bluuebunny/crossref_metadata_2025_split huggingface dataset:
Low-lying or malpositioned intrauterine devices and systems
Authors: Golightly Ellen , Gebbie Ailsa E 
Published: January 2014

IntroductionThe intrauterine device (IUD) and intrauterine system (IUS) are widely used forms of long-acting reversible contraception. Occasionally, IUD/IUS users have an ultrasound scan that shows a low-lying IUD/IUS or an IUD/IUS is found incidentally on scan to be low-lying within the uterus. No formal guidelines exist on the clinical implications of this scenario or the most appropriate management. We report here on a systematic review of the literature.MethodsA search of the online database PubMed was performed to identify articles relating to low-lying or malpositioned IUD/IUS.ResultsA total of 1101 articles was identified, and 15 were determined to be relevant to the research question.DiscussionThere is little published evidence to determine the nature and extent of the clinical relevance of a low-lying IUD. We recommend individualised management of these women, with particular caution in younger women and those with a history of previous IUD/IUS expulsion. Consideration may be given to attempting to readjust the IUD/IUS position, but if removal is performed, immediate replacement is essential if provision of alternative effective contraception has not been established.
Oral bisphosphonates do not increase the risk of severe upper gastrointestinal complications: a nested case–control study
Authors: Ghirardi Arianna , Scotti Lorenza , Vedova Gianluca Della , D’Oro Luca Cavalieri , Lapi Francesco , Cipriani Francesco , Caputi Achille P , Vaccheri Alberto , Gregori Dario , Gesuita Rosaria , Vestri Annarita , Staniscia Tommaso , Mazzaglia Giampiero , Corrao Giovanni 
Published: January 2014

Abstract

Background
Data on the effect of oral bisphosphonates (BPs) on risk of upper gastrointestinal complications (UGIC) are conflicting. We conducted a large population-based study from a network of Italian healthcare utilization databases aimed to assess the UGIC risk associated with use of BPs in the setting of secondary prevention of osteoporotic fractures.

Methods
A nested case–control study was carried out within a cohort of 68,970 patients aged 45 years or older, who have been hospitalized for osteoporotic fracture from 2003 until 2005. Cases were the 804 patients who experienced hospitalization for UGIC until 2007. Up to 20 controls were randomly selected for each case. Conditional logistic regression model was used to estimate odds ratio (OR) associated with current and past use of BPs (i.e. for drug dispensation within 30 days and over 31 days prior the outcome onset, respectively) after adjusting for several covariates.

Results
Compared with patients who did not use BPs, current and past users had OR (and 95% confidence interval) of 0.86 (0.60 to 1.22) and 1.07 (0.80 to 1.44) respectively. There was no difference in the ORs estimated according with BPs type (alendronate or risedronate) and regimen (daily or weekly), nor with co-therapies and comorbidities.

Conclusions
Further evidence that BPs dispensed for secondary prevention of osteoporotic fractures are not associated with increased risk of severe gastrointestinal complications is supplied from this study. Further research is required to clarify the role BPs and other drugs of co-medication in inducing UGIC.
The protective effect of baicalin against renal ischemia-reperfusion injury through inhibition of inflammation and apoptosis
Authors: Lin Miao , Li Long , Li Liping , Pokhrel Gaurab , Qi Guisheng , Rong Ruiming , Zhu Tongyu 
Published: January 2014

Abstract

Background
Renal ischemia-reperfusion injury (IRI) increases the rates of acute kidney failure, delayed graft function, and early mortality after kidney transplantation. The pathophysiology involved includes oxidative stress, mitochondrial dysfunction, and immune-mediated injury. The anti-oxidation, anti-apoptosis, and anti-inflammation properties of baicalin, a flavonoid glycoside isolated from Scutellaria baicalensis, have been verified. This study therefore assessed the effects of baicalin against renal IRI in rats.

Methods
Baicalin was intraperitoneally injected 30 min before renal ischemia. Serum and kidneys were harvested 24 h after reperfusion. Renal function and histological changes were assessed. Markers of oxidative stress, the Toll-like receptor (TLR)2 and TLR4 signaling pathway, mitochondrial stress, and cell apoptosis were also evaluated.

Results
Baicalin treatment decreased oxidative stress and histological injury, and improved kidney function, as well as inhibiting proinflammatory responses and tubular apoptosis. Baicalin pretreatment also reduced the expression of TLR2, TLR4, MyD88, p-NF-κB, and p-IκB proteins, as well as decreasing caspase-3 activity and increasing the Bcl-2/Bax ratio.

