bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identification and removal of ribosomal RNA sequences from metatranscriptomes
Authors: Schmieder Robert , Lim Yan Wei , Edwards Robert 
Published: December 2011

Abstract
Summary: Here, we present riboPicker, a robust framework for the rapid, automated identification and removal of ribosomal RNA sequences from metatranscriptomic datasets. The results can be exported for subsequent analysis, and the databases used for the web-based version are updated on a regular basis. riboPicker categorizes rRNA-like sequences and provides graphical visualizations and tabular outputs of ribosomal coverage, alignment results and taxonomic classifications.
Availability and implementation: This open-source application was implemented in Perl and can be used as stand-alone version or accessed online through a user-friendly web interface. The source code, user help and additional information is available at http://ribopicker.sourceforge.net/.
Contact: rschmied@sciences.sdsu.edu; rschmied@sciences.sdsu.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
Recombination rates across porcine autosomes inferred from high‐density linkage maps
Authors: Muñoz M. , Alves E. , Ramayo‐Caldas Y. , Casellas J. , Rodríguez C. , Folch J. M. , Silió L. , Fernández A. I. 
Published: December 2011

SummaryStudies of the variation in recombination rate across the genome provide a better understanding of evolutionary genomics and are also an important step towards mapping and dissecting complex traits in domestic animals. With the recent completion of the porcine genome sequence and the availability of a high‐density porcine single nucleotide polymorphism (SNP) array, it is now possible to construct a high‐density porcine linkage map and estimate recombination rate across the genome. A total of 416 animals were genotyped with the Porcine SNP60BeadChip, and high‐density chromosome linkage maps were constructed using CRI‐MAP, assuming the physical order of the Sscrofa10 assembly. The total linkage map length was 2018.79 cM, using 658 meioses and 14 503 SNPs. The estimated average recombination rate across the porcine autosomes was 0.86 cM/Mb. However, a large variation in recombination rate was observed among chromosomes. The estimated average recombination rates (cM/Mb) per chromosome ranged from 0.48 in SSC1 to 1.48 in SSC10, displaying a significant negative correlation with the chromosome sizes. In addition, the analysis of the variation in the recombination rates taking 1‐Mb sliding windows has allowed us to demonstrate the variation in recombination rates within chromosomes. In general, a larger recombination rate was observed in the extremes than in the centre of the chromosome. Finally, the ratio between female and male recombination rates was also inferred, obtaining a value of 1.38, with the heterogametic sex having the least recombination.
Compliance with focused antenatal care services: do health workers in rural Burkina Faso, Uganda and Tanzania perform all ANC procedures?
Authors: Conrad Paul , Schmid Gerhrd , Tientrebeogo Justin , Moses Arinaitwe , Kirenga Silvia , Neuhann Florian , Müller Olaf , Sarker Malabika 
Published: December 2011

AbstractObjective  To assess health workers’ compliance with the procedures set in the focused antenatal care (ANC) guidelines in rural Uganda, Tanzania and Burkina Faso; to compare the compliance within and among the three study sites; and to appraise the logistic and supply of the respective health facilities (HF).Methods  The cross‐sectional study was conducted in the rural HF in three African countries. This descriptive observational study took place in HF in Nouna, Burkina Faso (5), Iganga, Uganda (6) and Rufiji, Tanzania (7). In total, 788 ANC sessions and service provisions were observed, the duration of each ANC service provision was calculated, and the infrastructures of the respective HF were assessed.Results  Health workers in all HF performed most of the procedures but also omitted certain practices stipulated in the focused ANC guidelines. There was a substantial variation in provision of ANC services among HF within and among the country sites. The findings also revealed that the duration of first visits was <15 min and health workers spent even less time in subsequent visits in all three sites. Reagents for laboratory tests and drugs as outlined in the focus ANC guidelines were often out of stock in most facilities.Conclusion  Health workers in all three country sites failed to perform all procedures stipulated in the focused ANC guideline; this could not be always explained by the lack of supplies. It is crucial to point out the necessity of the core procedures of ANC repeatedly.
Ureteral replacement with appendix in pediatric renal transplantation
Authors: Corbetta Juan P. , Weller Santiago , Bortagaray Juan I. , Durán Victor , Burek Carol , Sager Cristian , Lopez Juan C. 
Published: December 2011

