Tensor Product Approximation (DMRG) and Coupled Cluster method in Quantum Chemistry

We present the Copupled Cluster (CC) method and the Density matrix Renormalization Grooup (DMRG) method in a unified way, from the perspective of recent developments in tensor product approximation. We present an introduction into recently developed hierarchical tensor representations, in particular tensor trains which are matrix product states in physics language. The discrete equations of full CI approximation applied to the electronic Schr\"odinger equation is casted into a tensorial framework in form of the second quantization. A further approximation is performed afterwards by tensor approximation within a hierarchical format or equivalently a tree tensor network. We establish the (differential) geometry of low rank hierarchical tensors and apply the Driac Frenkel principle to reduce the original high-dimensional problem to low dimensions. The DMRG algorithm is established as an optimization method in this format with alternating directional search. We briefly introduce the CC method and refer to our theoretical results. We compare this approach in the present discrete formulation with the CC method and its underlying exponential parametrization.Comment: 15 pages, 3 figure

How can mathematical models advance tuberculosis control in high HIV prevalence settings?

Existing approaches to tuberculosis (TB) control have been no more than partially successful in areas with high human immunodeficiency virus (HIV) prevalence. In the context of increasingly constrained resources, mathematical modelling can augment understanding and support policy for implementing those strategies that are most likely to bring public health and economic benefits. In this paper, we present an overview of past and recent contributions of TB modelling in this key area, and suggest a way forward through a modelling research agenda that supports a more effective response to the TB-HIV epidemic, based on expert discussions at a meeting convened by the TB Modelling and Analysis Consortium. The research agenda identified high-priority areas for future modelling efforts, including 1) the difficult diagnosis and high mortality of TB-HIV; 2) the high risk of disease progression; 3) TB health systems in high HIV prevalence settings; 4) uncertainty in the natural progression of TB-HIV; and 5) combined interventions for TB-HIV. Efficient and rapid progress towards completion of this modelling agenda will require co-ordination between the modelling community and key stakeholders, including advocates, health policy makers, donors and national or regional finance officials. A continuing dialogue will ensure that new results are effectively communicated and new policy-relevant questions are addressed swiftly

The ability of 1.23% acidulated phosphate fluoride gel to inhibit simulated endogenous erosion in tooth roots

The document attached has been archived with permission from the Australian Dental Association. An external link to the publisher’s copy is included.Background: Endogenous dental erosion is that produced by contact of gastric acids with tooth structure. It may affect exposed root cementum/ dentine as well as coronal enamel, causing marked loss of mineral. The aim of this study was to determine whether 1.23 per cent acidulated phosphate fluoride gel, if applied to the surface cementum at certain intervals during an erosive acid challenge, could provide any protection against demineralization. Materials and methods: Roots of preserved extracted human teeth were painted with a water and acid resistant varnish, leaving two windows (3x1mm) of exposed dentine. These were placed in a solution containing 0.06MHCl and 2.2mMCaHPO4, which has been shown to simulate gastric acid when it meets the tooth surface. The roots were placed in the erosive solution unprotected (controls), or subject to APF application for four minutes prior to and every 10, 30 or 120 minutes during the erosive challenge. Roots were removed at either 6 or 12 hours, washed thoroughly and cut into 120μm thick sections. Depths of demineralization were measured using an optical graticule under polarized light microscopy. Results: A high level of protection was provided when the roots were coated with APF gel every 10 or 30 minutes. Conclusions: APF gel will partially inhibit endogenous erosion of roots for up to 30 minutes if applied, for example, the night before a morning reflux episode. This should be considered along with other erosion control or reduction procedures for patients suffering from the effects of endogenous erosion.JGC Saunders and JM McIntyr

Uncovering opportunities for effective species conservation banking requires navigating technical and practical complexities

