bluuebunny/crossref_metadata_2025_split huggingface dataset:
Systematic significance of seed morphology in the genus Veronica (Plantaginaceae), with special reference to the Egyptian taxa
Authors: HASSAN Nasr M. , ABDEL KHALIK Kadry N. 
Published: August 2013

AbstractSeed morphology of 29 taxa including 9 subgenera belonging to the genus Veronica was compared using scanning electron microscopy to assess their diagnostic value for systematic studies. Subgenus Beccabunga is the largest in this study represented by nine taxa. Seed surface often varies from ridged reticulate or verrucose/granulate reticulate to rugose‐reticulate. Seed color and size have limited taxonomic significance as their variation is uninformative. Thereagainst, seed shape and seed coat ornamentation present informative characters that can be used efficiently in distinguishing the studied taxa. Our seed features support the DNA sequence data in showing close relationships between V. biloba and V. campylopoda, and between V. fruticans and V. fruticulosa. The present study indicates that V. anagallis‐aquatica, V. anagalloides, V. comosa, and V. catenata have more or less the same seed features; consequently, these four former species are most likely representing a single species as reported by earlier studies. Furthermore, V. polita and V. persica are very similar in terms of seed characteristics. Our results justify placement of V. peregina within subgenus Beccabunga and support the monophyly of the subgenus Veronica.
Treatment failure may lead to accelerated fibrosis progression in patients with chronic hepatitis C
Authors: Baran B. , Gulluoglu M. , Soyer O. M. , Ormeci A. C. , Gokturk S. , Evirgen S. , Yesil S. , Akyuz F. , Karaca C. , Demir K. , Kaymakoglu S. , Besisik F. 
Published: August 2013

SummaryChronic hepatitis C (CHC) patients with treatment failure (TF) remain at risk of continuing fibrosis progression. However, it has not been investigated whether there is an increased risk of accelerated fibrosis progression after failed interferon‐based therapy. We aimed to investigate long‐term influence of TF on fibrosis progression compared with untreated patients with CHC. We studied 125 patients with CHC who underwent paired liver biopsies from 1994 to 2012. Patients with advanced fibrosis were excluded from the analysis. Sixty‐three patients had TF, and 62 patients were treatment‐naïve (TN). Annual fibrosis progression rate (FPR) was calculated, and significant fibrosis progression (SFP) was defined as ≥2 stage increase in fibrosis during follow‐up. Multiple regression analyses were performed to find out independent predictors of FPR and SFP. Demographic characteristics and duration between paired liver biopsies were similar in TF and TN groups. Baseline alanine aminotransferase and gamma‐glutamyl transferase (GGT) levels (71 ± 31 vs 47 ± 22, P < 0.001 and 49 ± 39 vs 36 ± 28, P = 0.027, respectively), baseline mean fibrosis stage (2.2 ± 0.7 vs 1.9 ± 0.7, P = 0.018) and histologic activity index (6.3 ± 1.9 vs 4.3 ± 1.6, P < 0.001) were higher in the TF group compared with the TN group. In regression analyses, the strongest independent predictor of fibrosis progression was the GGT level (OR: 1.03, 95%CI 1.01–1.5, P < 0.001). Treatment experience (OR: 5.97, 95%CI 1.81–19.7, P = 0.003) also appeared as an independent predictor of both FPR and SFP. Failed interferon‐based CHC treatment may lead to accelerated FPR in the long‐term compared with the natural course.
A direct comparison of the effectiveness of two anti‐predator strategies under field conditions
Authors: Carroll J. , Sherratt T. N. 
Published: August 2013

