Cut-and-Run: A Distinct Mechanism by which V(D)J Recombination Causes Genome Instability.

V(D)J recombination is essential to generate antigen receptor diversity but is also a potent cause of genome instability. Many chromosome alterations that result from aberrant V(D)J recombination involve breaks at single recombination signal sequences (RSSs). A long-standing question, however, is how such breaks occur. Here, we show that the genomic DNA that is excised during recombination, the excised signal circle (ESC), forms a complex with the recombinase proteins to efficiently catalyze breaks at single RSSs both in vitro and in vivo. Following cutting, the RSS is released while the ESC-recombinase complex remains intact to potentially trigger breaks at further RSSs. Consistent with this, chromosome breaks at RSSs increase markedly in the presence of the ESC. Notably, these breaks co-localize with those found in acute lymphoblastic leukemia patients and occur at key cancer driver genes. We have named this reaction "cut-and-run" and suggest that it could be a significant cause of lymphocyte genome instability.

A human genome editing-based MLL::AF4 ALL model recapitulates key cellular and molecular leukemogenic features.

Cellular ontogeny and MLL breakpoint site influence the capacity of MLL-edited CD34+ hematopoietic cells to initiate and recapitulate infant patients' features in pro-B-cell acute lymphoblastic leukemia (B-ALL). We provide key insights into the leukemogenic determinants of MLL-AF4+ infant B-ALL.

Temporal analyses reveal a pivotal role for sense and antisense enhancer RNAs in coordinate immunoglobulin lambda locus activation.

Transcription enhancers are essential activators of V(D)J recombination that orchestrate non-coding transcription through complementary, unrearranged gene segments. How transcription is coordinately increased at spatially distinct promoters, however, remains poorly understood. Using the murine immunoglobulin lambda (Igλ) locus as model, we find that three enhancer-like elements in the 3' Igλ domain, Eλ3-1, HSCλ1 and HSE-1, show strikingly similar transcription factor binding dynamics and close spatial proximity, suggesting that they form an active enhancer hub. Temporal analyses show coordinate recruitment of complementary V and J gene segments to this hub, with comparable transcription factor binding dynamics to that at enhancers. We find further that E2A, p300, Mediator and Integrator bind to enhancers as early events, whereas YY1 recruitment and eRNA synthesis occur later, corresponding to transcription activation. Remarkably, the interplay between sense and antisense enhancer RNA is central to both active enhancer hub formation and coordinate Igλ transcription: Antisense Eλ3-1 eRNA represses Igλ activation whereas temporal analyses demonstrate that accumulating levels of sense eRNA boost YY1 recruitment to stabilise enhancer hub/promoter interactions and lead to coordinate transcription activation. These studies therefore demonstrate for the first time a critical role for threshold levels of sense versus antisense eRNA in locus activation.

Visuospatial memory in apraxia: Exploring quantitative drawing metrics to assess the representation of local and global information.

Neuropsychological evidence suggests that visuospatial memory is subserved by two separable processing systems, with dorsal underpinnings for global form and ventral underpinnings for the integration of part elements. Previous drawing studies have explored the effects of Gestalt organisation upon memory for hierarchical stimuli, and we here present an exploratory study of an apraxic dorsal stream patient's (MH) performance. We presented MH with a stimulus set (previously reported by Riddoch et al., Cognitive Neuropsychology, 20(7), 641-671, 2003) and devised a novel quantitative scoring system to obtain a finer grain of insight into performance. Stimuli possessed either good or poor Gestalt qualities and were reproduced in a copy condition and two visual memory conditions (with unlimited viewing before the model was removed, or with 3 s viewing). MH's copying performance was impaired in comparison to younger adult and age-matched older adult controls, with a variety of errors at the local level but relatively few at the global level. However, his performance in the visual memory conditions revealed impairments at the global level. For all participants, drawing errors were modulated by the Gestalt qualities of the stimuli, with accuracy at the global and local levels being lesser for poor global stimuli in all conditions. These data extend previous observations of this patient, and support theories that posit interaction between dorsal and ventral streams in the representation of hierarchical stimuli. We discuss the implications of these findings for our understanding of visuospatial memory in neurological patients, and also evaluate the application of quantitative metrics to the interpretation of drawings.

