A genomic mutational constraint map using variation in 76,156 human genomes.

The depletion of disruptive variation caused by purifying natural selection (constraint) has been widely used to investigate protein-coding genes underlying human disorders1-4, but attempts to assess constraint for non-protein-coding regions have proved more difficult. Here we aggregate, process and release a dataset of 76,156 human genomes from the Genome Aggregation Database (gnomAD)-the largest public open-access human genome allele frequency reference dataset-and use it to build a genomic constraint map for the whole genome (genomic non-coding constraint of haploinsufficient variation (Gnocchi)). We present a refined mutational model that incorporates local sequence context and regional genomic features to detect depletions of variation. As expected, the average constraint for protein-coding sequences is stronger than that for non-coding regions. Within the non-coding genome, constrained regions are enriched for known regulatory elements and variants that are implicated in complex human diseases and traits, facilitating the triangulation of biological annotation, disease association and natural selection to non-coding DNA analysis. More constrained regulatory elements tend to regulate more constrained protein-coding genes, which in turn suggests that non-coding constraint can aid the identification of constrained genes that are as yet unrecognized by current gene constraint metrics. We demonstrate that this genome-wide constraint map improves the identification and interpretation of functional human genetic variation.

Superstructure control of first-cycle voltage hysteresis in oxygen-redox cathodes.

In conventional intercalation cathodes, alkali metal ions can move in and out of a layered material with the charge being compensated for by reversible reduction and oxidation of the transition metal ions. If the cathode material used in a lithium-ion or sodium-ion battery is alkali-rich, this can increase the battery's energy density by storing charge on the oxide and the transition metal ions, rather than on the transition metal alone1-10. There is a high voltage associated with oxidation of O2- during the first charge, but this is not recovered on discharge, resulting in reduced energy density11. Displacement of transition metal ions into the alkali metal layers has been proposed to explain the first-cycle voltage loss (hysteresis)9,12-16. By comparing two closely related intercalation cathodes, Na0.75[Li0.25Mn0.75]O2 and Na0.6[Li0.2Mn0.8]O2, here we show that the first-cycle voltage hysteresis is determined by the superstructure in the cathode, specifically the local ordering of lithium and transition metal ions in the transition metal layers. The honeycomb superstructure of Na0.75[Li0.25Mn0.75]O2, present in almost all oxygen-redox compounds, is lost on charging, driven in part by formation of molecular O2 inside the solid. The O2 molecules are cleaved on discharge, reforming O2-, but the manganese ions have migrated within the plane, changing the coordination around O2- and lowering the voltage on discharge. The ribbon superstructure in Na0.6[Li0.2Mn0.8]O2 inhibits manganese disorder and hence O2 formation, suppressing hysteresis and promoting stable electron holes on O2- that are revealed by X-ray absorption spectroscopy. The results show that voltage hysteresis can be avoided in oxygen-redox cathodes by forming materials with a ribbon superstructure in the transition metal layers that suppresses migration of the transition metal.

A structural variation reference for medical and population genetics.

Structural variants (SVs) rearrange large segments of DNA1 and can have profound consequences in evolution and human disease2,3. As national biobanks, disease-association studies, and clinical genetic testing have grown increasingly reliant on genome sequencing, population references such as the Genome Aggregation Database (gnomAD)4 have become integral in the interpretation of single-nucleotide variants (SNVs)5. However, there are no reference maps of SVs from high-coverage genome sequencing comparable to those for SNVs. Here we present a reference of sequence-resolved SVs constructed from 14,891 genomes across diverse global populations (54% non-European) in gnomAD. We discovered a rich and complex landscape of 433,371 SVs, from which we estimate that SVs are responsible for 25-29% of all rare protein-truncating events per genome. We found strong correlations between natural selection against damaging SNVs and rare SVs that disrupt or duplicate protein-coding sequence, which suggests that genes that are highly intolerant to loss-of-function are also sensitive to increased dosage6. We also uncovered modest selection against noncoding SVs in cis-regulatory elements, although selection against protein-truncating SVs was stronger than all noncoding effects. Finally, we identified very large (over one megabase), rare SVs in 3.9% of samples, and estimate that 0.13% of individuals may carry an SV that meets the existing criteria for clinically important incidental findings7. This SV resource is freely distributed via the gnomAD browser8 and will have broad utility in population genetics, disease-association studies, and diagnostic screening.

The mutational constraint spectrum quantified from variation in 141,456 humans.

