bluuebunny/crossref_metadata_2025_split huggingface dataset:
The diatom genus Tetracyclus (Fragilariaceae, Bacillariophyta) from Chile
Authors: Williams David M. 
Published: September 2014

Ehrenberg referred only once to the diatom species Biblarium chilense Ehrenb. (1854: 301, 303, nom. nud.) in the text to his Mikrogeologie (Ehrenberg, 1854). His comments are relatively uninformative; he never published an illustration: “B[iblarium] chilense ist eine dem Bibl. compressum verwandte neue Art” (Ehrenberg, 1854: 301, and noted in the table on p. 303) “B[iblarium] chilense is a new species related to Bibl. compressum” (translation modified after Ralfs in Pritchard, 1862: 806) Consequently the name Biblarium chilense is a nomen nudum. Even so, some years later De Toni, observing neither illustration nor specimen, transferred it to Tetracyclus as Tetracyclus (chilensis) chilense (Ehrenb.) De Toni (De Toni 1892: 749).
Hill-Sachs Lesions in Shoulders With Traumatic Anterior Instability
Authors: Ozaki Ritsuro , Nakagawa Shigeto , Mizuno Naoko , Mae Tatsuo , Yoneda Minoru 
Published: September 2014

Background: In patients with traumatic anterior shoulder instability, a large Hill-Sachs lesion is a risk factor for postoperative recurrence. However, there is no consensus regarding the occurrence and enlargement of Hill-Sachs lesions. Purpose: To investigate the influence of the number of dislocations and subluxations on the prevalence and size of Hill-Sachs lesions evaluated by computed tomography (CT) with 3-dimensional reconstruction. Study Design: Cohort study (diagnosis); Level of evidence, 2. Methods: The prevalence and size of Hill-Sachs lesions were evaluated preoperatively by CT in 142 shoulders (30 with primary instability and 112 with recurrent instability) before arthroscopic Bankart repair. First, the prevalence of Hill-Sachs lesions was compared with the arthroscopic findings. Then, the size of Hill-Sachs lesions confirmed by arthroscopy was remeasured using the previous CT data. In addition, the relationship of Hill-Sachs lesions with the number of dislocations and subluxations was investigated. Results: Hill-Sachs lesions were detected in 90 shoulders by initial CT evaluation and were found in 118 shoulders at arthroscopy. The Hill-Sachs lesions missed by initial CT were 15 chondral lesions and 13 osseous lesions. However, all 103 osseous Hill-Sachs lesions were detected by reviewing the CT data. In patients with primary subluxation, the prevalence of Hill-Sachs lesions was 26.7%, and the mean length, width, and depth of the lesions (calculated as a percentage of the diameter of the humeral head) were 9.0%, 5.3%, and 2.1%, respectively, while the corresponding numbers for primary dislocation were 73.3%, 27.7%, 14.8%, and 7.0%, all showing statistically significant differences. Among all 142 shoulders, the corresponding numbers were, respectively, 56.3%, 20.7%, 11.2%, and 4.8% in patients who had subluxations but never a dislocation; 83.3%, 33.4%, 19.1%, and 7.6% in patients with 1 episode of dislocation; and 87.5%, 46.8%, 22.2%, and 10.2% in patients with ≥2 episodes, all showing statistically significant differences. There were no differences in lesion measurements in relation to the number of subluxations. Conclusion: Computed tomography is a useful imaging modality for evaluating Hill-Sachs lesions except for purely cartilaginous lesions. Hill-Sachs lesions were more frequent and larger when the primary episode was dislocation than when it was subluxation. Among patients with recurrent episodes of complete dislocation, the prevalence of Hill-Sachs lesions is increased, and the lesions are larger.
The Impact of Accelerometer Use in Exercise-Associated Hypoglycemia Prevention in Type 1 Diabetes
Authors: Stenerson Matthew , Cameron Fraser , Payne Shelby R. , Payne Sydney L. , Ly Trang T. , Wilson Darrell M. , Buckingham Bruce A. 
Published: September 2014

