bluuebunny/crossref_metadata_2025_split huggingface dataset:
Assessing the scientific research productivity of a leading toxicology journal: A case study of Human & Experimental Toxicology from 2003 to 2012
Authors: Zyoud Sa’ed H , Al-Jabi Samah W , Sweileh Waleed M , Awang Rahmat 
Published: February 2014

Background: Bibliometric studies are increasingly being used for research assessments. Bibliometric indicators involve the application of statistical methods to scientific publications to obtain the bibliographics for each journal. The main objective of this study was to conduct a bibliometric evaluation of Human & Experimental Toxicology retrieved from the Scopus database. Methods: This study obtained data from Scopus published from 1 January 2003 till 31 December 2012. The keywords entered in Scopus to accomplish the objective of this study were ‘Human’, ‘Experimental’ and ‘Toxicology’ as ‘Source Title’. Research productivity was evaluated based on a methodology developed and used in other bibliometric studies by analysing (a) total and trends in Human & Experimental Toxicology contributions in research between 2003 and 2012; (b) Human & Experimental Toxicology authorship patterns and productivity; (c) collaboration patterns; and (d) the citations received by the publications. Results: There were 1229 research articles published in Human & Experimental Toxicology. Of the articles included, 947 (77.1%) were original articles and 104 (8.5%) were review articles. The Hirsch-index of the retrieved documents was 35. The largest number of publications in Human & Experimental Toxicology was from the United States (19.6%), followed by India (12.8%) and Turkey (10.9%). The total number of citations was 9119, with a median (interquartile range) of 3 (1–9) in 6797 documents. The highest median (interquartile range) number of citations was 8 (2.7–12.7) for France, followed by 7.5 (2–22.5) for Iran and 6 (3–13.5) for the United Kingdom. The country most often citing articles that were published in Human & Experimental Toxicology was the United States, which made citations in 1508 documents, followed by India with citations in 792 documents. Conclusion: The documents in Human & Experimental Toxicology focus principally on original data, with very few review articles. Review articles tend to have higher citation rates than original articles, and hence, the editors and authors of Human & Experimental Toxicology might usefully promote the submission of reviews in the future to improve the impact of the journal.
Morbidity and mortality of sleep-disordered breathing: obstructive sleep apnoea and car crash
Authors: Phillips B. 
Published: February 2014

Educational aimsTo review the results of USA Department of Transportation meta-analysis regarding obstructive sleep apnoea (OSA) and car crash risk.To discuss factors beyond OSA that increase the risk of crash.SummaryUntreated OSA increases the risk of having a car crash two-fold. In addition, the severity of sleep-disordered breathing, degree of oxygen desaturation, self-reported sleepiness and body mass index (BMI) increase the risk of crash in OSA patients. Continuous positive airway pressure (CPAP) reduces the risk of car crash. The data are insufficient for other forms of treatment to date. Sleep loss, medications and driving conditions have also been found to be factors affecting the risk of crash.
Identification of asthma phenotypes in children
Authors: Lødrup Carlsen K.C. , Pijnenburg M. 
Published: February 2014

Educational aimsAid understanding of the complexity of linking clinical disease presentation of asthma with underlying mechanismsOutline possible advantages of improving this understandingSummaryThe lung is a highly complex organ that can only be understood by integrating the many aspects of its structure. There is increasing interest in defining childhood asthma phenotypes, following decades of research into understanding mechanisms of asthma development and their genetic background without significant breakthroughs. Despite the medical profession’s best efforts to define asthma, identify risk factors and natural development of asthma in birth cohorts, and find characteristics that distinguish one type of asthma from another, we still do not know the relevant characteristics of the various subgroups of childhood asthma. This review will briefly describe the importance of identifying childhood asthma phenotypes, the observable characteristics of the disease, and the previous and current approaches used to find them.
Functional modifications associated with gastrointestinal tract organogenesis during metamorphosis in Atlantic halibut (Hippoglossus hippoglossus)
Authors: Gomes Ana S , Kamisaka Yuko , Harboe Torstein , Power Deborah M , Rønnestad Ivar 
Published: February 2014

Abstract
Background
Flatfish metamorphosis is a hormone regulated post-embryonic developmental event that transforms a symmetric larva into an asymmetric juvenile. In altricial-gastric teleost fish, differentiation of the stomach takes place after the onset of first feeding, and during metamorphosis dramatic molecular and morphological modifications of the gastrointestinal (GI-) tract occur. Here we present the functional ontogeny of the developing GI-tract from an integrative perspective in the pleuronectiforme Atlantic halibut, and test the hypothesis that the multiple functions of the teleost stomach develop synchronously during metamorphosis.

