USP7 Acts as a Molecular Rheostat to Promote WASH-Dependent Endosomal Protein Recycling and Is Mutated in a Human Neurodevelopmental Disorder.

Endosomal protein recycling is a fundamental cellular process important for cellular homeostasis, signaling, and fate determination that is implicated in several diseases. WASH is an actin-nucleating protein essential for this process, and its activity is controlled through K63-linked ubiquitination by the MAGE-L2-TRIM27 ubiquitin ligase. Here, we show that the USP7 deubiquitinating enzyme is an integral component of the MAGE-L2-TRIM27 ligase and is essential for WASH-mediated endosomal actin assembly and protein recycling. Mechanistically, USP7 acts as a molecular rheostat to precisely fine-tune endosomal F-actin levels by counteracting TRIM27 auto-ubiquitination/degradation and preventing overactivation of WASH through directly deubiquitinating it. Importantly, we identify de novo heterozygous loss-of-function mutations of USP7 in individuals with a neurodevelopmental disorder, featuring intellectual disability and autism spectrum disorder. These results provide unanticipated insights into endosomal trafficking, illuminate the cooperativity between an ubiquitin ligase and a deubiquitinating enzyme, and establish a role for USP7 in human neurodevelopmental disease.

An inhibitor of complement C5 provides structural insights into activation.

The complement system is a crucial part of innate immune defenses against invading pathogens. The blood-meal of the tick Rhipicephalus pulchellus lasts for days, and the tick must therefore rely on inhibitors to counter complement activation. We have identified a class of inhibitors from tick saliva, the CirpT family, and generated detailed structural data revealing their mechanism of action. We show direct binding of a CirpT to complement C5 and have determined the structure of the C5-CirpT complex by cryoelectron microscopy. This reveals an interaction with the peripheral macro globulin domain 4 (C5_MG4) of C5. To achieve higher resolution detail, the structure of the C5_MG4-CirpT complex was solved by X-ray crystallography (at 2.7 Å). We thus present the fold of the CirpT protein family, and provide detailed mechanistic insights into its inhibitory function. Analysis of the binding interface reveals a mechanism of C5 inhibition, and provides information to expand our biological understanding of the activation of C5, and thus the terminal complement pathway.

Pulmonary gas exchange evaluated by machine learning: a computer simulation.

Using computer simulation we investigated whether machine learning (ML) analysis of selected ICU monitoring data can quantify pulmonary gas exchange in multi-compartment format. A 21 compartment ventilation/perfusion (V/Q) model of pulmonary blood flow processed 34,551 combinations of cardiac output, hemoglobin concentration, standard P50, base excess, VO2 and VCO2 plus three model-defining parameters: shunt, log SD and mean V/Q. From these inputs the model produced paired arterial blood gases, first with the inspired O2 fraction (FiO2) adjusted to arterial saturation (SaO2) = 0.90, and second with FiO2 increased by 0.1. 'Stacked regressor' ML ensembles were trained/validated on 90% of this dataset. The remainder with shunt, log SD, and mean 'held back' formed the test-set. 'Two-Point' ML estimates of shunt, log SD and mean utilized data from both FiO2 settings. 'Single-Point' estimates used only data from SaO2 = 0.90. From 3454 test gas exchange scenarios, two-point shunt, log SD and mean estimates produced linear regression models versus true values with slopes ~ 1.00, intercepts ~ 0.00 and R2 ~ 1.00. Kernel density and Bland-Altman plots confirmed close agreement. Single-point estimates were less accurate: R2 = 0.77-0.89, slope = 0.991-0.993, intercept = 0.009-0.334. ML applications using blood gas, indirect calorimetry, and cardiac output data can quantify pulmonary gas exchange in terms describing a 20 compartment V/Q model of pulmonary blood flow. High fidelity reports require data from two FiO2 settings.

Single-FiO2 lung modelling with machine learning: a computer simulation incorporating volumetric capnography.

