bluuebunny/crossref_metadata_2025_split huggingface dataset:
A plea for ‘genealogical thinking’ in comparative biology – a rebuttal to the reply of Szucsich, Wirkner, and Pass to my article ‘Deconstructing Morphology’
Authors: Scholtz Gerhard 
Published: November 2011

AbstractScholtz G. in press. A plea for ‘genealogical thinking’ in comparative biology – a rebuttal to the reply of Szucsich, Wirkner, and Pass to my article ‘Deconstructing Morphology’. —Acta Zoologica (Stockholm) 00: 1–4.Szucsich et al. (in press) claim that – in contrast to my statement – morphological thinking has to be ‘cladistic.’ Based on this premise, they stress the difference between the relationships among states of characters versus those among structures assigned to the same character state as implemented in numerical cladistic reasoning. SEA claim that my approach to the homology concept only deals with the problem of the integration of various character states into the same character, whereas the necessary relationships among structures assigned to the same state are not covered. Based on this distinction, SEA also criticise the application of similarity in my definition of homology. Furthermore, they address the issue of evolutionarily independent units.
Tool use in fishes
Authors: Brown Culum 
Published: November 2011

AbstractTool use was once considered the sole domain of humans. Over the last 40 years, however, it has become apparent that tool use may be widespread across the animal kingdom. Pioneering studies in primates have shaped the way we think about tool use in animals, but have also lead to a bias both in terms of our expectations about which animals should be capable of using tools and the working definition of tool use. Here I briefly examine tool use in terrestrial animals and consider the constraints of the current working definition of tool use in fishes. Fishes lack grasping limbs and operate underwater where there are clear constraints with respect to the physics of tool use that differ dramatically from the terrestrial environment. I then examine all of the documented accounts of tool use in fishes. The review reveals that tool use seems to be confined to a limited number of fish taxa, particularly the wrasse, which may show similarities with the greater than expected number of examples of tool use in primates and corvids amongst mammals and birds, respectively. As fish are seldom studied as intensely as birds and mammals, there is a clear need for further observation of tool use in fishes. It is likely that further examples will be unveiled allowing us to perform comparative analyses of the evolution of tool use in fish.
Patterns of Population Growth in Peri‐Urban Accra, Ghana
Authors: DOAN PETRA , ODURO CHARLES YAW 
Published: November 2011

AbstractUrbanization in Africa (and the wider developing world for that matter) has often been misunderstood by Western observers on the lookout for Western‐style cities and suburbs. In these parts of the world, rapid urbanization has led to continuing changes in the form and shape of cities, as peri‐urban zones shift swiftly from rural to urban. While some descriptions of the peri‐urban zone suggest an amorphous area filled with low‐income residents, others argue that the zone is highly diverse. Using population census data, spatial modeling and regression analysis, we show that urban expansion at the edge of the city of Accra, Ghana, is not amorphous and does indeed show some discernible patterns. These patterns are represented by four hypotheses tested in this study — the spreading pancake, development node, village magnet and ribbon hypotheses. While the assumption that urban growth occurs in concentric rings around a central city (represented by the spreading pancake model) holds for Accra, this pattern of growth combines with other patterns to create a still‐evolving urban form in the city's peri‐urban zone. These include clustering of growth around a port city, a number of old villages and along improved highways radiating from the city.RésuméEn Afrique (et dans le monde en développement en général), l'urbanisation a souvent été mal comprise par les observateurs occidentaux en quête de villes et banlieues de type occidental. Dans ces parties du monde, l'urbanisation accélérée a entraîné des modifications constantes dans la conformation des grandes villes, les terrains ruraux périphériques devenant rapidement des zones urbaines. Selon certaines descriptions, la périphérie est amorphe, envahie d'habitants à faible revenu; selon d'autres, elle est empreinte d'une grande diversité. À l'aide de données de recensement, d'une modélisation spatiale et d'une régression statistique, on peut montrer que l'expansion urbaine aux limites de la ville d'Accra au Ghana n'est pas amorphe et qu'elle présente des schémas tout à fait identifiables. Ceux‐ci correspondent aux quatre hypothèses évaluées dans cette étude: la crêpe étalée, le pôle de développement, les villages aimantés, le ruban. L'idée que la croissance urbaine se diffuse en cercles concentriques autour d'une ville centrale (modèle de la crêpe étalée) s'applique à Accra, mais ce modèle est associéà d'autres schémas pour créer une forme urbaine en évolution permanente dans sa périphérie. On trouve ainsi une concentration de croissance autour d'une ville portuaire, de plusieurs villages pré‐existants, ainsi que le long de grandes routes rénovées qui rayonnent à partir de la ville.
New grass phylogeny resolves deep evolutionary relationships and discovers C4 origins
Authors:   Grass Phylogeny Working Group II
Published: November 2011