Conclusions
Baicalin may attenuate renal ischemia-reperfusion injury by inhibiting proinflammatory responses and mitochondria-mediated apoptosis. These effects are associated with the TLR2/4 signaling pathway and mitochondrial stress.
Reusable three-dimensional nanostructured substrates for surface-enhanced Raman scattering
Authors: Zhu Zhendong , Li Qunqing , Bai Benfeng , Fan Shoushan 
Published: January 2014

Abstract
To date, fabricating three-dimensional (3D) nanostructured substrate with small nanogap was a laborious challenge by conventional fabrication techniques. In this article, we address a simple, low-cost, large-area, and spatially controllable method to fabricate 3D nanostructures, involving hemisphere, hemiellipsoid, and pyramidal pits based on nanosphere lithography (NSL). These 3D nanostructures were used as surface-enhanced Raman scattering (SERS) substrates of single Rhodamine 6G (R6G) molecule. The average SERS enhancement factor achieved up to 1011. The inevitably negative influence of the adhesion-promoting intermediate layer of Cr or Ti was resolved by using such kind of 3D nanostructures. The nanostructured quartz substrate is a free platform as a SERS substrate and is nondestructive when altering with different metal films and is recyclable, which avoids the laborious and complicated fabricating procedures.
Improvement of multimodal gesture and speech recognition performance using time intervals between gestures and accompanying speech
Authors: Miki Madoka , Kitaoka Norihide , Miyajima Chiyomi , Nishino Takanori , Takeda Kazuya 
Published: January 2014

AbstractWe propose an integrative method of recognizing gestures such as pointing, accompanying speech. Speech generated simultaneously with gestures can assist in the recognition of gestures, and since this occurs in a complementary manner, gestures can also assist in the recognition of speech. Our integrative recognition method uses a probability distribution which expresses the distribution of the time interval between the starting times of gestures and of the corresponding utterances. We evaluate the rate of improvement of the proposed integrative recognition method with a task involving the solution of a geometry problem.
De novo mutation in a male patient with Fabry disease: a case report
Authors: Iemolo Francesco , Pizzo Federica , Albeggiani Giuseppe , Zizzo Carmela , Colomba Paolo , Scalia Simone , Bartolotta Caterina , Duro Giovanni 
Published: January 2014

Abstract

Background
Fabry disease is an X-linked inherited metabolic condition where the deficit of the α-galactosidase A enzyme, encoded by the GLA gene, leads to glycosphingolipid storage, mainly globotriaosylceramide. To date, more than 600 mutations have been identified in human GLA gene that are responsible for FD, including missense and nonsense mutations, small and large deletions. Such mutations are usually inherited, and cases of de novo onset occur rarely.

Case presentation
In this article we report an interesting case of a 44-year-old male patient suffering from a severe form of Fabry disease, with negative family history. The patient showed signs such as cornea verticillata, angiokeratomas, cardiac and neurological manifestations, an end-stage renal disease and he had low α-galactosidase A activity. We detected, in this subject, the mutation c.493 G > C in the third exon of the GLA gene which causes the amino acid substitution D165H in the protein. This mutation affects the amino acid - belonging to the group of buried residues - involved, probably, in the preservation of the protein folding. Moreover, studies of multiple sequence alignment indicate that this amino acid is highly conserved, thus strengthening the hypothesis that it is a key amino acid to the enzyme functionality.
The study of the relatives of the patient showed that, surprisingly, none of the members of his family of origin had this genetic alteration, suggesting a de novo mutation. Only his 11-year-old daughter - showing acroparaesthesias and heat intolerance with reduced enzymatic activity - had the same mutation.

Conclusions
We suggest that a non-inherited mutation of the α-galactosidase A gene is responsible for Fabry disease in the patient who had reduced enzyme activity and classical clinical manifestations of the disease. In a family, it is rare to find only one Fabry disease affected subject with a de novo mutation. These findings emphasize the importance of early diagnosis, genetic counselling, studying the genealogical tree of the patients and starting enzyme replacement therapy to prevent irreversible vital organ damage that occurs during the course of the disease.
The efficacy of probiotics for monosodium glutamate-induced obesity: dietology concerns and opportunities for prevention
Authors: Savcheniuk Oleksandr A , Virchenko Oleksandr V , Falalyeyeva Tetyana M , Beregova Tetyana V , Babenko Lidia P , Lazarenko Liudmyla M , Demchenko Olga M , Bubnov Rostyslav V , Spivak Mykola Ya 
Published: January 2014

Abstract

Introduction
Obesity becomes endemic today. Monosodium glutamate was proved as obesogenic food additive. Probiotics are discussed to impact on obesity development.

Aims and objectives
The aim was to study the effects of probiotics on the development of monosodium glutamate (MSG)-induced obesity in rats.

