bluuebunny/crossref_metadata_2025_split huggingface dataset:
MetaMapp: mapping and visualizing metabolomic data by integrating information from biochemical pathways and chemical and mass spectral similarity
Authors: Barupal Dinesh K , Haldiya Pradeep K , Wohlgemuth Gert , Kind Tobias , Kothari Shanker L , Pinkerton Kent E , Fiehn Oliver 
Published: May 2012

AbstractBackgroundExposure to environmental tobacco smoke (ETS) leads to higher rates of pulmonary diseases and infections in children. To study the biochemical changes that may precede lung diseases, metabolomic effects on fetal and maternal lungs and plasma from rats exposed to ETS were compared to filtered air control animals. Genome- reconstructed metabolic pathways may be used to map and interpret dysregulation in metabolic networks. However, mass spectrometry-based non-targeted metabolomics datasets often comprise many metabolites for which links to enzymatic reactions have not yet been reported. Hence, network visualizations that rely on current biochemical databases are incomplete and also fail to visualize novel, structurally unidentified metabolites.ResultsWe present a novel approach to integrate biochemical pathway and chemical relationships to map all detected metabolites in network graphs (MetaMapp) using KEGG reactant pair database, Tanimoto chemical and NIST mass spectral similarity scores. In fetal and maternal lungs, and in maternal blood plasma from pregnant rats exposed to environmental tobacco smoke (ETS), 459 unique metabolites comprising 179 structurally identified compounds were detected by gas chromatography time of flight mass spectrometry (GC-TOF MS) and BinBase data processing. MetaMapp graphs in Cytoscape showed much clearer metabolic modularity and complete content visualization compared to conventional biochemical mapping approaches. Cytoscape visualization of differential statistics results using these graphs showed that overall, fetal lung metabolism was more impaired than lungs and blood metabolism in dams. Fetuses from ETS-exposed dams expressed lower lipid and nucleotide levels and higher amounts of energy metabolism intermediates than control animals, indicating lower biosynthetic rates of metabolites for cell division, structural proteins and lipids that are critical for in lung development.ConclusionsMetaMapp graphs efficiently visualizes mass spectrometry based metabolomics datasets as network graphs in Cytoscape, and highlights metabolic alterations that can be associated with higher rate of pulmonary diseases and infections in children prenatally exposed to ETS. The MetaMapp scripts can be accessed athttp://metamapp.fiehnlab.ucdavis.edu.
Prevalence and clinical features of respiratory syncytial virus in children hospitalized for community-acquired pneumonia in northern Brazil
Authors: Lamarão Letícia Martins , Ramos Francisco Luzio , Mello Wyller Alencar , Santos Mirleide Cordeiro , Barbagelata Luana Soares , Justino Maria Cleonice Aguiar , da Silva Alexandre Ferreira , Quaresma Ana Judith Pires Garcia , da Silva Veronilce Borges , Burbano Rommel Rodríguez , Linhares Alexandre Costa 
Published: May 2012

AbstractBackgroundChildhood pneumonia and bronchiolitis is a leading cause of illness and death in young children worldwide with Respiratory Syncytial Virus (RSV) as the main viral cause. RSV has been associated with annual respiratory disease outbreaks and bacterial co-infection has also been reported. This study is the first RSV epidemiological study in young children hospitalized with community-acquired pneumonia (CAP) in Belém city, Pará (Northern Brazil).MethodsWith the objective of determining the prevalence of RSV infection and evaluating the patients’ clinical and epidemiological features, we conducted a prospective study across eight hospitals from November 2006 to October 2007. In this study, 1,050 nasopharyngeal aspirate samples were obtained from hospitalized children up to the age of three years with CAP, and tested for RSV antigen by direct immunofluorescence assay and by Reverse Transcription Polymerase Chain Reaction (RT-PCR) for RSV Group identification.ResultsRSV infection was detected in 243 (23.1%) children. The mean age of the RSV-positive group was lower than the RSV-negative group (12.1 months vs 15.5 months,p<0.001) whereas gender distribution was similar. The RSV-positive group showed lower means of C-reactive protein (CRP) in comparison to the RSV-negative group (15.3 vs 24.0 mg/dL,p<0.05). Radiological findings showed that 54.2% of RSV-positive group and 50.3% of RSV-negative group had interstitial infiltrate. Bacterial infection was identified predominantly in the RSV-positive group (10% vs 4.5%, p<0.05). Rhinorrhea and nasal obstruction were predominantly observed in the RSV-positive group. A co-circulation of RSV Groups A and B was identified, with a predominance of Group B (209/227). Multivariate analysis revealed that age under 1 year (p<0.015), CRP levels under 48 mg/dL (p<0.001) and bacterial co-infection (p<0.032) were independently associated with the presence of RSV and, in the analyze of symptoms, nasal obstruction were independently associated with RSV-positive group (p<0.001).ConclusionThe present study highlights the relevance of RSV infection in hospitalized cases of CAP in our region; our findings warrant the conduct of further investigations which can help design strategies for controlling the disease.
Baicalin, a natural compound, promotes regulatory T cell differentiation
Authors: Yang Ji , Yang Xue , Li Ming 
Published: May 2012

