PLUMED 2: New feathers for an old bird

Enhancing sampling and analyzing simulations are central issues in molecular simulation. Recently, we introduced PLUMED, an open-source plug-in that provides some of the most popular molecular dynamics (MD) codes with implementations of a variety of different enhanced sampling algorithms and collective variables (CVs). The rapid changes in this field, in particular new directions in enhanced sampling and dimensionality reduction together with new hardware, require a code that is more flexible and more efficient. We therefore present PLUMED 2 here a,complete rewrite of the code in an object-oriented programming language (C++). This new version introduces greater flexibility and greater modularity, which both extends its core capabilities and makes it far easier to add new methods and CVs. It also has a simpler interface with the MD engines and provides a single software library containing both tools and core facilities. Ultimately, the new code better serves the ever-growing community of users and contributors in coping with the new challenges arising in the field.

Program summary

Program title: PLUMED 2

Catalogue identifier: AEEE_v2_0

Program summary URL: http://cpc.cs.qub.ac.uk/summaries/AEEE_v2_0.html

Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland

Licensing provisions: Yes

No. of lines in distributed program, including test data, etc.: 700646

No. of bytes in distributed program, including test data, etc.: 6618136

Distribution format: tar.gz

Programming language: ANSI-C++.

Computer: Any computer capable of running an executable produced by a C++ compiler.

Operating system: Linux operating system, Unix OSs.

Has the code been vectorized or parallelized?: Yes, parallelized using MPI.

RAM: Depends on the number of atoms, the method chosen and the collective variables used.

Classification: 3, 7.7, 23. Catalogue identifier of previous version: AEEE_v1_0.

Journal reference of previous version: Comput. Phys. Comm. 180 (2009) 1961.

External routines: GNU libmatheval, Lapack, Bias, MPI. (C) 2013 Elsevier B.V. All rights reserved.

A qualitative study of community pharmacists’ awareness of and involvement with intermediate care facilities

Rationale, aims and objectives: Intermediate care (IC) describes a range of services targeted at older people, aimed at preventing unnecessary hospitalisation, promoting faster recovery and maximising independence. The introduction of IC has created a new interface between primary and secondary care. Older people are known to be at an increased risk of medication-related problems when transferring between healthcare settings and pharmacists are often not included as part of IC multidisciplinary teams. This study aimed to explore community pharmacists’ (CPs) awareness of IC services and to investigate their views of and attitudes towards the medicines management aspects of such services, including the transfer of medication information.

Method: Semi-structured interviews were conducted, recorded, transcribed verbatim and analysed using a constant comparative approach with CPs practising in the vicinity of IC facilities in Northern Ireland, UK.

Results: Interviews were conducted with 16 CPs. Three themes were identified and named ‘left out of the loop’, ‘chasing things up’ and ‘closing the loop’. CPs felt that they were often ‘left out of the loop’ with regards to both their involvement with local IC services and communication across the healthcare interfaces. As a result, CPs resorted to ‘chasing things up’ as they had to proactively try to obtain information relating to patients’ medications. CPs viewed themselves as ideally placed to facilitate medicines management across the healthcare interfaces (i.e., ‘closing the loop’), but several barriers to potential services were identified.

Conclusion: CPs have limited involvement with IC services. There is a need for improvement of effective communication of patients’ medication information between secondary care, IC and community pharmacy. Increasing CP involvement may contribute to improving continuity of care across such healthcare interfaces, thereby increasing the person-centeredness of service provision.

Development of a new welfare assessment protocol for practical application in long-term dog shelters

In many European shelters, dogs may spend many years confined. A poor environment and inappropriate management may lead to a low quality of life. The absence of harmonised European regulatory frameworks defining the minimum requirements for shelter facilities makes the definition of welfare standards for kennelled dogs challenging. Here, a new protocol was developed and tested to help identify the main welfare issues for shelter dogs. Twenty-six indicators were identified including management, resource and animal based measures. Accuracy and interobserver reliability were checked between four assessors. The protocol was applied in 29 shelters (n=1308 dogs) in six European countries. Overall prevalence of poor health conditions was below 10%. Test-retest reliability and validity of the protocol were investigated with encouraging results. A logistic regression was carried out to assess the potential of the protocol as a tool to identify welfare hazards in shelter environments. Inappropriate space allowance, for example, was found to be a risk factor potentially affecting the animal's cleanliness, skin condition and body condition. The protocol was designed to be concise and easy to implement. Systematic data collection could help identify welfare problems that are likely to arise in certain shelter designs and thus determine improvement in animal care standards.

