bluuebunny/crossref_metadata_2025 huggingface dataset:
A global experimental dataset for assessing grain legume production
Authors: Cernay Charles , Pelzer Elise , Makowski David
Published: September 2016

Grain legume crops are a significant component of the human diet and animal feed and have an important role in the environment, but the global diversity of agricultural legume species is currently underexploited. Experimental assessments of grain legume performances are required, to identify potential species with high yields. Here, we introduce a dataset including results of field experiments published in 173 articles. The selected experiments were carried out over five continents on 39 grain legume species. The dataset includes measurements of grain yield, aerial biomass, crop nitrogen content, residual soil nitrogen content and water use. When available, yields for cereals and oilseeds grown after grain legumes in the crop sequence are also included. The dataset is arranged into a relational database with nine structured tables and 198 standardized attributes. Tillage, fertilization, pest and irrigation management are systematically recorded for each of the 8,581 crop*field site*growing season*treatment combinations. The dataset is freely reusable and easy to update. We anticipate that it will provide valuable information for assessing grain legume production worldwide.
A recurrent deletion in the SLC5A2 gene including the intron 7 branch site responsible for familial renal glucosuria
Authors: Zhao Xiangzhong , Cui Li , Lang Yanhua , liu Ting , Lu Jingru , Wang Cui , Tuffery-Giraud Sylvie , Bottillo Irene , Wang Xinsheng , Shao Leping
Published: September 2016

Familial renal glycosuria (FRG) is caused by mutations in the SLC5A2 gene, which codes for Na+-glucose co-transporters 2 (SGLT2). The aim of this study was to analyze and identify the mutations in 16 patients from 8 families with FRG. All coding regions, including intron-exon boundaries, were analyzed using PCR followed by direct sequence analysis. Six mutations in SLC5A2 gene were identified, including five missense mutations (c.393G > C, p.K131N; c.1003A > G, p.S335G; c.1343A > G, p.Q448R; c.1420G > C, p.A474P; c.1739G > A, p.G580D) and a 22-bp deletion in intron 7 (c.886(-10_-31)del) removing the putative branch point sequence. By the minigene studies using the pSPL3 plasmids, we confirmed that the deletion c.886(-10_-31)del acts as a splicing mutation. Furthermore, we found that this deletion causes exclusion of exon 8 in the SCL5A2 transcript in patients. The mutation c.886(-10_-31)del was present in 5 (62.5%) of 8 families and accounts for about 37.5% of the total alleles (6/16). In conclusion, six mutations resulting in FRG were found and the c.886(-10_-31)del may be the high frequency mutation that can be screened in FRG patients with uniallelic or negative SLC5A2 mutations.
A boron-centered radical: a potassium-crown ether stabilized boryl radical anion
Authors: Yuan Ningning , Wang Wenqing , Wu Ziye , Chen Sheng , Tan Gengwen , Sui Yunxia , Wang Xinping , Jiang Jun , Power Philip P.
Published: September 2016

A boron radical contact ion-pair has been isolated, an intermediate stage between free radical anions and neutral radicals of boron.
Studies of G-quadruplexes formed within self-assembled DNA mini-circles
Authors: Klejevskaja Beata , Pyne Alice L. B. , Reynolds Matthew , Shivalingam Arun , Thorogate Richard , Hoogenboom Bart W. , Ying Liming , Vilar Ramon
Published: September 2016

We have developed self-assembled DNA mini-circles that contain a G-quadruplex-forming sequence and demonstrate by FRET that the G-quadruplex unfolding kinetics are 10-fold slower than for the simpler 24-mer G-quadruplex that is commonly used for FRET experiments.
Carboxylation of multiwalled carbon nanotubes reduces their toxicity in primary human alveolar macrophages
Authors: Sweeney Sinbad , Hu Sheng , Ruenraroengsak Pakatip , Chen Shu , Gow Andrew , Schwander Stephan , Zhang Junfeng (Jim) , Chung Kian Fan , Ryan Mary P. , Porter Alexandra E. , Shaffer Milo S. , Tetley Teresa D.
Published: September 2016

Surface functionalisation of multiwalled carbon nanotubes (MWCNT) is commonly used to facilitate their various and diverse applications.
Design of a heterogeneous catalytic process for the continuous and direct synthesis of lactide from lactic acid
Authors: Upare Pravin P. , Yoon Ji Woong , Hwang Dong Won , Lee U-Hwang , Hwang Young Kyu , Hong Do-Young , Kim Jin Chul , Lee Jeong Hyeon , Kwak Sang Kyu , Shin Hyeyoung , Kim Hyungjun , Chang Jong-San
Published: September 2016

We present a continuous one-step reaction pathway for optically pure lactide under atmospheric conditions based on a novel SnO2–SiO2 nanocomposite catalyst.
Rapid, portable and cost-effective yeast cell viability and concentration analysis using lensfree on-chip microscopy and machine learning
Authors: Feizi Alborz , Zhang Yibo , Greenbaum Alon , Guziak Alex , Luong Michelle , Chan Raymond Yan Lok , Berg Brandon , Ozkan Haydar , Luo Wei , Wu Michael , Wu Yichen , Ozcan Aydogan
Published: September 2016

