bluuebunny/crossref_metadata_2025_split huggingface dataset:
Direct detection of the anti‐cancer drug 9‐phenylacridine in tissues by graphite rod laser desorption vacuum‐ultraviolet post‐ionization mass spectrometry
Authors: Liu Ping , Hu Yongjun , Chen Jiaxin , Yang Qing 
Published: June 2015

RationaleTraditionally, drug analysis in biological tissue by mass spectrometry has required complicated sample pre‐treatment, which not only wasted time, but also had adverse effects on the results. In order to assist assessment of potential drugs rapidly and accurately, a direct analytical method for drug detection in tissues is needed. The development of such a method is described in this study.MethodsAn anti‐cancer drug, 9‐phenylacridine (ACPH), injected into the kidney of mice, was directly analysed from tissues placed on the surface of a graphite rod by near‐infrared (1064 nm) laser desorption single photon ionization mass spectrometry (LD/SPI‐MS).ResultsThe LD/SPI‐MS method was successfully validated by direct analysis of ACPH in kidney sections of mice, without any complicated and time‐consuming sample pre‐treatment. The sensitivity of detection was down to about 100 fmol per spot and the wide linear dynamic range allowed quantitative detection of ACPH in complex biological samples. A drug‐time curve was acquired of ACPH in the kidney of mice after the drug had been injected into the caudal vein.ConclusionsIt was demonstrated that the anti‐tumor drug ACPH could be directly and rapidly detected by LD/SPI‐MS in biological tissues without any time‐consuming pre‐treatment procedure. This method could potentially be applied to the selective localization and analysis of small molecule drugs in tissues and to the study of the pharmacokinetics of new drugs. Copyright © 2015 John Wiley & Sons, Ltd.
Isomerization of fenbuconazole under UV‐visible irradiation – chemical and toxicological approaches
Authors: Lassalle Yannick , Nicol Edith , Genty Christophe , Bourcier Sophie , Bouchonnet Stéphane 
Published: June 2015

RationaleFenbuconazole is a fungicide commonly used for the protection of vineyards, vegetables and grain crops. Under UV‐visible irradiation, it undergoes isomerization through various cyclization processes. Isomeric structures were elucidated by liquid chromatography/high‐resolution multiple‐stage mass spectrometry (LC/HR‐MSn) coupling. The potential toxicities of these isomers were estimated by in silico tests.MethodsAqueous solutions of fenbuconazole and grapes treated with this fungicide were irradiated in a self‐made reactor equipped with a mercury vapor lamp. Analyses were carried out using high‐performance liquid chromatography (HPLC) coupled with Fourier transform ion cyclotron resonance mass spectrometry (FT‐ICRMS). High‐resolution m/z measurements, multiple‐stage mass spectrometry and isotopic labeling experiments allowed structural elucidation of the isomers of fenbuconazole. In silico toxicity estimations were carried out using the T.E.S.T. program.ResultsSeven isomers of fenbuconazole were detected after irradiation of the fungicide in aqueous solution; the major ones were also detected in the flesh of treated grapes irradiated under laboratory conditions. Elucidation of their chemical structures owing to high resolution measurements and multi‐stage collision induced dissociation experiments allowed confirmation of photo‐transformation pathways mainly dominated by cyclization processes. Photo‐induced isomers exhibited higher potential toxicities than fenbuconazole for Daphnia magna and fathead minnow species.ConclusionsUV‐visible irradiation of fenbuconazole in aqueous solution and on grapes leads to the formation of isomers, all of which being potentially much more toxic than the parent fungicide. Copyright © 2015 John Wiley & Sons, Ltd.
A high calorie diet causes memory loss, metabolic syndrome and oxidative stress into hippocampus and temporal cortex of rats
Authors: Treviño Samuel , Aguilar‐Alonso Patrícia , Flores Hernandez Jose Angel , Brambila Eduardo , Guevara Jorge , Flores Gonzalo , Lopez‐Lopez Gustavo , Muñoz‐Arenas Guadalupe , Morales‐Medina Julio Cesar , Toxqui Veronica , Venegas Berenice , Diaz Alfonso 
Published: June 2015