Genetic variants that inactivate protein-coding genes are a powerful source of information about the phenotypic consequences of gene disruption: genes that are crucial for the function of an organism will be depleted of such variants in natural populations, whereas non-essential genes will tolerate their accumulation. However, predicted loss-of-function variants are enriched for annotation errors, and tend to be found at extremely low frequencies, so their analysis requires careful variant annotation and very large sample sizes1. Here we describe the aggregation of 125,748 exomes and 15,708 genomes from human sequencing studies into the Genome Aggregation Database (gnomAD). We identify 443,769 high-confidence predicted loss-of-function variants in this cohort after filtering for artefacts caused by sequencing and annotation errors. Using an improved model of human mutation rates, we classify human protein-coding genes along a spectrum that represents tolerance to inactivation, validate this classification using data from model organisms and engineered human cells, and show that it can be used to improve the power of gene discovery for both common and rare diseases.

Vibrationally-resolved RIXS reveals OH-group formation in oxygen redox active Li-ion battery cathodes.

Vibrationally-resolved resonant inelastic X-ray scattering (VR-RIXS) at the O K-edge is emerging as a powerful tool for identifying embedded molecules in lithium-ion battery cathodes. Here, we investigate two known oxygen redox-active cathode materials: the commercial LixNi0.90Co0.05Al0.05O2 (NCA) used in electric vehicles and the high-capacity cathode material Li1.2Ni0.13Co0.13Mn0.54O2 (LRNMC) for next-generation Li-ion batteries. We report the detection of a novel vibrational RIXS signature for Li-ion battery cathodes appearing in the O K pre-peak above 533 eV that we attribute to OH-groups. We discuss likely locations and pathways for OH-group formation and accumulation throughout the active cathode material. Initial-cycle behaviour for LRNMC shows that OH-signal strength correlates with the cathodes state of charge, though reversibility is incomplete. The OH-group RIXS signal strength in long-term cycled NCA is retained. Thus, VR-RIXS offers a path for gaining new insights to oxygen reactions in battery materials.

The association of Greig syndrome and mastocytosis reveals the involvement of the hedgehog pathway in advanced mastocytosis.

Mastocytosis is a heterogeneous disease characterized by an abnormal accumulation of mast cells (MCs) in 1 or several organs. Although a somatic KIT D816V mutation is detected in ∼85% of patients, attempts to demonstrate its oncogenic effect alone have repeatedly failed, suggesting that additional pathways are involved in MC transformation. From 3 children presenting with both Greig cephalopolysyndactyly syndrome (GCPS, Mendelian Inheritance in Man [175700]) and congenital mastocytosis, we demonstrated the involvement of the hedgehog (Hh) pathway in mastocytosis. GCPS is an extremely rare syndrome resulting from haploinsufficiency of GLI3, the major repressor of Hh family members. From these familial cases of mastocytosis, we demonstrate that the Hh pathway is barely active in normal primary MCs and is overactive in neoplastic MCs. GLI3 and KIT mutations had a synergistic, tumorigenic effect on the onset of mastocytosis in a GCPS mouse model. Finally, Hh inhibitors suppressed neoplastic MC proliferation in vitro and extend the survival time of mice with aggressive systemic mastocytosis (ASM). This work revealed, for the first time, the involvement of Hh signaling in the pathophysiology of mastocytosis and demonstrated the cooperative effects of the KIT and Hh oncogenic pathways in mice with ASM, leading to the identification of new promising therapeutic targets.

Hepaticojejunostomy for bile duct injury: state of the art.

BACKGROUND: Hepaticojejunostomy (HJ) is the gold standard procedure for the reconstruction of the bile duct in many benign and malignant situations. One of the major situation is the bile duct injury (BDI) after cholecystectomy, either for early or late repair. This procedure presents some specificities associated to a debated management of BDI. PURPOSE: This article provides a state-of-the-art of the hepaticojejunostomy procedure focusing on bile duct injury including its indications and outcomes CONCLUSION: Performed at the right moment and respecting the technical rules, HJ provides a restoration of the biliary patency in the long term of 80 to 90%. It is the main surgical technique to repair BDI. Complications and failure of this procedure can be difficult to manage. That is why the primary repair requires an appropriate multidisciplinary approach associated with an expert high quality surgical technique.

Regression trees to identify combinations of farming practices that achieve the best overall intrinsic quality of milk.