Background: Exercise-associated hypoglycemia is a common adverse event in people with type 1 diabetes. Previous in silico testing by our group demonstrated superior exercise-associated hypoglycemia mitigation when a predictive low glucose suspend (PLGS) algorithm was augmented to incorporate activity data. The current study investigates the effectiveness of an accelerometer-augmented PLGS algorithm in an outpatient exercise protocol. Methods: Subjects with type 1 diabetes on insulin pump therapy participated in two structured soccer sessions, one utilizing the algorithm and the other using the subject’s regular basal insulin rate. Each subject wore their own insulin pump and a Dexcom G4™ Platinum continuous glucose monitor (CGM); subjects on-algorithm also wore a Zephyr BioHarness™ 3 accelerometer. The algorithm utilized a Kalman filter with a 30-minute prediction horizon. Activity and CGM readings were manually entered into a spreadsheet and at five-minute intervals, the algorithm indicated whether the basal insulin infusion should be on or suspended; any changes were then implemented by study staff. The rate of hypoglycemia during and after exercise (until the following morning) was compared between groups. Results: Eighteen subjects (mean age 13.4 ± 3.7 years) participated in two separate sessions 7-22 days apart. The difference in meter blood glucose levels between groups at each rest period did not achieve statistical significance at any time point. Hypoglycemia during the session was recorded in three on-algorithm subjects, compared to six off-algorithm subjects. In the postexercise monitoring period, hypoglycemia occurred in two subjects who were on-algorithm during the session and four subjects who were off-algorithm. Conclusions: The accelerometer-augmented algorithm failed to prevent exercise-associated hypoglycemia compared to subjects on their usual basal rates. A larger sample size may have achieved statistical significance. Further research involving an automated system, a larger sample size, and an algorithm design that favors longer periods of pump suspension is necessary.
Observation of anomalous linear photogalvanic effect and its dependence on wavelength in undoped InGaAs/AlGaAs multiple quantum well
Authors: Zhu Laipan , Liu Yu , Gao Hansong , Qin Xudong , Li Yuan , Wu Qing , Chen Yonghai 
Published: September 2014

Abstract
We observed an anomalous linear photogalvanic effect (ALPGE) in undoped InGaAs/AlGaAs multiple quantum well and studied its wavelength dependence in details. This effect is believed to originate from the optical momentum alignment effect and the inhomogeneity of light intensity. We find that the spot location with the maximum ALPGE current is wavelength independent. And the normalized ALPGE current decreasing at smaller wavelengths is attributed to the sharp decrease of the momentum and energy relaxation time. The electrical measurement of the spectra dependence of ALPGE is highly sensitive proving to be an effective method for detecting the momentum anisotropy of photoinduced carriers and band coupling.
Modification of light absorption in thin CuInS2 films by sprayed Au nanoparticles
Authors: Katerski Atanas , Kärber Erki , Acik Ilona Oja , Dolgov Leonid , Mere Arvo , Sildos Ilmo , Mikli Valdek , Krunks Malle 
Published: September 2014

Abstract
The chemical spray pyrolysis method was used to deposit CuInS2 (CIS) thin films and Au nanoparticles (NPs) in two configurations: glass/Au-NP layer covered with CuInS2 film (Au-NP/CIS) and glass/CuInS2 films covered with Au-NP layer (CIS/Au-NP). According to X-ray diffraction (XRD), the spray of 2 mM HAuCl4 aqueous solution with a volume of 2.5 to 15 ml onto a glass substrate at 340°C results in metallic Au nanoparticles with a similar mean crystallite size in the range of 30 - 38 nm. The mean crystallite sizes remain in the range of 15 - 20 nm when grown onto a CIS film. The prepared films show plasmonic light absorption with increasing intensity in the spectral range of 500- 800 nm when increasing the volume of HAuCl4 solution sprayed. When compared to bare CIS on glass, the absorptance was increased ca. 4.5 times in the case of glass/Au-NP/CIS and ca. 3 times in the case of glass/CIS/Au-NP configuration. The glass/Au-NP/CIS configuration had an advantage since Au-NP could be embedded without chemically damaging the CIS.
Structuring research methods and data with the research object model: genomics workflows as a case study
Authors: Hettne Kristina M , Dharuri Harish , Zhao Jun , Wolstencroft Katherine , Belhajjame Khalid , Soiland-Reyes Stian , Mina Eleni , Thompson Mark , Cruickshank Don , Verdes-Montenegro Lourdes , Garrido Julian , de Roure David , Corcho Oscar , Klyne Graham , van Schouwen Reinout , ‘t Hoen Peter A C , Bechhofer Sean , Goble Carole , Roos Marco 
Published: September 2014

Abstract

Background
One of the main challenges for biomedical research lies in the computer-assisted integrative study of large and increasingly complex combinations of data in order to understand molecular mechanisms. The preservation of the materials and methods of such computational experiments with clear annotations is essential for understanding an experiment, and this is increasingly recognized in the bioinformatics community. Our assumption is that offering means of digital, structured aggregation and annotation of the objects of an experiment will provide necessary meta-data for a scientist to understand and recreate the results of an experiment. To support this we explored a model for the semantic description of a workflow-centric Research Object (RO), where an RO is defined as a resource that aggregates other resources, e.g., datasets, software, spreadsheets, text, etc. We applied this model to a case study where we analysed human metabolite variation by workflows.