AbstractAposematism and crypsis are two widespread defensive strategies that have evolved in organisms to reduce attacks by predators. However, although both have been studied extensively, predation rates on unpalatable conspicuous prey have seldom been directly compared to those on palatable cryptic prey, and never in the field. In this study, we use established methods to compare the effectiveness of both defensive traits, by presenting artificial prey targets on trees where they were subject to attack by wild avian predators in a natural field setting. When partially consumed prey and those that had been completely removed were both treated as attacked by predators, there were no differences in attack rates between targets with the two defensive strategies. However, aposematic prey were completely consumed less often than cryptic prey, and partially consumed more often. This suggests that predators engage in taste rejection of unpalatable prey and/or feed on conspicuous prey more cautiously (‘go‐slow’ predation). We also observed significant differences in predation among experimental sites, in spite of their similarity and relatively close proximity, and among trials, which suggests that prey may experience highly variable predation in the wild. If aposematic prey are capable of surviving attacks by predators, then this represents a potential defensive benefit of aposematism over crypsis.
Influence of diet on prehension mode in cordylid lizards: a morphological and kinematic analysis
Authors: Broeckhoven C. , Mouton P. le F. N. 
Published: August 2013

AbstractLizards exhibit a variety of mechanisms to capture prey, including lingual prehension, jaw prehension and lingual pinning. Despite being the topic of numerous studies, the link between prehension mode and diet remains poorly understood, especially in clades where multiple prehension modes are present. We addressed this issue by comparing the feeding behaviour and tongue morphology of a termite‐eating specialist Ouroborus cataphractus with that of a closely related dietary generalist Karusasaurus polyzonus. We used high‐speed videography to test the effect of prey species (termite vs. small cricket) and prey size (small vs. large cricket) on prehension mode. In addition, we included several other cordylid lizards representing the major clades in the family into our analysis to examine whether the prehension modes present in O. cataphractus characterize all cordylid species or whether they represent isolated occurrences. Finally, we investigated the morphology of the tongue in Cordylidae, with emphasis on O. cataphractus and K. polyzonus, using light and scanning electron microscopy techniques. Our data showed that the consumption of termites in O. cataphractus has resulted in the evolution of a novel lingual prehension mode, during which the ventral surface of the tongue is used to apprehend prey. This is in contrast to other lizards, which use the dorsal surface of the tongue to contact prey. Moreover, we demonstrated that this novel lingual prehension mode is accompanied by distinct morphological elaborations of the tongue surface. None of the other cordylid lizards tested in our study used lingual prehension during prey capture, except K. polyzonus, which used the tongue in a very small percentage of feeding trials. Overall, this study suggests that dietary specialization might underlie the evolution of novel prehension mechanisms in lizards.
Maternal allergy is associated with surface‐bound IgE on cord blood basophils
Authors: Matson Adam P. , Cloutier Michelle M. , Dhongade Ashish , Puddington Lynn , Rafti Ektor 
Published: August 2013

AbstractBackgroundThe cell type(s) mediating the maternal influence on allergic disease in children remain unclear. We set out to define the relationship between maternal allergy and frequencies of cord blood (CB) basophils, and plasmacytoid dendritic cells (pDCs); to characterize surface‐bound IgE and FcεRI expressions on these cells; and to investigate the association between maternal and CB serum IgE levels with surface‐bound IgE and FcεRI expressions.MethodsOne hundred and three mother/infant dyads were recruited prenatally, and maternal allergic history was recorded. Maternal blood was collected prior to delivery, and CB was collected after birth. Flow cytometry was used to identify CB basophils and pDCs and to determine surface‐bound IgE and FcεRI expressions.ResultsFrequencies of CB basophils and pDCs were low and not related to maternal history of allergy. Percentages of CB basophils with surface‐bound IgE were significantly higher in infants of allergic mothers compared with infants of non‐allergic mothers (median, 59.60% vs. 19.70%, p = 0.01). IgE on CB basophils correlated with CB IgE levels (r = 0.72, p < 0.0001), but not with maternal IgE levels (r = 0.26, p = 0.06). IgE on CB pDCs was low and not significantly associated with maternal or CB IgE levels. Similarly, FcεRI expression by CB basophils and pDCs was not significantly associated with maternal or CB IgE levels.ConclusionsFrequencies of CB basophils and pDCs are not influenced by maternal allergy. CB basophils and pDCs have surface‐bound IgE and express FcεRI; however, only IgE on CB basophils appears influenced by maternal allergy.
Toric systems and mirror symmetry
Authors: Bocklandt Raf 
Published: August 2013

