bluuebunny/crossref_metadata_2025 huggingface dataset:
Peritoneal drainage versus laparotomy for perforated necrotising enterocolitis or spontaneous intestinal perforation: A retrospective cohort study
Authors: Rakshasbhuvankar Abhijeet , Rao Shripada , Minutillo Corrado , Gollow Ian , Kolar Satish
Published: November 2011

Aim:  Perforated necrotising enterocolitis (NEC) and spontaneous intestinal perforation (SIP) in preterm infants are associated with high morbidity and mortality. The optimum surgical management during the acute stage remains unclear. The aim of the study was to compare the outcomes of preterm infants (gestational age at birth <30 weeks) with perforated NEC or SIP undergoing primary peritoneal drainage (PD) versus laparotomy.

Methods:  This was a retrospective cohort study (January 2004 to February 2010). Initial search of hospital database followed by a review of the medical records was performed to identify eligible infants. Thirty‐nine infants were included in the study. Information regarding the baseline characteristics and outcomes of interest were recorded using the medical charts, radiology and laboratory databases. NEC was differentiated from SIP based on radiological, operative and clinical findings retrospectively for this study.

Results:  Among 39 infants, 19 underwent primary PD while 20 had primary laparotomy. Gestational age and birthweight were similar between the two groups. The composite outcome of mortality before discharge or hospital stay longer than 3 months post‐term was significantly worse in PD group (74% vs. 40%, P= 0.038).

Conclusions:  Preterm infants undergoing PD for NEC/SIP appeared to have increased risk of adverse outcome compared with laparotomy. More randomised controlled trials are necessary to confirm these findings.
Potential influence of sevelamer hydrochloride on responsiveness to erythropoiesis‐stimulating agents in haemodialysis patients
Authors: IKEE RYOTA , TSUNODA MASATAKA , SASAKI NAOMI , SATO NARITSUGU , HASHIMOTO NOBUO
Published: November 2011

Aim:  Vitamin D analogues, cinacalcet, and sevelamer play pivotal roles in the management of chronic kidney disease‐mineral bone disorder, and are noted to have pleiotropic effects. We examined whether these agents might be associated with the responsiveness to erythropoiesis‐stimulating agents (ESA).

Methods:  In this cross‐sectional study including haemodialysis patients treated with ESA, we searched for clinical parameters associated with the ESA resistance index, which was calculated as the weekly ESA dose divided by the patient's haemoglobin value.

Results:  Among 45 patients (male: female = 28 : 17, age 68 ± 10 years, haemodialysis duration 84 ± 60 months), vitamin D analogue, cinacalcet, and sevelamer were used in 95.6%, 26.7%, and 84.4% of the patients, respectively. Univariate analysis showed significant association of the ESA resistance index with transferrin saturation rate (TSAT), vitamin D analogue dose, and sevelamer dose. In multivariate analysis, the sevelamer dose and TSAT were found to be independent determinants of the ESA resistance index.

Conclusion:  Our preliminary data showed an independent association between sevelamer dose and the responsiveness to ESA in haemodialysis patients. Further studies are required to investigate the causal relationship between sevelamer and ESA responsiveness.
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

Scholtz 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

Tool 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.
Market access, organic farming and productivity: the effects of Fair Trade affiliation on Thai farmer producer groups*
Authors: Becchetti Leonardo , Conzo Pierluigi , Gianfreda Giuseppina
Published: November 2011

The study analyses the impact of Fair Trade (FT) and organic farming on a sample of FT rice producers in Thailand. It finds that per capita income from agriculture is positively and significantly affected by years of organic certification and FT affiliation. The estimated FT and organic certification contributions to producers’ economic well‐being are higher when account is taken of the relatively higher proportion of self‐consumption among affiliated farmers. But the per capita income effect does not translate into higher productivity owing to a concurrent increase in hours worked.
ADOLF GRÜNBAUM ON THE STEADY‐STATE THEORY AND CREATIO CONTINUA OF MATTER OUT OF NOTHING
Authors: Karimi Mirsaeid Mousavi
Published: November 2011

Abstract The ideas of creatio ex nihilo of the universe and creatio continua of new matter out of nothing entered the arena of natural science with the advent of the Big Bang and the steady‐state theories in the mid‐twentieth century. Adolf Grünbaum has tried to interpret the steady‐state theory in such a way, to show that the continuous formation of new matter out of nothing in this theory can be explained purely physically. In this paper, however, it will be shown that Grünbaum's interpretation encounters at least three problems: not distinguishing between material and efficient causes, inconsistency, and misconceiving the law of density conservation.
Patterns of Population Growth in Peri‐Urban Accra, Ghana
Authors: DOAN PETRA , ODURO CHARLES YAW
Published: November 2011

Urbanization 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.

