bluuebunny/crossref_metadata_2025_split huggingface dataset:
Noninvasive fetal genome sequencing: a primer
Authors: Snyder Matthew W. , Simmons LaVone E. , Kitzman Jacob O. , Santillan Donna A. , Santillan Mark K. , Gammill Hilary S. , Shendure Jay 
Published: April 2013

ABSTRACTWe recently demonstrated whole genome sequencing of a human fetus using only parental DNA samples and plasma from the pregnant mother. This proof‐of‐concept study demonstrated how samples obtained noninvasively in the first or second trimester can be analyzed to yield a highly accurate and substantially complete genetic profile of the fetus, including both inherited and de novo variation. Here, we revisit our original study from a clinical standpoint, provide an overview of the scientific approach, and describe opportunities and challenges along the path toward clinical adoption of noninvasive fetal whole genome sequencing. © 2013 John Wiley & Sons, Ltd.
Gentamicin Pharmacokinetics and Dosing in Neonates with Hypoxic Ischemic Encephalopathy Receiving Hypothermia
Authors: Frymoyer Adam , Meng Lina , Bonifacio Sonia L. , Verotta Davide , Guglielmo B. Joseph 
Published: April 2013

Study ObjectiveTo evaluate the pharmacokinetics of gentamicin in neonates with hypoxic ischemic encephalopathy (HIE) receiving hypothermia and to identify an empiric gentamicin dosing strategy in this population that optimizes achievement of target peak and trough concentrations.DesignPopulation pharmacokinetic study using retrospective medical record data.SettingTertiary neonatal intensive care unit.PatientsA total of 29 full‐term neonates diagnosed with HIE treated with hypothermia who received gentamicin and underwent therapeutic drug monitoringMeasurement and Main ResultsPatient demographics and gentamicin concentration data were retrospectively collected over a 2‐year period. A population‐based pharmacokinetic model was developed using nonlinear mixed‐effects modeling (NONMEM). Using the developed model, Monte Carlo simulations were performed to evaluate the probability of achieving target peak (> 6 mg/L) and trough (< 2 mg/L) gentamicin concentrations for various potential dosing regimens. A one‐compartment model best described the available gentamicin concentration data. Birthweight and serum creatinine significantly influenced gentamicin clearance. For the typical study neonate (birthweight 3.3 kg, serum creatinine 0.9 mg/dl), clearance was 0.034 L/hour/kg and volume was 0.52 L/kg. At a 24‐hour dosing interval, Monte Carlo simulations predicted target gentamicin peak and trough concentrations could not be reliably achieved at any dose. At a 36‐hour dosing interval, a dose of 4–5 mg/kg is predicted to achieve target gentamicin peak and trough concentrations in more than 90% of neonates.ConclusionsGentamicin clearance is decreased in neonates with HIE treated with hypothermia compared with previous reports in nonasphyxiated normothermic full‐term neonates. A prolonged 36‐hour dosing interval will be needed to achieve target gentamicin trough concentrations in this population. Further prospective evaluation of this dosing recommendation is needed.
Block copolymers prepared by polymeric radical addition cross‐coupling reaction to different double bonds
Authors: Zhang Chengyu , Wang Qi 
Published: April 2013

ABSTRACTWe present an efficient method for synthesis of block copolymer by radical addition cross‐coupling reaction between two different polymeric radicals and different double bonds. Two different monobromo polymers (P1‐Br and P2‐Br) were reacted with Cu(0)/N,N,N′,N″,N″‐pentamethyldiethylenetriamine in the presence of ethyl dithiobenzoate or 1,1‐diphenylethylene (X) and the block copolymer (P1‐X‐P2) can be obtained with high efficiency, which cannot be prepared by normal atom transfer radical coupling of mixture of P1‐Br and P2‐Br. © 2013 Wiley Periodicals, Inc. J. Polym. Sci., Part A: Polym. Chem. 2013, 51, 2817–2823.
Thermoresponsive gels based on ABA triblock copolymers: Does the asymmetry matter?
Authors: Ward Mark A. , Georgiou Theoni K. 
Published: April 2013

