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.

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.

Endogenous oxidized DNA bases and APE1 regulate the formation of G-quadruplex structures in the genome.

Formation of G-quadruplex (G4) DNA structures in key regulatory regions in the genome has emerged as a secondary structure-based epigenetic mechanism for regulating multiple biological processes including transcription, replication, and telomere maintenance. G4 formation (folding), stabilization, and unfolding must be regulated to coordinate G4-mediated biological functions; however, how cells regulate the spatiotemporal formation of G4 structures in the genome is largely unknown. Here, we demonstrate that endogenous oxidized guanine bases in G4 sequences and the subsequent activation of the base excision repair (BER) pathway drive the spatiotemporal formation of G4 structures in the genome. Genome-wide mapping of occurrence of Apurinic/apyrimidinic (AP) site damage, binding of BER proteins, and G4 structures revealed that oxidized base-derived AP site damage and binding of OGG1 and APE1 are predominant in G4 sequences. Loss of APE1 abrogated G4 structure formation in cells, which suggests an essential role of APE1 in regulating the formation of G4 structures in the genome. Binding of APE1 to G4 sequences promotes G4 folding, and acetylation of APE1, which enhances its residence time, stabilizes G4 structures in cells. APE1 subsequently facilitates transcription factor loading to the promoter, providing mechanistic insight into the role of APE1 in G4-mediated gene expression. Our study unravels a role of endogenous oxidized DNA bases and APE1 in controlling the formation of higher-order DNA secondary structures to regulate transcription beyond its well-established role in safeguarding the genomic integrity.

Psyllium reduces inulin-induced colonic gas production in IBS: MRI and in vitro fermentation studies.

OBJECTIVE: Health-promoting dietary fibre including inulin often triggers gastrointestinal symptoms in patients with IBS, limiting their intake. Our aim was to test if coadministering psyllium with inulin would reduce gas production. DESIGN: A randomised, four-period, four-treatment, placebo-controlled, crossover trial in 19 patients with IBS. Subjects ingested a 500 mL test drink containing either inulin 20 g, psyllium 20 g, inulin 20 g+ psyllium 20 g or dextrose 20 g (placebo). Breath hydrogen was measured every 30 min with MRI scans hourly for 6 hours. Faecal samples from a subset of the patients with IBS were tested using an in vitro fermentation model. Primary endpoint was colonic gas assessed by MRI. RESULTS: Colonic gas rose steadily from 0 to 6 hours, with inulin causing the greatest rise, median (IQR) AUC(0-360 min) 3145 (848-6502) mL·min. This was significantly reduced with inulin and psyllium coadministration to 618 (62-2345) mL·min (p=0.02), not significantly different from placebo. Colonic volumes AUC(0-360 min) were significantly larger than placebo for both inulin (p=0.002) and inulin and psyllium coadministration (p=0.005). Breath hydrogen rose significantly from 120 min after inulin but not psyllium; coadministration of psyllium with inulin delayed and reduced the maximum increase, AUC(0-360 min) from 7230 (3255-17910) ppm·hour to 1035 (360-4320) ppm·hour, p=0.007.Fermentation in vitro produced more gas with inulin than psyllium. Combining psyllium with inulin did not reduce gas production. CONCLUSIONS: Psyllium reduced inulin-related gas production in patients with IBS but does not directly inhibit fermentation. Whether coadministration with psyllium increases the tolerability of prebiotics in IBS warrants further study. TRIAL REGISTRATION NUMBER: NCT03265002.

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.

Impact of the source of fermentable carbohydrate on SCFA production by human gut microbiota in vitro - a systematic scoping review and secondary analysis.

