Molecular portraits of patients with intrahepatic cholangiocarcinoma who diverge as rapid progressors or long survivors on chemotherapy.

OBJECTIVE: Cytotoxic agents are the cornerstone of treatment for patients with advanced intrahepatic cholangiocarcinoma (iCCA), despite heterogeneous benefit. We hypothesised that the pretreatment molecular profiles of diagnostic biopsies can predict patient benefit from chemotherapy and define molecular bases of innate chemoresistance. DESIGN: We identified a cohort of advanced iCCA patients with comparable baseline characteristics who diverged as extreme outliers on chemotherapy (survival <6 m in rapid progressors, RP; survival >23 m in long survivors, LS). Diagnostic biopsies were characterised by digital pathology, then subjected to whole-transcriptome profiling of bulk and geospatially macrodissected tissue regions. Spatial transcriptomics of tumour-infiltrating myeloid cells was performed using targeted digital spatial profiling (GeoMx). Transcriptome signatures were evaluated in multiple cohorts of resected cancers. Signatures were also characterised using in vitro cell lines, in vivo mouse models and single cell RNA-sequencing data. RESULTS: Pretreatment transcriptome profiles differentiated patients who would become RPs or LSs on chemotherapy. Biologically, this signature originated from altered tumour-myeloid dynamics, implicating tumour-induced immune tolerogenicity with poor response to chemotherapy. The central role of the liver microenviroment was confrmed by the association of the RPLS transcriptome signature with clinical outcome in iCCA but not extrahepatic CCA, and in liver metastasis from colorectal cancer, but not in the matched primary bowel tumours. CONCLUSIONS: The RPLS signature could be a novel metric of chemotherapy outcome in iCCA. Further development and validation of this transcriptomic signature is warranted to develop precision chemotherapy strategies in these settings.

PICKLUSTER: a protein-interface clustering and analysis plug-in for UCSF ChimeraX.

SUMMARY: The identification and characterization of interfaces in protein complexes is crucial for understanding the mechanisms of molecular recognition. These interfaces are also attractive targets for protein inhibition. However, targeting protein interfaces can be challenging for large interfaces that consist of multiple interacting regions. We present PICKLUSTER [Protein Interface C(K)luster]-a program for identifying "sub-interfaces" in protein-protein complexes using distance clustering. The division of the interface into smaller "sub-interfaces" offers a more focused approach for targeting protein-protein interfaces. AVAILABILITY AND IMPLEMENTATION: PICKLUSTER is implemented as a plug-in for the molecular visualization program UCSF ChimeraX 1.4 and subsequent versions. It is freely available for download in the ChimeraX Toolshed and https://gitlab.com/topf-lab/pickluster.git.

Efficient quantum analytic nuclear gradients with double factorization.

Efficient representations of the Hamiltonian, such as double factorization, drastically reduce the circuit depth or the number of repetitions in error corrected and noisy intermediate-scale quantum (NISQ) algorithms for chemistry. We report a Lagrangian-based approach for evaluating relaxed one- and two-particle reduced density matrices from double factorized Hamiltonians, unlocking efficiency improvements in computing the nuclear gradient and related derivative properties. We demonstrate the accuracy and feasibility of our Lagrangian-based approach to recover all off-diagonal density matrix elements in classically simulated examples with up to 327 quantum and 18 470 total atoms in QM/MM simulations with modest-sized quantum active spaces. We show this in the context of the variational quantum eigensolver in case studies, such as transition state optimization, ab initio molecular dynamics simulation, and energy minimization of large molecular systems.

Cool birds: first evidence of energy-saving nocturnal torpor in free-living common swifts Apus apus resting in their nests.

Daily torpor is a means of saving energy by controlled lowering of the metabolic rate (MR) during resting, usually coupled with a decrease in body temperature. We studied nocturnal daily torpor under natural conditions in free-living common swifts Apus apus resting in their nests as a family using two non-invasive approaches. First, we monitored nest temperature (Tnest) in up to 50 occupied nests per breeding season in 2010-2015. Drops in Tnest were the first indication of torpor. Among 16 673 observations, we detected 423 events of substantial drops in Tnest of on average 8.6°C. Second, we measured MR of the families inside nest-boxes prepared for calorimetric measurements during cold periods in the breeding seasons of 2017 and 2018. We measured oxygen consumption and carbon dioxide production using a mobile indirect respirometer and calculated the percentage reduction in MR. During six torpor events observed, MR was gradually reduced by on average 56% from the reference value followed by a decrease in Tnest of on average 7.6°C. By contrast, MR only decreased by about 33% on nights without torpor. Our field data gave an indication of daily torpor, which is used as a strategy for energy saving in free-living common swifts.

