bluuebunny/crossref_metadata_2025_split huggingface dataset:
Maximal regularity for degenerate differential equations with infinite delay in periodic vector-valued function spaces
Authors: Lizama Carlos , Ponce Rodrigo 
Published: August 2013

AbstractLet A and M be closed linear operators defined on a complex Banach space X and let a ∈ L1(ℝ+) be a scalar kernel. We use operator-valued Fourier multipliers techniques to obtain necessary and sufficient conditions to guarantee the existence and uniqueness of periodic solutions to the equationwith initial condition Mu(0) = Mu(2π), solely in terms of spectral properties of the data. Our results are obtained in the scales of periodic Besov, Triebel–Lizorkin and Lebesgue vector-valued function spaces.
Predicting the risk of an endemic focus ofLeishmania tropicabecoming established in south-western Europe through the presence of its main vector,Phlebotomus sergentiParrot, 1917
Authors: BARÓN S. D. , MORILLAS-MÁRQUEZ F. , MORALES-YUSTE M. , DÍAZ-SÁEZ V. , GÁLLEGO M. , MOLINA R. , MARTÍN-SÁNCHEZ J. 
Published: August 2013

SUMMARYThe aim of the study was the construction of risk maps for exposure toPhlebotomus sergenti, the main vector ofLeishmania tropica, with a view to identifying hot spots for the potential establishment of this parasite in the southwest of Europe. Data were collected on the presence/absence of this vector and the ecological and climatic characteristics of 662 sampling sites located in the southeast, centre and northeast of the Iberian Peninsula (south-western Europe). The environmental factors associated with the distribution ofP. sergentiwere determined. The best predictors for the presence of this dipteran were ‘altitude’, ‘land use’, ‘land surface temperature’, ‘aspect’, ‘adjacent land cover’, ‘absence of vegetation in wall’ and the ‘absence of PVC pipes in the drainage holes of retaining walls’. Risk maps for exposure to the vector were drawn up based on these variables. The validation of the predictive risk model confirmed its usefulness in the detection of areas with a high risk ofP. sergentibeing present. These locations represent potential hot spots for an autochthonous focus ofL. tropicabecoming established. The risk maps produced forP. sergentipresence revealed several areas in the centre and south of the Iberian Peninsula to be the most prone to this process, which would make it possible for the disease to enter south-western Europe.
Acriflavine treatment promotes dyskinetoplasty inTrypanosoma cruzias revealed by ultrastructural analysis
Authors: MANCHESTER THIAGO , CAVALCANTI DANIELLE PEREIRA , ZOGOVICH MARCELO , DE SOUZA WANDERLEY , MOTTA MARIA CRISTINA MACHADO 
Published: August 2013

SUMMARYTrypanosomatid mitochondrial DNA is structured as a giant network of thousands of interlocked DNA molecules enclosed within the kinetoplast. The structure and replication mechanism of kinetoplast DNA (kDNA) is unique, thereby making it an excellent chemotherapeutic target. Alteration in the structural organization of kDNA can give rise to dyskinetoplastic (Dk) strains. In Dk cells, the kDNA is dispersed in clumps throughout the mitochondrial matrix and not organized into a network. In this work,Trypanosoma cruziepimastigotes were treated with acriflavine, a DNA intercalating drug, which promoted a decrease in cell proliferation and induced the appearance of Dk protozoa. In treated cells, the kinetoplast lost its normal disc-shaped structure because the fibrillar arrangement was reduced to a compact, amorphous mass within the mitochondrion. Moreover, basic proteins associated with kDNA were redistributed throughout the Dk protozoal kinetoplast. We sought to understand how the disruption of the kDNA leads to the emergence of the Dk phenotype with atomic force microscopy (AFM) analysis of isolated networks. Our results demonstrate that the detachment of minicircles from the kDNA disk promotes the disassembly of the network, thereby generating Dk cells. Our data strongly suggest that acriflavine inhibitsT. cruzimultiplication by interfering with kDNA replication.
Trypanosoma evansiinfection impairs memory, increases anxiety behaviour and alters neurochemical parameters in rats
Authors: WOLKMER PATRÍCIA , PAIM FRANCINE C. , DA SILVA CÁSSIA B. , GAI BIBIANA M. , CARVALHO FABIANO B. , DA SOUZA ANA CRISTINA G. , DA ROSA MICHELLE M. , DA SILVA ALEKSANDRO S. , PEREIRA PAULA R. , LOPES SONIA T. A. , NOGUEIRA CRISTINA W. , RUBIN MARIBEL A. , MONTEIRO SILVIA G. , MAZZANTI CINTHIA M. 
Published: August 2013

