bluuebunny/crossref_metadata_2025_split huggingface dataset:
RegTransBase – a database of regulatory sequences and interactions based on literature: a resource for investigating transcriptional regulation in prokaryotes
Authors: Cipriano Michael J , Novichkov Pavel N , Kazakov Alexey E , Rodionov Dmitry A , Arkin Adam P , Gelfand Mikhail S , Dubchak Inna 
Published: April 2013

Abstract

Background
Due to the constantly growing number of sequenced microbial genomes, comparative genomics has been playing a major role in the investigation of regulatory interactions in bacteria. Regulon inference mostly remains a field of semi-manual examination since absence of a knowledgebase and informatics platform for automated and systematic investigation restricts opportunities for computational prediction. Additionally, confirming computationally inferred regulons by experimental data is critically important.

Description
RegTransBase is an open-access platform with a user-friendly web interface publicly available at http://regtransbase.lbl.gov. It consists of two databases – a manually collected hierarchical regulatory interactions database based on more than 7000 scientific papers which can serve as a knowledgebase for verification of predictions, and a large set of curated by experts transcription factor binding sites used in regulon inference by a variety of tools. RegTransBase captures the knowledge from published scientific literature using controlled vocabularies and contains various types of experimental data, such as: the activation or repression of transcription by an identified direct regulator; determination of the transcriptional regulatory function of a protein (or RNA) directly binding to DNA or RNA; mapping of binding sites for a regulatory protein; characterization of regulatory mutations. Analysis of the data collected from literature resulted in the creation of Putative Regulons from Experimental Data that are also available in RegTransBase.

Conclusions
RegTransBase is a powerful user-friendly platform for the investigation of regulation in prokaryotes. It uses a collection of validated regulatory sequences that can be easily extracted and used to infer regulatory interactions by comparative genomics techniques thus assisting researchers in the interpretation of transcriptional regulation data.
TRACER: a resource to study the regulatory architecture of the mouse genome
Authors: Chen Chao-Kung , Symmons Orsolya , Uslu Veli Vural , Tsujimura Taro , Ruf Sandra , Smedley Damian , Spitz François 
Published: April 2013

Abstract

Background
Mammalian genes are regulated through the action of multiple regulatory elements, often distributed across large regions. The mechanisms that control the integration of these diverse inputs into specific gene expression patterns are still poorly understood. New approaches enabling the dissection of these mechanisms in vivo are needed.

Results
Here, we describe TRACER (http://tracerdatabase.embl.de), a resource that centralizes information from a large on-going functional exploration of the mouse genome with different transposon-associated regulatory sensors. Hundreds of insertions have been mapped to specific genomic positions, and their corresponding regulatory potential has been documented by analysis of the expression of the reporter sensor gene in mouse embryos. The data can be easily accessed and provides information on the regulatory activities present in a large number of genomic regions, notably in gene-poor intervals that have been associated with human diseases.

Conclusions
TRACER data enables comparisons with the expression pattern of neighbouring genes, activity of surrounding regulatory elements or with other genomic features, revealing the underlying regulatory architecture of these loci. TRACER mouse lines can also be requested for in vivo transposition and chromosomal engineering, to analyse further regions of interest.
Systematic antibody generation and validation via tissue microarray technology leading to identification of a novel protein prognostic panel in breast cancer
Authors: O´Leary Patrick C , Penny Sarah A , Dolan Roisin T , Kelly Catherine M , Madden Stephen F , Rexhepaj Elton , Brennan Donal J , McCann Amanda H , Pontén Fredrik , Uhlén Mathias , Zagozdzon Radoslaw , Duffy Michael J , Kell Malcolm R , Jirström Karin , Gallagher William M 
Published: April 2013

Abstract

Background
Although omic-based discovery approaches can provide powerful tools for biomarker identification, several reservations have been raised regarding the clinical applicability of gene expression studies, such as their prohibitive cost. However, the limited availability of antibodies is a key barrier to the development of a lower cost alternative, namely a discrete collection of immunohistochemistry (IHC)-based biomarkers. The aim of this study was to use a systematic approach to generate and screen affinity-purified, mono-specific antibodies targeting progression-related biomarkers, with a view towards developing a clinically applicable IHC-based prognostic biomarker panel for breast cancer.