Corbetta JP, Weller S, Bortagaray JI, Durán V, Burek C, Sager C, Lopez JC. Ureteral replacement with appendix in pediatric renal transplantation.Abstract: Ureteral necrosis is an uncommon complication following RT which can adversely affect outcome. Even though authors agree that the native ureter ought to be preserved, there are cases in which graft function can only be salvaged by ureteral substitution. The scant references in the literature on the use of the appendix for left ureteral replacement in children prompted us to report the following two cases in whom the technique was employed and to assess the evolution of graft function in these patients.
Parental Investment Theory and Nest Defence by Imperial Shags: Effects of Offspring Number, Offspring Age, Laying Date and Parent Sex
Authors: Svagelj Walter S. , Magdalena Trivellini María , Quintana Flavio 
Published: December 2011

AbstractNest defence is a common form of parental care employed by birds to improve the survival of their offspring. Theory predicts that parents should adjust their nest defence according to the value of the brood at stake, defending more intensively broods with high survival and reproductive prospects. We evaluated the influence of offspring number, offspring age, laying date and parent sex on nest‐defence intensity (NDI) of the Imperial Shag Phalacrocorax atriceps, a sexually dimorphic seabird with seasonal decline in offspring survival and very limited renesting potential. We also evaluated whether NDI was correlated within pairs and whether NDI of both members of the pair was correlated with incubation and breeding success. To elicit defensive behaviour, we simulated predation attempts using a Kelp Gull Larus dominicanus model. As predicted by theory, NDI was positively correlated with the number of offspring in the nest and offspring age. NDI during chick rearing was higher than that at early and late incubation, while no differences were found between incubation stages. Contrary to our prediction, we did not find differences in NDI according to laying date. NDI for males was higher than females, while NDI was also positively correlated within pairs. NDI was not statistically related to incubation or breeding success. These results suggest that other factors, such as laying date or parental quality and age, play a much larger role in determining the outcome and productivity of a nesting attempt. Our results provide partial support for parental investment theory; while parental defence increased with brood value according to offspring number and age, parental defence was not related to laying date, a factor strongly affecting offspring survival and recruitment probabilities in this species.
Adjustment to loss of the driving role following traumatic brain injury: A qualitative exploration with key stakeholders
Authors: Liddle Jacki , Fleming Jennifer , McKenna Kryss , Turpin Merrill , Whitelaw Penny , Allen Shelley 
Published: December 2011

Background/aims:  Community mobility is affected by an interruption to or cessation of driving following traumatic brain injury (TBI). This study aimed to examine loss of the driving role and to explore the outcomes associated with driving cessation from the perspectives of key people involved within the process: people with TBI, their family members and involved health professionals.
Methods:  A qualitative methodology was used, employing semi‐structured interviews with 15 individuals with TBI who had experienced driving cessation, 10 family members and 10 health professionals working with this population.
Results:  This article focuses on two themes, each with three subthemes. Being stuck: needs related to driving cessation had subthemes: (i) an emotional time, (ii) being normal and (iii) participation without driving. The second theme, A better way: suggestions to improve outcomes had subthemes: (i) information, (ii) support and trying it out and (iii) their family member’s roles and needs.
Conclusions:  Driving cessation following TBI is associated with emotional, identity, transport and participation‐related needs. An ongoing, individualised approach involving information, support and practical experiences may improve outcomes of driving cessation for people with TBI and their family members.
Using Short Message Service (SMS) to teach English idioms to EFL students
Authors: Hayati Abdolmajid , Jalilifar Alireza , Mashhadi Amir 
Published: December 2011

