bluuebunny/crossref_metadata_2025_split huggingface dataset:
Polyphosphate Accumulation in
Escherichia coli
in Response to Defects in DNA Metabolism
Authors: Amado Luciana , Kuzminov Andrei 
Published: October 2009

ABSTRACT

Phenol-chloroform extraction of [
32
P]orthophosphate-labeled
E
scherichia coli
cells followed by alkaline gel electrophoresis revealed, besides the expected chromosomal DNA, two non-DNA species that we have identified as lipopolysaccharides and polyphosphates by using a combination of biochemical and genetic techniques. We used this serendipitously found straightforward protocol for direct polyphosphate detection to quantify polyphosphate levels in
E. coli
mutants with diverse defects in the DNA metabolism. We detected increased polyphosphate accumulation in the
ligA
,
ligA recBCD
,
dut ung
, and
thyA
mutants. Polyphosphate accumulation may thus be an indicator of general DNA stress.
Purely functional lazy non-deterministic programming
Authors: Fischer Sebastian , Kiselyov Oleg , Shan Chung-chieh 
Published: October 2009

Functional logic programming and probabilistic programming have demonstrated the broad benefits of combining laziness (non-strict evaluation with sharing of the results) with non-determinism. Yet these benefits are seldom enjoyed in functional programming, because the existing features for non-strictness, sharing, and non-determinism in functional languages are tricky to combine.
We present a practical way to write purely functional lazy non-deterministic programs that are efficient and perspicuous. We achieve this goal by embedding the programs into existing languages (such as Haskell, SML, and OCaml) with high-quality implementations, by making choices lazily and representing data with non-deterministic components, by working with custom monadic data types and search strategies, and by providing equational laws for the programmer to reason about their code.
Safe functional reactive programming through dependent types
Authors: Sculthorpe Neil , Nilsson Henrik 
Published: October 2009

Functional Reactive Programming (FRP) is an approach to reactive programming where systems are structured as networks of functions operating on signals. FRP is based on the synchronous data-flow paradigm and supports both continuous-time and discrete-time signals (hybrid systems). What sets FRP apart from most other languages for similar applications is its support for systems with dynamic structure and for higher-order reactive constructs.
Statically guaranteeing correctness properties of programs is an attractive proposition. This is true in particular for typical application domains for reactive programming such as embedded systems. To that end, many existing reactive languages have type systems or other static checks that guarantee domain-specific properties, such as feedback loops always being well-formed. However, they are limited in their capabilities to support dynamism and higher-order data-flow compared with FRP. Thus, the onus of ensuring such properties of FRP programs has so far been on the programmer as established static techniques do not suffice.
In this paper, we show how dependent types allow this concern to be addressed. We present an implementation of FRP embedded in the dependently-typed language Agda, leveraging the type system of the host language to craft a domain-specific (dependent) type system for FRP. The implementation constitutes a discrete, operational semantics of FRP, and as it passes the Agda type, coverage, and termination checks, we know the operational semantics is total, which means our type system is safe.
Effective interactive proofs for higher-order imperative programs
Authors: Chlipala Adam , Malecha Gregory , Morrisett Greg , Shinnar Avraham , Wisnesky Ryan 
Published: October 2009

We present a new approach for constructing and verifying higher-order, imperative programs using the Coq proof assistant. We build on the past work on the Ynot system, which is based on Hoare Type Theory. That original system was a proof of concept, where every program verification was accomplished via laborious manual proofs, with much code devoted to uninteresting low-level details. In this paper, we present a re-implementation of Ynot which makes it possible to implement fully-verified, higher-order imperative programs with reasonable proof burden. At the same time, our new system is implemented entirely in Coq source files, showcasing the versatility of that proof assistant as a platform for research on language design and verification. Both versions of the system have been evaluated with case studies in the verification of imperative data structures, such as hash tables with higher-order iterators. The verification burden in our new system is reduced by at least an order of magnitude compared to the old system, by replacing manual proof with automation. The core of the automation is a simplification procedure for implications in higher-order separation logic, with hooks that allow programmers to add domain-specific simplification rules.
We argue for the effectiveness of our infrastructure by verifying a number of data structures and a packrat parser, and we compare to similar efforts within other projects. Compared to competing approaches to data structure verification, our system includes much less code that must be trusted; namely, about a hundred lines of Coq code defining a program logic. All of our theorems and decision procedures have or build machine-checkable correctness proofs from first principles, removing opportunities for tool bugs to create faulty verifications.
Experience report
Authors: Sampson Curt J. 
Published: October 2009