We demonstrate a field-portable and automatic yeast analysis platform that can rapidly measure cell concentration and viability using on-chip microscopy and machine learning.
Synthesis and photophysical properties of novel fluorescent materials containing 2,4,6-triphenylpyridine and 1,8-naphthalimide units using Suzuki reaction
Authors: Liu Hui-Yan , Chen Liang-Feng , Wang Hai-Ying , Wan Yu , Wu Hui
Published: September 2016

A series of novel 2,4,6-triphenylpyridine derivatives containing 1,8-naphthalimide groups have been prepared. The relationship of photoluminescence property of the products and the theoretical calculation analysis were investigated.
Zero thermal expansion with high Curie temperature in Ho2Fe16Cr alloy
Authors: Dan Shovan , Mukherjee S. , Mazumdar Chandan , Ranganathan R.
Published: September 2016

Ho2Fe16Cr with a highTCand moderate coercivity behaves like a zero thermal expansion material in the temperature range 13–330 K.
A bi-continuous network structure of p-DTS(FBTTh2)2/EP-PDI via selective solvent vapor annealing
Authors: Li Mingguang , Liang Qiuju , Zhao Qiaoqiao , Zhou Ke , Yu Xinhong , Xie Zhiyuan , Liu Jiangang , Han Yanchun
Published: September 2016

Donor selective solvent vapor annealing leads to the moderate phase-separated morphology accompanied by a pure crystalline phase with a medium size, which could maximize the carrier transport process without compromising exciton separation efficiency.
Modeling field emitter arrays using nonlinear line charge distribution
Authors: Biswas Debabrata , Singh Gaurav , Kumar Raghwendra
Published: September 2016

Modeling high aspect ratio field emitter arrays is a computational challenge due to the enormity of the resources involved. The line charge model (LCM) provides an alternate semi-analytical tool that has been used to model both infinite as well as finite sized arrays. It is shown that the linearly varying charge density used in the LCM generically mimics ellipsoidal emitters rather than a Cylindrical-Post-with-an-Ellipsoidal-Tip (CPET) that is typical of nanowires. Furthermore, generalizing the charge density beyond the linear regime allows for modeling shapes that are closer to a CPET. Emitters with a fixed base radius and a fixed apex radius are studied with a view to understanding the effect of nonlinearity on the tip enhancement factor and the emitter current in each case. Furthermore, an infinite square array of the CPET emitters is studied using the nonlinear line charge model, each having a height h=1500 μm and a base radius b=1.5 μm. It is found that for moderate external field strengths (0.3−0.4 V/μm), the array current density falls sharply for lattice spacings smaller than 43h. Beyond this value, the maximal array current density can be observed over a range of lattice spacings and falls gradually thereafter.
Differences between sexes, muscles and aging times on the quality of meat from Wagyu × Angus cattle finished in feedlot
Authors: Carvalho R. M. S. , Boari C. A. , Villela S. D. J. , Pires A. V. , Mourthé M. H. F. , Oliveira F. R. , Dumont M. A. , Gontijo R. P. , Lobo-Jr A. R. , Martins P. G. M. A.
Published: September 2016

Our objectives were to assess quality parameters and chemical composition, and to evaluate the effects of sex, muscle and aging time on the quality of meats from Wagyu × Angus cross cattle reared under tropical conditions. Analyses were performed on the longissimus thoracis, semitendinosus and triceps brachii muscles obtained from chilled carcasses of a total of 30, 24-month-old, male (immunocastrated) and female animals (15 each sex). An effect of sex (P ≤ 0.05) was observed for subcutaneous fat thickness, marbling score, and ribeye area. The longissimus thoracis muscle from males was less (P < 0.0001) marbled than that from females, but males had greater subcutaneous fat thickness (P = 0.0001) and greater ribeye area (P = 0.0411) compared with females. No effect of sex (P ≥ 0.05) was observed for fat colour measures. An interaction effect of sex and muscle (P < 0.03) was detected for cooking loss, yellow intensity (b*), ash, and fat. Main effect of sex was not observed (P > 0.07) only for the ultimate pH and water-holding capacity. Greater shear force and moisture values were observed (P < 0.01) in meat from males than that from females, but a greater value of luminance (L*), red intensity (a*), chroma (C), hue (Ho), dry matter and protein was observed (P < 0.001) in meat from females than that from males. Main effect of muscle was not observed only for water-holding capacity (P = 0.13). Ultimate pH and shear force values were lesser (P < 0.001) in the longissimus thoracis muscle compared with other muscles. The triceps brachii muscle had the least (P ≤ 0.001) L* and Ho values among muscles, whereas the semitendinosus muscle had the greatest values of a* and C (P < 0.001). The semitendinosus muscle presented the greatest (P < 0.01) protein content compared with other muscles, although not differing in moisture and dry matter content from the triceps brachii muscle. An interaction effect of sex × aging time was observed for ultimate pH (P = 0.0110), meat colour parameters (except for Ho; P ≤ 0.01), and fat L* (P = 0.0025). Greater cooking loss, shear force, and fat a* values were observed (P < 0.01) in meat from males than that from females, but greater values of meat Ho, fat a* and Ho, dry matter, and protein were observed (P ≤ 0.03) in meat from females than that from males. Meat aging of longissimus thoracis reduced shear force. Based on these findings, we recommend that meat from Wagyu × Angus cross cattle should be aged during 7 days because, although differences between 7 and 14 days were observed in either aging times, meat subjected to this process is considered as very tender, based on shear force values. In addition, aging in a shorter period of time can reflect on costs by reducing particularly those related with energy, due to less refrigeration time.
TBLT through the lens of applied linguistics
Authors: Bygate Martin
Published: September 2016