Abstract

Background
CD4+CD25+Foxp3+ regulatory T (Treg) cells inhibit autoimmunity and protect against tissue injury. The development of these Treg cells is controlled by the regulator protein Foxp3, which can be enhanced by the in vitro activation of Foxp3 in the presence of transforming growth factor-beta. However, little is known about alternative methods, such as the use of natural products, for controlling Foxp3-mediated Treg cell differentiation.

Method
HEK 293 T cells were transfected with Foxp3 expression plasmid, and then treated with different compounds, Foxp3 mRNA expression was determined by real-time RT-PCR. CD4+CD25-T cells were stimulated with Baicalin, Foxp3 protein expression were analyzed by flow cytometry and confocal microscopy, the regulatory function of T cells stimulated with Baicalin was detected by the carboxyfluorescien succinimidyl ester.

Results
We demonstrated that Baicalin, a compound isolated from the Chinese herb Huangqin, induced Foxp3 protein expression in cultured T cells, promoted Treg cell differentiation and regulatory activity. Our data also indicated that Baicalin restored Foxp3 expression following its initial interleukin-6-mediated inhibition and induced Foxp3 expression in vitro.

Conclusions
These data suggest that Baicalin may promote Treg cell differentiation and regulatory activity and may serve as a promising natural immunosuppressive compound for treating autoimmune inflammatory diseases.
Scapula alata in early breast cancer patients enrolled in a randomized clinical trial of post-surgery short-course image-guided radiotherapy
Authors: Adriaenssens Nele , De Ridder Mark , Lievens Pierre , Van Parijs Hilde , Vanhoeij Marian , Miedema Geertje , Voordeckers Mia , Versmessen Harijati , Storme Guy , Lamote Jan , Pauwels Stephanie , Vinh-Hung Vincent 
Published: May 2012

Abstract

Background
Scapula alata (SA) is a known complication of breast surgery associated with palsy of the serratus anterior, but it is seldom mentioned. We evaluated the risk factors associated with SA and the relationship of SA with ipsilateral shoulder/arm morbidity in a series of patients enrolled in a trial of post-surgery radiotherapy (RT).

Methods
The trial randomized women with completely resected stage I-II breast cancer to short-course image-guided RT, versus conventional RT. SA, arm volume and shoulder-arm mobility were measured prior to RT and at one to three months post-RT. Shoulder/arm morbidities were computed as a post-RT percentage change relative to pre-RT measurements.

Results
Of 119 evaluable patients, 13 (= 10.9%) had pre-RT SA. Age younger than 50 years old, a body mass index less than 25 kg/m2, and axillary lymph node dissection were significant risk factors, with odds ratios of 4.8 (P = 0.009), 6.1 (P = 0.016), and 6.1 (P = 0.005), respectively. Randomization group was not significant. At one to three months’ post-RT, mean arm volume increased by 4.1% (P = 0.036) and abduction decreased by 8.6% (P = 0.046) among SA patients, but not among non-SA patients. SA resolved in eight, persisted in five, and appeared in one patient.