I describe the initial attempt of experienced business software developers with minimal functional programming background to write a non-trivial, business-critical application entirely in Haskell. Some parts of the application domain are well suited to a mathematically-oriented language; others are more typically done in languages such as C++.
I discuss the advantages and difficulties of Haskell in these circumstances, with a particular focus on issues that commercial developers find important but that may receive less attention from the academic community.
I conclude that, while academic implementations of "advanced" programming languages arguably may lag somewhat behind implementations of commercial languages in certain ways important to businesses, this appears relatively easy to fix, and that the other advantages that they offer make them a good, albeit long-term, investment for companies where effective IT implementation can offer a crucial advantage to success.
Strict Contractive Conditions and Common Fixed Point Theorems in Cone Metric Spaces
Authors: Kadelburg Z. , Radenović S. , Rosić B. 
Published: October 2009

AbstractA lot of authors have proved various common fixed-point results for pairs of self-mappings under strict contractive conditions in metric spaces. In the case of cone metric spaces, fixed point results are usually proved under assumption that the cone is normal. In the present paper we prove common fixed point results under strict contractive conditions in cone metric spaces using only the assumption that the cone interior is nonempty. We modify the definition of property (E.A), introduced recently in the work by Aamri and Moutawakil (2002), and use it instead of usual assumptions about commutativity or compatibility of the given pair. Examples show that the obtained results are proper extensions of the existing ones.
Recent Developments in the Reform of English Law on Assisted Suicide
Authors: Shaw Julia 
Published: October 2009

AbstractAssisted suicide remains a deeply contested issue in the UK. Recently three Assisted Dying for the Terminally Ill Bills were introduced in a three year period, all of which failed. Despite the provision of clear and precise safeguards, at each reading the House of Lords fixed largely on the traditional slippery slope and sanctity of life positions; a disproportionate reliance on theological determinism in particular prevented informed rational debate. People are living longer often with chronic, incurable diseases and palliative care is frequently of poor quality or even unavailable in the UK and it is unacceptable that individuals 'suffering unbearably' in their final days have no available domestic alternative. Yet the courts have consistently declined to prosecute in cases where friends and relatives have accompanied terminally ill persons abroad to die, against the provisions of the 1961 Suicide Act s2(1). This article critically assesses recent developments in English law on assisted dying and considers the implications for a more inclusive and reasoned debate in the future.
Mail-Order Trade in Medicines in Europe — A Guide for Legislators to Protect Consumers
Authors: Seeberg-Elverfeldt Niels-J. 
Published: October 2009

AbstractThis article discusses mail-order trade in medicines. It explains why this trade has developed and why there is a need for strict safety standards. The European Court of Justice obliged member states to allow such trade in non prescription medicines but did not specify any safety standards. The 2007 resolution of the Council of Europe lays these down precisely. An analysis of the legal situation in the 30 EU and EEA states shows that they increasingly permit this trade. However, there are considerable deficits as regards the necessary safety standards. To protect consumers from illegal medicine sales via the internet, they should be able to easily identify legal products online. Legislators should act accordingly.
The mental gland of Bolitoglossa nicefori (Caudata: Plethodontidae)
Authors: González-León Ezequiel , Ramírez-Pinilla Martha Patricia 
Published: October 2009

AbstractThe mental gland of the plethodontid salamander Bolitoglossa nicefori was examined by macroscopic observation and light microscopy and compared with morphological descriptions of other species of Plethodontidae. The mental gland is an oval shaped pad which develops exclusively in reproductive males. It is composed of 255 to 710 simple glands of merocrine secretion arranged in a dorso-ventral disposition. The outlets of the glands are spindle-shaped or fusiform. Negative stain reaction for AB and PAS is consistent with results of the glandular components of mental glands from other Plethodontidae. Males of this species produce sperm continuously throughout the year: all examined adult males showed conspicuous mental glands. However, an evident and significant increase in the surface area of the mental gland pad, in the density of the glands, and in the number of tubular glands was observed in the males collected during the breeding season. At the histological level, a slight variation was observed among males in the height and diameter of the simple tubular glands, and significant variation was found in the diameter of the secretory granules. This variation may reflect the fact that, although males potentially can mate during all months of the year, females oviposit seasonally. During this defined season, the hypertrophy of the mental gland is the greatest.
Predation pressure, density-induced stress and tail regeneration: a casual-nexus situation or a bunch of independent factors?
Authors: Tsasi Gerasimia , Valakos Efstratios , Simou Chrysi , Pafilis Panayiotis 
Published: October 2009

