bluuebunny/crossref_metadata_2025_split huggingface dataset:
Reading Galileo’sDiscorsiin the Early Modern University*
Authors: Raphael Renée J. 
Published: June 2015

AbstractThis article examines the scholarly practices with which readers at three universities read select passages from Galileo’s 1638Discorsi,a work depicted by Galileo as one that eschewed the goals and methods of Aristotelian natural philosophy in favor of the quantitative and experimental ones characteristic of modern science. The article reveals that a group of readers — diverse in terms of institutional affiliation, disciplinary identity, geography, and attitude toward Galileo — approached Galileo’s text using the tools of what Ann Blair has termed “bookish” natural philosophy. It argues that, contrary to Galileo’s rhetoric, these readers saw old and new methods as interchangeable.
Operator Lipschitz estimates in the unitary setting
Authors: Ayre P. , Cowling M. , Sukochev F. 
Published: June 2015

We develop a Lipschitz estimate for unitary operators. More specifically, we show that for each

p
∈
(
1
,
∞
)

p\in (1,\infty )

there exists a constant

d
p

d_p

such that

‖
f
(
U
)
−
f
(
V
)
‖

p

≤

d
p

‖
U
−
V
‖

p

\left \Vert f(U) - f(V)\right \Vert _p \leq d_p \left \Vert U - V\right \Vert _p

for all Lipschitz functions

f
:

T

→

C

f: \mathbb {T} \to \mathbb {C}

and unitary operators

U
U

and

V
V

.
FinisherSC: a repeat-aware tool for upgrading de novo assembly using long reads
Authors: Lam Ka-Kit , LaButti Kurt , Khalak Asif , Tse David 
Published: June 2015

Abstract
We introduce FinisherSC, a repeat-aware and scalable tool for upgrading de novo assembly using long reads. Experiments with real data suggest that FinisherSC can provide longer and higher quality contigs than existing tools while maintaining high concordance.
Availability and implementation: The tool and data are available and will be maintained at http://kakitone.github.io/finishingTool/
Contact: dntse@stanford.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
Modelling the effect of antimicrobial treatment on carriage of hospital pathogens with application to MRSA
Authors: Verykouki E. , Kypraios T. , O'neill P.D. 
Published: June 2015

Abstract
Numerous studies have sought to assess the effectiveness of control measures aimed at reducing the spread of pathogens such as Methicillin-resistant Staphylococcus aureus (MRSA) in hospital settings. Far less is known about possible short-term effects of antibiotics and other antimicrobial treatments on pathogen carriage in patients. This paper is concerned with developing and applying methods for the analysis of detailed data on hospital patients which include information on patient treatments and screening tests for the pathogen in question. The carriage status (colonized, or not) of each patient is modelled as a Markov chain, and models for both perfect and imperfect test sensitivity are developed. Goodness-of-fit procedures based on simulation are also proposed. The methods are illustrated using both simulated data and data on MRSA.
Birth month affects lifetime disease risk: a phenome-wide method
Authors: Boland Mary Regina , Shahn Zachary , Madigan David , Hripcsak George , Tatonetti Nicholas P 
Published: June 2015

AbstractObjective An individual’s birth month has a significant impact on the diseases they develop during their lifetime. Previous studies reveal relationships between birth month and several diseases including atherothrombosis, asthma, attention deficit hyperactivity disorder, and myopia, leaving most diseases completely unexplored. This retrospective population study systematically explores the relationship between seasonal affects at birth and lifetime disease risk for 1688 conditions.Methods We developed a hypothesis-free method that minimizes publication and disease selection biases by systematically investigating disease-birth month patterns across all conditions. Our dataset includes 1 749 400 individuals with records at New York-Presbyterian/Columbia University Medical Center born between 1900 and 2000 inclusive. We modeled associations between birth month and 1688 diseases using logistic regression. Significance was tested using a chi-squared test with multiplicity correction.Results We found 55 diseases that were significantly dependent on birth month. Of these 19 were previously reported in the literature (P &lt; .001), 20 were for conditions with close relationships to those reported, and 16 were previously unreported. We found distinct incidence patterns across disease categories.Conclusions Lifetime disease risk is affected by birth month. Seasonally dependent early developmental mechanisms may play a role in increasing lifetime risk of disease.
Sequence-independent characterization of viruses based on the pattern of viral small RNAs produced by the host
Authors: Aguiar Eric Roberto Guimarães Rocha , Olmo Roenick Proveti , Paro Simona , Ferreira Flavia Viana , de Faria Isaque João da Silva , Todjro Yaovi Mathias Honore , Lobo Francisco Pereira , Kroon Erna Geessien , Meignin Carine , Gatherer Derek , Imler Jean-Luc , Marques João Trindade 
Published: June 2015