Ever since the establishment in the 1940’s of the distinguished journalLanguage Learning, a significant proportion of research in applied linguistics has defined itself as aiming to address practical problems of language teaching. Given the definition of applied linguistics as ‘the theoretical and empirical study of real world problems in which language has a central role’ (after Brumfit, 2001), an ambition to relate its work to practical language teaching problems is appropriate. Task-based language teaching is a subarea of applied linguistics which deliberately aims to link research to practice. With this in mind, this paper will seek to evaluate the extent to which TBLT research has to date engaged with — and helped address — the real world problems of language education. It then attempts to derive some implications for future directions of TBLT research as a part of an empirical applied linguistics.
AcCNET (

Ac

cessory Genome

C

onstellation

Net

work): comparative genomics software for accessory genome analysis using bipartite networks
Authors: Lanza Val F , Baquero Fernando , de la Cruz Fernando , Coque Teresa M
Published: September 2016

AcCNET (Accessory genome Constellation Network) is a Perl application that aims to compare accessory genomes of a large number of genomic units, both at qualitative and quantitative levels. Using the proteomes extracted from the analysed genomes, AcCNET creates a bipartite network compatible with standard network analysis platforms. AcCNET allows merging phylogenetic and functional information about the concerned genomes, thus improving the capability of current methods of network analysis. The AcCNET bipartite network opens a new perspective to explore the pangenome of bacterial species, focusing on the accessory genome behind the idiosyncrasy of a particular strain and/or population.

Availability and Implementation

AcCNET is available under GNU General Public License version 3.0 (GPLv3) from http://sourceforge.net/projects/accnet

Supplementary information

Supplementary data are available at Bioinformatics online.
An accessibility-incorporated method for accurate prediction of RNA–RNA interactions from sequence data
Authors: Kato Yuki , Mori Tomoya , Sato Kengo , Maegawa Shingo , Hosokawa Hiroshi , Akutsu Tatsuya
Published: September 2016

Motivation

RNA–RNA interactions via base pairing play a vital role in the post-transcriptional regulation of gene expression. Efficient identification of targets for such regulatory RNAs needs not only discriminative power for positive and negative RNA–RNA interacting sequence data but also accurate prediction of interaction sites from positive data. Recently, a few studies have incorporated interaction site accessibility into their prediction methods, indicating the enhancement of predictive performance on limited positive data.

Results

Here we show the efficacy of our accessibility-based prediction model RactIPAce on newly compiled datasets. The first experiment in interaction site prediction shows that RactIPAce achieves the best predictive performance on the newly compiled dataset of experimentally verified interactions in the literature as compared with the state-of-the-art methods. In addition, the second experiment in discrimination between positive and negative interacting pairs reveals that the combination of accessibility-based methods including our approach can be effective to discern real interacting RNAs. Taking these into account, our prediction model can be effective to predict interaction sites after screening for real interacting RNAs, which will boost the functional analysis of regulatory RNAs.

Availability and Implementation

The program RactIPAce along with data used in this work is available at https://github.com/satoken/ractip/releases/tag/v1.0.1.

Supplementary information

Supplementary data are available at Bioinformatics online.
Near-infrared spectroscopy of M dwarfs. IV. A preliminary survey on the carbon isotopic ratio in M dwarfs*
Authors: Tsuji Takashi
Published: September 2016

Carbon isotopic ratios are estimated in 48 M dwarfs based on the medium resolution near infrared spectra (λ/Δ λ ≈ 20000) of the 13CO (3,1) band. We find clear evidence for the presence of a 13CO feature for the first time in the spectra of M dwarfs. Spectral resolution of our observed data, however, is not high enough to analyze the 13CO feature directly. Instead, we compare the observed spectrum with synthetic spectra assuming 12C/13C = 10, 25, 50, 100, and 200 for each of 48 M dwarfs and estimate the best possible 12C/13C ratio by chi-square analysis. The resulting 12C/13C ratios in M dwarfs distribute from 39 to a lower limit of 200. The mean value of 31 M dwarfs for which 12C/13C ratios are determined (i.e., excluding those with the lower limit only) is (12C/13C)dM = 87 ± 21 (p.e.), and that of 48 M dwarfs including those with the lower limit of 200 is (12C/13C)dM > 127 ± 41 (p.e.). These results are somewhat larger than the 12C/13C ratio of the present interstellar matter (ISM) determined from the molecular lines observed in the millimeter and optical wavelength regions. Since the amount of 13C in the ISM has increased with time due to mass loss from evolved stars, the 12C/13C ratios in M dwarfs, reflecting those of the past ISM, should be larger than those of the present ISM. In M dwarfs, log 13C/12C plotted against log AC shows a large scatter without clear dependence on the metallicity. This result shows a marked contrast to log 16O/12C (= log AO/AC) plotted against log AC, which shows a rather tight correlation with a larger value at the lower metallicity. Such a contrast can be a natural consequence of 16O and 12C being primary products in stellar nuclear synthesis while 13C is a secondary product, at least partly.
The evolution of photospheric temperature in nova V2676 Oph toward the formation of C2 and CN during its near-maximum phase
Authors: Kawakita Hideyo , Arai Akira , Fujii Mitsugu
Published: September 2016

