Accurate nonrelativistic ground-state energies of 3d transition metal atoms

We present accurate nonrelativistic ground-state energies of the transition metal atoms of the 3d series calculated with Fixed-Node Diffusion Monte Carlo (FN-DMC). Selected multi-determinantal expansions obtained with the CIPSI method (Configuration Interaction using a Perturbative Selection made Iteratively) and including the most prominent determinants of the full CI expansion are used as trial wavefunctions. Using a maximum of a few tens of thousands determinants, fixed-node errors on total DMC energies are found to be greatly reduced for some atoms with respect to those obtained with Hartree-Fock nodes. The FN-DMC/(CIPSI nodes) ground-state energies presented here are, to the best of our knowledge, the most accurate values reported so far. Thanks to the variational property of FN-DMC total energies, the results also provide lower bounds for the absolute value of all-electron correlation energies, $|E_c|$.Comment: 5 pages, 3 table

Development of an in vitro microfluidic model to study the role of microenvironmental cells in oral cancer metastasis.

Metastasis occurs when cancer cells leave the primary tumour and travel to a secondary site to form a new lesion. The tumour microenvironment (TME) is recognised to greatly influence this process, with for instance the vascular system enabling the dissemination of the cells into other tissues. However, understanding the exact role of these microenvironmental cells during metastasis has proven challenging. Indeed, in vitro models often appear too simplistic, and the study of the interactions between different cell types in a 3D space is limited. On the other hand, even though in vivo models incorporate the TME, observing cells in real-time to understand their exact role is difficult. Horizontal compartmentalised microfluidic models are a promising new platform for metastasis studies. These devices, composed of adjacent microchannels, can incorporate multiple cell types within a 3D space. Furthermore, the transparency and thickness of these models also enables high quality real-time imaging to be performed. This paper demonstrates how these devices can be successfully used for oral squamous cell carcinoma (OSCC) metastasis studies, focusing on the role of the vascular system in this process. Conditions for co-culture of OSCC cells and endothelial cells have been determined and staining protocols optimised. Furthermore, several imaging analysis techniques for these models are described, enabling precise segmentation of the different cell types on the images as well as accurate assessment of their phenotype. These methods can be applied to any study aiming to understand the role of microenvironmental cell types in cancer metastatic dissemination, and overcome several challenges encountered with current in vitro and in vivo models. Hence, this new in vitro model capable of recapitulating important aspects of the cellular complexity of human metastatic dissemination can ultimately contribute to replacing animal studies in this field

Championing stochastic electronic structure methods with CHAMP

We present the recent progress in developing a high-performance and user-friendly program suite – the Cornell-Holland Ab-initio Materials Package (CHAMP) -- for performing accurate and efficient quantum Monte Carlo (QMC) calculations of molecular systems. A prominent capability of CHAMP is the efficient computation of analytical interatomic forces, also in combination with the fast evaluation of multi-determinant expansions and their derivatives. The code utilizes the latest processor instructions to perform vectorized tasks and is optimized for upcoming exascale computing facilities.The code offers various capabilities such as variational Monte Carlo (VMC), diffusion Monte Carlo (DMC), and optimization of many-body wave functions by energy minimization for ground and excited states. The other prominent features of CHAMP include the efficient computation of analytical interatomic forces and a compact formulation for the fast evaluation of multi-determinant expansions and their derivatives