Results
Onset of gastric function was determined with several approaches (anatomical, biochemical, molecular and in vivo observations). In vivo pH analysis in the GI-tract lumen combined with quantitative PCR (qPCR) of α and β subunits of the gastric proton pump (H
+
/K
+
-ATPase) and pepsinogen A2 indicated that gastric proteolytic capacity is established during the climax of metamorphosis. Transcript abundance of ghrelin, a putative orexigenic signalling molecule produced in the developing stomach, correlated (p < 0.05) with the emergence of gastric proteolytic activity, suggesting that the stomach’s role in appetite regulation occurs simultaneously with the establishment of proteolytic function. A 3D models series of the GI-tract development indicated a functional pyloric sphincter prior to first feeding. Observations of fed larvae in vivo confirmed that stomach reservoir function was established before metamorphosis, and was thus independent of this event. Mechanical breakdown of food and transportation of chyme through the GI-tract was observed in vivo and resulted from phasic and propagating contractions established well before metamorphosis. The number of contractions in the midgut decreased at metamorphic climax synchronously with establishment of the stomach’s proteolytic capacity and its increased peristaltic activity. Putative osmoregulatory competence of the GI-tract, inferred by abundance of Na
+
/K
+
-ATPase α transcripts, was already established at the onset of exogenous feeding and was unmodified by metamorphosis.

Conclusions
The functional specialization of the GI-tract was not exclusive to metamorphosis, and its osmoregulatory capacity and reservoir function were established before first feeding. Nonetheless, acid production and the proteolytic capacity of the stomach coincided with metamorphic climax, and also marked the onset of the stomach’s involvement in appetite regulation via ghrelin.
Predictors of expiratory flow limitation measured by forced oscillation technique in COPD
Authors: Mikamo Masashi , Shirai Toshihiro , Mori Kazutaka , Shishido Yuichiro , Akita Takefumi , Morita Satoru , Asada Kazuhiro , Fujii Masato , Suda Takafumi 
Published: February 2014

Abstract

Background
Expiratory flow limitation (EFL) during tidal breathing is common in patients with severe COPD, and a major determinant of dynamic hyperinflation and exercise limitation. EFL can be measured by the forced oscillation technique (FOT); however, the relevance to clinical parameters is not fully understood. We hypothesized that emphysema extent and pulmonary function would contribute independently to the degree of EFL.

Methods
Broadband frequency FOT and pulmonary function tests were performed in 74 patients with COPD to derive respiratory system resistance (Rrs) and reactance (Xrs), and the EFL index as expressed by the differences between inspiratory and expiratory phases of Xrs at 5 Hz (ΔX5). Emphysema extent was measured by high-resolution computed tomography and scored.

Results
On the basis of the median value of ΔX5 (0.55 cmH2O/L/s), patients were classified into a high or low EFL index group. In multivariate regression analyses, a high EFL index was independently predicted by emphysema score, peripheral airway obstruction (forced expiratory flow between 25% and 75% of forced vital capacity), hyperinflation (functional residual capacity), and airway caliber (whole-breath Rrs at 5 Hz).

Conclusions
EFL measured by FOT is a global measure of COPD that has separable etiologies and is useful for evaluating the disease condition.
Ethnobotany of dye plants in Dong communities of China
Authors: Liu Yujing , Ahmed Selena , Liu Bo , Guo Zhiyong , Huang Weijuan , Wu Xianjin , Li Shenghua , Zhou Jiangju , Lei Qiyi , Long Chunlin 
Published: February 2014

Abstract

Background
Dyes derived from plants have an extensive history of use for coloring food and clothing in Dong communities and other indigenous areas in the uplands of China. In addition to use as coloring agents, Dong communities have historically utilized dye plants for their value for enhancing the nutritive, medicinal and preservative properties of foods. However, the persistence of plant-derived dyes and associated cultural practices and traditional knowledge is threatened with rapid socio-economic change in China. Research is needed to document the ethnobotany of dye plants in indigenous communities towards their conservation and potential commercialization as a sustainable means of supporting local development initiatives.

