A new method for identification of protein (sub)families in a set of proteins based on hydropathy distribution in proteins

Structural similarity among proteins is reflected in the distribution of hydropathicity along the amino acids in the protein sequence. Similarities in the hydropathy distributions are obvious for homologous proteins within a protein family. They also were observed for proteins with related structures, even when sequence similarities were undetectable. Here we present a novel method that employs the hydropathy distribution in proteins for identification of (sub)families in a set of (homologous) proteins. We represent proteins as points in a generalized hydropathy space, represented by vectors of specifically defined features. The features are derived from hydropathy of the individual amino acids. Projection of this space onto principal axes reveals groups of proteins with related hydropathy distributions. The groups identified correspond well to families of structurally and functionally related proteins. We found that this method accurately identifies protein families in a set of proteins, or subfamilies in a set of homologous proteins. Our results show that protein families can be identified by the analysis of hydropathy distribution, without the need for sequence alignment. (C) 2005 Wiley-Liss, Inc.

The costs of caring for patients in a tertiary referral Australian intensive care unit

We determined the direct cost of an Intensive Care Unit (ICU) bed in a tertiary referral Australian ICU and the cost drivers thereof, by retrospectively analysing a number of prospectively designed Hospital- and Unit-specific electronic databases. The study period was a financial year, from 1 July 2002 to 30 June 2003. There were 1615 patients occupying 5692 fractional occupied bed days at a total cost of A$15,915,964, with an average length of stay of 3.69 days (range 0.5-77, median 1.06, interquartile range 2.33). The main cost driver not incorporated into this analysis was blood products (paid for centrally). The average costs of an ICU day and total stay per patient were A$2670 and A$9852 respectively. Staff-related charges were 68.76%, with consumables related expenditure making up 19.65%, clinical support services 9.55% and capital equipment 2.04%. Overtime charges and nursing agency staff were 19.4% of staff-related charges (2.9% for agency staff), 3.9% lower than expenditure associated with full-time employment charges, such as pension and leave. The emergency nature of ICU means it is difficult to accurately set a nursing establishment to cater for all admissions and therefore it is hard to decide what is an acceptable percentage difference between agency/overtime costs compared with the costs associated with full-time staff appointments. Consumable expenditure is likely to increase the most with new innovation and therapies. Using protocol driven practices may tighten and control costs incurred in ICU.

Nitrogen balance for an agroforestry system irrigated with saline, high nitrogen effluent

Land disposal is commonly used for urban and industrial wastewater, largely due to the high costs involved in alternative treatments or disposal systems. However, the viability of such systems depends on many factors, including the composition of the effluent water, soil type, the plant species grown, growth rate, and planting density. The objective of this study is to establish whether land disposal of nitrogen (N) rich effluent using an agroforestry system is sustainable, and determine the effect of irrigation rate and tree planting density on the N cycle and subsequent N removal. We examined systems for the sustainable disposal of a high strength industrial effluent. The challenge was to leach the salt, by using a sufficiently high rate of irrigation, while simultaneously ensuring that N did not leach from the soil profile. We describe the N balance for two plant systems irrigated with effluent, one comprising Eucalyptus tereticornis and Eucalyptus moluccana and a Rhodes grass (Chloris gayana) pasture, and the other, Rhodes grass pasture alone. Nitrogen balance was assessed from N inputs in effluent and rainfall, accumulation of N in the plant biomass, changes in soil N storage, N loss in run-off water, denitrification and N loss to the groundwater by deep-drainage. Biomass production was estimated from allometric relationships derived from yearly destructive harvesting of selected trees. The N content of that biomass was then calculated from measured N content of the various plant parts, and their mass. Approximately 300 kg N/ha/yr was assimilated into tree biomass at a planting density of 2500 tree/ha of E. moluccana. In addition to tree assimilation, pasture growth between the tree rows, which was regularly harvested, contributed substantially to N uptake. If the trees were harvested after two years of growth and grass harvested regularly, biomass removal of N by the mixed system would be about 700 kg N/ha/yr. The results of this study show that the current system of effluent disposal is not sustainable as the nitrate leaching from the soil profile far exceeds standards set out by the ANZECC guidelines. Hence additional means of N removal will need to be implemented. Biological N removal is an area that warrants further studies as it is aimed at reducing N levels in the effluent before irrigation. This will complement the current agroforestry system.