Routine HIV Screening in France: Clinical Impact and Cost-Effectiveness

BACKGROUND. In France, roughly 40,000 HIV-infected persons are unaware of their HIV infection. Although previous studies have evaluated the cost-effectiveness of routine HIV screening in the United States, differences in both the epidemiology of infection and HIV testing behaviors warrant a setting-specific analysis for France. METHODS/PRINCIPAL FINDINGS. We estimated the life expectancy (LE), cost and cost-effectiveness of alternative HIV screening strategies in the French general population and high-risk sub-populations using a computer model of HIV detection and treatment, coupled with French national clinical and economic data. We compared risk-factor-based HIV testing ("current practice") to universal routine, voluntary HIV screening in adults aged 18-69. Screening frequencies ranged from once to annually. Input data included mean age (42 years), undiagnosed HIV prevalence (0.10%), annual HIV incidence (0.01%), test acceptance (79%), linkage to care (75%) and cost/test (€43). We performed sensitivity analyses on HIV prevalence and incidence, cost estimates, and the transmission benefits of ART. "Current practice" produced LEs of 242.82 quality-adjusted life months (QALM) among HIV-infected persons and 268.77 QALM in the general population. Adding a one-time HIV screen increased LE by 0.01 QALM in the general population and increased costs by €50/person, for a cost-effectiveness ratio (CER) of €57,400 per quality-adjusted life year (QALY). More frequent screening in the general population increased survival, costs and CERs. Among injection drug users (prevalence 6.17%; incidence 0.17%/year) and in French Guyana (prevalence 0.41%; incidence 0.35%/year), annual screening compared to every five years produced CERs of €51,200 and €46,500/QALY. CONCLUSIONS/SIGNIFICANCE. One-time routine HIV screening in France improves survival compared to "current practice" and compares favorably to other screening interventions recommended in Western Europe. In higher-risk groups, more frequent screening is economically justifiable.Haute Autorite de Sante; the Institut de Veille Sanitaire; Sidaction; the Agence Nationale de Recherches sur le SIDA et les hepatites virales; the National Institute of Allergy and Infectious Diseases (R01 AI042006, K24 AI062476, P30 AI42851); the National Institute of Mental Health (R01 MH65869); the National Institute on Drug Abuse (R01 DA015612

Mutation Detection in Patients with Retinal Dystrophies Using Targeted Next Generation Sequencing

Retinal dystrophies (RD) constitute a group of blinding diseases that are characterized by clinical variability and pronounced genetic heterogeneity. The different nonsyndromic and syndromic forms of RD can be attributed to mutations in more than 200 genes. Consequently, next generation sequencing (NGS) technologies are among the most promising approaches to identify mutations in RD. We screened a large cohort of patients comprising 89 independent cases and families with various subforms of RD applying different NGS platforms. While mutation screening in 50 cases was performed using a RD gene capture panel, 47 cases were analyzed using whole exome sequencing. One family was analyzed using whole genome sequencing. A detection rate of 61% was achieved including mutations in 34 known and two novel RD genes. A total of 69 distinct mutations were identified, including 39 novel mutations. Notably, genetic findings in several families were not consistent with the initial clinical diagnosis. Clinical reassessment resulted in refinement of the clinical diagnosis in some of these families and confirmed the broad clinical spectrum associated with mutations in RD genes

The Changing Landscape for Stroke\ua0Prevention in AF: Findings From the GLORIA-AF Registry Phase 2

