bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Model based Survey of Colour Deconvolution in Diagnostic Brightfield Microscopy: Error Estimation and Spectral Consideration
Authors: Haub Peter , Meckel Tobias 
Published: July 2015

AbstractColour deconvolution is a method used in diagnostic brightfield microscopy to transform colour images of multiple stained biological samples into images representing the stain concentrations. It is applied by decomposing the absorbance values of stain mixtures into absorbance values of single stains. The method assumes a linear relation between stain concentration and absorbance, which is only valid under monochromatic conditions. Diagnostic applications, in turn, are often performed under polychromatic conditions, for which an accurate deconvolution result cannot be achieved. To show this, we establish a mathematical model to calculate non-monochromatic absorbance values based on imaging equipment typically used in histology and use this simulated data as the ground truth to evaluate the accuracy of colour deconvolution. We show the non-linear characteristics of the absorbance formation and demonstrate how it leads to significant deconvolution errors. In particular, our calculations reveal that polychromatic illumination causes 10-times higher deconvolution errors than sequential monochromatic LED illumination. In conclusion, our model can be used for a quantitative assessment of system components - and also to assess and compare colour deconvolution methods.
Identification of a novel lymphoid population in the murine epidermis
Authors: Almeida Francisca F. , Tenno Mari , Brzostek Joanna , Li Jackson LiangYao , Allies Gabriele , Hoeffel Guillaume , See Peter , Ng Lai Guan , Fehling Hans Jörg , Gascoigne Nicholas R. J. , Taniuchi Ichiro , Ginhoux Florent 
Published: July 2015

AbstractT cell progenitors are known to arise from the foetal liver in embryos and the bone marrow in adults; however different studies have shown that a pool of T cell progenitors may also exist in the periphery. Here, we identified a lymphoid population resembling peripheral T cell progenitors which transiently seed the epidermis during late embryogenesis in both wild-type and T cell-deficient mice. We named these cells ELCs (Epidermal Lymphoid Cells). ELCs expressed Thy1 and CD2, but lacked CD3 and TCRαβ/γδ at their surface, reminiscent of the phenotype of extra- or intra- thymic T cell progenitors. Similarly to Dendritic Epidermal T Cells (DETCs), ELCs were radioresistant and capable of self-renewal. However, despite their progenitor-like phenotype and expression of T cell lineage markers within the population, ELCs did not differentiate into conventional T cells or DETCs in in vitro, ex vivo or in vivo differentiation assays. Finally, we show that ELC expressed NK markers and secreted IFN-γ upon stimulation. Therefore we report the discovery of a unique population of lymphoid cells within the murine epidermis that appears related to NK cells with as-yet-unidentified functions.
Selective Generation of Dopaminergic Precursors from Mouse Fibroblasts by Direct Lineage Conversion
Authors: Tian Changhai , Li Yuju , Huang Yunlong , Wang Yongxiang , Chen Dapeng , Liu Jinxu , Deng Xiaobei , Sun Lijun , Anderson Kristi , Qi Xinrui , Li Yulong , Lee Mosley R. , Chen Xiangmei , Huang Jian , Zheng Jialin C. 
Published: July 2015

AbstractDegeneration of midbrain dopaminergic (DA) neurons is a key pathological event of Parkinson’s disease (PD). Limited adult dopaminergic neurogenesis has led to novel therapeutic strategies such as transplantation of dopaminergic precursors (DPs). However, this strategy is currently restrained by a lack of cell source, the tendency for the DPs to become a glial-restricted state and the tumor formation after transplantation. Here, we demonstrate the direct conversion of mouse fibroblasts into induced DPs (iDPs) by ectopic expression of Brn2, Sox2 and Foxa2. Besides expression with neural progenitor markers and midbrain genes including Corin, Otx2 and Lmx1a, the iDPs were restricted to dopaminergic neuronal lineage upon differentiation. After transplantation into MPTP-lesioned mice, iDPs differentiated into DA neurons, functionally alleviated the motor deficits and reduced the loss of striatal DA neuronal axonal termini. Importantly, no iDPs-derived astroctyes and neoplasia were detected in mouse brains after transplantation. We propose that the iDPs from direct reprogramming provides a safe and efficient cell source for PD treatment.
SIMULATED PHOTOEVAPORATIVE MASS LOSS FROM HOT JUPITERS IN 3D
Authors: Tripathi Anjali , Kratter Kaitlin M. , Murray-Clay Ruth A. , Krumholz Mark R. 
Published: July 2015

