bluuebunny/crossref_metadata_2025_split huggingface dataset:
Molecular phylogeny of Salmo of the western Balkans, based upon multiple nuclear loci
Authors: Pustovrh Gašper , Snoj Aleš , Bajec Simona Sušnik 
Published: February 2014

Abstract

Background
Classification of species within the genus Salmo is still a matter of discussion due to their high level of diversity and to the low power of resolution of mitochondrial (mt)DNA-based phylogeny analyses that have been traditionally used in evolutionary studies of the genus. We apply a new marker system based on nuclear (n)DNA loci to present a novel view of the phylogeny of Salmo representatives and we compare it with the mtDNA-based phylogeny.

Methods
Twenty-two nDNA loci were sequenced for 76 individuals of the brown trout complex: Salmo trutta (Danubian, Atlantic, Adriatic, Mediterranean and Duero mtDNA lineages), Salmo marmoratus (marble trout), Salmo obtusirostris (softmouth trout), and Salmo ohridanus (Ohrid belvica or belushka). Sequences were phylogenetically analyzed using maximum-likelihood and Bayesian Inference methods. The divergence time of the major clades was estimated using the program BEAST.

Results
The existence of five genetic units i.e. S. salar, S. ohridanus, S. obtusirostris, S. marmoratus and the S. trutta complex, including its major phylogenetic lineages was confirmed. Contrary to previous observations, S. obtusirostris was found to be sister to the S. trutta complex and the S. marmoratus clade rather than to the S. ohridanus clade. Reticulate evolution of S. obtusirostris was confirmed and a time for its pre-glacial origin suggested. S. marmoratus was found to be a separate species as S. trutta and S. obtusirostris. Relationships among lineages within the S. trutta complex were weakly supported and remain largely unresolved.

Conclusions
Nuclear DNA-based results showed a fairly good match with the phylogeny of Salmo inferred from mtDNA analyses. The comparison of nDNA and mtDNA data revealed at least four cases of mitochondrial–nuclear DNA discordance observed that were all confined to the Adriatic basin of the Western Balkans. Together with the well-known extensive morphological and genetic variability of Balkan trouts, this observation highlights an interesting and variegated evolutionary history of Salmo in this area.
Malondialdehyde mediates oxidized LDL-induced coronary toxicity through the Akt-FGF2 pathway via DNA methylation
Authors: Yang Tzu-Ching , Chen Yi-Jie , Chang Shwu-Fen , Chen Chu-Huang , Chang Po-Yuan , Lu Shao-Chun 
Published: February 2014

AbstractBackgroundOxidized LDL (oxLDL) is involved in the development of atherosclerotic heart disease through a mechanism that is not fully understood. In this study, we examined the role of malondialdehyde (MDA), an important oxidative stress epitope of oxLDL, in mediating coronary endothelial cytotoxicity.ResultsHuman coronary artery endothelial cells (HCAECs) were treated with oxLDL in the presence or absence of antibody against MDA (anti-MDA) or apoB100 (anti-apoB100). In HCAECs treated with oxLDL (100 μg/ml) alone, DNA synthesis, cell viability, and expression of prosurvival fibroblast growth factor 2 (FGF2) were significantly reduced (P< 0.01 vs phosphate buffered saline–treated cells). These inhibitory effects of oxLDL were significantly attenuated in HCAECs cotreated with anti-MDA (0.15 μg/ml;P< 0.05 vs oxLDL-treated cells), but not in those cotreated with anti-apoB100. When we tested the effects of a panel of signal transduction modifiers on the signal transduction pathways of MDA in oxLDL-treated HCAECs, we found that MDA-induced cytotoxicity was mediated partly through the Akt pathway. Using a reporter gene assay, we identified an oxLDL-response element in theFGF2promoter that was responsible for the transcriptional repression ofFGF2by oxLDL. The results of bisulfite genomic DNA sequencing showed that in HCAECs treated with oxLDL, the GC-rich promoter ofFGF2was heavily methylated at cytosine residues, whereas cotreatment with anti-MDA markedly reduced oxLDL-inducedFGF2promoter methylation.ConclusionOxLDL disrupts the growth and survival of HCAECs through an MDA-dependent pathway involving methylation of theFGF2promoter and repression ofFGF2transcription. This novel epigenetic mechanism of oxLDL may underlie its atherogenicity in patients with atherosclerotic cardiovascular disease.
NDM-1 Metallo-β-Lactamase and ArmA 16S rRNA methylase producing Providencia rettgeri clinical isolates in Nepal
Authors: Tada Tatsuya , Miyoshi-Akiyama Tohru , Dahal Rajan K , Sah Manoj K , Ohara Hiroshi , Shimada Kayo , Kirikae Teruo , Pokhrel Bharat M 
Published: February 2014

Abstract

Background
Drug-resistant Providencia rettgeri producing metallo-β-lactamase and 16S rRNA methylase has been reported in several countries. We analyzed P. rettgeri clinical isolates with resistance to carbapenems and aminoglycosides in a hospital in Nepal.