Background GLORIA-AF (Global Registry on Long-Term Oral Antithrombotic Treatment in Patients with Atrial Fibrillation) is a prospective, global registry program describing antithrombotic treatment patterns in patients with newly diagnosed nonvalvular atrial fibrillation at risk of stroke. Phase 2 began when dabigatran, the first non\u2013vitamin K antagonist oral anticoagulant (NOAC), became available. Objectives This study sought to describe phase 2 baseline data and compare these with the pre-NOAC era collected during phase 1. Methods During phase 2, 15,641 consenting patients were enrolled (November 2011 to December 2014); 15,092 were eligible. This pre-specified cross-sectional analysis describes eligible patients\u2019 baseline characteristics. Atrial fibrillation disease characteristics, medical outcomes, and concomitant diseases and medications were collected. Data were analyzed using descriptive statistics. Results Of the total patients, 45.5% were female; median age was 71 (interquartile range: 64, 78) years. Patients were from Europe (47.1%), North America (22.5%), Asia (20.3%), Latin America (6.0%), and the Middle East/Africa (4.0%). Most had high stroke risk (CHA2DS2-VASc [Congestive heart failure, Hypertension, Age  6575 years, Diabetes mellitus, previous Stroke, Vascular disease, Age 65 to 74 years, Sex category] score  652; 86.1%); 13.9% had moderate risk (CHA2DS2-VASc = 1). Overall, 79.9% received oral anticoagulants, of whom 47.6% received NOAC and 32.3% vitamin K antagonists (VKA); 12.1% received antiplatelet agents; 7.8% received no antithrombotic treatment. For comparison, the proportion of phase 1 patients (of N = 1,063 all eligible) prescribed VKA was 32.8%, acetylsalicylic acid 41.7%, and no therapy 20.2%. In Europe in phase 2, treatment with NOAC was more common than VKA (52.3% and 37.8%, respectively); 6.0% of patients received antiplatelet treatment; and 3.8% received no antithrombotic treatment. In North America, 52.1%, 26.2%, and 14.0% of patients received NOAC, VKA, and antiplatelet drugs, respectively; 7.5% received no antithrombotic treatment. NOAC use was less common in Asia (27.7%), where 27.5% of patients received VKA, 25.0% antiplatelet drugs, and 19.8% no antithrombotic treatment. Conclusions The baseline data from GLORIA-AF phase 2 demonstrate that in newly diagnosed nonvalvular atrial fibrillation patients, NOAC have been highly adopted into practice, becoming more frequently prescribed than VKA in Europe and North America. Worldwide, however, a large proportion of patients remain undertreated, particularly in Asia and North America. (Global Registry on Long-Term Oral Antithrombotic Treatment in Patients With Atrial Fibrillation [GLORIA-AF]; NCT01468701

Effect of alirocumab on mortality after acute coronary syndromes. An analysis of the ODYSSEY OUTCOMES randomized clinical trial

Background: Previous trials of PCSK9 (proprotein convertase subtilisin-kexin type 9) inhibitors demonstrated reductions in major adverse cardiovascular events, but not death. We assessed the effects of alirocumab on death after index acute coronary syndrome. Methods: ODYSSEY OUTCOMES (Evaluation of Cardiovascular Outcomes After an Acute Coronary Syndrome During Treatment With Alirocumab) was a double-blind, randomized comparison of alirocumab or placebo in 18 924 patients who had an ACS 1 to 12 months previously and elevated atherogenic lipoproteins despite intensive statin therapy. Alirocumab dose was blindly titrated to target achieved low-density lipoprotein cholesterol (LDL-C) between 25 and 50 mg/dL. We examined the effects of treatment on all-cause death and its components, cardiovascular and noncardiovascular death, with log-rank testing. Joint semiparametric models tested associations between nonfatal cardiovascular events and cardiovascular or noncardiovascular death. Results: Median follow-up was 2.8 years. Death occurred in 334 (3.5%) and 392 (4.1%) patients, respectively, in the alirocumab and placebo groups (hazard ratio [HR], 0.85; 95% CI, 0.73 to 0.98; P=0.03, nominal P value). This resulted from nonsignificantly fewer cardiovascular (240 [2.5%] vs 271 [2.9%]; HR, 0.88; 95% CI, 0.74 to 1.05; P=0.15) and noncardiovascular (94 [1.0%] vs 121 [1.3%]; HR, 0.77; 95% CI, 0.59 to 1.01; P=0.06) deaths with alirocumab. In a prespecified analysis of 8242 patients eligible for ≥3 years follow-up, alirocumab reduced death (HR, 0.78; 95% CI, 0.65 to 0.94; P=0.01). Patients with nonfatal cardiovascular events were at increased risk for cardiovascular and noncardiovascular deaths (P<0.0001 for the associations). Alirocumab reduced total nonfatal cardiovascular events (P<0.001) and thereby may have attenuated the number of cardiovascular and noncardiovascular deaths. A post hoc analysis found that, compared to patients with lower LDL-C, patients with baseline LDL-C ≥100 mg/dL (2.59 mmol/L) had a greater absolute risk of death and a larger mortality benefit from alirocumab (HR, 0.71; 95% CI, 0.56 to 0.90; Pinteraction=0.007). In the alirocumab group, all-cause death declined wit h achieved LDL-C at 4 months of treatment, to a level of approximately 30 mg/dL (adjusted P=0.017 for linear trend). Conclusions: Alirocumab added to intensive statin therapy has the potential to reduce death after acute coronary syndrome, particularly if treatment is maintained for ≥3 years, if baseline LDL-C is ≥100 mg/dL, or if achieved LDL-C is low. Clinical Trial Registration: URL: https://www.clinicaltrials.gov. Unique identifier: NCT01663402

