bluuebunny/crossref_metadata_2025_split huggingface dataset:
Influence of argon plasma on the deposition of Al2O3 film onto the PET surfaces by atomic layer deposition
Authors: Edy Riyanto , Huang Xiaojiang , Guo Ying , Zhang Jing , Shi Jianjun 
Published: February 2013

Abstract
In this paper, polyethyleneterephthalate (PET) films with and without plasma pretreatment were modified by atomic layer deposition (ALD) and plasma-assisted atomic layer deposition (PA-ALD). It demonstrates that the Al2O3 films are successfully deposited onto the surface of PET films. The cracks formed on the deposited Al2O3 films in the ALD, plasma pretreated ALD, and PA-ALD were attributed to the energetic ion bombardment in plasmas. The surface wettability in terms of water contact angle shows that the deposited Al2O3 layer can enhance the wetting property of modified PET surface. Further characterizations of the Al2O3 films suggest that the elevated density of hydroxyl -OH group improve the initial growth of ALD deposition. Chemical composition of the Al2O3-coated PET film was characterized by X-ray photoelectron spectroscopy, which shows that the content of C 1s reduces with the growing of O 1s in the Al2O3-coated PET films, and the introduction of plasma in the ALD process helps the normal growth of Al2O3 on PET in PA-ALD.
Persistence of Penaeus stylirostris densovirus delays mortality caused by white spot syndrome virus infection in black tiger shrimp (Penaeus monodon)
Authors: Molthathong Sudkhate , Jitrakorn Sarocha , Joyjinda Yutthana , Boonchird Chuenchit , Witchayachamnarnkul Boonsirm , Pongtippatee Pattira , Flegel Timothy , Saksmerprome Vanvimon 
Published: February 2013

Abstract

Background
Persistent infection of Penaeus stylirostris densovirus (PstDNV) (also called IHHNV) and its non-infectious inserts in the black tiger shrimp, Penaeus monodon (P. monodon) genome are commonly found without apparent disease. Here, we introduced the method of multiplex PCR in order to differentiate shrimp with viral inserts from ones with the infectious virus. The method allowed us to study the effect of pre-infection of IHHNV, in comparison to IHHNV inserts, on WSSV resistance in P. monodon.

Results
A multiplex PCR system was developed to amplify the entire IHHNV genome, ensuring the accurate diagnosis. Field samples containing IHHNV DNA templates as low as 20 pg or equivalent 150 viral copies can be detected by this method. By challenging the two groups of diagnosed shrimp with WSSV, we found that shrimp with IHHNV infection and those with viral inserts responded to WSSV differently. Considering cumulative mortality, average time to death of shrimp in IHHNV-infected group (day 14) was significantly delayed relative to that (day 10) of IHHNV-inserted group. Real-time PCR analysis of WSSV copy number indicated the lower amount of WSSV in the IHHNV-infected group than the virus-inserted group. The ratio of IHHNV: WSSV copy number in all determined IHHNV-infected samples ranged from approximately 4 to 300-fold.

Conclusion
The multiplex PCR assay developed herein proved optimal for convenient differentiation of shrimp specimens with real IHHNV infection and those with insert types. Diagnosed shrimp were also found to exhibit different WSSV tolerance. After exposed to WSSV, the naturally pre-infected IHHNV P. monodon were less susceptible to WSSV and, consequently, survived longer than the IHHNV-inserted shrimp.
Identification and MS-assisted interpretation of genetically influenced NMR signals in human plasma
Authors: Raffler Johannes , Römisch-Margl Werner , Petersen Ann-Kristin , Pagel Philipp , Blöchl Florian , Hengstenberg Christian , Illig Thomas , Meisinger Christa , Stark Klaus , Wichmann H-Erich , Adamski Jerzy , Gieger Christian , Kastenmüller Gabi , Suhre Karsten 
Published: February 2013

AbstractNuclear magnetic resonance spectroscopy (NMR) provides robust readouts of many metabolic parameters in one experiment. However, identification of clinically relevant markers in 1H NMR spectra is a major challenge. Association of NMR-derived quantities with genetic variants can uncover biologically relevant metabolic traits. Using NMR data of plasma samples from 1,757 individuals from the KORA study together with 655,658 genetic variants, we show that ratios between NMR intensities at two chemical shift positions can provide informative and robust biomarkers. We report seven loci of genetic association with NMR-derived traits (APOA1, CETP, CPS1, GCKR, FADS1, LIPC, PYROXD2) and characterize these traits biochemically using mass spectrometry. These ratios may now be used in clinical studies.
One-pot, Radiation-induced Graft Polymerization of Vinylsulfonic Acid onto Poly(ether ether ketone) and High Proton Conductivity of Its Membrane
Authors: Takahashi Katsuyuki , Nishide Hiroyuki 
Published: February 2013

