bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparison of 2 Delivery Vehicles for Viscous Budesonide to Treat Eosinophilic Esophagitis in Children
Authors: Rubinstein Eitan , Lee John J. , Fried Ari , Logvinenko Tanya , Ngo Peter , McDonald Douglas , Hait Elizabeth J. 
Published: May 2014

ABSTRACTObjectives:Oral viscous budesonide (OVB) using Splenda as a delivery vehicle has become an attractive therapeutic option for children with eosinophilic esophagitis (EoE). Many families are wary of giving the artificial sweetener in high doses to their children. The aim of the present study was to determine whether OVB mixed with Neocate Nutra, a hypoallergenic nutritional supplement, is at least as efficacious as OVB mixed with Splenda at healing EoE.Methods:Our institutional review board approved a retrospective chart review of patients with well‐documented EoE treated with OVB at the Boston Children's Hospital Eosinophilic Gastrointestinal Disorder program between June 2008 and June 2013. Primary outcome measured was histologic response defined as change in peak eosinophil count to <15 eosinophils per high‐power field (eos/HPF) after at least 10 weeks of OVB therapy.Results:A total of 46 children were treated with OVB mixed with Splenda, and 14 were treated with OVB mixed with Neocate Nutra. The 2 groups were not significantly different in their demographic (race, age, sex) or clinical (initial eosinophil count, proton pump inhibitor use, or concomitant dietary elimination) characteristics. On follow‐up endoscopy, 30 of 46 patients on Splenda and 13 of 14 patients on Neocate Nutra achieved histologic response. Mean pretreatment and posttreatment peak eosinophil counts for the children taking Neocate Nutra were 62 eos/HPF ([high‐power field] range 20–120 eos/HPF) and 9 eos/HPF (range 0–100 eos/HPF), respectively. Mean pretreatment and posttreatment peak eosinophil counts for the Splenda group were 59.5 eos/HPF (range 20–180 eos/HPF) and 25.5 eos/HPF (range 0–200 eos/HPF), respectively. The odds ratio (OR) of success with Neocate Nutra as compared with Splenda was 6.93 (95% CI 0.83–57.91, P = 0.0728), demonstrating the noninferiority of Neocate Nutra.Conclusions:We demonstrate that OVB mixed with Neocate Nutra is at least as effective as OVB mixed with Splenda at treating children with EoE. Neocate Nutra is an innovative, effective, and palatable mixing agent to create a viscous budesonide slurry for families who prefer not to use the standard recipe with Splenda.
Module organizational principles and dynamics in biological networks
Authors: Lin Chun-Yu , Lee Tsai-ling , Lin Yi-Wei , Lo Yu-Shu , Lin Chih-Ta , Yang Jinn-Moon 
Published: May 2014

AbstractA module is a group of closely related proteins that act in concert to perform specific biological functions through protein–protein interactions (PPIs) that occur in time and space. However, the underlying organizational principles of a module remain unclear. In this study, we collected CORUM module templates to infer respective module families, including 58,041 homologous modules in 1,678 species, and PPI families using searches of complete genomic database. We then derived PPI evolution scores (PPIES) and interface evolution scores (IES) to infer module elements, including core and ring components. Functions of core components were highly correlated (Pearson’sr= 0.98) with those of 11,384 essential genes. In comparison with ring components, core proteins and PPIs were conserved in multiple species. Subsequently, protein dynamics and module dynamics of biological networks and functional diversities confirmed that core components form dynamic biological network hubs and play key roles in various biological functions. PPIES and IES can reflect module organization principles and protein/module dynamics in biological networks. On the basis of the analyses of gene essentiality, module dynamics, network topology, and gene co-expression, the module organizational principles can be described as follows: 1) a module consists of core and ring components; 2) the core components play major roles in biological functions and collaborate with ring components to perform certain functions in some cases; 3) the core components are conserved and essential in module dynamics in time and space.
Depth‐related distribution of a key gene of the tetraether lipid biosynthetic pathway in marine Thaumarchaeota
Authors: Villanueva Laura , Schouten Stefan , Sinninghe Damsté Jaap S. 
Published: May 2014