AbstractCaudal autotomy, the self-induced tail shedding from the body, is a common defensive strategy in lizards. Tail loss is followed rapidly by regeneration, revealing the importance of a fully functional tail. Predation pressure has been traditionally correlated with autotomy performance. However there is a lack of evidence regarding the impact of predation regime on tail regeneration. Another important factor that has been neglected is the population density. Though it is well established that crowding alters various life-history traits, the impact of density on caudal regeneration remains understudied. In this paper we compared three island populations of the Aegean Wall Lizard (Podarcis erhardii) that have evolved under different levels of predation pressure: whereas the Naxos population is exposed to numerous predators the Kopries and Daskalio islet populations experience low predation pressure. To evaluate the effect of density-induced stress on caudal regeneration, lizards were treated under two conditions of housing, in single and crowded (six individuals) terraria. Tail sheding occurred prior to this treatment following a standardised method. The length of regenerated tail was recorded weekly. Regeneration rate was higher in single terraria when compared to crowded, reflecting the negative impact of crowding. However we failed to detect any statistically significant difference between single and crowded terraria in the case of Naxos. We believe that the underlying reason must be the heavy predation pressure under which rapid tail regeneration, even under unfavourable conditions, is crucial for survival. It seems that the imperious need for regeneration counteracts density-induced stress.
Testing the competitive exclusion principle using various niche parameters in a native (Natrix maura) and an introduced (N. tessellata) colubrid
Authors: Ursenbacher Sylvain , Christe Philippe , Metzger César 
Published: October 2009

AbstractDespite the increase of animal and plant introductions worldwide and the strong augmentation of the reptile trade, few invasive snake populations have been studied. Dice snakes (Natrix tessellata) were introduced to the shores of Lake Geneva (Switzerland) in the early 1920s, and are now well established. This region of introduction was previously inhabited by Viperine snakes (N. maura). Ever since these two species have been under monitoring (which began in 1996) the Viperine snake population has shown drastic decline. We examine here the possibility of trophic competition by analysing diet composition, prey size and trophic niche overlap. Spatial distribution is also assessed in order to address the question of spatial competitive exclusion. We found very similar diets, and thus a high trophic niche overlap, indicating no partitioning of the trophic resource. No arguments in favour of spatial competitive exclusion were found. Our study suggests that trophic competition may occur between the two natricines and that it may give an explanation for the drastic decline of the Viperine snake in this area. Other pathways potentially playing a role in the exclusion of the Viperine snake are discussed.
Diet of Hydromedusa tectifera (Testudines-Chelidae) in a mountain stream of Córdoba province, Argentina
Authors: Lescano Julián , Bonino Marcelo , Leynaud Gerardo , Haro José 
Published: October 2009

AbstractThe diet of Hydromedusa tectifera occurring in two mountain streams in the province of Córdoba is described through a comparative analysis of 154 individuals. Turtles were manually captured between August 2005 and August 2006 from streams at the localities of Tanti and Flor Serrana. Before being released, turtles were stomach-flushed, and sex and carapace length were recorded. The stomach contents were observed under stereomicroscope; prey items were identified and classified according to size and volume. The importance of the different items was quantified using the Index of Relative Importance (IRI). Similarity in the diet between sexes and among size classes and seasons of an annual cycle was evaluated using the simplified Morisita index. Trophic breadth was estimated with the Shannon diversity index. Detrended Correspondence Analysis (DCA) was used to evaluate differences in the diet between categories (sex, size classes). Forty-seven food items belonging to the following taxa were identified: leeches, annelids, gastropods, arachnids, insects, and fishes. According to the IRI value, the most important items in the diet of H. tectifera were larvae of Trichoptera (IRI = 33.5), fishes (IRI = 30), and naiads of Odonata (IRI = 25.2). The relative importance of the items varied with size of turtles but not with sex. Size of prey consumed increased with increasing turtle size. A greater trophic breadth was observed in smaller individuals.
Different habitats, different pressures? Analysis of escape behaviour and ectoparasite load in Podarcis sicula (Lacertidae) populations in different agricultural habitats
Authors: Corti Claudia , Biaggini Marta , Berti Roberto 
Published: October 2009

AbstractHuman agricultural activities can deeply alter the environment thus provoking major impacts on a variety of organisms. Agricultural habitats however can be very different from one another in terms of habitat structure and management intensity, presenting varying pressures and/or benefits for different species. Agro-ecosystems can have opposing effects on reptiles and in some circumstances the presence of a species can even been enhanced by agricultural practices. We focused our study on Podarcis sicula, a relatively widespread lacertid lizard commonly present in agro-environments in Italy. We examined escape behaviour, caudal autotomy rates and ectoparasite load (tick infestation) in populations living in two different land uses, olive tree plantations and vineyards. All three aspects seemed to be deeply influenced by habitat structure. Predation pressure, as evaluated by tail break frequency, was lower in olive tree plantations, the most structurally complex habitats. In this type of habitat lizard escape behaviour was characterised by a clear preference for olive trees as refuges: individuals ran farther distances on average to reach the trees and hid inside them for a relatively long time. In vineyards, on the contrary, a less clear escape strategy was observed, showing a use of more temporary refuges. Also tick (Ixodes ricinus) infestation differed among land uses, being higher in olive tree plantations, probably in relation to vegetation cover features. Differences were found also between managements (with a higher tick load in traditional cultivations) and sexes, with males being more parasitized.
How many Archaeolacerta inhabit the Corso-Sardinian Plate? Allozyme variation and differentiation in Archaeolacerta bedriagae (Camerano, 1885)
Authors: Bologna Marco , Capula Massimo , Salvi Daniele , Bombi Pierluigi 
Published: October 2009