AbstractIn their paper [Exceptional sequences of invertible sheaves on rational surfaces, Compositio Math. 147 (2011), 1230–1280], Hille and Perling associate to every cyclic full strongly exceptional sequence of line bundles on a toric weak del Pezzo surface a toric system, which defines a new toric surface. We interpret this construction as an instance of mirror symmetry and extend it to a duality on the set of toric weak del Pezzo surfaces equipped with a cyclic full strongly exceptional sequence.
On the algebraicity of the zero locus of an admissible normal function
Authors: Brosnan Patrick , Pearlstein Gregory 
Published: August 2013

AbstractWe show that the zero locus of an admissible normal function on a smooth complex algebraic variety is algebraic. In Part II of the paper, which is an appendix, we compute the Tannakian Galois group of the category of one-variable admissible real nilpotent orbits with split limit. We then use the answer to recover an unpublished theorem of Deligne, which characterizes the ${\mathrm{sl} }_{2} $-splitting of a real mixed Hodge structure.
Relations in the Sarkisov program
Authors: Kaloghiros Anne-Sophie 
Published: August 2013

AbstractThe Sarkisov program studies birational maps between varieties that are end products of the Minimal Model Program (MMP) on nonsingular uniruled varieties. If $X$ and $Y$ are terminal $ \mathbb{Q} $-factorial projective varieties endowed with a structure of Mori fibre space, a birational map $f: X\dashrightarrow Y$ is the composition of a finite number of elementary Sarkisov links. This decomposition is in general not unique: two such define a relation in the Sarkisov program. I define elementary relations, and show they generate relations in the Sarkisov program. Roughly speaking, elementary relations are the relations among the end products of suitable relative MMPs of $Z$ over $W$ with $\rho (Z/ W)= 3$.
Teleost fish models in membrane transport research: the PEPT1(SLC15A1) H+–oligopeptide transporter as a case study
Authors: Romano Alessandro , Barca Amilcare , Storelli Carlo , Verri Tiziano 
Published: August 2013

AbstractHuman genes for passive, ion‐coupled transporters and exchangers are included in the so‐called solute carrier (SLC) gene series, to date consisting of 52 families and 398 genes. Teleost fish genes for SLC proteins have also been described in the last two decades, and catalogued in preliminary SLC‐like form in 50 families and at least 338 genes after systematic GenBank database mining (December 2010–March 2011). When the kinetic properties of the expressed proteins are studied in detail, teleost fish SLC transporters always reveal extraordinary ‘molecular diversity’ with respect to the mammalian counterparts, which reflects peculiar adaptation of the protein to the physiology of the species and/or to the environment where the species lives. In the case of the H+–oligopeptide transporter PEPT1(SLC15A1), comparative analysis of diverse teleost fish orthologs has shown that the protein may exhibit very eccentric properties in terms of pH dependence (e.g. the adaptation of zebrafish PEPT1 to alkaline pH), temperature dependence (e.g. the adaptation of icefish PEPT1 to sub‐zero temperatures) and/or substrate specificity (e.g. the species‐specificity of PEPT1 for the uptake of l‐lysine‐containing peptides). The revelation of such peculiarities is providing new contributions to the discussion on PEPT1 in both basic (e.g. molecular structure–function analyses) and applied research (e.g. optimizing diets to enhance growth of commercially valuable fish).
Yersinia pestis Subverts the Dermal Neutrophil Response in a Mouse Model of Bubonic Plague
Authors: Shannon Jeffrey G. , Hasenkrug Aaron M. , Dorward David W. , Nair Vinod , Carmody Aaron B. , Hinnebusch B. Joseph 
Published: August 2013