Methods
We examined both in-house and publicly available breast cancer DNA microarray datasets relating to invasion and metastasis, thus identifying a cohort of candidate progression-associated biomarkers. Of these, 18 antibodies were released for extended analysis. Validated antibodies were screened against a tissue microarray (TMA) constructed from a cohort of consecutive breast cancer cases (n = 512) to test the immunohistochemical surrogate signature.

Results
Antibody screening revealed 3 candidate prognostic markers: the cell cycle regulator, Anillin (ANLN); the mitogen-activated protein kinase, PDZ-Binding Kinase (PBK); and the estrogen response gene, PDZ-Domain Containing 1 (PDZK1). Increased expression of ANLN and PBK was associated with poor prognosis, whilst increased expression of PDZK1 was associated with good prognosis. A 3-marker signature comprised of high PBK, high ANLN and low PDZK1 expression was associated with decreased recurrence-free survival (p < 0.001) and breast cancer-specific survival (BCSS) (p < 0.001). This novel signature was associated with high tumour grade (p < 0.001), positive nodal status (p = 0.029), ER-negativity (p = 0.006), Her2-positivity (p = 0.036) and high Ki67 status (p < 0.001). However, multivariate Cox regression demonstrated that the signature was not a significant predictor of BCSS (HR = 6.38; 95% CI = 0.79-51.26, p = 0.082).

Conclusions
We have developed a comprehensive biomarker pathway that extends from discovery through to validation on a TMA platform. This proof-of-concept study has resulted in the identification of a novel 3-protein prognostic panel. Additional biochemical markers, interrogated using this high-throughput platform, may further augment the prognostic accuracy of this panel to a point that may allow implementation into routine clinical practice.
Mortality among British Columbians testing for hepatitis C antibody
Authors: Yu Amanda , Spinelli John J , Cook Darrel A , Buxton Jane A , Krajden Mel 
Published: April 2013

Abstract

Background
Hepatitis C virus (HCV) infection is a major preventable and treatable cause of morbidity and mortality. The ability to link population based centralized laboratory HCV testing data with administrative databases provided a unique opportunity to compare mortality between HCV seronegative and seropositive individuals. Through the use of laboratory testing patterns and results, the objective of this study was to differentiate the viral effects of mortality due to HCV infection from risk behaviours/activities that are associated with acquisition of HCV infection.

Methods
Serological testing data from the British Columbia (BC) Centre for Disease Control Public Health Microbiology and Reference Laboratory from 1992–2004 were linked to the BC Vital Statistics Agency death registry. Four groups of HCV testers were defined by their HCV antibody (anti-HCV) testing patterns: single non-reactive (SNR); serial multiple tested non-reactive (MNR); reactive at initial testing (REAC); and seroconverter (SERO) (previously seronegative followed by reactive, a marker for incident infection). Standardized mortality ratios (SMRs) were calculated to compare the relative risk of all cause and disease specific mortality to that of the BC population for each serological group. Time dependent Cox proportional hazard regression was used to compare hazard ratios (HRs) among HCV serological groups.

Results
All anti-HCV testers had higher SMRs than the BC population. Referent to the SNR group, the REAC group had higher risks for liver (HR: 9.62; 95% CI=8.55-10.87) and drug related mortality (HR: 13.70; 95% CI=11.76-16.13). Compared to the REAC group, the SERO group had a lower risk for liver (HR: 0.53; 95% CI=0.24-0.99), but a higher risk for drug related mortality (HR: 1.54; 95% CI=1.12-2.05).

Conclusions
These findings confirm that individuals who test anti-HCV positive have increased mortality related to progressive liver disease, and that a substantial proportion of the mortality is attributable to drug use and risk behaviours/activities associated with HCV acquisition. Mortality reduction in HCV infected individuals will require comprehensive prevention programming to reduce the harms due to behaviours/activities which relate to HCV acquisition, as well as HCV treatment to prevent progression of chronic liver disease.
Dracaena arborea alleviates ultra-structural spermatogenic alterations in streptozotocin-induced diabetic rats
Authors: Wankeu-Nya Modeste , Florea Adrian , Bâlici Stefana , Watcho Pierre , Matei Horea , Kamanyi Albert 
Published: April 2013

Abstract

Background
Infertility is a common complication in diabetic men and experimental animals, mainly due to loss of germ cells by apoptotic cell death. The aim of this study was to evaluate the effects of aqueous and ethanol extracts of Dracaena arborea in streptozotocin-induced ultra-structural spermatogenic alterations in Wistar rats.