SummaryThe distribution of isoprenoid glycerol dialkyl glycerol tetraethers (GDGT) lipids synthesized by Thaumarchaeota has been shown to be temperature‐dependent in world oceans. Depth‐related differences in the ammonia monooxygenase (amoA) of Thaumarchaeota have led to the classification of ‘shallow’ and ‘deep water’ clusters, potentially affecting GDGT distributions. Here, we investigate if this classification is also reflected in a key gene of the thaumarchaeotal lipid biosynthetic pathway coding for geranylgeranylglyceryl phosphate (GGGP) synthase. We investigated metagenomic databases, suspended particulate matter and surface sediment of the Arabian Sea oxygen minimum zone. These revealed significant differences in amoA and GGGP synthase between ‘shallow’ and ‘deep water’ Thaumarchaeota. Intriguingly, amoA and GGGP synthase sequences of benthic Thaumarchaeota clustered with the ‘shallow water’ rather than with ‘deep water’ Thaumarchaeota. This suggests that pressure and temperature are unlikely factors that drive the differentiation, and suggests an important role of ammonia concentration that is higher in benthic and ‘shallow water’ niches. Analysis of the relative abundance of GDGTs in the Arabian Sea and in globally distributed surface sediments showed differences in GDGT distributions from subsurface to deep waters that may be explained by differences in the GGGP synthase, suggesting a genetic control on GDGT distributions.
Absence of Po2 change in fetal brain despite Po2 increase in placenta in response to maternal oxygen challenge
Authors: Huen I , Morris DM , Wright C , Sibley CP , Naish JH , Johnstone ED 
Published: May 2014

ObjectiveMagnetic resonance imaging allows the noninvasive observation of Po2 changes between air breathing and oxygen breathing through quantification of the magnetic longitudinal relaxation time T1. Changes in Po2 are proportional to changes in the longitudinal relaxation rate ΔR1 (where ΔR1 = 1/T1oxygen − 1/T1air). Knowledge of this response could inform clinical interventions using maternal oxygen administration antenatally to treat fetal growth restriction. We present in vivo measurements of the response of the fetal–placental unit to maternal hyperoxia.DesignProspective cohort.SettingLarge tertiary maternity hospital.SampleNine women undergoing low‐risk pregnancy (21–33 weeks of gestation) and five nonpregnant adults.MethodsDuring imaging the air supply to mothers was changed from medical air (21% oxygen) to medical oxygen (100% oxygen) and T1 was monitored over time in both the placenta and fetal brain using a periodically repeated magnetic resonance imaging sequence. To demonstrate that the method could detect a brain response, brain responses from five normal adult volunteers were measured using a similar imaging protocol.Main outcome measureChanges in T1 following oxygen challenge.ResultsNo significant ΔR1 (P = 0.42, paired t‐test) was observed in fetal brains. A significant placental ΔR1 (P = 0.0002, paired t‐test) of 0.02 ± 0.01/s (mean ± SD) was simultaneously observed in the same participants. In the brains of the nonpregnant adults, a significant ΔR1 (P = 0.01, paired t‐test) of 0.005 ± 0.002/s was observed.ConclusionShort‐term maternal oxygen administration does not improve fetal brain oxygenation, in contrast to the response observed in the adult brain.
Beef Credence Attributes: Implications of Substitution Effects on Consumers’ WTP
Authors: Viegas Inês , Nunes Luís Catela , Madureira Lívia , Fontes Magda Aguiar , Santos José Lima 
Published: May 2014

AbstractConsumers’ food choices are influenced by a wide variety of credence attributes, but the food industry faces problems assessing whether the price premiums that consumers are willing to pay for these attributes will be sufficient to offset higher production costs. In this context, consumers’ willingness to pay (WTP) for safer, cleaner and animal friendlier beef was investigated through a choice experiment. The relative importance of WTP for these attributes shows that consumers place the highest values on food safety, followed by animal welfare and finally environmental protection. WTP for different combinations of the three attributes cannot be obtained by independent valuation and summation due to the presence of significant substitution relationships. However, some suggestions for the relationships between these attributes can be proposed through an after‐survey analytical solution. The bias involved in separately valuing closely related attributes can potentially jeopardise the success of a differentiation strategy.
Chemotherapy mediates intestinal injury via p53/p53 upregulated modulator of apoptosis (PUMA) signaling pathway
Authors: Zhan Ya Shi , Tan Si Wei , Mao Wei , Jiang Jie , Liu Hui Ling , Wu Bin 
Published: May 2014