Methods
Five clinical isolates of multidrug-resistant P. rettgeri were obtained in a hospital in Nepal. Antimicrobial susceptibilities were determined using the microdilution method and entire genomes were sequenced to determine drug-resistant genes. Epidemiological analysis was performed by pulsed-field gel electrophoresis.

Results
Four of the 5 isolates were resistant to carbapenems (imipenem and meropenem), with MICs ≥16 mg/L, with the remaining isolate showing intermediate resistance to imipenem, with an MIC of 2 mg/L and susceptibility to meropenem with an MIC ≤1 mg/L. All 5 isolates had bla
VEB-1. Of the 4 carbapenem-resistant strains, 3 had bla
NDM-1 and 1 had bla
OXA-72. All isolates were highly resistant to aminoglycosides (MICs ≥1,024 mg/L) and harbored armA. As the result of pulsed-field gel electrophoresis pattern analysis in the 5 P. rettgeri isolates, 4 had identical PFGE patterns and the fifth showed 95.7% similarity.

Conclusions
This is the first report describing multidrug-resistant P. rettgeri strains harboring bla
NDM-1 or bla
OXA-72 and armA isolated from patients in Nepal.
Broadband antireflective silicon nanostructures produced by spin-coated Ag nanoparticles
Authors: Kim Joon Beom , Yeo Chan Il , Lee Yong Hwan , Ravindran Sooraj , Lee Yong Tak 
Published: February 2014

Abstract
We report the fabrication of broadband antireflective silicon (Si) nanostructures fabricated using spin-coated silver (Ag) nanoparticles as an etch mask followed by inductively coupled plasma (ICP) etching process. This fabrication technique is a simple, fast, cost-effective, and high-throughput method, making it highly suitable for mass production. Prior to the fabrication of Si nanostructures, theoretical investigations were carried out using a rigorous coupled-wave analysis method in order to determine the effects of variations in the geometrical features of Si nanostructures to obtain antireflection over a broad wavelength range. The Ag ink ratio and ICP etching conditions, which can affect the distribution, distance between the adjacent nanostructures, and height of the resulting Si nanostructures, were carefully adjusted to determine the optimal experimental conditions for obtaining desirable Si nanostructures for practical applications. The Si nanostructures fabricated using the optimal experimental conditions showed a very low average reflectance of 8.3%, which is much lower than that of bulk Si (36.8%), as well as a very low reflectance for a wide range of incident angles and different polarizations over a broad wavelength range of 300 to 1,100 nm. These results indicate that the fabrication technique is highly beneficial to produce antireflective structures for Si-based device applications requiring low light reflection.
Enhanced field electron emission properties of hierarchically structured MWCNT-based cold cathodes
Authors: Gautier Loïck-Alexandre , Le Borgne Vincent , Al Moussalami Samir , El Khakani My Ali 
Published: February 2014

Abstract
Hierarchically structured MWCNT (h-MWCNT)-based cold cathodes were successfully achieved by means of a relatively simple and highly effective approach consisting of the appropriate combination of KOH-based pyramidal texturing of Si (100) substrates and PECVD growth of vertically aligned MWCNTs. By controlling the aspect ratio (AR) of the Si pyramids, we were able to tune the field electron emission (FEE) properties of the h-MWCNT cathodes. Indeed, when the AR is increased from 0 (flat Si) to 0.6, not only the emitted current density was found to increase exponentially, but more importantly its associated threshold field (TF) was reduced from 3.52 V/μm to reach a value as low as 1.95 V/μm. The analysis of the J-E emission curves in the light of the conventional Fowler-Nordheim model revealed the existence of two distinct low-field (LF) and high-field (HF) FEE regimes. In both regimes, the hierarchical structuring was found to increase significantly the associated β
LF and β
HF field enhancement factors of the h-MWCNT cathodes (by a factor of 1.7 and 2.2, respectively). Pyramidal texturing of the cathodes is believed to favor vacuum space charge effects, which could be invoked to account for the significant enhancement of the FEE, particularly in the HF regime where a β
HF as high as 6,980 was obtained for the highest AR value of 0.6.
Vertical nanowire probes for intracellular signaling of living cells
Authors: Lee Ki-Young , Kim Ilsoo , Kim So-Eun , Jeong Du-Won , Kim Ju-Jin , Rhim Hyewhon , Ahn Jae-Pyeong , Park Seung-Han , Choi Heon-Jin 
Published: February 2014