AbstractArchaeolacerta bedriagae is a rock lizard endemic to Corsica and Sardinia. Four subspecies have been recozied to date on the basis of morphological traits. Previous allozyme investigations revealed high genetic differentiation among populations of the species. Based on these results some authors hypothesized that more than one species of Archaeolacerta may occur on Corsica and Sardinia. In this paper we investigated allozyme variation at 19 gene loci in 5 populations belonging to all subspecies of A. bedriagae in order to study genetic differentiation among populations from Corsica and Sardinia, and to compare our results with those obtained in previous studies carried out on allozyme variation and taxonomy of the species. Low levels of genetic differentiation (average Nei's D = 0.026) and heterogeneity (mean FST = 0.147) were found comparing the A. bedriagae populations, and there was no evidence of interruption or restriction of gene flow. This is in agreement with the available molecular and morphometric data, while it is not in accordance with allozyme data reported in the previous studies. Our data do not support the hypothesis of an unrecognized criptic species of Archaeolacerta in Corsica and Sardinia, and indicate that the definitive assessment of the taxonomic status of the A. bedriagae populations requires further investigation.
Conspicuous colouration of the vocal sac of a nocturnal chorusing treefrog: carotenoid-based?
Authors: Richardson Christina , Lengagne Thierry , Bellvert Floriant , Popovici Jean 
Published: October 2009

AbstractIn nocturnal chorusing anurans, mate choice has long been considered to be based exclusively on the highly conspicuous male calls. However an additional visual cue, the pulsing male vocal sac, has recently been shown to increase male attractiveness. In several species, including the European treefrog Hyla arborea, this organ is characterized by a bright orange colouration. In the present study, analysis of the pigments extracted from the vocal sacs of European treefrogs revealed the colouration of these organs to be based on several pigments, including three carotenoids, which are highly costly immune function enhancing molecules. This result raises the important question as to whether the carotenoid-based colouration of the vocal sac in H. arborea could constitute an additional visual cue used by females to discriminate male quality.
Relationships of Podarcis wall lizards from Algeria based on mtDNA data
Authors: Larbes Said , Harris D. James , Pinho Catarina , Lima Alexandra , Brito José Carlos , Carretero Miguel 
Published: October 2009

AbstractRecent molecular studies indicate that Podarcis wall lizards occurring in the southern region of the Iberian Peninsula and in North Africa, from south Morocco to eastern Tunisia, constitute a monophyletic group composed of several highly differentiated forms that appear to be incipient species. However, Algerian populations, which are geographically intermediate, have not been investigated so far. In this study we determine the levels of genetic variability between Algerian populations and other North African populations, using a more extensive sampling scheme covering most of the distribution range in this area. Our results show that North African Podarcis present high genetic diversity, comprising at least five highly divergent lineages. Two of these lineages were only detected in Algeria, which harbours most of the genetic diversity found within Podarcis from North Africa.
Food habits of Brazilian boid snakes: overview and new data, with special reference to Corallus hortulanus
Authors: Pizzatto Lígia , Marques Otavio , Facure Kátia 
Published: October 2009

AbstractThis study examines the diet of eight boid snakes: Boa c. constrictor, Boa c. amarali, Corallus caninus, C. hortulanus, Epicrates cenchria, E. crassus, E. assisi and Eunectes murinus mainly by analyzing the gut contents of preserved museum specimens, and includes a literature review to present an overview of the diet of Brazilian boids. Mammals constitute the primary prey consumed by the majority of the species. Birds are also frequently consumed by C. hortulanus and Boa contrictor, and are the most important prey for B. c. amarali. Ectotherms (mostly lizards) were only consumed by immature snakes. Such prey is rarely consumed by B. c. amarali and not recorded for Epicrates and Eunectes species in our dissections. C. caninus is likely a mammal specialist and Epicrates prey on birds more opportunistically. The niche overlap index varied from 0.27-0.52 for species occurring in the same bioma and geographic range but it is possible this overlap is lower as most sympatric species explore different macrohabitat. C. hortulanus exhibited a significant relationship between prey size and predator head size; this relationship did not differ among mature and immature snakes. In comparison to immature individuals heavier adult snakes fed on heavier prey items however, the ratio between prey/predator mass decreased with increase in predator mass (or size). Most boids exploit diurnal and nocturnal preys, probably using both sit-and-wait and active tactics. They feed on the ground but boas and C. hortulanus and possibly E. cenchria also exploit arboreal prey.