bluuebunny/crossref_metadata_2025_split huggingface dataset:
Estimating the prevalence of hepatitis C infection in New York City using surveillance data
Authors: BALTER S. , STARK J. H. , KENNEDY J. , BORNSCHLEGEL K. , KONTY K. 
Published: May 2013

SUMMARYHepatitis C virus is the most common chronic blood-borne infection in the USA. Based on results of a serosurvey, national prevalence is estimated to be 1·3% or 3·2 million people. Sub-national estimates are not available for most jurisdictions. Hepatitis C surveillance data was adjusted for death, out-migration, under-diagnosis, and undetectable blood RNA, to estimate prevalence in New York City (NYC). The prevalence of hepatitis C infection in adults aged ⩾20 years in NYC is 2·37% (range 1·53–4·90%) or 146 500 cases of hepatitis C. This analysis presents a mechanism for generating prevalence estimates using local surveillance data accounting for biases and difficulty in accessing hard to reach populations. As the cohort of patients with hepatitis C age and require additional medical care, local public health officials will need a method to generate prevalence estimates to allocate resources. This approach can serve as a guideline for generating local estimates using surveillance data that is less resource prohibitive.
Deriving session and union types for objects
Authors: BETTINI LORENZO , CAPECCHI SARA , DEZANI-CIANCAGLINI MARIANGIOLA , GIACHINO ELENA , VENNERI BETTI 
Published: May 2013

Guaranteeing that the parties of a network application respect a given protocol is a crucial issue.Session typesoffer a method for abstracting and validating structured communication sequences (sessions).Object-oriented programmingis an established paradigm for large scale applications.Union types, which behave as the least common supertypes of a set of classes, allow the implementation of unrelated classes with similar interfaces without additional programming. We have previously developed an integration of the features above into a class-based core language for building network applications, and this successfully amalgamated sessions and methods so that data can be exchanged flexibly according to communication protocols (session types).The first aim of the work reported in this paper is to provide a full proof of the type safety property for that core language by renewing syntax, typing and semantics. In this way, static typechecking guarantees that after a session has started, computation cannot get stuck on a communication deadlock.The second aim is to define a constraint-based type system that reconstructs the appropriate session types of session declarations instead of assuming that session types are explicitly given by the programmer. Such an algorithm can save programming work, and automatically presents an abstract view of the communications of the sessions.
Expression levels of mRNA for insulin-like growth factors 1 and 2, IGF receptors and IGF binding proteins in in vivo and in vitro grown bovine follicles
Authors: Rebouças Emanuela L. , Costa José J.N. , Passos Maria J. , Silva Anderson W.B. , Rossi Rodrigo O.D.S. , van den Hurk Robert , Silva José R.V. 
Published: May 2013

SummaryThis study investigated mRNA levels for insulin-like growth factors (IGFs) IGF1 (IGF-I) and IGF2 (IGF-II), IGF receptors (IGF1R and IGF2R), and binding proteins (IGFBP-1, IGFBP-2. IGFBP-3, IGFBP-4, IGFBP-5 and IGFBP-6) in bovine follicles of 0.2, 0.5 or 1.0 mm in diameter. mRNA expression levels in in vitro cultured follicles that reached approximately 0.5 mm were compared with that of in vivo grown follicles. IGF1R and IGF2R expression levels in 0.5 mm in vivo follicles were higher than in 1.0 or 0.2 mm follicles, respectively. IGFBP-1, IGFBP-2. IGFBP-3, IGFBP-4, IGFBP-5 and IGFBP-6 showed variable expression in the follicular size classes analyzed. In vitro grown follicles had significantly reduced expression levels for IGF1, IGF1R, IGFBP-3, IGFBP-5 and IGFBP-6 mRNA when compared with 0.2 mm follicles, but, when compared with in vivo grown follicles (0.5 mm), only IGFBP-1, IGFBP-2, IGFBP-3 and IGFBP-6 showed a reduction in their expression. In conclusion, IGFs, their receptors and IGFBPs showed variable expression of mRNA levels in the follicular size classes analyzed.
Akt/PKB plays role of apoptosis relay on entry into first mitosis of mouse embryo
Authors: Baran Vladimir , Fabian Dusan , Rehak Pavol 
Published: May 2013