Abstract
Virus surveillance in vector insects is potentially of great benefit to public health. Large-scale sequencing of small and long RNAs has previously been used to detect viruses, but without any formal comparison of different strategies. Furthermore, the identification of viral sequences largely depends on similarity searches against reference databases. Here, we developed a sequence-independent strategy based on virus-derived small RNAs produced by the host response, such as the RNA interference pathway. In insects, we compared sequences of small and long RNAs, demonstrating that viral sequences are enriched in the small RNA fraction. We also noted that the small RNA size profile is a unique signature for each virus and can be used to identify novel viral sequences without known relatives in reference databases. Using this strategy, we characterized six novel viruses in the viromes of laboratory fruit flies and wild populations of two insect vectors: mosquitoes and sandflies. We also show that the small RNA profile could be used to infer viral tropism for ovaries among other aspects of virus biology. Additionally, our results suggest that virus detection utilizing small RNAs can also be applied to vertebrates, although not as efficiently as to plants and insects.
Use of Oropharyngeal Washes to Diagnose and Genotype Pneumocystis jirovecii
Authors: Juliano Jonathan J. , Barnett Eric , Parobek Christian M. , Taylor Steve M. , Meshnick Steven R. , Stone Stephen , Chang Emily , Fong Serena , Huang Laurence 
Published: June 2015

Abstract
Pneumocystis jirovecii is a symbiotic respiratory fungus that presents in 2 clinical forms: pneumonia in immunocompromised patients or colonization, defined by the presence of the organism without associated clinical symptoms. Currently, diagnosis requires invasive bronchoscopy, which may not be available in some settings and is inappropriate for detecting colonization in healthy individuals. Noninvasive diagnostic techniques and molecular strain typing tools that can be used on these samples are critical for conducting studies to better understand transmission. We evaluated 2 real-time polymerase chain reaction (PCR) assays targeting dihydropteroate synthase and the major surface glycoprotein for detection in 77 oropharyngeal washes (OPWs) from 43 symptomatic human immunodeficiency virus-infected patients who underwent bronchoscopy. We also evaluated the ability of a new microsatellite (MS) genotyping panel to strain type infections from these samples. Each PCR used individually provided a high sensitivity (&gt;80%) for detection of pneumonia but a modest specificity (&lt;70%). When used in combination, specificity was increased to 100% with a drop in sensitivity (74%). Concentration of organisms by PCR in the OPW tended to be lower in colonized individuals compared with those with pneumonia, but differences in concentration could not clearly define colonization in symptomatic individuals. Oropharyngeal wash samples were genotyped using 6 MSs with ≥4 alleles successfully genotyped in the majority of colonized patients and ≥5 alleles in patients with pneumonia. The MS profile was consistent over time within patients with serial OPWs analyzed. Microsatellite genotyping on noninvasive samples may aid in studying the molecular epidemiology of this pathogen without requiring invasive diagnostic techniques.
The AKARI far-infrared all-sky survey maps
Authors: Doi Yasuo , Takita Satoshi , Ootsubo Takafumi , Arimatsu Ko , Tanaka Masahiro , Kitamura Yoshimi , Kawada Mitsunobu , Matsuura Shuji , Nakagawa Takao , Morishima Takahiro , Hattori Makoto , Komugi Shinya , White Glenn J. , Ikeda Norio , Kato Daisuke , Chinone Yuji , Etxaluze Mireya , Cypriano Elysandra F. 
Published: June 2015

Abstract
We present a far-infrared all-sky atlas from a sensitive all-sky survey using the Japanese AKARI satellite. The survey covers &gt; 99% of the sky in four photometric bands centred at 65 μm, 90 μm, 140 μm, and 160 μm, with spatial resolutions ranging from 1′ to 1${^{\prime\prime}_{.}}$5. These data provide crucial information on the investigation and characterisation of the properties of dusty material in the interstellar medium (ISM), since a significant portion of its energy is emitted between ∼ 50 and 200 μm. The large-scale distribution of interstellar clouds, their thermal dust temperatures, and their column densities can be investigated with the improved spatial resolution compared to earlier all-sky survey observations. In addition to the point source distribution, the large-scale distribution of ISM cirrus emission, and its filamentary structure, are well traced. We have made the first public release of the full-sky data to provide a legacy data set for use in the astronomical community.
Revealing progenitors of type Ia supernovae from their light curves and spectra
Authors: Kutsuna Masamichi , Shigeyama Toshikazu 
Published: June 2015