Location-routing problems of semi-obnoxious facilities: approaches and decision support

A presente tese resulta de um trabalho de investigação cujo objectivo se centrou no problema de localização-distribuição (PLD) que pretende abordar, de forma integrada, duas actividades logísticas intimamente relacionadas: a localização de equipamentos e a distribuição de produtos. O PLD, nomeadamente a sua modelação matemática, tem sido estudado na literatura, dando origem a diversas aproximações que resultam de diferentes cenários reais. Importa portanto agrupar as diferentes variantes por forma a facilitar e potenciar a sua investigação. Após fazer uma revisão e propor uma taxonomia dos modelos de localização-distribuição, este trabalho foca-se na resolução de alguns modelos considerados como mais representativos. É feita assim a análise de dois dos PLDs mais básicos (os problema capacitados com procura nos nós e nos arcos), sendo apresentadas, para ambos, propostas de resolução. Posteriormente, é abordada a localização-distribuição de serviços semiobnóxios. Este tipo de serviços, ainda que seja necessário e indispensável para o público em geral, dada a sua natureza, exerce um efeito desagradável sobre as comunidades contíguas. Assim, aos critérios tipicamente utilizados na tomada de decisão sobre a localização destes serviços (habitualmente a minimização de custo) é necessário adicionar preocupações que reflectem a manutenção da qualidade de vida das regiões que sofrem o impacto do resultado da referida decisão. A abordagem da localização-distribuição de serviços semiobnóxios requer portanto uma análise multi-objectivo. Esta análise pode ser feita com recurso a dois métodos distintos: não interactivos e interactivos. Ambos são abordados nesta tese, com novas propostas, sendo o método interactivo proposto aplicável a outros problemas de programação inteira mista multi-objectivo. Por último, é desenvolvida uma ferramenta de apoio à decisão para os problemas abordados nesta tese, sendo apresentada a metodologia adoptada e as suas principais funcionalidades. A ferramenta desenvolvida tem grandes preocupações com a interface de utilizador, visto ser direccionada para decisores que tipicamente não têm conhecimentos sobre os modelos matemáticos subjacentes a este tipo de problemas.

New sensing materials of molecularly-imprinted polymers for the selective recognition of Chlortetracycline

As a result of the stressful conditions in aquaculture facilities there is a high risk of bacterial infections among cultured fish. Chlortetracycline (CTC) is one of the antimicrobials used to solve this problem. It is a broad spectrum antibacterial active against a wide range of Gram-positive and Gram-negative bacteria. Numerous analytical methods for screening, identifying, and quantifying CTC in animal products have been developed over the years. An alternative and advantageous method should rely on expeditious and efficient procedures providing highly specific and sensitive measurements in food samples. Ion-selective electrodes (ISEs) could meet these criteria. The only ISE reported in literature for this purpose used traditional electro-active materials. A selectivity enhancement could however be achieved after improving the analyte recognition by molecularly imprinted polymers (MIPs). Several MIP particles were synthesized and used as electro-active materials. ISEs based in methacrylic acid monomers showed the best analytical performance according to slope (62.5 and 68.6 mV/decade) and detection limit (4.1 × 10−5 and 5.5 × 10−5 mol L−1). The electrodes displayed good selectivity. The ISEs are not affected by pH changes ranging from 2.5 to 13. The sensors were successfully applied to the analysis of serum, urine and fish samples.