The formation and fate of internal waves in the South China Sea.

Internal gravity waves, the subsurface analogue of the familiar surface gravity waves that break on beaches, are ubiquitous in the ocean. Because of their strong vertical and horizontal currents, and the turbulent mixing caused by their breaking, they affect a panoply of ocean processes, such as the supply of nutrients for photosynthesis, sediment and pollutant transport and acoustic transmission; they also pose hazards for man-made structures in the ocean. Generated primarily by the wind and the tides, internal waves can travel thousands of kilometres from their sources before breaking, making it challenging to observe them and to include them in numerical climate models, which are sensitive to their effects. For over a decade, studies have targeted the South China Sea, where the oceans' most powerful known internal waves are generated in the Luzon Strait and steepen dramatically as they propagate west. Confusion has persisted regarding their mechanism of generation, variability and energy budget, however, owing to the lack of in situ data from the Luzon Strait, where extreme flow conditions make measurements difficult. Here we use new observations and numerical models to (1) show that the waves begin as sinusoidal disturbances rather than arising from sharp hydraulic phenomena, (2) reveal the existence of >200-metre-high breaking internal waves in the region of generation that give rise to turbulence levels >10,000 times that in the open ocean, (3) determine that the Kuroshio western boundary current noticeably refracts the internal wave field emanating from the Luzon Strait, and (4) demonstrate a factor-of-two agreement between modelled and observed energy fluxes, which allows us to produce an observationally supported energy budget of the region. Together, these findings give a cradle-to-grave picture of internal waves on a basin scale, which will support further improvements of their representation in numerical climate predictions.

Contribution of cryopreservation to the cumulative live birth rate: a large multicentric cycle-based data analysis from the Italian National Registry.

PURPOSE: To estimate the contribution of cryopreservation to the cumulative live birth rate (CLBR) after law modification in Italy in the era of vitrification and freeze-all. METHODS: The Italian National Registry performed a cycle-based data collection. Nine Italian IVF clinics were involved incorporating a total of 10,260 fresh cycles performed between January 2015 and April 2016 resulting in 9273 oocyte retrievals and 3266 subsequent warming cycles from the same oocyte retrievals performed up to December 2016. Mean female age was 37 ± 4.3 years. Primary outcome measure was CLBR per oocyte retrieval. Confounding factors were tested in multivariate regression analysis, and the relative impact of cryopreservation to the CLBR in different patient categories was calculated. RESULTS: CLBR per oocyte retrieval was 32.6%, 26.5%, 18.7%, 13.0%, and 5.5% for women younger than 36, aged 36-39, 40-41, and older than 41 years, respectively. The total relative contribution of oocyte/embryo cryopreservation was 40.6% (95% CI 38.41-42.75). An association between maternal age, number of oocytes retrieved, fertilization rate, cryopreservation, and cumulative live birth was shown. When adjusted for confounders, a 2.3-fold increase was observed in the chance of live birth when cryopreservation was performed (OR 2.3; 95% CI 1.99-2.56). In high responder patients (> 15 oocytes retrieved) where freeze-all was applied in 67.6% of cycles to avoid the risk of hyper stimulation syndrome, the relative contribution of vitrification to the CLBR was 80.6%. CONCLUSIONS: Cryopreservation is essential in IVF and should always be available to patients to optimize success rates. Multicentric, cycle-based data analyses are crucial to provide infertile couples, clinicians, and regulatory bodies with accurate information on IVF effectiveness including fresh and cryopreserved cycles.

Correction to: Contribution of cryopreservation to the cumulative live birth rate: a large multicentric cycle-based data analysis from the Italian National Registry.

The original article unfortunately contained a mistake. The names of the collaborators were captured as authors of the article.

Meta-analysis of microsatellite instability in relation to clinicopathological characteristics and overall survival in gastric cancer.