We investigated whether machine learning (ML) analysis of ICU monitoring data incorporating volumetric capnography measurements of mean alveolar PCO2 can partition venous admixture (VenAd) into its shunt and low V/Q components without manipulating the inspired oxygen fraction (FiO2). From a 21-compartment ventilation / perfusion (V/Q) model of pulmonary blood flow we generated blood gas and mean alveolar PCO2 data in simulated scenarios with shunt values from 7.3% to 36.5% and a range of FiO2 settings, indirect calorimetry and cardiac output measurements and acid- base and hemoglobin oxygen affinity conditions. A 'deep learning' ML application, trained and validated solely on single FiO2 bedside monitoring data from 14,736 scenarios, then recovered shunt values in 500 test scenarios with true shunt values 'held back'. ML shunt estimates versus true values (n = 500) produced a linear regression model with slope = 0.987, intercept = -0.001 and R2 = 0.999. Kernel density estimate and error plots confirmed close agreement. With corresponding VenAd values calculated from the same bedside data, low V/Q flow can be reported as VenAd-shunt. ML analysis of blood gas, indirect calorimetry, volumetric capnography and cardiac output measurements can quantify pulmonary oxygenation deficits as percentage shunt flow (V/Q = 0) versus percentage low V/Q flow (V/Q > 0). High fidelity reports are possible from analysis of data collected solely at the operating FiO2.

Mouse models of patent ductus arteriosus (PDA) and their relevance for human PDA.

The ductus arteriosus (DA) is a unique fetal vascular shunt, which allows blood to bypass the developing lungs in utero. After birth, changes in complex signaling pathways lead to constriction and permanent closure of the DA. The persistent patency of the DA (PDA) is a common disorder in preterm infants, yet the underlying causes of PDA are not fully defined. Although limits on the availability of human DA tissues prevent comprehensive studies on the mechanisms of DA function, mouse models have been developed that reveal critical pathways in DA regulation. Over 20 different transgenic models of PDA in mice have been described, with implications for human DA biology. Similarly, we enumerate 224 human single-gene syndromes that are associated with PDA, including a small subset that consistently feature PDA as a prominent phenotype. Comparison and functional analyses of these genes provide insight into DA development and identify key regulatory pathways that may serve as potential therapeutic targets for the management of PDA.

The experimental evolution of human culture: flexibility, fidelity and environmental instability.

The past 2 Myr have seen both unprecedented environmental instability and the evolution of the human capacity for complex culture. This, along with the observation that cultural evolution occurs faster than genetic evolution, has led to the suggestion that culture is an adaptation to an unstable environment. We test this hypothesis by examining the ability of human social learning to respond to environmental changes. We do this by inserting human participants (n = 4800) into evolutionary simulations with a changing environment while varying the social information available to individuals across five conditions. We find that human social learning shows some signs of adaptation to environmental instability, including critical social learning, the adoption of up-and-coming traits and, unexpectedly, contrariness. However, these are insufficient to avoid significant fitness declines when the environment changes, and many individuals are highly conformist, which exacerbates the fitness effects of environmental change. We conclude that human social learning reflects a compromise between the competing needs for flexibility to accommodate environmental change and fidelity to accurately transmit valuable cultural information.

Heterozygous Deletion of Long Noncoding RNA AK127244 Is a Susceptibility Factor for Neurodevelopmental Delay.

Neurodevelopmental syndromes due to copy number variation are well-known clinical entities. While the numerical variation of gene-harboring regions has been widely investigated at both molecular and clinical levels, much less is understood about unbalanced expression of long noncoding RNAs. Few studies have been performed on the clinical consequences of such unbalanced expression. Heterozygous deletions of NRXN1 have been well described to cause neuropsychological features. Heterozygous deletion of adjacent long noncoding RNA AK127244, either isolated or combined with partial NRXN1 deletion, was recently reported in association with neurodevelopmental delay. In our retrospective study, we analyze a bicentric cohort of 4 individuals, comprising 2 siblings, which bear an isolated heterozygous deletion in long noncoding RNA AK127244 and present with nonsyndromic neurodevelopmental delay.