ABSTRACT
Ionizing stellar photons heat the upper regions of planetary atmospheres, driving atmospheric mass loss. Gas escaping from several hot, hydrogen-rich planets has been detected using UV and X-ray transmission spectroscopy. Because these planets are tidally locked, and thus asymmetrically irradiated, escaping gas is unlikely to be spherically symmetric. In this paper, we focus on the effects of asymmetric heating on local outflow structure. We use the Athena code for hydrodynamics to produce 3D simulations of hot Jupiter mass loss that jointly model wind launching and stellar heating via photoionization. Our fiducial planet is an inflated, hot Jupiter with radius

and mass

. We irradiate the initially neutral, atomic hydrogen atmosphere with 13.6 eV photons and compute the outflow’s ionization structure. There are clear asymmetries in the atmospheric outflow, including a neutral shadow on the planet’s nightside. Given an incident ionizing UV flux comparable to that of the Sun, we find a steady-state mass loss rate of

g s−1. The total mass loss rate and the outflow substructure along the substellar ray show good agreement with earlier 1D models, for two different fluxes. Our 3D data cube can be used to generate the outflow’s extinction spectrum during transit. As a proof of concept, we find absorption of stellar Lyα at Doppler-shifted velocities of up to ±50 km s−1. Our work provides a starting point for further 3D models that can be used to predict observable signatures of hot Jupiter mass loss.
Metabolic Syndrome and Cardiovascular Risk in Elderly Treated
Hypertensive Patients
Authors: Pierdomenico Sante D. , Pierdomenico Anna M. , Di Tommaso Roberta , Coccina Francesca , Di Carlo Silvio , Cuccurullo Franco , Porreca Ettore 
Published: July 2015

Abstract

BACKGROUND
The independent prognostic significance of the metabolic syndrome (MetS) in the elderly is not yet clear. We investigated the association between MetS and cardiovascular risk (composite endpoint of stroke and coronary events) in elderly treated hypertensive patients.

METHODS
Cardiovascular outcome was evaluated in 1,191 elderly treated hypertensive patients (≥60 years). Among them, 578 (48.5%) had MetS according to a modified joint interim statement definition (body mass index in place of waist circumference).

RESULTS
During the follow-up (9.1±4.9 years, range 0.4–20 years), 139 strokes and 120 coronary events occurred. In univariate analysis, patients with MetS had higher risk of the composite endpoint (hazard ratio (HR) 1.322, 95% confidence interval (CI) 1.035–1.688, P &lt; 0.05). Among the single components of MetS, only blood pressure (BP) level and impaired fasting glucose/diabetes were significantly associated with increased cardiovascular risk. After adjustment for age, previous events, estimated glomerular filtration rate (eGFR), left ventricular (LV) hypertrophy and left atrial (LA) enlargement, the prognostic relevance of MetS was attenuated (HR 1.245, 95% CI 0.974–1.591, P = 0.08). After further adjustment for the above-mentioned variables and ambulatory BP parameters and impaired fasting glucose/diabetes, Cox regression analysis showed that MetS was not independently associated with increased cardiovascular risk (HR 1.090, 95% CI 0.805–1.475, P = 0.58).

CONCLUSIONS
In elderly treated hypertensive patients, MetS is associated with increased cardiovascular risk, but not independently of BP and glucose levels and of organ damage.
SNPGenie: estimating evolutionary parameters to detect natural selection using pooled next-generation sequencing data
Authors: Nelson Chase W. , Moncla Louise H. , Hughes Austin L. 
Published: July 2015