Abstract
The single living cell action potential was measured in an intracellular mode by using a vertical nanoelectrode. For intracellular interfacing, Si nanowires were vertically grown in a controlled manner, and optimum conditions, such as diameter, length, and nanowire density, were determined by culturing cells on the nanowires. Vertical nanowire probes were then fabricated with a complimentary metal-oxide-semiconductor (CMOS) process including sequential deposition of the passivation and electrode layers on the nanowires, and a subsequent partial etching process. The fabricated nanowire probes had an approximately 60-nm diameter and were intracellular. These probes interfaced with a GH3 cell and measured the spontaneous action potential. It successfully measured the action potential, which rapidly reached a steady state with average peak amplitude of approximately 10 mV, duration of approximately 140 ms, and period of 0.9 Hz.
Age differences in the impact of forced swimming test on serotonin transporter levels in lateral septum and dorsal raphe
Authors: Ulloa Rosa-Elena , Díaz-Valderrama Aliyeri , Herrera-Pérez Jaime , León-Olea Martha , Martínez-Mota Lucía 
Published: February 2014

Abstract

Background
Forced swimming test (FST) is an animal model which evaluates behavioral despair and the effect of antidepressants such as the selective serotonin reuptake inhibitors; the FST modifies the expression of some receptors related to antidepressant response, but it is not known whether serotonin transporter (SERT), their main target, is affected by this test in animals of different ages. Antidepressant response has shown age-dependent variations which could be associated with SERT expression. The aim of the present study was to analyze changes in the SERT immunoreactivity (SERT-IR) in dorsal raphe and lateral septum of male rats from different age groups with or without behavioral despair induced by their exposure to the FST, since these two structures are related to the expression of this behavior.

Methods
Prepubertal (24 PN), pubertal (40 PN), young adult (3–5 months) and middle-aged (12 months) male rats were assigned to a control group (non-FST) or depressed group (FST, two sessions separated by 24 h). Changes in SERT-IR in dorsal raphe and lateral septum were determined with immunofluorescence.

Results
Pubertal and middle-aged rats showed higher levels of immobility behavior compared to prepubertal rats on the FST. SERT-IR showed an age-dependent increase followed by a moderate decrease in middle-aged rats in both structures; a decreased in SERT-IR in lateral septum and dorsal raphe of pubertal rats was observed after the FST.

Conclusions
Age differences were observed in the SERT-IR of structures related to behavioral despair; SERT expression was modified by the FST in lateral septum and dorsal raphe of pubertal rats.
Functional characterization of the N-terminal and C-terminal domains of a sesame group II phytocystatin
Authors: Cheng Mei-Ling , Tzen Jason T C , Shyu Douglas J H , Chou Wing-Ming 
Published: February 2014

Abstract

Background
Phytocystatins are natural inhibitors of cysteine protease, and may regulate endo- or exo-genous proteolytic activities in plants. They are classified into Group I and II differing by the presence of C-terminal extension of Group II. A cDNA fragment encoding a Group II phytosystatin, SiCYS was previously obtained from sesame seeds.

Results
SiCYS as well as its two structural domains, N-terminal and C-terminal domains (SiCYS-N and SiCYS-C), was expressed in Escherichia coli. The recombinant SiCYS and SiCYS-N showed inhibitory activity against papain. The K i values of SiCYS and SiCYS-N were ~1.9 ×10-8 M and ~7.9 ×10-8 M, respectively. All the three recombinants possessed comparable ability to inhibit spore germination of Trichoderma reesei, Aspergillus sydowii, and Helminthosporium sesamum. Similar protein profile including proteases in germinating seeds was found in proteins purified by the SiCYS, SiCYS-N or SiCYS-C coupling affinity column.

