bluuebunny/crossref_metadata_2025_split huggingface dataset:
Electronic states and spin-orbit splitting of lanthanum dimer
Authors: Liu Yang , Wu Lu , Zhang Chang-Hua , Krasnokutski Serge A. , Yang Dong-Sheng 
Published: July 2011

Lanthanum dimer (La2) was studied by mass-analyzed threshold ionization (MATI) spectroscopy and a series of multi-configuration ab initio calculations. The MATI spectrum exhibits three band systems originating from ionization of the neutral ground electronic state, and each system shows vibrational frequencies of the neutral molecule and singly charged cation. The three ionization processes are La2+ (a2∑g+) ← La2 (X1∑g+), La2+ (b2Π3/2, u) ← La2 (X1∑g+), and La2+ (b2Π1/2, u) ← La2 (X1∑g+), with the ionization energies of 39 046, 40 314, and 40 864 cm−1, respectively. The vibrational frequency of the X1Σg+ state is 207 cm−1, and those of the a2Σg+, b2Π3/2, u and b2Π1/2, u are 235.7, 242.2, and 240 cm−1. While X1Σg+ is the ground state of the neutral molecule, a2Σg+ and b2Πu are calculated to be the excited states of the cation. The spin-orbit splitting in the b2Πu ion is 550 cm−1. An X4Σg− state of La2+ was predicted by theory, but not observed by the experiment. The determination of a singlet ground state of La2 shows that lanthanum behaves differently from scandium and yttrium.
What is the Future of Agricultural Economics Departments and the Agricultural and Applied Economics Association?
Authors: Perry Gregory M. 
Published: July 2011

AbstractThe downward trends in Agricultural and Applied Economics Association (AAEA) membership and faculty numbers nationwide have many departments wondering about the future of agricultural economics. The author examines trends in undergraduate and graduate enrollment, as well as trends in extension and experiment‐station funding, to suggest what the prospects are for future survival and growth. Although there exist challenges like shrinking faculty numbers, agricultural economics programs still have a strong undergraduate element and address important research issues. Consequently, agricultural economics should remain viable for many years to come.
Comparative analysis of RNA-Seq alignment algorithms and the RNA-Seq unified mapper (RUM)
Authors: Grant Gregory R. , Farkas Michael H. , Pizarro Angel D. , Lahens Nicholas F. , Schug Jonathan , Brunk Brian P. , Stoeckert Christian J. , Hogenesch John B. , Pierce Eric A. 
Published: July 2011

Abstract
Motivation: A critical task in high-throughput sequencing is aligning millions of short reads to a reference genome. Alignment is especially complicated for RNA sequencing (RNA-Seq) because of RNA splicing. A number of RNA-Seq algorithms are available, and claim to align reads with high accuracy and efficiency while detecting splice junctions. RNA-Seq data are discrete in nature; therefore, with reasonable gene models and comparative metrics RNA-Seq data can be simulated to sufficient accuracy to enable meaningful benchmarking of alignment algorithms. The exercise to rigorously compare all viable published RNA-Seq algorithms has not been performed previously.
Results: We developed an RNA-Seq simulator that models the main impediments to RNA alignment, including alternative splicing, insertions, deletions, substitutions, sequencing errors and intron signal. We used this simulator to measure the accuracy and robustness of available algorithms at the base and junction levels. Additionally, we used reverse transcription–polymerase chain reaction (RT–PCR) and Sanger sequencing to validate the ability of the algorithms to detect novel transcript features such as novel exons and alternative splicing in RNA-Seq data from mouse retina. A pipeline based on BLAT was developed to explore the performance of established tools for this problem, and to compare it to the recently developed methods. This pipeline, the RNA-Seq Unified Mapper (RUM), performs comparably to the best current aligners and provides an advantageous combination of accuracy, speed and usability.
Availability: The RUM pipeline is distributed via the Amazon Cloud and for computing clusters using the Sun Grid Engine (http://cbil.upenn.edu/RUM).
Contact: ggrant@pcbi.upenn.edu; epierce@mail.med.upenn.edu
Supplementary Information:The RNA-Seq sequence reads described in the article are deposited at GEO, accession GSE26248.
miRDeep-P: a computational tool for analyzing the microRNA transcriptome in plants
Authors: Yang Xiaozeng , Li Lei 
Published: July 2011