ObjectiveThe aim of this study was to investigate the potential mechanism and signaling pathway involved in chemotherapy‐induced intestinal mucosal injury (CIMI), which is a common physiopathological problem in patients with cancer.MethodsFor the in vivo experiment, mice received intraperitoneal injection of 5‐fluorouracil (5‐FU) at a dose of 75 mg/kg/day for 1, 3 or 5 days. Villus height and crypt depth of the small intestine, cell apoptosis and proliferation were then examined to determine the extent of CIMI. The expressions of Akt, p53, PUMA and p21 were evaluated both in vivo in mice models and in vitro in the IEC‐6 and HCT116 cell lines.ResultsAfter 5‐FU therapy both the intestinal villus height (275.93 μm vs 164.52 μm, P < 0.001) and crypt depth (64.13 μm vs 42.48 μm, P < 0.001) were decreased. The apoptotic index was greatly increased from 0.32% to 15.84% (P < 0.001) and proliferation was suppressed (63.58% vs 39.15%, P < 0.001). Additionally, p53 expression was significantly increased in the intestinal crypt along with the expressions of PUMA and p21. Western blot showed that the administration of 5‐FU induced p53/PUMA‐mediated apoptosis and upregulated p21 expression to suppress cell proliferation.ConclusionChemotherapy might mediate intestinal injury via p53/PUMA‐mediated apoptotic signaling and the suppression of proliferation in response to p21.
‘Direct PCR’ optimization yields a rapid, cost‐effective, nondestructive and efficient method for obtaining DNA barcodes without DNA extraction
Authors: Wong Wing Hing , Tay Ywee Chieh , Puniamoorthy Jayanthi , Balke Michael , Cranston Peter S. , Meier Rudolf 
Published: May 2014

AbstractMacroinvertebrates that are collected in large numbers pose major problems in basic and applied biodiversity research: identification to species via morphology is often difficult, slow and/or expensive. DNA barcodes are an attractive alternative or complementary source of information. Unfortunately, obtaining DNA barcodes from specimens requires many steps and thus time and money. Here, we promote a short cut to DNA barcoding, that is, a nondestructive PCR method that skips DNA extraction (‘direct PCR’) and that can be used for a broad range of invertebrate taxa. We demonstrate how direct PCR can be optimized for the larvae and adults of nonbiting midges (Diptera: Chironomidae), a typical invertebrate group that is abundant, contains important bioindicator species, but is difficult to identify based on morphological features. After optimization, direct PCR yields high PCR success rates (>90%), preserves delicate morphological features (e.g. details of genitalia, and larval head capsules) while allowing for the recovery of genomic DNA. We also document that direct PCR can be successfully optimized for a wide range of other invertebrate taxa that need routine barcoding (flies: Culicidae, Drosophilidae, Dolichopodidae, Sepsidae; sea stars: Oreasteridae). Key for obtaining high PCR success rates is optimizing (i) tissue quantity, (ii) body part, (iii) primer pair and (iv) type of Taq polymerase. Unfortunately, not all invertebrates appear suitable because direct PCR has low success rates for other taxa that were tested (e.g. Coleoptera: Dytiscidae, Copepoda, Hymenoptera: Formicidae and Odonata). It appears that the technique is less successful for heavily sclerotized insects and/or those with many exocrine glands.
Challenges to barcoding an entire flora
Authors: Elliott Tammy L. , Jonathan Davies T. 
Published: May 2014