Abstract
A poly(vinylsulfonic acid) (PVSA)-grafted poly(ether ether ketone) (PEEK) was simply prepared by one-pot, γ-ray radiation-induced graft polymerization of the vinylsulfonic acid (VSA) solution dissolving PEEK. The VSA-highly-grafted PEEK membrane possessed high ion exchange capacity (e.g., 7.2 mequiv g−1) and showed proton conductivity in the order of 10−1 and 10−3–10−6 S cm−1 under hydrated and nonhumidified conditions, respectively.
Controlled Encapsulation of Photoresponsive Macromolecules in Porous Coordination Polymer
Authors: Uemura Takashi , Washino Gosuke , Yanai Nobuhiro , Kitagawa Susumu 
Published: February 2013

Abstract
A photoresponsive controlled adsorption system based on a porous coordination polymer (PCP) was fabricated, using azobenzene tethered with poly(ethylene glycol) (PEG-AB) as macromolecular guests. Specific adsorption behavior of trans-PEG-AB into the nanochannels of a PCP was observed in an EtOH medium. When this composite was irradiated with UV light in EtOH, isomerization of PEG-AB from the trans to the cis form resulted in release of PEG-AB because of the large changes in the molecular shape and solubility of PEG-AB. Subsequent visible light irradiation induced photoisomerization of PEG-AB, which led to readsorption of PEG-AB into the nanochannels.
Synthesis, Characterization, and Optical Properties of Zn1−xCoxO Nanostructures
Authors: Zhu Lu-Ping , Huang Hua , Wang Ling-Ling , Bing Nai-Ci , Liao Gui-Hong , Wang Li-Jun 
Published: February 2013

Abstract
Zn1−xCoxO nanostructures (x = 0, 0.01, 0.02, and 0.04) were synthesized by a solvothermal process. The samples were characterized by XRD, SEM, TEM, EDS, and UV–vis spectroscopy. The structure and morphology analyses showed that Co doping can slightly promote ZnO crystallinity and influence the nanostructure morphology but cannot change the crystal structures of ZnO samples. The optical measurements showed that Co doping can enhance the visible light absorption abilities of the ZnO samples and that the band-gap energies of the Zn1−xCoxO nanostructures can be effectively tuned from 3.25 to 2.85 eV.
Quantitative structural characterization of the lignins from the stem and pith of bamboo (Phyllostachys pubescens)
Authors: Wen Jia-Long , Sun Shao-Long , Xue Bai-Liang , Sun Run-Cang 
Published: February 2013

Abstract
Milled wood lignins (MWL) were isolated from the stem (MWLS) and pith (MWLP) of bamboo (Phyllostachys pubescens). The nonacetylated and acetylated bamboo MWLs were investigated by Fourier transform infrared, quantitative 13C-nuclear magnetic resonance (NMR), 2D heteronuclear single quantum coherence (HSQC) NMR, and 31P-NMR spectroscopy. The MWL consists of p-hydroxyphenyl (1–2%), guaiacyl (21–31%), and syringyl (67–78%) units associated with p-coumarates and ferulates. A modified quantitative 13C-NMR and 2D-HSQC analysis has demonstrated that the predominant intermonomeric linkages are of the type β-O-4 (45–49 per 100 C9 units, i.e., per C900) along with small amounts of other structural units such as resinols (3.6–7.4 per C900), tetrahydrofuran (2.0–2.3 per C900), phenylcoumaran (2.8–4.5 per C900), spirodienones (1.3–2.3 per C900), and α,β-diaryl ethers (2.8–2.9 per C900). MWLP contained more p-coumarates than MWLS. The various degrees of γ-acylation (17–27%) were positively associated with S/G ratios in the lignins; however, γ-acylation was inversely correlated to the ratio between β-β and β-O-4 side chains in these lignin fractions. Moreover, a flavonoid compound (tricin) was also detected in the MWLS but not in MWLP. The two MWLs are very similar in terms of molecular weights and the contents of OHphen and OHaliph.
Methylation of the nuclear poly(A)-binding protein by type I protein arginine methyltransferases – how and why
Authors: Wahle Elmar , Moritz Bodo 
Published: February 2013