Material and methods
We included 45 Wistar male rats and divided into three groups (n = 15). Newborn rats of group 1 (control) received subcutaneously 8 μl/g saline. Group 2 received 3 to 4 mg/g MSG subcutaneously on the second, fourth, sixth, eighth and tenth day of life. Within 4 months after birth, rats were on a standard diet. Group 3 received an aqueous solution of probiotics mixture (2:1:1 Lactobacillus casei IMVB-7280, Bifidobacterium animalis VKL, B. animalis VKB) at the dose of 5 × 109 CFU/kg (50 mg/kg) intragastrically. Administration of probiotics was started at the age of 4 weeks just after weaning and continued for 3 months during 2-week courses. Group 2 received intragastrically 2.5 ml/kg water. Organometric and biochemical parameters in all groups of rats were analyzed over 4 months. The concentration of adiponectin was determined in serum, and leptin - in adipose tissue.

Results
Administration of MSG led to the development of obesity in rats; body weight had increased by 7.9% vs controls (p < 0.05); body length had increased by 5.4% (p < 0.05). Body mass index and Lee index and visceral fat mass had increased (p < 0.001). Under the neonatal injection of MSG, the concentration of total cholesterol, triglycerides, VLDL cholesterol and LDL cholesterol significantly increased (p < 0.001), in comparison with controls. Adipose-derived hormones changed in MSG obesity rats: adiponectin decreased by 58.8% (p < 0.01), and leptin concentration in adipose tissue had increased by 74.7% (p < 0.01). The probiotic therapy of rats from group 3 prevented obesity development. Parameters of rats treated with probiotic mixture did not differ from that in the control.

Conclusions
The introduction of MSG to newborn rats caused the obesity in adulthood. Periodic administration of probiotic mixture to rat injected with MSG neonatally resulted in recovery of lipid metabolism and prevention of the obesity development.
Phylogenetic analyses of Begonia sect. Coelocentrum and allied limestone species of China shed light on the evolution of Sino-Vietnamese karst flora
Authors: Chung Kuo-Fang , Leong Wai-Chao , Rubite Rosario Rivera , Repin Rimi , Kiew Ruth , Liu Yan , Peng Ching-I 
Published: January 2014

Abstract

Background
The picturesque limestone karsts across the Sino-Vietnamese border are renowned biodiversity hotspot, distinguished for extremely high endemism of calciphilous plants restricted to caves and cave-like microhabitats that have functioned as biological refugia on the otherwise harsh habitats. To understand evolutionary mechanisms underlying the splendid limestone flora, dated phylogeny is reconstructed for Asian Begonia, a species-rich genus on limestone substrates represented by no less than 60 species in southern China, using DNA sequences of nrITS and chloroplast rpL16 intron. The sampling includes 94 Begonia species encompassing most major Asian clades with a special emphasized on Chinese species.

Results
Except for two tuberous deciduous species and a species with upright stems, a majority of Sino-Vietnamese limestone Begonia (SVLB), including sect. Coelocentrum (19 species sampled) and five species of sect. Diploclinium, Leprosae, and Petermannia, are rhizomatous and grouped in a strongly supported and yet internally poorly resolved clade (Clade SVLB), suggesting a single evolutionary origin of the adaptation to limestone substrates by rhizomatous species, subsequent species radiation, and a strong tendency to retain their ancestral niche. Divergence-time estimates indicate a late Miocene diversification of Clade SVLB, coinciding with the onset of the East Asian monsoon and the period of extensive karstification in the area.

Conclusions
Based on our phylogenetic study, Begonia sect. Coelocentrum is recircumscribed and expanded to include other members of the Clade SVLB (sect. Diploclinium: B. cavaleriei, B. pulvinifera, and B. wangii; sect. Leprosae: B. cylindrica and B. leprosa; sect. Petermannia: B. sinofloribunda). Because species of Clade SVLB have strong niche conservatism to retain in their ancestral habitats in cave-like microhabitats and Begonia are generally poor dispersers prone to diversify allopatrically, we propose that extensive and continuous karstification of the Sino-Vietnamese limestone region facilitated by the onset of East Asian monsoon since the late Miocene has been the major driving force for species accumulation via geographic isolation in Clade SVLB. Morphologically species of Clade SVLB differ mainly in vegetative traits without apparent adaptive value, suggesting that limestone Begonia radiation is better characterized as non-adaptive, an underappreciated speciation mode crucial for rapid species accumulations in organisms of low vagility and strong niche conservatism.
Bioactive Terpenoids and Flavonoids from Daucus littoralis Smith subsp. hyrcanicus Rech.f, an Endemic Species of Iran
Authors: Yousefbeyk Fatemeh , Gohari Ahmad Reza , Hashemighahderijani Zeinabsadat , Ostad Sayed Nasser , Salehi Sourmaghi Mohamad Hossein , Amini Mohsen , Golfakhrabadi Fereshteh , Jamalifar Hossein , Amin Gholamreza 
Published: January 2014

Abstract

Background

Daucus littoralis Smith subsp. hyrcanicus Rech.f. (Apiaceae) is an endemic species in northern parts of Iran where it is commonly named Caspian carrot. The fruits have been used as condiment.

