bluuebunny/crossref_metadata_2025_split huggingface dataset:
Transient decrease in serum potassium level during ischemic attack of acute coronary syndrome: Paradoxical contribution of plasma glucose level and glycohemoglobin
Authors: Sekiyama Hiroshi , Nagoshi Tomohisa , Komukai Kimiaki , Matsushima Masato , Katoh Daisuke , Ogawa Kazuo , Minai Kosuke , Ogawa Takayuki , Yoshimura Michihiro 
Published: January 2013

Abstract

Background
Although a decrease in serum potassium level has been suggested to be a fairly common observation in acute coronary syndrome (ACS), there have so far been no definitive reports directly demonstrating the transient potassium decrease (the potassium dip) during ischemic attack of ACS compared to stable phase in individual patients. To understand the pathophysiological significance of the potassium dip, we examined the changes in serum potassium level throughout ischemic attack and evaluated the clinical factors affecting it.

Methods
The degree of the potassium dip during ischemic attack (as indicated by ΔK, ΔK = K at discharge − K on admission) was examined in 311 consecutive patients with ACS who required urgent hospitalization in our institution.

Results
Serum potassium level during ischemic attack was significantly decreased compared to that during stable phase (P < 0.001). Multiple regression analysis revealed that plasma glucose level during attack was the sole factor which was positively correlated with ΔK (P < 0.01), while HbA1c level was negatively correlated (P < 0.05). The medication profiles and renal function had no impact on ΔK. A longer hospitalization period, higher incidence of myocardial infarction and higher peak creatine kinase level were observed in patients with a larger ΔK.

Conclusions
We have clearly demonstrated that there is a transient decrease in serum potassium level during ischemic attack of ACS compared to stable phase. The degree of the potassium dip was tightly correlated with glucose level, which overwhelmed the diabetic condition, and it also indicates the disease severity. The present study therefore promotes awareness of the significance of monitoring potassium level in parallel with glucose level in patients with ACS.
Graphitic carbon grown on fluorides by molecular beam epitaxy
Authors: Jerng Sahng-Kyoon , Lee Jae Hong , Kim Yong Seung , Chun Seung-Hyun 
Published: January 2013

Abstract
We study the growth mechanism of carbon molecules supplied by molecular beam epitaxy on fluoride substrates (MgF2, CaF2, and BaF2). All the carbon layers form graphitic carbon with different crystallinities depending on the cation. Especially, the growth on MgF2 results in the formation of nanocrystalline graphite (NCG). Such dependence on the cation is a new observation and calls for further systematic studies with other series of substrates. At the same growth temperature, the NCG on MgF2 has larger clusters than those on oxides. This is contrary to the general expectation because the bond strength of the carbon-fluorine bond is larger than that of the carbon-oxygen bond. Our results show that the growth of graphitic carbon does not simply depend on the chemical bonding between the carbon and the anion in the substrate.
Structural, phylogenetic and docking studies of D-amino acid oxidase activator (DAOA), a candidate schizophrenia gene
Authors: Sehgal Sheikh Arslan , Khattak Naureen Aslam , Mir Asif 
Published: January 2013

Abstract

Background
Schizophrenia is a neurodegenerative disorder that occurs worldwide and can be difficult to diagnose. It is the foremost neurological disorder leading to suicide among patients in both developed and underdeveloped countries. D-amino acid oxidase activator (DAOA), also known as G72, is directly implicated in the glutamateric hypothesis of schizophrenia. It activates D-amino acid oxidase, which oxidizes D-serine, leading to modulation of the N-methyl-D-aspartate receptor.

Methods
MODELLER (9v10) was utilized to generate three dimensional structures of the DAOA candidate gene. The HOPE server was used for mutational analysis. The Molecular Evolutionary Genetics Analysis (MEGA5) tool was utilized to reconstruct the evolutionary history of the candidate gene DAOA. AutoDock was used for protein-ligand docking and Gramm-X and PatchDock for protein-protein docking.