BACKGROUND: Several associations between microsatellite instability (MSI) and other clinicopathological factors have been reported in gastric cancer, but the results have been ambiguous. This systematic review and meta-analysis investigated the relationship between MSI and overall survival and clinicopathological characteristics of patients with gastric cancer. METHODS: A systematic literature search of the PubMed, Cochrane and Ovid databases until 31 January 2016 was performed in accordance with the PRISMA statement. The articles were screened independently according to PICO (population, intervention, comparator, outcome) eligibility criteria. All eligible articles were evaluated independently by two reviewers for risk of bias according to the Quality In Prognosis Study tool. RESULTS: Overall, 48 studies with a total of 18 612 patients were included. MSI was found in 9·2 per cent of patients (1718 of 18 612), and was associated with female sex (odds ratio (OR) 1·57, 95 per cent c.i. 1·31 to 1·89; P < 0·001), older age (OR 1·58, 2·20 to 1·13; P < 0·001), intestinal Laurén histological type (OR 2·23, 1·94 to 2·57; P < 0·001), mid/lower gastric location (OR 0·38, 0·32 to 0·44; P < 0·001), lack of lymph node metastases (OR 0·70, 0·57 to 0·86, P < 0·001) and TNM stage I-II (OR 1·77, 1·47 to 2·13; P < 0·001). The pooled hazard ratio for overall survival of patients with MSI versus those with non-MSI gastric cancer from 21 studies was 0·69 (95 per cent c.i. 0·56 to 0·86; P < 0·001). CONCLUSION: MSI in gastric cancer was associated with good overall survival, reflected in several favourable clinicopathological tumour characteristics.

Early urological care of patients with spinal cord injury.

PURPOSE: After spinal cord injury (SCI), the initial goals of urological management include maintaining safe storage of urine with efficient bladder emptying, maximising urinary continence, and minimising the risk of urological complications. METHODS: This review was performed according to the methodology recommended by the Joint SIU-ICUD International Consultation. Embase and Medline databases were used to identify literature relevant to the early urological care of SCI patients. Recommendations were developed by consensus and graded using a modified Oxford system which identifies level of evidence (LOE) and grade of recommendation (GOR). RESULTS: Clinicians must ensure appropriate bladder emptying immediately after SCI (LOE 3, GOR A) and perform the initial neuro-urological assessment within 3 months after injury (LOE 3, GOR A), including history, validated questionnaires, bladder diary, physical examination, measurement of renal function, and urinary tract imaging (LOE 4, GOR B). Urodynamics, if available video-urodynamics, must be performed to detect and specify lower urinary tract dysfunction (LOE 1, GOR A). Spontaneous voiding and/or intermittent catheterization must be considered in appropriate patients once they are medically stable (LOE 3, GOR A). Antimuscarinics are the first-line and intradetrusor botulinum toxin A injections are the second-line treatment for neurogenic detrusor overactivity (LOE 1, GOR A). Irreversible surgical interventions should be delayed until the second year after injury due to the potential for neurological recovery (LOE 4, GOR B). CONCLUSIONS: Careful clinical assessment and pertinent urological testing including urodynamic investigation are necessary for appropriate counselling and treatment of new SCI patients.

Early neurological care of patients with spinal cord injury.

PURPOSE: Considering the major clinical challenges of managing patients with spinal cord injury (SCI), we summarized the relevant aspects of the early (within 1 year after SCI) neurological care emphasizing common standards. METHODS: This review was performed according to the methodology recommended by the Joint SIU-ICUD International Consultation. Embase and Medline databases were used to identify literature relevant to the early neurological care of SCI patients. Recommendations were developed by consensus and graded using a modified Oxford system which identifies level of evidence (LOE) and grade of recommendation (GOR). RESULTS: Emergency health care providers must address altered mental status, evidence of intoxication, suspected extremity fracture/distracting injury, focal neurological deficit and spinal pain/tenderness to determine the risk of SCI in a trauma patient [LOE 1, GOR A]. Neurogenic shock must be recognized and treated [LOE 3, GOR A]. Spine surgeons should consider early decompression and spine fixation/stabilization, where indicated, and should promote early active rehabilitation to improve functional recovery [LOE 2, GOR B]. Clinicians should refer SCI patients to specialized SCI rehabilitation centers [LOE 4, GOR B], must apply interventions to prevent venous thromboembolism (i.e., compression devices and low-molecular weight heparin/unfractionated heparin) after acute SCI respecting contraindications [LOE 1, GOR A]. Contemporary guidelines to manage pain must be employed [LOE 1, GOR A] and methods to reduce the risk of pressure ulcers should be used [LOE 3, GOR B]. CONCLUSIONS: Early treatment, prevention of associated complications and individualized patient-targeted rehabilitation programs provided by a specialized interdisciplinary team are crucial to optimize the outcome after SCI.

Congenital Neuronal Ceroid Lipofuscinosis with a Novel CTSD Gene Mutation: A Rare Cause of Neonatal-Onset Neurodegenerative Disorder.