Abstract
In the single degenerate (SD) scenario of type Ia supernovae (SNe Ia), the collision of the ejecta with its companion results in stripping hydrogen-rich matter from the companion star. This hydrogen-rich matter might leave its trace in the light curves and/or spectra. In this paper, we perform radiation hydrodynamical simulations of this collision for three binary systems. As a result, we find that the emission from the shock-heated region is not as strong as in previous studies. This weak emission, however, may be a result of our underestimation of the coupling between the gas and radiation in the shock interaction. Therefore, though our results suggest that the observed early light curves of SNe Ia cannot rule out a binary system with a short separation as the progenitor system, more elaborate numerical studies will be needed to reach a fair conclusion. Alternatively, our results indicate that the feature observed in the early phase of a recent type Ia SN 2014J might result from interaction of the ejecta with a red giant companion star. We also discuss the dependence of spectral features of Hα and Si ii absorption lines on viewing angles and investigate whether they can constrain the event rate of the SD progenitor.
Eddington limit for a gaseous stratus with finite optical depth
Authors: Fukue Jun 
Published: June 2015

Abstract
The Eddington luminosity of a spherical source is usually defined for a uniformly extending normal plasma. We usually suppose that the gas can accrete to the central object at the sub-Eddington luminosity, while it would be blown off from the central luminous source in the super-Eddington case. We reconsider this central dogma of the Eddington limit under the radiative transfer effect for the purely scattering case, using analytical and numerical methods. For the translucent isolated gas cloud (stratus) with finite optical depth, the concept of the Eddington luminosity is drastically changed. In an heuristic way, we find that the critical condition is approximately expressed as Γ = (1 + μ* + τc)/2, where Γ (=L/LE) is the central luminosity L normalized by the Eddington luminosity LE, τc is the optical depth of the stratus, and μ* ($=\sqrt{1-R_*^2/R^2}$) is the direction cosine of the central object, R* being the radius of the central object, and R the distance from the central object. When the optical depth of the stratus is around unity, the classical Eddington limit roughly holds for the stratus; Γ ∼ 1. However, when the optical depth is greater than unity, the critical condition becomes roughly Γ ∼ τc/2, and the stratus would infall on to the central source even at the highly super-Eddington luminosity. When the optical depth is less than unity, on the other hand, the critical condition reduces to Γ ≳ (1 + μ*)/2, and the stratus could be blown off in some limited ranges, depending on μ*. This new concept of the Eddington limit for the isolated stratus could drastically change the accretion and outflow physics of highly inhomegeneous plasmas, with relevance for astrophysical jets and winds and supermassive black hole formation.
Attitudes towards HIV testing via home-sampling kits ordered online (RUClear pilots 2011–12)
Authors: Ahmed-Little Y. , Bothra V. , Cordwell D. , Freeman Powell D. , Ellis D. , Klapper P. , Scanlon S. , Higgins S. , Vivancos R. 
Published: June 2015

Background
The burden of disease relating to undiagnosed HIV infection is significant in the UK. BHIVA (British HIV Association) recommends population screening in high prevalence areas, expanding outside traditional antenatal/GUM settings.

Methods
RUClear 2011–12 piloted expanding HIV testing outside traditional settings using home-sampling kits (dry-blood-spot testing) ordered online. Greater Manchester residents (≥age 16) could request testing via an established, online chlamydia testing service (www.ruclear.co.uk). Participant attitudes towards this new service were assessed. Qualitative methods (thematic analysis) were used to analyse free-text data submitted by participants via hard copy questionnaires issued in all testing kits.

Results
79.9% (2447/3062) participants completed questionnaires, of which 30.9% (756/2447) provided free-text data. Participants overwhelmingly supported the service, valuing particularly accessibility and convenience, allowing individuals to order tests any time of day and self-sample comfortably at home; avoiding the invasive nature of venipuncture and avoiding the need for face-to-face interaction with health services. The pilot was also clinically and cost-effective.