Many studies over the last 30 years have shown the effects of farming practices on milk compounds. Combinations of practices may have antagonistic or synergistic effects on milk compounds, but these combination effects remain underinvestigated. Research needs to focus on overall intrinsic milk quality (including sensory, technological, health, and nutritional dimensions) and identify the combinations that can optimize it. The aim of this study was to identify which combinations of farming practices achieved the best scores for sensory, technological, health, and nutritional dimensions and for overall intrinsic milk quality. Ninety-nine private farms were visited once each to sample their bulk tank milk and survey their farming practices. The surveyed practices concerned herd characteristics, feeding management, housing conditions, and milking and milk storage conditions on the day of test. Analyses of bulk tank milk were designed to evaluate the overall intrinsic quality of the milk for 2 target products: raw milk cheese and semi-skimmed UHT milk. Regression trees were then used to identify the combinations of farming practices that achieved the best scores on each dimension and on overall intrinsic quality of the milk. Breed and diet (type of forage) were the most influential factors for sensory and health dimensions and for technological and nutritional dimension scores, respectively, in the cheese assessment. Overall cheese quality was highly positively correlated with these 4 dimension scores. Therefore, breed and diet emerged as the most influential practices in the regression tree for overall cheese quality. However, the combinations of practices that resulted in the best quality scores differed according to dimension studied and product targeted. This suggests that advice on farming practices to improve intrinsic milk quality needs to be adapted according to the end-purpose of the collected milk. This innovative approach combining on-farm data and regression trees provides farm managers with a valuable and practical tool to prioritize practices in terms of their role in shaping milk quality, and to identify the combinations of practices that promote good milk quality and practice thresholds or modalities needed to achieve it.

Optical phased array neural probes for beam-steering in brain tissue.

Implantable silicon neural probes with integrated nanophotonic waveguides can deliver patterned dynamic illumination into brain tissue at depth. Here, we introduce neural probes with integrated optical phased arrays and demonstrate optical beam steering in vitro. Beam formation in brain tissue is simulated and characterized. The probes are used for optogenetic stimulation and calcium imaging.

Impact of cirrhosis in patients undergoing laparoscopic liver resection in a nationwide multicentre survey.

BACKGROUND: The aim was to analyse the impact of cirrhosis on short-term outcomes after laparoscopic liver resection (LLR) in a multicentre national cohort study. METHODS: This retrospective study included all patients undergoing LLR in 27 centres between 2000 and 2017. Cirrhosis was defined as F4 fibrosis on pathological examination. Short-term outcomes of patients with and without liver cirrhosis were compared after propensity score matching by centre volume, demographic and tumour characteristics, and extent of resection. RESULTS: Among 3150 patients included, LLR was performed in 774 patients with (24·6 per cent) and 2376 (75·4 per cent) without cirrhosis. Severe complication and mortality rates in patients with cirrhosis were 10·6 and 2·6 per cent respectively. Posthepatectomy liver failure (PHLF) developed in 3·6 per cent of patients with cirrhosis and was the major cause of death (11 of 20 patients). After matching, patients with cirrhosis tended to have higher rates of severe complications (odds ratio (OR) 1·74, 95 per cent c.i. 0·92 to 3·41; P = 0·096) and PHLF (OR 7·13, 0·91 to 323·10; P = 0·068) than those without cirrhosis. They also had a higher risk of death (OR 5·13, 1·08 to 48·61; P = 0·039). Rates of cardiorespiratory complications (P = 0·338), bile leakage (P = 0·286) and reoperation (P = 0·352) were similar in the two groups. Patients with cirrhosis had a longer hospital stay than those without (11 versus 8 days; P = 0·018). Centre expertise was an independent protective factor against PHLF in patients with cirrhosis (OR 0·33, 0·14 to 0·76; P = 0·010). CONCLUSION: Underlying cirrhosis remains an independent risk factor for impaired outcomes in patients undergoing LLR, even in expert centres.