Results
We present the application of the workflow-centric RO model for our bioinformatics case study. Three workflows were produced following recently defined Best Practices for workflow design. By modelling the experiment as an RO, we were able to automatically query the experiment and answer questions such as “which particular data was input to a particular workflow to test a particular hypothesis?”, and “which particular conclusions were drawn from a particular workflow?”.

Conclusions
Applying a workflow-centric RO model to aggregate and annotate the resources used in a bioinformatics experiment, allowed us to retrieve the conclusions of the experiment in the context of the driving hypothesis, the executed workflows and their input data. The RO model is an extendable reference model that can be used by other systems as well.

Availability
The Research Object is available at http://www.myexperiment.org/packs/428

The Wf4Ever Research Object Model is available at http://wf4ever.github.io/ro
Antibiotic stewardship in the intensive care unit
Authors: Luyt Charles-Edouard , Bréchot Nicolas , Trouillet Jean-Louis , Chastre Jean 
Published: September 2014

AbstractThe rapid emergence and dissemination of antimicrobial-resistant microorganisms in ICUs worldwide constitute a problem of crisis dimensions. The root causes of this problem are multifactorial, but the core issues are clear. The emergence of antibiotic resistance is highly correlated with selective pressure resulting from inappropriate use of these drugs. Appropriate antibiotic stewardship in ICUs includes not only rapid identification and optimal treatment of bacterial infections in these critically ill patients, based on pharmacokinetic-pharmacodynamic characteristics, but also improving our ability to avoid administering unnecessary broad-spectrum antibiotics, shortening the duration of their administration, and reducing the numbers of patients receiving undue antibiotic therapy. Either we will be able to implement such a policy or we and our patients will face an uncontrollable surge of very difficult-to-treat pathogens.
Propensity-matched analysis of the effect of preoperative intraaortic balloon pump in coronary artery bypass grafting after recent acute myocardial infarction on postoperative outcomes
Authors: Yu Pey-Jen , Cassiere Hugh A , Dellis Sophia L , Kohn Nina , Manetta Frank , Hartman Alan R 
Published: September 2014

Abstract
Introduction
There is substantial variability in the preoperative use of intraaortic balloon pumps (IABPs) in patients undergoing coronary artery bypass grafting post myocardial infarction. The objective of this study is to determine the effect of preoperative IABPs on postsurgical outcomes in this subset of patients.

Methods
From 2007 to 2012, 877 patients underwent isolated coronary artery bypass post myocardial infarction. Four hundred and six patients were propensity-score matched based on the likelihood of receiving a preoperative balloon pump. Total blood transfusion requirements, composite in-hospital morbidity and/or mortality end point, total hours in the intensive care unit, and length of hospital stay were compared between the two groups.

Results
No significant differences in demographics, preoperative risk factors, intraoperative variables or length of hospital stay were found between patients with and without balloon pumps after propensity score matching. Compared to patients without balloon pumps, a higher percentage of patients with preoperative IABPs required transfusions. Patients with preoperative balloon pumps were more likely to have the composite end point of in-hospital morbidity (24.1% versus 12.8%, P <0.004), and increased hours in the intensive care unit (median hours: 69.0 versus 46.0, P <0.013) as compared to patients without balloon pumps.

Conclusions
The use of preoperative IABPs in patients undergoing isolated coronary artery bypass grafting after myocardial infarction is associated with increased transfusion requirements, increased in-hospital morbidity and longer postoperative intensive care unit stay as compared to patients without IABPs.
Thyroid Nodules in an 11-Year DanThyr Follow-Up Study
Authors: Krejbjerg Anne , Bjergved Lena , Pedersen Inge Bülow , Knudsen Nils , Jørgensen Torben , Perrild Hans , Ovesen Lars , Rasmussen Lone Banke , Laurberg Peter 
Published: September 2014

Context:
Limited longitudinal data are available on changes in the thyroid gland structure in a population and how this is influenced by iodine fortification (IF).