ABSTRACTThe majority of humanYersinia pestisinfections result from introduction of bacteria into the skin by the bite of an infected flea. Once in the dermis,Y. pestiscan evade the host’s innate immune response and subsequently disseminate to the draining lymph node (dLN). There, the pathogen replicates to large numbers, causing the pathognomonic bubo of bubonic plague. In this study, several cytometric and microscopic techniques were used to characterize the early host response to intradermal (i.d.)Y. pestisinfection. Mice were infected i.d. with fully virulent or attenuated strains of dsRed-expressingY. pestis, and tissues were analyzed by flow cytometry. By 4 h postinfection, there were large numbers of neutrophils in the infected dermis and the majority of cell-associated bacteria were associated with neutrophils. We observed a significant effect of the virulence plasmid (pCD1) on bacterial survival and neutrophil activation in the dermis. Intravital microscopy of i.d.Y. pestisinfection revealed dynamic interactions between recruited neutrophils and bacteria. In contrast, very few bacteria interacted with dendritic cells (DCs), indicating that this cell type may not play a major role early inY. pestisinfection. Experiments using neutrophil depletion and a CCR7 knockout mouse suggest that dissemination ofY. pestisfrom the dermis to the dLN is not dependent on neutrophils or DCs. Taken together, the results of this study show a very rapid, robust neutrophil response toY. pestisin the dermis and that the virulence plasmid pCD1 is important for the evasion of this response.IMPORTANCEYersinia pestisremains a public health concern today because of sporadic plague outbreaks that occur throughout the world and the potential for its illegitimate use as a bioterrorism weapon. Since bubonic plague pathogenesis is initiated by the introduction ofY. pestisinto the skin, we sought to characterize the response of the host’s innate immune cells to bacteria early after intradermal infection. We found that neutrophils, innate immune cells that engulf and destroy microbes, are rapidly recruited to the injection site, irrespective of strain virulence, indicating thatY. pestisis unable to subvert neutrophil recruitment to the site of infection. However, we saw a decreased activation of neutrophils that were associated withY. pestisstrains harboring the pCD1 plasmid, which is essential for virulence. These findings indicate a role for pCD1-encoded factors in suppressing the activation/stimulation of these cellsin vivo.
Clathrin- and Arp2/3-Independent Endocytosis in the Fungal Pathogen Candida albicans
Authors: Epp Elias , Nazarova Elena , Regan Hannah , Douglas Lois M. , Konopka James B. , Vogel Jackie , Whiteway Malcolm 
Published: August 2013

ABSTRACT

Clathrin-mediated endocytosis (CME) is conserved among eukaryotes and has been extensively analyzed at a molecular level. Here, we present an analysis of CME in the human fungal pathogen
Candida albicans
that shows the same modular structure as those in other fungi and mammalian cells. Intriguingly,
C. albicans
is perfectly viable in the absence of Arp2/3, an essential component of CME in other systems. In
C. albicans
, Arp2/3 function remains essential for CME as all 15 proteins tested that participate in CME, including clathrin, lose their characteristic dynamics observed in wild-type (WT) cells. However, since
arp2
/
3
cells are still able to endocytose lipids and fluid-phase markers, but not the Ste2 and Mup1 plasma membrane proteins, there must be an alternate clathrin-independent pathway we term Arp2/3-independent endocytosis (AIE). Characterization of AIE shows that endocytosis in
arp2
mutants relies on actin cables and other Arp2/3-independent actin structures, as inhibition of actin functions prevented cargo uptake in
arp2
/
3
mutants. Transmission electron microscopy (TEM) showed that
arp2
/
3
mutants still formed invaginating tubules, cell structures whose proper functions are believed to heavily rely on Arp2/3. Finally, Prk1 and Sjl2, two proteins involved in patch disassembly during CME, were not correctly localized to sites of endocytosis in
arp2
mutants, implying a role of Arp2/3 in CME patch disassembly. Overall,
C. albicans
contains an alternative endocytic pathway (AIE) that relies on actin cable function to permit clathrin-independent endocytosis (CIE) and provides a system to further explore alternate endocytic routes that likely exist in fungal species.