Liver Transplantation in Children with Urea Cycle Disorders: The Importance of Minimizing Waiting Time.

Liver transplantation (LT) for children with urea cycle disorders (UCDs) is capable of correcting the enzymatic defect and preventing progressive neurologic injury. We describe the characteristics and outcomes of pediatric LT recipients with UCDs. We identified all pediatric (<18 years) LT candidates with UCDs in the United Network for Organ Sharing (UNOS) database (February 2002 to September 2020). Multivariable Cox and logistic regression were used to determine risk factors for graft loss and cognitive delay, respectively. Of 424 patients, 1.9% (8/424) experienced waitlist mortality and 95.0% underwent LT (403/424). The most frequently encountered UCDs in our cohort were ornithine transcarbamylase deficiency (46.2%), citrullinemia (20.3%), and argininosuccinic aciduria (ASA; 12.9%). The 1-, 3-, and 5-year graft survival rates were 90.4%, 86.3%, and 85.2%, respectively. Multivariable analysis showed a decreased risk of graft loss with increasing weight at LT (adjusted hazard ratio [aHR], 0.96; 95% confidence interval [CI], 0.94-0.99; P = 0.02), male sex (aHR, 0.49; 95% CI, 0.28-0.85; P = 0.01), and ASA diagnosis (aHR, 0.29; 95% CI, 0.09-0.98; P = 0.047), when adjusting for location (intensive care/hospital/home) and graft type (both P ≥ 0.65). In multivariable logistic regression, waitlist time (adjusted odds ratio [aOR], 1.10; 95% CI, 1.02-1.17; P = 0.009) and male sex (aOR, 1.71; 95% CI, 1.02-2.88; P = 0.04) were associated with increased odds of long-term cognitive delay. Waitlist duration is associated with a long-term risk of cognitive delay. Given excellent long-term outcomes, early LT evaluation should be considered in all children with UCDs to prevent progressive neurologic injury and optimize cognitive outcomes.

Nicotine exposure of male mice produces behavioral impairment in multiple generations of descendants.

Use of tobacco products is injurious to health in men and women. However, tobacco use by pregnant women receives greater scrutiny because it can also compromise the health of future generations. More men smoke cigarettes than women. Yet the impact of nicotine use by men upon their descendants has not been as widely scrutinized. We exposed male C57BL/6 mice to nicotine (200 µg/mL in drinking water) for 12 wk and bred the mice with drug-naïve females to produce the F1 generation. Male and female F1 mice were bred with drug-naïve partners to produce the F2 generation. We analyzed spontaneous locomotor activity, working memory, attention, and reversal learning in male and female F1 and F2 mice. Both male and female F1 mice derived from the nicotine-exposed males showed significant increases in spontaneous locomotor activity and significant deficits in reversal learning. The male F1 mice also showed significant deficits in attention, brain monoamine content, and dopamine receptor mRNA expression. Examination of the F2 generation showed that male F2 mice derived from paternally nicotine-exposed female F1 mice had significant deficits in reversal learning. Analysis of epigenetic changes in the spermatozoa of the nicotine-exposed male founders (F0) showed significant changes in global DNA methylation and DNA methylation at promoter regions of the dopamine D2 receptor gene. Our findings show that nicotine exposure of male mice produces behavioral changes in multiple generations of descendants. Nicotine-induced changes in spermatozoal DNA methylation are a plausible mechanism for the transgenerational transmission of the phenotypes. These findings underscore the need to enlarge the current focus of research and public policy targeting nicotine exposure of pregnant mothers by a more equitable focus on nicotine exposure of the mother and the father.

Foraging zebra finches (Taeniopygia guttata) are public information users rather than conformists.