New methods for detecting antibiotic resistant bacteria and preventing their spread

Methicillin resistant Staphylococcus aureus (MRSA) bacteria have emerged in the early 1980's in numerous health care institutions around the world. The main transmission mechanism within hospitals and healthcare facilities is through the hands of health care workers. Resistant to several antibiotics, the MRSA is one of the most feared pathogens in the hospital setting since it is very difficult to eradicate with the standard treatments. There are still a limited number of anti-MRSA antibiotics but the first cases of resistance to these compounds have already been reported and their frequency is likely to increase in the coming years. Every year, the MRSA infections result in major human and financial costs, due to the high associated mortality and expenses related to the required care. Measures towards a faster detection of resistant bacteria and establishment of appropriate antibiotic treatment parameters are fundamental. Also as part as infection prevention, diminution of bacteria present on the commonly touched surfaces could also limit the spread and selection of antibiotic resistant bacteria. During my thesis, projects were developed around MRSA and antibiotic resistance investigation using innovative technologies. The thesis was subdivided in three main parts with the use of atomic force microscopy AFM for antibiotic resistance detection in part 1, the importance of the bacterial inoculum size in the selection of antibiotic resistance in part 2 and the testing of antimicrobial surfaces creating by sputtering copper onto polyester in part 3. In part 1 the AFM was used two different ways, first for the measurement of stiffness (elasticity) of bacteria and second as a nanosensor for antibiotic susceptibility testing. The stiffness of MRSA with different susceptibility profiles to vancomycin was investigated using the stiffness tomography mode of the AFM and results have demonstrated and increased stiffness in the vancomycin resistant strains that also paralleled with increased thickness of the bacterial cell wall. Parts of the AFM were also used to build a new antibiotic susceptibility-testing device. This nano sensor was able to measure vibrations emitted from living bacteria that ceased definitively upon antibiotic exposure to which they were susceptible but restarted after antibiotic removal to which they were resistant, allowing in a matter of minute the assessment of antibiotic susceptibility determination. In part 2 the inoculum effect (IE) of vancomycin, daptomycin and linezolid and its importance in antibiotic resistance selection was investigated with MRSA during a 15 days of cycling experiment. Results indicated that a high bacterial inoculum and a prolonged antibiotic exposure were two key factors in the in vitro antibiotic resistance selection in MRSA and should be taken into consideration when choosing the drug treatment. Finally in part 3 bactericidal textile surfaces were investigated against MRSA. Polyesters coated after 160 seconds of copper sputtering have demonstrated a high bactericidal activity reducing the bacterial load of at least 3 logio after one hour of contact. -- Au cours des dernières décennies, des bactéries multirésistantes aux antibiotiques (BMR) ont émergé dans les hôpitaux du monde entier. Depuis lors, le nombre de BMR et la prévalence des infections liées aux soins (IAS) continuent de croître et sont associés à une augmentation des taux de morbidité et de mortalité ainsi qu'à des coûts élevés. De plus, le nombre de résistance à différentes classes d'antibiotiques a également augmenté parmi les BMR, limitant ainsi les options thérapeutiques disponibles lorsqu'elles ont liées a des infections. Des mesures visant une détection plus rapide des bactéries résistantes ainsi que l'établissement des paramètres de traitement antibiotiques adéquats sont primordiales lors d'infections déjà présentes. Dans une optique de prévention, la diminution des bactéries présentes sur les surfaces communément touchées pourrait aussi freiner la dissémination et l'évolution des bactéries résistantes. Durant ma thèse, différents projets incluant des nouvelles technologies et évoluant autour de la résistance antibiotique ont été traités. Des nouvelles technologies telles que le microscope à force atomique (AFM) et la pulvérisation cathodique de cuivre (PCC) ont été utilisées, et le Staphylococcus aureus résistant à la méticilline (SARM) a été la principale BMR étudiée. Deux grandes lignes de recherche ont été développées; la première visant à détecter la résistance antibiotique plus rapidement avec l'AFM et la seconde visant à prévenir la dissémination des BMR avec des surfaces crées grâce à la PCC. L'AFM a tout d'abord été utilisé en tant que microscope à sonde locale afin d'investiguer la résistance à la vancomycine chez les SARMs. Les résultats ont démontré que la rigidité de la paroi augmentait avec la résistance à la vancomycine et que celle-ci corrélait aussi avec une augmentation de l'épaisseur des parois, vérifiée grâce à la microscopie électronique. Des parties d'un AFM ont été ensuite utilisées afin de créer un nouveau dispositif de test de sensibilité aux antibiotiques, un nanocapteur. Ce nanocapteur mesure des vibrations produites par les bactéries vivantes. Après l'ajout d'antibiotique, les vibrations cessent définitivement chez les bactéries sensibles à l'antibiotique. En revanche pour les bactéries résistantes, les vibrations reprennent après le retrait de l'antibiotique dans le milieu permettant ainsi, en l'espace de minutes de détecter la sensibilité de la bactérie à un antibiotique. La PCC a été utilisée afin de créer des surfaces bactéricides pour la prévention de la viabilité des BMR sur des surfaces inertes. Des polyesters finement recouverts de cuivre (Cu), connu pour ses propriétés bactéricides, ont été produits et testés contre des SARMs. Une méthode de détection de viabilité des bactéries sur ces surfaces a été mise au point, et les polyesters obtenus après 160 secondes de pulvérisation au Cu ont démontré une excellente activité bactéricide, diminuant la charge bactérienne d'au moins 3 logio après une heure de contact. En conclusion, l'utilisation de nouvelles technologies nous a permis d'évoluer vers de méthodes de détection de la résistance antibiotique plus rapides ainsi que vers le développement d'un nouveau type de surface bactéricide, dans le but d'améliorer le diagnostic et la gestion des BMR.