ABSTRACTThe aim of this study was to investigate the effect of the asymmetry of the triblock copolymers on their thermoresponsive self‐assembly behavior. To this end, nine ABA‐type triblock copolymers with n‐butyl methacrylate and 2‐(dimethylamino)ethyl methacrylate (DMAEMA) consisting of the A and the B blocks, respectively, were synthesized. Polymers of three different DMAEMA contents (50, 60, and 70 wt %) were synthesized while varying the length ratio of the two hydrophobic A blocks. Specifically, one symmetric ABA triblock copolymer and two asymmetric ABA′ triblock copolymers with the length of the second A block to be twice or four times bigger than the length of the first A block (AB2A and AB4A triblock copolymer) were synthesized for each DMAEMA composition. Three statistical copolymers were also synthesized for comparison. The thermoresponsive behavior of the copolymers was studied and it was found that the cloud point and rheological properties of the polymers were strongly affected by the architecture (statistical vs. block) and less strongly by the DMAEMA composition and the asymmetry of the polymers. Nevertheless, interestingly the asymmetry of the ABA triblock copolymers did influence the thermoresponsive behavior with the more symmetric polymers presenting a sol–gel transition at lower temperatures. © 2013 Wiley Periodicals, Inc. J. Polym. Sci., Part A: Polym. Chem. 2013, 51, 2850–2859.
Lyapunov exponent and bifurcation characteristics in synchronous machines with an internal fault
Authors: Shariatmadar Seyed Mohammad , Nazarzadeh Jalal , Abedi Mehrdad 
Published: April 2013

AbstractIn this paper, first, turn‐to‐turn fault in a synchronous machine stator winding is investigated, and its inductances are derived with the winding function method. Then, using the nonlinear control theory, the first‐order Poincaré map of the synchronous machine is computed, and a new extended Poincaré map of the machine is established. Also, the characteristic multipliers of the synchronous machine are calculated by the Poincaré map. This new map is capable of analyzing electrical machines in the nonlinear and unbalanced cases for evaluation of stability, bifurcation, and chaos phenomena. The results show that the new map is an effective technique for modeling and analyzing any AC electrical machines. The characteristic multipliers and the Lyapunov exponents of the extended map indicate the system's condition. Chaotic phenomena are observed in some machines with internal faults. Since chaotic systems have a continuous spectrum and various kinds of frequencies in their spectrum, identification of the internal fault location is not easy with harmonic analyses such as Fourier spectrum method on the excitation current in synchronous machines. © 2013 Institute of Electrical Engineers of Japan. Published by John Wiley & Sons, Inc.
Experiment of an electric water heater with autonomous frequency regulation
Authors: Kondoh Junji 
Published: April 2013

AbstractIntegration of wind power generation into power systems has been limited because of the problem of frequency regulation during light‐load periods at night in some areas in Japan. As a solution, autonomous frequency regulation by electric water heaters (EWHs) has been proposed. A control board to control the power consumption of an EWH is fabricated. It measures both the power system frequency and thermal energy stored in a hot‐water tank, and then turns on/off a heating element according to a control algorithm. It is confirmed that the board can measure power system frequency every 1 s with a resolution of better than 0.01 Hz and that it can measure the vertical temperature distribution in the storage tank with an acceptable accuracy to calculate the future power consumption ratio, which is a parameter that decides the turn on/off of the heating element while considering end‐user comfort. Then, an EWH with autonomous frequency regulation is fabricated by embedding the board, and the EWH is operated to investigate the performance. © 2013 Institute of Electrical Engineers of Japan. Published by John Wiley & Sons, Inc.
Sediment discharge division at two tidally influenced river bifurcations
Authors: Sassi M. G. , Hoitink A. J. F. , Vermeulen B. , Hidayat H. 
Published: April 2013

Key Points
Bed‐load and suspended‐load division functions at bifurcations are different
3D effects of the suspended sediment transport at bifurcations can be limited
Sediment transport rates can be estimated from boat‐mounted ADCPs
How changes in fibril‐level organization correlate with the macrolevel behavior of articular cartilage
Authors: Nickien Mieke , Thambyah Ashvin , Broom Neil 
Published: April 2013

