bluuebunny/crossref_metadata_2025_split huggingface dataset:
Instability of 8E5 calibration standard revealed by digital PCR risks inaccurate quantification of HIV DNA in clinical samples by qPCR
Authors: Busby Eloise , Whale Alexandra S. , Ferns R. Bridget , Grant Paul R. , Morley Gary , Campbell Jonathan , Foy Carole A. , Nastouli Eleni , Huggett Jim F. , Garson Jeremy A. 
Published: April 2017

AbtractEstablishing a cure for HIV is hindered by the persistence of latently infected cells which constitute the viral reservoir. Real-time qPCR, used for quantification of this reservoir by measuring HIV DNA, requires external calibration; a common choice of calibrator is the 8E5 cell line, which is assumed to be stable and to contain one HIV provirus per cell. In contrast, digital PCR requires no external calibration and potentially provides ‘absolute’ quantification. We compared the performance of qPCR and dPCR in quantifying HIV DNA in 18 patient samples. HIV DNA was detected in 18 by qPCR and in 15 by dPCR, the difference being due to the smaller sample volume analysed by dPCR. There was good quantitative correlation (R2 = 0.86) between the techniques but on average dPCR values were only 60% of qPCR values. Surprisingly, investigation revealed that this discrepancy was due to loss of HIV DNA from the 8E5 cell calibrant. 8E5 extracts from two other sources were also shown to have significantly less than one HIV DNA copy per cell and progressive loss of HIV from 8E5 cells during culture was demonstrated. We therefore suggest that the copy number of HIV in 8E5 extracts be established by dPCR prior to use as calibrator.
Phonon-mediated repulsion, sharp transitions and (quasi)self-trapping in the extended Peierls-Hubbard model
Authors: Sous J. , Chakraborty M. , Adolphs C. P. J. , Krems R. V. , Berciu M. 
Published: April 2017

AbstractWe study two identical fermions, or two hard-core bosons, in an infinite chain and coupled to phonons by interactions that modulate their hopping as described by the Peierls/Su-Schrieffer-Heeger (SSH) model. We show that exchange of phonons generates effective nearest-neighbor repulsion between particles and also gives rise to interactions that move the pair as a whole. The two-polaron phase diagram exhibits two sharp transitions, leading to light dimers at strong coupling and the flattening of the dimer dispersion at some critical values of the parameters. This dimer (quasi)self-trapping occurs at coupling strengths where single polarons are mobile. This illustrates that, depending on the strength of the phonon-mediated interactions, the coupling to phonons may completely suppress or strongly enhance quantum transport of correlated particles.
A reconfigurable all-optical ultrasound transducer array for 3D endoscopic imaging
Authors: Alles Erwin J. , Fook Sheung Nora , Noimark Sacha , Zhang Edward Z. , Beard Paul C. , Desjardins Adrien E. 
Published: April 2017

AbstractA miniature all-optical ultrasound imaging system is presented that generates three-dimensional images using a stationary, real acoustic source aperture. Discrete acoustic sources were sequentially addressed by scanning a focussed optical beam across the proximal end of a coherent fibre bundle; high-frequency ultrasound (156% fractional bandwidth centred around 13.5 MHz) was generated photoacoustically in the corresponding regions of an optically absorbing coating deposited at the distal end. Paired with a single fibre-optic ultrasound detector, the imaging probe (3.5 mm outer diameter) achieved high on-axis resolutions of 97 μm, 179 μm and 110 μm in thex,yandzdirections, respectively. Furthermore, the optical scan pattern, and thus the acoustic source array geometry, was readily reconfigured. Implementing four different array geometries revealed a strong dependency of the image quality on the source location pattern. Thus, by employing optical technology, a miniature ultrasound probe was fabricated that allows for arbitrary source array geometries, which is suitable for three-dimensional endoscopic and laparoscopic imaging, as was demonstrated onex vivoporcine cardiac tissue.
Holocene winter climate variability in Central and Eastern Europe
Authors: Perșoiu Aurel , Onac Bogdan P. , Wynn Jonathan G. , Blaauw Maarten , Ionita Monica , Hansson Margareta 
Published: April 2017