The molecular formation of C2 and CN in the dust-forming classical nova V2676 Oph occurs during its near-maximum phase. We investigated the temporal evolution of the photospheric temperature of the nova as it approached molecular formation during its early phase. The effective temperature of the nova around the maximum decreased from ∼7000 K to ∼5000 K over the course of ∼3 d. The molecules formed at temperatures of <∼5000 K. Such low temperatures of nova photosphere and low expansion velocities along with carbon-rich atmosphere might play an important role in achieving conditions favorable to the molecular formation of C2 and CN in V2676 Oph.
Validation of the ‘CHRESI’ questionnaire on habits related to sun exposure during childhood
Authors: Blázquez-Sánchez Nuria , De Troya-Martín Magdalena , Rivas-Ruiz Francisco , Bueno-Fernández Sara , Fernández-Morano Maria Teresa , Arias-Santiago Salvador
Published: September 2016

Sun exposure in childhood is the main risk determinant for skin cancer in adulthood. Several questionnaires have been used to examine behaviour patterns in terms of sun exposure in childhood, but none have been subjected to a rigorous analysis of their measurement properties. To evaluate the psychometric properties of a questionnaire adapted to investigate children’s sun exposure behaviour, a two-stage validation study was carried out. First, in a transverse study, the questionnaire was administered to a sample of 333 children recruited from schools, and the validity and internal consistency were analysed. Second, 32 children recruited in a hospital setting were interviewed for the test–retest analysis. All the items in the ‘Photoprotection habits’ category were significantly correlated. Principal components analysis showed that two components accounted for over 53% of the variance. The Cronbach’s α-coefficient was 0.63 for the first component and 0.43 for the second. In the stability analysis, the percentage of absolute agreement exceeded 70% for all the questions. The Questionnaire on Habits RElated to Sun exposure during Infancy (CHRESI) questionnaire examines sun protection habits by children. Its proven reliability, validity and stability make it a useful tool both in epidemiologic research and in the development and evaluation of campaigns to reduce the risk of skin cancer.
Chronic Sarpogrelate Treatment Reveals 5-HT7 Receptor in the Serotonergic Inhibition of the Rat Vagal Bradycardia
Authors: García-Pedraza José Ángel , García Mónica , Martín María Luisa , Eleno Nélida , Morán Asunción
Published: September 2016

5-Hydroxytryptamine (5-HT) modulates the cardiac parasympathetic neurotransmission, inhibiting the bradyarrhythmia by 5-HT2receptor activation. We aimed to determine whether the chronic selective 5-HT2blockade (sarpogrelate) could modify the serotonergic modulation on vagal cardiac outflow in pithed rat. Bradycardic responses in rats treated with sarpogrelate (30 mg·kg−1·d−1; orally) were obtained by electrical stimulation of the vagal fibers (3, 6, and 9 Hz) or intravenous (IV) injections of acetylcholine (1, 5, and 10 μg/kg). 5-HT7receptor expression was quantified by Western blot in vagus nerve and right atrium. The IV administration of 5-HT (10–200 μg/kg) dose dependently decreased the vagally induced bradycardia, and agonists 5-CT (5-HT1/7), 8-OH-DPAT (5-HT1A), or AS-19 (5-HT7) (50 μg/kg each) mimicked the 5-HT–induced inhibitory effect. Neither agonists CGS-12066B (5-HT1B), L-694,247 (5-HT1D), nor 1-phenylbiguanide (5-HT3) modified the electrically-induced bradycardic responses. Moreover, SB-258719 (5-HT7antagonist) abolished the 5-HT–, 5-CT–, 8-OH-DPAT–, and AS-19–induced bradycardia inhibition; 5-HT or AS-19 did not modify the bradycardia induced by IV acetylcholine; and 5-HT7receptor was expressed in both the vagus nerve and the right atrium. Our outcomes suggest that blocking chronically 5-HT2receptors modifies the serotonergic influence on cardiac vagal neurotransmission exhibiting 5-HT as an exclusively inhibitory agent via prejunctional 5-HT7receptor.
Tetramethylpyrazine and Astragaloside IV Synergistically Ameliorate Left Ventricular Remodeling and Preserve Cardiac Function in a Rat Myocardial Infarction Model
Authors: Wang Chuying , Li Yumei , Yang Xinxin , Bi Shengnan , Zhang Yajie , Han Dong , Zhang Dafang
Published: September 2016