Abstract: In the USA, Species Conservation Banking is a prominent example of compensatory biodiversity impact mitigation, with an annual market value estimated at US$354.2 million. Species Conservation Banking represents a useful case study of a well‐established program that can provide empirical insights into the practicalities of implementing quantitative compensatory biodiversity mitigation on‐the‐ground. Using semi‐structured key‐informant interviews structured around well‐established technical challenges to compensatory mitigation, this study aimed to understand (i) how and why these challenges are or are not addressed in practice; and (ii) how these challenges relate to practical challenges faced by conservation banking stakeholders on‐the‐ground. Challenges identified included: (i) defining trading currencies and equivalence, (ii) regulatory and political uncertainty, (iii) regulatory agency capacity, will and knowledge, (iv) lack of policies, standards, and competition with other mitigation mechanisms, (v) long‐term uncertainty/longevity, and (vi) lack of species knowledge and data transparency. These challenges are numerous, diverse, interlinked and transdisciplinary, and collectively inhibit the ability of practitioners to resolve underlying technical challenges—a finding likely applicable to related biodiversity offset programs. To help address challenges and navigate this complexity, we formulate several recommendations for conservation banking stakeholders to improve the chances of beneficial biodiversity outcomes being achieved

Identifying opportunities to deliver effective and efficient outcomes from business-biodiversity action

Data Availability: The data that has been used is confidential.Supporting information The interview guide (S1), thematic framework (S2), research information document (S3), prior informed consent form (S4), information on how the research met qualitative research transparency criteria (S5), expanded tables of quotes (S6) and an observational standpoint (S7) are included in the supporting information: supplementary material is available online at https://www.sciencedirect.com/science/article/pii/S1462901122003720?via%3Dihub#sec0115 .Copyright © 2022 The Author(s). Business-biodiversity action is increasingly seen as critical for delivering conservation goals, but such action needs to be effective. Using detailed semi-structured interviews with leading business-biodiversity professionals and consultants we aimed to understand the actions currently taken and why, how actions are decided upon, and current challenges that hinder effective, efficient action. The scale and type of action varied by sector, driven largely by the risks (reputational, financial) of inaction. Cost-effectiveness was important to businesses, but the limited quantification of the economic consequences of biodiversity action hindered uptake. Indirect evidence sources were generally used to guide decision-making including using expert consultants, guidance, standards or certifications. Acquiring better evidence of cost-effectiveness, particularly if embedded within these indirect sources, could improve practice. A diverse set of challenges emerged that impeded business engagement with biodiversity, effective decision-making, and action implementation. We discuss opportunities to address them and thus improve the effectiveness of business-biodiversity action.The work was completed as part of T.B.W’s PhD funded by the Balfour Studentship, Department of Zoology, University of Cambridge. W.J.S & S.O.P's research received funding from The David and Claudia Harding Foundation, MAVA, the A. G. Leventis Foundation, and Arcadi

Colored Motifs Reveal Computational Building Blocks in the C. elegans Brain

Background: Complex networks can often be decomposed into less complex sub-networks whose structures can give hints about the functional organization of the network as a whole. However, these structural motifs can only tell one part of the functional story because in this analysis each node and edge is treated on an equal footing. In real networks, two motifs that are topologically identical but whose nodes perform very different functions will play very different roles in the network. Methodology/Principal Findings: Here, we combine structural information derived from the topology of the neuronal network of the nematode C. elegans with information about the biological function of these nodes, thus coloring nodes by function. We discover that particular colorations of motifs are significantly more abundant in the worm brain than expected by chance, and have particular computational functions that emphasize the feed-forward structure of information processing in the network, while evading feedback loops. Interneurons are strongly over-represented among the common motifs, supporting the notion that these motifs process and transduce the information from the sensor neurons towards the muscles. Some of the most common motifs identified in the search for significant colored motifs play a crucial role in the system of neurons controlling the worm's locomotion. Conclusions/Significance: The analysis of complex networks in terms of colored motifs combines two independent data sets to generate insight about these networks that cannot be obtained with either data set alone. The method is general and should allow a decomposition of any complex networks into its functional (rather than topological) motifs as long as both wiring and functional information is available

Near-critical free-surface flows: Real fluid flow analysis

An open channel flow with a flow depth close to the critical depth is characterised by a curvilinear streamline flow field that results in steady free surface undulations. Near critical flows of practical relevance encompass the undular hydraulic jump when the flow changes from supercritical (F > 1) to subcritical (F 1). So far these flows were mainly studied based on ideal fluid flow computations, for which the flow is assumed irrotational and, thus, shear forces are absent. While the approach is accurate for critical flow conditions (F = 1) in weir and flumes, near-critical flows involve long distances reaches, and the effect of friction on the flow properties cannot be neglected. In the present study the characteristics of near-critical free-surface flows are reanalysed based on a model accounting for both the streamline curvature and friction effects. Based on the improved model, some better agreement with experimental results is found, thereby highlighting the main frictional features of the flow profiles

Impact and cost-effectiveness of current and future tuberculosis diagnostics: the contribution of modelling.