Short chain fatty acids (SCFA) are produced by bacterial fermentation of non-digestible carbohydrates (NDC) and have many potential tissue and SCFA specific actions, from providing fuel for colonic cells to appetite regulation. Many studies have described the fermentation of different carbohydrates, often using in vitro batch culture. As evidence-based critical evaluation of substrates selectively promoting production of individual SCFA is lacking, we performed a systematic scoping literature review. Databases were searched to identify relevant papers published between 1900 and 12/06/2016. Search terms included In vitro batch fermentation and In vitro short chain fatty acid production. Articles were considered for essential criteria allowing equivalent comparison of SCFA between NDC. Seventy seven articles were included in the final analysis examining 29 different carbohydrates. After 24-hour fermentation, galacto-oligosaccharide ranked highest for butyrate and total SCFA production and second for acetate production. Rhamnose ranked highest for propionate production. The lowest SCFA production was observed for kiwi fiber, polydextrose, and cellulose. This review demonstrates that choosing a substrate to selectively enhance a specific SCFA is difficult, and the molar proportion of each SCFA produced by individual substrates may be misleading. Instead the rate and ratio of SCFA production should be evaluated in parallel.

A Randomized Comparison of Positional Stability: The EZ-Blocker Versus Left-Sided Double-Lumen Endobronchial Tubes in Adult Patients Undergoing Thoracic Surgery.

OBJECTIVE: To assess if there is a difference in the repositioning rate of the EZ-Blocker versus a left-sided double-lumen endobronchial tube (DLT) in patients undergoing thoracic surgery and one-lung ventilation. DESIGN: Prospective, randomized. SETTING: Single center, university hospital. PARTICIPANTS: One hundred sixty-three thoracic surgery patients. INTERVENTIONS: Patients were randomized to either EZ-Blocker or a DLT. MEASUREMENTS AND MAIN RESULTS: The primary outcome was positional stability of either the EZ-Blocker or a left-sided double-lumen endobronchial tube, defined as the number of repositionings per hour of surgery and one-lung ventilation. Secondary outcomes included an ordinal isolation score from 1 to 3, in which 1 was poor, up to 3, which represented excellent isolation, and a visual analog postoperative sore throat score (0-100) on postoperative days (POD) one and two. Rate of repositionings per hour during one-lung ventilation and surgical manipulation in left-sided cases was similar between the two devices: 0.08 ± 0.15 v 0.11 ± 0.3 (p = 0.72). In right-sided cases, the rate of repositioning was higher in the EZ-Blocker group compared with DLT: 0.38 ± 0.65 v 0.09 ± 0.21 (p = 0.03). Overall, mean isolation scores for the EZ-Blocker versus the DLT were 2.76 v 2.92 (p = 0.04) in left-sided cases and 2.70 v 2.83 (p = 0.22) in right-sided cases. Median sore throat scores for left sided cases were 0 v 5 (p = 0.13) POD one and 0 v 5 (p = 0.006) POD two for the EZ-Blocker and left-sided DLT, respectively. CONCLUSION: For right-sided procedures, the positional stability of the EZ-Blocker is inferior to a DLT. In left-sided cases, the rate of repositioning for the EZ-Blocker and DLT are not statistically different.

Optimization of an Assay To Determine Colonization Resistance to Clostridioides difficile in Fecal Samples from Healthy Subjects and Those Treated with Antibiotics.

A healthy, intact gut microbiota is often resistant to colonization by gastrointestinal pathogens. During periods of dysbiosis, however, organisms such as Clostridioides difficile can thrive. We describe an optimized in vitro colonization resistance assay for C. difficile in stool (CRACS) and demonstrate the utility of this assay by assessing changes in colonization resistance following antibiotic exposure. Fecal samples were obtained from healthy volunteers (n = 6) and from healthy subjects receiving 5 days of moxifloxacin (n = 11) or no antibiotics (n = 10). Samples were separated and either not manipulated (raw) or sterilized (autoclaved or filtered) prior to inoculation with C. difficile ribotype 027 spores and anaerobic incubation for 72 h. Different methods of storing fecal samples were also investigated in order to optimize the CRACS. In healthy, raw fecal samples, incubation with spores did not lead to increased C. difficile total viable counts (TVCs) or cytotoxin detection. In contrast, increased C. difficile TVCs and cytotoxin detection occurred in sterilized healthy fecal samples or those from antibiotic-treated individuals. The CRACS was functional with fecal samples stored at either 4°C or -80°C but not with those stored with glycerol (12% or 30% [vol/vol]). Our data show that the CRACS successfully models in vitro the loss of colonization resistance and subsequent C. difficile proliferation and toxin production. The CRACS could be used as a proxy for C. difficile infection in clinical studies or to determine if an individual is at risk of developing C. difficile infection or other potential infections occurring due to a loss of colonization resistance.