AbstractThis study aimed to gauge the efficacy of three modes of instruction of English idioms, ie, Short Message Service (SMS)‐based learning, contextual learning and self‐study learning. More precisely, this study capitalized on the push aspect of SMS affordance to deliver bite‐sized English idiom lessons on spaced intervals to the learners irrespective of the traditionally inherent problems in most teaching classrooms of English as a Foreign Language learning contexts and thus promote regular study. Students' perceptions and attitudes toward mobile learning and the application of SMS in teaching and learning English (idioms) were also sought by conducting a poststudy survey. Overall, the results revealed that students receiving short mini‐lessons on their mobile phones via SMS were more enthusiastic and learned more than their counterparts on paper or contextual groups.Practitioner NotesWhat is already known about this topic
Among different functions a mobile phone can afford, its Short Message Service (SMS) has been widely used to transmit and receive general and educational contents.
SMS affordance of mobile phones has been used to teach language components such as grammar and vocabulary.
The efficiency of teaching English idioms via SMS in comparison with other methods (eg, contextual learning and self‐study approaches) has not been examined in the Mobile Assisted Language Learning practices simultaneously.
What this paper adds
Gauging the comparative efficacy of SMS‐based instruction of English idioms in contrast with two other instruction modes, ie, contextual learning and self‐study simultaneously.
Delivering bite‐sized SMS‐based English idiom lessons to the learners beyond the constraints of the traditional classrooms and promoting regular study.
Seeking students' perceptions and attitudes toward mobile learning and the application of SMS in teaching and learning English idioms by conducting a poststudy survey.
Implications for practice and/or policy
Insights gathered from the comparative integration of mobile devices, particularly mobile phones and its different affordances into teaching classrooms of English as a Foreign Language learning contexts, are considered to have important implications for the educators and technologists to harness the potential of mobile technologies and design appropriate tasks that pave the way for the widespread use of this platform for language learning on a large scale.
A deep understanding of the mobile devices used and the possibilities associated with them is needed in order to better design the mobile learning (m‐learning) activities.
Embarking on an m‐learning project entails designing particular activities tailored to the needs of students involved in the learning process.
Towards Understanding Variations in Social Care for Older People in England
Authors: Brand Christian , Hughes Jane , Challis David 
Published: December 2011

AbstractIndicators of the public provision of old age social care are routinely recorded in England and have been used for diverse purposes including performance monitoring. Despite long‐term policy guidance promoting more homogeneous service provision, large variations can still be observed between local authorities (the providers of state‐funded social care). Our aim is to better understand such variations in a small selection of key aggregate indicators. Drawing on multiple data sources and pursuing a two‐step strategy, we first assess the explanatory power of a set of structural predictors and then add to the models a set of specific care management ‘process’ predictors. We find that structural factors beyond the control of local authorities explain a considerable share of the observable variation. The additional explanatory power of care management characteristics is small in comparison. Therefore, our findings suggest that caution must be taken when aggregate indicators of service provision are used for performance monitoring purposes, as a degree of autonomy over outcomes may be implied which in light of the empirical evidence is unrealistic. Past attempts to influence the aggregate pattern of service provision – apparently seeking greater ‘territorial justice’– are likely to have had adverse implications for service users and the uniformity of service delivery across England. Questions are raised about the adequate role of central government in a policy environment characterized by longstanding local government responsibility.
HIV‐related stigma and NGO‐isation in India: a historico‐empirical analysis
Authors: Nambiar Devaki 
Published: December 2011

AbstractIn response to World Bank critiques in 2007, the Indian Ministry of Health and Family Welfare declared that human immunodeficiency virus (HIV)‐related stigma was a barrier to the participation of non‐governmental organisations (NGOs) in the implementation of HIV prevention targeted interventions. Taking a deeper view of HIV‐related stigma as a historically inflected process of devaluation, this article details the history and transformation of NGO involvement in the HIV epidemic from 1986 through economic liberalisation in the 1990s up to the Second National AIDS Control Programme (NACP II 1999–2006). It additionally examines findings from interviews and participant observation of NGO workers (N = 24) from four targeted intervention NGOs in Delhi funded under NACP II. Analysis reveals that a second wave of HIV‐related NGO involvement has mushroomed in the past two decades, affording NGO workers multiple pathways to credibility in the Indian response to the epidemic. Contradictions embedded in the overlap of these pathways produce stigma, reflecting ‘adverse incorporation’ of the NGO workers. Drawing upon noteworthy exceptions to this trend from the first wave of Indian HIV‐related NGOs, the article calls for NGO participation as an explicitly political project of addressing the social inequalities that shape stigma as well as vulnerability to illness writ large.
Cued Recall and Other Cognitive Tasks to Facilitate Dementia Recognition in Primary Care
Authors: Fuchs Angela , Wiese Birgitt , Altiner Attila , Wollny Anja , Pentzek Michael 
Published: December 2011