Methods
Diabetic animals were orally treated with Millipore water (10 ml/kg), sildenafil citrate (1.44 mg/kg) or Dracaena arborea aqueous (500 mg/kg) and ethanol (100 mg/kg) extracts for three weeks. A group of non diabetic rats received Millipore water (10 ml/kg) and served as healthy control group. Blood glucose was monitored at the beginning and the end of the study. One day after the last treatment, animals were sacrificed and the testes immediately removed were morphologically observed and prepared for electron microscopy analysis of spermatogenesis.

Results
Our results showed that Dracaena arborea was devoid of any anti-hyperglycemic activity. In the untreated diabetic rats, hyperglycemia severely damaged the testes morphology as well as the spermatogenic process as evidenced by the: thickness of basement membrane of the seminiferous tubule; mitochondria alteration; abnormal spermatocyte cells displaying polymorphous nuclei, cytoplasmic vacuolization and necrosis; and disorganization and degeneration of sperm germ cells. Administration of sildenafil citrate and Dracaena arborea extracts to the diabetic rats improved testes morphology and reversed, although not completely, the impairment of spermatogenesis; this alleviating effect was more pronounced in animals treated with the aqueous extract (500 mg/kg) of Dracaena arborea.

Conclusion

Dracaena arborea improves testes morphology and restores spermatogenesis in type 1 diabetic rats, without having major anti-hyperglycemic properties. These effects could be attributed to saponins, flavonoids, phenols and sterols revealed in this plant, which could be a useful component in the treatment of diabetes-induced testicular dysfunction.
Could the Sasang constitution itself be a risk factor of abdominal obesity?
Authors: Jang Eunsu , Baek Younghwa , Park Kihyun , Lee Siwoo 
Published: April 2013

Abstract

Background
Abdominal obesity (AO) is a medical condition in which excess body fat accumulates in the abdomen. It may cause adverse effects on health and result in reduced life expectancy or increased health problems. While various genetic approaches have explained the risks of AO in Western society, the Sasang constitution (SC) has been identified as a risk factor in Korean medicine. Different SC types are associated with different fat distribution, body shapes and susceptibility to diseases. We evaluated whether the SC type could be a risk for AO in a cross-sectional study among Koreans.

Methods
In total, 2,528 subjects aged over 30 years were recruited from 23 medical clinics. We collected waist circumference (WC), weight, height, and some clinical information for AO from the subjects. A Chi-square test and a one-way ANOVA were performed according to SC type (p < .05), while multiple logistic regression was used to produce odds ratios (ORs).

Results
The rates of AO in Tae-eumin (TE), Soeumin (SE), and Soyangin (SY) types were 63.7%, 14.7%, and 32.8% in males and 84.8%, 41.7%, and 52.8% in females, respectively. The TE type was associated with increased AO prevalence compared with the SE and SY types in males (OR 1.79; 95% CI 1.02–3.15, p = 0.044 and OR 1.74; 95% CI 1.18–2.58, p = 0.006, respectively) and females (OR 1.51; 95% CI 1.03–2.23, p = 0.037 and OR 1.88; 95% CI 1.32–2.68, p < 0.001, respectively) after adjusting for age, BMI, hypertension, diabetes mellitus, hypertriglyceridemia, and low HDL cholesterol.

Conclusions
This study suggested that SC, particularly the TE type, might be significantly and independently associated with AO and could be considered a risk factor in predicting AO.
Effective treatment with a tetrandrine/chloroquine combination for chloroquine-resistant falciparum malaria in Aotus monkeys
Authors: Ye Zuguang , Van Dyke Knox , Rossan Richard N 
Published: April 2013

Abstract

Background
In vitro evidence indicates that tetrandrine (TT) can potentiate the action of chloroquine 40-fold against choloquine-resistant Plasmodium falciparum. The key question emanating from that study is “would tetrandine and chloroquine be highly effective in a live Aotus monkey model with chloroquine-resistant parasites”. This study was designed to closely mimic the pharmacological/anti-malarial activity in man.

Methods
The Vietnam Smith/RE strain of P. falciparum, which is chloroquine-resistant was used in this study. Previous experimental procedures were followed. Panamanian owl monkeys (Aotus) were inoculated with 5×106 erythrocytes parasitized with the CQ-resistant strain of P. falciparum. Oral drug treatment was with CQ (20 mg/kg) and/or tetrandrine at 15 mg/Kg, 30 mg/Kg or 60 mg/Kg or 25 mg/Kg depending on experimental conditions.