SummaryThe cell-cycle regulators that control meiotic divisions also regulate the events that accompany the oocyte-to-zygote transition. Thus, the meiotic machinery functions as an internal pacemaker that propels the oocyte toward embryogenesis. The preimplantation embryo expresses a number of receptors that are important for initial activity of the phosphatidylinositol 3-kinase–protein kinase B (PI3K-Akt/PKB) pathway. The complete PI3K-Akt/PKB-CDK1 cascade is implicated as a key regulator of a number of cellular functions. Selective inhibition of protein kinase B (Akt/PKB) with inhibitor SH6 and cyclin-dependent kinase 1 (CDK1) with inhibitor roscovitine arrest development of the 1-cell preimplantation mouse embryo before entry into the first mitosis. The pronuclei of these inhibited embryos migrate to one another, but do not progress to pronuclei envelope breakdown and pronuclear fusion running immediately before the onset of mitosis. SH6-treated 1-cell mouse embryos showed a high occurrence of apoptosis features (nuclear fragmentation, positive terminal deoxynucleotidyl transferase dUTP nick end labelling (TUNEL), active caspase-3 in both cytoplasm and nucleoplasm). In the Akt/PKB-inhibited embryos, the active phosphorylated form Ser473Akt/PKB was not detected in pronuclear areas when compared with inhibitor-free controls. Although CDK1-inhibited 1-cell embryos also failed to enter into the first mitosis, the presence of apoptotic cell death features was not observed. In the roscovitine-treated embryos, Ser473Akt/PKB was detected in the pronuclei independently of CDK1 activity. We conclude that Akt/PKB plays an important role during entry of the 1-cell mouse embryo into the first mitosis, and probably functions as a relay in the cell-cycle stage. We assume that Akt/PKB is the primary target responsible for mediating anti-apoptotic signals in the 1-cell mouse embryo.
Dynamics of Carbon Nanotube Tipped Atomic Force Microscopy in Liquid
Authors: Korayem Moharam Habibnejad , Ebrahimi Nazila 
Published: May 2013

AbstractCarbon nanotubes (CNT) are proper tips for atomic force microscopes (AFMs) as a result of their small tip diameter, high aspect ratio, and high flexibility. For nanoscale imaging of soft biological specimens, a CNT tipped AFM is an ideal tool. In this article we review the application of CNTs as AFM tips and present related research about the forces applied from liquids on nanotubes. Then a dynamic mode CNT tipped AFM in liquid is modeled and simulated. The simulation results are compared with experimental results. For modeling and simulation, a continuous beam model and a forward-time simulation method are used. The simulation results show that when a CNT tip vibrates in liquid, the oscillation amplitude and resonance frequency are changed compared to the state of oscillation in air. The small structure of CNTs reduces the hydrodynamic forces, and the liquid environment reduces the adhesive forces between the CNT tip and the sample. These two factors make CNTs a good choice as an AFM tip.
Insight into the Compositional and Structural Nano Features of AlN/GaN DBRs by EELS-HAADF
Authors: Eljarrat Alberto , López-Conesa Lluís , Magén César , Gačević Žarko , Fernández-Garrido Sergio , Calleja Enrique , Estradé Sónia , Peiró Francesca 
Published: May 2013

AbstractIII-V nitride (AlGa)N distributed Bragg reflector devices are characterized by combined high-angle annular dark-field (HAADF) and electron energy loss spectroscopy (EELS) in the scanning transmission electron microscope. Besides the complete structural characterization of the AlN and GaN layers, the formation of AlGaN transient layers is revealed using Vegard law on profiles of the position of the bulk plasmon peak maximum. This result is confirmed by comparison of experimental and simulated HAADF intensities. In addition, we present an advantageous method for the characterization of nano-feature structures using low-loss EELS spectrum image (EEL-SI) analysis. Information from the materials in the sample is extracted from these EEL-SI at high spatial resolution.The log-ratio formula is used to calculate the relative thickness, related to the electron inelastic mean free path. Fitting of the bulk plasmon is performed using a damped plasmon model (DPM) equation. The maximum of this peak is related to the chemical composition variation using the previous Vegard law analysis. In addition, within the context of the DPM, information regarding the structural properties of the material can be obtained from the lifetime of the oscillation. Three anomalous segregation regions are characterized, revealing formation of metallic Al islands.
Variation of PTV dose distribution on patient size in prostate VMAT and IMRT: a dosimetric evaluation using the PTV dose–volume factor
Authors: Chow James C. L. , Jiang Runqing , Markel Daniel 
Published: May 2013