An Examination of Sex Differences in a Disease-Specific Model of Disordered Eating Behaviors in Type 1 Diabetes.

OBJECTIVE: Preliminary evidence supports the integration of type 1 diabetes (T1D) disease-specific factors into eating disorder risk models. The current study explored whether cross-sectional associations among constructs included in the modified dual pathway model of eating disorder risk for individuals with T1D are similar across sex among adolescents and young adults with T1D. METHODS: Original study participants were recruited from the T1D Exchange Clinic Network, a U.S. registry of individuals with T1D. Online surveys included measures of general eating disorder risk factors, hypothesized T1D-specific risk factors, and a T1D-specific eating disorder questionnaire. The current study is a secondary analysis with the adolescents (13-17 years; n = 307; 46.9% female) and young adults (18-25 years; n = 313; 62.6% female) from the original sample. In the absence of strong measurement invariance for all measures of interest, sex-specific path models were estimated among the adolescent and young adult cohorts. RESULTS: Only two paths emerged as significant in the female, but not male, adolescent model. In the young adult cohort, all significant paths were the same across sex. CONCLUSIONS: Both general and T1D-specific risk factors are associated with disordered eating behaviors in the T1D population. Patterns of associations were similar across male and female youth with T1D, suggesting that sex-specific prevention approaches to disordered eating behaviors among T1D youth may not be warranted.

Antinociceptive activity of thiazole-containing cyclized DAMGO and Leu-(Met) enkephalin analogs.

Numerous studies demonstrate the promise of opioid peptides as analgesics, but poor oral bioavailability has limited their therapeutic development. This study sought to increase the oral bioavailability of opioid peptides by cyclization, using Hantzsch-based macrocyclization strategies to produce two new series of cyclized DAMGO and Leu/Met-enkephalin analogs. Opioid receptor affinity and selectivity for compounds in each series were assessed in vitro with radioligand competition binding assays. Compounds demonstrated modest affinity but high selectivity for the mu, delta, and kappa opioid receptors (MOR, DOR and KOR), while selectivity for mu opioid receptors varied by structure. Antinociceptive activity of each compound was initially screened in vivo following intracerebroventricular (i.c.v.) administration and testing in the mouse 55 °C warm-water tail-withdrawal test. The four most active compounds were then evaluated for dose- and time-dependent antinociception, and opioid receptor selectivity in vivo. Cyclic compounds 1924-10, 1936-1, 1936-7, and 1936-9 produced robust and long- lasting antinociception with ED50 values ranging from 0.32-0.75 nmol following i.c.v. administration mediated primarily by mu- and delta-opioid receptor agonism. Compounds 1924-10, 1936-1 and 1936-9 further displayed significant time-dependent antinociception after oral (10 mg kg-1, p.o.) administration. A higher oral dose (30 mg kg-1. p.o.) of all four cyclic peptides also reduced centrally-mediated respiration, suggesting successful penitration into the CNS. Overall, these data suggest cyclized opioid peptides synthesized by a Hantzsch-based macrocyclization strategy can retain opioid agonist activity to produce potent antinociception in vivo while conveying improved bioavailability following oral administration.

Test of the modified dual pathway model of eating disorders in individuals with type 1 diabetes.