Abstract
Motivation: Ultra-deep sampling of small RNA libraries by next-generation sequencing has provided rich information on the microRNA (miRNA) transcriptome of various plant species. However, few computational tools have been developed to effectively deconvolute the complex information.
Results: We sought to employ the signature distribution of small RNA reads along the miRNA precursor as a model in plants to profile expression of known miRNA genes and to identify novel ones. A freely available package, miRDeep-P, was developed by modifying miRDeep, which is based on a probabilistic model of miRNA biogenesis in animals, with a plant-specific scoring system and filtering criteria. We have tested miRDeep-P on eight small RNA libraries derived from three plants. Our results demonstrate miRDeep-P as an effective and easy-to-use tool for characterizing the miRNA transcriptome in plants.
Availability: http://faculty.virginia.edu/lilab/miRDP/
Contact: ll4jn@virginia.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
Fishery-dependent information and the ecosystem approach: what role can fishers and their knowledge play in developing countries?
Authors: Mathew Sebastian 
Published: July 2011

Abstract
Mathew, S. 2011. Fishery-dependent information and the ecosystem approach: what role can fishers and their knowledge play in developing countries? – ICES Journal of Marine Science, 68: 1805–1808. An ecosystem approach to fishery management is as much a mechanism to deal with the impact of fishing on targeted, associated, and dependent fish stocks, and on the habitat, as it is to deal with the impact of habitat degradation from natural and anthropogenic factors on fishing. In developing countries, often with little institutional capacity for generating timely and reliable information for managing fisheries, effective integration of the knowledge possessed by fishers and their communities regarding, for example, oceanographic, biological, economic, social, and cultural aspects can contribute to an ecosystem approach to fisheries. The challenge is to identify and validate such knowledge and to create policy and legal space to integrate it into management, also drawing upon good practice in industrialized countries. An attempt is made to identify such knowledge, to discuss its salient aspects, and to look at the conditions under which its practical value can be enhanced and integrated into formal fishery-management systems in developing countries.
Hemorrhagic Shock-induced Endothelial Cell Activation in a Spontaneous Breathing and a Mechanical Ventilation Hemorrhagic Shock Model Is Induced by a Proinflammatory Response and Not by Hypoxia
Authors: van Meurs Matijs , Wulfert Francis M. , Jongman Rianne M. , Schipper Martin , Houwertjes Martin C. , Vaneker Michiel , Scheffer Gert Jan , Teppema Luc J. , Aarts Leon P. H. J. , Heeringa Peter , Zijlstra Jan G. , Molema Grietje 
Published: July 2011

Introduction
The interaction between neutrophils and activated endothelium is essential for the development of multiple organ dysfunction in patients with hemorrhagic shock (HS). Mechanical ventilation frequently is used in patients with HS. The authors sought to investigate the consequences of mechanical ventilation of mice subjected to HS on microvascular endothelial activation in the lung and kidney.

Methods
Anesthetized wild type C57BL/6 male mice were subjected to controlled hemorrhage; subgroups of mice were mechanically ventilated during the HS insult. To study the effect of acute hypoxia on the mice, the animals were housed in hypoxic cages. Gene expression levels was assessed by quantitative real-time polymerase chain reaction. Protein expression was assessed by immunohistochemistry and enzyme-linked immunosorbent assay.

Results
Ninety minutes after the shock induction, a vascular bed-specific, heterogeneous proinflammatory endothelial activation represented by E-selectin, vascular cell adhesion molecule 1, and intercellular adhesion molecule 1 expression was seen in kidney and lung. No differences in adhesion molecules between the spontaneously breathing and mechanically ventilated mice were found. Concentrations of the proinflammatory cytokines chemokine (C-X-C motif) ligand 1 (11.0-fold) and interleukin-6 (21.7-fold) were increased after 90 min of HS. Two hours of 6% oxygen did not induce the expression of E-selectin, vascular cell adhesion molecule 1, and intercellular adhesion molecule 1 in the kidneys and the lung.