En 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

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.
L1 in English language learning: a research study in a Greek regional context
Authors: Giannikas Christina N.
Published: November 2011

The amount of the target language (TL) and whether or not the first language (L1) should be used in the young language learners' classroom is currently receiving a great amount of attention in the field. The present study investigates language learning within a Greek regional context where teachers are reluctant to maximize TL use, due to traditional teaching trends and adherence to the curriculum. The study aims to support the hypothesis that TL can be maximized by creating a student‐centred environment where learners are encouraged to use a significant amount of TL and increase their interest by offering more chances to practice authentic communication. The results of the study provide the understanding of the child's willingness to communicate and explore the TL.
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.x

Purpose: 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

Background

Recent 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.

Aims

This 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.

Methods

The 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.

Results

The 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.

Conclusions

Increased 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.
Biology, Ideology, and Epistemology: How Do We Know Political Attitudes Are Inherited and Why Should We Care?
Authors: Smith Kevin , Alford John R. , Hatemi Peter K. , Eaves Lindon J. , Funk Carolyn , Hibbing John R.
Published: November 2011

Evidence that political attitudes and behavior are in part biologically and even genetically instantiated is much discussed in political science of late. Yet the classic twin design, a primary source of evidence on this matter, has been criticized for being biased toward finding genetic influence. In this article, we employ a new data source to test empirically the alternative, exclusively environmental, explanations for ideological similarities between twins. We find little support for these explanations and argue that even if we treat them as wholly correct, they provide reasons for political science to pay more rather than less attention to the biological basis of attitudes and behaviors. Our analysis suggests that the mainstream socialization paradigm for explaining attitudes and behaviors is not necessarily incorrect but is substantively incomplete.
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

Aim

To systematically review the literature and to determine the clinical performance of conservative surgery (CS) for the treatment of intrabony defects (ID).

Methods

RCTs 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.

Results

Twenty‐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.

Conclusions

The 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.
What is the Probability of Patients who are Nonambulatory after Stroke Regaining Independent Walking? a Systematic Review
Authors: Preston Elisabeth , Ada Louise , Dean Catherine M. , Stanton Rosalyn , Waddington Gordon
Published: November 2011

Patients after stroke who are nonambulatory require resources, and independent walking becomes a major determinant of the ability to participate in activities of daily living. Our objective was to determine the probability of walking for patients who are nonambulatory in the first month after stroke. We performed a systematic review and meta-analysis of consecutive, prospective studies of nonambulatory patients within the first month after stroke in rehabilitation and acute units. The outcomes were the probability of achieving independent walking at three-, six- and 12 months after stroke. Twenty-six studies were included in the review. Seventeen studies comprising 2856 participants were entered into meta-analyses. For initially nonambulatory stroke patients managed in a rehabilitation unit, the probability of independent walking was 0·60 (95% CI 0·47–0·74, 1373 participants) at three-months, 0·65 (95% CI 0·53–0·77, 444 participants) at six-months and 0·91 (95% CI 0·81–1·00, 24 participants) at 12 months. For patients managed in an acute unit, the probability of independent walking was 0·39 (95% CI 0·27–0·52, 634 participants) at three-months, 0·69 (95% CI 0·46–0·92, 405 participants) at six-months and 0·74 (95% CI 0·59–0·88, 34 participants) at 12 months. 60% of patients managed in a rehabilitation unit who are nonambulatory in the first month after stroke will regain independent walking compared with 39% of those managed in an acute unit. This information can be used clinically to make decisions about allocation of rehabilitation resources, education of patients and carers, and for discharge planning.
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

Denitrification 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

Introduction

Laparoscopy for small bowel obstruction (SBO) has increasingly been performed for the advantages minimally invasive surgery provides. However, its benefit remains unclear.

Methods

From 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.

Results

Laparoscopic 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).