Summary
Grasses rank among the world’s most ecologically and economically important plants. Repeated evolution of the C4 syndrome has made photosynthesis highly efficient in many grasses, inspiring intensive efforts to engineer the pathway into C3 crops. However, comparative biology has been of limited use to this endeavor because of uncertainty in the number and phylogenetic placement of C4 origins.
We built the most comprehensive and robust molecular phylogeny for grasses to date, expanding sampling efforts of a previous working group from 62 to 531 taxa, emphasizing the C4‐rich PACMAD (Panicoideae, Arundinoideae, Chloridoideae, Micrairoideae, Aristidoideae and Danthonioideae) clade. Our final matrix comprises c. 5700 bp and is > 93% complete.
For the first time, we present strong support for relationships among all the major grass lineages. Several new C4 lineages are identified, and previously inferred origins confirmed. C3/C4 evolutionary transitions have been highly asymmetrical, with 22–24 inferred origins of the C4 pathway and only one potential reversal.
Our backbone tree clarifies major outstanding systematic questions and highlights C3 and C4 sister taxa for comparative studies. Two lineages have emerged as hotbeds of C4 evolution. Future work in these lineages will be instrumental in understanding the evolution of this complex trait.
Intellectual ability and executive function in pediatric moyamoya vasculopathy
Authors: WILLIAMS TRICIA S , WESTMACOTT ROBYN , DLAMINI NOMAZULU , GRANITE LEEOR , DIRKS PETER , ASKALAN RAND , MACGREGOR DAUNE , MOHARIR MAHENDRANATH , DEVEBER GABRIELLE 
Published: November 2011

Aim  Moyamoya vasculopathy is characterized by progressive stenosis of the major arteries of the Circle of Willis, resulting in compromised cerebral blood flow and increased risk of stroke. The objectives of the current study were to examine intellectual and executive functioning of children with moyamoya and to evaluate the impact of moyamoya type, stroke (clinical or silent), vasculopathy laterality, and disease duration on neurocognitive abilities.Method  Thirty pediatric participants (mean age 10y 10mo, SD 4y; 18 females, 12 males) completed age‐appropriate Wechsler Intelligence Scales before any therapeutic revascularization procedures. Reports of executive function were obtained from parents and teachers using the Behavior Rating Index of Executive Function.Results  Children with moyamoya scored significantly lower than the test standardization samples on all indices of intelligence and ratings of executive functioning (p<0.001). Patients did not differ by type of moyamoya or history of stroke. Patients with bilateral disease and stroke scored significantly lower than those with unilateral disease on measures of overall intellectual function (p=0.035) and verbal comprehension (p=0.04). Deficits in metacognitive executive functions were also more pronounced in bilateral patients according to teacher ratings.Interpretation  Children with moyamoya are at risk for intellectual and executive problems, exacerbated by bilateral disease and clinical stroke history.
The position of ELT practitioners in Mexican public universities
Authors: Farmer Frank , Mercau María Virginia , López Guadalupe Blanco 
Published: November 2011

English Language Teaching (ELT) staff in Mexican universities may be academics or technicians, depending on the status accorded by the university. This paper reports a survey of the academic qualifications and duties of 185 ELT staff in seven Mexican public universities and relates these to the Mexican government's standards for university lecturers in general (Programa para el Mejoramiento del Profesorado [PROMEP]). It was found that the proportion of ELT staff officially accredited with a desirable PROMEP profile was low, and that other staff varied from the PROMEP profile in different ways and to different degrees. Possible reasons for the wide variation in the position of ELT staff in tertiary institutions are explored and discussed in this paper, and suggestions are made for follow‐up studies.El personal docente de inglés de las universidades mexicanas se clasifica en técnicos o académicos dependiendo del acuerdo establecido por las universidades. Este estudio presenta los resultados de una encuesta sobre el perfil académico y las actividades que realizan 185 profesores de inglés que trabajan en siete universidades públicas mexicanas, relacionándolos con el modelo con que el gobierno mexicano califica el desempeño de todos los profesores universitarios que gozan de una contratación definitiva (PROMEP). Se observó que el número de profesores de inglés que acreditaron oficialmente el perfil deseable PROMEP fue bajo y que el resto de ellos tiene un perfil que difiere del de PROMEP en diferentes maneras y grados. En el artículo se analizan las posibles razones para esta gran variedad de perfiles de los profesores de inglés y se hacen sugerencias respecto a los estudios futuros que se podrían hacer.
Prevalence and associated factors for pterygium and pinguecula in a South Indian population
Authors: Asokan Rashima , Venkatasubbu Ramesh S , Velumuri Lokapavani , Lingam Vijaya , George Ronnie 
Published: November 2011