Social learning enables adaptive information acquisition provided that it is not random but selective. To understand species typical decision-making and to trace the evolutionary origins of social learning, the heuristics social learners use need to be identified. Here, we experimentally tested the nature of majority influence in the zebra finch. Subjects simultaneously observed two demonstrator groups differing in relative and absolute numbers (ratios 1 : 2/2 : 4/3 : 3/1 : 5) foraging from two novel food sources (black and white feeders). We find that demonstrator groups influenced observers' feeder choices (social learning), but that zebra finches did not copy the majority of individuals. Instead, observers were influenced by the foraging activity (pecks) of the demonstrators and in an anti-conformist fashion. These results indicate that zebra finches are not conformist, but are public information users.

Tin deposition on ruthenium and its influence on blistering in multi-layer mirrors.

An atomistic description of tin deposition on ruthenium and its effect on blistering damage is of great interest in extreme ultraviolet (EUV) lithography. In EUV machines, tin debris from the EUV-emitting tin plasma may be deposited on the mirrors in the optical path. Tin facilitates the formation of hydrogen-filled blisters under the ruthenium top layer of the multi-layer mirrors. We have used Density Functional Theory (DFT) to show that tin deposition on a clean ruthenium surface exhibits a film-plus-islands (Stranski-Krastanov) growth mode, with the first atomic layer bonding strongly to the substrate. We find that a single tin layer allows hydrogen to reach the ruthenium surface and subsurface more easily than on clean ruthenium, but hydrogen penetration through the tin film becomes progressively more difficult when more layers are added. The results indicate that hydrogen penetration and blistering occur when only a thin layer of tin is present.

Hyperlactatemia in diabetic ketoacidosis is common and can be prolonged: lactate time-series from 25 intensive care admissions.

Hyperlactatemia is a documented complication of diabetic ketoacidosis (DKA). Lactate responses during DKA treatment have not been studied and were the focus of this investigation. Blood gas and electrolyte data from 25 DKA admissions to ICU were sequenced over 24 h from the first Emergency Department sample. Hyperlactatemia (> 2 mmol/L) was present in 22 of 25 DKA presentations [mean concentration = 3.2 mmol/L]. In 18 time-series (72%), all concentrations normalized in ≤ 2.6 h (aggregate decay t1/2 = 2.29 h). In the remaining 7 (28%), hyperlactatemia persisted > 12 h. These were females (P = 0.04) with relative anemia (hemoglobin concentrations 131 v 155 g/L; P = 0.004) and lower nadir glucose concentrations (5.2 v 8.0 mmol/L, P = 0.003). Their aggregate glucose decay curve commenced higher (42 mmol/L v 29 mmol/L), descending towards a lower asymptote (8 mmol/L v 11 mmol/L). Tonicity decay showed similar disparities. There was equivalent resolution of metabolic acidosis and similar lengths of stay in both groups. Hyperlactatemia is common in DKA. Resolution is often rapid, but high lactates can persist. Females with high glucose concentrations corrected aggressively are more at risk. Limiting initial hyperglycemia correction to ≥ 11 mmol/L may benefit.

Duplicated Enhancer Region Increases Expression of CTSB and Segregates with Keratolytic Winter Erythema in South African and Norwegian Families.

Keratolytic winter erythema (KWE) is a rare autosomal-dominant skin disorder characterized by recurrent episodes of palmoplantar erythema and epidermal peeling. KWE was previously mapped to 8p23.1-p22 (KWE critical region) in South African families. Using targeted resequencing of the KWE critical region in five South African families and SNP array and whole-genome sequencing in two Norwegian families, we identified two overlapping tandem duplications of 7.67 kb (South Africans) and 15.93 kb (Norwegians). The duplications segregated with the disease and were located upstream of CTSB, a gene encoding cathepsin B, a cysteine protease involved in keratinocyte homeostasis. Included in the 2.62 kb overlapping region of these duplications is an enhancer element that is active in epidermal keratinocytes. The activity of this enhancer correlated with CTSB expression in normal differentiating keratinocytes and other cell lines, but not with FDFT1 or NEIL2 expression. Gene expression (qPCR) analysis and immunohistochemistry of the palmar epidermis demonstrated significantly increased expression of CTSB, as well as stronger staining of cathepsin B in the stratum granulosum of affected individuals than in that of control individuals. Analysis of higher-order chromatin structure data and RNA polymerase II ChIA-PET data from MCF-7 cells did not suggest remote effects of the enhancer. In conclusion, KWE in South African and Norwegian families is caused by tandem duplications in a non-coding genomic region containing an active enhancer element for CTSB, resulting in upregulation of this gene in affected individuals.