Neuronal ceroid lipofuscinoses represent a heterogeneous group of early onset neurodegenerative disorders that are characterized by progressive cognitive and motor function decline, visual loss, and epilepsy. The age of onset has been historically used for the phenotypic classification of this group of disorders, but their molecular genetic delineation has now enabled a better characterization, demonstrating significant genetic heterogeneity even among individuals with a similar phenotype. The rare Congenital Neuronal Ceroid Lipofuscinosis (CLN10) caused by mutations in the CTSD gene encoding for cathepsin D is associated with a dramatic presentation with onset before or around birth. We report on a female born to consanguineous parents who presented at birth with severe neonatal encephalopathy with massive cerebral and cerebellar shrinking on magnetic resonance imaging. Whole exome sequencing with targeted bioinformatic analysis of a panel of genes associated with prenatal/perinatal onset of neurodegenerative disease was performed and revealed the presence of a novel homozygous in-frame deletion in CTSD. Additional functional studies further confirmed the pathogenic character of this variant and established the diagnosis of CLN10 in the patient.

Cultivating nature-based solutions: The governance of communal urban gardens in the European Union.

In many countries in the European Union (EU), the popularity of communal urban gardening (CUG) on allotments and community gardens is on the rise. Given the role of this practice in increasing urban resilience, most notably social resilience, municipalities in the Global North are promoting CUG as a nature-based solution (NbS). However, the mechanisms by which institutional actors can best support and facilitate CUG are understudied, which could create a gap between aspiration and reality. The aim of this study is therefore to identify what governance arrangements contribute to CUG delivering social resilience. Through the EU GREEN SURGE project, we studied six CUG initiatives from five EU-countries, representing different planning regimes and traditions. We selected cases taking a locally unique or innovative approach to dealing with urban challenges. A variety of actors associated with each of the cases were interviewed to achieve as complete a picture as possible regarding important governance arrangements. A cross-case comparison revealed a range of success factors, varying from clearly formulated objectives and regulations, municipal support, financial resources and social capital through to the availability of local food champions and facilitators engaging in community building. Municipalities can support CUG initiatives by moving beyond a rigid focus on top-down control, while involved citizens can increase the impact of CUG by pursuing political, in addition to hands-on, activities. We conclude that CUG has clear potential to act as a nature-based solution if managed with sensitivity to local dynamics and context.

Risk Perception and Psychological Distress in Genetic Counselling for Hereditary Breast and/or Ovarian Cancer.

Oncological Genetic Counselling (CGO) allows the identification of a genetic component that increases the risk of developing a cancer. Individuals' psychological reactions are influenced by both the content of the received information and the subjective perception of their own risk of becoming ill or being a carrier of a genetic mutation. This study included 120 participants who underwent genetic counselling for breast and/or ovarian cancer. The aim of the study was to examine the relation between their cancer risk perception and the genetic risk during CGO before receiving genetic test results, considering the influence of some psychological variables, in particular distress, anxiety and depression. Participants completed the following tools during a psychological interview: a socio-demographic form, Cancer Risk Perception (CRP) and Genetic Risk Perception (GRP), Hospital Anxiety and Depression Scale (HADS) and Distress Thermometer (DT). The data seem to confirm our hypothesis. Positive and significant correlations were found between the observed variables. Moreover, genetic risk perception determined an increase in depressive symptomatology and cancer risk perception led to an increase in anxious symptomatology, specifically in participants during cancer treatment. The present results suggest the importance of assessing genetic and cancer risk perception in individuals who undergo CGO, to identify those who are at risk of a decrease in psychological well-being and of developing greater psychological distress.

Neuronal and astrocytic involvement in striped dolphins (Stenella coeruleoalba) with morbilliviral encephalitis.

Dolphin morbillivirus (DMV), a highly pathogenic agent, may cause peculiar, "brain-only" forms of infection (BOFDI), in which viral antigen and/or genome is found exclusively in the brain from striped dolphins (Stenella coeruleoalba). These BOFDIs show morphopathological similarities with subacute sclerosing panencephalitis and old dog encephalitis (ODE) in measles virus-infected patients and in canine distemper virus-infected dogs, respectively. The brain tissue from 3 BOFDI-affected striped dolphins was investigated by means of double labelling-indirect immunofluorescence (DL-IIF) and ultrastructurally, in order to characterize the DMV-targeted neuronal and non-neuronal cell populations, along with the associated submicroscopic findings. Viral colonization of calbindin-immunoreactive (IR) and nitric oxide synthase-IR neurons was detected in the cerebral parenchyma from the 3 DMV-infected dolphins under study, associated with nuclear (chromatin) and cytoplasmic (mitochondrial) ultrastructural changes. Furthermore, a limited viral targeting of brain astrocytes was found in these animals, all of which exhibited a prominent astrogliosis/astrocytosis. To the best of our knowledge, those herein reported should be the first submicroscopic pathology and neuropathogenetic data about BOFDI in striped dolphins. In this respect, the marked astrogliosis/astrocytosis and the low viral colonization of brain astrocytes in the 3 DMV-infected dolphins under investigation are of interest from the comparative pathology and viral neuropathogenesis standpoints, when compared with ODE-affected dogs, in whose brain a non-cytolytic, astrocyte-to-astrocyte infectious spread has been recently documented. Further studies aimed at characterizing the complex DMV-host interactions in BOFDI-affected striped dolphins are needed.