ANÁLISE DAS MUDANÇAS DOS FATORES DETERMINANTES DA ESTRUTURA DE CAPITAL EM FUNÇÃO DO CICLO DE VIDA DAS EMPRESAS BRASILEIRAS SÃO BERNARDO DO CAMPO

As várias teorias acerca da estrutura de capital despertam interesse motivando diversos estudos sobre o assunto sem, no entanto, ter um consenso. Outro tema aparentemente pouco explorado refere-se ao ciclo de vida das empresas e como ele pode influenciar a estrutura de capital. Este estudo teve como objetivo verificar quais determinantes possuem maior relevância no endividamento das empresas e se estes determinantes alteram-se dependendo do ciclo de vida da empresa apoiada pelas teorias Trade Off, Pecking Order e Teoria da Agência. Para alcançar o objetivo deste trabalho foi utilizado análise em painel de efeito fixo sendo a amostra composta por empresas brasileiras de capital aberto, com dados secundários disponíveis na Economática® no período de 2005 a 2013, utilizando-se os setores da BM&FBOVESPA. Como resultado principal destaca-se o mesmo comportamento entre a amostra geral, alto e baixo crescimento pelo endividamento contábil para o determinante Lucratividade apresentando uma relação negativa, e para os determinantes Oportunidade de Crescimento e Tamanho, estes com uma relação positiva. Para os grupos de alto e baixo crescimento alguns determinantes apresentaram resultados diferentes, como a singularidade que resultou significância nestes dois grupos, sendo positiva no baixo crescimento e negativa no alto crescimento, para o valor colateral dos ativos e benefício fiscal não dívida apresentaram significância apenas no grupo de baixo crescimento. Para o endividamento a valor de mercado foi observado significância para o Benefício fiscal não dívida e Singularidade. Este resultado reforça o argumento de que o ciclo de vida influência a estrutura de capital

Seeing blur:'Motion sharpening' without motion

It is widely supposed that things tend to look blurred when they are moving fast. Previous work has shown that this is true for sharp edges but, paradoxically, blurred edges look sharper when they are moving than when stationary. This is 'motion sharpening'. We show that blurred edges also look up to 50% sharper when they are presented briefly (8-24 ms) than at longer durations (100-500 ms) without motion. This argues strongly against high-level models of sharpening based specifically on compensation for motion blur. It also argues against a recent, low-level, linear filter model that requires motion to produce sharpening. No linear filter model can explain our finding that sharpening was similar for sinusoidal and non-sinusoidal gratings, since linear filters can never distort sine waves. We also conclude that the idea of a 'default' assumption of sharpness is not supported by experimental evidence. A possible source of sharpening is a nonlinearity in the contrast response of early visual mechanisms to fast or transient temporal changes, perhaps based on the magnocellular (M-cell) pathway. Our finding that sharpening is not diminished at low contrast sets strong constraints on the nature of the nonlinearity.

An experimental analysis of operating conditions in cold roll-forming

A detailed literature survey confirmed cold roll-forming to be a complex and little understood process. In spite of its growing value, the process remains largely un-automated with few principles used in set-up of the rolling mill. This work concentrates on experimental investigations of operating conditions in order to gain a scientific understanding of the process. The operating conditions are; inter-pass distance, roll load, roll speed, horizontal roll alignment. Fifty tests have been carried out under varied operating conditions, measuring section quality and longitudinal straining to give a picture of bending. A channel section was chosen for its simplicity and compatibility with previous work. Quality measurements were measured in terms of vertical bow, twist and cross-sectional geometric accuracy, and a complete method of classifying quality has been devised. The longitudinal strain profile was recorded, by the use of strain gauges attached to the strip surface at five locations. Parameter control is shown to be important in allowing consistency in section quality. At present rolling mills are constructed with large tolerances on operating conditions. By reduction of the variability in parameters, section consistency is maintained and mill down-time is reduced. Roll load, alignment and differential roll speed are all shown to affect quality, and can be used to control quality. Set-up time is reduced by improving the design of the mill so that parameter values can be measured and set, without the need for judgment by eye. Values of parameters can be guided by models of the process, although elements of experience are still unavoidable. Despite increased parameter control, section quality is variable, if only due to variability in strip material properties. Parameters must therefore be changed during rolling. Ideally this can take place by closed-loop feedback control. Future work lies in overcoming the problems connected with this control.