Methods
Semi-structured surveys on plants used for coloring agents and associated traditional knowledge were conducted in fifteen Dong villages of Tongdao County in Hunan Province of South Central China during 2011–2012. Transect walks were carried out with key informants identified from semi-structured surveys to collect samples and voucher specimens for each documented plant species for taxonomic identification.

Results
Dong households at the study sites utilize the flowers, bark, stems, tubers and roots of 13 plant species from 9 families as dyes to color their customary clothing and food. Out of the documented plants, a total of 7 are used for coloring food, 3 for coloring clothing and 3 for both food and clothing. Documented plants consist of 3 species that yield black pigments, 3 for brownish red/russet pigments, 3 for red pigments, 2 for dark blue pigments and 2 for yellow pigments. In addition to dyes, the plants have multiple uses including medicinal, ornamental, sacrificial, edible, and for timber.

Conclusions
The use of dyes derived from plants persists at the study sites for their important role in expressing Dong cultural identity through customary clothing and food. Further research is needed to evaluate the safety of dye plants, their efficacy in enhancing food items and their commercial potential. Conservation policies and management plans are called for to preserve these ethnobotanical resources in a sustainable manner that supports local livelihoods while maintaining cultural practices.
Persistent negative visual aura in migraine without headache: a case report
Authors: Lim Jisun , Jo Kwang Deog , Lee Moon Kyu , Jang Wooyoung 
Published: February 2014

Abstract

Introduction
Persistent migraine aura without headache is an extremely rare condition. The International Headache Society defines various subtypes of migraines, including “persistent migraine aura without infarction” and “typical aura without headache.”

Case presentation
We describe the case of a 21-year-old Asian woman with a history of migraine without aura who had (as her first aura episode) persistent negative visual symptoms without headache for 6 months. We detected no lesions that could cause her persistent visual symptoms. Based on the patient’s history of migraine without aura and responsiveness to furosemide and lamotrigine, we concluded that the visual symptoms in this case were related to migraine visual auras.

Conclusions
Persistent visual aura without headache overlapped the criteria for the two migraine subtypes mentioned above and thus did not fit an exact diagnosis. Therefore, we assert that new criteria are needed to encompass uncertain visual symptoms of migraine aura.
Cardiac performance, biomarkers and gene expression studies in previously sedentary men participating in half-marathon training
Authors: Vance Danica D , Chen Gordon L , Stoutenberg Mark , Myerburg Robert J , Jacobs Kevin , Nathanson Lubov , Perry Arlette , Seo David , Goldschmidt-Clermont Pascal J , Rampersaud Evadnie 
Published: February 2014

Abstract

Background
The mechanisms through which exercise reduces cardiovascular disease are not fully understood. We used echocardiograms, cardiac biomarkers and gene expression to investigate cardiovascular effects associated with exercise training.

Methods
Nineteen sedentary men (22–37 years) completed a 17-week half-marathon training program. Serial measurements of resting heart rate, blood pressure, maximum oxygen consumption, lipids, C-reactive protein, cardiac troponin T, echocardiograms and blood for gene expression were obtained from baseline to peak training. Controls included 22 sedentary men who did not exercise.

Results
Among the training group, VO2 max increased from 37.1 to 42.0 ml/kg/min (p < 0.001). Significant changes were seen in left ventricular wall thickness and mass, stroke volume, resting heart rate and blood pressure (p < 0.001). The control group demonstrated no significant changes. Expression profiling in the training group identified 10 significantly over-expressed and 53 significantly under-expressed loci involved in inflammatory pathways. Dividing the training group into high and low responders based on percent change in VO2 max identified loci that differentiated these two groups at baseline and after training.