Results
A suitable template (1ZCA) was selected by employing BLASTp on the basis of 33% query coverage, 27% identity and E-value 4.9. The Rampage evaluation tool showed 91.1% favored region, 4.9% allowed region and 4.1% outlier region in DAOA. ERRAT demonstrated that the predicted model had a 50.909% quality factor. Mutational analysis of DAOA revealed significant effects on hydrogen bonding and correct folding of the DAOA protein, which in turn affect protein conformation. Ciona was inferred as the outgroup. Tetrapods were in their appropriate clusters with bifurcations. Human amino acid sequences are conserved, with chimpanzee and gorilla showing more than 80% homology and bootstrap value based on 1000 replications. Molecular docking analysis was employed to elucidate the binding mode of the reported ligand complex for DAOA. The docking experiment demonstrated that DAOA is involved in major amino acid interactions: the residues that interact most strongly with the ligand C28H28N3O5PS2 are polar but uncharged (Gln36, Asn38, Thr 122) and non-polar hydrophobic (Ile119, Ser171, Ser21, Ala31). Protein-protein docking simulation demonstrated two ionic bonds and one hydrogen bond involving DAOA. Lys-7 of the receptor protein interacted with Lys-163 and Asp-2037. Tyr-03 interacted with Arg-286 of the ligand protein and formed a hydrogen bond.

Conclusion
The predicted interactions might serve to inhibit the disease-related allele. It is assumed that current bioinformatics methods will contribute significantly to identifying, analyzing and curing schizophrenia. There is an urgent need to develop effective drugs for schizophrenia, and tools for examining candidate genes more accurately and efficiently are required.
Identification of EBV infection in adults with egg specific food allergy
Authors: Pan Yang , Nie Zhiyang , Zhang Yuan , Zhang Kuo , Li Jinming , Wang Lunan 
Published: January 2013

Abstract

Background
Food allergy has been reported increasingly around the world during the past several decades. Epstein-Barr virus (EBV), a common herpesvirus with high infection rate, is now suspected to be a risk or protective factor in food allergy. The aim of the study was to investigate the possible role of EBV infection in IgE-mediated food allergy.

Methods
34 patients with an egg allergy and 34 healthy controls participated in this study. Egg allergy was confirmed by open-food challenge. Serum anti-viral capsid antigen (VCA), anti-Epstein-Barr nuclear antigen 1 (EBNA-1) IgG and egg specific (yolk and white)-IgE levels were evaluated by enzyme linked immunosorbent assay (ELISA). At the same time, EBV DNA as well as viral miRNAs in these samples was quantified by real-time PCR.

Results
The results showed that serum anti EBNA-1 IgG and two viral miRNAs (miR-BART1-5p and miR-BART7) were highly expressed in patients with egg allergy compared with healthy controls (p < 0.05, < 0.001 and < 0.01, respectively). Moreover, the expressions of anti EBNA-1 specific IgG, miR-BART1-5p and miR-BART7 positively correlated with the level of egg-specific IgE (p < 0.05, < 0.01 and < 0.01, respectively). The differences in anti VCA IgG concentration and EBV DNA copy number between the allergy patients and control individuals were not statistically significant.

Conclusions
The high expression of EBV-specific antibody and miRNAs indicated that EBV infection might play a promoting role in IgE-mediated egg food allergy, and viral miRNAs-related immunomodulatory pathway was likely involved in this allergy process.
MRI characterisation of adult onset alpha-methylacyl-coA racemase deficiency diagnosed by exome sequencing
Authors: Haugarvoll Kristoffer , Johansson Stefan , Tzoulis Charalampos , Haukanes Bjørn Ivar , Bredrup Cecilie , Neckelmann Gesche , Boman Helge , Knappskog Per Morten , Bindoff Laurence A 
Published: January 2013

Abstract

Background
Correct diagnosis is pivotal to understand and treat neurological disease. Herein, we report the diagnostic work-up utilizing exome sequencing and the characterization of clinical features and brain MRI in two siblings with a complex, adult-onset phenotype; including peripheral neuropathy, epilepsy, relapsing encephalopathy, bilateral thalamic lesions, type 2 diabetes mellitus, cataract, pigmentary retinopathy and tremor.

Methods
We applied clinical and genealogical investigations, homozygosity mapping and exome sequencing to establish the diagnosis and MRI to characterize the cerebral lesions.