ObjectivesTo compare the accuracy of commonly used tasks with that of the Visual Association Test (VAT), a conceptually different test involving cued recall of pictorial stimuli, in the recognition of dementia within primary care.DesignA cross‐sectional diagnostic study of concurrent validity.SettingTwenty‐nine German primary care practices.ParticipantsFour hundred twenty‐three individuals in primary care participating in a longitudinal cohort study.MeasurementsParticipants underwent a comprehensive neuropsychological interview. The validated clinical dementia diagnosis was used as reference standard. Index tests comprised the VAT, Mini‐Cog, clock drawing, verbal fluency, episodic memory, and subjective complaints. Validity parameters were calculated; possible confounders of test performance (age, sex, education, comorbidity, depression, language) were evaluated.ResultsTwenty‐one participants (5%) had dementia according to the reference standard. The VAT distinguished dementia from nondementia with a sensitivity of 95.2% (95% confidence interval (CI) = 86.1–100.0), a specificity of 96.0% (95% CI = 94.1–97.9), a positive predictive value (PPV) of 55.6% (95% CI = 39.3–71.8), and a negative predictive value (NPV) of 99.7% (95% CI = 99.2–100.0). The next‐most‐accurate tasks were the Mini‐Cog and immediate and delayed recall. Their sensitivity and NPV are similar to those of the VAT, but their PPV and specificity were significantly lower than those of the VAT. Age and depression affected all test scores.ConclusionThe VAT (cued recall of pictorial material) is superior to other tasks for the recognition of dementia in terms of higher specificity and PPV. Age‐specific cutoff scores may improve the validity of all tests.
Caudal Mediastinal Paraesophageal Abscesses in 7 Dogs
Authors: Brissot Hervé N. , Burton Carolyn A. , Doyle Ronan S. , Bray Jonathan P. 
Published: December 2011

ObjectiveTo report clinical, imaging, and surgical findings associated with caudal mediastinal paraesophageal abscesses (CMPA) in dogs and outcome after surgical treatment.Study designCase series.AnimalsDogs (n = 7) with CMPA.MethodsMedical records (April 2005–January 2010) were reviewed for dogs with CMPA treated surgically. Retrieved data were signalment, history, clinical findings, diagnostic investigations, surgical findings, surgical procedures performed, and postoperative recovery. Long‐term follow‐up information was obtained by telephone questionnaire of owners and referring veterinarians.ResultsMedian sternotomy (5 dogs) or lateral thoracotomy (2 dogs) was used for access to CMPA, which were drained and partially debrided surgically. In 5 dogs, omentalization of the abscess cavity was performed through a diaphragmatic incision. Foreign material was not identified within any abscess. All dogs were discharged from the hospital and had full recovery.ConclusionsCMPA should be suspected when there is regurgitation and pyrexia associated with a mass or enlargement in the caudal mediastinum. CMPA appears to have a good prognosis after aggressive surgical therapy.
ORGANIC GEOCHEMISTRY AND PETROLOGY OF A LOWER JURASSIC (PLIENSBACHIAN) PETROLEUM SOURCE ROCK FROM AÏT MOUSSA, MIDDLE ATLAS, MOROCCO
Authors: Sachse V. F. , Leythaeuser D. , Grobe A. , Rachidi M. , Littke R. 
Published: December 2011