Cortical reorganization in multiple sclerosis after intrathecal baclofen therapy.

Our objective was to assess the role of Intrathecal Baclofen Therapy (ITB) in the cortical reorganization in a patient affected by multiple sclerosis (MS) undergoing physical therapy. We reported a case of a woman affected by MS and severe spasticity, who performed an fMRI examination, before and after the ITB implantation. The subject showed controlateral motor cortex activation after motor task. After a month of ITB implantation, patient showed ipsilateral and controlateral motor cortex activation although with a broader extension. fMRI examination supported the hypothesis of a central influence in patients who undergo physiotherapy and therapy with ITB.

Tailored and Externally Corrected Coupled Cluster with Quantum Inputs.

We propose to use wave function overlaps obtained from a quantum computer as inputs for the classical split-amplitude techniques, tailored and externally corrected coupled cluster, to achieve balanced treatment of static and dynamic correlation effects in molecular electronic structure simulations. By combining insights from statistical properties of matchgate shadows, which are used to measure quantum trial state overlaps, with classical correlation diagnostics, we can provide quantum resource estimates well into the classically no longer exactly solvable regime. We find that rather imperfect wave functions and remarkably low shot counts are sufficient to cure qualitative failures of plain coupled cluster singles doubles and to obtain chemically precise dynamic correlation energy corrections. We provide insights into which wave function preparation schemes have a chance of yielding quantum advantage, and we test our proposed method using overlaps measured on Google's Sycamore device.

Road-Map to Epicardial Approach for Catheter Ablation of Ventricular Tachycardia in Structural Heart Disease: Results From a 10-Year Tertiary-Center Experience.

BACKGROUND: Epicardial approach in ventricular tachycardia (VT) ablation is still regarded as a second-step strategy, due to the risk of complications. We evaluated the frequency that epicardial ablation targets were identified and ablation performed following pericardial access compared with unnecessary pericardial access for different VT causes and potential markers of epicardial VT. METHODS: All VT ablation procedures including epicardial approach over a 10-year period were included. First-line epicardial approach was indicated in arrhythmogenic right ventricular cardiomyopathy (ARVC) and postmyocarditis VT; in patients with idiopathic dilated cardiomyopathy (IDCM) and postmyocardial infarction, indications resulted from available imaging techniques or 12-lead VT morphology. The epicardial approach was considered useful if epicardial ablation was performed after epicardial mapping. Feasibility, complications, and long-term outcome were reported. RESULTS: Four hundred and eighty-eight subjects with a median age of 60 years (interquartile range, 47-65) and of left ventricle ejection fraction 41% (interquartile range, 30-55) underwent 626 epicardial VT ablations. Percutaneous access had a success rate of 92.2% and a complication rate of 3.6%. Overall, epicardial approach was, respectively, indicated to 11.8% of postmyocardial infarction patients, 49.5% in IDCM, 94% in myocarditis, and 90.7% in ARVC. Epicardial ablation at the first ablation attempt was performed in 9.3% of postmyocardial infarction patients, 28.8% in IDCM, 86.5% in myocarditis, and 81.3% in patients with ARVC. In first-line epicardial group, ARVC and myocarditis showed the highest odds for epicardial ablation (OR, 4.057 [95% CI, 1.299-8.937]; P=0.007; OR, 3.971 [95% CI, 1.376-11.465]; P=0.005, respectively). IDCM independently predicted unnecessary epicardial approach (OR, 2.7 [95% CI, 1.7-4.3]; P<0.001). After a follow-up of 41 months (interquartile range, 19-64), patients with IDCM experienced higher rate of recurrences and mortality compared with other causes. CONCLUSIONS: Epicardial approach is integral part of ablation armamentarium regardless of the VT cause, with high feasibility and low complication rate in experienced centers. Our data support its use at first ablation attempt in VTs related to ARVC and myocarditis.