Conclusions
Hemorrhagic shock leads to an early and reversible proinflammatory endothelial activation in kidney and lung. HS-induced endothelial activation is not changed by mechanical ventilation during the shock phase. Hypoxia alone does not lead to endothelial activation. The observed proinflammatory endothelial activation is mostly ischemia- or reperfusion-dependent and not related to hypoxia.
Pregnancy in acromegaly: experience from two referral centers and systematic review of the literature
Authors: Cheng Sonia , Grasso Ludovica , Martinez‐Orozco Jose A. , Al‐Agha Rany , Pivonello Rosario , Colao Annamaria , Ezzat Shereen 
Published: July 2011

SummaryBackground  Acromegaly results from increased growth hormone and its target insulin‐like growth factor‐1, most commonly due to a pituitary tumour. As it is frequently accompanied by infertility, little is known about the course of this disease in pregnancy.Objective  We describe 13 new pregnancies in acromegalic women and compare their outcomes in a systematic review of the literature.Methods  We collected clinical, biochemical, imaging, and outcomes data during and following pregnancy and performed a systematic review for a total of 47 pregnancies. An extended analysis of 106 pregnancies was also performed.Results  In 13 newly described cases, pregnancy was un‐complicated without need for additional surgical intervention. In these pregnancies, adjunctive medical therapy was required in three patients. This was in the form of somatostatin analogs (SA) (3/13) as well as pegvisomant in 1/13 to control symptomatic and biochemical progression. One 37‐year‐old female succeeded in having two separate pregnancies 2 years apart both without need for any form of medical therapy. Review of an additional 34 published reports allowed for an analysis of outcomes in 47 pregnancies. Adjunctive medical therapy during pregnancy was required in 15 of these cases where 12 received SA and an additional three received dopamine agonists. None of these patients developed endocrine or neurologic complications during pregnancy. In an extended analysis of 106 pregnancies, treatment during pregnancy appears to be associated with good disease control but increased risk of microsomic or macrosomic newborns depending on the medical agent used.Conclusions  In 13 newly described pregnancies along with systematic review of an additional 34 cases indicate that pregnancy in treated acromegalic women can proceed without significant complications or teratogenicity. Medical treatment during pregnancy with DA or SA appears to be associated with altered neonatal weight. Nevertheless, gestation may have a beneficial impact on acromegaly control both during and following pregnancy.
Fine needle aspiration (FNA) cytology of extra‐adrenal paragangliomas
Authors: RANA R. S. , DEY P. , DAS A. 
Published: July 2011

Fine needle aspiration (FNA) cytology of extra‐adrenal paragangliomasWe studied nine histologically proved cases of extra‐adrenal paragangliomas. Of these, eight cases were correctly diagnosed preoperatively by FNA cytology. Salient cytological features included clusters and discretely scattered cells, with occasional acinar configuration. The cells showed moderate to abundant slightly basophilic cytoplasm with ill‐defined margins and round to oval nuclei with mild to marked nuclear pleomorphism. Fine reddish intracytoplasmic granules were also noted (six cases). Cytological features along with clinical data are quite diagnostic of paragangliomas. A correct preoperative cytological diagnosis helps to prevent undue surgical complications.Cytologie par ponction aspiration à l'aiguille fine des paragangliomes extra‐surrénaliensNous avons étudié 9 cas de paragangliomes extra‐surrénaliens histologiquement prouvés. Huit cas sur 9 ont été correctement diagnostiqués, à titre pré‐opératoire, par cytologie par ponction aspiration à l'aiguille fine. Les caractéristiques cytologiques principales sont la présence d'amas, une dispersion cellulaire modérée et d'occasionnelles formations acineuses. Les cellules comportent un cytoplasme légèrement basophile, moyennement à très abondant, avec des limites mal définies ainsi qu'un noyau rond ou ovale, dont le pléomorphisme nucléaire est modéré ou plus nettement marqué. Le présence de fines granulations rougeâtres intra‐cytoplasmiques a également été notée (6 cas). Ces caractères cytologiques, associés aux données cliniques, permettent pratiquement le diagnostic des paragangliomes. Un diagnostic cytologique pré‐opératoire correct favorise la prévention des complications chirurgicales indésirables.FNP extraadrenaler ParagangliomeNeun histologisch gesicherte Fälle extraadrenaler Paragangliome werden vorgestellt. Präoperativ waren 8 der Fälle zytologisch durch FNP richtig diagnostiziert worden. Charakteristisch waren Einzelzellen und z.T. azinäre Verbände. Die Zellen zeigten mässig bis reichlich, leicht basophiles, unscharf begrenztes Zytoplasma und rund‐ovale Kerne mit leichter bis ausgeprägter Pleomorphie. In 6 Fällen lagen feine, rote Granula im Zytoplasma vor. Das zytologische Bild in Zusammenschau mit den klinischen Daten erlaubt eine sichere Diagnose. Auf diese Weise können die operativen Risiken vermindert werden.
Disentangling direct and indirect effects of water table drawdown on above‐ and belowground plant litter decomposition: consequences for accumulation of organic matter in boreal peatlands
Authors: Straková Petra , Penttilä Timo , Laine Jukka , Laiho Raija 
Published: July 2011