Tetramethylpyrazine (TMP) and astragaloside IV (AGS-IV) are herbal ingredients that have been demonstrated in animal models to limit infarct size and protect cardiomyocytes in the acute phase of myocardial infarction (MI), yet their long-term cardioprotective effects have not been evaluated. In this study, TMP and/or AGS-IV were administrated to rats for 14 days after MI. Echocardiography revealed that the left ventricular (LV) dimensions and cardiac function were preserved in the MI rats with TMP and AGS-IV treatment, compared with untreated MI rats. Moreover, the LV dimensions and cardiac function in the MI rats with TMP and AGS-IV cotreatment were comparable with the sham-operated rats. In addition, TMP and AGS-IV synergistically inhibited LV fibrosis by attenuating MI-induced collagen deposition and elevation of transforming growth factor β1. TMP and AGS-IV, alone or in synergy, enhanced angiogenesis in the infarcted myocardium and reduced cardiac hypertrophy of the remote myocardium after MI. Furthermore, TMP and AGS-IV mutually upregulated the expression of Sonic hedgehog (Shh), Smoothened, and Glioblastoma-2, the receptor and signal transducer of Shh signaling pathway, in the infarcted myocardium. In summary, in the circumstance of the irreversible ischemic injury, the antifibrotic, and pro-angiogenic properties of TMP and AGS-IV on the nonaffected tissues contribute to the cardioprotection in the healing phase post MI, and the cardioprotective effects are likely to be mediated through the Shh pathway.
CILIOCHOROIDAL EFFUSION AND ACUTE MACULAR NEURORETINOPATHY ASSOCIATED WITH CERVICAL TRACTION THERAPY
Authors: Dedania Vaidehi S. , Ghodasra Devon H. , Kay Christine N. , Roseman Robert , Johnson Mark W.
Published: September 2016

Purpose:

To report an unusual case of ciliochoroidal effusion and presumed acute macular neuroretinopathy associated with cervical traction therapy for the treatment of cervical spinal stenosis.

Methods:

Case report.

Results:

A 75-year-old man reported sudden onset of a wedge-shaped paracentral scotoma in the right eye. Fundus examination showed a ciliochoroidal effusion in the right eye. Optical coherence tomography revealed intraretinal fluid in both eyes without leakage on fluorescein angiography. B-scan ultrasonography and anterior segment ultrasound biomicroscopy of the right eye showed peripheral ciliochoroidal effusion. He had recently started intensive cervical traction therapy for the treatment of cervical spinal stenosis. There was spontaneous resolution of the choroidal effusion and intraretinal fluid after stopping cervical traction treatments. Optical coherence tomography imaging after resolution of the intraretinal fluid revealed thinning of the outer nuclear layer and attenuation of the ellipsoid and interdigitation zones corresponding to a persistent paracentral scotoma, consistent with acute macular neuroretinopathy.

Conclusion:

This is the first report of adverse ocular effects of cervical traction. We postulate that venous and arterial compromise during cervical traction therapy resulted in both ciliochoroidal effusion and a watershed infarct in the outer retina.
Legionnaires Disease With Focal Neurologic Deficits and a Reversible Lesion in the Splenium of the Corpus Callosum
Authors: Raybould Jillian E. , Conroy Megan E. , Timpone Joseph G. , Kumar Princy N.
Published: September 2016

Patients with Legionnaires pneumonia frequently present with neurologic abnormalities but normal neuroimaging findings. We present a case of a healthy 52-year-old man presenting with severe Legionella pneumonia and a unique constellation of focal neurologic deficits including bowel and bladder incontinence, hemiparesis, and ataxia with progression to somnolence. A transient lesion was identified at the splenium of the corpus callosum on magnetic resonance imaging. His recovery was marked by prolonged limb and oral apraxia, but the patient improved with an early combination antibiotic treatment and the late use of corticosteroids. To our knowledge, this is the ninth case reported in the English literature of a patient presenting with Legionnaires disease with neurologic deficits and a reversible lesion at the splenium of the corpus callosum. We present a review of the literature including previous cases, with a focus on neurologic examination, neuroimaging findings, combination antibiotic therapy, and the use of corticosteroids.
Implementing Effective Policy in a National Mental Health Reengagement Program for Veterans
Authors: Smith Shawna N. , Lai Zongshan , Almirall Daniel , Goodrich David E. , Abraham Kristen M. , Nord Kristina M. , Kilbourne Amy M.
Published: September 2016

Policy is a powerful motivator of clinical change, but implementation success can depend on organizational characteristics. This article used validated measures of organizational resources, culture, and climate to predict uptake of a nationwide Veteran's Health Administration (VA) policy aimed at implementing Re-Engage, a brief care management program that reestablishes contact with veterans with serious mental illness lost to care. Patient care databases were used to identify 2738 veterans lost to care. Local recovery coordinators (LRCs) were to update disposition for 2738 veterans at 158 VA facilities and, as appropriate, facilitate a return to care. Multivariable regression was used to assess organizational culture and climate as predictors of early policy compliance (via LRC presence) and uptake at 6 months. Higher composite climate and culture scores were associated with higher odds of having a designated LRC but were not predictive of higher uptake. Sites with LRCs had significantly higher rates of updated documentation than sites without LRCs.
Expanding Advocacy for Head Trauma Vision Research Funding
Authors: Jorkasky James F. , Goodrich Gregory L.
Published: September 2016

In this article, we explore the roles of media, research, and advocacy in education and research funding. All three have played critical roles in advancing our understanding of eye, vision, and brain injuries in sports and in the military.
Fundus Autofluorescence in Age-related Macular Degeneration
Authors: Ly Angelica , Nivison-Smith Lisa , Assaad Nagi , Kalloniatis Michael
Published: September 2016