Paediatric playground and tree-related injuries: Hospital admissions in the Midland region of New Zealand.

AIM: To examine the incidence and outcomes of paediatric playground and tree-related injuries in the Midland region of New Zealand. METHODS: A retrospective review of Midland Trauma Registry hospitalisation data between January 2012 and December 2018 was undertaken. Cases included children aged 0-14 years hospitalised for playground and tree-related injuries. Demographic and event information, injury severity and hospital-related outcomes were examined. RESULTS: Playground and tree-related hospitalisations (n = 1941) occurred with an age-standardised rate of 144.3/100 000 (confidence interval (CI) 127.3-161.3) and increased 1.4% (CI 1.3-4.2%) annually. The highest incidence was observed in 5-9-year olds (248.8/100 000) with 0-4 and 10-14-year olds at 86.0 and 89.2/100 000, respectively. Injuries most commonly occurred at home, school or pre-school (77.1%), 93.7% were due to falls and, the upper extremity was the most frequently injured body region (69.9%), particularly due to forearm (55.6%) and upper arm (34.7%) fractures. Tree-related incidents comprised 11.6% of all injuries and explained 57.1% of injuries classified as major severity. Fifty-eight percent of children were hospitalised for 1 day and 97.0% for less than 5 days. Estimated hospital costs were NZ$1.2 million annually with a median of NZ$3898 per incident. Injuries classified as minor severity accounted for 86.5% of the total estimated cost. CONCLUSION: Children aged 5-9 years' experience high rates of costly hospitalisation for playground and tree-related injuries. Targeted injury prevention initiatives, particularly in the home and school environments, are imperative to reduce the incidence and burden of playground and tree-related injuries to affected children, their families and hospital resources.

Thinking outside of the box II: Disrupting the cognitive map.

A number of influential spatial learning theories posit that organisms encode a viewpoint independent (i.e. allocentric) representation of the global boundary shape of their environment in order to support spatial reorientation and place learning. In contrast to the trial and error learning mechanisms that support domain-general processes, a representation of the global-shape of the environment is thought to be encoded automatically as part of a cognitive map, and without interference from other spatial cues. To date, however, this core theoretical assumption has not been appropriately examined. This is because previous attempts to address this question have failed to employ tasks that fully dissociate reorientation based on an allocentric representation of global-shape from egocentric reorientation strategies. Here, we address this issue in two experiments. Participants were trained to navigate to a hidden goal on one side of a virtual arena (e.g. the inside) before being required to find the same point on the alternative side (e.g. the outside). At test, performing the correct search behaviour requires an allocentric representation of the global boundary-shape. Using established associative learning procedures of overshadowing and blocking, we find that search behaviour at test is disrupted when participants were able to form landmark-goal associations during training. These results demonstrate that encoding of an allocentric representation of boundary information is susceptible to interference from landmark cues, and is not acquired through special means. Instead, the results suggest that allocentric representations of environmental boundaries are acquired through the same kind of error-correction mechanisms that support domain-general non-spatial learning.

Cultural differences in attention: Eye movement evidence from a comparative visual search task.

Individual differences in visual attention have been linked to thinking style: analytic thinking (common in individualistic cultures) is thought to promote attention to detail and focus on the most important part of a scene, whereas holistic thinking (common in collectivist cultures) promotes attention to the global structure of a scene and the relationship between its parts. However, this theory is primarily based on relatively simple judgement tasks. We compared groups from Great Britain (an individualist culture) and Saudi Arabia (a collectivist culture) on a more complex comparative visual search task, using simple natural scenes. A higher overall number of fixations for Saudi participants, along with longer search times, indicated less efficient search behaviour than British participants. Furthermore, intra-group comparisons of scan-path for Saudi participants revealed less similarity than within the British group. Together, these findings suggest that there is a positive relationship between an analytic cognitive style and controlled attention.

Outcomes in Adults With Acute Liver Failure Between 1998 and 2013: An Observational Cohort Study.