AbstractThe primary structural components of articular cartilage are the zonally differentiated interconnected network of collagen fibrils and proteoglycans, the latter having the potential to bind large amounts of water. Both components exist in a coupled relationship that gives rise to its remarkable mechanical properties. The response of cartilage to compression is governed both by the degree to which the hydrated proteoglycans are constrained within this fibrillar network and the ease with which the matrix fluid can be displaced. The functional properties of cartilage are therefore closely linked to the integrity of the fibrillar network. Our current understanding of this network has been derived via studies conducted at the macro, micro, and ultrastructural levels. Of particular interest to joint researchers and clinicians are issues relating to how the network structure varies both directionally and with zonal depth, how its integrity is maintained via mechanisms of fibril interconnectivity, and how it is modified by ageing, degeneration, and trauma. Physical models have been developed to explore modes of interconnectivity. Combined micromechanical and structural studies confirm the critical role that this interconnectivity must play but detailed descriptions at the molecular level remain elusive. Current computationally based models of cartilage have in some cases implemented the fibrillar component, albeit simplistically, as a separate structure. Considering how important a role fibril network interconnectivity plays in actual tissue structure and mechanical behavior, and especially how it changes with degeneration, a major challenge facing joint tissue modellers is how to incorporate such a feature in their models. WIREs Syst Biol Med 2013, 5:495–509. doi: 10.1002/wsbm.1220This article is categorized under:

Models of Systems Properties and Processes > Organ, Tissue, and Physiological Models
Adequacy of Lymph Node Retrieval for Ampullary Cancer and Its Association with Improved Staging and Survival
Authors: Partelli Stefano , Crippa Stefano , Capelli Paola , Neri Anna , Bassi Claudio , Zamboni Giuseppe , Barugola Giuliano , Falconi Massimo 
Published: April 2013

AbstractBackgroundThe aim of the present study was to determine the optimal number of lymph nodes (LN) examined to stage pN0 tumors after surgery for ampulla of Vater carcinoma (AVC).MethodsWe reviewed retrospectively 127 patients with AVC who underwent pancreaticoduodenectomy (1990–2008). Univariate and multivariate analysis was performed.ResultsFifty‐nine patients (46.5 %) were pN0, whereas 68 patients (53.5 %) were pN1. The 5‐year disease‐specific survival (DSS) was worse for pN1 patients than for pN0 patients (46 vs. 77 %; P < 0.0001). In the pN0 cohort, the optimal cut‐off number of LN analyzed was found to be 12. The 5‐year DSS for patients with ≤12 LN was 50 %, compared with 89 % in those with >12 LN (P = 0.001). By multivariate analysis, a LN count >12 was the only independent predictor associated with improved survival (HR 0.16, P = 0.003) among pN0 patients. Among pN1 patients, a LN count >12 was associated with a significantly better 5‐year DSS (59 vs. 22 %; P = 0.027). Patients with a lymph node ratio (LNR) >0.20 had a 5‐year DSS of 24 %, compared with 58 % in those with 0 < LNR ≤ 0.20 (P = 0.038).ConclusionsRemoval of more than 12 LN for examination is associated with improved survival rate after surgery for AVC in both pN0 and pN1 patients.
Small High‐Density Lipoprotein (HDL) Subclasses are Increased with Decreased Activity of HDL‐Associated Phospholipase A2 in Subjects with Prediabetes
Authors: Filippatos Theodosios D. , Rizos Evangelos C. , Tsimihodimos Vasilios , Gazi Irene F. , Tselepis Alexandros D. , Elisaf Moses S. 
Published: April 2013

AbstractAlterations in high‐density lipoprotein (HDL) subclass distribution, as well as in the activities of HDL‐associated enzymes, have been associated with increased cardiovascular disease (CVD) risk. HDL subclass distribution and the activities of HDL‐associated enzymes remain unknown in prediabetic patients, a condition also associated with increased CVD risk. The aim of the present study was to assess any differences in HDL subclass distribution (using polyacrylamide gel electrophoresis) and in activities of HDL‐associated enzymes between prediabetic (impaired fasting glucose, IFG, n = 80) and non‐prediabetic subjects (n = 105). Subjects with prediabetes had significantly increased waist circumference, blood pressure and triacylglycerol (TAG) levels compared with subjects with fasting glucose levels <100 mg/dL (all p < 0.05). The proportion of small HDL3 over HDL cholesterol (HDL‐C) was significantly increased in prediabetic subjects compared with their controls (p < 0.05). The activity of the anti‐atherogenic HDL‐associated lipoprotein‐associated phospholipase A2 (HDL‐LpPLA2) was significantly lower in subjects with prediabetes (p < 0.05), whereas the activity of paraoxonase 1 (using both paraoxon and phenyl acetate as substrates) did not significantly differ between subjects with or without prediabetes. In a stepwise linear regression analysis, the proportion of small HDL3 over HDL‐C concentration was independently associated with the presence of prediabetes and with total cholesterol and TAG concentration (positively), as well as with HDL‐C levels (negatively). We also observed a trend of increased small dense low‐density lipoprotein cholesterol levels in prediabetic subjects compared with their controls. Subjects with IFG exhibit increased proportion of small HDL3 particles combined with decreased activity of the anti‐atherogenic HDL‐LpPLA2.
PDE5-Is for the Treatment of Concomitant ED and LUTS/BPH
Authors: Gacci M. , Sebastianelli A. , Salvi M. , Vignozzi L. , Corona G. , McVary K. T. , Kaplan S. A. , Oelke M. , Maggi M. , Carini M. 
Published: April 2013