AbstractAmong abundant reconstructions of Holocene climate in Europe, only a handful has addressed winter conditions, and most of these are restricted in length and/or resolution. Here we present a record of late autumn through early winter air temperature and moisture source changes in East-Central Europe for the Holocene, based on stable isotopic analysis of an ice core recovered from a cave in the Romanian Carpathian Mountains. During the past 10,000 years, reconstructed temperature changes followed insolation, with a minimum in the early Holocene, followed by gradual and continuous increase towards the mid-to-late-Holocene peak (between 4-2 kcal BP), and finally by a decrease after 0.8 kcal BP towards a minimum during the Little Ice Age (AD 1300–1850). Reconstructed early Holocene atmospheric circulation patterns were similar to those characteristics of the negative phase of the North Atlantic Oscillation (NAO), while in the late Holocene they resembled those prevailing in the positive NAO phase. The transition between the two regimes occurred abruptly at around 4.7 kcal BP. Remarkably, the widespread cooling at 8.2 kcal BP is not seen very well as a temperature change, but as a shift in moisture source, suggesting weaker westerlies and increased Mediterranean cyclones penetrating northward at this time.
RETRACTED ARTICLE: MicroRNA-27a-3p Modulates the Wnt/β-Catenin Signaling Pathway to Promote Epithelial-Mesenchymal Transition in Oral Squamous Carcinoma Stem Cells by Targeting SFRP1
Authors: Qiao Bin , He Bao-Xia , Cai Jing-Hua , Tao Qian , King-yin Lam Alfred 
Published: April 2017

AbstractThis study aimed to elucidate how microRNA27a-3p (miR-27a-3p) modulates the Wnt/β-catenin signaling pathway to promote the epithelial-mesenchymal transition (EMT) in oral squamous carcinoma stem cells (OSCSCs) by targeting secreted frizzled-related protein 1 (SFRP1). Flow cytometry was used to sort OSCSCs from the SCC-9 and Tca8113 cell lines. The OSCSCs were randomly assigned into the miR-27a-3p inhibitors group, the miR-27a-3p inhibitors-NC group, the si-SFRP1 group, the si-SFRP1 + miR-27a-3p inhibitors group and the blank group. A luciferase reporter, immunofluorescence and Transwell assays were performed to detect luciferase activity, SFRP1, and cell migration and invasion, respectively. The mRNA expression of miR-27a-3p, SFRP1 and EMT markers (E-cadherin, N-cadherin, vimentin and ZEB1) were detected using qRT-PCR. The protein expression of SFRP1, EMT markers and the proteins of the Wnt/β-catenin signaling pathway was detected by Western blotting. OSCSCs showed up-regulated miR-27a-3p, Wnt/β-catenin signaling pathway-related proteins, vimentin, N-cadherin and ZEB1 and down-regulated SFRP1 and E-cadherin. MiR-27a-3p targeted SFRP1. Down-regulated miR-27a-3p resulted in increased E-cadherin and SFRP1 but decreased vimentin, N-cadherin, ZEB1, the Wnt/β-catenin signaling pathway-related proteins, and invasive and migratory cells. Silenced SFRP1 reversed this effect. We found that miR-27a-3p modulated the Wnt/β-catenin signaling pathway to promote EMT in OSCSCs by down-regulating SFRP1.
Transcriptome Analysis of Mango (Mangifera indica L.) Fruit Epidermal Peel to Identify Putative Cuticle-Associated Genes
Authors: Tafolla-Arellano Julio C. , Zheng Yi , Sun Honghe , Jiao Chen , Ruiz-May Eliel , Hernández-Oñate Miguel A. , González-León Alberto , Báez-Sañudo Reginaldo , Fei Zhangjun , Domozych David , Rose Jocelyn K. C. , Tiznado-Hernández Martín E. 
Published: April 2017