Results
A recessive genetic defect was suspected in two siblings of healthy, but consanguineous parents. Homozygosity mapping revealed three shared homozygous regions and exome sequencing, revealed a novel homozygous c.367 G>A [p.Asp123Asn] mutation in the α-methylacyl-coA racemase (AMACR) gene in both patients. The genetic diagnosis of α-methylacyl-coA racemase deficiency was confirmed by demonstrating markedly increased pristanic acid levels in blood (169 μmol/L, normal <1.5 μmol/L). MRI studies showed characteristic degeneration of cerebellar afferents and efferents, including the dentatothalamic tract and thalamic lesions in both patients.

Conclusions
Metabolic diseases presenting late are diagnostically challenging. We show that appropriately applied, homozygosity mapping and exome sequencing can be decisive for establishing diagnoses such as late onset α-methylacyl-coA racemase deficiency, an autosomal recessive peroxisomal disorder with accumulation of pristanic acid. Our study also highlights radiological features that may assist in diagnosis. Early diagnosis is important as patients with this disorder may benefit from restricted dietary phytanic and pristanic acid intake.
ASAP: an environment for automated preprocessing of sequencing data
Authors: Torstenson Eric S , Li Bingshan , Li Chun 
Published: January 2013

Abstract

Background
Next-generation sequencing (NGS) has yielded an unprecedented amount of data for genetics research. It is a daunting task to process the data from raw sequence reads to variant calls and manually processing this data can significantly delay downstream analysis and increase the possibility for human error. The research community has produced tools to properly prepare sequence data for analysis and established guidelines on how to apply those tools to achieve the best results, however, existing pipeline programs to automate the process through its entirety are either inaccessible to investigators, or web-based and require a certain amount of administrative expertise to set up.

Findings
Advanced Sequence Automated Pipeline (ASAP) was developed to provide a framework for automating the translation of sequencing data into annotated variant calls with the goal of minimizing user involvement without the need for dedicated hardware or administrative rights. ASAP works both on computer clusters and on standalone machines with minimal human involvement and maintains high data integrity, while allowing complete control over the configuration of its component programs. It offers an easy-to-use interface for submitting and tracking jobs as well as resuming failed jobs. It also provides tools for quality checking and for dividing jobs into pieces for maximum throughput.

Conclusions
ASAP provides an environment for building an automated pipeline for NGS data preprocessing. This environment is flexible for use and future development. It is freely available at http://biostat.mc.vanderbilt.edu/ASAP.
Susceptibility of eight species members in the Anopheles hyrcanus group to nocturnally subperiodic Brugia malayi
Authors: Saeung Atiporn , Hempolchom Chayanit , Baimai Visut , Thongsahuan Sorawat , Taai Kritsana , Jariyapan Narissara , Chaithong Udom , Choochote Wej 
Published: January 2013

Abstract

Background
Filariasis, caused by Brugia malayi, is a public health problem in Thailand. Currently, at least two locations in southern Thailand are reported to be active endemic areas. Two and four Mansonia species are primary and secondary vectors, respectively, of the nocturnally subperiodic race, whereas, Coquillettidia crassipes is a vector of the diurnally subperiodic race. Although several Anopheles species have been incriminated extensively as natural and/or suspected vectors of B. malayi, little is known about vector competence between indigenous Anopheles and this filaria in Thailand. Thus, the susceptibility levels of eight species members in the Thai An. hyrcanus group to nocturnally subperiodic B. malayi are presented herein, and the two main refractory factors that affect them in different degrees of susceptibility have been elucidated.

Methods

Aedes togoi (a control vector), An. argyropus, An. crawfordi, An. nigerrimus, An. nitidus, An. paraliae, An. peditaeniatus, An. pursati and An. sinensis were allowed to feed artificially on blood containing B. malayi microfilariae, and dissected 14 days after feeding. To determine factors that take effect at different susceptibility levels, stain-smeared blood meals were taken from the midguts of Ae. togoi, An. peditaeniatus, An. crawfordi, An. paraliae, An. sinensis and An. nitidus immediately after feeding, and their dissected-thoraxes 4 days post blood-feedings were examined consecutively for microfilariae and L1 larvae.