AbstractBackgroundWe propose to use the PTV dose–volume factor (PDVF) to evaluate treatment plans of prostate volumetric modulated arc therapy (VMAT) and intensity modulated radiotherapy (IMRT).PurposePDVF was used to compare the variation of planning target volume (PTV) coverage between VMAT and IMRT because of weight loss of patient.Materials and methodsVMAT and IMRT plans of five patients (prostate volume = 32–86·5 cm3) using the 6 MV photon beams were created with the external contour reduced by depths of 0·5–2 cm to reflect the weight loss. Moreover, integral doses (volume integral of the patient dose) and prostate tumour control probability (TCP) were calculated.ResultsWe found that reduced depth resulted in PDVF decreasing 0·03 ± 4·7 × 10−4 (VMAT) and 0·04 ± 9·7 × 10−3 (IMRT) per cm for patients. The decrease of PDVF or degradation of PTV coverage was found more significant in IMRT plans than VMAT with patient size reduction. The integral dose did not change significantly between VMAT and IMRT, while the prostate TCP increased with an increase of reduced depth.ConclusionWe concluded that PDVF can be successfully used to evaluate the variation of PTV coverage because of weight loss of patient in prostate VMAT and IMRT. Degradation of PTV coverage in prostate VMAT is less significant than IMRT regarding patient size reduction.
Pivotal role of P450–P450 interactions in CYP3A4 allostery: the case of α-naphthoflavone
Authors: Davydov Dmitri R. , Davydova Nadezhda Y. , Sineva Elena V. , Kufareva Irina , Halpert James R. 
Published: May 2013

We investigated the relationship between oligomerization of CYP3A4 (cytochrome P450 3A4) and its response to ANF (α-naphthoflavone), a prototypical heterotropic activator. The addition of ANF resulted in over a 2-fold increase in the rate of CYP3A4-dependent debenzylation of 7-BFC [7-benzyloxy-4-(trifluoromethyl)coumarin] in HLM (human liver microsomes), but failed to produce activation in BD Supersomes™ or Baculosomes® containing recombinant CYP3A4 and NADPH-CPR (cytochrome P450 reductase). However, incorporation of purified CYP3A4 into Supersomes™ containing only recombinant CPR reproduced the behaviour observed with HLM. The activation in this system was dependent on the surface density of the enzyme. Although no activation was detectable at an L/P (lipid/P450) ratio ≥750, it reached 225% at an L/P ratio of 140. To explore the relationship between this effect and CYP3A4 oligomerization, we probed P450–P450 interactions with a new technique that employs LRET (luminescence resonance energy transfer). The amplitude of LRET in mixed oligomers of the haem protein labelled with donor and acceptor fluorophores exhibited a sigmoidal dependence on the surface density of CYP3A4 in Supersomes™. The addition of ANF eliminated this sigmoidal character and increased the degree of oligomerization at low enzyme concentrations. Therefore the mechanisms of CYP3A4 allostery with ANF involve effector-dependent modulation of P450–P450 interactions.
Probing quantum coherence in qubit arrays
Authors: Almeida J , de Groot P C , Huelga S F , Liguori-Schremp A M , Plenio M B 
Published: May 2013

Abstract
We discuss how the observation of population localization effects in periodically driven systems can be used to quantify the presence of quantum coherence in interacting qubit arrays. Essential for our proposal is the fact that these localization effects persist beyond tight-binding Hamiltonian models. This result is of special practical relevance in those situations where direct system probing using tomographic schemes becomes infeasible beyond a very small number of qubits. As a proof of principle, we study analytically a Hamiltonian system consisting of a chain of superconducting flux qubits under the effect of a periodic driving. We provide extensive numerical support of our results in the simple case of a two-qubit chain. For this system we also study the robustness of the scheme against different types of noise and disorder. We show that localization effects underpinned by quantum coherent interactions should be observable within realistic parameter regimes in chains with a larger number of qubits.
Detection of significantly differentially methylated regions in targeted bisulfite sequencing data
Authors: Hebestreit Katja , Dugas Martin , Klein Hans-Ulrich 
Published: May 2013