Enhancing pnemonia surveillance in acute care facilities in post SARS era : a Canadian hospital surveillance study, 2003-2004 influenza season

A retrospective study of patients hospitalized with influenza and/or pneumonia in a Niagara area community hospital for the influenza season 2003-04 was designed with the main goal of enhancing pneumonia surveillance in acute care facilities and the following specific objectives: 1) identify etiologies, factors, and clinical presentation associated with pneumonia; 2) assess the ODIN score on ICU patients to predict outcomes of severe pneumonia; 3) identify the frequency of pneumonia and influenza in a hospital setting; and 4) develop a hospital pneumonia electronic surveillance tool. A total of 172 patients' charts (50% females) were reviewed and classified into two groups: those with diagnosis of pneumonia (n=132) and those without pneumonia (n=40). The latter group consisted mainly of patients with influenza (85%). Most patients were young (<10yrs) or elderly (>71yrs). Presenting body temperature <38°C, cough symptoms, respiratory and cardiac precomorbidities were common in both groups. Pneumonia was more frequent in males (p= .032) and more likely community-acquired (98%) than nosocomial (2%). No evidence of ventilator-associated pneumonia was found. Microbiology testing in 72% of cases detected 19 different pathogens. In pneumonia patients the most common organisms were Streptococcus pneumoniae (3%), Respiratory syncytial virus (4%), and Influenza A virus (2%). Conversely, Influenza A virus was identified in 73% of non-pneumonia patients. Community-acquired influenza was more common (80%) than nosocomial influenza (20%). The ODIN score was a good predictor of mortality and the new electronic surveillance tool was an effective prototype to monitor patients in acute care, especially during influenza season. The results of this study provided baseline data on respiratory illness surveillance and demonstrated that future research, including prospective studies, is warranted in acute care facilities.

The Design and Construction of Facilities for Handling Cattle

The article focuses on the following: Cattle Perception, How to prevent Balking, Solid Fences, Flight Zone, Curved Race more Efficient, Curved Race and Crowd Pen Dimensions, Loading Ramps, Working Corral for a Large Ranch, Squeeze Chutes and Headgates, Calf Tables, Artificial Insemination Chute, New Restraint Ideas, Dipping Vats, Bruise and Injury Prevention, Washable Facilities.