Citation information:Rashima A, Ramesh S Ve, Lokapavani V, Vijaya L & George R. Prevalence and associated factors for pterygium and pinguecula in a South Indian population.Ophthalmic Physiol Opt2011. doi: 10.1111/j.1475‐1313.2011.00882.xAbstractPurpose: To describe the prevalence and factors associated with pterygium and pinguecula in a south Indian population.Methods: The Chennai Glaucoma Study examined 7774 (Urban 3850, Rural 3924) subjects aged above 40 years. All subjects underwent a comprehensive ophthalmic evaluation. Personal history, occupation and lifetime ultraviolet exposure were documented. The presence of pterygium and pinguecula on slit‐lamp examination was recorded. The prevalence of pterygium and pinguecula, differences in the rural and urban populations and their association with age, gender, residence, nature of occupation, lifetime ultraviolet radiation exposure, tobacco use (smoking/smokeless), alcohol use, diabetes mellitus and hypertension were analyzed.Results: The mean age of the subjects was 54.6 (SD: 10.6) years. Pterygium was present in either eye of 740 subjects (9.5%, 95% CI: 8.6–10.4%), of which 329 subjects were male and 411 subjects were female. The prevalence of pterygium differed significantly (OR: 4.60 95% CI: 3.82–5.56,p < 0.0001) between the urban (144, 3.7%, 95% CI: 3.1–4.3%) and the rural population (596, 15.2%, 95% CI: 14.1–16.3%). Pinguecula was present in either eye of 875 subjects (11.3%, 95% CI: 10.5–12.0%), of which 368 subjects were male and 507 subjects were female. The prevalence of pinguecula differed significantly (OR: 2.94, 95% CI: 2.51–3.43,p < 0.0001) between the urban (238, 6.2%, 95% CI: 5.4–6.9%) and the rural population (637, 16.2%, 95% CI: 15.1–17.4%). Pinguecula and pterygium were significantly associated with rural residence (p < 0.0001). We found rural residence and exposure to higher lifetime UV exposure to be significantly associated with the presence of pterygium (p < 0.0001). Non‐use of spectacles was found to be associated with both pterygium (OR: 1.41, 95% CI: 1.12–1.79) and pinguecula (OR: 1.69, 95% CI: 1.38–2.08). The presence of pterygium and pinguecula was not associated with smoking, use of alcohol, nature of work, diabetes and hypertension.Conclusion: The prevalence of pterygium and pinguecula a South Indian population were 9.5% and 11.3% respectively. Rural residence were associated with presence of both pterygium and pinguecula. Higher lifetime UV exposure was associated with the presence of pterygia.
Foxp3+ regulatory T cells are associated with the natural history of chronic hepatitis B and poor prognosis of hepatocellular carcinoma
Authors: Wang Fengmei , Jing Xiang , Li Ge , Wang Tao , Yang Bin , Zhu Zhengyan , Gao Yingtang , Zhang Qin , Yang Yankai , Wang Yijun , Wang Peng , Du Zhi 
Published: November 2011

AbstractBackgroundRecent studies have focused on regulatory T cells (Tregs) in chronic hepatitis B (CHB) and hepatocellular carcinoma (HCC) and they were also conducted independently of each other.AimsThis study tried to characterize Tregs in blood and tumour infiltration, and to explore the correlations between Tregs and the context of chronic hepatitis B in HCC patients.MethodsThe liver‐resident Tregs and CD8+ T cells on core biopsy were investigated using immunohistochemistry staining in individuals (n = 209) with CHB (n = 47), HCC (n = 137) or healthy controls (n = 25). Circulating Tregs were detected in the above patients with CHB (n = 27) or HCC (n = 101) by flow cytometry.ResultsThe number of tumour‐infiltrating and circulating FoxP3+ Tregs was significantly high in patients with CHB (P < 0.001). However, there were fewer intratumoural Tregs in patients with advanced HCC than those in patients with early stage HCC (P = 0.043); In contrast, the circulating Tregs frequency increased during the progression of HCC (P = 0.024). Increased tumour‐infiltrating and circulating FoxP3+ Tregs were associated with poor overall survival (P = 0.041, 0.002 respectively) and a shorter time to recurrence (P = 0.049, 0.002 respectively) in patients with early stage HCC. Tumour‐infiltrating Foxp3 + Tregs were related to chronic hepatitis B natural history in HCC (P = 0.012). Neither tumour‐infiltrating CD8+ T cells nor balance of intratumoural Tregs and CD8+ T cells correlated with prognosis of HCC.ConclusionsIncreased Foxp3+ Tregs may represent a prognostic predictor in patients with early stage HCC. The CHB natural history influenced density of tumour‐infiltrating Tregs in hepatocellular carcinoma patients with chronic hepatitis B viruses infection.
Delayed‐type hypersensitivity responses to HIV Gag p24 relate to clinical outcome after peptide‐based therapeutic immunization for chronic HIV infection
Authors: KRAN ANNE‐MARTE B. , SOMMERFELT MAJA A. , BAKSAAS INGEBJØRG , SØRENSEN BIRGER , KVALE DAG 
Published: November 2011