Conclusion

The 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 FEM Approach for Simulation of Metal Foam Filled Tubes
Authors: Strano Matteo
Published: November 2011

The combination of thin metal cases or tubes with a filling made of metal foams is interesting and promising for many applications in mechanical engineering. Components made of an outer hollow thin compact metal structure and a cellular lightweight core are especially suited to energy absorption applications. In order to allow for an efficient product/process design with a concurrent engineering approach, reliable and computationally affordable finite element method (FEM) calculations are required by both product and process engineers. The structural performance of these complex composite parts must be numerically predicted, in order to find the optimal combination of outer structure and metal foam properties. While FEM simulation at large deformations of bending, crushing, etc. of thin sheets and tubes is state of the art, the accurate FEM simulation of the mechanical behavior of metal foams cannot be considered fully established. In this paper the three most common methods for FEM simulation of metal foam materials are discussed: (a) homogenization approach, (b) realistic reconstruction of tomographic data, and (c) repetition of standard unit cells. A new effective approach is proposed, suited for simulation of composite, metal foam filled, structures of realistic dimensions. The approach is based on meshing the metal foam by replicating a unit cell made of 32 triangular shell elements, and then by randomizing the nodal position in order to emulate the intrinsic homogeneity of foam morphology. The method is validated by means of different experimental tests. The results show that the proposed method correctly predicts the behavior of foam structures in axial compression. The method slightly overestimated the actual load registered in three point bending tests. Several improvements are described and discussed in the paper, such as randomization of nodal positions of the mesh, in order to reduce the overestimation of forces. An FEM approach for the simulation of large deformations of metal foam filled metal structure (e.g., tubes) suited for the design of realistic large dimensions structural components has been presented. The proposed method shows some innovative features with respect to the available scientific literature, such as a configuration based on octahedral unit cells with low number of triangular shell elements. Randomization of nodal positions of each unit cell has been implemented as a method for better representing the intrinsic variability of metal foams and for reducing the stiffness of the simulated structure.
Open Source Physics
Authors: Christian Wolfgang , Esquembre Francisco , Barbato Lyle
Published: November 2011

A curriculum resource designed around interactive computer-based modeling brings
computational physics to students of all levels.
Pelagic Fishing at 42,000 Years Before the Present and the Maritime Skills of Modern Humans
Authors: O’Connor Sue , Ono Rintaro , Clarkson Chris
Published: November 2011

Abundant fish remains from a shelter in East Timor imply that humans were fishing the deep sea by 43,000 years ago.
The Unfolded Protein Response: From Stress Pathway to Homeostatic Regulation
Authors: Walter Peter , Ron David
Published: November 2011

The vast majority of proteins that a cell secretes or displays on its surface first enter the endoplasmic reticulum (ER), where they fold and assemble. Only properly assembled proteins advance from the ER to the cell surface. To ascertain fidelity in protein folding, cells regulate the protein-folding capacity in the ER according to need. The ER responds to the burden of unfolded proteins in its lumen (ER stress) by activating intracellular signal transduction pathways, collectively termed the unfolded protein response (UPR). Together, at least three mechanistically distinct branches of the UPR regulate the expression of numerous genes that maintain homeostasis in the ER or induce apoptosis if ER stress remains unmitigated. Recent advances shed light on mechanistic complexities and on the role of the UPR in numerous diseases.
Stress-Related Noradrenergic Activity Prompts Large-Scale Neural Network Reconfiguration
Authors: Hermans Erno J. , van Marle Hein J. F. , Ossewaarde Lindsey , Henckens Marloes J. A. G. , Qin Shaozheng , van Kesteren Marlieke T. R. , Schoots Vincent C. , Cousijn Helena , Rijpkema Mark , Oostenveld Robert , Fernández Guillén
Published: November 2011

Acute stress leads to reorganization of large-scale neural network connectivity in the brain that is driven by noradrenaline.
The Essence of Quiescence
Authors: Coller Hilary A.
Published: November 2011

Is cell quiescence a distinct state or does it represent a series of growth rates that cells use to adjust to their environment?
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

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.
Comparative Study of Different Sources of Pertussis Toxin (PT) as Coating Antigens in IgG Anti-PT Enzyme-Linked Immunosorbent Assays
Authors: Kapasi Aditi , Meade Bruce D. , Plikaytis Brian , Pawloski Lucia , Martin Monte D. , Yoder Sandra , Rock Michael T. , Coddens Séverine , Haezebroeck Valérie , Fievet-Groyne Françoise , Bixler Garvin , Jones Charles , Hildreth Stephen , Edwards Kathryn M. , Messonnier Nancy E. , Tondella Maria L.
Published: November 2011