AbstractPristine peatlands are carbon (C)‐accumulating wetland ecosystems sustained by a high water table (WT) and consequent anoxia that slows down decomposition. Persistent WT drawdown as a response to climate and/or land‐use change affects decomposition either directly through environmental factors such as increased oxygenation, or indirectly through changes in plant community composition. This study attempts to disentangle the direct and indirect effects of WT drawdown by measuring the relative importance of environmental parameters (WT depth, temperature, soil chemistry) and litter type and/or litter chemical quality on the 2‐year decomposition rates of above‐ and belowground litter (altogether 39 litter types). Consequences for organic matter accumulation were estimated based on the annual litter production. The study sites were chosen to form a three‐stage chronosequence from pristine (undrained) to short‐term (years) and long‐term (decades) WT drawdown conditions at three nutrient regimes. The direct effects of WT drawdown were overruled by the indirect effects through changes in litter type composition and production. Short‐term responses to WT drawdown were small. In long‐term, dramatically increased litter inputs resulted in large accumulation of organic matter in spite of increased decomposition rates. Furthermore, the quality of the accumulated matter greatly changed from that accumulated in pristine conditions. Our results show that the shift in vegetation composition as a response to climate and/or land‐use change is the main factor affecting peatland ecosystem C cycle, and thus dynamic vegetation is a necessity in any model applied for estimating responses of C fluxes to changing environment. We provide possible grouping of litter types into plant functional types that the models could utilize. Furthermore, our results clearly show a drop in soil summer temperature as a response to WT drawdown when an initially open peatland converts into a forest ecosystem, which has not yet been considered in the existing models.
The large Amazonian peatland carbon sink in the subsiding Pastaza‐Marañón foreland basin, Peru
Authors: Lähteenoja Outi , Reátegui Yully Rojas , Räsänen Matti , Torres Dennis Del Castillo , Oinonen Markku , Page Susan 
Published: July 2011

AbstractThe carbon (C) dynamics of tropical peatlands can be of global importance, because, particularly in Southeast Asia, they are the source of considerable amounts of C released to the atmosphere as a result of land‐use change and fire. In contrast, the existence of tropical peatlands in Amazonia has been documented only recently. According to a recent study, the 120 000 km2 subsiding Pastaza‐Marañón foreland basin in Peruvian Amazonia harbours previously unstudied and up to 7.5 m thick peat deposits. We studied the role of these peat deposits as a C reserve and sink by measuring peat depth, radiocarbon age and peat and C accumulation rates at 5–13 sites. The basal ages varied from 1975 to 8870 cal yr bp, peat accumulation rates from 0.46 to 9.31 mm yr−1 and C accumulation rates from 28 to 108 g m−2 yr−1. The total peatland area and current peat C stock within the area of two studied satellite images were 21 929 km2 and 3.116 Gt (with a range of 0.837–9.461 Gt). The C stock is 32% (with a range of 8.7–98%) of the best estimate of the South American tropical peatland C stock and 3.5% (with a range of 0.9–10.7%) of the best estimate of the global tropical peatland C stock. The whole Pastaza‐Marañón basin probably supports about twice this peatland area and peat C stock. In addition to their contemporary geographical extent, these peatlands probably also have a large historical (vertical) extension because of their location in a foreland basin characterized by extensive river sedimentation, peat burial and subsidence for most of the Quaternary period. Burial of peat layers in deposits of up to 1 km thick Quaternary river sediments removes C from the short‐term C cycle between the biosphere and atmosphere, generating a long‐term C sink.
Treatment outcomes and dental anxiety in 18‐year‐olds with MIH, comparisons with healthy controls – a longitudinal study
Authors: JÄLEVIK BIRGITTA , KLINGBERG GUNILLA 
Published: July 2011

