bluuebunny/crossref_metadata_2025_split huggingface dataset:
The circadian schedule for childhood acute lymphoblastic leukemia maintenance therapy does not influence event‐free survival in the NOPHO ALL92 protocol
Authors: Clemmensen Kim K.B. , Christensen Regitse H. , Shabaneh Diana N. , Harila‐Saari Arja , Heyman Mats , Jonsson Olafur G. , Wesenberg Finn , Rosthøj Susanne , Schmiegelow Kjeld ,   On behalf of the Nordic Society of Pediatric Hematology, Oncology (NOPHO)
Published: November 2013

BackgroundThe event‐free survival of childhood acute lymphoblastic leukemia (ALL) has been reported to be superior when oral methotrexate (MTX) and 6‐mercaptopurine (6MP) maintenance therapy (MT) is administered in the evening compared to the morning.ProcedureIn the ALL92 MT study we prospectively registered the intake of MTX/6MP. The registration was done when blood samples for erythrocyte MTX/6MP metabolite measurements were collected, and referred to the time of intake in the period since last registration. Nine thousand one hundred ninety‐five registrations in total. The administration of MTX/6MP was scored as morning, midday, or evening.ResultsOf 532 patients, 296 took their medication consistently in the evening, 129 in the evening 50.0–99.9% of the time, and 101 in the evening <50% of the time, six did not have any registrations. The circadian schedule did not differ significantly by age, sex, MTX/6MP doses, and average absolute neutrophil counts. The circadian schedule groups did differ on risk groups (P = 0.003) with fewer HR patients in the 50–99.9% group, and there was a negative correlation between percentage of time on evening schedule and average WBC (Spearman's rho −0.15;P = 0.0004). Average WBC was not associated with relapse on ALL92. In a Cox multivariate model the circadian schedule of MTX/6MP was not of prognostic significance for the risk of relapse, and the 10‐year cumulative relapse risk was below 20% in all groups.ConclusionAn evening schedule may still be recommended based on the previous publications, but in this study morning administration of MTX and 6MP does not seem to impact EFS. Pediatr Blood Cancer 2014;61:653–658. © 2013 Wiley Periodicals, Inc.
ApoA‐I mutations, L202P and K131del, in HDL from heterozygotes with low HDL‐C
Authors: Ljunggren Stefan , Levels Johannes H. M. , Turkina Maria V. , Sundberg Sofie , Bochem Andrea E. , Hovingh Kees , Holleboom Adriaan G. , Lindahl Mats , Kuivenhoven Jan Albert , Karlsson Helen 
Published: November 2013

PurposeMutations in apolipoprotein A‐I (apoA‐I) may affect plasma high‐density lipoprotein (HDL) cholesterol levels and the risk for cardiovascular disease but little is known about the presence and effects of circulating apoA‐I variants. This study investigates whether the apoA‐I mutations, apoA‐IL202P and apoA‐IK131del, are present on plasma HDL particles derived from heterozygote carriers and whether this is associated to changes in HDL protein composition.Experimental designPlasma HDL of heterozygotes for either apoA‐IL202P or apoA‐IK131del and family controls was isolated using ultracentrifugation. HDL proteins were separated by 2DE and analyzed by MS.ResultsApoA‐I peptides containing apoA‐IL202P or apoA‐IK131del were identified in HDL from heterozygotes. The apoA‐IL202P mutant peptide was less abundant than wild‐type peptide while the apoA‐IK131del mutant peptide was more abundant than wild‐type peptide in the heterozygotes. Two‐dimensional gel electrophoresis analyses indicated that, compared to controls, HDL in apoA‐IL202P carriers contained less apoE and more zinc‐α‐2‐glycoprotein while HDL from the apoA‐IK131del heterozygotes contained more alpha‐1‐antitrypsin and transthyretin.Conclusions and clinical relevanceBoth apoA‐IL202P and apoA‐IK131del were identified in HDL. In heterozygotes, these mutations have markedly differential effects on the concentration of wild‐type apoA‐I in the circulation, as well as the HDL proteome, both of which might affect the clinical phenotype encountered in the heterozygous carriers.
Enhanced expression of endoinulinase from Aspergillus niger by codon optimization in Pichia pastoris and its application in inulooligosaccharide production
Authors: He Miao , Wu Dan , Wu Jing , Chen Jian 
Published: November 2013