Conclusion
Intensive exercise training leads to significant increase in cardiac and hemodynamic performance, and significant changes in expression of genes involved in immune and inflammatory response.
Effects of mutations and deletions in the human optineurin gene
Authors: Turturro Sanja , Shen Xiang , Shyam Rajalekshmy , Yue Beatrice YJT , Ying Hongyu 
Published: February 2014

Abstract
Optineurin is a gene associated with normal tension glaucoma (NTG) and amyotrophic lateral sclerosis (ALS). Foci formation and functional consequences including Golgi fragmentation, impairment of vesicle trafficking and apoptosis were observed previously upon overexpression and/or mutation of optineurin.
In the current study, a total of 15 GFP tagged constructs that included NTG (E50K and 2 bp-AG insertion), ALS (exon 5 deletion, R96L, Q398X, and E478G) and non-disease (L157A and D474N) associated mutants and a series of deletion fragments were cloned into mammalian expression vectors and transfected into RGC5 and/or Neuro2A cells to evaluate whether their expression confer the optineurin phenotypes. The cells were monitored for foci formation and stained by immunofluorescence with anti-GM130 to analyze the Golgi integrity. Transferrin uptake experiments were performed to evaluate the protein trafficking process and apoptosis was assessed with the active caspase 3/7 detection kit. We demonstrated that cells expressing E50K and R96L optineurin exhibited all of the optineurin phenotypes. Q398X mutant did not induce foci formation, but triggered Golgi fragmentation, impairment of transferrin uptake and increase in apoptosis. The 2 bp-AG insertion mutant had a nuclear localization, compromised the transferrin uptake and strongly induced apoptosis. The foci formation, which might not predict the rest of the phenotypes, appeared to require both the leucine zipper and ubiquitin binding domains of the optineurin sequence. Interactions of optineurin with proteins including Rab8, myosin VI, huntingtin and transferrin receptor might directly determine whether the Golgi and protein trafficking phenotypes would be manifested. Examination of mutants and deletion fragments located at various sites of optineurin gene provide clues as to what regions of the gene may play a critical role in the development of pathologic consequences.
Ontological specification of quality of chronic disease data in EHRs to support decision analytics: a realist review
Authors: Rahimi Alireza , Liaw Siaw-Teng , Ray Pradeep , Taggart Jane , Yu Hairong 
Published: February 2014

Abstract
This systematic review examined the current state of conceptualization and specification of data quality and the role of ontology based approaches to develop data quality based on "fitness for purpose" within the health context. A literature review was conducted of all English language studies, from January 2000-March 2013, which addressed data/information quality, fitness for purpose of data, used and implemented ontology-based approaches. Included papers were critically appraised with a "context-mechanism-impacts/outcomes" overlay. We screened 315 papers, excluded 36 duplicates, 182 on abstract review and 46 on full-text review; leaving 52 papers for critical appraisal. Six papers conceptualized data quality within the "fitness for purpose" definition. While most agree with a multidimensional definition of DQ, there is little consensus on a conceptual framework. We found no reports of systematic and comprehensive ontological approaches to DQ based on fitness for purpose or use. However, 16 papers used ontology-specified implementations in DQ improvement, with most of them focusing on some dimensions of DQ such as completeness, accuracy, correctness, consistency and timeliness. The majority of papers described the processes of the development of DQ in various information systems. There were few evaluative studies, including any comparing ontological with non-ontological approaches, on the assessment of clinical data quality and the performance of the application.
Estrogen receptor beta as a novel target of androgen receptor action in breast cancer cell lines
Authors: Rizza Pietro , Barone Ines , Zito Domenico , Giordano Francesca , Lanzino Marilena , De Amicis Francesca , Mauro Loredana , Sisci Diego , Catalano Stefania , Wright Karin Dahlman , Gustafsson Jan-ake , Andò Sebastiano 
Published: February 2014

Abstract
Introduction
The two isoforms of estrogen receptor (ER) alpha and beta play opposite roles in regulating proliferation and differentiation of breast cancers, with ER-alpha mediating mitogenic effects and ER-beta acting as a tumor suppressor. Emerging data have reported that androgen receptor (AR) activation inhibits ER-positive breast cancer progression mainly by antagonizing ER-alpha signaling. However, to date no studies have specifically evaluated a potential involvement of ER-beta in the inhibitory effects of androgens.

Methods
ER-beta expression was examined in human breast cancer cell lines using real-time PCR, Western blotting and small interfering RNA (siRNA) assays. Mutagenesis studies, electromobility shift assay (EMSA) and chromatin immunoprecipitation (ChIP) analysis were performed to assess the effects of mibolerone/AR on ER-beta promoter activity and binding.