A 3Rs approach to tumour metastasis: investigating the role of cancer stem cells in the metastasis of oral squamous cell carcinoma using an in vitro microfluidic model

300,000 cases of oral squamous cell carcinoma (OSCC) are diagnosed every year, and around 30% of patients exhibit metastatic spread. Metastasis is a complex process by which cancer cells travel to a secondary site to form a new tumour. Previous work has suggested that cancer stem cells (CSCs) are capable of driving metastasis by switching between epithelial and mesenchymal states. However, the role they play in the interactions with the vascular system, a key component of the tumour microenvironment (TME) recognised to greatly influence metastasis, remains unclear. Here, I used microfluidic devices, a promising new in vitro model, to study these interactions. I fabricated these devices using photolithography and soft lithography techniques and used them to co-culture endothelial cells with OSCC cells in a fibrin gel, to assess the interactions between these two cell types in a 3-dimensional (3D) environment. After developing and optimising this OSCC metastasis-on-a-chip model, I uncovered a two-way communication between cancer cells and endothelial cells that greatly changes the behaviour of both cell types. Most interestingly, cancer cell invasion undergoes marked changes and is significantly reduced in the presence of endothelial cells. Imaging of the matrix shows that endothelial cells degrade and remodel the matrix when undergoing sprouting angiogenesis in the fibrin gel. This remodelled environment restricts OSCC cell migration in the matrix, and full epithelial-to-mesenchymal transition (EMT) is suppressed – instead invasion progresses through streaming of epithelial tumour cells through pre-existing tracks made by endothelial cells. Immunofluorescent staining of the cells in the invasive streams demonstrates features that have been associated with partial EMT in metastatic CSCs. These findings may represent the generation of a vascular niche that acts to modify the surrounding TME and, through this, influences the invasive CSC phenotype

BIONFORMATICS ANALYSIS OF THE STRIPED (MORONE SAXATILIS) BASS HOXA2A AND HOXA2B GENOMIC DNA SUGGESTS EVOLUTIONARY CONSERVATION OF GENE REGULATION

Hoxa2 is an evolutionarily conserved developmental regulatory gene that functions to pattern the rhombomeres and pharyngeal arches, or tissue primordia that give rise to many cranial nerves and craniofacial skeletal elements, respectively, in vertebrates. Bioinformatics and reporter gene assays in the mouse (Mus musculus) and chick (Gallus gallus) embryos have shown the presence of several genomic DNA regulatory sequences within and around the Hoxa2 gene. These sequences were shown to direct Hoxa2 gene expression in the rhombomeres and pharyngeal arches. Several teleost fishes contain two Hoxa2 genes, hoxa2a and hoxa2b, due to a whole genome duplication at the incipient stage of teleost evolution. Recent bioinformatics and reporter gene assays have shown that many of the regulatory sequences identified for Hoxa2 of mouse and chick are also present for hoxa2a and a2b of several teleost fishes, including zebrafish (Danio rerio), Japanese medaka (Oryzias latipes), pufferfish (Takifugu rubripes), and Nile tilapia (Oreochromis niloticus). The current study attempts to expand our understanding of the Hoxa2 regulatory elements in teleost fishes by analyzing unpublished genomic hoxa2a and a2b sequences of striped bass (Morone saxatilis). We used the software program Geneious® to perform comparative genomic sequence analyses of the Striped bass hoxa2a and a2b sequences with orthologous sequences from mouse, chick, zebrafish, medaka, pufferfish, and tilapia. Preliminary results suggest that the regulatory sequences that direct mouse and chick Hoxa2 gene expression in the rhombomeres and pharyngeal arches are conserved for striped bass hoxa2a and a2b. These results support the expression patterns of striped bass hoxa2a and a2b, which are also expressed in the same domains