IMPORTANCE
There is a well-established process of endocytosis that is generally used by eukaryotic cells termed clathrin-mediated endocytosis (CME). Although the details are somewhat different between lower and higher eukaryotes, CME appears to be the dominant endocytic process in all eukaryotes. While fungi such as
Saccharomyces cerevisiae
have proven excellent models for dissecting the molecular details of endocytosis, loss of CME is so detrimental that it has been difficult to study alternate pathways functioning in its absence. Although the fungal pathogen
Candida albicans
has a CME pathway that functions similarly to that of
S. cerevisiae
, inactivation of this pathway does not compromise growth of yeast-form
C. albicans
. In these cells, lipids and fluid-phase molecules are still endocytosed in an actin-dependent manner, but membrane proteins are not. Thus,
C. albicans
provides a powerful model for the analysis of CME-independent endocytosis in lower eukaryotes.
Genome and Transcriptome Adaptation Accompanying Emergence of the Definitive Type 2 Host-Restricted Salmonella enterica Serovar Typhimurium Pathovar
Authors: Kingsley Robert A. , Kay Sally , Connor Thomas , Barquist Lars , Sait Leanne , Holt Kathryn E. , Sivaraman Karthi , Wileman Thomas , Goulding David , Clare Simon , Hale Christine , Seshasayee Aswin , Harris Simon , Thomson Nicholas R. , Gardner Paul , Rabsch Wolfgang , Wigley Paul , Humphrey Tom , Parkhill Julian , Dougan Gordon 
Published: August 2013

ABSTRACTSalmonella entericaserovar Typhimurium definitive type 2 (DT2) is host restricted toColumba livia(rock or feral pigeon) but is also closely related toS. Typhimurium isolates that circulate in livestock and cause a zoonosis characterized by gastroenteritis in humans. DT2 isolates formed a distinct phylogenetic cluster withinS. Typhimurium based on whole-genome-sequence polymorphisms. Comparative genome analysis of DT2 94-213 andS. Typhimurium SL1344, DT104, and D23580 identified few differences in gene content with the exception of variations within prophages. However, DT2 94-213 harbored 22 pseudogenes that were intact in other closely relatedS. Typhimurium strains. We report a novelin silicoapproach to identify single amino acid substitutions in proteins that have a high probability of a functional impact. One polymorphism identified using this method, a single-residue deletion in the Tar protein, abrogated chemotaxis to aspartatein vitro. DT2 94-213 also exhibited an altered transcriptional profile in response to culture at 42°C compared to that of SL1344. Such differentially regulated genes included a number involved in flagellum biosynthesis and motility.IMPORTANCEWhereasSalmonella entericaserovar Typhimurium can infect a wide range of animal species, some variants within this serovar exhibit a more limited host range and altered disease potential. Phylogenetic analysis based on whole-genome sequences can identify lineages associated with specific virulence traits, including host adaptation. This study represents one of the first to link pathogen-specific genetic signatures, including coding capacity, genome degradation, and transcriptional responses to host adaptation within aSalmonellaserovar. We performed comparative genome analysis of reference and pigeon-adapted definitive type 2 (DT2)S. Typhimurium isolates alongside phenotypic and transcriptome analyses, to identify genetic signatures linked to host adaptation within the DT2 lineage.
Evaluating a complex system-wide intervention using the difference in differences method: the Delivering Choice Programme
Authors: Round Jeff , Drake Robyn , Kendall Edward , Addicott Rachael , Agelopoulos Nicky , Jones Louise 
Published: August 2013

ObjectivesWe report the use of difference in differences (DiD) methodology to evaluate a complex, system-wide healthcare intervention. We use the worked example of evaluating the Marie Curie Delivering Choice Programme (DCP) for advanced illness in a large urban healthcare economy.MethodsDiD was selected because a randomised controlled trial was not feasible. The method allows for before and after comparison of changes that occur in an intervention site with a matched control site. This enables analysts to control for the effect of the intervention in the absence of a local control. Any policy, seasonal or other confounding effects over the test period are assumed to have occurred in a balanced way at both sites. Data were obtained from primary care trusts. Outcomes were place of death, inpatient admissions, length of stay and costs.ResultsSmall changes were identified between pre- and post-DCP outputs in the intervention site. The proportion of home deaths and median cost increased slightly, while the number of admissions per patient and the average length of stay per admission decreased slightly. None of these changes was statistically significant.ConclusionsEffects estimates were limited by small numbers accessing new services and selection bias in sample population and comparator site. In evaluating the effect of a complex healthcare intervention, the choice of analysis method and output measures is crucial. Alternatives to randomised controlled trials may be required for evaluating large scale complex interventions and the DiD approach is suitable, subject to careful selection of measured outputs and control population.