AbstractEpidemiologic data in adult men exhibit a strong relationship between erectile dysfunction (ED) and lower urinary tract symptoms suggestive of benign prostatic hyperplasia (LUTS/BPH), indicating that men affected by ED should also be investigated for LUTS/BPH and those presenting with storage or voiding LUTS should be investigated for co-morbid ED. Common pathophysiolgical mechanisms underlying both LUTS/BPH and ED, including alteration of NO/cGMP or RhoA/Rho-kinase signaling and/or vascular or neurogenic dysfunction, are potential targets for proposed phosphodiesterase type 5 inhibitors (PDE5-Is). Several randomized controlled trials and only a few reviews including all commercially available PDE5-Is demonstrated the safety and efficacy of these drugs in the improvement of erectile function and urinary symptoms, in patients affected either by ED, LUTS, or both conditions.
Modified Z method to calculate melting curve by molecular dynamics
Authors: Wang Shuaichuang , Zhang Gongmu , Liu Haifeng , Song Haifeng 
Published: April 2013

We extend the recently proposed Z method of estimating the melting temperature from a complete liquid and propose a modified Z method to calculate the melting temperature from a solid-liquid coexistence state. With the simulation box of rectangular parallelepiped, an initial structure of perfect lattice can run in the microcanonical ensemble to achieve steady solid-liquid coexistence state. The melting pressure and temperature are estimated from the coexistence state. For the small system with 1280 atoms, the simulation results show that the melting curve of copper has a good agreement with the experiments and is identical in accuracy with the results of the two-phase coexistence method with 24 000 atoms in the literature. Moreover, the method is conceptually simpler than the two-phase coexistence method.
Online scholarly publishing in China: Who? What? How?
Authors: Jie XU , Xiaoqun YUAN 
Published: March 2013

ABSTRACTThis overview describes the general situation of online scholarly publishing in China from both the supply and demand points of view. Based on desk research, online survey, and face‐to‐face interviews, we identify scholars' perceptions as well as expectations of the current online publishing system. We offer some personal recommendations for change. We then provide a list of business models for stakeholders.
Ranking journals: could Google Scholar Metrics be an alternative to Journal Citation Reports and Scimago Journal Rank?
Authors: DELGADO‐LÓPEZ‐CÓZAR Emilio , CABEZAS‐CLAVIJO Álvaro 
Published: March 2013

ABSTRACTThe launch of Google Scholar Metrics as a tool for assessing scientific journals may be serious competition for Thomson Reuters' Journal Citation Reports, and for the Scopus‐powered Scimago Journal Rank. A review of these bibliometric journal evaluation products is performed. We compare their main characteristics from different approaches: coverage, indexing policies, search and visualization, bibliometric indicators, results analysis options, economic cost, and differences in their ranking of journals. Despite its shortcomings, Google Scholar Metrics is a helpful tool for authors and editors in identifying core journals. As an increasingly useful tool for ranking scientific journals, it may also challenge established journals products.
Simplifying e‐book and print production
Authors: BORGSTROM Liam 
Published: March 2013

ABSTRACTWhile XML‐based single‐source publishing is a powerful tool for streamlining the book publishing industry, it may not be the right one for every sector of the industry. For an industry that is part cultural and part industrial, the traditional workflow allows for creativity at every stage and this craft focus still deserves a place in defining how the industry functions. With simple and familiar tools, it can be possible to integrate elements of old and new principles to create a workflow that is streamlined and advantageous without being too radical a shift in practice. This article describes the factors that are important to creating publications in both digital and physical formats.
Information workflow of academic researchers in the evolving information environment: an interview study
Authors: NEWMAN Michael L. , SACK John 
Published: March 2013