AbstractMango fruit (Mangifera indica L.) are highly perishable and have a limited shelf life, due to postharvest desiccation and senescence, which limits their global distribution. Recent studies of tomato fruit suggest that these traits are influenced by the expression of genes that are associated with cuticle metabolism. However, studies of these phenomena in mango fruit are limited by the lack of genome-scale data. In order to gain insight into the mango cuticle biogenesis and identify putative cuticle-associated genes, we analyzed the transcriptomes of peels from ripe and overripe mango fruit using RNA-Seq. Approximately 400 million reads were generated and de novo assembled into 107,744 unigenes, with a mean length of 1,717 bp and with this information an online Mango RNA-Seq Database (http://bioinfo.bti.cornell.edu/cgi-bin/mango/index.cgi) which is a valuable genomic resource for molecular research into the biology of mango fruit was created. RNA-Seq analysis suggested that the pathway leading to biosynthesis of the cuticle component, cutin, is up-regulated during overripening. This data was supported by analysis of the expression of several putative cuticle-associated genes and by gravimetric and microscopic studies of cuticle deposition, revealing a complex continuous pattern of cuticle deposition during fruit development and involving substantial accumulation during ripening/overripening.
Invasion of Ancestral Mammals into Dim-light Environments Inferred from Adaptive Evolution of the Phototransduction Genes
Authors: Wu Yonghua , Wang Haifeng , Hadly Elizabeth A. 
Published: April 2017

AbstractNocturnality is a key evolutionary innovation of mammals that enables mammals to occupy relatively empty nocturnal niches. Invasion of ancestral mammals into nocturnality has long been inferred from the phylogenetic relationships of crown Mammalia, which is primarily nocturnal, and crown Reptilia, which is primarily diurnal, although molecular evidence for this is lacking. Here we used phylogenetic analyses of the vision genes involved in the phototransduction pathway to predict the diel activity patterns of ancestral mammals and reptiles. Our results demonstrated that the common ancestor of the extant Mammalia was dominated by positive selection for dim-light vision, supporting the predominate nocturnality of the ancestral mammals. Further analyses showed that the nocturnality of the ancestral mammals was probably derived from the predominate diurnality of the ancestral amniotes, which featured strong positive selection for bright-light vision. Like the ancestral amniotes, the common ancestor of the extant reptiles and various taxa in Squamata, one of the main competitors of the temporal niches of the ancestral mammals, were found to be predominate diurnality as well. Despite this relatively apparent temporal niche partitioning between ancestral mammals and the relevant reptiles, our results suggested partial overlap of their temporal niches during crepuscular periods.
Estimating the irreversible pressure drop across a stenosis by quantifying turbulence production using 4D Flow MRI
Authors: Ha Hojin , Lantz Jonas , Ziegler Magnus , Casas Belen , Karlsson Matts , Dyverfeldt Petter , Ebbers Tino 
Published: April 2017

AbstractThe pressure drop across a stenotic vessel is an important parameter in medicine, providing a commonly used and intuitive metric for evaluating the severity of the stenosis. However, non-invasive estimation of the pressure drop under pathological conditions has remained difficult. This study demonstrates a novel method to quantify the irreversible pressure drop across a stenosis using 4D Flow MRI by calculating the total turbulence production of the flow. Simulation MRI acquisitions showed that the energy lost to turbulence production can be accurately quantified with 4D Flow MRI within a range of practical spatial resolutions (1–3 mm; regression slope = 0.91, R2 = 0.96). The quantification of the turbulence production was not substantially influenced by the signal-to-noise ratio (SNR), resulting in less than 2% mean bias at SNR > 10. Pressure drop estimation based on turbulence production robustly predicted the irreversible pressure drop, regardless of the stenosis severity and post-stenosis dilatation (regression slope = 0.956, R2 = 0.96). In vitro validation of the technique in a 75% stenosis channel confirmed that pressure drop prediction based on the turbulence production agreed with the measured pressure drop (regression slope = 1.15, R2 = 0.999, Bland-Altman agreement = 0.75 ± 3.93 mmHg).
Differences in salicylic acid glucose conjugations by UGT74F1 and UGT74F2 from Arabidopsis thaliana
Authors: George Thompson Alayna M. , Iancu Cristina V. , Neet Kenneth E. , Dean John V. , Choe Jun-yong 
Published: April 2017