Ireland:from racism without ‘race’, to ‘racism without racists’

The Irish have been relentlessly racialized in their diaspora settings, yet little historical work engages with “race” to understand Irish history on the island of Ireland. This article provides an interpretation of two key periods of Irish history—the second half of the sixteenth century and the period since 1996—through the lens of racialization. I argue that Ireland's history is exceptional in its capacity to reveal key elements of the history of the development of race as an idea and a set of practices. The English colonization of Ireland was underpinned by a form of racism reliant on linking bodies to unchanging hierarchically stacked cultures, without reference to physical differences. For example, the putative unproductiveness of the Gaelic Irish not only placed them at a lower level of civilization than the industrious English but it also authorizes increasingly draconian ways of dealing with the Irish populace. The period since 1996, during which Ireland has become a country of immigration, illustrates how racism has undergone a transformation into the object of official state policies to eliminate it. Yet it flourishes as part of a globalized set of power relations that has brought immigrants to the developing Irish economy. In response to immigration the state simultaneously exerts neoliberal controls and reduces pathways to citizenship through residence while passing antiracism legislation. Today, the indigenous nomadic Travellers and asylum seekers are the ones that are seen as pathologically unproductive. Irish history thus demonstrates that race is not only about color but also very much about culture. It also illustrates notable elements of the West's journey from racism without race to racism without racists.

Estimating the scope for savings in referrals and drug prescription costs in the general Practice units of a UK primary care trust

This paper explores the potential for cost savings in the general Practice units of a Primary Care Trust (PCT) in the UK. We have used Data Envelopment Analysis (DEA) to identify benchmark Practices, which offer the lowest aggregate referral and drugs costs controlling for the number, age, gender, and deprivation level of the patients registered with each Practice. For the remaining, non-benchmark Practices, estimates of the potential for savings on referral and drug costs were obtained. Such savings could be delivered through a combination of the following actions: (i) reducing the levels of referrals and prescriptions without affecting their mix (£15.74 m savings were identified, representing 6.4% of total expenditure); (ii) switching between inpatient and outpatient referrals and/or drug treatment to exploit differences in their unit costs (£10.61 m savings were identified, representing 4.3% of total expenditure); (iii) seeking a different profile of referral and drug unit costs (£11.81 m savings were identified, representing 4.8% of total expenditure). © 2012 Elsevier B.V. All rights reserved.

Interval data without sign restrictions in DEA

Conventional DEA models assume deterministic, precise and non-negative data for input and output observations. However, real applications may be characterized by observations that are given in form of intervals and include negative numbers. For instance, the consumption of electricity in decentralized energy resources may be either negative or positive, depending on the heat consumption. Likewise, the heat losses in distribution networks may be within a certain range, depending on e.g. external temperature and real-time outtake. Complementing earlier work separately addressing the two problems; interval data and negative data; we propose a comprehensive evaluation process for measuring the relative efficiencies of a set of DMUs in DEA. In our general formulation, the intervals may contain upper or lower bounds with different signs. The proposed method determines upper and lower bounds for the technical efficiency through the limits of the intervals after decomposition. Based on the interval scores, DMUs are then classified into three classes, namely, the strictly efficient, weakly efficient and inefficient. An intuitive ranking approach is presented for the respective classes. The approach is demonstrated through an application to the evaluation of bank branches. © 2013.

Representing "Recursive" Default Logic in Modal Logic

The "recursive" definition of Default Logic is shown to be representable in a monotonic Modal Quantificational Logic whose modal laws are stronger than S5. Specifically, it is proven that a set of sentences of First Order Logic is a fixed-point of the "recursive" fixed-point equation of Default Logic with an initial set of axioms and defaults if and only if the meaning of the fixed-point is logically equivalent to a particular modal functor of the meanings of that initial set of sentences and of the sentences in those defaults. This is important because the modal representation allows the use of powerful automatic deduction systems for Modal Logic and because unlike the original "recursive" definition of Default Logic, it is easily generalized to the case where quantified variables may be shared across the scope of the components of the defaults.

Representing Default Logic in Modal Logic

The nonmonotonic logic called Default Logic is shown to be representable in a monotonic Modal Quantificational Logic whose modal laws are stronger than S5. Specifically, it is proven that a set of sentences of First Order Logic is a fixed-point of the fixed-point equation of Default Logic with an initial set of axioms and defaults if and only if the meaning or rather disquotation of that set of sentences is logically equivalent to a particular modal functor of the meanings of that initial set of sentences and of the sentences in those defaults. This result is important because the modal representation allows the use of powerful automatic deduction systems for Modal Logic and because unlike the original Default Logic, it is easily generalized to the case where quantified variables may be shared across the scope of the components of the defaults thus allowing such defaults to produce quantified consequences. Furthermore, this generalization properly treats such quantifiers since both the Barcan Formula and its converse hold.