Results and Discussion
Parasitaemia was cleared rapidly with CQ and TT while CQ treatment alone was ineffective. Recrudescence of malaria occurred after seven days post-infection. However, four animals were treated orally with TT and CQ parasites were cleared. It is likely that monkeys were cured via a combination of both drug and host immune responses. A single Aotus monkey infected with P. falciparum and untreated with drugs, died. No side effects were observed with these drug treatments.

Conclusions
This combination of chloroquine and tetrandrine forms the basis of a new attack on chloroquine-resistant malaria - one based upon inhibition of the basis of chloroquine resistance, the multiple drug resistance pump. Previous studies demonstrated that the parasite MDR pump was found on parasite membranes using 3H azidopine photoaffinity labelling.
Since MDR-based choloroquine resistance is induced by chloroquine, the basis of the action of tetrandrine is the following: 1) tetrandrine inhibits the MDR pump by stimulating MDR ATPase which limits the energy of the pump by depletion of parasite ATP, 2) tetrandrine blocks the genetic factor which controls the induction of the pump. Therefore, it appears that the parasite cannot outsmart these mechanisms and produce a new mode of resistance. Only time will tell if this is correct.
Maternal iron intake at mid-pregnancy is associated with reduced fetal growth: results from Mothers and Children’s Environmental Health (MOCEH) study
Authors: Hwang Ji-Yun , Lee Ji-Yeon , Kim Ki-Nam , Kim Hyesook , Ha Eun-Hee , Park Hyesook , Ha Mina , Kim Yangho , Hong Yun-Chul , Chang Namsoo 
Published: April 2013

Abstract

Background
Iron supplementation is a common recommendation for pregnant women to prevent iron deficiency during pregnancy. There is an increasing concern about excessive iron consumption as a general iron prophylaxis by pregnant women without any due consideration about their dietary iron intake or iron status. Our present study investigated the association between total iron intake from diet and supplements and fetal growth in 337 pregnant women at mid-pregnancy in South Korea.

Methods
Iron intake from diet and supplements was examined by a 24-hour recall method. Subjects were divided into three groups based on tertiles of total iron intake levels. Fetal biometry was assessed by ultrasonography at mid-pregnancy.

Results
About 99% of the non-supplement users had iron intake below the recommended nutrient intake (RNI) for pregnant women (24 mg), whereas 64.9% of supplement users had iron intake above the upper level (UL) (45 mg). In the babies of mothers in the third tertile of iron intake (>17.04 mg), biparietal diameter, abdominal circumference, and femur length were lower by 0.41 cm (P =0.019), 0.41 cm (P = 0.027), and 0.07 cm (P = 0.051), respectively, than the babies of mothers in the second tertile of iron intake (11.49 ~ 17.04 mg).

Conclusion
These results suggest that excessive maternal iron intake at mid-pregnancy is associated with reduced fetal growth. Iron supplementation for pregnant women should be individualized according to their iron status. Appropriate diet education is needed for pregnant women so that they can consume adequate amounts of iron from food and supplements.
Autoinflammatory gene polymorphisms and susceptibility to UK juvenile idiopathic arthritis
Authors: Hinks Anne , Martin Paul , Thompson Susan D , Sudman Marc , Stock Carmel J , Thomson Wendy , Day Thomas G , Packham Jon ,   Childhood arthritis prospective study (CAPS),   BSPAR study group, Ramanan Athimalaipet V , Donn Rachelle P 
Published: April 2013

Abstract

Background
To investigate the autoinflammatory hereditary periodic fever syndrome genes MVK and TNFRSF1A, and the NLRP1 and IL1 genes, for association with juvenile idiopathic arthritis (JIA).

Methods
For MVK, TNFRSF1A and NLRP1 pair-wise tagging SNPs across each gene were selected and for IL1A SNPs from a prior meta-analysis were included. 1054 UK Caucasian JIA patients were genotyped by Sequenom iPlex MassARRAY and allele and genotype frequencies compared with 5380 unrelated healthy UK Caucasian controls.

Results
Four SNPs were significantly associated with UK JIA: rs2071374 within intron 4 of IL1A (ptrend=0.006), rs2228576 3’ of TNFRSF1A (ptrend=0.009) and 2 SNPs, rs11836136 and rs7957619, within MVK (ptrend=0.006, ptrend=0.005 respectively). In all cases the association appeared to be driven by the systemic-onset JIA (SoJIA) subtype. Genotype data for the two MVK SNPs was available in a validation cohort of 814 JIA (oligoarticular and RF negative polyarticular) cases and 3058 controls from the US. Replication was not confirmed, however, further suggesting that this association is specific to SoJIA.