AbstractSalicylic acid (SA) is a signaling molecule utilized by plants in response to various stresses. Through conjugation with small organic molecules such as glucose, an inactive form of SA is generated which can be transported into and stored in plant vacuoles. In the model organism Arabidopsis thaliana, SA glucose conjugates are formed by two homologous enzymes (UGT74F1 and UGT74F2) that transfer glucose from UDP-glucose to SA. Despite being 77% identical and with conserved active site residues, these enzymes catalyze the formation of different products: UGT74F1 forms salicylic acid glucoside (SAG), while UGT74F2 forms primarily salicylic acid glucose ester (SGE). The position of the glucose on the aglycone determines how SA is stored, further metabolized, and contributes to a defense response. We determined the crystal structures of the UGT74F2 wild-type and T15S mutant enzymes, in different substrate/product complexes. On the basis of the crystal structures and the effect on enzyme activity of mutations in the SA binding site, we propose the catalytic mechanism of SGE and SAG formation and that SA binds to the active site in two conformations, with each enzyme selecting a certain binding mode of SA. Additionally, we show that two threonines are key determinants of product specificity.
Statistical estimator for simultaneous noise and mismatch suppression in SAR ADC
Authors: Banerjee I. , Sanyal A. 
Published: April 2017

A statistical estimator based on maximum‐likelihood estimation theory is developed to simultaneously reduce capacitor mismatch and noise in a successive approximation register analogue‐to‐digital converter (SAR ADC). After the SAR ADC has finished quantisation, the residue voltage is available at the comparator input and is estimated accurately by using the statistical estimator. The ADC resolution is improved by subtracting the estimated residue from the digital output. The same technique of residue extraction is used to estimate mismatches in the capacitive digital‐to‐analogue converter. A 7 dB improvement is shown in signal‐to‐noise‐plus‐distortion ratio by using the statistical estimator for an 11‐bit SAR over a wide range of capacitance mismatch and ADC noise.
The lexical semantic variation hypothesis
Authors: Francez Itamar , Koontz-Garboden Andrew 
Published: April 2017

Abstract
This chapter lays out the main hypothesis about variation in the form of property concept sentences explored in the book—the Lexical Semantic Variation Hypothesis—and introduces the semantics of qualities that underlies the analyses developed in the rest of the book. The hypothesis is that property concept lexemes can have two different kinds of denotation: sets of individuals or qualities. Building on the observation that quality-denoting property concept lexemes, when nominal, have mass noun characteristics, we propose an explicit semantics of qualities is proposed, showing how it captures the facts of possessive property concept sentences and comparatives in Ulwa. The semantic structure of qualities is compared to that of degrees on scales, and motivations for an ontology of qualities are discussed.
Meaning and category: Semantic constraints on parts of speech
Authors: Francez Itamar , Koontz-Garboden Andrew 
Published: April 2017

Abstract
Taking the Lexical Semantic Variation Hypothesis and the well-known fact that property concept lexemes vary in lexical category as the points of departure, it is considered whether there is any correlation between the meaning of a property concept lexeme and its lexical category. A novel observation is made about a lexical gap: while nouns across languages can denote qualities as well as sets of individuals, adjectives can never denote qualities. A derivation of this gap is proposed from the assumption that lexical adjectives must be able to affect non-trivial subsective modification.
Importing Coordination
Authors: Page John 
Published: April 2017

Abstract
Recent writing on industrial policy stresses the need for coordination between the public and private sectors. This chapter examines the performance of one public–private coordination mechanism, Presidential Investors’ Advisory Councils (PIACs), in Ethiopia, Senegal, Tanzania, and Uganda. It finds that the councils have been better at focusing attention on a donor-driven agenda of regulatory reforms than they have been at addressing the binding constraints to private investment. Notwithstanding their name, the actual level of presidential commitment to the PIACs varies quite substantially. None have established a track record of experimentation, effective implementation, and evaluation of the impact of decisions taken.
The pre-Industrial Revolution, 1500–1700
Authors: Allen Robert C. 
Published: April 2017

Abstract
‘The pre-Industrial Revolution, 1500–1700’ uses the cloth industry in Witney, a small Oxfordshire market town, as an example of the many themes of both the pre- and main Industrial Revolution. During the Industrial Revolution, the technology changed and so did the organization of work, but these changes did not benefit the workforce. Despite the decline in employment and real wages, the woven blanket industry remained the economic basis of the town for two more centuries. England’s success in the global economy had important effects beyond the growth of cities and rural manufacturing. These include the agricultural revolution, the coal revolution, the high wage economy, and the expansion of literacy.
Why the Industrial Revolution was British
Authors: Allen Robert C. 
Published: April 2017

