bluuebunny/crossref_metadata_2025_split huggingface dataset:
Incorporating domain knowledge in chemical and biomedical named entity recognition with word representations
Authors: Munkhdalai Tsendsuren , Li Meijing , Batsuren Khuyagbaatar , Park Hyeon Ah , Choi Nak Hyeon , Ryu Keun Ho 
Published: June 2015

Abstract

Background
Chemical and biomedical Named Entity Recognition (NER) is an essential prerequisite task before effective text mining can begin for biochemical-text data. Exploiting unlabeled text data to leverage system performance has been an active and challenging research topic in text mining due to the recent growth in the amount of biomedical literature.
We present a semi-supervised learning method that efficiently exploits unlabeled data in order to incorporate domain knowledge into a named entity recognition model and to leverage system performance. The proposed method includes Natural Language Processing (NLP) tasks for text preprocessing, learning word representation features from a large amount of text data for feature extraction, and conditional random fields for token classification. Other than the free text in the domain, the proposed method does not rely on any lexicon nor any dictionary in order to keep the system applicable to other NER tasks in bio-text data.

Results
We extended BANNER, a biomedical NER system, with the proposed method. This yields an integrated system that can be applied to chemical and drug NER or biomedical NER. We call our branch of the BANNER system BANNER-CHEMDNER, which is scalable over millions of documents, processing about 530 documents per minute, is configurable via XML, and can be plugged into other systems by using the BANNER Unstructured Information Management Architecture (UIMA) interface.
BANNER-CHEMDNER achieved an 85.68% and an 86.47% F-measure on the testing sets of CHEMDNER Chemical Entity Mention (CEM) and Chemical Document Indexing (CDI) subtasks, respectively, and achieved an 87.04% F-measure on the official testing set of the BioCreative II gene mention task, showing remarkable performance in both chemical and biomedical NER. BANNER-CHEMDNER system is available at: https://bitbucket.org/tsendeemts/banner-chemdner.
What is the effect of phasing out long-chain per- and polyfluoroalkyl substances on the concentrations of perfluoroalkyl acids and their precursors in the environment? A systematic review protocol
Authors: Land Magnus , de Wit Cynthia A , Cousins Ian T , Herzke Dorte , Johansson Jana , Martin Jonathan W 
Published: June 2015

Abstract
Background
There is a growing concern in Sweden and elsewhere that continued emissions of per- and polyfluoroalkyl substances (PFASs) may cause environmental as well as human health effects. PFASs are a broad class of man-made substances that have been produced and used in both commercial products and industrial processes for more than 60 years. Although the production and use of some PFASs has been phased-out in some parts of the world, it is not known what effect these actions to date have had on PFAS concentrations in the environment. Owing to the wide diversity of PFASs, it is difficult to generalize their properties, environmental fate and production histories. However, the strength and stability of the C-F bond renders the perfluoroalkyl moieties resistant to heat and environmental degradation. Several PFASs are now occurring even in very remote areas in large parts of the world, but the environmental transport and fate of substances within this group is not well understood. A systematic review may be able to determine whether the concentrations of these substances in different environments are changing in any particular direction with time, and whether the phase-outs have had any effects on the concentration trends.

Methods
Searches for primary research studies reporting on temporal variations of PFAS concentrations in the environment will be performed in the scientific literature as well as in other reports. Relevant samples include both abiotic and biological samples including humans. No particular time, document type, language or geographical constraints will be applied. Two authors will screen all retrieved articles. Double screening of about 10% of the articles will be performed by all authors at both title/abstract and full-text levels. Kappa tests will be used to test if the screening is consistent. Relevant articles will be critically appraised by four authors (double checking of 25% of the articles). Quality assessment will focus on selection bias, dating of samples, sample integrity and analytical procedures. Data synthesis will be based on statistical analysis of temporal concentration trends.
Lactococcus garvieae: a small bacteria and a big data world
Authors: López-Campos Guillermo , Aguado-Urda Mónica , Blanco María Mar , Gibello Alicia , Cutuli María Teresa , López-Alonso Victoria , Martín-Sánchez Fernando , Fernández-Garayzábal José F 
Published: June 2015

Abstract

Objective
To describe the importance of bioinformatics tools to analyze the big data yielded from new "omics" generation-methods, with the aim of unraveling the biology of the pathogen bacteria Lactococcus garvieae.