Conclusion
SiCYS exhibited more effective papain-inhibitory activity than SiCYS-N; while SiCYS-C had almost no inhibitory activity. All displayed similar antifungal activities indicating that there is no correlation between antifungal and papain-inhibitory activities. Structural and sequence analyses suggest that the C-terminal domain of SiCYS may be originated from gene duplication to enhance its inhibitory activity.
Development of a sustainable process for the production of polymer grade lactic acid
Authors: Bapat Susmit S , Aichele Clint P , High Karen A 
Published: February 2014

Abstract
Lactic acid is a commonly occurring substance in nature, ranging from existence in micro-organisms to the human body. Traditionally, lactic acid has applications in industries such as food, chemicals, pharmaceuticals and textiles. In this work, a sustainable process for the production of polymer grade lactic acid (99 wt. % on dry basis) from crude lactic acid was simulated. The simulation was performed using Aspen Plus® version 8.2. The thermodynamic model used for the process was NRTL – Hayden O’Connell due to the polar nature and non-ideal behavior of the species involved. The process was carried out in three stages. First, crude lactic acid was obtained by reacting calcium lactate with sulfuric acid. The second stage consisted of esterification of lactic acid by reactive distillation. A RadFrac column was used for this purpose which also facilitated easy separation of methyl lactate from methanol and water. Pure methyl lactate obtained from the second stage was then hydrolyzed in the third stage using pure lactic acid as an auto-catalyst to obtain the desired product. Use of pure lactic acid as an auto-catalyst helped to achieve the required purity as it minimized contamination. The process was optimized using sensitivity analysis in Aspen Plus®.
Production traits in F1 and F2 crosses with naturalized hair breed Santa Inês ewes
Authors: da Silva Alessandra Ferreira , McManus Concepta , do Prado Paim Tiago , Dallago Bruno Stéfano Lima , Esteves Geisa Isilda Ferreira , Louvandini Helder , Neto José Braccini , Lucci Carolina Madeira 
Published: February 2014

Abstract
The once bred ewe slaughter method proposes the use of female lamb to produce a lamb and then both are slaughtered, increasing income and high quality meat production. Thus, this study evaluated the growth and reproduction performance of ewe lamb from Santa Inês (SI), a naturalized genetic resource, and their crosses (Dorper x Santa Inês (DOR), Texel x Santa Inês (TEX), Ile de France x Santa Inês (ILE)), as well as the survivability and development of their offspring. The animals were weighed monthly from birth to 12-months age. Samples of milk were collected on approximately 30 days of lactation. The physical-chemical analysis of milk was performed. SI females (2.94 kg) had significantly lower birth weight than DOR (3.80 kg) and TEX (3.87 kg). ILE females had higher weaning weight and weight at 12 months than SI females, which reflected in higher daily weight gain (ADG) (108.46 g/day) than TEX and SI. The pregnancy rates at 12 months were ILE (57.14%), TEX (25%), DOR (50%), and SI (28.57%), with TEX and SI differing of ILE and DOR (p = 0.03). Therefore, in semi-confinement and in a once-bred ewe production system using crossbreeding and allying meat production and reproduction, we recommend the use of Dorper and Ile de France breeds for crossbreeding with Santa Inês females. These results demonstrated the useful of a local genetic resource in productive system aiming a low cost meat production.
Clinical disease activity and acute phase reactant levels are discordant among patients with active rheumatoid arthritis: acute phase reactant levels contribute separately to predicting outcome at one year
Authors: Kay Jonathan , Morgacheva Olga , Messing Susan P , Kremer Joel M , Greenberg Jeffrey D , Reed George W , Gravallese Ellen M , Furst Daniel E 
Published: February 2014

Abstract
Introduction
Clinical trials of new treatments for rheumatoid arthritis (RA) typically require subjects to have an elevated acute phase reactant (APR), in addition to tender and swollen joints. However, despite the elevation of individual components of the Clinical Disease Activity Index (CDAI) (tender and swollen joint counts and patient and physician global assessment), some patients with active RA may have normal erythrocyte sedimentation rate (ESR) and/or C-reactive protein (CRP) levels and thus fail to meet entry criteria for clinical trials. We assessed the relationship between CDAI and APRs in the Consortium of Rheumatology Researchers of North America (CORRONA) registry by comparing baseline characteristics and one-year clinical outcomes of patients with active RA, grouped by baseline APR levels.