Conclusion
The relationship of SA with lower body mass index suggests that SA might have been underestimated in overweight patients. Despite apparent resolution of SA in most patients, pre-RT SA portended an increased risk of shoulder/arm morbidity. We argue that SA warrants further investigation. Incidentally, the observation of SA occurring after RT in one patient represents the second case of post-RT SA reported in the literature.
Oocyte activation and phospholipase C zeta (PLCζ): diagnostic and therapeutic implications for assisted reproductive technology
Authors: Ramadan Walaa M , Kashir Junaid , Jones Celine , Coward Kevin 
Published: May 2012

AbstractInfertility affects one in seven couples globally and has recently been classified as a disease by the World Health Organisation (WHO). Whilein-vitrofertilisation (IVF) offers effective treatment for many infertile couples, cases exhibiting severe male infertility (19–57%) often remain difficult, if not impossible to treat. In such cases, intracytoplasmic sperm injection (ICSI), a technique in which a single sperm is microinjected into the oocyte, is implemented. However, 1–5% of ICSI cycles still fail to fertilise, affecting over 1000 couples per year in the UK alone. Pregnancy and delivery rates for IVF and ICSI rarely exceed 30% and 23% respectively. It is therefore imperative that Assisted Reproductive Technology (ART) protocols are constantly modified by associated research programmes, in order to provide patients with the best chances of conception. Prior to fertilisation, mature oocytes are arrested in the metaphase stage of the second meiotic division (MII), which must be alleviated to allow the cell cycle, and subsequent embryogenesis, to proceed. Alleviation occurs through a series of concurrent events, collectively termed ‘oocyte activation’. In mammals, oocytes are activated by a series of intracellular calcium (Ca2+) oscillations following gamete fusion. Recent evidence implicates a sperm-specific phospholipase C, PLCzeta (PLCζ), introduced into the oocyte following membrane fusion as the factor responsible. This review summarises our current understanding of oocyte activation failure in human males, and describes recent advances in our knowledge linking certain cases of male infertility with defects in PLCζ expression and activity. Systematic literature searches were performed using PubMed and the ISI-Web of Knowledge. Databases compiled by the United Nations and World Health Organisation databases (UNWHO), and the Human Fertilization and Embryology Authority (HFEA) were also scrutinised. It is clear that PLCζ plays a fundamental role in the activation of mammalian oocytes, and that genetic, molecular, or biochemical perturbation of this key enzyme is strongly linked to human infertility where oocyte activation is deficient. Consequently, there is significant scope for our understanding of PLCζ to be translated to the ART clinic, both as a novel therapeutic agent with which to rescue oocyte activation deficiency (OAD), or as a prognostic/diagnostic biomarker of oocyte activation ability in target sperm samples.
CXCL13 is the major determinant for B cell recruitment to the CSF during neuroinflammation
Authors: Kowarik Markus C , Cepok Sabine , Sellner Johann , Grummel Verena , Weber Martin S , Korn Thomas , Berthele Achim , Hemmer Bernhard 
Published: May 2012

Abstract

Background
The chemokines and cytokines CXCL13, CXCL12, CCL19, CCL21, BAFF and APRIL are believed to play a role in the recruitment of B cells to the central nervous system (CNS) compartment during neuroinflammation. To determine which chemokines/cytokines show the strongest association with a humoral immune response in the cerebrospinal fluid (CSF), we measured their concentrations in the CSF and correlated them with immune cell subsets and antibody levels.

Methods
Cytokine/chemokine concentrations were measured in CSF and serum by ELISA in patients with non-inflammatory neurological diseases (NIND, n = 20), clinically isolated syndrome (CIS, n = 30), multiple sclerosis (MS, n = 20), Lyme neuroborreliosis (LNB, n = 8) and patients with other inflammatory neurological diseases (OIND, n = 30). Albumin, IgG, IgA and IgM were measured by nephelometry. CSF immune cell subsets were determined by seven-color flow cytometry.

Results
CXCL13 was significantly elevated in the CSF of all patient groups with inflammatory diseases. BAFF levels were significantly increased in patients with LNB and OIND. CXCL12 was significantly elevated in patients with LNB. B cells and plasmablasts were significantly elevated in the CSF of all patients with inflammatory diseases. CXCL13 showed the most consistent correlation with CSF B cells, plasmablasts and intrathecal Ig synthesis.