SUMMARYThe aim of this study was to investigate neurochemical and enzymatic changes in rats infected withTrypanosoma evansi, and their interference in the cognitive parameters. Behavioural assessment (assessment of cognitive performance), evaluation of cerebral L-[3H]glutamate uptake, acetylcholinesterase (AChE) activity and Ca+2and Na+, K+-ATPase activity were evaluated at 5 and 30 days post infection (dpi). This study demonstrates a cognitive impairment in rats infected withT. evansi. At 5 dpi memory deficit was demonstrated by an inhibitory avoidance test. With the chronicity of the disease (30 dpi) animals showed anxiety symptoms. It is possible the inhibition of cerebral Na+, K+-ATPase activity, AChE and synaptosomal glutamate uptake are involved in cognitive impairment in infected rats byT. evansi. The understanding of cerebral host–parasite relationship may shed some light on the cryptic symptoms of animals and possibly human infection where patients often present with other central nervous system (CNS) disorders.
Cost-effectiveness of combining systematic identification and treatment of co-morbid major depression for people with chronic diseases: the example of cancer
Authors: Walker S. , Walker J. , Richardson G. , Palmer S. , Wu Q. , Gilbody S. , Martin P. , Hansen C. Holm , Sawhney A. , Murray G. , Sculpher M. , Sharpe M. 
Published: August 2013

BackgroundCo-morbid major depression occurs in approximately 10% of people suffering from a chronic medical condition such as cancer. Systematic integrated management that includes both identification and treatment has been advocated. However, we lack information on the cost-effectiveness of this combined approach, as published evaluations have focused solely on the systematic (collaborative care) treatment stage. We therefore aimed to use the best available evidence to estimate the cost-effectiveness of systematic integrated management (both identification and treatment) compared with usual practice, for patients attending specialist cancer clinics.MethodWe conducted a cost-effectiveness analysis using a decision analytic model structured to reflect both the identification and treatment processes. Evidence was taken from reviews of relevant clinical trials and from observational studies, together with data from a large depression screening service. Sensitivity and scenario analyses were undertaken to determine the effects of variations in depression incidence rates, time horizons and patient characteristics.ResultsSystematic integrated depression management generated more costs than usual practice, but also more quality-adjusted life years (QALYs). The incremental cost-effectiveness ratio (ICER) was £11 765 per QALY. This finding was robust to tests of uncertainty and variation in key model parameters.ConclusionsSystematic integrated management of co-morbid major depression in cancer patients is likely to be cost-effective at widely accepted threshold values and may be a better way of generating QALYs for cancer patients than some existing medical and surgical treatments. It could usefully be applied to other chronic medical conditions.
Linking minds and brains
Authors: BARLOW HORACE 
Published: August 2013

AbstractWhen I first came across William James’ dictum that “ … this sense of sameness is the very keel and backbone of our thinking,” I thought he had foreseen the importance of cross-correlation in the brain, and told myself to find out how he had reached this conclusion. When I finally did this a year or two ago, I slowly came to realize that I had completely misunderstood him; from the full quote it is absolutely clear that his dictum cannot be referring to the process by which a cortical simple cell responds selectively to the orientation of features in a visual image, as I had originally supposed. If one translates the original dictum into two more prosaic modern versions, his version would say: “Our minds could not think at all without neural circuits in our brains that compute auto-correlations,” but in my mistaken interpretation the last word would be “cross-correlations.” Others may have made the same mistake, but the difference is profound, and finding what he really meant has been a revelation to me. This essay explains the revelation, describes how to determine experimentally whether the brain does auto- or cross-correlation, and gives the result of preliminary experiments showing clearly that it does both. A revised view of the visual cortex as autocorrelator as well as cross-correlator claims to tell us what complex cells in the visual cortex do, and it assigns a role to its columnar structure that is as important to fulfilling that role as the concept of the receptive field has been to understanding the simple cells’ fulfillment of theirs. The new view has compelling features, broad implications, and suggests a plausible model of how neural circuits in the cortex achieve thought, but it needs further testing.
Pharmacometric Analyses to Support Early Development Decisions for LY2878735: A Novel Serotonin Norepinephrine Reuptake Inhibitor
Authors: Raddad E , Melhem MR , Sloan‐Lancaster JS , Miller JW , Van Wart SA , Rubino CM 
Published: August 2013