Methods
In a series of in vitro assays, antioxidant (DPPH and FRAP assays), cytotoxic and antimicrobial activities of different extracts of roots and fruits were evaluated for the first time. The separation and purification of the compounds were carried out on the most potent extracts using various chromatographic methods and identified by spectroscopic data (1H and 13C NMR).

Results
The results showed that among the extracts only fruit methanol extract (FME) has significant antioxidant activity (IC50 = 145.93 μg.ml-1 in DPPH assay and 358 ± 0.02 mmol FeII/g dry extract in FRAP assay). The radical scavenging activity of FME at 400 μg.ml-1 was comparable with α-tocopherol (40 μg.ml-1) and with BHA (100 μg.ml-1) (p > 0.05). FME did not show any toxicity against cancerous and normal cell lines. Fruit ethyl acetate extract (FEE) had cytotoxic activity against breast carcinoma and hepatocellular carcinoma cells (IC50 168.4 and 185 μg.ml-1, respectively), while it did not possess antioxidant activity in comparison with α-tocopherol and BHA as standard compounds. Ethyl acetate and methanol extract of fruits showed antimicrobial activity against Staphylococcus aureus (MIC: 3.75 mg.ml-1) and Candida albicans (MIC: 15.6 and 7.8 mg.ml-1, respectively). Four terpenoids were isolated form FEE including: β- sitosterol (1), stigmasterol (2), caryophyllene oxide (3), β-amyrin (4). Also, three flavonoids namely quercetin 3-O-β-glucoside (5), quercetin 3-O-β- galactoside (6) and luteolin (7) were isolated from FME.

Conclusion
This study showed that FEE and FME of D. littoralis Smith subsp. hyrcanicus Rech.f. had the highest biological activities which may be correlated with in vitro cytotoxic, antimicrobial and antioxidant activities of terpenoids and flavonoids components of the extracts.
Comparison of pesticide residues in surface water and ground water of agriculture intensive areas
Authors: Lari Summaiya Z , Khan Noor A , Gandhi Kavita N , Meshram Tejal S , Thacker Neeta P 
Published: January 2014

Abstract
The organochlorines (OClPs) and organophosphates (OPPs) pesticides in surface and ground water having intensive agriculture activity were investigated to evaluate their potential pollution and risks on human health. As per USEPA 8081 B method, liquid-liquid extraction followed by Gas-Chromatographic technique with electron capture detector and mass selective detector (GC-MS) were used for monitoring of pesticides. Among organochlorines, α,β,γ,δ HCH’s, aldrin, dicofol, DDT and its derivatives, α,β endosulphan’s and endosulphan-sulphate were analysed; dichlorovos, ethion, parathion-methyl, phorate, chlorpyrifos and profenofos were determined among organophosphates.
As compared to ground water, higher concentrations of OClPs and OPPs were found in surface water. Throughout the monitoring study, α - HCH (0.39 μg/L in Amravati region),α - endosulphan (0.78 μg/L in Yavatmal region), chlorpyrifos (0.25 μg/L in Bhandara region) and parathion-methyl (0.09 μg/L in Amravati region) are frequently found pesticide in ground water, whereas α,β,γ-HCH (0.39 μg/L in Amravati region), α,β - endosulphan (0.42 μg/L in Amravati region), dichlorovos (0.25 μg/L in Yavatmal region), parathion-methyl (0.42 μg/L in Bhandara region), phorate (0.33 μg/L in Yavatmal region) were found in surface water.
Surface water was found to be more contaminated than ground water with more number of and more concentrated pesticides. Among pesticides water samples are found to be more contaminated by organophosphate than organochlorine. Pesticides in the surface water samples from Bhandara and Yavatmal region exceeded the EU (European Union) limit of 1.0 μg/L (sum of pesticide levels in surface water) but were within the WHO guidelines for individual pesticides.
Removal of Zn(II) from electroplating effluent using yeast biofilm formed on gravels: batch and column studies
Authors: Basak Geetanjali , V Lakshmi , Chandran Preethy , Das Nilanjana 
Published: January 2014

Abstract

Background
Present study deals with the removal of Zn(II) ions from effluent using yeast biofilm formed on gravels.

