bluuebunny/crossref_metadata_2025_split huggingface dataset:
A review of paediatric tuberculosis in Denmark: 10-year trend, 2000–2009
Authors: Hatleberg Camilla Ingrid , Prahl Julie B. , Rasmussen Jeppe Nørgaard , Andersen Peter Henrik , Bjerrum Stephanie , Thomsen Vibeke Østergaard , Johansen Isik Somuncu 
Published: August 2013

Paediatric tuberculosis (TB) is a key indicator for recent transmission and presents a reservoir for the disease. We describe trends in epidemiology, microbiological characteristics and treatment outcome in Denmark between 2000 and 2009. Data were retrieved from the national TB surveillance system and the International Reference Laboratory of Mycobacteriology.In total, 323 TB cases were reported in children aged <15 years, accounting for 7.6% of all notified cases in Denmark. The overall incidence rate of childhood TB declined from 4.1 per 100 000 to 1.9 per 100 000 in the study period. Immigrant children comprised 79.6% of all cases, with the highest incidence rate of 94.1 per 100 000 children in 2001. In contrast to immigrant children, the majority of Danish children were aged <5 years and had a known exposure to TB. Pulmonary TB was the commonest presentation. Only half of the cases were culture confirmed.We observed an overall decreasing trend in the child to adult notification ratio, but a slight increase in the ratio when calculated specifically for ethnic Danes.Childhood TB needs continuous attention with a special focus on risk groups. Emphasis on improving early TB case detection, contact tracing and further implementation of preventive treatment is necessary.
Ontology based molecular signatures for immune cell types via gene expression analysis
Authors: Meehan Terrence F , Vasilevsky Nicole A , Mungall Christopher J , Dougall David S , Haendel Melissa A , Blake Judith A , Diehl Alexander D 
Published: August 2013

AbstractBackgroundNew technologies are focusing on characterizing cell types to better understand their heterogeneity. With large volumes of cellular data being generated, innovative methods are needed to structure the resulting data analyses. Here, we describe an ‘Ontologically BAsed Molecular Signature’ (OBAMS) method that identifies novel cellular biomarkers and infers biological functions as characteristics of particular cell types. This method finds molecular signatures for immune cell types based on mapping biological samples to the Cell Ontology (CL) and navigating the space of all possible pairwise comparisons between cell types to find genes whose expression is core to a particular cell type’s identity.ResultsWe illustrate this ontological approach by evaluating expression data available from the Immunological Genome project (IGP) to identify unique biomarkers of mature B cell subtypes. We find that using OBAMS, candidate biomarkers can be identified at every strata of cellular identity from broad classifications to very granular. Furthermore, we show that Gene Ontology can be used to cluster cell types by shared biological processes in order to find candidate genes responsible for somatic hypermutation in germinal center B cells. Moreover, throughin silicoexperiments based on this approach, we have identified genes sets that represent genes overexpressed in germinal center B cells and identify genes uniquely expressed in these B cells compared to other B cell types.ConclusionsThis work demonstrates the utility of incorporating structured ontological knowledge into biological data analysis - providing a new method for defining novel biomarkers and providing an opportunity for new biological insights.
Identification, expression, and comparative genomic analysis of the IPT and CKX gene families in Chinese cabbage (Brassica rapa ssp. pekinensis)
Authors: Liu Zhenning , Lv Yanxia , Zhang Mei , Liu Yapei , Kong Lijun , Zou Minghua , Lu Gang , Cao Jiashu , Yu Xiaolin 
Published: August 2013

Abstract

Background
Cytokinins (CKs) have significant roles in various aspects of plant growth and development, and they are also involved in plant stress adaptations. The fine-tuning of the controlled CK levels in individual tissues, cells, and organelles is properly maintained by isopentenyl transferases (IPTs) and cytokinin oxidase/dehydrogenases (CKXs). Chinese cabbage is one of the most economically important vegetable crops worldwide. The whole genome sequencing of Brassica rapa enables us to perform the genome-wide identification and functional analysis of the IPT and CKX gene families.

Results
In this study, a total of 13 BrIPT genes and 12 BrCKX genes were identified. The gene structures, conserved domains and phylogenetic relationships were analyzed. The isoelectric point, subcellular localization and glycosylation sites of the proteins were predicted. Segmental duplicates were found in both BrIPT and BrCKX gene families. We also analyzed evolutionary patterns and divergence of the IPT and CKX genes in the Cruciferae family. The transcription levels of BrIPT and BrCKX genes were analyzed to obtain an initial picture of the functions of these genes. Abiotic stress elements related to adverse environmental stimuli were found in the promoter regions of BrIPT and BrCKX genes and they were confirmed to respond to drought and high salinity conditions. The effects of 6-BA and ABA on the expressions of BrIPT and BrCKX genes were also investigated.