Kran A‐MB, Sommerfelt MA, Baksaas I, Sørensen B, Kvale D. Delayed‐type hypersensitivity responses to HIV Gag p24 relate to clinical outcome after peptide‐based therapeutic immunization for chronic HIV infection. APMIS 2012; 120: 204–9.Therapeutic immunization in chronic HIV infection aims to induce durable, HIV‐specific immune responses capable of controlling disease progression, but immunological correlates of clinical efficacy are poorly defined. We have previously immunized 38 patients with a mixture of four short Gag p24‐like conserved peptides (Vacc‐4x) targeting skin dendritic cells. Antiretroviral treatment (ART) was initially stopped after completed immunizations and resumed post‐protocol during regular clinical follow‐up according to current guidelines. Four years after enrolment, Vacc‐4x‐specific cellular responses were evaluated in vivo by delayed‐type hypersensitivity (DTH) skin test, and in vitro by a T‐cell proliferation assay. Kaplan–Meier product‐limit estimates were used to analyse time until ART was resumed. Peptide‐specific cellular immune responses induced by Vacc‐4x had persisted 4 years after the last immunization in terms of unchanged DTH independent of ART and detectable proliferative T‐cell responses which correlated to the native peptides (R = 0.73, p = 0.01). Circulating bifunctional (IFN‐γ and IL‐10) Vacc‐4x‐specific T‐cell clones were detected in 43% of patients. Subjects with the strongest post‐immunization DTH responses appeared to start ART later compared with DTH low responders (p = 0.07). These data suggest that DTH responses should be further evaluated as a new and convenient tool for predicting clinical efficacy in trials testing therapeutic immunizations.
Clinical performance of access flap surgery in the treatment of the intrabony defect. A systematic review and meta‐analysis of randomized clinical trials
Authors: Graziani Filippo , Gennai Stefano , Cei Silvia , Cairo Francesco , Baggiani Angelo , Miccoli Mario , Gabriele Mario , Tonetti Maurizio 
Published: November 2011

AbstractAimTo systematically review the literature and to determine the clinical performance of conservative surgery (CS) for the treatment of intrabony defects (ID).MethodsRCTs on ID treatment with 12 months of follow‐up were identified through electronic databases and hand‐searched journals. Primary outcomes were tooth survival, clinical attachment (CAL) gain, probing depth (PD) reduction and gingival recession increase (REC). Weighted means and forest plots were calculated for each outcome variable 12 months after surgery. Long‐term stability was explored with RCTs of at least 24 months of follow‐up. Subgroup analysis was performed according to the type of flap.ResultsTwenty‐seven trials reporting 647 subjects and 734 defects were identified. Twelve months after CS, tooth survival was 98% (IQ: 96.77–100), CAL gain 1.65 mm (95% CI: 1.37–1.94; p < 0.0001), PD reduction 2.80 mm (CI: 2.43–3.18; p < 0.0001) and REC increase 1.26 mm (CI: 0.94–1.49; p < 0.0001). Longer follow‐up showed similar findings. CI of CAL gain were 1.44–3.52 for recently introduced papilla preservation flaps and 1.25–1.89 mm for access flaps.ConclusionsThe treatment of intrabony defect with CS is associated with high tooth retention and improvement of periodontal clinical parameters. Clinical performance may vary according to the type of surgical flap used.
Differential responses of nirK‐ and nirS‐carrying bacteria to denitrifying conditions in the anoxic rice field soil
Authors: Yuan Quan , Liu Pengfei , Lu Yahai 
Published: November 2011