Abstract
Asymmetric dimethylation of arginine side chains in proteins is a frequent posttranslational modification, catalyzed by type I protein arginine methyltransferases (PRMTs). This article summarizes what is known about this modification in the nuclear poly(A)-binding protein (PABPN1). PABPN1 contains 13 dimethylated arginine residues in its C-terminal domain. Three enzymes, PRMT1, 3, and 6, can methylate PABPN1. Although 26 methyl groups are transferred to one PABPN1 molecule, the PRMTs do so in a distributive reaction, i.e., only a single methyl group is transferred per binding event. As PRMTs form dimers, with the active sites accessible from a small central cavity, backbone conformation around the methyl-accepting arginine is an important determinant of substrate specificity. Neither the association of PABPN1 with poly(A) nor its role in poly(A) tail synthesis is affected by arginine methylation. At least at low protein concentration, methylation does not affect the protein’s tendency to oligomerize. The dimethylarginine residues of PABPN1 are located in the binding site for its nuclear import receptor, transportin. Arginine methylation weakens this interaction about 10-fold. Very recent evidence suggests that arginine methylation as a way of fine-tuning the interactions between transportin and its cargo may be a general mechanism.
Functional gold nanoparticles for sensing applications
Authors: Zhang Guomei 
Published: February 2013

AbstractNanoparticle-based technologies have played important roles in providing opportunities for the development of a new generation of sensing tools. Because of their unique optical, chemical, electrical, and catalytic properties, gold nanoparticles (AuNPs) have been extensively studied for biological and chemical detections as well as analytical applications. AuNP-based sensors are expected to change the foundations of sensing and detecting biomolecules and metal ions. The ease of surface functionalization of AuNPs allows chemists to create the desired functionalities for specific applications. In this review, we will discuss the use of surface-functionalized AuNPs for fabricating smart sensors that are capable of detecting heavy metal ions, glucose, and specific biomolecules such as protein and DNA.
Marker Density and Read Depth for Genotyping Populations Using Genotyping-by-Sequencing
Authors: Beissinger Timothy M , Hirsch Candice N , Sekhon Rajandeep S , Foerster Jillian M , Johnson James M , Muttoni German , Vaillancourt Brieanne , Buell C Robin , Kaeppler Shawn M , de Leon Natalia 
Published: February 2013

Abstract
Genotyping-by-sequencing (GBS) approaches provide low-cost, high-density genotype information. However, GBS has unique technical considerations, including a substantial amount of missing data and a nonuniform distribution of sequence reads. The goal of this study was to characterize technical variation using this method and to develop methods to optimize read depth to obtain desired marker coverage. To empirically assess the distribution of fragments produced using GBS, ∼8.69 Gb of GBS data were generated on the Zea mays reference inbred B73, utilizing ApeKI for genome reduction and single-end reads between 75 and 81 bp in length. We observed wide variation in sequence coverage across sites. Approximately 76% of potentially observable cut site-adjacent sequence fragments had no sequencing reads whereas a portion had substantially greater read depth than expected, up to 2369 times the expected mean. The methods described in this article facilitate determination of sequencing depth in the context of empirically defined read depth to achieve desired marker density for genetic mapping studies.
Genetic Networks Inducing Invasive Growth in Saccharomyces cerevisiae Identified Through Systematic Genome-Wide Overexpression
Authors: Shively Christian A , Eckwahl Matthew J , Dobry Craig J , Mellacheruvu Dattatreya , Nesvizhskii Alexey , Kumar Anuj 
Published: February 2013

Abstract
The budding yeast Saccharomyces cerevisiae can respond to nutritional and environmental stress by implementing a morphogenetic program wherein cells elongate and interconnect, forming pseudohyphal filaments. This growth transition has been studied extensively as a model signaling system with similarity to processes of hyphal development that are linked with virulence in related fungal pathogens. Classic studies have identified core pseudohyphal growth signaling modules in yeast; however, the scope of regulatory networks that control yeast filamentation is broad and incompletely defined. Here, we address the genetic basis of yeast pseudohyphal growth by implementing a systematic analysis of 4909 genes for overexpression phenotypes in a filamentous strain of S. cerevisiae. Our results identify 551 genes conferring exaggerated invasive growth upon overexpression under normal vegetative growth conditions. This cohort includes 79 genes lacking previous phenotypic characterization. Pathway enrichment analysis of the gene set identifies networks mediating mitogen-activated protein kinase (MAPK) signaling and cell cycle progression. In particular, overexpression screening suggests that nuclear export of the osmoresponsive MAPK Hog1p may enhance pseudohyphal growth. The function of nuclear Hog1p is unclear from previous studies, but our analysis using a nuclear-depleted form of Hog1p is consistent with a role for nuclear Hog1p in repressing pseudohyphal growth. Through epistasis and deletion studies, we also identified genetic relationships with the G2 cyclin Clb2p and phenotypes in filamentation induced by S-phase arrest. In sum, this work presents a unique and informative resource toward understanding the breadth of genes and pathways that collectively constitute the molecular basis of filamentation.
Sex-Specific Pattern Formation During Early Drosophila Development
Authors:   Manu, Ludwig Michael Z , Kreitman Martin 
Published: February 2013