Objective:
Our objective was to clarify how IF influenced thyroid gland structure in 2 regions with different iodine intake at baseline (Copenhagen, mild iodine deficiency [ID]; Aalborg, moderate ID).

Design and Setting:
We conducted a longitudinal population-based study (DanThyr) where participants were examined before (1997) and after (2008) the Danish mandatory IF of salt (2000).

Participants:
We examined 2465 adults, and ultrasonography was performed by the same sonographers using the same equipment, after controlling performances.

Main Outcome Measure:
Change in thyroid gland structure was evaluated.

Results:
The follow-up period saw an increased prevalence of multinodularity (9.8%–13.8 %, P &lt; .001), especially in the previously moderate ID region of Aalborg (9.1%–15.4%, P &lt; .001), whereas no change in prevalence was seen for solitary nodules (5.6%–5.1%, P = .34). In individual participants, changes in thyroid structure and disappearance of thyroid nodules during the 11 years was common with an overall normalization rate of 21.2 (95% confidence interval [CI] = 17.9–24.9) per 1000 person-years. Solitary nodules had a significantly higher normalization rate than multiple nodules (normalization rate ratio 0.47 [95% CI = 0.32–0.67]). A regional difference (Aalborg vs Copenhagen) was seen between normalization rates of multiple nodules (normalization rate ratio 0.29 [95% CI = 0.12–0.64]), but not for solitary nodules (normalization rate ratio 0.81 [95% CI = 0.53–1.21]).

Conclusions:
Changes in the thyroid gland structure with both appearance and disappearance of thyroid nodules are common after an iodization program.
Synthesis of α-Aminophosphonates in the Presence of a Magnetic Recyclable Fe3O4@SiO2-2mimSO3H Nanocatalyst
Authors: Shakourian-Fard Mehdi , Rezayan Ali Hossein , Kheirjou Somayyeh , Bayat Ahmad , Hashemi Mohammad Mahmoodi 
Published: September 2014

Abstract
A highly efficient magnetic Brønsted acid catalyst was synthesized based on immobilization of 2-methylimidazole functionalized by chlorosulfonic acid on the surface of silica-coated magnetic nanoparticles (Fe3O4@SiO2-2mimSO3H). The catalyst has an excellent activity and recyclable for at least 6 reaction runs and is proven to be highly effective in the synthesis of α-aminophosphonate compounds in a green way. The facile recovery of the catalyst is carried out by applying an external magnet device. It is both “green” and efficient. The catalyst was fully characterized by techniques of TEM, SEM, FT-IR, TGA, and elemental analysis (CHNS).
Synthesis of 8-Substituted Adenine and Adenosine Libraries and the Binding to pre-miR-29a
Authors: Fukuzumi Takeo , Aikawa Haruo , Harada Yasue , Sugai Ayako , Murata Asako , Nakatani Kazuhiko 
Published: September 2014

Abstract
A small chemical library of 8-substituted adenine and adenosine derivatives was synthesized and examined for binding to pre-miR-29a. We found that one compound showed the affinity with 61 nM of Kd and a 10-fold stronger binding than the double-stranded RNA.
Plasticizer-Promoted Thermal Crosslinking of a Dynamic Covalent Polymer with Complementarily Reactive Alkoxyamine Units in the Side Chain under Bulk Conditions
Authors: Su Jing , Imato Keiichi , Sato Tomoya , Ohishi Tomoyuki , Takahara Atsushi , Otsuka Hideyuki 
Published: September 2014

Abstract
Plasticizer-promoted thermal crosslinking reactions of an alkoxyamine-appended poly(methyl methacrylate)-based dynamic covalent polymer were successfully performed under bulk conditions. The films of the dynamic covalent polymer with complementarily reactive alkoxyamine side chains and dibutyl phthalate as a plasticizer were prepared and their crosslinking behavior was observed at 100 °C.
Practical Synthesis of Poly(2-methoxyaniline-5-phosphonic acid), a Self-Doped Conducting Polyaniline Bearing Phosphonic Acid
Authors: Abe Yasushi , Amaya Toru , Hirao Toshikazu 
Published: September 2014

Abstract
A practical synthetic approach for poly(2-methoxyaniline-5-phosphonic acid) was developed. The improved method for the monomer synthesis was appropriate for scale-up in view of the yield, purification, and cost compared to the previous method. Polymerization was also performed in a gram scale.
Improving Penetration Forecasts Using Social Interactions Data
Authors: Toubia Olivier , Goldenberg Jacob , Garcia Rosanna 
Published: September 2014