Fundus autofluorescence (FAF) provides detailed insight into the health of the retinal pigment epithelium (RPE). This is highly valuable in age-related macular degeneration (AMD) as RPE damage is a hallmark of the disease. The purpose of this paper is to critically appraise current clinical descriptions regarding the appearance of AMD using FAF and to integrate these findings into a chair-side reference. A wide variety of FAF patterns have been described in AMD, which is consistent with the clinical heterogeneity of the disease. In particular, FAF imaging in early to intermediate AMD has the capacity to reveal RPE alterations in areas that appear normal on funduscopy, which aids in the stratification of cases and may have visually significant prognostic implications. It can assist in differential diagnoses and also represents a reliable, sensitive method for distinguishing reticular pseudodrusen. FAF is especially valuable in the detection, evaluation, and monitoring of geographic atrophy and has been used as an endpoint in clinical trials. In neovascular AMD, FAF reveals distinct patterns of classic choroidal neovascularization noninvasively and may be especially useful for determining which eyes are likely to benefit from therapeutic intervention. FAF represents a rapid, effective, noninvasive imaging method that has been underutilized, and incorporation into the routine assessment of AMD cases should be considered. However, the practicing clinician should also be aware of the limitations of the modality, such as in the detection of foveal involvement and in the distinction of phenotypes (hypo-autofluorescent drusen from small areas of geographic atrophy).
Evaluation of the SVOne Handheld Autorefractor in a Pediatric Population
Authors: Rosenfield Mark , Ciuffreda Kenneth J.
Published: September 2016

Purpose

The SVOne is a portable, Hartmann-Shack wavefront aberrometer, which can be attached to a smartphone to determine the refractive error of the eye objectively. Previous results have shown the device to provide measurements equivalent to those of standard clinical techniques in young, healthy adults. The aim of the present study was to compare the findings of the SVOne with retinoscopy, subjective refraction, and two commercially available autorefractors (Retinomax-3 and WAM-5500) in a pediatric population.

Method

The refractive error of the right eye was assessed both without and with cycloplegia in 40 visually normal children between 5 and 17 years of age (mean age = 11.3 years) using the five techniques described above. Further, to assess repeatability of the instruments, the entire procedure was repeated in a subgroup of five subjects. All data were analyzed in terms of power vectors (M, J0, and J45).

Results

No significant difference was observed between the mean values of M (spherical equivalent) for the different techniques. Retinoscopy showed the best agreement with subjective refraction, both without and with cycloplegia, followed by the open-field WAM-5500. The most repeatable procedures, when measured without and with cycloplegia, were the WAM-5500 and retinoscopy, respectively. Measurements with the SVOne showed a decline in repeatability under cycloplegia.

Conclusions

The results indicate that the SVOne provides measurements of refractive error in a normal, pediatric population that are not significantly different from other subjective and objective procedures. Accurate alignment along the visual axis, especially when measuring through a dilated pupil, is critical. This instrument is valuable for vision screenings, for examinations taking place outside the clinical office, and a starting point for the refractive assessment.
Identifying the Species Threat Hotspots from Global Supply Chains
Authors: Moran Daniel , Kanemoto Keiichiro
Published: September 2016

Summary Sentence

Spatially explicit footprints make it possible to locate biodiversity hotspots linked to global supply chains.

Identifying species threat hotspots has been a successful approach for setting conservation priorities. One major challenge in conservation is that in many hotspots export industries continue to drive overexploitation. Conservation measures must consider not just the point of impact, but also the consumer demand that ultimately drives resource use. To understand which species threat hotspots are driven by which consumers, we have developed a new approach to link a set of biodiversity footprint accounts to the hotspots of threatened species on the IUCN Red List. The result is a map connecting global supply chains to impact locations. Connecting consumption to spatially explicit hotspots driven by production has not been done before on a global scale. Locating biodiversity threat hotspots driven by consumption of goods and services can help connect conservationists, consumers, companies, and governments in order to better target conservation actions.
Learning of speech categories in humans and Zebra Finches
Authors: Botskaris D. , Kriengwatana B. , ten Cate C.
Published: September 2016

The survival of organisms depends highly on their ability to adjust their behavior according to proper categorizations of various events. More than one strategy can be used in categorization. One is the Rule-Based (RB) strategy and the other is Information-Integration (II) strategy. In this research we analyzed the differences between avian and human cognition. Twelve Greek listeners and four Zebra finches were tested in speech category learning tasks. In particular, both humans and Zebra finches had to categorize between Dutch vowels that differ on duration, frequency or both depending on the condition. Feedback was given for correct and incorrect responses. The results showed that humans and Zebra finches are probably using the same methods of learning depending on the categorization tasks that they are exposed to. If Zebra Finches are actually able to acquire (RB) and (II) category structures using the same strategies as humans, the utility of multiple systems of categorization might not be restricted to primates as current literature suggest.
TRANSPORTIN1 Promotes the Association of MicroRNA with ARGONAUTE1 in Arabidopsis
Authors: Cui Yuwei , Fang Xiaofeng , Qi Yijun
Published: September 2016