ANTECEDENTES: El objetivo de este estudio fue analizar el impacto de la cirrosis en los resultados a corto plazo después de la resección hepática laparoscópica (laparoscopic liver resection, LLR) en un estudio de cohortes multicéntrico nacional. MÉTODOS: Este estudio retrospectivo incluyó todos los pacientes sometidos a LLR en 27 centros entre 2000 y 2017. La cirrosis se definió como fibrosis F4 en el examen histopatológico. Los resultados a corto plazo de los pacientes con hígado cirrótico (cirrhotic liver CL) (pacientes CL) y los pacientes con hígado no cirrótico (non-cirrhotic liver, NCL) (pacientes NCL) se compararon después de realizar un emparejamiento por puntaje de propension del volumen del centro, las características demográficas y del tumor, y la extensión de la resección. RESULTADOS: Del total de 3.150 pacientes incluidos, se realizó LLR en 774 (24,6%) pacientes CL y en 2.376 (75,4%) pacientes NCL. Las tasas de complicaciones graves y mortalidad en el grupo de pacientes CL fueron del 10,6% y 2,6%, respectivamente. La insuficiencia hepática posterior a la hepatectomía (post-hepatectomy liver failure, PHLF) fue la principal causa de mortalidad (55% de los casos) y se produjo en el 3,6% de los casos en pacientes CL. Después del emparejamiento, los pacientes CL tendieron a tener tasas más altas de complicaciones graves (razón de oportunidades, odds ratio, OR 1,74; i.c. del 95% 0,92-0,41; P = 0,096) y de PHLF (OR 7,13; i.c. del 95% 0,91-323,10; P = 0,068) en comparación con los pacientes NCL. Los pacientes CL estuvieron expuestos a un mayor riesgo de mortalidad (OR 5,13; i.c. del 95% 1,08-48,6; P = 0,039) en comparación con los pacientes NCL. Los pacientes CL presentaron tasas similares de complicaciones cardiorrespiratorias graves (P = 0,338), de fuga biliar (P = 0,286) y de reintervenciones (P = 0,352) que los pacientes NCL. Los pacientes CL tuvieron una estancia hospitalaria más larga (11 versus 8 días; P = 0,018) que los pacientes NCL. La experiencia del centro fue un factor protector independiente de PHLF (OR 0,33; i.c. del 95% 0,14-0,76; P = 0,010) pacientes CL. CONCLUSIÓN: La presencia de cirrosis subyacente sigue siendo un factor de riesgo independiente de peores resultados en pacientes sometidos a resección hepática laparoscópica, incluso en centros con experiencia.

PREIMPLANTATION GENETIC TESTING: Preimplantation genetic testing for polygenic disease risk.

Since its introduction to clinical practice, preimplantation genetic testing (PGT) has become a standard of care for couples at risk of having children with monogenic disease and for chromosomal aneuploidy to improve outcomes for patients with infertility. The primary objective of PGT is to reduce the risk of miscarriage and genetic disease and to improve the success of infertility treatment with the delivery of a healthy child. Until recently, the application of PGT to more common but complex polygenic disease was not possible, as the genetic contribution to polygenic disease has been difficult to determine, and the concept of embryo selection across multiple genetic loci has been difficult to comprehend. Several achievements, including the ability to obtain accurate, genome-wide genotypes of the human embryo and the development of population-level biobanks, have now made PGT for polygenic disease risk applicable in clinical practice. With the rapid advances in embryonic polygenic risk scoring, diverse considerations beyond technical capability have been introduced.

R-CHOP appears to be the best first-line treatment for second primary diffuse large B cell lymphoma: a cancer registry study.

Second primary diffuse large B cell lymphoma (spDLBCL) is defined as a metachronous tumor occurring after a first primary cancer. To date, while R-CHOP is the standard first-line treatment for de novo DLBCL, no available data show that R-CHOP is the optimal treatment for spDLBCL. This exploratory study aimed to investigate treatment of spDLBCL. From 2008 to 2015, the Poitou-Charentes general cancer registry recorded 68 cases of spDLBCL ≤ 80 years old, having received a first-line treatment with either R-CHOP (78%) or other regimens (22%). Patients without R-CHOP have worse overall survival in univariate (HR 2.89 [1.33-6.24], P = 0.007) and multivariate (HR 2.98 [1.34-6.67], P = 0.008) analyses. Patients without R-CHOP more frequently had PS > 1 (67% vs. 28%, P = 0.007) and prior chemotherapy (60% vs. 26%, P = 0.02), which suggests that both of these factors influence a clinician's decision to not use R-CHOP. Prior chemotherapy had no prognostic impact in univariate and multivariate analyses; this result could call into question the risk-benefit balance of not using R-CHOP to prevent toxicity. In our study, one DLBCL out of ten occurred after a first primary cancer, and as regards de novo DLBCL, R-CHOP appeared to be the best first-line treatment. Larger series are needed to confirm these results.

Modern slavery and public health: a rapid evidence assessment and an emergent public health approach.