Results
The susceptibility rates of Ae. togoi, An. peditaeniatus, An. crawfordi, An. nigerrimus, An. argyropus, An. pursati, An. sinensis, An. paraliae and An. nitidus to B. malayi were 70–95%, 70–100%, 80–85%, 50–65%, 60%, 60%, 10%, 5%, and 0%, respectively. These susceptibility rates related clearly to the degrees of normal larval development in thoracic muscles, i.e., Ae. togoi, An. peditaeniatus, An. crawfordi, An. paraliae, An. sinensis and An. nitidus yielded normal L1 larvae of 93.15%, 96.34%, 97.33%, 23.60%, 15.38% and 0%, respectively.

Conclusions

An. peditaeniatus, An. crawfordi, An. nigerrimus, An. argyropus and An. pursati were high potential vectors. An. paraliae and An. sinensis were low potential vectors, while An. nitidus was a refractory vector. Two refractory mechanisms; direct toxicity and/or melanotic encapsulation against filarial larval were involved in the refractoriness of development in the thoracic muscles of the mosquito.
Comparative efficacy of tandem autologous versus autologous followed by allogeneic hematopoietic cell transplantation in patients with newly diagnosed multiple myeloma: a systematic review and meta-analysis of randomized controlled trials
Authors: Kharfan-Dabaja Mohamed A , Hamadani Mehdi , Reljic Tea , Nishihori Taiga , Bensinger William , Djulbegovic Benjamin , Kumar Ambuj 
Published: January 2013

Abstract

Background
Despite advances in understanding of clinical, genetic, and molecular aspects of multiple myeloma (MM) and availability of more effective therapies, MM remains incurable. The autologous-allogeneic (auto-allo) hematopoietic cell transplantation (HCT) strategy is based on combining cytoreduction from high-dose (chemo- or chemoradio)-therapy with adoptive immunotherapy. However, conflicting results have been reported when an auto-allo HCT approach is compared to tandem autologous (auto-auto) HCT. A previously published meta-analysis has been reported; however, it suffers from serious methodological flaws.

Methods
A systematic search identified 152 publications, of which five studies (enrolling 1538 patients) met inclusion criteria. All studies eligible for inclusion utilized biologic randomization.

Results
Assessing response rates by achievement of at least a very good partial response did not differ among the treatment arms [risk ratio (RR) (95% CI) = 0.97 (0.87-1.09), p = 0.66]; but complete remission was higher in the auto-allo HCT arm [RR = 1.65 (1.25-2.19), p = 0.0005]. Event-free survival did not differ between auto-allo HCT group versus auto-auto HCT group using per-protocol analysis [hazard ratio (HR) = 0.78 (0.58-1.05)), p = 0.11] or using intention-to-treat analysis [HR = 0.83 (0.60-1.15), p = 0.26]. Overall survival (OS) did not differ among these treatment arms whether analyzed on per-protocol [HR = 0.88 (0.33-2.35), p = 0.79], or by intention-to-treat [HR = 0.80 (0.48-1.32), p = 0.39] analysis. Non-relapse mortality (NRM) was significantly worse with auto-allo HCT [RR (95%CI) = 3.55 (2.17-5.80), p < 0.00001].

Conclusion
Despite higher complete remission rates, there is no improvement in OS with auto-allo HCT; but this approach results in higher NRM in patients with newly diagnosed MM. At present, totality of evidence suggests that an auto-allo HCT approach for patients with newly diagnosed myeloma should not be offered outside the setting of a clinical trial.
XRCC3 Thr241Met gene polymorphisms and lung cancer risk: a meta-analysis
Authors: Zhan Ping , Wang Qin , Qian Qian , Yu Li-Ke 
Published: January 2013

Abstract
Many studies have examined the association between the XRCC3 Thr241Met gene polymorphism and lung cancer risk in various populations, but their results have been inconsistent. To assess this relationship more precisely, a meta-analysis was performed. The PubMed, Embase, Web of Science, and CNKI database was searched for case–control studies published up to July 2012. Data were extracted and pooled odds ratios (OR) with 95% confidence intervals (CI) were calculated.
Ultimately, 17 studies, comprising 4123 lung cancer cases and 5597 controls were included. Overall, for T allele carriers (TC + TT) versus the wild-type homozygotes (CC), the pooled OR was 0.95 (95% CI = 0.87-1.04 P = 0.228 for heterogeneity), for TT versus CC the pooled OR was 0.99 (95% CI = 0.86-1.15 P = 0.315 for heterogeneity). In the stratified analysis by ethnicity, histological types of lung cancer and smoking status, no any significantly risks were found for (C/T + T/T) vs C/C or T/T vs C/C. No publication bias was found by using the funnel plot and Egger's test.
Overall, there is no evidence showing a significant correlation between XRCC3 Thr241Met polymorphism and lung cancer risk stratified analysis by ethnicity, histology and smoking status.
Method to quantify live and dead cells in multi-species oral biofilm by real-time PCR with propidium monoazide
Authors: Àlvarez Gerard , González Marta , Isabal Sergio , Blanc Vanessa , León Rubén 
Published: January 2013