In Arabidopsis thaliana, microRNAs (miRNAs) are mainly loaded into ARGONAUTE1 (AGO1) to posttranscriptionally regulate gene expression. We previously found that ENHANCED MiRNA ACTIVITY1 (EMA1), an importin β family protein, negatively regulates miRNA loading into AGO1. In this study, through a suppressor screening of ema1, we identified another importin β protein, TRANSPORTIN1 (TRN1), as a regulatory component in the miRNA pathway. Mutation of TRN1 did not reduce miRNA accumulation, but it impaired miRNA activity. We found that TRN1 interacted with AGO1. Mutation of the three conserved residues required for cargo recognition of TRN1 reduced its interaction with AGO1 and compromised its function in regulating miRNA activity. Intriguingly, TRN1 dysfunction did not change the cytoplasmic-nuclear distribution of miRNAs and AGO1 but reduced the amount of miRNAs associated with AGO1. These results indicate that TRN1 positively regulates miRNA activity by promoting the association of miRNAs with AGO1, and they reveal opposing roles of two importin β family proteins in miRNA loading.
The library and the academic resource center
Authors: Pun Raymond
Published: September 2016

Purpose

– This paper aims to explore the library’s on-going relationship with the academic resource center (ARC), and how over the past two years, there have been new services and programs thriving as a result of this collaboration. The paper presents three case studies that demonstrate the library’s collaboration with the ARC and assesses the opportunities and challenges in working with this department in a new university.

Design/methodology/approach

– The approach of this paper is to explore three case studies on how the library collaborated with the ARC in supporting students. The case studies explore the opportunities for partnerships in developing innovative services, programs and resources. Librarians are integral members of the ARC and are embedded in this community by providing support to the department as well.

Findings

– The paper finds that collaborations between the library and the ARC are mutually beneficial: academic libraries may consider partnering with tutoring centers to create synergies in enhancing the students’ research experience. However, not all collaborative projects or programs are successful or repeatable in success. They are still opportunities to build and strengthen the relationship between the library and the ARC.

Originality/value

– This paper presents three case studies on how the library works closely with the “Global Academic Fellows” (GAF) from the ARC. The GAFs work closely with faculty and librarians as they teach, tutor and collaborate with different university departments to create programs or initiatives that enrich the student experience and the university. Their roles have been instrumental in collaborating with the library to create innovative programs, events and support services throughout the two years since the university opened in 2013.
The usability study on the multicultural children’s book project of the National Library for Children and Young Adults (NLCY) in Korea
Authors: Jeong Wooseob
Published: September 2016

Purpose

– The purpose of this study is to identify usability issues on a storytelling digital library with six languages provided by the National Library for Children and Young Adults (NLCY) in Korea, and to provide suggestions for future improvement to create a better interface.

Design/methodology/approach

– In this study, usability issues at the multicultural children’s book project Web site of the NLCY were identified, with comparison between the previous interface and the current one, based on the findings of established literature on children’s use of computer applications and web interface.

Findings

– Suggestions for improvements include brighter colors, bigger fonts and graphics, more lively animation and sound, easier navigation, consistent interface, summary availability, better organization of information and labeling and multilingual searching and browsing function. A user study is being planned for future development.

Originality/value

– There is a great value in making 400 children’s books available to the public at the NLCY digital library in six different languages with their original pictures animated and their stories performed in a storytelling mode. However, to provide more pleasant access to the valuable site, particularly for children users, there is much room for improvement in terms of the user interface. Based on these findings, a user study is being planned for future development, which should be more intuitive for users, particularly children.
Migrating a specialized locally created database into WorldCat
Authors: Nelson David N. , Hansard Larry , Turney Linda
Published: September 2016

Purpose

– The purpose of this paper is to describe the process and the personnel skills required for converting a non-MARC database file into a MARC file for uploading to both OCLC and a local catalog. It also examines the various decisions that need to be made when mapping from one file structure to another.

Design/methodology/approach

– Applied–Database record conversion.

Findings

– While MARCEDIT is a remarkably powerful tool for cataloging and database maintenance purposes, dealing with non-MARC records requires additional programming skills and tools for the successful completion of a file conversion project.

Practical implications

– Discusses the importance of converting locally produced databases, especially those with bibliographic content, to national and international standards to significantly increase their discoverability.

Originality/value

– Provides an overview of file conversion issues and considerations.
Separation of novel phosphoproteins of Porphyromonas gingivalis using phosphate‐affinity chromatography
Authors: Izumigawa Masashi , Hasegawa Yoshiaki , Ikai Ryota , Horie Toshi , Inomata Megumi , Into Takeshi , Kitai Noriyuki , Yoshimura Fuminobu , Murakami Yukitaka
Published: September 2016

Phosphorylation of serine, threonine and tyrosine is a central mechanism for regulating the structure and function of proteins in both eukaryotes and prokaryotes. However, the action of phosphorylated proteins present in Porphyromonas gingivalis, a major periodontopathogen, is not fully understood. Here, six novel phosphoproteins that possess metabolic activities were identified, namely PGN_0004, PGN_0375, PGN_0500, PGN_0724, PGN_0733 and PGN_0880, having been separated by phosphate‐affinity chromatography. The identified proteins were detectable by immunoblotting specific to phosphorylated Ser (P‐Ser), P‐Thr, and/or P‐Tyr. These results imply that novel phosphorylated proteins might play an important role for regulation of metabolism in P. gingivalis.
Joint up/down decomposition and reconstruction using three‐component streamers with or without ghost model: the sampling theory
Authors: Tang Zijian , Campman Xander
Published: September 2016