LY2878735 is a novel dual serotonin (5‐hydroxytryptamine (5‐HT)) and norepinephrine (NE) reuptake inhibitor (SNRI) in development for chronic pain indications. In vitro profile suggests a more balanced profile as compared with other SNRI's, which is expected to confer superior clinical efficacy. LY2878735 is metabolized partly by the genetically polymorphic cytochrome P450 (CYP) 2D6 pathway, raising pharmacokinetic (PK) variability concerns. Phase 1 PK and biomarker data were analyzed by pharmacometric methods to characterize the balance between dual‐target engagement and adverse effects on heart rate (HR) and blood pressure (BP). A narrow range of plasma LY2878735 levels was associated with an acceptable balance. As compared with poor metabolizers (PM), CYP2D6 extensive metabolizers (EM) have 21‐ and threefold higher clearance and distribution volume, respectively. Even with a CYP2D6‐based dosing paradigm, a superior therapeutic index comparable to duloxetine, a widely used SNRI, was not achievable and LY2878735 development was thus terminated. Model‐based approach effectively synthesizes PK‐pharmacodynamic (PD) relationships, enabling efficient early development decisions.CPT: Pharmacometrics & Systems Pharmacology (2013) 2, e66; doi:10.1038/psp.2013.43; published online 21 August 2013
Use of a Biomarker in Exposure–Response Analysis to Support Dose Selection for Fingolimod
Authors: Lee J‐Y , Wang Y 
Published: August 2013

Fingolimod 0.5 mg q.d. (once daily) has been approved for the treatment of patients with relapsing and remitting forms of multiple sclerosis (RRMS). Fingolimod at two doses (0.5 and 1.25 mg) showed superior effectiveness in the frequency of relapse with little difference between the two dose groups. At the same time, fingolimod manifests a number of dose‐dependent adverse events. Given the safety concerns and similar effect size at both dose groups, it was reasonable to raise the question whether doses even lower than 0.5 mg would produce sufficient effectiveness. Therefore, our analysis focused on estimating the effect size of the primary endpoint at doses lower than 0.5 mg via exposure–response analysis. Specifically, we aim to show how biomarker data can be used as a bridge in exposure–response analysis to estimate the clinical endpoint response at certain doses when the direct relationship between exposure and the clinical endpoint can not be quantified reliably.CPT: Pharmacometrics & Systems Pharmacology (2013) 2, e67; doi:10.1038/psp.2013.44; published online 21 August 2013
Switching regulator using a high step‐up voltage converter for fuel‐cell modules
Authors: Leyva‐Ramos Jesus , Lopez‐Cruz Juan Manuel , Ortiz‐Lopez Maria Guadalupe , Diaz‐Saldierna Luis Humberto 
Published: August 2013

A typical fuel‐cell stack produces a low DC voltage with wide variations; therefore a DC–DC switching converter is required to step up and regulate the output voltage. In this work, a model based on electrical variables is developed for a fuel‐cell stack. This model is later combined with the model of a high step‐up voltage converter to obtain a combined model that incorporates the behaviour of fuel‐cell stack. The resulting model is then used to design an average‐current mode controller for a switching regulator. To test the proposed regulator, a power module with polymer electrolyte membrane fuel cells is used as an input source. This module delivers an output voltage between 26 and 42 V depending on the current being drawn. Experimental results exhibit the robustness of the switching regulator to step changes in the output load and the output voltage of the fuel‐cell stack.
Design of a zero‐voltage‐switching large‐air‐gap wireless charger with low electric stress for electric vehicles
Authors: Duan Chen , Jiang Chenguang , Taylor Allan , Bai Kevin (Hua) 
Published: August 2013