AbstractReal-time PCR (qPCR) is a widely used technique in analysing environmental and clinical microbiological samples. However, its main limitation was its inability to discriminate between live and dead cells.Recently, propidium monoazide (PMA) together with qPCR has been used to overcome this problem, with good results for different bacterial species in different types of samples.Our objective was to implement this technique for analysing mortality in multi-species oral biofilms formedin vitrowith five oral bacteria:Streptococcus oralis,Streptococcus gordonii,Veillonella parvula,Fusobacterium nucleatumandPrevotella intermedia. We also tested its effectiveness on biofilms treated with an antiseptic solution containing 0.07% w/w cetylpyridinium chloride (CPC).Standardisation of the qPCR-PMA method was performed on pure, heat-killed planktonic cultures of each species, detecting mortality higher than 4 log inS. oralis,S. gordoniiandF. nucleatumand higher than 2 forV. parvulaandP. intermedia. We obtained similar results for all species when using CPC.When we analysed biofilms with qPCR-PMA, we found that the mortality in the non-CPC treated multi-species biofilms was lower than 1 log for all species. After treatment with CPC, the viability reduction was higher than 4 log inS. oralisandS. gordonii, higher than 3 log inF. nucleatumandP. intermediaand approximately 2 inV. parvula.In short, we standardised the conditions for using qPCR-PMA in 5 oral bacterial species and proved its usefulness for quantification of live and dead cells in multi-species oral biofilms formedin vitro, after use of an antiseptic.
Comparison of percent density from raw and processed full-field digital mammography data
Authors: Vachon Celine M , Fowler Erin EE , Tiffenberg Gail , Scott Christopher G , Pankratz V Shane , Sellers Thomas A , Heine John J 
Published: January 2013

Abstract
Introduction
Mammographic density has been established as a strong risk factor for breast cancer, primarily using digitized film mammograms. Full-field digital mammography (FFDM) is replacing film mammography, has different properties than film, and provides both raw and processed clinical display representation images. We evaluated and compared FFDM raw and processed breast density measures and their associations with breast cancer.

Methods
A case-control study of 180 cases and 180 controls matched by age, postmenopausal hormone use, and screening history was conducted. Mammograms were acquired from a General Electric Senographe 2000D FFDM unit. Percent density (PD) was assessed for each FFDM representation using the operator-assisted Cumulus method. Reproducibility within image type (n = 80) was assessed using Lin's concordance correlation coefficient (rc). Correlation of PD between image representations (n = 360) was evaluated using Pearson's correlation coefficient (r) on the continuous measures and the weighted kappa statistic (κ) for quartiles. Conditional logistic regression was used to estimate odds ratios (ORs) for the PD and breast cancer associations for both image representations with 95% confidence intervals. The area under the receiver operating characteristic curve (AUC) was used to assess the discriminatory accuracy.

Results
Percent density from the two representations provided similar intra-reader reproducibility (rc= 0.92 for raw and rc= 0.87 for processed images) and was correlated (r = 0.82 and κ = 0.64). When controlling for body mass index, the associations of quartiles of PD with breast cancer and discriminatory accuracy were similar for the raw (OR: 1.0 (ref.), 2.6 (1.2 to 5.4), 3.1 (1.4 to 6.8), 4.7 (2.1 to 10.6); AUC = 0.63) and processed representations (OR: 1.0 (ref.), 2.2 (1.1 to 4.1), 2.2 (1.1 to 4.4), 3.1 (1.5 to 6.6); AUC = 0.64).

Conclusions
Percent density measured with an operator-assisted method from raw and processed FFDM images is reproducible and correlated. Both percent density measures provide similar associations with breast cancer.