Connection design without accurate LV feeder load data:an argument for LV monitoring

Since privatisation, maintenance of DNO LV feeder maximum demand information has gradually demised in some Utility Areas, and it is postulated that lack of knowledge about 11kV and LV electrical networks is resulting in a less economical and energy efficient Network as a whole. In an attempt to quantify the negative impact, this paper examines ten postulated new connection scenarios for a set of real LV load readings, in order to find the difference in design solutions when LV load readings were and were not known. The load profiles of the substations were examined in order to explore the utilisation profile. It was found that in 70% of the scenarios explored, significant cost differences were found. These cost differences varied by an average of 1000%, between schemes designed with and without load readings. Obviously, over designing a system and therefore operating more, underutilised transformers becomes less financially beneficial and less energy efficient. The paper concludes that new connection design is improved in terms of cost when carried out based on known LV load information and enhances the case for regular maximum feeder demand information and/or metering of LV feeders. © 2013 IEEE.

Medicines optimisation for young people with juvenile arthritis and other long-term conditions:system-level barriers to engagement

To explore the views of pharmacy and rheumatology stakeholders about system-related barriers to medicines optimisation activities with young people with long-term conditions. A three-phase consensus-building study comprising (1) focus groups with community and hospital pharmacists; (2) semi-structured telephone interviews with lay and professional adolescent rheumatology stakeholders and pharmacy policymakers, and (3) multidisciplinary discussion groups with community and hospital pharmacists and rheumatology staff. Qualitative verbatim transcripts from phases 1 and 2 were subjected to framework analysis. Themes from phase 1 underpinned a briefing for phase 2 interviewees. Themes from phases 1 and 2 generated elements of good pharmacy practice and current/future pharmacy roles for ranking in phase 3. Results from phase 3 prioritisation and ranking exercises were captured on self-completion data collection forms, entered into an Excel spreadsheet and subjected to descriptive statistical analysis. Institutional ethical approval was given by Aston University Health and Life Sciences Research Ethics Committee. Four focus groups were conducted with 18 pharmacists across England, Scotland and Wales (7 hospital, 10 community and 1 community/public health). Fifteen stakeholders took part in telephone interviews (3 pharmacist commissioners; 2 pharmacist policymakers; 2 pharmacy staff members (1 community and 1 hospital); 4 rheumatologists; 1 specialist nurse, and 3 lay juvenile arthritis advocates). Twenty-five participants took part in three discussion groups in adolescent rheumatology centres across England and Scotland (9 community pharmacists; 4 hospital pharmacists; 6 rheumatologists; 5 specialist nurses, and 1 physiotherapist). In all phases of the study, system-level issues were acknowledged as barriers to more engagement with young people and families. Community pharmacists in the focus groups reported that opportunities for engaging with young people were low if parents collected prescriptions alone, which was agreed by other stakeholders. Moreover, institutional/company prescription collection policies – an activity largely disallowed for a young person under 16 without an accompanying parent - were identified by hospital and community pharmacists as barriers to open discussion and engagement. Few community pharmacists reported using Medicines Use Review (England/Wales) or Chronic Medication Service (Scotland) as a medicines optimisation activity with young people; many were unsure about consent procedures. Despite these limitations, rheumatology stakeholders ranked highly the potential of pharmacists empowering young people with general health care skills, such as repeat prescription ordering. The pharmacy profession lacks vision for its role in the care of young people with long-term conditions. Pharmacists and rheumatology stakeholders identified system-level barriers to more engagement with young people who take medicines regularly. We acknowledge that the modest number of participants may have had a specific interest and thus bias for the topic, but this underscores their frank admission of the challenges. Professional guidance and policy, practice frameworks and institutional/company policies must promote flexibility for pharmacy staff to recognise and empower young people who are able to give consent and take responsibility for medicines activities. This will increase mutual confidence and trust, and foster pharmacy’s role in teaching general health care skills. In this way, pharmacists will be able to build long-term relationships with young people and families.