Evidence of systematic approaches to innovation in facilities management

Purpose – This paper seeks to examine the nature of “service innovation” in the facilities management (FM) context. It reviews recent thinking on “service innovation” as distinct from “product innovation”. Applying these contemporary perspectives it describes UK case studies of 11 innovations in different FM organisations. These include both in-house client-based innovations and third-party innovations. Design/methodology/approach – The study described in the paper encompasses 11 different innovations that constitute a mix of process, product and practice innovations. All of the innovations stem from UK-based organisations that were subject to in-depth interviews regarding the identification, screening, commitment of resources and implementation of the selected innovations. Findings – The research suggested that service innovation is highly active in the UK FM sector. However, the process of innovation rarely followed a common formalized path. Generally, the innovations were one-shot commitments at the early stage. None of the innovations studied failed to proceed to full adoption stage. This was either due to the reluctance of participating organisations to volunteer “tested but unsuccessful” innovations or the absence of any trial methods that might have exposed an innovations shortcomings. Research limitations/implications – The selection of innovations was restricted to the UK context. Moreover, the choice of innovations was partly determined by the innovating organisation. This selection process appeared to emphasise “one-shot” high profile technological innovations, typically associated with software. This may have been at the expense of less resource intensive, bottom-up innovations. Practical implications – This paper suggests that there is a role for “research and innovation” teams within larger FM organisations, whether they are client-based or third-party. Central to this philosophy is an approach that is open to the possibility of failure. The innovations studied were risk averse with a firm commitment to proceed at the early stage. Originality/value – This paper introduces new thinking on the subject of “service innovation” to the context of FM. It presents research and development as a planned solution to innovation. This approach will enable service organisations to fully test and exploit service innovations.

The untethered facilities manager

Facilities managers have a host of skills to sustain the functionality of complex buildings, often not provided by them directly, but by the team of specialists they draw upon to effectively plan for the future, whether the resource be money, space or technology. Building intelligence presents a challenge in terms of understanding a wholly new approach to the building management. This paper asks if the intelligent building of today meets the needs of the facilities management team. Does it enable them to manage their asset more effectively? New technologies are converging that will enable a radically new approach to maintenance, enabling remote smart sensing or remote condition based monitoring (CBM). Some of the design and economic issues that arise from this radically new approach to managing built assets are highlighted and the possibilities for a maintenance environment, where wires, power cables and data loggers become a thing of the past, is described.

Recent trends in UK Government policy on the provision and management of leisure facilities

Since the first election victory of the Thatcher administration in 1979, Britain has witnessed a cultural transformation from the municipal socialism of the post-World War 2 Welfare State to a form of post-industrial entrepreneurialism. This has had a profound effect on all aspects of civil society, not least the redefinition of the role of active leisure from the 1950s evocation of 'Sport For All' to the market rationality of the 1980s. The transformation has signalled a shift from government support for active leisure as an element of citizen rights to the use of leisure to promote the government's interest in legitimating a new social order based not on rights but on means. Thus access to active living is no longer a societal goal for all, but a discretionary consumer good, the consumption of which signifies 'active' citizenship. It furthermore signifies differentiation from the growing mass of 'deviants' who are unwilling or unable to embrace this new construction of citizenship and are, therefore, increasingly denied access to active living and, hence, active citizenship.

The impact of information and communications technology on commercial real estate in the new economy

Purpose – This paper seeks to critically review the conceptual frameworks that have been developed for assessing the impact of information and communications technology (ICT) on real estate. Design/methodology/approach – The research is based on a critical review of existing literature and draws from examples of previous empirical research in the field. Findings – The paper suggests that a “socio-technical framework” is more appropriate to examine ICT impact in real estate than other “deterministic” frameworks. Therefore, ICT is an important part of the new economy, but must be seen in the context of a number of other social and economic factors. Research limitations/implications – The research is based on a qualitative assessment of existing frameworks, and by using examples from commercial real estate, assesses the extent to which a “socio-technical” framework can aid understanding of ICT impact. Practical implications – The paper is important in highlighting a number of the main issues in conceptualising ICT impact in real estate and also critically examines the emergence of a new economy in the information society within the general context of real estate. The paper also highlights research gaps in the field. Originality/value – The paper deconstructs the myths of the “death of real estate” and “productivity increase means jobs loss”, in relation to office real estate. Finally, it examines some of the ways in which ICT is impacting on real estate and suggests the most important components for a future research agenda in the field of ICT and real estate impact, and will be of value to property investors, facilities managers, developers, financiers, and others.