Conclusion
Testing via home-sampling kits ordered online (dry-blood-spot testing) was felt to be an acceptable and convenient method for accessing a HIV test. Many individuals undertook HIV testing where they would otherwise not have been tested at all. Expansion of similar services may increase the uptake of HIV testing.
Biological Impact of Transpulmonary Driving Pressure in Experimental Acute Respiratory Distress Syndrome
Authors: Samary Cynthia S. , Santos Raquel S. , Santos Cíntia L. , Felix Nathane S. , Bentes Maira , Barboza Thiago , Capelozzi Vera L. , Morales Marcelo M. , Garcia Cristiane S. N. B. , Souza Sergio A. L. , Marini John J. , Gama de Abreu Marcelo , Silva Pedro L. , Pelosi Paolo , Rocco Patricia R. M. 
Published: June 2015

AbstractAbstract
Different combinations of tidal volume and positive end-expiratory pressure (PEEP) were used to create a range of driving pressures in a rat model of acute respiratory distress syndrome due to tracheal instillation of endotoxin for 24 h. Low transpulmonary driving pressure was associated with alveolar collapse and high driving pressure was associated with hyperinflation. The combination of a tidal volume of 6 ml/kg predicted body weight and the lowest PEEP and driving pressure to maintain oxygenation in a normal range minimized ventilator-induced lung injury even in the presence of alveolar collapse.
Supplemental Digital Content is available in the text.

Background:
Ventilator-induced lung injury has been attributed to the interaction of several factors: tidal volume (VT), positive end-expiratory pressure (PEEP), transpulmonary driving pressure (difference between transpulmonary pressure at end-inspiration and end-expiration, ΔP,L), and respiratory system plateau pressure (Pplat,rs).

Methods:
Forty-eight Wistar rats received Escherichia coli lipopolysaccharide intratracheally. After 24 h, animals were randomized into combinations of VT and PEEP, yielding three different ΔP,L levels: ΔP,LLOW (VT = 6 ml/kg, PEEP = 3 cm H2O); ΔP,LMEAN (VT = 13 ml/kg, PEEP = 3 cm H2O or VT = 6 ml/kg, PEEP = 9.5 cm H2O); and ΔP,LHIGH (VT = 22 ml/kg, PEEP = 3 cm H2O or VT = 6 ml/kg, PEEP = 11 cm H2O). In other groups, at low VT, PEEP was adjusted to obtain a Pplat,rs similar to that achieved with ΔP,LMEAN and ΔP,LHIGH at high VT.

Results:
At ΔP,LLOW, expressions of interleukin (IL)-6, receptor for advanced glycation end products (RAGE), and amphiregulin were reduced, despite morphometric evidence of alveolar collapse. At ΔP,LHIGH (VT = 6 ml/kg and PEEP = 11 cm H2O), lungs were fully open and IL-6 and RAGE were reduced compared with ΔP,LMEAN (27.4 ± 12.9 vs. 41.6 ± 14.1 and 0.6 ± 0.2 vs. 1.4 ± 0.3, respectively), despite increased hyperinflation and amphiregulin expression. At ΔP,LMEAN (VT = 6 ml/kg and PEEP = 9.5 cm H2O), when PEEP was not high enough to keep lungs open, IL-6, RAGE, and amphiregulin expression increased compared with ΔP,LLOW (41.6 ± 14.1 vs. 9.0 ± 9.8, 1.4 ± 0.3 vs. 0.6 ± 0.2, and 6.7 ± 0.8 vs. 2.2 ± 1.0, respectively). At Pplat,rs similar to that achieved with ΔP,LMEAN and ΔP,LHIGH, higher VT and lower PEEP reduced IL-6 and RAGE expression.