Abstract
Summary: New applications of next-generation sequencing technologies use pools of DNA from multiple individuals to estimate population genetic parameters. However, no publicly available tools exist to analyse single-nucleotide polymorphism (SNP) calling results directly for evolutionary parameters important in detecting natural selection, including nucleotide diversity and gene diversity. We have developed SNPGenie to fill this gap. The user submits a FASTA reference sequence(s), a Gene Transfer Format (.GTF) file with CDS information and a SNP report(s) in an increasing selection of formats. The program estimates nucleotide diversity, distance from the reference and gene diversity. Sites are flagged for multiple overlapping reading frames, and are categorized by polymorphism type: nonsynonymous, synonymous, or ambiguous. The results allow single nucleotide, single codon, sliding window, whole gene and whole genome/population analyses that aid in the detection of positive and purifying natural selection in the source population.
Availability and implementation: SNPGenie version 1.2 is a Perl program with no additional dependencies. It is free, open-source, and available for download at https://github.com/hugheslab/snpgenie.
Contact: nelsoncw@email.sc.edu or austin@biol.sc.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
Zakat on retirement and pension plans
Authors: Rahman Shafiqur 
Published: July 2015

Purpose
– This paper aims to compare and contrast alternative pension plans in the market place and their status as zakatable wealth or property. These plans differ in terms of who is responsible for providing funds for pension benefit to the retirees upon retirement and who is responsible for bearing investment risk. Whether a pension plan is subject to zakat immediately or upon receipt at retirement depends on immediate accessibility to and ownership of the funds in the account. It makes no difference whether employer and/or the employee is (are) responsible for funding the plan and who bears the investment risk.

Design/methodology/approach
– Descriptive and analytical methods were used.

Findings
– There is consensus among Muslim jurists and shariah scholars that mandatory retirement plans offered as a part of compensation and benefit package for a job are subject to zakat when money is received upon retirement and non-mandatory plans offered as replacement for or supplement to employer-sponsored plans with voluntary employee participation are subject to zakat in each year of employment.

Originality/value
– There is no prior research work in the extant literature examining zakatability of alternative retirement plans offered in the US marketplace. This paper fills this void and provides a comprehensive survey and analysis of all available retirement plans and their treatment with respect to zakat.
Mental representation of brands: a schema-based approach to consumers’ organization of market knowledge
Authors: Halkias Georgios 
Published: July 2015

Purpose
– This paper aims to review the notion of schemata in consumer behavior, placing particular emphasis on the conceptualization of brand knowledge, and illustrate how schema theory may act as a unifying conceptual framework to study what consumers know about products and brands. Extant research on how consumers conceptualize brands lacks a single, coherent theoretical framework. The literature is fragmented into different approaches that may prevent comparisons across studies and make it difficult to draw conclusive results.

Design/methodology/approach
– The paper discusses the central tenets of schema theory and then presents the structure of schematic knowledge and the main typology of consumer schemata. It focuses on the brand schema, delineating its internal properties and drawing analogies with other approaches used to describe consumers’ mental representation of brands.

Findings
– Schema theory can provide a comprehensive framework to analyze how consumers perceive brand information. A cognitive schema specifies the parameters of knowledge content, discriminates between different types of information and indicates how various pieces of information relate to one another. Importantly, the internal structure of schemata remains stable across conceptual domains, allowing to investigate brand-specific knowledge in different contexts and in conjunction with superordinate and subordinate knowledge structures.

Originality/value
– This is the first systematic review of the notion of schemata in consumer behavior. It thoroughly describes how schema theory from psychology has been applied in marketing research to describe the organization of market knowledge and illustrates how it may function as an analytical tool.
Crowding out, diversion, and benefit/cost assessments in fertilizer subsidy programs in sub‐Saharan Africa: a comment on Jayne, T.S., Mather, D., Mason, N., Ricker‐Gilbert, J., 2013. How do fertilizer subsidy programs affect total fertilizer use in sub‐Saharan Africa? Crowding out, diversion, and benefit/cost assessments. Agric. Econ. 44(6), 687–703
Authors: Dorward A. R. , Chirwa E. W. 
Published: July 2015

AbstractJayne et al. make a valuable contribution to emerging empirical evidence on agricultural input subsidy programs in Africa by examining the effects of corrupt “diversion” of subsidized fertilizers on the displacement or crowding out effects of farmers’ purchases of subsidized fertilizer on purchases of unsubsidized fertilizer. Unfortunately, their estimation of the effects of this on economic and financial benefit cost ratios (BCRs) is methodologically flawed and, for Malawi, is also undermined by problematic use of data. This comment presents a consistent methodology for revised estimates of both economic BCR and fiscal efficiency for the Malawi program. This shows that the underlying economic BCR of subsidized fertilizers in Malawi has been higher than estimated by Jayne et al. and is largely unaffected by diversion and displacement, but that the fiscal efficiency of investments in the program is strongly affected by diversion and displacement in program implementation.
Emergence of methicillin‐resistant coagulase‐negative staphylococci resistant to linezolid with rRNA gene C2190T and G2603T mutations
Authors: Cidral Thiago André , Carvalho Maria Cícera , Figueiredo Agnes Marie Sá , de Melo Maria Celeste Nunes 
Published: July 2015