Methods
The paper provides the vision of the large volume of data generated from genome sequences, gene expression profiles by microarrays and other experimental methods that require biomedical informatics methods for management and analysis.

Results
The use of biomedical informatics methods improves the analysis of big data in order to obtain a comprehensive characterization and understanding of the biology of pathogenic organisms, such as L. garvieae.

Conclusions
The "Big Data" concepts of high volume, veracity and variety are nowadays part of the research in microbiology associated with the use of multiple methods in the "omic" era. The use of biomedical informatics methods is a requisite necessary to improve the analysis of these data.
Genetically engineering encapsulin protein cage nanoparticle as a SCC-7 cell targeting optical nanoprobe
Authors: Moon Hyojin , Lee Jisu , Kim Hansol , Heo Somin , Min Junseon , Kang Sebyung 
Published: June 2015

Abstract

Background
Protein cage nanoparticles are promising nanoplatform candidates for efficient delivery systems of diagnostics and/or therapeutics because of their uniform size and structure as well as high biocompatibility and biodegradability. Encapsulin protein cage nanoparticle is used to develop a cell-specific targeting optical nanoprobe.

Results
FcBPs are genetically inserted and successfully displayed on the surface of encapsulin to form FcBP-encapsulin. Selectively binding of FcBP-encapsulin to SCC-7 is visualized with fluorescent microscopy.

Conclusions
Encapsulin protein cage nanoparticle is robust enough to maintain their structure at high temperature and easily acquires multifunctions on demand through the combination of genetic and chemical modifications.
Simple clinical indicators for early psoriatic arthritis detection
Authors: Caso Francesco , Costa Luisa , Atteno Mariangela , Del Puente Antonio , Cantarini Luca , Lubrano Ennio , Scarpa Raffaele 
Published: June 2015

Abstract

Background
Diagnosis of psoriatic arthritis (PsA), in a period of 12 months from the onset of the first articular episode, permits of identifying the early form defined as “early PsA”. The recognition of the disease in this phase leads to better outcome.
The aim of this study was to identify peculiar clinical and/or laboratory findings that could be useful for the diagnosis of “early PsA”.

Findings
Thirty-five patients with early onset of arthritis were observed. The following data were collected for each patient: family and personal history, physical examination, tender and swollen joint counts (TJC, SJC), tender entheseal count, presence of dactylitis and low back pain (LBP), and laboratory tests.
Among the 35 total patients, 24 showed skin and/or nail psoriasis or a family history of psoriasis.
The remaining 11 patients showed absence of concomitant or previous psoriasis and/or familiarity for psoriasis. The comparison between the two groups showed that patients with psoriasis had a significant presence of LBP, dactylitis and enthesitis than patients with psoriasis.

Conclusions
The study confirms that the distinctive clinical findings of PsA is psoriasis, but also LBP, dactylitis and enthesitis have a relevant role in early identification. A low number of SJC and TJC are frequently observed in early phases of PsA than in other forms of early arthritis. These aspects could be mostly helpful when psoriasis is not detected or can follow arthritis in absence of familiar positivity, making difficult PsA diagnosis.
In conclusion, careful medical history, clinical examination and first-level laboratory investigations are useful to characterize early phases of PsA.
Isolation and functional characterization of novel biosurfactant produced by Enterococcus faecium
Authors: Sharma Deepansh , Saharan Baljeet Singh , Chauhan Nikhil , Procha Suresh , Lal Sohan 
Published: June 2015

Abstract
The objective of the present study was to isolate the biosurfactant (BS) producing lactic acid bacteria (LAB) from traditional fermented food (buttermilk) and its functional and structural characterization. BS isolated from strain MRTL9 reduced surface tension from 72.0 to 40.2 mN m-1. The critical micelle concentration (CMC) of BS was 2.25 mg ml-1 with emulsification efficiency (E24) after 24 h of 64% against kerosene oil. The cell bound BS was partially purified by silica gel column chromatography and found as glycolipid. The gas chromatography and mass spectroscopy data revealed the fatty acid as hexadecanoic acid. Xylose was determined as hydrophilic moiety. The BS was found to be stable to pH changes over a range of 4.0-12.0, being most effective at pH 7 and showed no apparent loss of surface tension and emulsification efficiency after heat treatment at 120°C for 15 min. The outcomes of cellular toxicity showed lower toxicity of BS in comparison to SDS and rhamnolipids. Current study confirmed the preventive anti-adhesion activity of BS. These amphiphilic molecules, interferes with the microbial adhesion and found to be least cytotoxic with cellular compatibility with mouse fibroblasts cells.
Hyperbaric oxygen therapy ameliorates acute brain injury after porcine intracerebral hemorrhage at high altitude
Authors: Zhu Hai-tao , Bian Chen , Yuan Ji-chao , Liao Xiao-jun , Liu Wei , Zhu Gang , Feng Hua , Lin Jiang-kai 
Published: June 2015