Methods
This was an observational study of 9,135 RA patients who had both ESR and CRP drawn and a visit at which CDAI was >2.8 (not in remission).

Results
Of 9,135 patients with active RA, 58% had neither elevated ESR nor CRP; only 16% had both elevated ESR and CRP and 26% had either ESR or CRP elevated. Among the 4,228 patients who had a one-year follow-up visit, both baseline and one-year follow-up modified Health Assessment Questionnaire (mHAQ) and CDAI scores were lowest for patients with active RA but with neither APR elevated; both mHAQ and CDAI scores increased sequentially with the increase in number of elevated APR levels at baseline. Each individual component of the CDAI followed the same trend, both at baseline and at one-year follow-up. The magnitude of improvement in both CDAI and mHAQ scores at one year was associated positively with the number of APRs elevated at baseline.

Conclusions
In a large United States registry of RA patients, APR levels often do not correlate with disease activity as measured by joint counts and global assessments. These data strongly suggest that it is appropriate to obtain both ESR and CRP from RA patients at the initial visit. Requiring an elevation in APR levels as a criterion for inclusion of RA patients in studies of experimental agents may exclude some patients with active disease.
Identification and characterization of locus-specific methylation patterns within novel loci undergoing hypermethylation during breast cancer pathogenesis
Authors: Wojdacz Tomasz K , Windeløv Johanne A , Thestrup Britta B , Damsgaard Tine E , Overgaard Jens , Hansen Lise Lotte 
Published: February 2014

Abstract
Introduction
Despite similar clinical and pathological features, large numbers of breast cancer patients experience different outcomes of the disease. This, together with the fact that the incidence of breast cancer is growing worldwide, emphasizes an urgent need for identification of new biomarkers for early cancer detection and stratification of patients.

Methods
We used ultrahigh-resolution microarrays to compare genomewide methylation patterns of breast carcinomas (n = 20) and nonmalignant breast tissue (n = 5). Biomarker properties of a subset of discovered differentially methylated regions (DMRs) were validated using methylation-sensitive high-resolution melting (MS-HRM) in a case–control study on a panel of breast carcinomas (n = 275) and non-malignant controls (n = 74).

Results
On the basis of microarray results, we selected 19 DMRs for large-scale screening of cases and controls. Analysis of the screening results showed that all DMRs tested displayed significant gains of methylation in the cancer tissue compared to the levels in control tissue. Interestingly, we observed two types of locus-specific methylation, with loci undergoing either predominantly full or heterogeneous methylation during carcinogenesis. Almost all tested DMRs (17 of 19) displayed low-level methylation in nonmalignant breast tissue, independently of locus-specific methylation patterns in cases.

Conclusions
Specific loci can undergo either heterogeneous or full methylation during carcinogenesis, and loci hypermethylated in cancer frequently show low-level methylation in nonmalignant tissue.
Genetic ancestry of participants in the National Children’s Study
Authors: Smith Erin N , Jepsen Kristen , Arias Angelo D , Shepard Peter J , Chambers Christina D , Frazer Kelly A 
Published: February 2014

Abstract
Background
The National Children’s Study (NCS) is a prospective epidemiological study in the USA tasked with identifying a nationally representative sample of 100,000 children, and following them from their gestation until they are 21 years of age. The objective of the study is to measure environmental and genetic influences on growth, development, and health. Determination of the ancestry of these NCS participants is important for assessing the diversity of study participants and for examining the effect of ancestry on various health outcomes.

Results
We estimated the genetic ancestry of a convenience sample of 641 parents enrolled at the 7 original NCS Vanguard sites, by analyzing 30,000 markers on exome arrays, using the 1000 Genomes Project superpopulations as reference populations, and compared this with the measures of self-reported ethnicity and race. For 99% of the individuals, self-reported ethnicity and race agreed with the predicted superpopulation. NCS individuals self-reporting as Asian had genetic ancestry of either South Asian or East Asian groups, while those reporting as either Hispanic White or Hispanic Other had similar genetic ancestry. Of the 33 individuals who self-reported as Multiracial or Non-Hispanic Other, 33% matched the South Asian or East Asian groups, while these groups represented only 4.4% of the other reported categories.

Conclusions
Our data suggest that self-reported ethnicity and race have some limitations in accurately capturing Hispanic and South Asian populations. Overall, however, our data indicate that despite the complexity of the US population, individuals know their ancestral origins, and that self-reported ethnicity and race is a reliable indicator of genetic ancestry.