ABSTRACTA high calorie intake can induce the appearance of the metabolic syndrome (MS), which is a serious public health problem because it affects glucose levels and triglycerides in the blood. Recently, it has been suggested that MS can cause complications in the brain, since chronic hyperglycemia and insulin resistance are risk factors for triggering neuronal death by inducing a state of oxidative stress and inflammatory response that affect cognitive processes. This process, however, is not clear. In this study, we evaluated the effect of the consumption of a high‐calorie diet (HCD) on both neurodegeneration and spatial memory impairment in rats. Our results demonstrated that HCD (90 day consumption) induces an alteration of the main energy metabolism markers, indicating the development of MS in rats. Moreover, an impairment of spatial memory was observed. Subsequently, the brains of these animals showed activation of an inflammatory response (increase in reactive astrocytes and interleukin1‐β as well as tumor necrosis factor‐α) and oxidative stress (reactive oxygen species and lipid peroxidation), causing a reduction in the number of neurons in the temporal cortex and hippocampus. Altogether, these results suggest that a HCD promotes the development of MS and contributes to the development of a neurodegenerative process and cognitive failure. In this regard, it is important to understand the relationship between MS and neuronal damage in order to prevent the onset of neurodegenerative disorders. Synapse 69:421–433, 2015. © 2015 Wiley Periodicals, Inc.
Mid-term results of a physiotherapist-led Ponseti service for the management of non-idiopathic and idiopathic clubfoot
Authors: Dunkley Mia , Gelfer Yael , Jackson Debbie , Parnell Evette , Armstong Jennifer , Rafter Cristina , Eastwood Deborah M. 
Published: June 2015

Background The Ponseti method is the preferred treatment for idiopathic clubfoot. Although popularised by orthopaedic surgeons it has expanded to physiotherapists and other health practitioners. This study reviews the results of a physiotherapist-led Ponseti service for idiopathic and non-idiopathic clubfeet and compares these results with those reported by other groups. Method A prospective cohort of clubfeet (2005–2012) with a minimum 2-year follow-up after correction was reviewed. Physiotherapists treated 91 children—41 patients (69 feet) had non-idiopathic deformities and 50 children (77 feet) were idiopathic. Objective outcomes were evaluated and compared to results from other groups managing similar patient cohorts. Results The mean follow-up was 4.6 years (range 2–8.3 years) for both groups. The non-idiopathic group required a median of 7 casts to correct the clubfoot deformity with an 83 % tenotomy rate compared to a median of 5 casts for the idiopathic group with a 63 % tenotomy rate. Initial correction was achieved in 96 % of non-idiopathic feet and in 100 % of idiopathic feet. Recurrence requiring additional treatment was higher in the non-idiopathic group with 40 % of patients (36 % of feet) sustaining a relapse as opposed to 8 % (6 % feet) in the idiopathic group. Surgery was required in 26 % of relapsed non-idiopathic feet and 6 % of idiopathic. Conclusions Although Ponseti treatment was not as successful in non-idiopathic feet as in idiopathic feet, deformity correction was achieved and maintained in the mid-term for the majority of feet. These results compare favourably to other specialist orthopaedic-based services for Ponseti management of non-idiopathic clubfeet. Level of evidence Prognostic Level III.
A multi‐center, randomized, open‐label, parallel group study of a natural micronized progesterone vaginal tablet as a luteal support agent in Japanese women undergoing assisted reproductive technology
Authors: Fujiwara Toshihiro 
Published: June 2015

AbstractPurposeTo verify sufficient progesterone supplementation during the luteal phase and to determine the efficacy and safety of a natural micronized progesterone vaginal tablet (FE 999913) in Japanese women undergoing in vitro fertilization‐embryo transfer or intracytoplasmic sperm injection.MethodsIn a multi‐center, randomized, open‐label, parallel group trial, 108 subjects were randomized to receive FE 999913 vaginally twice daily (n = 54) or three times daily (n = 54) for up to 10 weeks. Primary endpoints were the proportion of subjects with serum progesterone concentration ≥10 ng/ml on day 5 and ongoing pregnancy rate at week 5.ResultsNinety‐four subjects completed the trial and 90 subjects underwent embryo transfer. The proportion of subjects with serum progesterone concentration ≥10 ng/ml on day 5 was 98.9 % and the lower limit of 95 % CI of the difference between the current trial and MEGASET trial was −3.6 %, which was within the non‐inferiority criterion. The ongoing pregnancy rate was 22.2 %, which is similar to that in actual clinical settings in Japan. No safety concerns were observed.ConclusionsFE 999913 was useful in this trial from the aspects of sufficient supplementation of progesterone, comparable pregnancy rate with that in clinical practice in Japan, and safety.Clinical trial registrationClinicalTrials.gov identifier: NCT01710514.
Interaction Between Parental Psychosis and Early Motor Development and the Risk of Schizophrenia in a General Population Birth Cohort
Authors: Keskinen E. , Marttila A. , Marttila R. , Jones P.B. , Murray G.K. , Moilanen K. , Koivumaa-Honkanen H. , Mäki P. , Isohanni M. , Jääskeläinen E. , Miettunen J. 
Published: June 2015