Organic‐rich silty marls and limestones (Pliensbachian to earliest Toarcian) exposed at Aït Moussa in Boulemane Province are the only known example of an effective petroleum source rock in the Middle Atlas of Morocco. In this study, petrological and organic‐geochemical analyses (vitrinite reflectance measurements, Rock‐Eval pyrolysis, GC‐MS) were carried out in order to evaluate the maturity, quality and quantity of the organic matter (OM) and to investigate the depositional environment of these source rocks. Results indicate the presence of Type I/II kerogen which was deposited under marine conditions with an input of predominantly algal‐derived organic matter. The presence of woody particles indicates minor input of terrestrial material. Organic‐geochemical and biomarker analyses are consistent with deposition of carbonate‐rich sediments under oxygen‐depleted but not anoxic conditions. In terms of thermal maturity, the sediments have reached the oil window (0.5–0.6 %VRt) but not peak oil generation, although petroleum generation and migration are indicated by organic geochemical and microscopic evidence.Kinetic parameters derived from an investigation of petroleum generation characteristics show that the kerogen decomposes within a narrow temperature interval due to the fairly homogenous structure of the algal‐derived organic matter. The kinetic parameters together with vitrinite reflectance data were used to construct a ID model of the burial, thermal and maturation history of the Aït Moussa locality. The model suggested that deepest burial (approx. 3200 m) for the Pliensbachian succession took place in the Eocene (approx. 40 Ma). Two phases of hydrocarbon generation occurred, the first in the Late Jurassic/Early Cretaceous (approx. 150 Ma), and the second at the time of deepest burial (Eocene).
IMPACT OF DIAGENESIS ON RESERVOIR QUALITY IN RAMP CARBONATES: GIALO FORMATION (MIDDLE EOCENE), SIRT BASIN, LIBYA
Authors: Swei G. H. , Tucker Maurice E. 
Published: December 2011

The reservoir quality of Middle Eocene carbonates in the intracratonic Sirt Basin is strongly influenced by depositional facies and various diagenetic processes. Based on data from core samples and well logs from five boreholes in the Assumood and Sahl gasfields in the subsurface of the north‐central Sirt Basin, six major carbonate facies (and fourteen microfacies) are distinguished in the Middle Eocene Gialo Formation (thickness ∼1100 ft/335 m). Wackestones‐packstones dominate the Gialo Formation with abundant grains of larger benthic foraminifera, especially nummulites, in a matrix composed mostly of finely comminuted bioclastic material. Sediments were deposited as a mosaic of facies on a broad carbonate ramp in moderate‐energy nummulite‐packstone banks, with locally restricted back‐bank lagoons and fore‐bank areas of foraminiferal debris passing to offshore lime mudstones.Marine diagenesis was minor with micritization of bioclasts and rare vadose marine fibrous cements. Sparry calcite cements are ubiquitous and were precipitated during shallow to moderate burial from seawater and/or meteoric water, the latter largely unaffected by surface‐pedogenic processes. This is indicated by the fabrics and pre‐ and post‐compaction precipitation of drusy spar and echinoderm overgrowths, and supported by their bright‐to‐dull luminescence and low negative δ18O signatures (‐2.68 to ‐4.16%° PDB). Some early neomorphic alteration of calcitic bioclasts is suggested by bright CL and marine to low negative δ18O values (‐1.06 to –3.93%° PDB). Bioclastic grains have δ13C values ranging between 0.76 and 1.19%° PDB, interpreted as marine signatures. Similar low positive δ13C values of the cements (0.9 to 1.05 %°) indicate a source of carbonate from dissolution of grains and/or seawater/meteoric water, but without any near‐surface/soil effects. Dissolution of grains and matrix, notably originally aragonitic grains but also the originally high‐Mg calcite nummulites, was a major porosity‐enhancing process, and took place from shallow to moderate burial depths. Fractures may locally have increased porosity too.Shallow‐water packstones/rudstones containing both primary intergranular and secondary biomouldic porosity have the best reservoir quality and these are concentrated in the upper parts (top ∼100 ft/30 m) of the wells, with porosity‐permeability decreasing downwards. This trend relates to the broad, large‐scale facies pattern of more mud‐dominated facies giving way upwards to more grainy, nummulite‐dominated facies as a result of an overall shallowing of the depositional environment. In addition, the influx of meteoric waters in the upper part of the Gialo platform, before drowning and deposition of the overlying Augila Shale, increased porosity through dissolution. This integrated study has helped in understanding the reservoir heterogeneity and hydrocarbon potential of the Gialo carbonates.