AbstractMotivation: Bisulfite sequencing is currently the gold standard to obtain genome-wide DNA methylation profiles in eukaryotes. In contrast to the rapid development of appropriate pre-processing and alignment software, methods for analyzing the resulting methylation profiles are relatively limited so far. For instance, an appropriate pipeline to detect DNA methylation differences between cancer and control samples is still required.Results: We propose an algorithm that detects significantly differentially methylated regions in data obtained by targeted bisulfite sequencing approaches, such as reduced representation bisulfite sequencing. In a first step, this approach tests all target regions for methylation differences by taking spatial dependence into account. A false discovery rate procedure controls the expected proportion of incorrectly rejected regions. In a second step, the significant target regions are trimmed to the actually differentially methylated regions. This hierarchical procedure detects differentially methylated regions with increased power compared with existing methods.Availability: R/Bioconductor package BiSeq.Contact: katja.hebestreit@uni-muenster.deSupplementary information: Supplementary data are available at Bioinformatics online.
TrioVis: a visualization approach for filtering genomic variants of parent–child trios
Authors: Sakai Ryo , Sifrim Alejandro , Vande Moere Andrew , Aerts Jan 
Published: May 2013

Abstract
Summary: TrioVis is a visual analytics tool developed for filtering on coverage and variant frequency for genomic variants from exome sequencing of parent–child trios. In TrioVis, the variant data are organized by grouping each variant based on the laws of Mendelian inheritance. Taking three Variant Call Format files as input, TrioVis allows the user to test different coverage thresholds (i.e. different levels of stringency), to find the optimal threshold values tailored to their hypotheses and to gain insights into the global effects of filtering through interaction.
Availability: Executables, source code and sample data are available at https://bitbucket.org/biovizleuven/triovis. Screencast is available at http://vimeo.com/user6757771/triovis.
Contact: ryo.sakai@esat.kuleuven.be
N‐terminal pro brain natriuretic peptide‐guided management in patients with heart failure and preserved ejection fraction: findings from the Trial of Intensified versus standard Medical therapy in Elderly patients with Congestive Heart Failure (TIME‐CHF)
Authors: Maeder Micha T. , Rickenbacher Peter , Rickli Hans , Abbühl Heidi , Gutmann Marc , Erne Paul , Vuilliomenet André , Peter Martin , Pfisterer Matthias , Brunner‐La Rocca Hans‐Peter ,   for the TIME‐CHF Investigators
Published: May 2013

AimsTo assess the effects of an NT‐proBNP‐guided medical management on 18‐month outcomes in patients with heart failure (HF) and preserved LVEF (HFpEF).Methods and resultsPatients with HFpEF (LVEF >45%; n = 123) and HF with reduced LVEF (HFrEF; LVEF ≤45%; n = 499) with age ≥60 years, NYHA class ≥ II, and elevated NT‐proBNP (>400 ng/L or >800 ng/L depending on age) were randomized to medical therapy titrated only to reduce symptoms to NYHA ≤II (symptom‐guided) or also to reduce NT‐proBNP below the inclusion threshold (NT‐proBNP‐guided) during a 6‐month period. Patients were followed for an additional 12 months. Despite similar treatment escalation, NT‐proBNP reduction and symptom relief were less in HFpEF than in HFrEF. Hospitalization‐free survival at 18 months was worse in HFpEF than in HFrEF (P = 0.02), while survival and HF hospitalization‐free survival did not differ. Among HFpEF patients, NT‐proBNP reduction and symptom relief were similar in the symptom‐guided (n = 59) and NT‐proBNP‐guided (n = 64) group despite more aggressive treatment in the NT‐proBNP‐guided group. In contrast to effects in HFrEF, NT‐proBNP‐guided management tended to worsen 18‐month outcomes in HFpEF, with P‐values for the interactions between LVEF stratum and management strategy of 0.2 for hospitalization‐free survival, 0.03 for survival, and 0.01 for HF hospitalization‐free survival.ConclusionsOutcomes in HFpEF were not better than in HFrEF, and opposite effects of NT‐proBNP‐guided management were observed in HFpEF compared with HFrEF. These preliminary findings suggest that, in contrast to HFrEF, NT‐proBNP‐guided therapy may not be beneficial in HFpEF.Trial registrationISRCTN43596477.
Long‐term Outcomes for Infants With Intestinal Atresia Studied at Children's National Medical Center
Authors: Nusinovich Yevgeniya , Revenis Mary , Torres Clarivet 
Published: May 2013