Virtuális árhatás a Budapesti Értéktőzsdén = Virtual price effects on the Budapest stock exchange

Az árhatásfüggvények azt mutatják meg, hogy egy adott értékű megbízás mekkora relatív árváltozást okoz. Az árhatásfüggvény ismerete a piaci szereplők számára fontos szerepet játszik a jövőben benyújtandó ajánlataikhoz kapcsolódó árhatás előrejelzésében, a kereskedés árváltozásból eredő többletköltségének becslésében, illetve az optimális kereskedési algoritmus kialakításában. Az általunk kidolgozott módszer révén a piaci szereplők a teljes ajánlati könyv ismerete nélkül egyszerűen és gyorsan tudnak virtuális árhatásfüggvényt meghatározni, ugyanis bemutatjuk az árhatásfüggvény és a likviditási mértékek kapcsolatát, valamint azt, hogy miként lehet a Budapesti Likviditási Mérték (BLM) idősorából ár ha tás függ vényt becsülni. A kidolgozott módszertant az OTP-részvény idősorán szemléltetjük, és a részvény BLM-adatsorából a 2007. január 1-je és 2011. június 3-a közötti időszakra virtuális árhatás függvényt becsülünk. Empirikus elemzésünk során az árhatás függ vény időbeli alakulásának és alapvető statisztikai tulajdonságainak vizsgálatát végezzük el, ami révén képet kaphatunk a likviditás hiányában fellépő tranzakciós költségek múltbeli viselkedéséről. Az így kapott információk például a dinamikus portfólióoptimalizálás során lehetnek a kereskedők segítségére. / === / Price-effect equations show what relative price change a commission of a given value will have. Knowledge of price-effect equations plays an important part in enabling market players to predict the price effect of their future commissions and to develop an optimal trading algorithm. The method devised by the authors allows a virtual price-effect equation to be defined simply and rapidly without knowledge of the whole offer book, by presenting the relation between the price-effect equation and degree of liquidity, and how to estimate the price-effect equation from the time line of the Budapest Liquidity Measure (BLM). The methodology is shown using the time line for OTP shares and the virtual price-effect equation estimated for the 1 January 2007 to 3 June 2011 period from the shares BML data set. During the empirical analysis the authors conducted an examination of the tendency of the price-effect equation over time and for its basic statistical attributes, to yield a picture of the past behaviour of the transaction costs arising in the absence of liquidity. The information obtained may, for instance, help traders in dynamic portfolio optimization.

Az államcsőd költségei régen és ma (Costs of sovereign defaults now and long ago)

Az államoknak nyújtott hitelekre gyakran gondolunk biztonságos befektetésként, lehetetlen vagy legalábbis valószerűtlen kimenetelként kezelve az államcsőd lehetőségét. Pedig államcsődök azóta vannak, amióta szuverén államok hitelt vesznek fel, és még csak nem is ritka eseményekről van szó. Amikor egy-egy válság vagy csődesemény felhívja erre a figyelmünket, a leggyakrabban elhangzó kérdés az, hogy miért következett be a csőd. Ebben a tanulmányban a szerző ennél furcsább kérdésre hívja fel a figyelmet: mi késztet egy hitelt felvevő államot arra, hogy visszafizesse hiteleit, vagyis miért nem megy csődbe? Ez rögtön felvet egy további, talán még meglepőbb problémát: miért kap egyáltalán egy szuverén állam hitelt? Ezekre a kérdésekre már régóta tudni véljük a választ: azért, mert az államcsődnek költségei vannak. A lehetséges költségek és a hozzájuk kapcsolódó empirikus kutatások értelmezésével és rendszerezésével, az ellentmondások feltárásával azonban a szerző felhívja a figyelmet arra, hogy bár elképzeléseink vannak és lehetnek, valójában nem ismerjük a törlesztést kikényszerítő és így az államadósságok létezését biztosító mechanizmusokat. Talán éppen azért nem, mert az államcsőd lehetséges politikai, gazdasági következményei - azaz költségei - idővel legalább annyira változnak, mint öltözködési, étkezési és közlekedési szokásaink. ____ Loans to sovereign states are often referred to as safe investments, treating default as an impossible or at least improbable event. Yet sovereign defaults have been arising ever since countries borrowed money. They are not rare at all. When a debt crisis or default event draws attention to the problem, the commonest question put is why defaults occur. This paper stresses the need to ask a less common question as well: why sovereign states repay loans, why they do not default. Consequent on that is why rational lenders give money to countries. The answer to these questions seems to be because defaults are costly. The paper reviews and systematizes possible cost types and explores inconsistencies in the related literature, to show that the mechanisms supporting the existence of sovereign debts are not precisely known. One reason why costs of defaults are challenging to study may be that the possible political and economic consequences of defaults change over time.