AbstractBackgroundDelayed motor development in infancy and family history of psychosis are both associated with increased risk of schizophrenia, but their interaction is largely unstudied.AimTo investigate the association of the age of achieving motor milestones and parental psychosis and their interaction in respect to risk of schizophrenia.MethodsWe used data from the general population-based prospective Northern Finland Birth Cohort 1966 (n = 10,283). Developmental information of the cohort members was gathered during regular visits to Finnish child welfare clinics. Several registers were used to determine the diagnosis of schizophrenia among the cohort members and psychosis among the parents. Altogether 152 (1.5%) individuals had schizophrenia by the age of 46 years, with 23 (15.1%) of them having a parent with psychosis. Cox regression analysis was used in analyses.ResultsParental psychosis was associated (P < 0.05) with later achievement of holding the head up, grabbing an object, and walking without support. In the parental psychosis group, the risk for schizophrenia was increased if holding the head up (hazard ratio [HR]: 2.46; degrees of freedom [df] = 1; 95% confidence interval [95% CI]: 1.07–5.66) and touching the thumb with the index finger (HR: 1.84; df = 1; 95% CI: 1.11–3.06) was later. In the group without parental psychosis, a delay in the following milestones increased the risk of schizophrenia: standing without support and walking without support. Parental psychosis had an interaction with delayed touching thumb with index finger (HR: 1.87; df = 1; 95% CI: 1.08–3.25) when risk of schizophrenia was investigated.ConclusionsParental psychosis was associated with achieving motor milestones later in infancy, particularly the milestones that appear early in a child's life. Parental psychosis and touching the thumb with the index finger had a significant interaction on risk of schizophrenia. Genetic risk for psychosis may interact with delayed development to raise future risk of schizophrenia, or delayed development may be a marker of other risk processes that interact with genetic liability to cause later schizophrenia.
A National Network of Schizophrenia Expert Centres: an Innovative Tool to Bridge the Research-Practice Gap
Authors: Schürhoff F. , Fond G. , Berna F. , Bulzacka E. , Vilain J. , Capdevielle D. , Misdrahi D. , Leboyer M. , Llorca P.-M. 
Published: June 2015

AbstractSchizophrenia is probably the most severe psychiatric disorder with much suffering for the patients and huge costs for the society. Efforts to provide optimal care by general practitioners and psychiatrists are undermined by the complexity of the disorder and difficulties in applying clinical practice guidelines and new research findings to the spectrum of cases seen in day-to-day practice. An innovative model of assessment aimed at improving global care of people with schizophrenia provided by the French national network of schizophrenia expert centres is being described. Each centre has established strong links to local health services and provides support to clinicians in delivering personalized care plans. A common set of assessment tools has been adopted by the ten centres spread over the whole French territory. A web application, e-schizo©has been created to record data in a common computerized medical file. This network offers systematic, comprehensive, longitudinal, and multi-dimensional assessments of cases including a medical workup and an exhaustive neuropsychological evaluation. This strategy offers an effective way to transfer knowledge and share expertise. This network is a great opportunity to improve the global patient care and is conceived as being an infrastructure for research from observational cohort to translational research.
A graph-based method for fitting planar B-spline curves with intersections
Authors: Bo Pengbo , Luo Gongning , Wang Kuanquan 
Published: June 2015