AbstractDNA barcodes are species‐specific genetic markers that allow taxonomic identification of biological samples. The promise of DNA barcoding as a rapid molecular tool for conducting biodiversity inventories has catalysed renewed efforts to document and catalogue the diversity of life, parallel to the large‐scale sampling conducted by Victorian naturalists. The unique contribution of DNA barcode data is in its ability to identify biotic material that would be impossible to classify using traditional taxonomic keys. However, the utility of DNA barcoding relies upon the construction of accurate barcode libraries that provide a reference database to match to unidentified samples. Whilst there has been much debate in the literature over the choice and efficacy of barcode markers, there has been little consideration of the practicalities of generating comprehensive barcode reference libraries for species‐rich floras. Here, we discuss several challenges to the generation of such libraries and present a case study from a regional biodiversity hotspot in southern Quebec. We suggest that the key challenges include (i) collection of specimens for rare or ephemeral species, (ii) limited access to taxonomic expertise necessary for reliable identification of reference specimens and (iii) molecular challenges in amplifying and matching barcode data. To be most effective, we recommend that sampling must be both flexible and opportunistic and conducted across the entire growing season by expert taxonomists. We emphasize that the success of the global barcoding initiative will depend upon the close collaboration of taxonomists, plant collectors, and molecular biologists.
Psychometric examination of the Persian version of Osteoarthritis Knee and Hip Quality of Life questionnaire
Authors: Saffari Mohsen , Emami Meybodi Mohammad Kazem , Koenig Harold G. , Pakpour Amir H. , Rshidi Jahan Hojat 
Published: May 2014

AbstractAimOsteoarthritis is a serious and prevalent health problem that creates considerable disability when it involves the knee or hip joints. The aim of the study was to adapt and validate the Osteoarthritis Knee and Hip Quality of Life (OAKHQOL) questionnaire for use in a Persian‐speaking population.MethodsA total of 434 patients were recruited. The forward‐backward translation process was used to develop the Persian version. Participants were asked to complete the Short Form 12 Health Survey, EuroQoL, visual analog scale for pain and the OAKHQOL questionnaire. Reliability was assessed using Cronbach's alpha and the test‐retest method. The structure of the questionnaire was evaluated by exploratory factor analysis. The OAKHQOL was correlated with related measures to establish construct validity. Convergent and discriminant validity were examined with demographic and clinical variables. Comparisons were performed between patients with different severity grades of osteoarthritis.ResultsThe mean age of participants was 61.9 (SD 12.1) and the majority were female (91.2%). Principal component analysis demonstrated a five‐factor solution that explained 58.4% of the variance. Cronbach's alpha coefficients ranged between 0.74 and 0.89 for all domains of the questionnaire with the exception of the social activities domain. The kappa for test‐retest reliability was 0.85. The OAKHQOL demonstrated good discriminative and convergent validity. Construct validity was established by determining significant relationships between related measures. The results of known‐groups validity indicated different scores on most domains (P < 0.001) across different levels of disease severity.ConclusionThe questionnaire may be used as a valid and reliable measure for assessing quality of life among Iranian patients with lower limb osteoarthritis.
Spatial targeting of infectious disease control: identifying multiple, unknown sources
Authors: Verity Robert , Stevenson Mark D. , Rossmo D. Kim , Nichols Richard A. , Le Comber Steven C. 
Published: May 2014

Summary

Geographic profiling (GP) was originally developed as an analytical tool in criminology, where it uses the spatial locations of linked crimes (for example murder, rape or arson) to identify areas that are most likely to include the offender's residence. The technique has been extremely successful in this field and is now widely used by police forces and investigative agencies around the world. More recently, the same method has been applied to biological data, notably in spatial epidemiology, where it uses the locations of disease cases to identify infection sources: the identification of these sources is critical to control efforts of diseases such as malaria, since targeted intervention is more efficient and cost‐effective than untargeted intervention.

Here, we solve the problem of identifying multiple sources, even when the number of sources is unknown – a requirement for many biological studies. We present a new, rigorous mathematical and computational method and show why previous Bayesian methods were often outperformed by the empirically developed criminal geographic targeting (CGT) algorithm used in criminology.

We use simulations and real‐world examples to compare our model to both the CGT algorithm and to an existing Bayesian model. We demonstrate that our method combines the advantages of both previous methods, particularly in cases featuring large data sets and multiple sources.