In an effort to improve the reliability and reproducibility of serological assays forBordetella pertussis, a collaborative study was conducted to compare four different sources of pertussis toxin (PT) as coating antigens in the immunoglobulin G (IgG) anti-PT enzyme-linked immunosorbent assay (ELISA). Four sources of PT were used as coating antigens in the IgG anti-PT ELISA in four different testing laboratories (labs A to D) to determine whether the different antigen preparations and different laboratories influenced assay results. A panel of 60 sera consisting of deidentified human specimens from previous vaccination trials of healthy adults and infants and clinical specimens from outbreak settings was tested. In the four laboratories, each sample was tested three times with the four PT antigens according to the standard coating optimization and IgG anti-PT ELISA testing procedures used in that laboratory. Differences among the antigens, as well as intra- and interlaboratory variability, were evaluated. Excellent agreement was observed with the test panel results among the four antigens within each laboratory. Concordance correlation coefficient (rc) measurements among the different antigens ranged from 0.99, 0.99 to 1.00, 1.00, and 0.97 to 1.00 for labs A to D, respectively. The comparisons between pairs of laboratories also indicated a high degree of concordance for each PT preparation, withrcmeasurements between 0.90 and 0.98, 0.93 and 0.99, 0.92 and 0.98, and 0.93 and 0.99 for antigens 1 to 4, respectively. Relatively minor differences in results were observed among laboratories or among antigens, suggesting that the four PT antigens are quite similar and could be considered for acceptance in harmonized immunoassays used for serodiagnosis or vaccine evaluation.
Risk of injury and concussion associated with team performance and penalty minutes in competitive youth ice hockey
Authors: Emery Carolyn A , Kang Jian , Schneider Kathryn J , Meeuwisse Willem H
Published: November 2011

Objective

To determine if there is an association between the risk of all injury or concussion and win–loss records or penalty minutes in competitive youth ice hockey players (ages 11–14).

Design, setting, participants

This is a secondary data analysis of a 2-year cohort study in Alberta and Quebec on the 2007/2008 (Pee Wee) and 2008/2009 (Bantam) seasons.

Main outcome measures

Incidence rate ratios (IRRs) were estimated based on Poisson regression for game-related injury and concussion and adjusted for cluster by team.

Results

A total of 140 teams from Alberta (n=2081) and 137 teams (n=2018) from Quebec were included in the analysis. There were 451 game-related injuries (121 concussions) from Alberta and 280 (62 concussions) from Quebec. For game-related injuries, the IRR between players from teams with more than 50% wins and players with less or equal to 50% wins was 0.78 (95% CI 0.64–0.95) for all injuries, 0.75 (95% CI 0.52–1.08) for concussions, 0.64 (95% CI 0.47–0.88) for injuries resulting in time loss of more than 7 days, and 0.74 (95% CI 0.39–1.40) for concussions resulting in time loss of more than 10 days; adjusting for clustering by team and other important risk factors (ie, province, age, level of play, previous injury, weight and position). There was no association found between the total penalty minutes per game and game-related injury or concussion.

Conclusions

There was a significant association found between team performance (ie, win/loss/tie record) and injury risk with a 22% lower injury rate and 36% lower injury rate resulting in less than 7 days time loss in Pee Wee and Bantam ice hockey teams winning more than 50% of all season games. Total penalty minutes per game were not associated with injury or concussion rates.
NOTE ON TWO-DIMENSIONAL GAUGED LIFSHITZ MODELS
Authors: SON EDWIN J. , KIM WONTAE
Published: November 2011

We fermionize the two-dimensional free Lifshitz scalar field in order to identify what the gauge-covariant couplings are, and then they are bosonized back to get the gauged Lifshitz scalar field theories. We show that they give the same physical modes with those of the corresponding Lorentz invariant gauged scalar theories, although the dispersion relations are different.
Assessment of cellular mechanisms contributing to cAMP compartmentalization in pulmonary microvascular endothelial cells
Authors: Feinstein Wei P. , Zhu Bing , Leavesley Silas J. , Sayner Sarah L. , Rich Thomas C.
Published: November 2011