The landscape of diagnostic testing for tuberculosis (TB) is changing rapidly, and stakeholders need urgent guidance on how to develop, deploy and optimize TB diagnostics in a way that maximizes impact and makes best use of available resources. When decisions must be made with only incomplete or preliminary data available, modelling is a useful tool for providing such guidance. Following a meeting of modelers and other key stakeholders organized by the TB Modelling and Analysis Consortium, we propose a conceptual framework for positioning models of TB diagnostics. We use that framework to describe modelling priorities in four key areas: Xpert(®) MTB/RIF scale-up, target product profiles for novel assays, drug susceptibility testing to support new drug regimens, and the improvement of future TB diagnostic models. If we are to maximize the impact and cost-effectiveness of TB diagnostics, these modelling priorities should figure prominently as targets for future research

Drinking contexts and their association with acute alcohol‐related harm : a systematic review of event‐level studies on adults' drinking occasions

Issues Event‐level alcohol research can inform prevention efforts by determining whether drinking contexts—such as people or places—are associated with harmful outcomes. This review synthesises evidence on associations between characteristics of adults' drinking occasions and acute alcohol‐related harm. Approach We systematically searched Ovid MEDLINE, Ovid PsycInfo and the Web of Science Social Sciences Citation Index. Eligible papers used quantitative designs and event‐level data collection methods. They linked one or more drinking contexts to acute alcohol‐related harm. Following extraction of study characteristics, methods and findings, we assessed study quality and narratively synthesised the findings. PROSPERO ID: CRD42018119701. Key Findings Searches identified 95 eligible papers, 65 (68%) of which study young adults and 62 (65%) of which are set in the United States, which limits generalisability to other populations. These papers studied a range of harms from assault to drink driving. Study quality is good overall although measures often lack validation. We found substantial evidence for direct effects of drinking context on harms. All of the contextual characteristics types studied (e.g. people, place, timing, psychological states, drink type) were consistently associated with harms. Certain contexts were frequently studied and associated with harms, in particular, weekend drinking, drinking in licensed premises and concurrent illicit drug use. Implications The findings of our review indicate target drinking contexts for prevention efforts that are consistently associated with increased acute alcohol‐related harm. Conclusion A large range of contextual characteristics of drinking occasions are directly associated with acute alcohol‐related harm, over and above levels of consumption

Diagnosis of Cystic Fibrosis: Consensus Guidelines from the Cystic Fibrosis Foundation.

OBJECTIVE: Cystic fibrosis (CF), caused by mutations in the CF transmembrane conductance regulator (CFTR) gene, continues to present diagnostic challenges. Newborn screening and an evolving understanding of CF genetics have prompted a reconsideration of the diagnosis criteria. STUDY DESIGN: To improve diagnosis and achieve standardized definitions worldwide, the CF Foundation convened a committee of 32 experts in CF diagnosis from 9 countries to develop clear and actionable consensus guidelines on the diagnosis of CF and to clarify diagnostic criteria and terminology for other disorders associated with CFTR mutations. An a priori threshold of ≥80% affirmative votes was required for acceptance of each recommendation statement. RESULTS: After reviewing relevant literature, the committee convened to review evidence and cases. Following the conference, consensus statements were developed by an executive subcommittee. The entire consensus committee voted and approved 27 of 28 statements, 7 of which needed revisions and a second round of voting. CONCLUSIONS: It is recommended that diagnoses associated with CFTR mutations in all individuals, from newborn to adult, be established by evaluation of CFTR function with a sweat chloride test. The latest mutation classifications annotated in the Clinical and Functional Translation of CFTR project (http://www.cftr2.org/index.php) should be used to aid in diagnosis. Newborns with a high immunoreactive trypsinogen level and inconclusive CFTR functional and genetic testing may be designated CFTR-related metabolic syndrome or CF screen positive, inconclusive diagnosis; these terms are now merged and equivalent, and CFTR-related metabolic syndrome/CF screen positive, inconclusive diagnosis may be used. International Statistical Classification of Diseases and Related Health Problems, 10th Revision codes for use in diagnoses associated with CFTR mutations are included