Abstract
In the present study, the endoinulinase gene (EnInu) from Aspergillus niger CICIM F0620 was optimized according to the codon usage of Pichia pastoris and both the native and the optimized gene were expressed in P. pastoris. Use of the optimized gene resulted in the secretion of recombinant endoinulinase activity that reached 1,349 U ml−1, 4.18 times that observed using the native gene. This is the highest endoinulinase activity reported to date. The recombinant enzyme was optimally active at pH 6.0 and 60 °C. Moreover, inulooligosaccharides production from inulin was studied using the recombinant enzyme produced from the optimized gene. After 8 h under optimal conditions, which included 400 g l−1 inulin, an enzyme concentration of 40 U g−1 substrate, 50 °C and pH 6.0, the inulooligosaccharide yield was 91 %. The high substrate concentration and short reaction time described here should reduce production costs distinctly, compared with the conditions used in previous studies. Thus, this study may provide the basis for the industrial use of this recombinant endoinulinase for the production of inulooligosaccharides.
Genomics-enabled discovery of phosphonate natural products and their biosynthetic pathways
Authors: Ju Kou-San , Doroghazi James R , Metcalf William W 
Published: November 2013

Abstract
Phosphonate natural products have proven to be a rich source of useful pharmaceutical, agricultural, and biotechnology products, whereas study of their biosynthetic pathways has revealed numerous intriguing enzymes that catalyze unprecedented biochemistry. Here we review the history of phosphonate natural product discovery, highlighting technological advances that have played a key role in the recent advances in their discovery. Central to these developments has been the application of genomics, which allowed discovery and development of a global phosphonate metabolic framework to guide research efforts. This framework suggests that the future of phosphonate natural products remains bright, with many new compounds and pathways yet to be discovered.
Stripe rust resistance and genes in Chinese wheat cultivars and breeding lines
Authors: Zeng Qing-Dong , Han De-Jun , Wang Qi-Lin , Yuan Feng-Ping , Wu Jian-Hui , Zhang Li , Wang Xiao-Jie , Huang Li-Li , Chen Xian-Ming , Kang Zhen-Sheng 
Published: November 2013

AbstractStripe rust, caused by Puccinia striiformis f. sp. tritici (Pst), is one of the most important diseases on wheat in China. To assess resistance in wheat cultivars and breeding lines in China, 330 leading cultivars and 164 advanced breeding lines were evaluated with stripe rust. In the greenhouse tests, seedlings of the entries were inoculated separately with several Pst pathotypes. In the field tests, the entries were evaluated for stripe rust resistance in Yangling, Shaanxi Province artificially inoculated and in Tianshui, Gansu Province under natural infection of Pst. The oversummering/wintering and spring epidemic zones of resistance genes were postulated using molecular markers for Yr5, Yr9, Yr10, Yr15, Yr17, Yr18, and Yr26, in combination with resistance spectra. Out of the 494 wheat entries, 16 (3.24 %) entries had all-stage resistance (ASR) in all race tests, 99 (20.04 %) had adult-plant resistance (APR), 28 (5.67 %) were considered to have slow-rusting (SR), and 351 (71.05 %) were susceptible to one or more races in both seedling and adult-plant stages. Advanced breeding lines had a higher percentage (37.2 %) of resistant entries (The sum of ASR, APR and SR) than leading cultivars (24.85 %). Among the epidemic regions, southern Gansu had a higher percentage of resistant entries than any other regions. Based on stripe rust reactions and molecular markers, two cultivars were found to possibly have Yr5 while no entries have Yr10 or Yr15. Resistance genes Yr9, Yr17, Yr18, and Yr26 were found in 134 (29.4 %), 45 (9.1 %), 10 (2 %), and 15 (3 %) entries, respectively.
Large‐scale features affect spatial variation in seed dispersal by birds in juniper woodlands
Authors: Tellería José L. , Carrascal Luis M. , Santos Tomás 
Published: November 2013