Conclusions
The expansion of BrIPT and BrCKX genes after speciation from Arabidopsis thaliana is mainly attributed to segmental duplication events during the whole genome triplication (WGT) and substantial duplicated genes are lost during the long evolutionary history. Genes produced by segmental duplication events have changed their expression patterns or may adopted new functions and thus are obtained. BrIPT and BrCKX genes respond well to drought and high salinity stresses, and their transcripts are affected by exogenous hormones, such as 6-BA and ABA, suggesting their potential roles in abiotic stress conditions and regulatory mechanisms of plant hormone homeostasis. The appropriate modulation of endogenous CKs levels by IPT and CKX genes is a promising approach for developing economically important high-yielding and high-quality stress-tolerant crops in agriculture.
Odor naming and interpretation performance in 881 schizophrenia subjects: association with clinical parameters
Authors: Kästner Anne , Malzahn Dörthe , Begemann Martin , Hilmes Constanze , Bickeböller Heike , Ehrenreich Hannelore 
Published: August 2013

Abstract

Background
Olfactory function tests are sensitive tools for assessing sensory-cognitive processing in schizophrenia. However, associations of central olfactory measures with clinical outcome parameters have not been simultaneously studied in large samples of schizophrenia patients.

Methods
In the framework of the comprehensive phenotyping of the GRAS (Göttingen Research Association for Schizophrenia) cohort, we modified and extended existing odor naming (active memory retrieval) and interpretation (attribute assignment) tasks to evaluate them in 881 schizophrenia patients and 102 healthy controls matched for age, gender and smoking behavior. Associations with emotional processing, neuropsychological test performance and disease outcome were studied.

Results
Schizophrenia patients underperformed controls in both olfactory tasks. Odor naming deficits were primarily associated with compromised cognition, interpretation deficits with positive symptom severity and general alertness. Contrasting schizophrenia extreme performers of odor interpretation (best versus worst percentile; N=88 each) and healthy individuals (N=102) underscores the obvious relationship between impaired odor interpretation and psychopathology, cognitive dysfunctioning, and emotional processing (all p<0.004).

Conclusions
The strong association of performance in higher olfactory measures, odor naming and interpretation, with lead symptoms of schizophrenia and determinants of disease severity highlights their clinical and scientific significance. Based on the results obtained here in an exploratory fashion in a large patient sample, the development of an easy-to-use clinical test with improved psychometric properties may be encouraged.
Applying the trigger review method after a brief educational intervention: potential for teaching and improving safety in GP specialty training?
Authors: McKay John , de Wet Carl , Kelly Moya , Bowie Paul 
Published: August 2013

Abstract

Background
The Trigger Review Method (TRM) is a structured approach to screening clinical records for undetected patient safety incidents (PSIs) and identifying learning and improvement opportunities. In Scotland, TRM participation can inform GP appraisal and has been included as a core component of the national primary care patient safety programme that was launched in March 2013. However, the clinical workforce needs up-skilled and the potential of TRM in GP training has yet to be tested. Current TRM training utilizes a workplace face-to-face session by a GP expert, which is not feasible. A less costly, more sustainable educational intervention is necessary to build capability at scale. We aimed to determine the feasibility and impact of TRM and a related training intervention in GP training.

Methods
We recruited 25 west of Scotland GP trainees to attend a 2-hour TRM workshop. Trainees then applied TRM to 25 clinical records and returned findings within 4-weeks. A follow-up feedback workshop was held.

Results
21/25 trainees (84%) completed the task. 520 records yielded 80 undetected PSIs (15.4%). 36/80 were judged potentially preventable (45%) with 35/80 classified as causing moderate to severe harm (44%). Trainees described a range of potential learning and improvement plans. Training was positively received and appeared to be successful given these findings. TRM was valued as a safety improvement tool by most participants.

Conclusion
This small study provides further evidence of TRM utility and how to teach it pragmatically. TRM is of potential value in GP patient safety curriculum delivery and preparing trainees for future safety improvement expectations.
Carbon dioxide fixation by Calvin-Cycle enzymes improves ethanol yield in yeast
Authors: Guadalupe-Medina Víctor , Wisselink H Wouter , Luttik Marijke AH , de Hulster Erik , Daran Jean-Marc , Pronk Jack T , van Maris Antonius JA 
Published: August 2013

Abstract

Background
Redox-cofactor balancing constrains product yields in anaerobic fermentation processes. This challenge is exemplified by the formation of glycerol as major by-product in yeast-based bioethanol production, which is a direct consequence of the need to reoxidize excess NADH and causes a loss of conversion efficiency. Enabling the use of CO2 as electron acceptor for NADH oxidation in heterotrophic microorganisms would increase product yields in industrial biotechnology.