Abstract
The deleterious effects of different X-chromosome dosage in males and females are buffered by a process called dosage compensation, which in Drosophila is achieved through a doubling of X-linked transcription in males. The male-specific lethal complex mediates this process, but is known to act only after gastrulation. Recent work has shown that the transcription of X-linked genes is also upregulated in males prior to gastrulation; whether it results in functional dosage compensation is not known. Absent or partial early dosage compensation raises the possibility of sex-biased expression of key developmental genes, such as the segmentation genes controlling anteroposterior patterning. We assess the functional output of early dosage compensation by measuring the expression of even-skipped (eve) with high spatiotemporal resolution in male and female embryos. We show that eve has a sexually dimorphic pattern, suggesting an interaction with either X-chromosome dose or the sex determination system. By manipulating the gene copy number of an X-linked transcription factor, giant (gt), we traced sex-biased eve patterning to gt dose, indicating that early dosage compensation is functionally incomplete. Despite sex-biased eve expression, the gene networks downstream of eve are able to produce sex-independent segmentation, a point that we establish by measuring the proportions of segments in elongated germ-band embryos. Finally, we use a whole-locus eve transgene with modified cis regulation to demonstrate that segment proportions have a sex-dependent sensitivity to subtle changes in Eve expression. The sex independence of downstream segmentation despite this sensitivity to Eve expression implies that additional autosomal gene- or pathway-specific mechanisms are required to ameliorate the effects of partial early dosage compensation.
The Draft Genome and Transcriptome of Panagrellus redivivus Are Shaped by the Harsh Demands of a Free-Living Lifestyle
Authors: Srinivasan Jagan , Dillman Adler R , Macchietto Marissa G , Heikkinen Liisa , Lakso Merja , Fracchia Kelley M , Antoshechkin Igor , Mortazavi Ali , Wong Garry , Sternberg Paul W 
Published: February 2013

Abstract
Nematodes compose an abundant and diverse invertebrate phylum with members inhabiting nearly every ecological niche. Panagrellus redivivus (the “microworm”) is a free-living nematode frequently used to understand the evolution of developmental and behavioral processes given its phylogenetic distance to Caenorhabditis elegans. Here we report the de novo sequencing of the genome, transcriptome, and small RNAs of P. redivivus. Using a combination of automated gene finders and RNA-seq data, we predict 24,249 genes and 32,676 transcripts. Small RNA analysis revealed 248 microRNA (miRNA) hairpins, of which 63 had orthologs in other species. Fourteen miRNA clusters containing 42 miRNA precursors were found. The RNA interference, dauer development, and programmed cell death pathways are largely conserved. Analysis of protein family domain abundance revealed that P. redivivus has experienced a striking expansion of BTB domain-containing proteins and an unprecedented expansion of the cullin scaffold family of proteins involved in multi-subunit ubiquitin ligases, suggesting proteolytic plasticity and/or tighter regulation of protein turnover. The eukaryotic release factor protein family has also been dramatically expanded and suggests an ongoing evolutionary arms race with viruses and transposons. The P. redivivus genome provides a resource to advance our understanding of nematode evolution and biology and to further elucidate the genomic architecture leading to free-living lineages, taking advantage of the many fascinating features of this worm revealed by comparative studies.
Thrombophilia and Arteriovenous Fistula Survival in ESRD
Authors: Salmela Birgitta , Hartman Jari , Peltonen Seija , Albäck Anders , Lassila Riitta 
Published: February 2013

Summary

Background and objectives
The role of thrombophilia in failing arteriovenous fistula (AVF) among patients with ESRD undergoing hemodialysis is not established. This study aimed to assess whether AVF primary patency is associated with thrombophilia and coagulation abnormalities.