Abstract
‘Why the Industrial Revolution was British’ shows that the Industrial Revolution was Britain’s response to the challenges of globalization. First, world trade brought new products to Britain including Chinese porcelain and Indian cotton cloth. They were in high demand and British firms sought to imitate them. Second, growth in trade and empire opened new markets for British products, and the ensuing expansion of production and commerce generated high wages and cheap energy. Competing in that environment was the overriding engineering challenge that British industry so creatively met. Third, commercial expansion and increased wages aided British industry in meeting the challenge of foreign competition by improving workforce health, literacy, and skills.
The condition of England
Authors: Allen Robert C. 
Published: April 2017

Abstract
‘The condition of England’ considers why the upswing in technological progress caused such widespread suffering for so many people for so long. It begins with a broad question: how did the technological revolution change the structure of society? It looks at social tables, dividing the population into six social classes—the landed classes, bourgeoisie, lower middle class, farmers, workers, and cottagers and paupers—and how they changed from 1688 to 1867. It is no surprise that the share of national income going to farmers and land owners declined during the Industrial Revolution, but why did workers fall behind capitalists and why did some workers do so much better than others?
Water as a liquid—and as glass(es)
Authors: Finney John 
Published: April 2017

Abstract
For a liquid to flow, the molecules must move. So can a liquid have a structure? ‘Water as a liquid—and as glass(es)’ illustrates that it can; under normal temperature and pressure conditions, the structure of liquid is represented by the random network model. Important structural data on water have been obtained from the scattering of neutrons and X-rays: the four-fold tetrahedral motif dominates, but the data also tell us how the real structure differs from the reference random network, both under normal conditions and as temperature and pressure changes. Water’s dynamical aspects when it is heated, put under pressure, becomes supercritical, and is supercooled are considered. Three distinct amorphous ice structures are also discussed.
The emergence and state of the HIV and AIDS epidemic
Authors: Whiteside Alan 
Published: April 2017

Abstract
‘The emergence and state of the HIV and AIDS epidemic’ outlines the emergence of HIV/AIDS, charting the current state of the disease globally. Acquired Immunodeficiency Syndrome (AIDS) is caused by the Human Immunodeficiency Virus (HIV) virus. The spread of AIDS is a complex, long-wave, epidemic event, with waves of spread followed by waves of impact. The future of HIV/AIDS is, epidemiologically, reasonably predictable. Unless the virus mutates and becomes more easily transmitted it will be contained. Science is advancing, with new treatments becoming available and technological prevention methods, microbicides, and vaccines in the pipeline. The impacts are less certain, but will be confined to the worst affected countries and most marginal groups.
Illness, death, and the demographic impact
Authors: Whiteside Alan 
Published: April 2017

Abstract
‘Illness, death, and the demographic impact’ outlines how the effects of AIDS can be measured through demographic indicators. Demographic consequences of AIDS may include: increased deaths especially among adults; rising infant and child mortality; falling life expectancy; changes in the population size, growth, and structure; and growing numbers of orphans. How serious these impacts are depends on the location, size, and age of the epidemic; the underlying demographics of a country; and, increasingly, the availability and uptake of treatment. The impacts of AIDS continue to be felt by families and communities after death. There is evidence that AIDS deaths have more serious consequences for survivors than deaths from other causes.
Development, numbers, and politics
Authors: Whiteside Alan 
Published: April 2017

Abstract
‘Development, numbers, and politics’ first considers the Millennium Development Goals (MDGs) set by the United Nations in 2000 and explains how achieving some of them was difficult due to high HIV prevalence in some countries. It goes on to discuss the changing viewpoints of the links between AIDS, conflict, and security, and why accurate data on HIV/AIDS are important for its management. There is limited potential political impact from AIDS, but what is important is ensuring treatment is available and affordable. Political and economic failure has widespread implications for the health system and is harder to manage.
Treatment and prevention dilemmas
Authors: Whiteside Alan 
Published: April 2017

Abstract
AIDS is still a major threat. ‘Treatment and prevention dilemmas’ shows that prevention and public health programmes are the most cost-effective way to health. HIV infection is preventable through biomedical strategies, such as ensuring safe blood and blood products by screening donors and testing donations; social interventions advising behaviour change, such as using condoms, having fewer partners, and practicing monogamy or abstinence; and—crucial to behaviour change—community mobilization and leadership. AIDS treatment developments are described along with the current state of antiretroviral therapy. Looking ahead, prevention remains the priority—while HIV infected people can live normal, productive lives, it is challenging and expensive.