Metabolic Rate Interacts with Resource Availability to Determine Individual Variation in Microhabitat Use in the Wild.

Ecological pressures such as competition can lead individuals within a population to partition resources or habitats, but the underlying intrinsic mechanisms that determine an individual's resource use are not well understood. Here we show that an individual's own energy demand and associated competitive ability influence its resource use, but only when food is more limiting. We tested whether intraspecific variation in metabolic rate leads to microhabitat partitioning among juvenile Atlantic salmon (Salmo salar) in natural streams subjected to manipulated nutrient levels and subsequent per capita food availability. We found that individual salmon from families with a higher baseline (standard) metabolic rate (which is associated with greater competitive ability) tended to occupy faster-flowing water, but only in streams with lower per capita food availability. Faster-flowing microhabitats yield more food, but high metabolic rate fish only benefited from faster growth in streams with high food levels, presumably because in low-food environments the cost of a high metabolism offsets the benefits of acquiring a productive microhabitat. The benefits of a given metabolic rate were thus context dependent. These results demonstrate that intraspecific variation in metabolic rate can interact with resource availability to determine the spatial structuring of wild populations.

Limitations of exome sequencing in detecting rare and undiagnosed diseases.

While exome sequencing (ES) is commonly the final diagnostic step in clinical genetics, it may miss diagnoses. To clarify the limitations of ES, we investigated the diagnostic yield of genetic tests beyond ES in our Undiagnosed Diseases Network (UDN) participants. We reviewed the yield of additional genetic testing including genome sequencing (GS), copy number variant (CNV), noncoding variant (NCV), repeat expansion (RE), or methylation testing in UDN cases with nondiagnostic ES results. Overall, 36/54 (67%) of total diagnoses were based on clinical findings and coding variants found by ES and 3/54 (6%) were based on clinical findings only. The remaining 15/54 (28%) required testing beyond ES. Of these, 7/15 (47%) had NCV, 6/15 (40%) CNV, and 2/15 (13%) had a RE or a DNA methylation disorder. Thus 18/54 (33%) of diagnoses were not solved exclusively by ES. Several methods were needed to detect and/or confirm the functional effects of the variants missed by ES, and in some cases by GS. These results indicate that tests to detect elusive variants should be considered after nondiagnostic preliminary steps. Further studies are needed to determine the cost-effectiveness of tests beyond ES that provide diagnoses and insights to possible treatment.

Biased transformation erases traditions sustained by conformist transmission.

Conformist transmission is a cognitively simple decision-making process by which observers are disproportionately likely to follow the majority. It has been studied in multiple species because theory suggests it can create stable cultural variation. However, the current theory assumes that while conformist transmission favours the majority, it is otherwise unbiased and does not systematically transform information, even though such biases are widely documented. Here, we relax this assumption, requiring conformist observers to infer the size of the majority from finite observations of their group mates. Because such inference can be subject to bias, it can lead to the biased transformation of transmitted information. We find that when individuals are biased (even weakly) the capacity of conformist transmission to sustain traditions is reduced and, in many cases, removed entirely. This suggests that the emphasis on conformist transmission as a source of stable cultural variation may be misplaced.

Liver Transplantation for Propionic Acidemia: A Multicenter-linked Database Analysis.