Abstract
Introduction
Intracerebral hemorrhage (ICH) at high altitude is not well understood to date. This study investigates the effects of high altitude on ICH, and examines the acute neuroprotection of hyperbaric oxygen (HBO) therapy against high-altitude ICH.

Methods
Minipigs were placed in a hypobaric chamber for 72 h before the operation. ICH was induced by an infusion of autologous arterial blood (3 ml) into the right basal ganglia. Animals in the high-altitude ICH group received HBO therapy (2.5 ATA for 60 min) 30 min after ICH. Blood gas, blood glucose and brain tissue oxygen partial pressure (PbtO2) were monitored continuously for animals from all groups, as were microdialysis products including glucose, lactate, pyruvate and glutamate in perihematomal tissue from 3 to 12 h post-ICH.

Results
High-altitude ICH animals showed significantly lower PbtO2, higher lactate/pyruvate ratio (LPR) and glutamate levels than low-altitude ICH animals. More severe neurological deficits, brain edema and neuronal damage were also observed in high-altitude ICH. After HBO therapy, PbtO2 was significantly increased and LPR and glutamate levels were significantly decreased. Brain edema, neurological deficits and neuronal damage were also ameliorated.

Conclusions
The data suggested a more serious disturbance of tissue oxygenation and cerebral metabolism in the acute stage after ICH at high altitude. Early HBO treatment reduced acute brain injury, perhaps through a mechanism involving the amelioration of the derangement of cerebral oxygenation and metabolism following high-altitude ICH.
Identification of two novel mammographic density loci at 6Q25.1
Authors: Brand Judith S , Li Jingmei , Humphreys Keith , Karlsson Robert , Eriksson Mikael , Ivansson Emma , Hall Per , Czene Kamila 
Published: June 2015

Abstract
Introduction
Mammographic density (MD) is a strong heritable and intermediate phenotype for breast cancer, but much of its genetic variation remains unexplained. We performed a large-scale genetic association study including 8,419 women of European ancestry to identify MD loci.

Methods
Participants of three Swedish studies were genotyped on a custom Illumina iSelect genotyping array and percent and absolute mammographic density were ascertained using semiautomated and fully automated methods from film and digital mammograms. Linear regression analysis was used to test for SNP-MD associations, adjusting for age, body mass index, menopausal status and six principal components. Meta-analyses were performed by combining P values taking sample size, study-specific inflation factor and direction of effect into account.

Results
Genome-wide significant associations were observed for two previously identified loci: ZNF365 (rs10995194, P = 2.3 × 10−8 for percent MD and P = 8.7 × 10−9 for absolute MD) and AREG (rs10034692, P = 6.7 × 10−9 for absolute MD). In addition, we found evidence of association for two variants at 6q25.1, both of which are known breast cancer susceptibility loci: rs9485370 in the TAB2 gene (P = 4.8 × 10−9 for percent MD and P = 2.5 × 10−8 for absolute MD) and rs60705924 in the CCDC170/ESR1 region (P = 2.2 × 10−8 for absolute MD). Both regions have been implicated in estrogen receptor signaling with TAB2 being a potential regulator of tamoxifen response.