Our approach provides an increase in search efficiency over other methods and is likely to lead to improved targeting of interventions and more efficient use of resources. We suggest that the Dirichlet process mixture (DPM) model provides a useful and practical tool for conservation biologists and epidemiologists that can be used to inform management decisions and public health policy.
Aging impairs peritoneal but not bone marrow‐derived macrophage phagocytosis
Authors: Linehan Eimear , Dombrowski Yvonne , Snoddy Rachel , Fallon Padraic G. , Kissenpfennig Adrien , Fitzgerald Denise C. 
Published: May 2014

SummaryAging results in deterioration of the immune system, which is associated with increased susceptibility to infection and impaired wound healing in the elderly. Phagocytosis is an essential process in both wound healing and immune defence. As such, age‐related impairments in phagocytosis impact on the health of the elderly population. Phagocytic efficiency in peritoneal macrophages, bone marrow‐derived macrophages and bone marrow monocytes from young and old mice was investigated. Aging significantly impaired phagocytosis by peritoneal macrophages, both in vitro and in vivo. However, bone marrow‐derived macrophages and bone marrow monocytes did not exhibit age‐related impairments in phagocytosis, suggesting no intrinsic defect in these cells. We sought to investigate underlying mechanisms in age‐related impairments in phagocytosis by peritoneal macrophages. We hypothesized that microenvironmental factors in the peritoneum of old mice impaired macrophage phagocytosis. Indeed, macrophages from young mice injected into the peritoneum of old mice exhibited impaired phagocytosis. Proportions of peritoneal immune cells were characterized, and striking increases in numbers of T cells, B1 and B2 cells were observed in the peritoneum of old mice compared with young mice. In addition, B cell‐derived IL‐10 was increased in resting and LPS‐activated peritoneal cell cultures from old mice. These data demonstrate that aging impairs phagocytosis by tissue‐resident peritoneal macrophages, but not by bone marrow‐derived macrophages/monocytes, and suggest that age‐related defects in macrophage phagocytosis may be due to extrinsic factors in the tissue microenvironment. As such, defects may be reversible and macrophages could be targeted therapeutically in order to boost immune function in the elderly.
A nomogram for calculating the maximum dose of local anaesthetic
Authors: Williams D. J. , Walker J. D. 
Published: May 2014

SummaryToxic dose limits (mg.kg−1) for local anaesthetics based on body weight are well‐established, but calculation of the maximum safe volume (ml) of a given agent and formulation is complex, and frequently results in errors. We therefore developed a nomogram to perform this calculation. We compared the performance of the nomogram with a spreadsheet and a general purpose calculator using simulated clinical data. Bland‐Altman analysis showed close agreement between the nomogram and spreadsheet, with bias of −0.07 ml and limits of agreement of −0.38 to +0.24 ml (correlation coefficient r2 = 0.9980; p < 0.001). The nomogram produced fewer and smaller errors compared with the calculator. Our nomogram calculates the maximum safe volume (ml) of local anaesthetic to a clinically acceptable degree of accuracy. It facilitates rapid cross‐checking of dosage calculations performed by electronic or other means at negligible cost, and can potentially reduce the incidence of local anaesthetic toxicity.
Comparison of the duration of neuromuscular blockade following a single bolus dose of rocuronium during laparoscopic gynaecological surgery vs conventional open surgery
Authors: Wang T. , Huang S. , Geng G. 
Published: May 2014

SummaryWe investigated whether laparoscopic vs open surgical approaches affected the duration of neuromuscular blockade following a single bolus dose of rocuronium. Fifty‐three female patients underwent either laparoscopic or open gynaecological surgery. Rocuronium 0.6 mg.kg−1 was administered to achieve neuromuscular blockade in all subjects, and adductor pollicis train‐of‐four responses following ulnar nerve stimulation were monitored with mechanomyography. The mean (SD) time from injection of rocuronium until spontaneous recovery of the first twitch, and to 5% and 25% of baseline, was significantly prolonged in the laparoscopic group (27.2 (8.3) min, 31.3 (9.1) min and 38.1 (10.6) min, respectively) compared with the open surgery group (21.1 (5.8) min, 25.6 (6.3) min and 31.2 (6.7) min, respectively). Changes in liver function both before surgery and at 24 h postoperatively were similar between the two groups (p > 0.05). Our findings suggest that neuromuscular blockade may be prolonged following a single bolus dose of rocuronium given during laparoscopic procedures.