Cyclic AMP signals encode information required to differentially regulate a wide variety of cellular responses; yet it is not well understood how information is encrypted within these signals. An emerging concept is that compartmentalization underlies specificity within the cAMP signaling pathway. This concept is based on a series of observations indicating that cAMP levels are distinct in different regions of the cell. One such observation is that cAMP production at the plasma membrane increases pulmonary microvascular endothelial barrier integrity, whereas cAMP production in the cytosol disrupts barrier integrity. To better understand how cAMP signals might be compartmentalized, we have developed mathematical models in which cellular geometry as well as total adenylyl cyclase and phosphodiesterase activities were constrained to approximate values measured in pulmonary microvascular endothelial cells. These simulations suggest that the subcellular localizations of adenylyl cyclase and phosphodiesterase activities are by themselves insufficient to generate physiologically relevant cAMP gradients. Thus, the assembly of adenylyl cyclase, phosphodiesterase, and protein kinase A onto protein scaffolds is by itself unlikely to ensure signal specificity. Rather, our simulations suggest that reductions in the effective cAMP diffusion coefficient may facilitate the formation of substantial cAMP gradients. We conclude that reductions in the effective rate of cAMP diffusion due to buffers, structural impediments, and local changes in viscosity greatly facilitate the ability of signaling complexes to impart specificity within the cAMP signaling pathway.
Alcohol reduces airway hyperresponsiveness (AHR) and allergic airway inflammation in mice
Authors: Oldenburg Peter J. , Poole Jill A. , Sisson Joseph H.
Published: November 2011

There is very limited knowledge about the effects of alcohol on airway hyperresponsiveness and inflammation in asthma. Historical accounts of alcohol administration to patients with breathing problems suggest that alcohol may have bronchodilating properties. We hypothesized that alcohol exposure will alter airway hyperresponsiveness (AHR) and pulmonary inflammation in a mouse model of allergic asthma. To test this hypothesis, BALB/c mice were fed either 18% alcohol or water and then sensitized and challenged with ovalbumin (OVA). AHR was assessed by means of ventilation or barometric plethysmography and reported as either total lung resistance or enhanced pause, respectively. Airway inflammation was assessed by total and differential cell counts in bronchoalveolar lavage fluid (BALF), cytokine levels in BALF, lung histology, and serum immunoglobulin E (IgE) levels. Alcohol feeding significantly blocked methacholine-induced increases in AHR compared with water-fed controls. Alcohol feeding significantly reduced total cell numbers (64%) as well as the number of eosinophils (84%) recruited to the lungs of these mice. Modest changes in lung pathology were also observed. Alcohol exposure led to a reduction of IgE in the serum of the EtOH OVA mice. These data demonstrate that alcohol exposure blunts AHR and dampens allergic airway inflammation indices in allergic mice and suggest that there may be an important role for alcohol in the modulation of asthma. These data provide an in vivo basis for previous clinical observations in humans substantiating the bronchodilator properties of alcohol and for the first time demonstrates an alcohol-induced reduction of allergic inflammatory cells in a mouse model of allergic asthma.
Hypoxia-inducible factor-1α regulates KCNMB1 expression in human pulmonary artery smooth muscle cells
Authors: Ahn Yong-Tae , Kim Yu-Mee , Adams Eloa , Lyu Shu-Chen , Alvira Cristina M. , Cornfield David N.
Published: November 2011

Previously, we observed that hypoxia increases the expression of the β1-subunit ( KCNMB1) of the calcium-sensitive potassium channel (BKCa). Herein, we elucidate the mechanism whereby hypoxia increases KCNMB1 expression in human pulmonary artery smooth muscle cells (hPASMC). In response to hypoxia, the expression of both the transcription factor hypoxia-inducible factor 1-α ( HIF-1α) and KCNMB1 are increased. Knockdown of HIF-1α using a shRNA plasmid blocked the hypoxic induction of KCNMB1 expression. Chromatin immunoprecipitation (ChIP) demonstrated HIF-1α binding to three discrete regions of the human KCNMB1 promoter known to contain hypoxia response elements (HREs). A KCNMB1 promoter reporter assay combined with site-directed mutagenesis identified two adjacent HREs located between −3,540 bp and −3,311 bp that are essential for the hypoxic induction of KCNMB1 promoter activity. Furthermore, additional ChIP assays demonstrated recruitment of the HIF-1α transcriptional coactivator, p300, to this same promoter region. Treatment of hPASMC with the histone deacetylase inhibitor, trichostatin, prolonged the increase in KCNMB1 observed with hypoxia, suggesting that alterations in chromatin remodeling function to limit the hypoxic induction of KCNMB1. Finally, KCNMB1 knockdown potentiated the hypoxia-induced increase in cytosolic calcium in hPASMC, highlighting the contribution of the β1-subunit in modulating vascular SMC tone in response to acute hypoxia. In conclusion, HIF-1α increases KCNMB1 expression in response to hypoxia in hPASMC by binding to two HREs located at −3,540 to −3,311 of the KCNMB1 promoter. We speculate that selective modulation of KCNMB1 expression may serve as a novel therapeutic approach to address diseases characterized by an increase in vascular tone.