BACKGROUND: Acute liver failure (ALF) is a rare syndrome of severe, rapid-onset hepatic dysfunction-without prior advanced liver disease-that is associated with high morbidity and mortality. Intensive care and liver transplantation provide support and rescue, respectively. OBJECTIVE: To determine whether changes in causes, disease severity, treatment, or 21-day outcomes have occurred in recent years among adult patients with ALF referred to U.S. tertiary care centers. DESIGN: Prospective observational cohort study. (ClinicalTrials .gov: NCT00518440). SETTING: 31 liver disease and transplant centers in the United States. PATIENTS: Consecutively enrolled patients-without prior advanced liver disease-with ALF (n = 2070). MEASUREMENTS: Clinical features, treatment, and 21-day outcomes were compared over time annually for trends and were also stratified into two 8-year periods (1998 to 2005 and 2006 to 2013). RESULTS: Overall clinical characteristics, disease severity, and distribution of causes remained similar throughout the study period. The 21-day survival rates increased between the two 8-year periods (overall, 67.1% vs. 75.3%; transplant-free survival [TFS], 45.1% vs. 56.2%; posttransplantation survival, 88.3% vs. 96.3% [P < 0.010 for each]). Reductions in red blood cell infusions (44.3% vs. 27.6%), plasma infusions (65.2% vs. 47.1%), mechanical ventilation (65.7% vs. 56.1%), and vasopressors (34.9% vs. 27.8%) were observed, as well as increased use of N-acetylcysteine (48.9% vs. 69.3% overall; 15.8% vs. 49.4% [P < 0.001] in patients with ALF not due to acetaminophen toxicity). When examined longitudinally, overall survival and TFS increased throughout the 16-year period. LIMITATIONS: The duration of enrollment, the number of patients enrolled, and possibly the approaches to care varied among participating sites. The results may not be generalizable beyond such specialized centers. CONCLUSION: Although characteristics and severity of ALF changed little over 16 years, overall survival and TFS improved significantly. The effects of specific changes in intensive care practice on survival warrant further study. PRIMARY FUNDING SOURCE: National Institutes of Health.

Thinking outside of the box: Transfer of shape-based reorientation across the boundary of an arena.

The way in which human and non-human animals represent the shape of their environments remains a contentious issue. According to local theories of shape learning, organisms encode the local geometric features of the environment that signal a goal location. In contrast, global theories of shape learning suggest that organisms encode the overall shape of the environment. There is, however, a surprising lack of evidence to support this latter claim, despite the fact that common behaviours seem to require encoding of the global-shape of an environment. We tested one such behaviour in 5 experiments, in which human participants were trained to navigate to a hidden goal on one side of a virtual arena (e.g. the inside) before being required to find the same point on the alternative side (e.g. the outside). Participants navigated to the appropriate goal location, both when inside and outside the virtual arena, but only when the shape of the arena remained the same between training and test (Experiments 1a and 1b). When the arena shape was transformed between these stages, participants were lost (Experiments 2a and 2b). When training and testing was conducted on the outside of two different-shaped arenas that shared local geometric cues participants once again explored the appropriate goal location (Experiment 3). These results provide core evidence that humans encode a global representation of the overall shape of the environments in, or around, which they navigate.

Gender and menopause impact severity of fibrosis among patients with nonalcoholic steatohepatitis.

UNLABELLED: Estrogens inhibit stellate cell activation and fibrogenesis. Thus, gender and reproductive states may influence the degree of fibrosis in patients with nonalcoholic steatohepatitis (NASH). To investigate the association between gender, menopause, and the severity of liver fibrosis in patients with NASH, we analyzed 541 adult patients enrolled from our Duke Liver Clinics (n = 338) and the Duke Metabolic and Weight Loss Surgery Program (n = 203) who had a histologic diagnosis of NASH. Multiple ordinal logistic regression models were used to assess the association between gender, menopause, and severity of liver fibrosis. Overall, men, premenopausal, and postmenopausal women composed 35.1%, 28.4%, and 36.5% of the population, respectively. The mean age was 48 years and 22% had advanced fibrosis. After adjusting for covariates (enrolling site, grades of portal inflammation, and hepatocyte ballooning) and potential confounders (race, body mass index, diabetes/prediabetes, hypertension), adjusted cumulative odd ratio (ACOR) and 95% confidence interval (CI) for greater fibrosis severity was 1.4 (0.9, 2.1) (P = 0.17) for postmenopausal women and 1.6 (1.0, 2.5) (P = 0.03) for men, having premenopausal women as a reference. There was borderline interaction between gender and age group divided by age 50, the average age at menopause in the U.S. (P = 0.08): ACOR and 95% CI of having greater fibrosis severity in men compared to women was 1.8 (1.1, 2.9) for patients with age <50 years (P = 0.02) and 1.2 (0.7, 2.1) for patients with age ≥50 years (P = 0.59). CONCLUSION: Men are at a higher risk of having more severe fibrosis compared to women before menopause, while postmenopausal women have a similar severity of liver fibrosis compared to men. These findings may be explained by the protective effects of estrogen against fibrogenesis.