This paper addresses two artefacts inherent to marine towed‐streamer surveys: 1) ghost reflections and 2) too sparse a sampling in the crossline direction. A ghost reflection is generated when an upcoming reflection bounces off the sea surface back into the sensors and can, in principle, be removed by decomposing the measured wavefield into its up‐ and downgoing constituents. This process requires a dense sampling of the wavefield in both directions along and perpendicular to the streamers. A dense sampling in the latter direction is, however, often impossible due to economical and operational constraints. Recent multi‐component streamers have been designed to record the spatial gradients on top of the pressure, which not only benefits the wavefield decomposition but also facilitates a lower‐than‐Nyquist sampling rate of the pressure. In this paper, wavefield reconstruction and deghosting are posed as a joint inverse problem. We present two approaches to establish a system matrix that embeds both a deghosting and an interpolation operator. The first approach is derived with a ghost model, whereas the second approach is derived without a ghost model. The embodiment of a ghost model leads to an even lower sampling rate but relies on a more restrictive assumption on the sea surface.
tipdatingbeast: an r package to assist the implementation of phylogenetic tip‐dating tests using beast
Authors: Rieux Adrien , Khatchikian Camilo E.
Published: September 2016

Molecular tip dating of phylogenetic trees is a growing discipline that uses DNA sequences sampled at different points in time to coestimate the timing of evolutionary events with rates of molecular evolution. In this context, beast, a program for Bayesian analysis of molecular sequences, is the most widely used phylogenetic tool. Here, we introduce tipdatingbeast, an r package built to assist the implementation of various phylogenetic tip‐dating tests using beast. tipdatingbeast currently contains two main functions. The first one allows preparing date‐randomization analyses, which assess the temporal signal of a data set. The second function allows performing leave‐one‐out analyses, which test for the consistency between independent calibration sequences and allow pinpointing those leading to potential bias. We apply those functions to an empirical data set and supply practical guidance for results interpretation.
Predictive modelling of ecological patterns along linear‐feature networks
Authors: Ladle Andrew , Avgar Tal , Wheatley Matthew , Boyce Mark S.
Published: September 2016

Ecological patterns and processes often take place within linear‐feature networks, and this has implications when analysing the spatial configuration of such patterns or processes across a landscape.

One such pattern is the use of landscapes by human recreationists: an important variable in animal habitat selection and behaviour. Due to the difficulty in obtaining data, ecologists tend to use coarse metrics such as linear‐feature density, while the extent and timing of human activity are often ignored. Remote detector equipment and its increasing use in ecological studies allow for large volumes of data on human activity to be collected. However, the analysis of these data still can be challenging.

Using a combination of generalised linear mixed‐effects models and network‐based ordinary kriging, we developed a method for estimating spatial and temporal variations in motorised and non‐motorised activities across a complex linear‐feature network. Trail cameras were set up between 2012 and 2014 and monitored motorised and non‐motorised activities at 238 different trail sites across a 2824 km2 region of the eastern slopes and foothills of central Alberta's Rocky Mountains.

We evaluate the predictive capacity of this approach, demonstrate its application and discuss its merits and limitations. This method offers a straightforward analysis that can be applied to remotely acquired data to give a useful metric for assessing wildlife responses to human activity, and has potential application beyond the highlighted example.
Adalimumab or infliximab as monotherapy, or in combination with an immunomodulator, in the treatment of Crohn's disease
Authors: Cosnes J. , Sokol H. , Bourrier A. , Nion‐Larmurier I. , Wisniewski A. , Landman C. , Marteau P. , Beaugerie L. , Perez K. , Seksik P.
Published: September 2016

Background

The comparative efficacy of adalimumab (ADA) and infliximab (IFX) in Crohn's disease, and the benefit of initial combotherapy with an immunomodulator, are debated.

Aim

To assess the best anti‐TNF treatment regimens in Crohn's disease.

Methods

We included 906 biologic‐naïve Crohn's disease patients [median age, 31 years (24–41)] and performed a retrospective analysis of 1284 therapeutic exposures to ADA (n = 521) or IFX (n = 763) between 2006 and 2015. An immunomodulator was associated during the first 4–6 months (initial combotherapy) during 706 therapeutic exposures (55%). Median duration of anti‐TNF therapy was 39 months (IQR 17–67). Primary outcomes were 6‐month and 2‐year response rates and drug survival. Logistic regression with propensity scoring and Cox proportional hazard analysis determined variables associated with outcomes.

Results

The response rates at 6 months and 2 years were 64% and 44% on ADA mono, 86% and 70% on ADA combo, 72% and 45% on IFX mono, and 84% and 68% on IFX combotherapy, respectively. Differences between ADA and IFX were not significant, whereas combotherapy was superior to monotherapy (P < 0.001). Drug survival was longer with combotherapy vs. monotherapy [adjusted hazard ratio 2.17 (1.72–2.70)] and not significantly different between ADA and IFX. During subsequent anti‐TNF exposures, IFX combotherapy fared better than other groups regarding response rates, drug survival, disease activity, hospitalisations and abdominal surgery.

Conclusion

In this retrospective analysis of a large tertiary centre cohort of Crohn's disease patients, ADA and IFX had similar efficacy as first line treatment, while initial combotherapy with an immunomodulator improved all outcome measures.