We propose an approach for using individual-level data on social interactions (e.g., number of recommendations received by consumers, number of recommendations given by adopters, number of social ties) to improve the aggregate penetration forecasts made by extant diffusion models. We capture social interactions through an individual-level hazard rate in such a way that the resulting aggregate penetration process is available in closed form and nests extant diffusion models. The parameters of the model may be estimated by combining early aggregate penetration data with social interactions data collected from a sample of consumers in as few as one time period. We illustrate our approach by applying it to the mixed influence model (Bass model) and the more recent asymmetric influence model. A field study conducted in collaboration with a consumer packaged goods company and a marketing research company confirms that incorporating social interactions data using the proposed approach has the potential to result in improved aggregate penetration forecasts in managerially relevant settings. This paper was accepted by Pradeep Chintagunta, marketing.
Probabilistic Selling in Quality-Differentiated Markets
Authors: Zhang Zelin , Joseph Kissan , Subramaniam Ramanathan 
Published: September 2014

Probabilistic selling—the sale of synthetic products consisting of a lottery between two distinct goods—has been extensively analyzed in horizontal markets. In this research, we investigate probabilistic selling in quality-differentiated markets. This is an important new dimension of inquiry because of the widespread prevalence of quality-differentiated markets as well as significant differences in the preference structure across these markets. In fact, this latter consideration casts doubt as to whether probabilistic selling will even emerge in quality-differentiated markets. We find that probabilistic selling emerges in quality-differentiated markets as a way to profitably dispose excess capacity; moreover, probabilistic selling remains viable even under endogenous quality choice. In addition, in markets where sellers employ “strong” quality differentiation, the introduction of an intermediate probabilistic good actually causes closer quality levels in a product line and enhances consumer welfare. In contrast, in markets where sellers employ “weak” quality differentiation, the introduction of an intermediate probabilistic good increases quality separation and degrades consumer welfare. Overall, we view our contribution as one of characterizing the optimality, implementation, and policy implications of probabilistic selling in quality-differentiated markets. This paper was accepted by Pradeep Chintagunta, marketing.
RNA-Seq Alignment to Individualized Genomes Improves Transcript Abundance Estimates in Multiparent Populations
Authors: Munger Steven C , Raghupathy Narayanan , Choi Kwangbom , Simons Allen K , Gatti Daniel M , Hinerfeld Douglas A , Svenson Karen L , Keller Mark P , Attie Alan D , Hibbs Matthew A , Graber Joel H , Chesler Elissa J , Churchill Gary A 
Published: September 2014

Abstract
Massively parallel RNA sequencing (RNA-seq) has yielded a wealth of new insights into transcriptional regulation. A first step in the analysis of RNA-seq data is the alignment of short sequence reads to a common reference genome or transcriptome. Genetic variants that distinguish individual genomes from the reference sequence can cause reads to be misaligned, resulting in biased estimates of transcript abundance. Fine-tuning of read alignment algorithms does not correct this problem. We have developed Seqnature software to construct individualized diploid genomes and transcriptomes for multiparent populations and have implemented a complete analysis pipeline that incorporates other existing software tools. We demonstrate in simulated and real data sets that alignment to individualized transcriptomes increases read mapping accuracy, improves estimation of transcript abundance, and enables the direct estimation of allele-specific expression. Moreover, when applied to expression QTL mapping we find that our individualized alignment strategy corrects false-positive linkage signals and unmasks hidden associations. We recommend the use of individualized diploid genomes over reference sequence alignment for all applications of high-throughput sequencing technology in genetically diverse populations.
Purifying Selection, Drift, and Reversible Mutation with Arbitrarily High Mutation Rates
Authors: Charlesworth Brian , Jain Kavita 
Published: September 2014

Abstract
Some species exhibit very high levels of DNA sequence variability; there is also evidence for the existence of heritable epigenetic variants that experience state changes at a much higher rate than sequence variants. In both cases, the resulting high diversity levels within a population (hyperdiversity) mean that standard population genetics methods are not trustworthy. We analyze a population genetics model that incorporates purifying selection, reversible mutations, and genetic drift, assuming a stationary population size. We derive analytical results for both population parameters and sample statistics and discuss their implications for studies of natural genetic and epigenetic variation. In particular, we find that (1) many more intermediate-frequency variants are expected than under standard models, even with moderately strong purifying selection, and (2) rates of evolution under purifying selection may be close to, or even exceed, neutral rates. These findings are related to empirical studies of sequence and epigenetic variation.