AbstractFruit–frugivore interactions have received great attention from evolutionary, ecological and applied perspectives. However, despite the fact that large‐scale approaches may offer new insights on fruit–frugivore interactions, little work has been devoted to exploring the factors shaping large‐scale variation of seed dispersal. This paper studies the spatial variation in seeds regurgitated within pellets by wintering thrushes (genusTurdus) in a set of 26 Spanish juniper (Juniperus thurifera) woodlands scattered along a latitudinal gradient during two winters of contrasting cone and bird abundance. It explicitly explores whether pellet rain variation among woodlands was related to changes in vegetation cover, temperature, day length duration and bird abundance. Top regression models in the Akaike information criterion framework explained 34 % and 70 % of variance in pellet numbers in low and high crop and bird abundance years, respectively. In both winters, the spatial variation in pellets correlated to thrush abundance and day length duration. Pellet abundance linked to cone distribution only in the year of high crop, in which many migratory, extra‐Iberian thrushes arrived to exploit the resource. Strong dependence of seed dispersion on large‐scale features affecting bird numbers (e.g. the arrival of extra‐Iberian migratory birds) and feeding behaviour (e.g. latitudinal variation in day length duration) suggests a primary role for variables acting at large scale on this mutualistic interaction.
Differential Expressions of G0/G1 Switch Gene 2 and Comparative Gene Identification‐58 are Associated with Fat Content in Bovine Muscle
Authors: Ahn Jinsoo , Li Xiang , Choi Young Min , Shin Sangsu , Oh Shin‐Ae , Suh Yeunsu , Nguyen Trang Hoa , Baik Myunggi , Hwang Seongsoo , Lee Kichoon 
Published: November 2013

AbstractRegulation of lipolysis in muscle is a potential mechanism affecting marbling in beef carcasses and fat accumulation in muscles of humans, which is a known risk factor for type 2 diabetes. Adipose triglyceride lipase‐mediated lipolysis is inhibited by G0/G1 switch gene 2 (G0S2) and co‐activated by comparative gene identification‐58 (CGI‐58). In this study, bovine G0S2 and CGI‐58 were sequenced, and expressions of these genes were compared among various tissues and in muscles between bulls and steers with different degrees of marbling. The protein coding sequences of bovine G0S2 and CGI‐58 revealed breed‐specific SNPs, causing two amino acid variations for each protein. Bovine CGI‐58 mRNA showed two isoforms from alternative splicing. The G0S2 gene was preferentially expressed in fat and, to a lesser degree, in the liver; whereas, CGI‐58 was highly expressed in the muscle and fat (P < 0.05), suggesting their association with lipid metabolism in those tissues. The longissimus dorsi muscle (LM) of steers showed higher FABP4, G0S2 and CGI‐58 mRNA expression levels than the LM of bulls, implying the roles of those genes more in marbling of steers than in that of bulls. The G0S2 expression was markedly higher in the intramuscular fat (IMF) (P < 0.001); whereas, the CGI‐58 expression was significantly higher in the pure muscle portion of the LM of steers (P < 0.01), suggesting that G0S2 and CGI‐58 may regulate IMF and intramyocellular triglycerides, respectively. Taken together, our data suggest that G0S2 and CGI‐58 are associated with fat content in bovine species.
Hydrophobic, mechanical, and tribological properties of fluorine incorporated hydrogenated fullerene-like carbon films
Authors: Qiang Li , Zhang Bin , Gao Kaixiong , Gong Zhenbin , Zhang Junyan 
Published: November 2013

Abstract
Fluorine-incorporated hydrogenated fullerene-like nanostructure amorphous carbon films (F-FLC) were synthesized by employing the direct current plasma enhanced chemical vapor deposition (dc-PECVD) technique using a mixture of methane (CH4), tetra-fluoromethane (CF4), and hydrogen (H2) as the working gases. The effect of the fluorine content on the bonding structure, surface roughness, hydrophobic, mechanical, and tribological properties of the films was systematically investigated using Fourier transform infrared spectroscopy (FTIR), X-ray photoelectron spectroscopy (XPS), Raman analysis, atomic force microscope (AFM), contact angle goniometer, nano-indenter, and reciprocating ball-on-disc tester, respectively. The fluorine content in the films increased from 0 to 2.1 at.% as the CF4 gas flow ratio increased from 0 to 3 sccm, and incorporated fluorine atoms existed in the form of C-F
X
(X = 1, 2, 3) bonds in the film. The fullerene nanostructure embedded in the hydrogenated amorphous carbon films was confirmed by Raman analysis. The water contact angle was significantly increased because of fluorine doping, which indicates that the hydrophobicity of the carbon films could be adjusted to some extent by the fluorine doping. The hardness and elastic modulus of the films remained relatively high (22 GPa) as the fluorine content increased. Furthermore, the friction coefficient of the carbon films was significantly reduced and the wear resistance was enhanced by fluorine doping.
The neurobiology of autism spectrum disorders
Authors: Parellada M. , Penzol M.J. , Pina L. , Moreno C. , González-Vioque E. , Zalsman G. , Arango C. 
Published: November 2013