Conclusions
We identified two novel MD loci at 6q25.1. These findings underscore the importance of 6q25.1 as a susceptibility region and provide more insight into the mechanisms through which MD influences breast cancer risk.
Global genetic analyses reveal strong inter-ethnic variability in the loss of activity of the organic cation transporter OCT1
Authors: Seitz Tina , Stalmann Robert , Dalila Nawar , Chen Jiayin , Pojar Sherin , Dos Santos Pereira Joao N. , Krätzner Ralph , Brockmöller Jürgen , Tzvetkov Mladen V. 
Published: June 2015

Abstract
Background
The organic cation transporter OCT1 (SLC22A1) mediates the uptake of vitamin B1, cationic drugs, and xenobiotics into hepatocytes. Nine percent of Caucasians lack or have very low OCT1 activity due to loss-of-function polymorphisms in OCT1 gene. Here we analyzed the global genetic variability in OCT1 to estimate the therapeutic relevance of OCT1 polymorphisms in populations beyond Caucasians and to identify evolutionary patterns of the common loss of OCT1 activity in humans.

Methods
We applied massively parallel sequencing to screen for coding polymorphisms in 1,079 unrelated individuals from 53 populations worldwide. The obtained data was combined with the existing 1000 Genomes data comprising an additional 1,092 individuals from 14 populations. The identified OCT1 variants were characterized in vitro regarding their cellular localization and their ability to transport 10 known OCT1 substrates. Both the population genetics data and transport data were used in tandem to generate a world map of loss of OCT1 activity.

Results
We identified 16 amino acid substitutions potentially causing loss of OCT1 function and analyzed them together with five amino acid substitutions that were not expected to affect OCT1 function. The variants constituted 16 major alleles and 14 sub-alleles. Six major alleles showed improper subcellular localization leading to substrate-wide loss in activity. Five major alleles showed correct subcellular localization, but substrate-specific loss of activity. Striking differences were observed in the frequency of loss of OCT1 activity worldwide. While most East Asian and Oceanian individuals had completely functional OCT1, 80 % of native South American Indians lacked functional OCT1 alleles. In East Asia and Oceania the average nucleotide diversity of the loss-of-function variants was much lower than that of the variants that do not affect OCT1 function (ratio of 0.03) and was significantly lower than the theoretically expected heterozygosity (Tajima’s D = −1.64, P < 0.01).

Conclusions
Comprehensive genetic analyses showed strong global variations in the frequency of loss of OCT1 activity with selection pressure for maintaining OCT1 activity in East Asia and Oceania. These results not only enable pharmacogenetically-based optimization of drug treatment worldwide, but may help elucidate the functional role of human OCT1.
The class of $(\alpha,\psi)$-type contractions in b-metric spaces and fixed point theorems
Authors: Samet Bessem 
Published: June 2015

AbstractWe study the existence and uniqueness of fixed points for self-operators defined in a b-metric space and belonging to the class of $(\alpha,\psi)$
(
α
,
ψ
)
-type contraction mappings. The obtained results generalize and unify several existing fixed point theorems in the literature.
Curcumin as a double-edged sword for stem cells: dose, time and cell type-specific responses to curcumin
Authors: Attari Fatemeh , Zahmatkesh Maryam , Aligholi Hadi , Mehr Shahram Ejtemaei , Sharifzadeh Mohammad , Gorji Ali , Mokhtari Tahmineh , Khaksarian Mojtaba , Hassanzadeh Gholamreza 
Published: June 2015

Abstract

Background
The beneficial effects of curcumin which includes its antioxidant, anti-inflammatory and cancer chemo-preventive properties have been identified. Little information is available regarding the optimal dose and treatment periods of curcumin on the proliferation rate of different sources of stem cells.

Methods
In this study, the effect of various concentrations of curcumin on the survival and proliferation of two types of outstanding stem cells which includes bone marrow stem cells (BMSCs) and adult rat neural stem/progenitor cells (NS/PCs) at different time points was investigated. BMSCs were isolated from bilateral femora and tibias of adult Wistar rats. NS/PCs were obtained from subventricular zone of adult Wistar rat brain. The curcumin (0.1, 0.5, 1, 5 and 10 μM/L) was added into a culture medium for 48 or 72 h. Fluorescent density of 5-bromo-2′-deoxyuridine (Brdu)-positive cells was considered as proliferation index. In addition, cell viability was assessed by MTT assay.

Results
Treatment of BMSCs with curcumin after 48 h, increased cell survival and proliferation in a dose-dependent manner. However, it had no effect on NSCs proliferation except a toxic effect in the concentration of 10 μM of curcumin. After a 72 h treatment period, BMSCs and NS/PCs survived and proliferated with low doses of curcumin. However, high doses of curcumin administered for 72 h showed toxic effects on both stem cells.