OBJECTIVE: Adolescents and young adults with type 1 diabetes (T1D) demonstrate high rates of disordered eating behaviors (DEBs) and may experience physiological and psychological vulnerabilities not currently included in established risk models of DEBs. This study examined associations among constructs included in the recently proposed T1D-specific modified dual pathway model and examined age as a moderator of these associations. METHOD: Participants included adolescents (n = 307; age M = 15.71, SD = 1.33), young adults (n = 313; age M = 21.20, SD = 2.10), and adults (n = 198; age M = 30.51, SD = 2.81) recruited via the T1D Exchange Clinic Registry. Data were collected from participants' medical records and from self-report questionnaires assessing dietary regimen, dietary restraint, body dissatisfaction, hunger/satiety, diabetes-specific negative affect, and DEBs. Multiple group path modeling was used to test hypotheses. RESULTS: Approximately 31% of participants were at risk for an eating disorder. The original modified dual pathway model had poor model fit. The addition of three empirically defensible paths improved model fit. Diabetes-specific dietary regimen, diabetes-specific negative affect, and hunger/satiety disruption all were associated with DEBs. A fully varying multiple group model by age fit best; however, only the dietary restraint to DEBs pathway demonstrated a distinct pattern across age cohort, which attenuated from the adolescent to the adult cohort. DISCUSSION: This study provides preliminary support for associations proposed in the modified dual pathway model and suggests potential for intervening on disease-specific risk factors of DEBs in a T1D population.

A Simple Method for Estimating Hand Hygiene Use Among Anesthesia Personnel: Development, Validation, and Use in a Quality Improvement Project.

BACKGROUND: Frequent hand hygiene by anesthesia personnel may be an important factor in reducing contamination of IV lines and medication access ports and may reduce hospital-acquired infections. Measurement of hand hygiene frequency at the individual clinician level by direct observation or electronic devices is cumbersome and expensive. We developed and validated a simple method for estimating hand hygiene frequency by individual anesthesia providers and utilized it in a quality improvement initiative to increase hand hygiene use. METHODS: Pump-style, alcohol-based hand hygiene container weight at the anesthesia work station was measured before and after each surgical operation and converted to estimated number of accesses (pumps) per hour. Video observation was used to validate the estimated hand hygiene use. A quality improvement initiative utilized periodic measurement of hand hygiene frequency via the validated method, and incorporated individual provider feedback, email reminders, monthly departmental performance reports, and reminders in the electronic anesthesia record. Segmented linear regression was used to evaluate the effect of the intervention on hand hygiene use. RESULTS: Delivered product per pump was consistent for containers at least half-full and averaged (mean ± SD) 0.92 ± 0.13 g per pump. Video observation in 26 cases showed a strong correlation between observed hand hygiene episodes and estimated hand hygiene use frequency based on weight change of the container (linear regression, R = 0.97, P < .0001). Median hand hygiene frequency was near 0 at baseline but increased progressively throughout the intervention period (segmented linear regression, overall R = 0.76, P < .0001; change of intercept or mean hand hygiene after initiation of intervention [parameter estimate ± SE] [0.970 ± 0.29], P = .0008). CONCLUSIONS: A low-cost, simple method for measuring individual anesthesia clinician use of hand hygiene intraoperatively based on container weight change is feasible and sufficiently accurate to support a quality improvement initiative to increase its use.

Procedural Challenges During Intubation in Patients With Oropharyngeal Masses: A Prospective Observational Study.