ABSTRACTDigital journals have been widely adopted by academic researchers and have nearly replaced printed journals in many contexts. The adoption of digital books is accelerating. The transition to digital information has changed information workflows of researchers by transforming the methods they use to find, store, retrieve, and use information from monographs, journals, and other sources. It has also changed the needs and expectations of scholars in relation to research information. To investigate these changes, 45 researchers in science, medicine, engineering, social sciences, and humanities at Stanford University were interviewed regarding information workflow and preferences. Results are compared with the findings of the e‐Journal User Study (eJUSt), completed in 2002.
Market‐oriented reform in Chinese scholarly publishing
Authors: Qing FANG , Lifang XU 
Published: March 2013

ABSTRACTThe Chinese government initiated a policy of 'corporatization of cultural entities' in 2003. Most Chinese book publishing houses were required to complete this transformation by 2006 and journal publishers by 2012. Chinese academic publishers, who no longer receive any general subsidies and allowances from government, have struggled to survive since then. During the reform process, many Chinese journals charged their authors page fees, and academic book publishers raised the prices of their publications. The continuing existence of other subsidies, however, means that there is still a degree of dependency in the Chinese system, and it will take time for its academic publishers to grow into real market players and to enhance their competitiveness.
Understanding the needs of international authors
Authors: MUDRAK Benjamin 
Published: March 2013

ABSTRACTResearch and scholarly publication are global endeavors, and English‐language journals are receiving more and more manuscript submissions from international authors. A better understanding of the challenges faced by researchers who are not native English speakers will enable journal publishers to improve the process of submission for all authors, ensuring that the best papers are published in an efficient manner. We surveyed a sample of international researchers to determine what they perceived as challenges inherent to submission to English‐language journals and found that they desire assistance with manuscript formatting and responding to reviewers, as well as clear policies about pre‐submission inquiries and conflicts of interest. Taking into account these survey results and the experience our company has with international authors, we suggest several small changes to a journal's website, including clearer English and prominent links to select policies and guidelines, that may greatly simplify the submission process for second language authors.
Fast simulation of reconstructed phylogenies under global time-dependent birth–death processes
Authors: Höhna Sebastian 
Published: March 2013

Abstract
Motivation: Diversification rates and patterns may be inferred from reconstructed phylogenies. Both the time-dependent and the diversity-dependent birth–death process can produce the same observed patterns of diversity over time. To develop and test new models describing the macro-evolutionary process of diversification, generic and fast algorithms to simulate under these models are necessary. Simulations are not only important for testing and developing models but play an influential role in the assessment of model fit.
Results: In the present article, I consider as the model a global time-dependent birth–death process where each species has the same rates but rates may vary over time. For this model, I derive the likelihood of the speciation times from a reconstructed phylogenetic tree and show that each speciation event is independent and identically distributed. This fact can be used to simulate efficiently reconstructed phylogenetic trees when conditioning on the number of species, the time of the process or both. I show the usability of the simulation by approximating the posterior predictive distribution of a birth–death process with decreasing diversification rates applied on a published bird phylogeny (family Cettiidae).
Availability: The methods described in this manuscript are implemented in the R package TESS, available from the repository CRAN (http://cran.r-project.org/web/packages/TESS/).
Contact: hoehna@math.su.se
Supplementary information: Supplementary data are available at Bioinformatics online.
First Report of Tobacco ringspot virus Infecting Ajuga reptans in Ohio
Authors: Fisher John R. 
Published: April 2013

In the fall of 2011, a bugleweed sample tested positive for Tobacco ringspot virus (TRSV). Immunocapture RT-PCR using cDNAs from bound virions with RNA-dependent RNA polymerase (RdRp) and coat protein (CP) specific primers both amplified strong, distinct products. Cloned RdRp and CP amplicons were 89% and 97% identical, respectively, to GenBank accessions U50869.1 and AY363727.1, respectively. These results represent the first confirmed report of TRSV infecting Ajuga reptans in Ohio. Accepted for publication 11 January 2012. Published 1 March 2013.