Autoimmune hepatitis.

Autoimmune hepatitis is a disease of the hepatic parenchyma that can present in acute or chronic forms. In common with many autoimmune diseases, autoimmune hepatitis is associated with non-organ-specific antibodies in the context of hepatic autoimmunity. This dichotomy has made definition of a unifying hypothesis in the pathophysiology of the disease difficult, although data from the past 8 years have drawn attention to the role of regulatory T cells. Several triggers have been identified, and the disease arises in genetically susceptible individuals. Clinical and biochemical remission is achievable in up to 85% of cases. For the remaining patients, alternative immunosuppression strategies are an option. Liver transplantation provides an excellent outcome for patients with acute liver failure or complications of end-stage liver disease, including hepatocellular carcinoma. Variant or overlapping syndromes are worthy of consideration when unexpected disease features arise.

Literacy effects on language and vision: emergent effects from an amodal shared resource (ASR) computational model.

Learning to read and write requires an individual to connect additional orthographic representations to pre-existing mappings between phonological and semantic representations of words. Past empirical results suggest that the process of learning to read and write (at least in alphabetic languages) elicits changes in the language processing system, by either increasing the cognitive efficiency of mapping between representations associated with a word, or by changing the granularity of phonological processing of spoken language, or through a combination of both. Behavioural effects of literacy have typically been assessed in offline explicit tasks that have addressed only phonological processing. However, a recent eye tracking study compared high and low literate participants on effects of phonology and semantics in processing measured implicitly using eye movements. High literates' eye movements were more affected by phonological overlap in online speech than low literates, with only subtle differences observed in semantics. We determined whether these effects were due to cognitive efficiency and/or granularity of speech processing in a multimodal model of speech processing - the amodal shared resource model (ASR, Smith, Monaghan, & Huettig, 2013a,b). We found that cognitive efficiency in the model had only a marginal effect on semantic processing and did not affect performance for phonological processing, whereas fine-grained versus coarse-grained phonological representations in the model simulated the high/low literacy effects on phonological processing, suggesting that literacy has a focused effect in changing the grain-size of phonological mappings.

Children with autism are neither systematic nor optimal foragers.

It is well established that children with autism often show outstanding visual search skills. To date, however, no study has tested whether these skills, usually assessed on a table-top or computer, translate to more true-to-life settings. One prominent account of autism, Baron-Cohen's "systemizing" theory, gives us good reason to suspect that they should. In this study, we tested whether autistic children's exceptional skills at small-scale search extend to a large-scale environment and, in so doing, tested key claims of the systemizing account. Twenty school-age children with autism and 20 age- and ability-matched typical children took part in a large-scale search task in the "foraging room": a purpose-built laboratory, with numerous possible search locations embedded into the floor. Children were instructed to search an array of 16 (green) locations to find the hidden (red) target as quickly as possible. The distribution of target locations was manipulated so that they appeared on one side of the midline for 80% of trials. Contrary to predictions of the systemizing account, autistic children's search behavior was much less efficient than that of typical children: they showed reduced sensitivity to the statistical properties of the search array, and furthermore, their search patterns were strikingly less optimal and less systematic. The nature of large-scale search behavior in autism cannot therefore be explained by a facility for systemizing. Rather, children with autism showed difficulties exploring and exploiting the large-scale space, which might instead be attributed to constraints (rather than benefits) in their cognitive repertoire.