BACKGROUND: In patients who undergo surgery for oropharyngeal masses, intubation is almost always successful. However, technical aspects of airway management, including bag mask ventilation and oxygenation, may still be difficult. Although rates of airway difficulty and intubation success in these patients have been studied, these data may not reflect difficulty with individual components of the intubation process. We hypothesized that rates of complications with individual elements of the intubation process would not be reflected in the rate of eventual intubation success. To test our hypothesis, we observed the process of airway management and resulting complications with oxygenation and bag mask ventilation in patients with oropharyngeal masses undergoing otorhinolaryngology procedures under general anesthesia. METHODS: Forty-four patients with oropharyngeal masses scheduled for surgery were observed during the process of airway management. Observers recorded the number of airway devices used, the overall number of intubation attempts, the number and type of manual maneuvers required during bag mask ventilation, and the incidence of oxygen desaturation. The eventual intubation success rate was also recorded. RESULTS: All 44 patients (100%; 95% CI, 92%-100%) were successfully intubated. Thirty-six (81.8%) of 44 patients were intubated asleep and 8 (18.2%) of 44 were intubated awake using flexible fiberoptic bronchoscopy. Thirty-one (86.1%) of 36 patients who were intubated asleep received bag mask ventilation before intubation, while the other 5 patients underwent a rapid sequence induction. Twenty-seven (61.4%) of 44 patients (95% CI, 45%-75%) had ≥1 complication during airway management. Ten (23%) of 44 patients (95% CI, 11%-37%) required ≥3 attempts to intubate, 21 (68%) of 31 patients (95% CI, 49%-83%) had difficult mask ventilation, and 15 patients (34%; 95% CI, 20%-50%) experienced desaturation (oxygen saturation measured by pulse oximetry, <95%). CONCLUSIONS: We found that, although all patients were successfully intubated, clinicians frequently encountered complications with both intubation and mask ventilation. These complications required frequent use of additional manual maneuvers during mask ventilation and a high incidence of oxygen desaturation. The difficulty of airway management in patients with oropharyngeal masses may not be effectively assessed by success rate alone.

Effects of Cannabidiol on Morphine Conditioned Place Preference in Mice.

This study sought to determine whether the cannabis constituent cannabidiol attenuates the development of morphine reward in the conditioned place preference paradigm. Separate groups of mice received either saline or morphine in combination with one of four doses of cannabidiol using three sets of drug/no-drug conditioning trials. After drug-place conditioning, morphine mice displayed robust place preference that was attenuated by 10 mg/kg cannabidiol. Further, when administered alone, this dose of cannabidiol was void of rewarding and aversive properties. The finding that cannabidiol blocks opioid reward suggests that this compound may be useful in addiction treatment settings.

Effects of Delta-9-Tetrahydrocannabinol and Cannabidiol on Cisplatin-Induced Neuropathy in Mice.

Sativex, a cannabinoid extract with a 1 : 1 ratio of tetrahydocannabinol and cannabidiol, has been shown to alleviate neuropathic pain associated with chemotherapy. This research examined whether tetrahydocannabinol or cannabidiol alone could attenuate or prevent cisplatin-induced tactile allodynia. In experiment 1, mice (C57BL/6) received eight administrations of 2.3 mg/kg cisplatin or saline solution IP every other day to induce tactile allodynia. Mice were then administered vehicle, 100 mg/kg gabapentin, 2 mg/kg tetrahydocannabinol, or 2 mg/kg cannabidiol IP and tested 60 min later on an electronic Von Frey. In experiment 2, prevention studies, cannabidiol (0.0, 0.5, 1.0, and 2.0 mg/kg) or tetrahydocannabinol (0.0, 0.5, 1.0, and 2.0 mg/kg) was given IP 30 min prior to cisplatin administration (2.3 or 1.0 mg/kg) utilizing a six-dose alternate day protocol. In both studies, tactile responses to the hind paws were quantified in g of force using an electronic Von Frey prior to and after the cisplatin administration protocol. Cisplatin produced a reduction in g of force indicative of neuropathy that was attenuated by gabapentin, tetrahydocannabinol, and cannabidiol but not prevented by either cannabinoid. These data demonstrate that each of the major constituents of Sativex alone can achieve analgesic effects against cisplatin neuropathy.

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.

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.

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.

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.