This study proposes a design and development of a wireless power transfer system to charge the battery in electric vehicles. A parallel–parallel topology is adopted to realise 10–15 cm‐distance power transfer using the resonance theory. Finite‐element method is used to extract the coil parameters. The advantages of the proposed design compared with the previous similar research are (i) low operational frequency (42 kHz) which avoids the electromagnetic interference to the on‐board automotive electronics equipment and (ii) low electric stress to the semi‐conductor switches through using zero‐voltage‐switching technique. A 2 kW prototype to charge 200 V battery was built to experimentally verify the theoretical analysis. The overall system efficiency is ∼ 86%.
Zero‐voltage switching current‐fed flyback converter for power factor correction application
Authors: Quang Nha Trong , Chiu Huang‐Jen , Lo Yu‐Kang , Alam Mohammed Mahmood 
Published: August 2013

Previous research on flyback power factor correction (PFC) converters exposes some inherent shortcomings, such as high‐voltage spike on the metal oxide semiconductor field effect transistor (MOSFET), frequency variation, pulsating input current and hard switching operation. This study presents a new topology for PFC applications named zero‐voltage switching (ZVS) current‐fed flyback converter to not only achieve spike‐free voltage, ZVS on the MOSFETs, but also improve the input current quality. By utilising quasi‐z‐source configuration, the voltage spikes on the MOSFET are effectively eliminated using only a capacitive clamper, resulting in no‐loss consumption. Low‐voltage MOSFETs with low on‐resistance Rds(on) are used to improve the efficiency. In addition, by taking advantage of the average current mode control with the continuous conduction mode operation, the input current perfectly tracks the input voltage. To demonstrate the circuit's feasibility, a 100–140 V input, 28 V/5 A output laboratory prototype was built. The experimental results showed that the proposed topology completely eliminated the voltage spikes on the MOSFETs. The efficiency was improved using low Rds(on) MOSFETs, and ZVS was achieved. In summary, the proposed topology meets the high efficiency and high‐input current quality requirements.
Integral‐resonant control for stand‐alone voltage source inverters
Authors: Lidozzi Alessandro , Lo Calzo Giovanni , Solero Luca , Crescimbini Fabio 
Published: August 2013

This study deals with a newly‐conceived voltage control method for three‐phase four‐leg voltage source inverters (VSIs) which are being required in autonomous power generating units devoted to supply both three‐phase and single‐phase electrical loads in four‐wire electric power distribution systems. To deal with VSI operating conditions providing three‐phase voltage supply of both unbalanced loads and non‐linear loads, an integral + resonant (I + R) voltage control structure is discussed and experimentally verified by means of a 25 kVA rated power converter prototype. It is shown that the proposed voltage control allows simplifying the overall control configuration, achieving zero‐overhead power factor regulation and fast compensation of load unbalances. Further to that, a complete current limiting strategy is described and tested under different load conditions.
Accurate identification of polyadenylation sites from 3′ end deep sequencing using a naïve Bayes classifier
Authors: Sheppard Sarah , Lawson Nathan D. , Zhu Lihua Julie 
Published: August 2013

Abstract
Motivation: 3′ end processing is important for transcription termination, mRNA stability and regulation of gene expression. To identify 3′ ends, most techniques use an oligo-dT primer to construct deep sequencing libraries. However, this approach can lead to identification of artifactual polyadenylation sites due to internal priming in homopolymeric stretches of adenines. Although heuristic filters have been applied in these cases, they typically result in a high proportion of both false-positive and -negative classifications. Therefore, there is a need to develop improved algorithms to better identify mis-priming events in oligo-dT primed sequences.
Results: By analyzing sequence features flanking 3′ ends derived from oligo-dT-based sequencing, we developed a naïve Bayes classifier to classify them as true or false/internally primed. The resulting algorithm is highly accurate, outperforms previous heuristic filters and facilitates identification of novel polyadenylation sites.
Contact: nathan.lawson@umassmed.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
Determination of genomic copy number alteration emphasizing a restriction site-based strategy of genome re-sequencing
Authors: Zheng Caihong , Miao Xuexia , Li Yanen , Huang Ying , Ruan Jue , Ma Xi , Wang Li , Wu Chung-I , Cai Jun 
Published: August 2013