OBJECTIVES: Propionic acidemia (PA) is a rare inborn error of metabolism resulting from deficiency in the enzyme necessary for catabolism of branched-chain amino acids, some odd chain fatty acids and cholesterol. Despite optimal medical management, PA often leads to acute and progressive neurological injury. Reports on liver transplantation (LT) as a cellular therapy are limited and varied. The objective of this study was to examine the largest collection of patients who underwent LT for PA. METHODS: Examining the Scientific Registry of Transplant Recipients and the Pediatric Health Information System administrative billing databases, we performed a multicenter, retrospective analysis of LT over a 16-year period. During this period, 4849 pediatric LT were performed out of which 23 were done for PA at 10 different centers. RESULTS: The majority of recipients were 5 years of age or younger and had status 1b exception points at the time of transplant. The 1-, 3-, and 5-year graft survival for PA LT recipients was 84.6% and the 1-, 3, and 5-year patient survival was 89.5%. There was no significant difference in graft or patient survival between PA and non-PA LT recipients. Despite historical data to the contrary, we did not find an increased incidence of hepatic arterial thrombosis in patients undergoing LT for PA. Patients in the PA LT group, however, had a significantly higher postoperative rate of readmission compared with the non-PA LT group (90.5% vs 72.8%, P = 0.021). CONCLUSION: LT for children with PA is a viable treatment option with acceptable outcomes.

Hydrogen diffusion out of ruthenium-an ab initio study of the role of adsorbates.

Hydrogen permeation into mirrors used in extreme ultraviolet lithography results in the formation of blisters, which are detrimental to reflectivity. An understanding of the mechanism via which hydrogen ends up at the interface between the top ruthenium layer and the underlying bilayers is necessary to mitigate the blistering damage. In this study, we use density functional theory to examine the ways in which hydrogen, having entered the near-surface interstitial voids, can migrate further into the metal or to its surface. We show that with hydrogen and tin adsorbed on the ruthenium surface, diffusion to the surface is blocked for interstitial hydrogen in the metal, making diffusion further into the metal more likely than out-diffusion. The dependence on surface conditions matches and confirms similar findings on hydrogen permeation into metals. This suggests control and modification of surface conditions as a way to influence hydrogen retention and blistering.

Reducing complexity in acid-base diagnosis - how far should we go?

PURPOSE: To place in context the potential value of isolated plasma strong ion difference (SID) calculations and strong ion gap (SIG) calculations versus suggested cut-down versions such as SIDa adj and the BICgap respectively. METHODS: Stewart's physical chemical approach is seen as a mathematical model of isolated plasma not displacing traditional Copenhagen and Boston approaches. Scanning tools for unmeasured ions based on the Principle of Electrical Neutrality such as the SIG and suggested cut-down versions such as the albumin adjusted anion gap and the BICgap are evaluated for accuracy and clinical usefulness. RESULTS: Plasma SID and abbreviations such as SIDa adj are not independent variables in vivo since they vary with PCO due to Gibbs Donnan ion traffic. They can also exhibit positive and negative bias, and SID values must be partnered with non-volatile weak acid concentrations when evaluating metabolic acid-base status. The BICgap calculation is a cut down version of the SIG fixed for pH 7.4. It includes phosphate but is otherwise similar in form to the albumin corrected anion gap, with similar sensitivity and specificity characteristics. CONCLUSIONS: Clinicians are unlikely to find SID calculations or cut-down versions such as the SIDa adj clinically useful. The albumin corrected anion gap is in current use and easily determined by mental arithmetic from point of care anion gap printouts plus recent plasma albumin measurements. Any slight advantage of the BICgap would be offset by the complexity of its calculation.

A theory limited in scope and evidence.

What promised to be a refreshing addition to cumulative cultural evolution, by moving the focus from cultural transmission to technological innovation, falls flat through a lack of thoroughness, explanatory power, and data. A comprehensive theory of cumulative cultural change must carefully integrate all existing evidence in a cohesive multi-level account. We argue that the manuscript fails to do so convincingly.