SummaryDenitrification occurs actively in rice field soils. In the present study, the responses of nirK and nirS denitrifier communities to nitrate addition in the anoxic rice soil were determined through molecular analyses of nitrite reductase genes nirK and nirS and 16S rRNA genes. Denitrification occurred rapidly when nitrate was added at the beginning of anoxic incubation (experiment I). The structure of nirK‐type denitrifiers did not change; but their abundance as determined by quantitative (real‐time) PCR increased in nitrate treatments compared with control. Both the structure and abundance of nirS denitrifiers remained unaffected in experiment I. The rate of denitrification was slowed down when nitrate was added 20 days after the onset of anoxic incubation (experiment II). The structure and abundance of nirK‐type denitrifier community did not respond to nitrate addition; but the nirS community changed substantially in this experiment. The copy number of nirS genes increased by an order of magnitude in the treatments of 5 mM and 10 mM nitrate compared with control. The terminal restriction fragment length polymorphism (T‐RFLP) analysis of nirS genes revealed that the 100 bp T‐RF substantially increased in the nitrate treatments. Cloning and sequence analysis indicated that this T‐RF had similarity of up to 90% with Herbaspirillum sp. T‐RFLP profiles of the bacterial 16S rRNA genes also showed that Herbaspirillum sp. increased after nitrate amendments. Collectively, the nirK‐type denitrifiers were probably active at the beginning of anaerobic incubation, while the nirS denitrifiers, especially those related with Herbaspirillum sp. probably were more active when anaerobic condition was fully developed.
Clinical outcomes of laparoscopic adhesiolysis for mechanical small bowel obstruction
Authors: Okamoto H , Wakana H , Kawashima K , Fukasawa T , Fujii H 
Published: November 2011

AbstractIntroductionLaparoscopy for small bowel obstruction (SBO) has increasingly been performed for the advantages minimally invasive surgery provides. However, its benefit remains unclear.MethodsFrom January 2004 to July 2011, we enrolled 28 consecutive patients who underwent a laparoscopic operation for SBO, secondary to postoperative adhesions. We compared the results of SBO patients treated laparoscopically with those of 25 patients who underwent conventional open laparotomy in a retrospective matched‐pair analysis.ResultsLaparoscopic treatment was completed in 25 patients (89%), including 17 laparoscopic‐assisted cases. The mean procedural time was 112 minutes in the laparoscopic group and 79 minutes in the open group (P < 0.05). Patients resumed oral intake after a mean of 3 days in the laparoscopic group compared with a mean of 6.5 days in the open group (P < 0.05). The length of hospital stay was 11 and 22 days (P < 0.05), respectively, in the laparoscopic and open groups. Postoperative complications occurred in two patients in the laparoscopy group and 14 patients in the open group (P < 0.05).ConclusionThe laparoscopic approach was effective for the management of mechanical SBO in selected patients. Furthermore, minimally invasive laparoscopic adhesiolysis is also feasible and brings the benefit of cosmetic results.
A New MIC1-MAG1 Recombinant Chimeric Antigen Can Be Used Instead of the Toxoplasma gondii Lysate Antigen in Serodiagnosis of Human Toxoplasmosis
Authors: Holec-Gąsior Lucyna , Ferra Bartłomiej , Drapała Dorota , Lautenbach Dariusz , Kur Józef 
Published: November 2011

ABSTRACT

This study presents an evaluation of the MIC1 (microneme protein 1)-MAG1 (matrix antigen 1)
Toxoplasma gondii
recombinant chimeric antigen for the serodiagnosis of human toxoplasmosis for the first time. The recombinant MIC1-MAG1 antigen was obtained as a fusion protein containing His tags at the N- and C-terminal ends using an
Escherichia coli
expression system. After purification by metal affinity chromatography, the chimeric protein was tested for usefulness in an enzyme-linked immunosorbent assay (ELISA) for the detection of anti-
T. gondii
immunoglobulin G (IgG). One hundred ten sera from patients at different stages of infection and 40 sera from seronegative patients were examined. The results obtained for the MIC1-MAG1 chimeric antigen were compared with those of IgG ELISAs using a
Toxoplasma
lysate antigen (TLA), a combination of recombinant antigens (rMIC1ex2-rMAG1) and single recombinant proteins (rMIC1ex2 and rMAG1). The sensitivity of the IgG ELISA calculated from all of the positive serum samples was similar for the MIC1-MAG1 chimeric antigen (90.8%) and the TLA (91.8%), whereas the sensitivities of the other antigenic samples used were definitely lower, at 69.1% for the mixture of antigens, 75.5% for the rMIC1ex2, and 60% for rMAG1. This study demonstrates that the MIC1-MAG1 recombinant chimeric antigen can be used instead of the TLA in the serodiagnosis of human toxoplasmosis.