Assessing the relationship between eating disorder psychopathology and autistic traits in a non-clinical adult population.

PURPOSE: Previous research demonstrates a genetic and behavioural link between eating disorders and autism spectrum disorders, and a recent study (Coombs et al. in Br J Clin Psychol 50:326-338, 2011) extends this link to typical populations, showing a positive correlation between behaviours in typically developing children. The purpose of the present study was to examine whether this relationship continues beyond development, by studying the link between behaviours in a non-clinical adult population. METHODS: We examined associations between performance on measures relating to autistic traits and disordered eating. Undergraduate students, equally balanced by gender and by subject studied (i.e. humanity or science), completed three tasks: to measure autistic traits, participants were administered the Embedded Figures Test (EFT) and the Autism-Spectrum Quotient (AQ). Eating disorder symptomatology was measured by the Eating Attitudes Test (Eat-26). RESULTS: Our data revealed a significant positive correlation between scores on the AQ and Eat-26. Multiple linear regressions showed that higher scores on the AQ were particularly associated with higher scores on the Bulimia & Food Preoccupation subscale of the Eat-26. EFT performance was positively related to behaviours associated with autism and eating disorders, although not reliably so. CONCLUSIONS: These data support the broader link between autistic traits and disordered eating in the non-clinical population, and demonstrate that it extends into adulthood (a time at which autistic behaviours can decrease). This work carries implications for the development of cognitive therapies for people with eating disorders.

Liver function and portal-systemic shunting quantified by the oral cholate challenge test and risk for large oesophageal varices.

BACKGROUND: The quantitative HepQuant SHUNT test of liver function and physiology generates a disease severity index (DSI) that correlates with risk for clinical complications, such as large oesophageal varices (LEVs). A derivative test, HepQuant DuO, generates an equivalent DSI and simplifies testing by requiring only oral administration of the test solution and two blood samples at 20 and 60 min. AIMS: Since the DSIs measured from DuO and SHUNT are equivalent, we compared the diagnostic performance for large oesophageal varices (LEVs) between the DSIs measured from DuO and SHUNT tests. METHODS: This study combined the data from two prospectively conducted US studies: HALT-C and SHUNT-V. A total of 455 subjects underwent both the SHUNT test and esophagogastroduodenoscopy (EGD). RESULTS: DSI scores correlated with the probability of LEVs (p < 0.001) and demonstrated a stepwise increase from healthy lean controls without liver disease to subjects with chronic liver disease and no, small or large varices. Furthermore, a cutoff of DSI ≤ 18.3 from DuO had a sensitivity of 0.98 (missing only one case) and, if applied to the endoscopy (EGD) decision, would have prevented 188 EGDs (41.3%). The AUROC for DSI from DuO did not differ from that of the reference SHUNT test method (0.82 versus 0.81, p = 0.3500). CONCLUSIONS: DSI from HepQuant DuO links liver function and physiology to the risk of LEVs across a wide spectrum of patient characteristics, disease aetiologies and liver disease severity. DuO is minimally invasive, easy to administer, quantitative and may aid the decision to avoid or perform EGD for LEVs.

Associations of depression, anxiety and antidepressants with histological severity of nonalcoholic fatty liver disease.

BACKGROUND: Depression and anxiety are common in patients with nonalcoholic fatty liver disease (NAFLD). However, their associations with histological severity of NAFLD are unknown. AIM: This study examined the association(s) of depression, anxiety and antidepressant pharmacotherapy with severity of histological features in patients with NAFLD. METHODS: We analysed 567 patients with biopsy-proven NAFLD enrolled in the Duke NAFLD Clinical Database. Depressive and anxiety symptoms were assessed using the Hospital Anxiety & Depression Scale (HADS). The associations of depression and anxiety with severity of histological features of NAFLD were analysed using multiple logistic (or ordinal logistic) regression models with and without adjusting for confounding factors. RESULT: Subclinical and clinical depression was noted in 53% and 14% of patients respectively. Subclinical and clinical anxiety was noted in 45% and 25% of patients respectively. After adjusting for confounders, depression was significantly associated with more severe hepatocyte ballooning in a dose-dependent manner (likelihood ratio test, P = 0.0201); adjusted cumulative odds ratio (COR) of subclinical and clinical depression for having a higher grade of hepatocyte ballooning were 2.1 [95% CI, 1.0, 4.4] and 3.6 [95% CI, 1.4, 8.8]. CONCLUSIONS: In patients with NAFLD, depression was associated with more severe hepatocyte ballooning. Further investigation exploring pathobiological mechanisms underlying the observed associations and potential effects of antidepressant pharmacotherapy on NAFLD liver histology is warranted.