Design, setting, participants, & measurements
This observational study screened 219 patients between 2002 and 2004 for thrombophilia before AVF surgery. Thrombophilia included factor V Leiden and prothrombin G20210A mutations, protein C and antithrombin activities, and protein S. Coagulation abnormalities included high factor VIII:C, homocysteine, fibrinogen, and D-dimer levels; presence of antiphospholipid antibodies; and short thrombin time. We reviewed patient charts for comorbid conditions, AVF maturation and interventions, kidney transplantation, and patient survival (mean follow-up duration, 3.6 [range, 2.3–5.8] years). Primary patency from the AVF placement and functional primary patency from the first AVF cannulation were analyzed with Kaplan-Meier and Cox proportional hazards models.

Results
Thrombophilia was present in 9% of the patients, and coagulation abnormalities occurred in 77%. One-year primary patency was 68%; 46% of the AVF failures occurred before the initiation of hemodialysis. Female sex (hazard ratio [HR], 2.6; 95% confidence interval [CI], 1.7–4.1) and thrombophilia (HR, 2.2; 95% CI, 1.2–4.2) were independent risk factors for loss of primary patency. Thrombophilia mutations or low antithrombin level (HR, 3.8), female sex (HR, 2.5), and diabetes (HR, 1.9) were associated with shortened functional primary patency of AVF.

Conclusions
Against the background of frequent coagulation abnormalities, thrombophilia and female sex predispose patients with ESRD to access failure, mostly due to thrombosis or stenosis.
Metabolic Syndrome, ESRD, and Death in CKD
Authors: Navaneethan Sankar D. , Schold Jesse D. , Kirwan John P. , Arrigain Susana , Jolly Stacey E. , Poggio Emilio D. , Beddhu Srinivasan , Nally Joseph V. 
Published: February 2013

Summary

Background and objectives
Previous studies reported an association between metabolic syndrome , incident CKD, and proteinuria. This study examined the associations between metabolic syndrome and its components with ESRD and death among those patients with stages 3 and 4 CKD (estimated GFR=15–59 ml/min per 1.73 m2).

Design, setting, participants, & measurements
Patients with stages 3 and 4 CKD (n=25,868) who had data relating to metabolic syndrome and were followed in our health care system were identified using an electronic medical record-based registry. Cox proportional hazards models and competing risk analyses were used to study the associations between metabolic syndrome, its components (elevated BP, low HDL cholesterol, elevated serum triglycerides, impaired glucose metabolism, and obesity), and all-cause mortality and ESRD while adjusting for demographics, comorbid conditions, use of relevant medications, and renal function.

Results
Sixty percent of the study population (n=15,605) had metabolic syndrome. In the multivariate-adjusted analysis, presence of metabolic syndrome was associated with an increased risk for ESRD (hazard ratio=1.33, 95% confidence interval=1.08, 1.64) but not death (hazard ratio=1.04, 95% confidence interval=0.97, 1.12) during a mean follow-up of 2.3 years. Among the individual components of metabolic syndrome, impaired glucose metabolism, elevated triglycerides, and hypertension were associated with increased risk for ESRD, whereas low HDL cholesterol and impaired glucose metabolism were associated with higher risk of death.

Conclusions
Presence of metabolic syndrome is associated with ESRD but not death in patients with stages 3 and 4 CKD.
Prenatally diagnosed fetal omphalocele at 11 week gestation — a case report
Authors: Protrka Zoran , Dimitrijevic Aleksandra , Kastratovic Tatjana , Djuric Janko , Arsenijevic Petar , Novakovic Tanja , Milosavljevic Milos 
Published: February 2013

Abstract
Omphalocele is the most common congenital defect of the abdominal wall and in a large percentage of cases it is associated with chromosomal anomalies. In this case report during the regular ultrasound examination at 11 weeks of gestation, omphalocela, whose scope was 90% of fetal abdomen, was diagnosed. Karyotype analysis showed the presence of chromosomal aberrations 47 XX + 18 (Edwards syndrome). After the presentation of the severity of congenital anomalies and characteristic of the Edwards syndrome patient decided to terminate the pregnancy.
Colonic metastasis of a Renal Cell Carcinoma: Case report and brief review of the literature
Authors: Tsamis Dimitrios , Larentzakis Andreas , Skiada Dimitra , Panousopoulos Sotirios-Georgios , Toutouzas Konstantinos , Theodorou Dimitrios , Katsaragakis Stylianos 
Published: February 2013

Abstract