The aim of this article were to determinate the mechanism of linezolid resistance in coagulase‐negative methicillin‐resistant staphylococci from hospitals in the northeast of Brazil. We identified the isolates using VITEK® 2 and MALDI‐TOF. Susceptibility to antibiotics was measured by the disk‐diffusion method and by Etest®. Extraction of the whole genome DNA was performed, followed by screening of all the strains for the presence of mecA and cfr genes. The domain V region of 23S rRNA gene was sequenced and then aligned with a linezolid‐susceptible reference strain. Pulsed‐field gel electrophoresis (PFGE) macro‐restriction analysis was performed. Three linezolid‐resistant Staphylococcus hominis and two linezolid‐resistant Staphylococcus epidermidis strains were analyzed. The isolates showed two point mutations in the V region of the 23S rRNA gene (C2190T and G2603T). We did not detect the cfr gene in any isolate by PCR. The S. hominis showed the same pulsotype, while the S. epidermidis did not present any genetic relation to each other. In conclusion, this study revealed three S. hominis and two S. epidermidis strains with resistance to linezolid due to a double mutation (C2190T and G2603T) in the domain V of the 23S rRNA gene. For the first time, the mutation of C2190T in S. epidermidis is described. This study also revealed the clonal spread of a S. hominis pulsotype between three public hospitals in the city of Natal, Brazil. These findings highlight the importance of continued vigilance of linezolid resistance in staphylococci.
Resting‐State Functional Brain Networks in Parkinson's Disease
Authors: Baggio Hugo C. , Segura Bàrbara , Junque Carme 
Published: July 2015

SummaryThe network approach is increasingly being applied to the investigation of normal brain function and its impairment. In the present review, we introduce the main methodological approaches employed for the analysis of resting‐state neuroimaging data in Parkinson's disease studies. We then summarize the results of recent studies that used a functional network perspective to evaluate the changes underlying different manifestations of Parkinson's disease, with an emphasis on its cognitive symptoms. Despite the variability reported by many studies, these methods show promise as tools for shedding light on the pathophysiological substrates of different aspects of Parkinson's disease, as well as for differential diagnosis, treatment monitoring and establishment of imaging biomarkers for more severe clinical outcomes.
Jewellery: alloy composition and release of nickel, cobalt and lead assessed with the EU synthetic sweat method
Authors: Hamann Dathan , Thyssen Jacob P. , Hamann Carsten R. , Hamann Curtis , Menné Torkil , Johansen Jeanne D. , Spiewak Radoslaw , Maibach Howard , Lundgren Lennart , Lidén Carola 
Published: July 2015

SummaryBackgroundSeveral studies have shown nickel and cobalt release from jewellery by using spot tests, but the metal composition of jewellery is largely unknown.ObjectivesTo evaluate the metal composition of a large worldwide sample of mainly inexpensive jewellery items, and investigate the release of nickel, cobalt and lead from a subsample by using EN 1811:1998‐required methods.MethodsA total of 956 metallic jewellery components were examined with X‐ray fluorescence spectroscopy. A subsample of 96 jewellery items purchased in the United States were investigated for nickel, cobalt and lead release by the use of artificial sweat immersion and plasma optical emission spectroscopy.ResultsEighteen elements were detected. The 10 most frequently occurring were, in order of frequency, copper, iron, zinc, nickel, silver, chromium, tin, manganese, lead, and cobalt. Release of nickel was noted from 79 of the 96 US samples (0.01–98 µg/cm2/week), release of cobalt from 35 samples (0.02–0.5 µg/cm2/week), and release of lead from 37 samples (0.03–2718 µg/cm2/week).ConclusionsWe present here a comprehensive list of the most frequently encountered metals in jewellery and fashion accessories. Different allergenic and non‐allergenic metals are utilized. We also report the frequent release of nickel, cobalt and lead from these objects, despite legislative restrictions.
Treating codeine dependence with buprenorphine: Dose requirements and induction outcomes from a retrospective case series in New South Wales, Australia
Authors: Nielsen Suzanne , Bruno Raimondo , Murnion Bridin , Dunlop Adrian , Degenhardt Louisa , Demirkol Apo , Muhleisen Peter , Lintzeris Nicholas 
Published: July 2015