OBJECTIVES: Modern slavery is a human rights violation and a global public health concern. To date, criminal justice approaches have dominated attempts to address it. Modern slavery has severe consequences for people's mental and physical health, and there is a pressing need to identify and implement effective preventative measures. As such, a public health approach to modern slavery requires elucidation. The objectives of this study were to explore the case for public health involvement in addressing modern slavery and the components of a public health approach and to develop a globally relevant framework for public health action. STUDY DESIGN: A Rapid Evidence Assessment. METHODS: This study is a rapid systematic review of published literature and stakeholder consultation. RESULTS: The accounts of 32 consultees and evidence from 17 papers including reviews, commentaries and primary studies were included in the evidence assessment. A strong ethical rationale for public health engagement in addressing modern slavery was evident. Multilevel and multicomponent interventional strategies were identified across global, national, regional, local and service levels. Although public health could add value to existing approaches, multiple barriers and tensions exist. CONCLUSION: Published literature and stakeholder opinion indicate an emergent public health approach to modern slavery. It involves intervention at multiple levels and is guided by a rights-based, survivor-centred and trauma-informed approach. This synthesis offers an important early step in the construction of a globally relevant public health approach to modern slavery.

[Haemophilic ankle arthropathy : case reports and review of the literature]. / Arthropathie hémophilique de la cheville : description de deux cas et revue de la littérature.

Haemophilic arthropathy affects about half of the patients who suffer from haemophilia. Despite the fact that it's one of the main morbidity factors of haemophilia and that the pathophysiology of its mechanism is slowly better understood, its management is still under discussion. The cases of two men (53 and 54 years old) who suffer from ankle haemophilic arthropathy since several years are reported. For both cases, different aspects of the management are investigated, including a medicated and a physiotherapy approach, and an adequate orthotic. Other treatments are available and sometimes used, such as radio- or arthroscopic synovectomy, corticosteroids or platelet-rich plasma in?ltration or visco-supplementation.

L'arthropathie hémophilique affecte environ la moitié des hémophiles. Malgré le fait qu'elle soit un des facteurs principaux de morbidité dans l'hémophilie et que la physiopathologie de ce mécanisme soit de mieux en mieux comprise, sa prise en charge est toujours sujette à discussion. Nous décrivons le cas de deux hommes (âgés de 53 et 54 ans) qui souffrent d'arthropathie hémophilique de cheville depuis plusieurs années. Pour chacun, différents aspects de prise en charge ont été investigués, dont les approches médicamenteuses, rééducatives, et de port d'orthèse adéquate. D'autres prises en charge sont également disponibles et parfois utilisées, comme la radiosynovectomie ou la synovectomie arthroscopique, les in?ltrations par dérivés cortisonés ou de plasma riche en plaquettes (PRP), ou encore une visco-supplémentation.

Heterogeneity of virological suppression in the national antiretroviral programme of Cameroon (ANRS 12288 EVOLCAM).

OBJECTIVES: In terms of HIV infection, western and central Africa is the second most affected region world-wide, and the gap between the regional figures for the testing and treatment cascade and the Joint United Nations Programme on HIV/AIDS (UNAIDS) 90-90-90 targets is particularly worrying. We assessed the prevalence of virological suppression in patients routinely treated in 19 hospitals in Cameroon. METHODS: A cross-sectional survey was performed in adult patients receiving antiretroviral therapy (ART) in the Centre and Littoral regions. The prevalences of virological suppression (<1000 HIV-1 RNA copies/mL) were compared among all 19 hospitals using the χ2 test. Potential individual and health care-related determinants of virological suppression were assessed using multivariate logistic regression models. RESULTS: A total of 1700 patients (74% women; median age 41 years; median time on ART 3.7 years) were included in the study. The prevalence of virological suppression was 82.4% overall (95% confidence interval 80.5-84.2%). It ranged from 57.1 to 97.4% according to the individual hospital (P < 0.001). After adjustment, virological suppression was associated with age, CD4 cell count at ART initiation, disclosure of HIV status to family members, interruption of ART for more than two consecutive days, and location of patient's residence and hospital (rural/urban). These factors did not explain the heterogeneity of virological suppression between the study hospitals (P < 0.001). CONCLUSIONS: The overall prevalence of virological suppression was reassuring. Nevertheless, the heterogeneity of virological suppression among hospitals highlights that, in addition to programme-level data, health facility-level data are crucial in order to tailor the national AIDS programme's interventions with a view to achieving the third UNAIDS 90 target.