Results
A hitherto unexplored strategy to address this redox challenge is the functional expression in yeast of enzymes from autotrophs, thereby enabling the use of CO2 as electron acceptor for NADH reoxidation. Functional expression of the Calvin cycle enzymes phosphoribulokinase (PRK) and ribulose-1,5-bisphosphate carboxylase (Rubisco) in Saccharomyces cerevisiae led to a 90% reduction of the by-product glycerol and a 10% increase in ethanol production in sugar-limited chemostat cultures on a mixture of glucose and galactose. Co-expression of the Escherichia coli chaperones GroEL and GroES was key to successful expression of CbbM, a form-II Rubisco from the chemolithoautotrophic bacterium Thiobacillus denitrificans in yeast.

Conclusions
Our results demonstrate functional expression of Rubisco in a heterotrophic eukaryote and demonstrate how incorporation of CO2 as a co-substrate in metabolic engineering of heterotrophic industrial microorganisms can be used to improve product yields. Rapid advances in molecular biology should allow for rapid insertion of this 4-gene expression cassette in industrial yeast strains to improve production, not only of 1st and 2nd generation ethanol production, but also of other renewable fuels or chemicals.
Effect of salting-out on distribution behavior of di(2-ethylhexyl) phthalate and its analogues between water and sediment
Authors: Yuwatini Erini , Hata Noriko , Kuramitz Hideki , Taguchi Shigeru 
Published: August 2013

Abstract
A higher enrichment of organic pollutant, di(2-ethylhexyl) phthalate (DEHP) was found in estuary of Oyabe River and Jinzu River, Japan. Based on this, the distribution of DEHP between water and bed sediment was investigated as a model of organic pollutant through both the field investigation and laboratory experiment. The laboratory experiment was performed to examine the effect of seawater, organic matter in sediment and hydrophobicity (log K

ow
) of organic pollutants. The result showed that salting-out effect due to the high salinity in seawater and organic matter in sediment contributed towards the increasing of DEHP distribution between water and sediment. Furthermore, the hydrophobicity of organic pollutant also enhances the distribution between water and sediment to a higher magnitude in the presence of seawater.
Formation of Two-dimensionally Ordered Diarylethene Annulated Isomer at the Liquid/HOPG Interface upon In Situ UV Irradiation
Authors: Sakano Takeshi , Imaizumi Yohei , Hirose Takashi , Matsuda Kenji 
Published: August 2013

Abstract
A unique photoinduced change in the molecular ordering of a photochromic diarylethene derivative having amide groups was investigated at the liquid/highly oriented pyrolytic graphite (HOPG) interface by scanning tunneling microscopy (STM). Ordering of the diarylethene was stabilized by the hydrogen-bonded network of amide groups. The open- and the closed isomers formed characteristic stripe-patterned orderings; a different hydrogen-bonding network was formed in each case. In situ UV irradiation resulted in the exclusive formation of a third molecular ordering γ that is composed of the photoirreversible annulated isomer. No photoisomerized molecule was detected in the 2-D orderings, i.e., the open-ring isomer in the ordering of the closed-ring isomer and vice versa, despite the similarity in their molecular structures.
Mean Field Equilibrium in Dynamic Games with Strategic Complementarities
Authors: Adlakha Sachin , Johari Ramesh 
Published: August 2013

We study a class of stochastic dynamic games that exhibit strategic complementarities between players; formally, in the games we consider, the payoff of a player has increasing differences between her own state and the empirical distribution of the states of other players. Such games can be used to model a diverse set of applications, including network security models, recommender systems, and dynamic search in markets. Stochastic games are generally difficult to analyze, and these difficulties are only exacerbated when the number of players is large (as might be the case in the preceding examples). We consider an approximation methodology called mean field equilibrium to study these games. In such an equilibrium, each player reacts to only the long-run average state of other players. We find necessary conditions for the existence of a mean field equilibrium in such games. Furthermore, as a simple consequence of this existence theorem, we obtain several natural monotonicity properties. We show that there exist a “largest” and a “smallest” equilibrium among all those where the equilibrium strategy used by a player is nondecreasing, and we also show that players converge to each of these equilibria via natural myopic learning dynamics; as we argue, these dynamics are more reasonable than the standard best-response dynamics. We also provide sensitivity results, where we quantify how the equilibria of such games move in response to changes in parameters of the game (for example, the introduction of incentives to players).
A systematic review and meta-regression of mobile-bearingversusfixed-bearing total knee replacement in 41 studies
Authors: van der Voort P. , Pijls B. G. , Nouta K. A. , Valstar E. R. , Jacobs W. C. H. , Nelissen R. G. H. H. 
Published: August 2013