Conclusions
These findings suggest that curcumin survival and proliferative effects depend on its concentration, treatment period and the type of stem cells. Appropriate application of these results may be helpful in the outcome of combination therapy of stem cells and curcumin.
Bone morphogenetic protein 2 gene transduction enhances the osteogenic potential of human urine-derived stem cells
Authors: Guan Junjie , Zhang Jieyuan , Zhu Zhenzhong , Niu Xin , Guo Shangchun , Wang Yang , Zhang Changqing 
Published: June 2015

Abstract
Introduction
Urine-derived stem cells (USCs) have the ability to differentiate into osteogenic lineage. Previous studies have raised the possibility that USCs could be used for bone repair. To harness the power of USCs in promoting bone regeneration, methods must be developed to induce USCs to osteogenic lineage efficiently. The present study investigates the effect of lentivirus-encoded bone morphogenetic protein 2 (BMP2) gene transduction on the osteogenic potential of USCs.

Methods
USCs were isolated from voided urine and transduced with Lentiviral vector encoding BMP2. An in vitro study was performed to detect Lentiviral-BMP2 transduced USCs differentiated towards osteogenic lineage. Furthermore, Lentiviral-BMP2 transduced USCs were transplanted in vivo to examine the ectopic bone formation ability. After six weeks, retrieval samples were obtained for immunostaining and histological analysis.

Results
The results showed that the transduction efficiencies were over 90%, and transduced USCs had high expression levels of the BMP2 gene and secreted BMP2 protein. Alkaline activity and mineral deposition staining demonstrated that transduced USCs differentiate into osteogenic lineages without the addition of osteogenic supplements. Transduced USCs also showed high expression of bone-related markers, including runt-related protein-2 (Runx2) and osteocalcin (OCN), confirming this lentiviral-BMP2 construct provides sufficient stimuli for osteogenic differentiation. Histological analysis indicated that the transduced USCs induced robust new bone formation in nude mice. Six weeks after transplantation, human derived cells were observed to participate in bone formation.

Conclusions
These results demonstrate that BMP2 gene transduction provides an effective method to enhance the osteogenic potential of USCs.
The cerebral embolism evoked by intra-arterial delivery of allogeneic bone marrow mesenchymal stem cells in rats is related to cell dose and infusion velocity
Authors: Cui Li-li , Kerkelä Erja , Bakreen Abdulhameed , Nitzsche Franziska , Andrzejewska Anna , Nowakowski Adam , Janowski Miroslaw , Walczak Piotr , Boltze Johannes , Lukomska Barbara , Jolkkonen Jukka 
Published: June 2015

Abstract
Introduction
Intra-arterial cell infusion is an efficient delivery route with which to target organs such as the ischemic brain. However, adverse events including microembolisms and decreased cerebral blood flow were recently reported after intra-arterial cell delivery in rodent models, raising safety concerns. We tested the hypothesis that cell dose, infusion volume, and velocity would be related to the severity of complications after intra-arterial cell delivery.

Methods
In this study, 38 rats were subjected to a sham middle cerebral artery occlusion (sham-MCAO) procedure before being infused with allogeneic bone-marrow mesenchymal stem cells at different cell doses (0 to 1.0 × 106), infusion volumes (0.5 to 1.0 ml), and infusion times (3 to 6 minutes). An additional group (n = 4) was infused with 1.0 × 106 cells labeled with iron oxide for in vivo tracking of cells. Cells were infused through the external carotid artery under laser Doppler flowmetry monitoring 48 hours after sham-MCAO. Magnetic resonance imaging (MRI) was performed 24 hours after cell infusion to reveal cerebral embolisms or hemorrhage. Limb placing, cylinder, and open field tests were conducted to assess sensorimotor functions before the rats were perfused for histology.

Results
A cell dose-related reduction in cerebral blood flow was noted, as well as an increase in embolic events and concomitant lesion size, and sensorimotor impairment. In addition, a low infusion velocity (0.5 ml/6 minutes) was associated with high rate of complications. Lesions on MRI were confirmed with histology and corresponded to necrotic cell loss and blood-brain barrier leakage.

Conclusions
Particularly cell dose but also infusion velocity contribute to complications encountered after intra-arterial cell transplantation. This should be considered before planning efficacy studies in rats and, potentially, in patients with stroke.