Developing temporary manufacturing facilities for residential building: a case of the modern flying factory

The building industry is often berated for its short comings in meeting up with the demand for the provision of new housing. Addressing the need for new housing stock is a challenge that has led to debates among professional bodies, the construction sector, housing industry and government. The introduction of new manufacturing technologies is often offered as a solution, but the challenges of increasing the amount of off-site construction in residential building are well known and well-rehearsed. The modern flying factory (MFF) is a concept that involves the manufacture of specific components or modules in temporary off- or near- site locations using relatively simple and quick to set up and dismantle technologies and processes. The aim is to produce short batches and hence achieve some of the benefits of off-site manufacture on a much smaller scale than in dedicated factory environments. A case study of a modern flying factory being set up to produce pre-assembled utility cupboards for a large residential development in London is presented, involving participant observation and informal interviews with key actors on the design and operationalising of the process. The case reveals that although there are costs, efficiency and health and safety benefits to using MFF approaches, there are also challenges to overcome over the time required to set up and establish the process for relatively short runs, and in evaluating whether the MFF or traditional site based production is most effective for particular aspects of projects.

Contingent Edis: a new contractual framework for minimizing the risk of incentive failures

Granting economic development incentives (or “EDIs”) has become commonplace throughout the United States, but the efficiency of these mechanisms is generally unwarranted. Both the politicians granting, and the companies seeking, EDIs have incentives to overestimate the EDIs benefits. For politicians, ribbon–cutting ceremonies can be the highly desirable opportunity to please political allies and financiers, and the same time that they demonstrate to the population that they are successful in promoting economic growth – even when the population would be better off otherwise. In turn, businesses are naturally prone to seek governmental aid. This explains in part why EDIs often “fail” (i.e. don’t pay–off). To increase transparency and mitigate the risk of EDI failure, local and state governments across the country have created a number of accountability mechanisms. The general trait of these accountability mechanisms is that they apply controls to some of the sub–risks that underlie the risk of EDI failure. These sub–risks include the companies receiving EDIs not generating the expected number of jobs, not investing enough in their local facilities, not attracting the expected additional businesses investments to the jurisdiction, etc. The problem with such schemes is that they tackle the problem of EDI failure very loosely. They are too narrow and leave multiplier effects uncontrolled. I propose novel contractual framework for implementing accountability mechanisms. My suggestion is to establish controls on the risk of EDI failure itself, leaving its underlying sub–risks uncontrolled. I call this mechanism “Contingent EDIs”, because the EDIs are made contingent on the government achieving a preset target that benchmarks the risk of EDI failure. If the target is met, the EDIs will ex post kick in; if not, then the EDIs never kick in.

Developing new radiotherapy techniques using linac based gamma radiation sources

A major challenge in cancer radiotherapy is to deliver a lethal dose of radiation to the target volume while minimizing damage to the surrounding normal tissue. We have proposed a model on how treatment efficacy might be improved by interfering with biological responses to DNA damage using exogenous electric fields as a strategy to drastically reduce radiation doses in cancer therapy. This approach is demonstrated at this Laboratory through case studies with prokaryotes (bacteria) and eukaryotes (yeast) cells, in which cellkilling rates induced by both gamma radiation and exogenous electric fields were measured. It was found that when cells exposed to gamma radiation are immediately submitted to a weak electric field, cell death increases more than an order of magnitude compared to the effect of radiation alone. This finding suggests, although does not prove, that DNA damage sites are reached and recognized by means of long-range electric DNA-protein interaction, and that exogenous electric fields could destructively interfere with this process. As a consequence, DNA repair is avoided leading to massive cell death. Here we are proposing the use this new technique for the design and construction of novel radiotherapy facilities associated with linac generated gamma beams under controlled conditions of dose and beam intensity.