Mobile-bearing (MB) total knee replacement (TKR) was introduced to reduce the risk of aseptic loosening and wear of polyethylene inserts. However, no consistent clinical advantages of mobile- over fixed-bearing (FB) TKR have been found. In this study we evaluated whether mobile bearings have an advantage over fixed bearings with regard to revision rates and clinical outcome scores. Furthermore, we determined which modifying variables affected the outcome.A systematic search of the literature was conducted to collect clinical trials comparing MB and FB in primary TKR. The primary outcomes were revision rates for any reason, aseptic loosening and wear. Secondary outcomes included range of movement, Knee Society score (KSS), Oxford knee score (OKS), Short-Form 12 (SF-12) score and radiological parameters. Meta-regression techniques were used to explore factors modifying the observed effect.Our search yielded 1827 publications, of which 41 studies met our inclusion criteria, comprising over 6000 TKRs. Meta-analyses showed no clinically relevant differences in terms of revision rates, clinical outcome scores or patient-reported outcome measures between MB and FB TKRs. It appears that theoretical assumptions of superiority of MB over FB TKR are not borne out in clinical practice.Cite this article: Bone Joint J 2013;95-B:1209–16.
Anthro-tourism, documentary film and method
Authors: Peters Roanne 
Published: August 2013

Abstract
The lines between tourist and an anthropologist have become increasingly blurred. The idea of the Anthro-tourist is discussed in terms of a self-reflexive experience in the Kalahari Desert. A conceptual framework is developed through a case study of a reflexive video, I am, You Are? (2003). Auto-ethnographic reflections on personal encounters with the ≠Khomani Bushmen is offered as this author’s comparative experience in light of the commodification of indigenous cultures through tourism as well as the construction of the ‘self’ and ‘other’ relationships. Both tourists and anthropologists have a similar interest in the exotic. Anthropologists, however, aim to educate society through film and video rather than to advertise the exotic.
Is Laser Disinfection an Effective Adjunctive Treatment to Bone Augmentation for Peri‐Implantitis? A Review of Current Evidence
Authors: Geisinger Maria L. , Holmes Carolyn M. , Vassilopoulos Philip J. , Geurs Nicolaas C. , Reddy Michael S. 
Published: August 2013

Focused Clinical Question:In patients with endosseous dental implants that demonstrate peri‐implantitis, does surgical bone augmentation with adjunctive laser implant surface disinfection have an effect on implant survival rates, and do these rates differ based on laser treatment modality?Clinical Scenario:A 55‐year‐old female presents 10 years after implant placement at sites #18 and #20 (Fig. 1). She demonstrates a 9‐mm probing depth mesially and distally at implant #20. Bleeding on probing is present at all six sites around implant #20. The patient has not noted any discomfort, and suppuration has not been noted on clinical examination. Her medical history is significant for osteoarthritis, gastroesophageal reflux disease, and anxiety. She reports taking ibuprofen as needed for pain, 150 mg ranitidine twice daily, and 20 mg citalopram daily. The patient is concerned about the possibility of implant loss and states that she wants to save and treat the implant, if possible. During flap reflection, a circumferential defect at implant #20 is noted intrasurgically (Fig. 2).
Long-Term Hydrothermal Proppant Performance
Authors: Raysoni Neelam , Weaver Jim 
Published: August 2013

Summary
The hydrothermal degradation of alumina-based proppants, which can lead to significant loss of fracture conductivity, has been the topic of recent papers. Most of these studies were necessarily compromised either by being performed on too short of a time scale to produce geochemical effects or by using unrealistic temperature conditions to accelerate the geochemical reactions. Those studies, however, provided insight that geochemical reactions likely occur during production from hydraulically generated fractures and gave evidence of possible long-term proppant instability.
This paper presents proppant-pack-permeability and proppant-crush-strength data collected from a selection of hydrothermal tests performed in sealed test cells packed with proppant and formation material, with no flow and no mechanical closure stress. Long-term proppant performance was determined by evaluating the proppant after 0, 15, 45, 90, and 180 days of hydrothermal exposure at 300 and 450°F, resulting in verification that proppants degrade continuously with time at all temperatures. A typical longterm proppant-testing result was 80% loss in proppant-pack permeability and 40% loss in proppant crush strength, with just 180-days exposure at 300°F at typical reservoir pH. These tests were performed both with and without formation material present to demonstrate the impact of reservoir/proppant compatibility. Scanning-electron-microscope (SEM) and energy-dispersive X-ray (EDX) spectroscopy analyses verified that dynamic molecular rearrangement occurs over the entire temperature range, though at an accelerated rate as temperature increased. Extensive effort was made to quantify both the accuracy and repeatability of testing procedures used in this study and will be presented. This involves measurement of pack permeability using water before and after hydrothermal exposure, and single-proppant-grain crush-strength determination using Weibull statistical analyses.
This paper presents substantial data to support the importance of proppant compatibility when selecting the best proppant for long-term fracture conductivity. It also suggests that methods in addition to American Petroleum Institute (API) crush and conductivity procedures need to be developed and implemented to rank proppant performance properly.