Methods
The biofilm forming ability of Candida rugosa and Cryptococcus laurentii was evaluated using XTT (2,3-bis[2-methoxy-4-nitro-5-sulfophenyl]-2H-tetrazolium-5-carboxanilide) reduction assay and monitored by scanning electron microscopy (SEM), and Confocal laser scanning microscopy (CLSM). Copious amount of extracellular polymeric substances (EPS) produced by yeast species was quantified and characterized by Fourier transform infrared spectroscopy (FT-IR).

Results
Yeast biofilm formed on gravels by C. rugosa and C. laurentii showed 88% and 74.2% removal of Zn(II) ions respectively in batch mode. In column mode, removal of Zn(II) ions from real effluent was found to be 95.29% by C. rugosa biofilm formed on gravels.

Conclusion
The results of the present study showed that there is a scope to develop a cost effective method for the efficient removal of Zn(II) from effluent using gravels coated with yeast biofilm.
A 45-bp insertion/deletion polymorphism of UCP2 gene is associated with metabolic syndrome
Authors: Hashemi Mohammad , Rezaei Hamzeh , Kaykhaei Mahmoud-Ali , Taheri Mohsen 
Published: January 2014

Abstract
Background
Metabolic syndrome (MeS) is being recognized as a risk factor for insulin resistance and cardiovascular disease. The present study was aimed to find out the possible association between 45-bp I/D polymorphism of uncoupling protein 2 (UCP2) and MeS.

Methods
DNA was extracted from peripheral blood of 151 subjects with and 149 subjects without MeS. 45-bp I/D variant of UCP2 was detected using polymerase chain reaction (PCR).

Results
Our finding showed that 45-bp I/D polymorphism was associated with protection against MeS (OR = 0.56, 95% CI = 0.34-0.92, p = 0.020 D/I vs DD and OR = 0.54, 95% CI = 0.34-0.86, p = 0.009; D/I + I/I vs D/D). The I allele decreased the risk of MeS (OR = 0.62, 95% CI = 0.44-0.90, p = 0.011) in comparison with D allele.

Conclusion
In conclusion, our result suggests that 45-bp I/D polymorphism is associated with the risk of MeS, which remains to be cleared.
dCLIP: a computational approach for comparative CLIP-seq analyses
Authors: Wang Tao , Xie Yang , Xiao Guanghua 
Published: January 2014

AbstractAlthough comparison of RNA-protein interaction profiles across different conditions has become increasingly important to understanding the function of RNA-binding proteins (RBPs), few computational approaches have been developed for quantitative comparison of CLIP-seq datasets. Here, we present an easy-to-use command line tool, dCLIP, for quantitative CLIP-seq comparative analysis. The two-stage method implemented in dCLIP, including a modified MA normalization method and a hidden Markov model, is shown to be able to effectively identify differential binding regions of RBPs in four CLIP-seq datasets, generated by HITS-CLIP, iCLIP and PAR-CLIP protocols. dCLIP is freely available at http://qbrc.swmed.edu/software/.
Mammalian conserved ADAR targets comprise only a small fragment of the human editosome
Authors: Pinto Yishay , Cohen Haim Y , Levanon Erez Y 
Published: January 2014

Abstract
Background
ADAR proteins are among the most extensively studied RNA binding proteins. They bind to their target and deaminate specific adenosines to inosines. ADAR activity is essential, and the editing of a subset of their targets is critical for viability. Recently, a huge number of novel ADAR targets were detected by analyzing next generation sequencing data. Most of these novel editing sites are located in lineage-specific genomic repeats, probably a result of overactivity of editing enzymes, thus masking the functional sites. In this study we aim to identify the set of mammalian conserved ADAR targets.

Results
We used RNA sequencing data from human, mouse, rat, cow, opossum, and platypus to define the conserved mammalian set of ADAR targets. We found that the conserved mammalian editing sites are surprisingly small in number and have unique characteristics that distinguish them from non-conserved ones. The sites that constitute the set have a distinct genomic distribution, tend to be located in genes encoding neurotransmitter receptors or other synapse related proteins, and have higher editing and expression levels. We also found a high consistency of editing levels of this set within mice strains and between human and mouse. Tight regulation of editing in these sites across strains and species implies their functional importance.

Conclusions
Despite the discovery of numerous editing targets, only a small number of them are conserved within mammalian evolution. These sites are extremely highly conserved and exhibit unique features, such as tight regulation, and probably play a pivotal role in mammalian biology.