ABSTRACTObjectives:Intestinal atresia is a common cause of intestinal obstruction in neonates. The predominant cause of late complications in these children is prolonged dependence on parenteral nutrition (PN). Our aims were to analyze the outcomes for patients with intestinal atresia at our institution, and to see how these changed with the implementation of an intestinal rehabilitation program (IRP).Methods:This is a retrospective cohort study. The patient population is all children with intestinal atresias (118 patients) treated at our institution from July 2000 to June 2010, 20 of whom became PN dependent.Results:Survival to hospital discharge was 95% for all patients, and 100% for those who had isolated atresia. Twenty of 118 patients (17%) were PN dependent beyond initial hospital discharge. At discharge, their median intestinal length was 22.5 cm, and they required PN for a mean of 88.5% of energy needs. Of these 20 patients, 2 died, 2 received transplants, and 2 transferred away for transplantation. The remaining 14 joined the IRP. Their mean energy requirement from PN is presently 10%, down from 87% at IRP enrollment, and 10 patients fully weaned off PN. Eleven of the 14 children had hyperbilirubinemia, with mean direct bilirubin of 7.5 mg/dL. All resolved their cholestasis during an average of 12 weeks.Conclusions:These results compare favorably with those reported in earlier periods. With programs such as the IRP, patients with short bowel secondary to intestinal atresia can show improvement in liver function and nutritional parameters, and discontinue PN, avoiding the need for transplantation.
Grounded theory: an inductive method for supply chain research
Authors: Randall Wesley S. , Mello John E. 
Published: May 2013

PurposeDevelopment of theory remains an essential step in the evolution of supply chain management as an integrative business discipline. Supply chain research often involves phenomena possessing complex behavioral dimensions at both the individual and organizational levels. Such complexity can require the utilization of holistic and inductive approaches in order to more fully understand the behaviors associated with the phenomena. This paper aims to provide a step‐by‐step guide intended to increase researchers' understanding of the use of grounded theory (GT) methodology in supply chain contexts.Design/methodology/approachThe paper argues for GT as an appropriate method for studying emerging supply chain phenomena using an inductive, holistic approach.FindingsGT is positioned in a holistic framework of research methodologies. Next a step‐by‐step explanation of the grounded theory process is offered, illustrated by examples from the authors' own research.Originality/valueThis paper links the complex “system of systems” nature characteristic of supply chains to the need for a holistic research approach such as grounded theory. It also provides a guide for researchers, reviewers, and editors to judge sound GT. Moreover, from a practical perspective, the in‐vivo nature of GT provides recognizable solutions to managerial problems.
Dealing with supply chain risks
Authors: Wieland Andreas , Wallenburg Carl Marcus 
Published: May 2013

PurposeThe effects of supply chain risk management (SCRM) on the performance of a supply chain remain unexplored. It is assumed that SCRM helps supply chains to cope with vulnerabilities both proactively by supporting robustness and reactively by supporting agility. Both dimensions are assumed to have an influence on the supply chain's customer value and on business performance. The aim of this research is to provide clarity by empirically testing these hypotheses and scrutinizing the findings by the means of case studies.Design/methodology/approachThe research is empirical. Survey data were collected from 270 manufacturing companies for hypotheses testing via structural equation modeling. Additionally, qualitative data were collected to explore the nature of non‐hypothesized findings.FindingsIt is found that SCRM is important for agility and robustness of a company. Both agility and robustness show to be important in improving performance. While agility has a strong positive effect only on the supply chain's customer value, but not directly on business performance, robustness has a strong positive effect on both performance dimensions. This important finding directs the strategic attention from agility‐centered supply chains to ones that are both robust and agile. The case studies provide insights to the fact that robustness can be considered a basic prerequisite to deal with supplier‐side risks, while agility is necessary to deal with customer‐side risks. The amount of agility and robustness needs to fit to the competitive strategy.Practical implicationsSince volatility has increasingly become a prevalent state of supply chains, companies need to consider robustness to be of primary importance to withstand everyday risks and exceptions.Originality/valueThis is the first study to view the relationship between SCRM, agility/robustness, and performance.