell proliferation. Over a weeklong course of acute anemia recovery, we observed that erythroid gene activation mediated by S14E-like cis elements occurs during a phase coincident with low hematocrit and high progenitor activities, with distinct transcriptional programs activated at earlier and later time points. Our results define a genome-wide mechanism in which S14E-like enhancers control transcriptional responses during erythroid regeneration. These findings provide a framework to understand anemia-specific transcriptional mechanisms, ineffective erythropoiesis, anemia recovery, and phenotypic variability within human populations.

Refining the conceptualization and assessment of internalized weight stigma: A mixed methods approach.

Internalized weight stigma has gained increasing attention in empirical studies, though questions remain about the adequacy of existing measures. The current study utilized a mixed methods approach, including a novel semi-structured interview, to revisit the conceptualization of internalized weight stigma and explore in more depth the stereotypes and impacts of weight reported by individuals with high scores on the widely-used Weight Bias Internalization Scale. All participants were interviewed as part of the screening procedures for two clinical trials (Study 1 n = 84, mean age=47.8 years, 83.3% women, 67.9% Black, mean BMI=39.2 kg/m2; Study 2 n = 129, mean age=50.0 years, 88.4% women, 65.1% white, mean BMI=37.8 kg/m2). The most common weight stereotypes identified were being lazy, lacking willpower or self-control, and having poor eating habits. Up to 66% of participants reported that they did not endorse negative weight stereotypes or apply them to themselves. The most highly identified impacts of weight were on self-image (>70%) and emotions (68-83%), followed by social (37-62%) and health concerns (20-25%). Approximately 60% of participants indicated that weight affected their self-directed thoughts and feelings "very much" to "extremely." Findings have implications for understanding and assessing internalized weight stigma in research and in clinical settings where interventions are needed.

Digital Mental Health Interventions: Differences in Diet Culture Intervention Framing.

Diet culture is a societal norm that ranks thin bodies as superior to other body types and has been associated with negative outcomes, such as eating disorders. Wellness has evolved into a term that is often used to promote diet culture messages. One possible way to combat diet culture is through single-session, digital mental health interventions (DMHIs), which allow for increased access to brief public health treatments. The framing of DMHIs is critical to ensure that the target population is reached. Participants (N = 397) were enrolled in a single-session DMHI, which was framed as either a Diet Culture Intervention (n = 201) or a Wellness Resource (n = 196). Baseline group differences in eating disorder pathology, body image, weight stigma concerns, fat acceptance, and demographic characteristics were analyzed. Across groups, participants reported moderately high eating disorder pathology, low-to-moderate levels of body dissatisfaction, moderate levels of fat acceptance, and either very low or very high weight stigma concerns. Participants in the Diet Culture Intervention group reported higher levels of fat acceptance than those in the Wellness Resource group (p < 0.001). No other framing group differences were identified, though post hoc analyses revealed differences based on recruitment source (i.e., social media versus undergraduate research portal). This study found that framing a DMHI as targeting diet culture or as a Wellness Resource can result in the successful recruitment of individuals at risk of disordered eating. Framing a DMHI as a Wellness Resource may increase recruitment of individuals with low levels of fat acceptance, which may be particularly important for dismantling diet culture, disordered eating, and weight stigma concerns. Future research should assess DMHI framing in other populations, such as men and adolescents.

Hybrid metagenome assemblies link carbohydrate structure with function in the human gut microbiome.

Complex carbohydrates that escape small intestinal digestion, are broken down in the large intestine by enzymes encoded by the gut microbiome. This is a symbiotic relationship between microbes and host, resulting in metabolic products that influence host health and are exploited by other microbes. However, the role of carbohydrate structure in directing microbiota community composition and the succession of carbohydrate-degrading microbes, is not fully understood. In this study we evaluate species-level compositional variation within a single microbiome in response to six structurally distinct carbohydrates in a controlled model gut using hybrid metagenome assemblies. We identified 509 high-quality metagenome-assembled genomes (MAGs) belonging to ten bacterial classes and 28 bacterial families. Bacterial species identified as carrying genes encoding starch binding modules increased in abundance in response to starches. The use of hybrid metagenomics has allowed identification of several uncultured species with the functional potential to degrade starch substrates for future study.