Conclusions
CXCL13 seems to be the major determinant for B cell recruitment to the CNS compartment in different neuroinflammatory diseases. Thus, elevated CSF CXCL13 levels rather reflect a strong humoral immune response in the CNS compartment than being specific for a particular disease entity.
An ethnobotanical survey of medicinal plants used in Terai forest of western Nepal
Authors: Singh Anant Gopal , Kumar Akhilesh , Tewari Divya Darshan 
Published: May 2012

Abstract
Background
Nepal Himalayas have been known as a rich source for valuable medicinal plants since Vedic periods. Present work is the documentation of indigenous knowledge on plant utilization as natural remedy by the inhabitants of terai forest in Western Nepal.

Methods
Study was conducted during 2010–2011 following standard ethnobotanical methods. Data about medicinal uses of plants were collected by questionnaire, personal interview and group discussion with pre identified informants. Voucher specimens were collected with the help of informants, processed into herbarium following standard methods, identified with the help of pertinent floras and taxonomic experts, and submitted in Department of Botany, Butwal Multiple Campus, Tribhuvan University, Nepal for future references.

Results
During the present study 66 medicinal plant species belonging to 37 families and 60 genera has been documented. These plants were used to treat various diseases and ailments grouped under 11 disease categories, with the highest number of species (41) being used for gastro-intestinal disorders, followed by dermatological disorders (34). In the study area the informants’ consensus about usages of medicinal plants ranges from 0.93 to 0.97 with an average value of 0.94. Herbs (53%) were the primary source of medicine, followed by trees (23%). Curcuma longa (84%) and Azadirachta indica (76%) are the most frequently and popularly used medicinal plant species in the study area. Acacia catechu, Bacopa monnieri, Bombax ceiba, Drymaria diandra, Rauvolfia serpentina, and Tribulus terrestris are threatened species which needs to be conserved for future use.

Conclusions
The high degree of consensus among the informants suggests that current use and knowledge are still strong, and thus the preservation of today's knowledge shows good foresight in acting before much has been lost. The connections between plant use and conservation are also important ones, especially as the authors note that neither the local inhabitants nor the government is addressing the potential loss of valuable species in this region.
Prevalence of and factors associated with daily smoking among Inner Mongolia medical students in China: a cross-sectional questionnaire survey
Authors: Bian Jiang , Du Maolin , Liu Zhiyue , Fan Yancun , Eshita Yuki , Sun Juan 
Published: May 2012

Abstract

Background
To date, no study on smoking behavior of medical students in Inner Mongolia has been reported. The aim of the present study was to determine the 1-month prevalence of and factors associated with daily smoking among medical students in Inner Mongolia of China, to assist interventions designed to reduce the smoking behavior of medical college students in this region.

Methods
During December 2010 and January 2011 a cross-sectional survey was conducted among medical students at the Inner Mongolia Medical College using a self-administered questionnaire. The questionnaire consisted of three sections: students’ basic information, attitude on smoking behavior, and smoking status of the student daily smokers. Students who smoked every day in the last 30 days were regarded as daily smokers. Factors associated with smoking were identified using binary logistic regression analysis.

Results
A total of 6044 valid surveys were returned. The overall prevalence of daily smoking was 9.8% while the prevalence of daily smoking among males and females were 29.4% and 1.7%, respectively. Males in the Faculty of Medicine Information Management had the highest daily smoking rate (48.9%). Logistic regression models found that the main factors associated with daily smoking among male medical students were highest year of study (OR = 3.62; CI: 1.18–11.05); attitude towards smoking behavior Do not care about people smoking around you (OR = 2.75; CI: 2.08–3.64); and Smoking is harmful to their health (OR = 4.40; CI: 2.21–8.75). The main factor associated with daily smoking among female medical students was attitude towards smoking behavior Eliminate smoking on campus (OR = 0.11; CI: 0.06–0.23). Both for male and female medical students, there was no association between ethnicity and cigarette daily smoking. In regard to smoking status, more than 60% of daily smokers began smoking in high school, 61.3% smoked less than 5 cigarettes per day, 62.9% of the daily smokers’ families opposed their smoking behavior, and after an hour of not smoking 74.6% daily smokers did not feel uncomfortable.