AbstractData is progressively and robustly accumulating regarding the biological basis of autism. Autism spectrum disorders (ASD) are currently considered a group of neurodevelopmental disorders with onset very early in life and a complex, heterogeneous, multifactorial aetiology. A comprehensive search of the last five years of the Medline database was conducted in order to summarize recent evidence on the neurobiological bases of autism. The main findings on genetic influence, neuropathology, neurostructure and brain networks are summarized. In addition, findings from peripheral samples of subjects with autism and animal models, which show immune, oxidative, mitochondrial dysregulations, are reported. Then, other biomarkers from very different systems associated with autism are reported. Finally, an attempt is made to try and integrate the available evidence, which points to a oligogenetic, multifactorial aetiology that converges in an aberrant micro-organization of the cortex, with abnormal functioning of the synapses and abnormalities in very general physiological pathways (such as inflammatory, immune and redox systems).
Up‐regulation of alpha‐smooth muscle actin in cardiomyocytes from non‐hypertrophic and non‐failing transgenic mouse hearts expressing N‐terminal truncated cardiac troponin I
Authors: Kern Stephanie , Feng Han-Zhong , Wei Hongguang , Cala Steven , Jin J.-P. 
Published: November 2013

We previously reported that a restrictive N‐terminal truncation of cardiac troponin I (cTnI‐ND) is up‐regulated in the heart in adaptation to hemodynamic stresses. Over‐expression of cTnI‐ND in the hearts of transgenic mice revealed functional benefits such as increased relaxation and myocardial compliance. In the present study, we investigated the subsequent effect on myocardial remodeling. The alpha‐smooth muscle actin (α‐SMA) isoform is normally expressed in differentiating cardiomyocytes and is a marker for myocardial hypertrophy in adult hearts. Our results show that in cTnI‐ND transgenic mice of between 2 and 3 months of age (young adults), a significant level of α‐SMA is expressed in the heart as compared with wild‐type animals. Although blood vessel density was increased in the cTnI‐ND heart, the mass of smooth muscle tissue did not correlate with the increased level of α‐SMA. Instead, immunocytochemical staining and Western blotting of protein extracts from isolated cardiomyocytes identified cardiomyocytes as the source of increased α‐SMA in cTnI‐ND hearts. We further found that while a portion of the up‐regulated α‐SMA protein was incorporated into the sarcomeric thin filaments, the majority of SMA protein was found outside of myofibrils. This distribution pattern suggests dual functions for the up‐regulated α‐SMA as both a contractile component to affect contractility and as possible effector of early remodeling in non‐hypertrophic, non‐failing cTnI‐ND hearts.
Reproductive performance after conservative surgical treatment of postpartum hemorrhage
Authors: Rasheed Salah M. , Amin Magdy M. , Abd Ellah Ahmed H. , Abo Elhassan Ahmed M. , El Zahry Mazen A. , Wahab Hala A. 
Published: November 2013