Conclusion:
In the acute respiratory distress syndrome model used in this experiment, two strategies minimized ventilator-induced lung injury: (1) low VT and PEEP, yielding low ΔP,L and Pplat,rs; and (2) low VT associated with a PEEP level sufficient to keep the lungs open.
Human Milk Fortification Increases Bnip3 Expression Associated With Intestinal Cell Death In Vitro
Authors: Diehl‐Jones William , Archibald Alyssa , Gordon Joseph W. , Mughal Wajihah , Hossain Zakir , Friel James K. 
Published: June 2015

ABSTRACTObjectives:The aim of the present study was to determine the in vitro effect(s) of a bovine‐based human breast milk fortifier (HMF) on human intestinal cells. HMF increases the expression of BCL2/adenovirus E1B 19 kDa protein‐interacting protein (Bnip3) and cell death; the prostaglandin analogue misoprostol will rescue this effect.Methods:Cultured intestinal cells were exposed to in vitro–digested human breast milk (BM) ± HMF. Intracellular oxidation, cell damage/cell death, and BNIP3 expression were measured after exposure.Results:In vitro–digested BM + HMF significantly increased intracellular oxidation, cell damage, and cell death in enterocyte cell cultures compared with either saline or BM controls, an effect that was rescued by the prostaglandin analogue, misoprostol. Bnip3 transcript and Bnip3 protein levels were significantly increased in vitro after treatment with BM + HMF. We also provide evidence that transfection of enterocytes with Bnip3 increases cell death, an effect that is rescued by a nonfunctional Bnip3 splice variant.Conclusions:Our data support the hypothesis that HMF increases intestinal Bnip3 in vitro, and that the gene product triggers cell death. We suggest that misoprostol is a promising therapy, which may reduce intestinal cell death.
Segmenting Microarrays with Deep Neural Networks
Authors: Jones Andrew 
Published: June 2015

AbstractMicroarray images consist of thousands of spots, e ach of which corresponds to a different biological material. The microarray segmentation problem is to work out which pixels belong to which spots, even in presence of noise and corruption. We propose a solution based on deep neural networks, which achieves excellent results both on simulated and experimental data. We have made the source code for our solution available on Github under a permissive license.
Social media models, technologies, and applications
Authors: Ngai Eric W.T. , Moon Ka-leung Karen , Lam S.S. , Chin Eric S. K. , Tao Spencer S.C. 
Published: June 2015

Purpose– In recent years, social media have attracted considerable attention. Hence, the purpose of this paper is to conduct a critical literature review of social media research with the aim of developing a conceptual framework to explain how social media applications are supported by various social media tools and technologies and underpinned by a set of personal and social behavior theories or models.Design/methodology/approach– This study adopted a two-stage approach. The first stage involves a critical literature review of academic journals in social media research, followed by the proposal of a conceptual framework that highlights the tools and technologies as well as theories and models that serve as the foundation of social media applications. The second stage involves the use of an actual case to demonstrate how the proposed framework facilitates the development of a social media application for a regional division of an international non-government organization.Findings– The literature review indicated that social media have been applied in diverse business areas with the support of various social media tools and technologies and underpinned by a range of personal and social behavior theories and models. Based upon such findings, a conceptual social media application framework was devised and its usability illustrated via a real-life case study. Managerial implications are also discussed.Research limitations/implications– Social media covers a wide range of research topics and thus, the literature review presented in this study may not be exhaustive. Nevertheless, the proposed framework and case study can both serve as reference for future research and provide recommendations for practitioners in the design and development of their own social media applications.Practical implications– This study not only explains the importance of applying social media in various business sectors, but also enhances the understanding of the infrastructure of social media applications. The study also provides insights for improving the efficiency of application solutions. Organizations are advised to adopt social media in their business based on the proposed conceptual framework.Originality/value– With a literature review of social media research and a real-life case study, this study presents a conceptual framework using extant theories and models to form a foundation for social media applications. The framework extends existing knowledge on the design and development of information systems.
Solving two-dimensional Markov chain model for call centers
Authors: Liang Chih-Chin , Luh Hsing 
Published: June 2015

Purpose
– The purpose of this paper is to develop a novel model of a call center that must treat calls with distinctly different service depending on whether they orginate from VIP or regular customers. VIP calls must be responded to immediately but regular calls can be routed to a retrial queue if the operators are busy.

Design/methodology/approach
– This study’s proposed model can easily reveal the optimal arrangement of operators while minimizing computational time and without losing any precision of the performance measure when dealing with a call center with more operators.

Findings
– Based on the results of the comparison between the exact method and the proposed approximation method, the approach shows that the larger the number of operators or inbound calls, the smaller the error between the two methods.

Originality/value
– This investigation presents a computational method and management cost function intended to identify the optimal number of operators for a call center. Because of computational limitations, many operators could not be easily analyzed using the exact method. For the manager of a call center, the sooner the optimal solution is found, the faster business strategies are deployed. This study develops an approximation method and compares it with the exact method.