Results
In this study, we demonstrate that mibolerone, a synthetic androgen ligand, up-regulates ER-beta mRNA and protein levels in ER-positive breast cancer cells. Transient transfection experiments, using a vector containing the human ER-beta promoter region, show that mibolerone increases basal ER-beta promoter activity. Site-directed mutagenesis and deletion analysis reveal that an androgen response element (ARE), TGTTCT motif located at positions −383 and −377, is critical for mibolerone-induced ER-beta up-regulation in breast cancer cells. This occurs through an increased recruitment of AR to the ARE site within the ER-beta promoter region, along with an enhanced occupancy of RNA polymerase II. Finally, silencing of ER-beta gene expression by RNA interference is able to partially reverse the effects of mibolerone on cell proliferation, p21 and cyclin D1 expression.

Conclusions
Collectively, these data provide evidence for a novel mechanism by which activated AR, through an up-regulation of ER-beta gene expression, inhibits breast cancer cell growth.
Feasibility and reliability of an automated controller of inspired oxygen concentration during mechanical ventilation
Authors: Saihi Kaouther , Richard Jean-Christophe M , Gonin Xavier , Krüger Thomas , Dojat Michel , Brochard Laurent 
Published: February 2014

Abstract
Introduction
Hypoxemia and high fractions of inspired oxygen (FiO2) are concerns in critically ill patients. An automated FiO2 controller based on continuous oxygen saturation (SpO2) measurement was tested. Two different SpO2-FiO2 feedback open loops, designed to react differently based on the level of hypoxemia, were compared. The results of the FiO2 controller were also compared with a historical control group.

Methods
The system measures SpO2, compares with a target range (92% to 96%), and proposes in real time FiO2 settings to maintain SpO2 within target. In 20 patients under mechanical ventilation, two different FiO2-SpO2 open loops were applied by a dedicated research nurse during 3 hours, each in random order. The times spent in and outside the target SpO2 values were measured. The results of the automatic controller were then compared with a retrospective control group of 30 ICU patients. SpO2-FiO2 values of the control group were collected over three different periods of 6 hours.

Results
Time in the target range was higher than 95% with the controller. When the 20 patients were separated according to the median PaO2/FiO2 (160(133-176) mm Hg versus 239(201-285)), the loop with the highest slope was slightly better (P = 0.047) for the more-hypoxemic patients. Hyperoxemia and hypoxemia durations were significantly shorter with the controller compared with usual care: SpO2 target range was reached 90% versus 24%, 27% and 32% (P < .001) with the controller, compared with three historical control-group periods.

Conclusion
A specific FiO2 controller is able to maintain SpO2 reliably within a predefined target range. Two different feedback loops can be used, depending on the initial PaO2/FiO2; with both, the automatic controller showed excellent performance when compared with usual care.
Antimicrobial peptide LL-37 promotes bacterial phagocytosis by human macrophages
Authors: Wan Min , van der Does Anne M , Tang Xiao , Lindbom Lennart , Agerberth Birgitta , Haeggström Jesper Z 
Published: February 2014

AbstractLL-37/hCAP-18 is the only human member of the cathelicidin family and plays an important role in killing various pathogens, as well as in immune modulation. In this study, we investigated the effect of LL-37 on bacterial phagocytosis by macrophages and demonstrate that LL-37 enhances phagocytosis of IgG-opsonized Gram-negative and Gram-positive bacteria in a dose- and time-dependent manner by dTHP-1 cells. In addition, LL-37 enhanced phagocytosis of nonopsonized Escherichia coli by human macrophages. Consistently, LL-37 elevated the expression of FcγRs on macrophages but not the complement receptors CD11b and -c. Further studies revealed that the expression of TLR4 and CD14 is also increased on LL-37-treated macrophages. Several lines of evidence indicated that the FPR2/ALX receptor mediated LL-37-induced phagocytosis. However, TLR4 signaling was also coupled to the phagocytic response, as a specific TLR4 antibody significantly suppressed phagocytosis of IgG-opsonized E. coli and nonopsonized E. coli by dTHP-1 cells. Finally, macrophages from Cnlp−/− mice exhibited diminished bacterial phagocytosis compared with macrophages from their WT littermates. In conclusion, we demonstrate a novel, immune-modulatory mechanism of LL-37, which may contribute to bacterial clearance.