Covered transjugular intrahepatic portosystemic shunts: accuracy of ultrasound in detecting shunt malfunction.

OBJECTIVE: The purpose of this study was to determine the accuracy of ultrasound for detecting transjugular intrahepatic portosystemic shunt (TIPS) malfunction in covered stents in comparison with bare metal stents. MATERIALS AND METHODS: During a 6-year period, 126 TIPS angiography examinations were performed in 78 patients who had undergone a recent TIPS ultrasound examination. Radiology reports and images were retrospectively reviewed, and the sensitivity and specificity of sonographic parameters for detecting TIPS dysfunction were calculated using TIPS angiography and portosystemic gradient as the reference standards. RESULTS: Of 126 paired studies, 43 were in bare metal TIPS and 83 were in covered TIPS. Peak shunt velocity of covered and bare metal TIPS measured by ultrasound showed comparable sensitivities for detection of shunt dysfunction, using both depressed (< 90 cm/s) and elevated (> 200 cm/s) peak shunt velocity criteria. However, a depressed velocity was more specific in covered TIPS (0.939 vs 0.550, p < 0.001) whereas elevated velocity was more specific in bare TIPS (0.485 vs 0.800, p = 0.041). An interval change in peak TIPS velocity greater than 25% was significantly more sensitive in detection of dysfunction in covered TIPS (0.815 vs 0.400, p = 0.015) whereas detection based on main portal vein velocities (≤ 30 cm/s) was not statistically different in the two groups. CONCLUSION: Our data suggest that the accuracy of ultrasound for detection of TIPS shunt malfunction is at least as high in covered stents as in bare metal stents. Diagnostic performance for several sonographic parameters varied significantly between bare and covered stents, suggesting the need for optimization of sonographic criteria for covered stents.

The development of path integration: combining estimations of distance and heading.

Efficient daily navigation is underpinned by path integration, the mechanism by which we use self-movement information to update our position in space. This process is well understood in adulthood, but there has been relatively little study of path integration in childhood, leading to an underrepresentation in accounts of navigational development. Previous research has shown that calculation of distance and heading both tend to be less accurate in children as they are in adults, although there have been no studies of the combined calculation of distance and heading that typifies naturalistic path integration. In the present study, 5-year-olds and 7-year-olds took part in a triangle-completion task, where they were required to return to the start point of a multi-element path using only idiothetic information. Performance was compared to a sample of adult participants, who were found to be more accurate than children on measures of landing error, heading error, and distance error. Seven-year-olds were significantly more accurate than 5-year-olds on measures of landing error and heading error, although the difference between groups was much smaller for distance error. All measures were reliably correlated with age, demonstrating a clear development of path integration abilities within the age range tested. Taken together, these data make a strong case for the inclusion of path integration within developmental models of spatial navigational processing.

Evidence for spatial navigational impairments in hydrocephalus patients without spina bifida.

The cognitive sequelae of hydrocephalus have mostly been explored with standardised clinical tasks. The aim of the present research was determine whether impairments on these abstract tasks extend to everyday spatial and navigational behaviour. Patients with hydrocephalus, but without spina bifida, were compared to a control group on tests of searching behaviour, landmark memory, route learning, and path integration. Participants with hydrocephalus displayed reduced sensitivity to spatial cueing, less accurate route-learning, and significantly less accurate spatial updating. These data represent an important empirical demonstration of spatial navigational impairments due to hydrocephalus outside of the context of spina bifida. We discuss some of the cognitive, neural, and individual differences factors that might contribute to this particular pattern of impairments.