Abstract
The problem of fitting B-spline curves to planar point clouds is studied in this paper. A novel method is proposed to deal with the most challenging case where multiple intersecting curves or curves with self-intersection are necessary for shape representation. A method based on Delauney Triangulation of data points is developed to identify connected components which is also capable of removing outliers. A skeleton representation is utilized to represent the topological structure which is further used to create a weighted graph for deciding the merging of curve segments. Different to existing approaches which utilize local shape information near intersections, our method considers shape characteristics of curve segments in a larger scope and is thus capable of giving more satisfactory results. By fitting each group of data points with a B-spline curve, we solve the problems of curve structure reconstruction from point clouds, as well as the vectorization of simple line drawing images by drawing lines reconstruction.
When donating is liberating: The role of product and consumer characteristics in the appeal of cause‐related products
Authors: Zemack‐Rugar Yael , Rabino Rebecca , Cavanaugh Lisa A. , Fitzsimons Gavan J. 
Published: June 2015

AbstractThe present work examines the effectiveness of pairing a charitable donation with a product purchase. We propose a compensatory process, in which the guilt‐laundering properties of charitable donations are more appealing the more consumption guilt is experienced. Consumption guilt is dependent on both product type (hedonic vs. utilitarian) and consumer characteristics (guilt‐sensitivity), such that adding a charitable donation to hedonic products is more impactful than adding the same donation to utilitarian products, especially for guilt‐sensitive consumers. As a result of the impact of product type and guilt‐sensitivity, several non‐intuitive findings emerge. For example, guilt‐sensitive consumers, who normally indulge in hedonic consumption the least, indulge at least as much as their less guilt‐sensitive counterparts when hedonic products are paired with a charitable donation. Moreover, guilt‐sensitive consumers are relatively insensitive to the nature of the supported cause, indulging in hedonic consumption even when it supports disliked causes. Six studies demonstrate the impact of adding charitable donations to products as well as the unique role that consumption guilt and its alleviation play in the underlying process.
Biliary stenting for unresectable cholangiocarcinoma: A population‐based study of long‐term outcomes and hospital costs in Taiwan
Authors: Yang Ling‐Chun , Shi Hon‐Yi , Huang Jian‐Wei , Lee King‐Teh 
Published: June 2015

AbstractFew studies have compared percutaneous biliary stenting (PBS) and endoscopic biliary stenting (EBS) in terms of long‐term effects on cholangiocarcinoma (CC), and few have systematically evaluated outcome associations in Taiwan. This study aimed to compare long‐term outcomes between two treatments for unresectable CC: PBS and EBS. After propensity score matching (PSM) to reduce the effect of selection bias, 1002 CC patients were included in this analysis: 501 in the PBS group and 501 in the EBS group. The Kaplan‐Meier method was used to construct the survival curve for all CC patients, and the Cox proportional hazards model was used for multivariate assessment of outcome predictors. After PSM, group comparisons revealed a significantly longer length of stay in the PBS group compared to the EBS group (25 days vs. 19 days, respectively; p < 0.001). Hospital costs were also significantly higher in the PBS group than in the EBS group (US$126,575 vs. US$89,326, respectively; p < 0.001). The median survival time was 3.7 months in all CC patients, 3.5 months in the PBS group, and 4.0 months in the EBS group. The 1‐year, 3‐year, and 5‐year survival rates were 17.6%, 6.1%, and 3.2% in all CC patients; 16.6%, 4.8%, and 3.2% in the PBS group; and 18.6%, 7.27%, and 3% in the EBS group, respectively. The most important predictor of survival is extrahepatic CC. Medical professionals and healthcare providers should carefully consider the use of EBS for initial treatment of obstructive jaundice in patients with unresectable CC.
Posterior predictive checks to quantify lack-of-fit in admixture models of latent population structure
Authors: Mimno David , Blei David M. , Engelhardt Barbara E. 
Published: June 2015

SignificanceBayesian models, including admixture models, are a powerful framework for articulating complex assumptions about large-scale genetic data; such models are widely used to explore data or to study population-level statistics of interest. However, we assume that a Bayesian model does not oversimplify the complexities in the data, to the point of invalidating our analyses. Here, we develop and study procedures for quantitatively evaluating admixture models of genetic data. Using four large genetic studies, we demonstrate that model checking should be an important part of the modern genetic data analysis pipeline. Our methods help to support inferences drawn from recovered population structure, to protect scientists from being misled by a misspecified model class, and to point scientists toward useful model extensions.
Metabolome-scale de novo pathway reconstruction using regioisomer-sensitive graph alignments
Authors: Yamanishi Yoshihiro , Tabei Yasuo , Kotera Masaaki 
Published: June 2015