Starch hydrogels as targeted colonic drug delivery vehicles.

Targeted colonic drug delivery systems are needed for the treatment of endemic colorectal pathologies, such as Crohn's disease, ulcerative colitis, and colorectal cancer. These drug delivery vehicles are difficult to formulate, as they need to remain structurally intact whilst navigating a wide range of physiological conditions across the upper gastrointestinal tract. In this work we show how starch hydrogel bulk structural and molecular level parameters influence their properties as drug delivery platforms. The in vitro protocols mimic in vivo conditions, accounting for physiological concentrations of gastrointestinal hydrolytic enzymes and salts. The structural changes starch gels undergo along the entire length of the human gastrointestinal tract have been quantified, and related to the materials' drug release kinetics for three different drug molecules, and interactions with the large intestinal microbiota. It has been demonstrated how one can modify their choice of starch in order to fine tune its corresponding hydrogel's pharmacokinetic profile.

Safety and Pharmacokinetics of Intranasally Administered Heparin.

PURPOSE: Intranasally administered unfractionated heparin (UFH) and other sulfated polysaccharides are potential prophylactics for COVID-19. The purpose of this research was to measure the safety and pharmacokinetics of clearance of intranasally administered UFH solution from the nasal cavity. METHODS: Double-blinded daily intranasal dosing in C57Bl6 mice with four doses (60 ng to 60 µg) of UFH was carried out for fourteen consecutive days, with both blood coagulation measurements and subject adverse event monitoring. The pharmacokinetics of fluorescent-labeled UFH clearance from the nasal cavity were measured in mice by in vivo imaging. Intranasal UFH at 2000 U/day solution with nasal spray device was tested for safety in a small number of healthy human subjects. RESULTS: UFH showed no evidence of toxicity in mice at any dose measured. No significant changes were observed in activated partial thromboplastin time (aPTT), platelet count, or frequency of minor irritant events over vehicle-only control. Human subjects showed no significant changes in aPTT time, international normalized ratio (INR), or platelet count over baseline measurements. No serious adverse events were observed. In vivo imaging in a mouse model showed a single phase clearance of UFH from the nasal cavity. After 12 h, 3.2% of the administered UFH remained in the nasal cavity, decaying to background levels by 48 h. CONCLUSIONS: UFH showed no toxic effects for extended daily intranasal dosing in mice as well as humans. The clearance kinetics of intranasal heparin solution from the nasal cavity indicates potentially protective levels for up to 12 h after dosing.

Safety and Pharmacokinetics of Intranasally Administered Heparin.

PURPOSE: Intranasally administered unfractionated heparin (UFH) and other sulfated polysaccharides are potential prophylactics for COVID-19. The purpose of this research was to measure the safety and pharmacokinetics of clearance of intranasally administered UFH solution from the nasal cavity. METHODS: Double-blinded daily intranasal dosing in C57Bl6 mice with four doses (60 ng to 60 µg) of UFH was carried out for fourteen consecutive days, with both blood coagulation measurements and subject adverse event monitoring. The pharmacokinetics of fluorescent-labeled UFH clearance from the nasal cavity were measured in mice by in vivo imaging. Intranasal UFH at 2000 U/day solution with nasal spray device was tested for safety in a small number of healthy human subjects. RESULTS: UFH showed no evidence of toxicity in mice at any dose measured. No significant changes were observed in activated partial thromboplastin time (aPTT), platelet count, or frequency of minor irritant events over vehicle-only control. Human subjects showed no significant changes in aPTT time, international normalized ratio (INR), or platelet count over baseline measurements. No serious adverse events were observed. In vivo imaging in a mouse model showed a single phase clearance of UFH from the nasal cavity. After 12 hours, 3.2% of the administered UFH remained in the nasal cavity, decaying to background levels by 48 hours. CONCLUSIONS: UFH showed no toxic effects for extended daily intranasal dosing in mice as well as humans. The clearance kinetics of intranasal heparin solution from the nasal cavity indicates potentially protective levels for up to 12 hours after dosing.