Abstract
Motivation: Copy number abbreviation (CNA) is one type of genomic aberration that is often induced by genome instability and is associated with diseases such as cancer. Determination of the genome-wide CNA profile is an important step in identifying the underlying mutation mechanisms. Genomic data based on next-generation sequencing technology are particularly suitable for determination of high-quality CNA profile. Now is an important time to reevaluate the use of sequencing techniques for CNA analysis, especially with the rapid growth of the different targeted genome and whole-genome sequencing strategies.
Results: In this study, we provide a comparison of resequencing strategies, with regard to their utility, applied to the same hepatocellular carcinoma sample for copy number determination. These strategies include whole-genome, exome and restriction site-associated DNA (RAD) sequencing. The last of these strategies is a targeted sequencing technique that involves cutting the genome with a restriction enzyme and isolating the targeted sequences. Our data demonstrate that RAD sequencing is an efficient and comprehensive strategy that allows the cost-effective determination of CNAs. Further investigation of RAD sequencing data led to the finding that a precise measurement of the allele frequency would be a helpful complement to the read depth for CNA analysis for two reasons. First, knowledge of the allele frequency helps to resolve refined calculations of allele-specific copy numbers, which, in turn, identify the functionally important CNAs that are under natural selection on the parental alleles. Second, this knowledge enables deconvolution of CNA patterns in complex genomic regions.
Contact: juncai@big.ac.cn or ciwu@uchicago.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
ProteoStats—a library for estimating false discovery rates in proteomics pipelines
Authors: Yadav Amit Kumar , Kadimi Puneet Kumar , Kumar Dhirendra , Dash Debasis 
Published: August 2013

Abstract
Summary: Statistical validation of peptide assignments from a large-scale shotgun proteomics experiment is a critical step, and various methods for evaluating significance based on decoy database search are in practice. False discovery rate (FDR) estimation of peptide assignments assesses global significance and corrects for multiple comparisons. Various approaches have been proposed for FDR estimation but unavailability of standard tools or libraries leads to development of many in-house scripts followed by manual steps that are error-prone and low-throughput. The ProteoStats library provides an open-source framework for developers with many FDR estimation and visualization features for several popular search algorithms. It also provides accurate q-values, which can be easily integrated in any proteomics pipeline to provide automated, accurate, high-throughput statistical validation and minimize manual errors.
Availability: https://sourceforge.net/projects/mssuite/files/ProteoStats/.
Contact: ddash@igib.res.in or aky.compbio@gmail.com or amit.yadav@igib.in
Supplementary information: Supplementary data are available at Bioinformatics online.
A quantitative assessment of the mechanical strength of the polar pteropod Limacina helicina antarctica shell
Authors: Teniswood Clara M. H. , Roberts Donna , Howard William R. , Bradby Jodie E. 
Published: August 2013

AbstractTeniswood, C. M. H., Roberts, D., Howard, W. R., and Bradby, J. E. 2013. A quantitative assessment of the mechanical strength of the polar pteropod Limacina helicina antarctica shell. – ICES Journal of Marine Science, 70: . This work directly measures the mechanical properties of pteropod shells collected from the Southern Ocean on the 2007 midsummer Subantarctic Zone Sensitivity to Environmental Change (SAZ-Sense) voyage. Shells from the common Southern Ocean pteropod Limacina helicina antarctica were subjected to mechanical analyses in combination with detailed morphological studies. Average hardness and modulus of 2.30 ± 0.07 GPa and 45.27 ± 0.91 GPa, respectively were calculated from several hundred nanoindentation measurements taken from multiple positions across twelve shells of the same species collected under identical conditions. Quantitative data such as these are critical to establish a reference point for future comparative studies and to both understand and evaluate the implications of further ocean acidification on the structural integrity of these common polar calcifiers, particularly in light of their role in the Southern Ocean carbon cycle and food web.