Abstract
Motivation: Recent advances in mass spectrometry and related metabolomics technologies have enabled the rapid and comprehensive analysis of numerous metabolites. However, biosynthetic and biodegradation pathways are only known for a small portion of metabolites, with most metabolic pathways remaining uncharacterized.
Results: In this study, we developed a novel method for supervised de novo metabolic pathway reconstruction with an improved graph alignment-based approach in the reaction-filling framework. We proposed a novel chemical graph alignment algorithm, which we called PACHA (Pairwise Chemical Aligner), to detect the regioisomer-sensitive connectivities between the aligned substructures of two compounds. Unlike other existing graph alignment methods, PACHA can efficiently detect only one common subgraph between two compounds. Our results show that the proposed method outperforms previous descriptor-based methods or existing graph alignment-based methods in the enzymatic reaction-likeness prediction for isomer-enriched reactions. It is also useful for reaction annotation that assigns potential reaction characteristics such as EC (Enzyme Commission) numbers and PIERO (Enzymatic Reaction Ontology for Partial Information) terms to substrate–product pairs. Finally, we conducted a comprehensive enzymatic reaction-likeness prediction for all possible uncharacterized compound pairs, suggesting potential metabolic pathways for newly predicted substrate–product pairs.
Contact: maskot@bio.titech.ac.jp
A generic methodological framework for studying single cell motility in high-throughput time-lapse data
Authors: Schoenauer Sebag Alice , Plancade Sandra , Raulet-Tomkiewicz Céline , Barouki Robert , Vert Jean-Philippe , Walter Thomas 
Published: June 2015

Abstract
Motivation: Motility is a fundamental cellular attribute, which plays a major part in processes ranging from embryonic development to metastasis. Traditionally, single cell motility is often studied by live cell imaging. Yet, such studies were so far limited to low throughput. To systematically study cell motility at a large scale, we need robust methods to quantify cell trajectories in live cell imaging data.
Results: The primary contribution of this article is to present Motility study Integrated Workflow (MotIW), a generic workflow for the study of single cell motility in high-throughput time-lapse screening data. It is composed of cell tracking, cell trajectory mapping to an original feature space and hit detection according to a new statistical procedure. We show that this workflow is scalable and demonstrates its power by application to simulated data, as well as large-scale live cell imaging data. This application enables the identification of an ontology of cell motility patterns in a fully unsupervised manner.
Availability and implementation: Python code and examples are available online (http://cbio.ensmp.fr/∼aschoenauer/motiw.html)
Contact: thomas.walter@mines-paristech.fr
Supplementary information: Supplementary data are available at Bioinformatics online.
De novo meta-assembly of ultra-deep sequencing data
Authors: Mirebrahim Hamid , Close Timothy J. , Lonardi Stefano 
Published: June 2015

Abstract
We introduce a new divide and conquer approach to deal with the problem of de novo genome assembly in the presence of ultra-deep sequencing data (i.e. coverage of 1000x or higher). Our proposed meta-assembler Slicembler partitions the input data into optimal-sized ‘slices’ and uses a standard assembly tool (e.g. Velvet, SPAdes, IDBA_UD and Ray) to assemble each slice individually. Slicembler uses majority voting among the individual assemblies to identify long contigs that can be merged to the consensus assembly. To improve its efficiency, Slicembler uses a generalized suffix tree to identify these frequent contigs (or fraction thereof). Extensive experimental results on real ultra-deep sequencing data (8000x coverage) and simulated data show that Slicembler significantly improves the quality of the assembly compared with the performance of the base assembler. In fact, most of the times, Slicembler generates error-free assemblies. We also show that Slicembler is much more resistant against high sequencing error rate than the base assembler.
Availability and implementation: Slicembler can be accessed at http://slicembler.cs.ucr.edu/.
Contact: hamid.mirebrahim@email.ucr.edu