Conclusions
These findings extend the observations of the relevance of studying monogenic loci as candidates for complex diseases. We provide novel evidence of association of MVK and TNFRSF1A with UK JIA, specifically driven by association with SoJIA and further confirm that the IL1A SNP association with SoJIA is subtype specific. Replication is required in independent cohorts.
Efficient CD44-targeted magnetic resonance imaging (MRI) of breast cancer cells using hyaluronic acid (HA)-modified MnFe2O4 nanocrystals
Authors: Lee Taeksu , Lim Eun-Kyung , Lee Jaemin , Kang Byunghoon , Choi Jihye , Park Hyo Seon , Suh Jin-Suck , Huh Yong-Min , Haam Seungjoo 
Published: April 2013

AbstractTargeted molecular imaging with hyaluronic acid (HA) has been highlighted in the diagnosis and treatment of CD44-overexpressing cancer. CD44, a receptor for HA, is closely related to the growth of cancer including proliferation, metastasis, invasion, and angiogenesis. For the efficient detection of CD44, we fabricated a few kinds of HA-modified MnFe2O4nanocrystals (MNCs) to serve as specific magnetic resonance (MR) contrast agents (HA-MRCAs) and compared physicochemical properties, biocompatibility, and the CD44 targeting efficiency. Hydrophobic MNCs were efficiently phase-transferred using aminated polysorbate 80 (P80) synthesized by introducing spermine molecules on the hydroxyl groups of P80. Subsequently, a few kinds of HA-MRCAs were fabricated, conjugating different ratios of HA on the equal amount of phase-transferred MNCs. The optimized conjugation ratio of HA against magnetic content was identified to exhibit not only effective CD44 finding ability but also high cell viability throughin vitroexperiments. The results of this study demonstrate that the suggested HA-MRCA shows strong potential to be used for accurate tumor diagnosis.
Diameter-sensitive biocompatibility of anodic TiO2 nanotubes treated with supercritical CO2 fluid
Authors: Lan Ming-Ying , Liu Chia-Pei , Huang Her-Hsiung , Chang Jeng-Kuei , Lee Sheng-Wei 
Published: April 2013

Abstract
This work reports on the diameter-sensitive biocompatibility of anodic TiO2 nanotubes with different nanotube diameters grown by a self-ordering process and subsequently treated with supercritical CO2 (ScCO2) fluid. We find that highly hydrophilic as-grown TiO2 nanotubes become hydrophobic after the ScCO2 treatment but can effectively recover their surface wettability under UV light irradiation as a result of photo-oxidation of C-H functional groups formed on the nanotube surface. It is demonstrated that human fibroblast cells show more obvious diameter-specific behavior on the ScCO2-treated TiO2 nanotubes than on the as-grown ones in the range of diameters of 15 to 100 nm. This result can be attributed to the removal of disordered Ti(OH)4 precipitates from the nanotube surface by the ScCO2 fluid, thus resulting in purer nanotube topography and stronger diameter dependence of cell activity. Furthermore, for the smallest diameter of 15 nm, ScCO2-treated TiO2 nanotubes reveal higher biocompatibility than the as-grown sample.
Channel characteristics of MIMO–WLAN communications at 60 GHz for various corridors
Authors: Liao Shu-Han , Chiu Chien-Ching , Chen Chien-Hung , Ho Min-Hui 
Published: April 2013

Abstract
A comparison of 4 × 4 multiple-input multiple-output wireless local area network wireless communication characteristics for six different geometrical shapes is investigated. These six shapes include the straight shape corridor with rectangular cross section, the straight shape corridor with arched cross section, the curved shape corridor with rectangular cross section, the curved shape corridor with arched cross section, the L-shape corridor, and the T-shape corridor. The impulse responses of these corridors are computed by applying shooting and bouncing ray/image (SBR/Image) techniques along with inverse Fourier transform. By using the impulse response of these multipath channels, the mean excess delay, root mean square (RMS) delay spread for these six corridors can be obtained. Numerical results show that the capacity for the rectangular cross section corridors is smaller than those for the arched cross section corridors regardless of the shapes. And the RMS delay spreads for the T-and the L-shape corridors are greater than the other corridors.