AbstractIntroduction and AimsCodeine dependence is an emerging public health concern, yet no studies have specifically examined the treatment of codeine dependence. Given the lower potency of codeine it cannot be assumed that buprenorphine dose requirements for heroin dependence will generalise to codeine. This is the first study to examine buprenorphine treatment for codeine dependence.Design and MethodsRetrospective case series of 19 codeine‐dependent treatment entrants who received sublingual buprenorphine maintenance treatment through six specialist inpatient and outpatient treatment centres. Baseline codeine doses and buprenorphine dose at days 7 and 28 were collected, in addition to details on general demographics, pain and mental health, substance use and outcomes after 28 days of buprenorphine treatment.ResultsA significant linear relationship was found between initial codeine dose and dose of buprenorphine given at days 7 and 28 for the codeine dose range of 50–960 mg day−1 (mean: 564 mg; 95% confidence interval 431–696 mg). Median buprenorphine dose was 12.0 mg (interquartile range 9.5 mg, range 4–32 mg) at day 7 and 16.0 mg (interquartile range 13.5 mg, range 4–32 mg) at day 28. Buprenorphine doses received were markedly higher than estimated codeine doses based on standard dose conversion tables.Discussion and ConclusionsWith increasing presentations relating to codeine dependence, these findings provide important guidance to clinicians. Buprenorphine doses were consistently higher than doses estimated based on the dose of codeine consumed, and were comparable with doses used in the treatment of dependence with heroin and more potent prescription opioids. [Nielsen S, Bruno R, Murnion B, Dunlop A, Degenhardt L, Demirkol A, Muhleisen P, Lintzeris N. Treating codeine dependence with buprenorphine: Dose requirements and induction outcomes from a retrospective case series in New South Wales, Australia. Drug Alcohol Rev 2015]
Triptans attenuate circadian responses to light
Authors: Basu Priyoneel , Ie Naomi , Wensel Adrienne L. , Baskerville Joelle D. , Smith Victoria M. , Antle Michael C. 
Published: July 2015

AbstractDaily exposure to light synchronizes the circadian clock, located in the suprachiasmatic nucleus (SCN), to external day/night cycles. These responses to light can be modified by serotonergic drugs, such as serotonin 5HT1B receptor agonists. Triptans are specific 5HT1B agonists prescribed to treat migraines. Here, we examined the effects of two triptans (zolmitriptan and sumatriptan) on photic phase resetting in Syrian hamsters. Pre‐treatment with intra‐SCN sumatriptan significantly attenuates, and at higher doses completely blocks, phase advances to light during the late night. Pre‐treatment with systemic zolmitriptan significantly attenuates both light‐induced phase advances and phase delays. Neither of these drugs, nor their vehicles, causes phase shifts on their own. Pre‐treatment with zolmitriptan also significantly reduces the expression of light‐induced c‐fos in the SCN. Neither zolmitriptan nor vehicle alone induces significant c‐fos expression in the SCN. Finally, pre‐treatment with zolmitriptan does not attenuate phase shifts to intra‐SCN N‐methyl‐d‐aspartate injections, indicating that the mechanism of action for zolmitriptan is likely to be through activation of presynaptic 5HT1B receptors on retinal terminals, thereby decreasing light‐induced neurotransmitter release. As triptans are commercially available medications, there is potential for their use in blocking unwanted photic phase shifting during shift‐work or jet‐lag. Additionally, triptans may also affect the circadian clock in patients receiving them regularly for migraines. Finally, our results may hint at the mechanism by which triptans can alleviate the photophobia that frequently accompanies migraines, namely by activating 5HT1B receptors on retinal terminals elsewhere in the brain, and thereby diminishing visually‐evoked neurotransmitter signalling in those areas.