AbstractObjectiveTo evaluate the impact of bilateral internal iliac artery ligation (BIL), bilateral uterine artery ligation (BUAL), step‐wise uterine devascularization (SWUD), and B‐Lynch on infertility, ovarian reserve, and pregnancy outcome.MethodsThe study included 168 infertile or pregnant patients—recruited at outpatient clinics in Egypt—who had previously undergone uterine‐sparing surgery (BIL [group I], n = 59; SWUD [group II], n = 65); BUAL [group III], n = 2; and B‐Lynch [group IV], n = 42). One‐way analysis of variance was used to compare the prevalence of infertility, the status of ovarian reserve, and the prevalence and type of relevant maternal and/or fetal obstetric complications between the groups.ResultsGroups II and IV had the highest prevalences of infertility. The ovarian reserve was significantly lower in group II. Unexplained infertility was the predominant cause of infertility in group I, anovulation and premature ovarian failure in group II, and endometriosis and intrauterine adhesions in group IV. The frequency of obstetric complications, particularly placenta previa and preterm labor, was high in group IV.ConclusionOf the 4 procedures, BIL had the least deleterious effect on reproductive performance; SWUD increased the risk of premature ovarian failure, and B‐Lynch increased the risks of endometriosis, intrauterine adhesions, placenta previa, and preterm labor.
Trial-to-trial, uncertainty-based adjustment of decision boundaries in visual categorization
Authors: Qamar Ahmad T. , Cotton R. James , George Ryan G. , Beck Jeffrey M. , Prezhdo Eugenia , Laudano Allison , Tolias Andreas S. , Ma Wei Ji 
Published: November 2013

Significance
Categorization is an important part of perception and cognition. For example, an animal must successfully categorize a disturbing sound as being due to the wind or to a predator. Computationally, categorization amounts to applying decision boundaries to noisy stimulus measurements. Here, we examine how these decision boundaries change as the quality of the sensory evidence varies unpredictably from trial to trial. We show that both humans and monkeys adjust their decision boundaries from trial to trial, often near-optimally. We further show how a neural network can perform this computation near-optimally. Our results might lead to a better understanding of categorization.
Acceptability of a Computerized Brief Intervention for Alcohol among Abstinent but At-Risk Pregnant Women
Authors: Pollick Sarah A. , Beatty Jessica R. , Sokol Robert J. , Strickler Ronald C. , Chang Grace , Svikis Dace S. , Tzilos Golfo K. , Ondersma Steven J. 
Published: November 2013

Background Limitations in time and training have hindered widespread implementation of alcohol-based interventions in prenatal clinics. Also, despite the possibility of underreporting or relapse, many at-risk women report that they quit drinking after pregnancy confirmation so that interventions focusing on current drinking may seem unnecessary. The Computerized Brief Intervention for Alcohol Use in Pregnancy (C-BIAP) was designed to (a) be implemented via a handheld device in prenatal clinics, and (b) use a modified brief intervention strategy with women who screen at-risk but report no current drinking. Methods The authors administered the C-BIAP to 18 T-ACE (Tolerance, Annoyance, Cut Down, and Eye Opener)-positive pregnant African American women who provided quantitative and qualitative feedback. Results The C-BIAP received high ratings of acceptability; qualitative feedback was also positive overall and suggested good acceptance of abstinence themes. Conclusions Technology may be a feasible and acceptable method for brief intervention delivery with pregnant women who do not report current drinking.
Sequence alignment visualization in HTML5 without Java
Authors: Gille Christoph , Birgit Weyand , Gille Andreas 
Published: November 2013

Abstract
Motivation: Java has been extensively used for the visualization of biological data in the web. However, the Java runtime environment is an additional layer of software with an own set of technical problems and security risks. HTML in its new version 5 provides features that for some tasks may render Java unnecessary.
Results: Alignment-To-HTML is the first HTML-based interactive visualization for annotated multiple sequence alignments. The server side script interpreter can perform all tasks like (i) sequence retrieval, (ii) alignment computation, (iii) rendering, (iv) identification of a homologous structural models and (v) communication with BioDAS-servers. The rendered alignment can be included in web pages and is displayed in all browsers on all platforms including touch screen tablets. The functionality of the user interface is similar to legacy Java applets and includes color schemes, highlighting of conserved and variable alignment positions, row reordering by drag and drop, interlinked 3D visualization and sequence groups. Novel features are (i) support for multiple overlapping residue annotations, such as chemical modifications, single nucleotide polymorphisms and mutations, (ii) mechanisms to quickly hide residue annotations, (iii) export to MS-Word and (iv) sequence icons.
Conclusion: Alignment-To-HTML, the first interactive alignment visualization that runs in web browsers without additional software, confirms that to some extend HTML5 is already sufficient to display complex biological data. The low speed at which programs are executed in browsers is still the main obstacle. Nevertheless, we envision an increased use of HTML and JavaScript for interactive biological software.
Availability and implementation: Under GPL at: http://www.bioinformatics.org/strap/toHTML/.
Contact: christoph.gille@charite.de