International Journal of Paediatric Dentistry 2012; 22: 85–91Background.  In a previous study, 9‐year‐old children with severe Molar Incisor Hypomineralization (MIH) had undergone dental treatment of their first molars nearly ten times as often as children in a control group. They also showed more management problems (BMP) and fear and anxiety (DFA).Aim.  To assess the long‐term outcomes of dental treatments, dental anxiety, and patients’ satisfaction in adolescents with MIH.Design.  Sixty‐seven patients, identical with those in the baseline study, were studied at age 18‐years. The participants answered the Children’s Fear Survey Schedule – Dental Subscale the Dental Visit Satisfaction Scale (DVSS). Data were compiled from the dental records concerning dental health, number of restorative treatments and BMP.Results.  Molar Incisor Hypomineralization group had a significantly higher DMFT, and had undergone treatment of their permanent first molars 4.2 times as often as the controls. BMP was still significantly more common in the MIH group. However, DFS was reduced in MIH group and increased in the control groups. The DVSS scores did not differ between the groups.Conclusions.  Patients with severe MIH had a poorer dental health and were still more treatment consuming at age 18‐years. However, their dental fear was now at the same level as the controls.
Nurses’ perceptions of an electronic patient record from a patient safety perspective: a qualitative study
Authors: Stevenson Jean E. , Nilsson Gunilla 
Published: July 2011

stevenson j.e. & nilsson g. (2012) Nurses’ perceptions of an electronic patient record from a patient safety perspective: a qualitative study. Journal of Advanced Nursing68(3), 667–676.AbstractAims.  The overall aim of this study was to explore nurses’ perceptions of using an electronic patient record in everyday practice, in general ward settings. This paper reports on the patient safety aspects revealed in the study.Background.  Electronic patient records are widely used and becoming the main method of nursing documentation. Emerging evidence suggests that they fail to capture the essence of clinical practice and support the most frequent end‐users: nurses. The impact of using electronic patient records in general ward settings is under‐explored.Method.  In 2008, focus group interviews were conducted with 21 Registered Nurses. This was a qualitative study and the data were analysed by content analysis. At the time of data collection, the electronic patient record system had been in use for approximately 1 year.Findings.  The findings related to patient safety were clustered in one main category: ‘documentation in everyday practise’. There were three sub‐categories: vital signs, overview and medication module. Nurses reported that the electronic patient record did not support nursing practice when documenting crucial patient information, such as vital signs.Conclusions.  Efforts should be made to include the views of nurses when designing an electronic patient record to ensure it suits the needs of nursing practice and supports patient safety. Essential patient information needs to be easily accessible and give support for decision‐making.
The role of school nurses in delivering accessible health services for primary and secondary school students in Hong Kong
Authors: Lee Regina LT 
Published: July 2011

Aims.  To explore and describe the distinctive role of nurses in delivering school health services for primary and secondary school students in Hong Kong.Background.  The practical responsibility of nurses in delivering school health services has not been established. There is no literature on this topic and, in particular, nothing has been written from the perspective of the practitioner in communities in Hong Kong.Design.  A qualitative design using semi‐structured interviews was employed.Methods.  Thirteen school nurses were recruited and interviewed in 2006. The narratives were analysed using content analysis steps to identify categories.Results.  Seven categories were formulated. School nurses described their roles as providers, counsellors, leaders, promoters, collaborators, referrers and administrators and housekeepers. The school nurses also reported that they needed to maintain a diverse range of skills and knowledge, such as effective communication skills and clinical updated knowledge, to cope with the demands and the diversity of their roles and to support the health and educational needs of the students and their local communities.Conclusion.  The future development of the ‘one school, one nurse’ policy envisaged by the current government for ordinary schools in Hong Kong will not occur unless the role of school nurses is clearly delineated and valued by society as reducing school children’s and adolescents’ risk‐taking behaviours and promoting the health and well‐being of school children and adolescents.Relevance to clinical practice.  The findings provide relevant information for school nurse leaders and school nurse policy makers to understand how school nurses are practicing and promoting child and adolescent health services, which can inform regional and national policy and practice.