Conclusions
Antismoking education should be further promoted in Inner Mongolia medical students, with consideration given to the factors associated with daily smoking behavior found in the present study.
A selective aryl hydrocarbon receptor modulator 3,3'-Diindolylmethane inhibits gastric cancer cell growth
Authors: Yin Xiao-Fei , Chen Jie , Mao Wei , Wang Yu-Hong , Chen Min-Hu 
Published: May 2012

Abstract

Background
Aryl hydrocarbon receptor (AhR) is a ligand-activated transcription factor associated with gastric carcinogenesis. 3,3'-Diindolylmethane (DIM) is a relatively non-toxic selective AhR modulator. This study was to detect the effects of DIM on gastric cancer cell growth.

Methods
Gastric cancer cell SGC7901 was treated with DIM at different concentrations (0,10,20,30,40,50 μmol/L) with or without an AhR antagonist, resveratrol. The expression of AhR and Cytochrome P4501A1 (CYP1A1), a classic target gene of AhR pathway, were detected by RT-PCR and Western blot; cell viability was measured by MTT assay, and the changes in cell cycle and apoptosis were analyzed by flow cytometry.

Results
RT-PCR and western-blot showed that with the increase of the concentration of DIM, AhR protein gradually decreased and CYP1A1 expression increased, suggesting that DIM activated the AhR pathway and caused the translocation of AhR from cytoplasm to nucleus. MTT assay indicated that the viability of SGC7901 cells was significantly decreased in a concentration- and time-dependent manner after DIM treatment and this could be partially reversed by resveratrol. Flow cytometry analysis showed that DIM arrested cell cycle in G1 phase and induced cell apoptosis.

Conclusion
Selective aryl hydrocarbon receptor modulator 3,3'-Diindolylmethane inhibits SGC7901 cell proliferation by inducing apoptosis and delaying cell cycle progression. AhR may be a potential therapeutic target for gastric cancer treatment.
Antipsychotic use and diagnosis of delirium in the intensive care unit
Authors: Swan Joshua T , Fitousis Kalliopi , Hall Jeffrey B , Todd S Rob , Turner Krista L 
Published: May 2012

Abstract
Introduction
Delirium is an independent risk factor for prolonged hospital length of stay (LOS) and increased mortality. Several antipsychotics have been studied for the treatment of intensive care unit (ICU) delirium that has led to a high variability in prescribing patterns for these medications. We hypothesize that in clinical practice the documentation of delirium is lower than the incidence of delirium reported in prospective clinical trials. The objective of this study was to document the incidence of delirium diagnosed in ICU patients and to describe the utilization of antipsychotics in the ICU.

Methods
This was a retrospective, observational, cohort study conducted at 71 United States academic medical centers that reported data to the University Health System Consortium Clinical Database/Resource Manager. It included all patients 18 years of age and older admitted to the hospital between 1 January 2010 and 30 June 2010 with at least one day in the ICU.

Results
Delirium was diagnosed in 6% (10,034 of 164,996) of hospitalizations with an ICU admission. Antipsychotics were administered to 11% (17,764 of 164,996) of patients. Of the antipsychotics studied, the most frequently used were haloperidol (62%; n = 10,958) and quetiapine (31%; n = 5,448). Delirium was associated with increased ICU LOS (5 vs. 3 days, P < 0.001) and hospital LOS (11 vs. 6 days, P < 0.001), but not in-hospital mortality (8% vs. 9%, P = 0.419). Antipsychotic exposure was associated with increased ICU LOS (8 vs. 3 days, P < 0.001), hospital LOS (14 vs. 5 days, P < 0.001) and mortality (12% vs. 8%, P < 0.001). Of patients with antipsychotic exposure in the ICU, absence of a documented mental disorder (32%, n = 5,760) was associated with increased ICU LOS (9 vs. 7 days, P < 0.001), hospital LOS (16 vs. 13 days, P < 0.001) and in-hospital mortality (19% vs. 9%, P < 0.001) compared to patients with a documented mental disorder (68%, n = 12,004).

Conclusions
The incidence of documented delirium in ICU patients is lower than that documented in previous prospective studies with active screening. Antipsychotics are administered to 1 in every 10 ICU patients. When administration occurs in the absence of a documented mental disorder, antipsychotic use is associated with an even higher ICU and hospital LOS, as well as in-hospital mortality.