bluuebunny/crossref_metadata_2025_split huggingface dataset:
Collecting wild Miscanthus germplasm in Asia for crop improvement and conservation in Europe whilst adhering to the guidelines of the United Nations’ Convention on Biological Diversity
Authors: Huang Lin S , Flavell Richard , Donnison Iain S , Chiang Yu-Chung , Hastings Astley , Hayes Charlotte , Heidt Chris , Hong Hao , Hsu Tsai-Wen , Humphreys Mervyn , Jackson Julian , Norris John , Schwarz Kai-Uwe , Squance Michael , Swaller Timothy , Thomas Ian David , Van Assche Wilfriede , Xi Qingguo , Yamada Toshihiko , Youell Sue , Clifton-Brown John 
Published: December 2018

Abstract

Background and Aims
Germplasm with diverse, agronomically relevant traits forms the foundation of a successful plant breeding programme. Since 1993, the United Nations has been advocating the implementation of the Convention on Biological Diversity (CBD) and the subsequent 2002 Bonn Guidelines as international best practice on germplasm collection and use. In 2006, a European team made an expedition to Asia to collect wild germplasm of Miscanthus, a C4 perennial rhizomatous grass, for breeding an environmentally adaptable, resilient and high-yielding bioenergy crop. We outline general aspects of germplasm collection, conservation, breeding and biomass production evaluation while following the CBD’s guidelines, respecting biodiversity and conservation needs, and the ethical use of genetic resources.

Methods
Effective protocols, quarantine, methods for collecting seed and rhizomes, and a genebank for conservation were established. Versatile informatics and database architecture were used to assist in selection, flowering synchronization, crossing, evaluation, phenotyping and data integration. Approaches were formulated to comply with the CBD guidelines.

Key Results
A total of 303 accessions of M. sinensis, M. sacchariflorus and M. floridulus were collected from 158 geographically and environmentally diverse locations. These species were shown to accumulate different amounts of aerial biomass due to combinations of stem count, height and thickness. Progeny from one interspecies cross accumulated more biomass in early trials and has shown double the yield performance in years 3–4 compared with the existing commercial cultivar M. × giganteus. An example of an F1 hybrid has already demonstrated the long-term potential of exploiting this collection for a breeding programme.

Conclusions
By conforming to the CBD principles, the authors’ international collaboration provides a practical example of implementing the CBD. The collection widened the genetic diversity of Miscanthus available to allow for breeding of novel hybrids that exhibit more diverse traits to increase yield and resilience for growth on marginal land and in climate-challenged environments.
A novel measure of non-coding genome conservation identifies genomic regulatory blocks within primates
Authors: Nash Alexander J , Lenhard Boris 
Published: December 2018

AbstractMotivationClusters of extremely conserved non-coding elements (CNEs) mark genomic regions devoted to cis-regulation of key developmental genes in Metazoa. We have recently shown that their span coincides with that of topologically associating domains (TADs), making them useful for estimating conserved TAD boundaries in the absence of Hi-C data. The standard approach—detecting CNEs in genome alignments and then establishing the boundaries of their clusters—requires tuning of several parameters and breaks down when comparing closely related genomes.ResultsWe present a novel, kurtosis-based measure of pairwise non-coding conservation that requires no pre-set thresholds for conservation level and length of CNEs. We show that it performs robustly across a large span of evolutionary distances, including across the closely related genomes of primates for which standard approaches fail. The method is straightforward to implement and enables detection and comparison of clusters of CNEs and estimation of underlying TADs across a vastly increased range of Metazoan genomes.Availability and implementationThe data generated for this study, and the scripts used to generate the data, can be found at https://github.com/alexander-nash/kurtosis_conservation.Supplementary informationSupplementary data are available at Bioinformatics online.
A databank for intracellular electrophysiological mapping of the adult somatosensory cortex
Authors: da Silva Lantyer Angelica , Calcini Niccolò , Bijlsma Ate , Kole Koen , Emmelkamp Melanie , Peeters Manon , Scheenen Wim J J , Zeldenrust Fleur , Celikel Tansu 
Published: December 2018

Abstract

Background
Neurons in the supragranular layers of the somatosensory cortex integrate sensory (bottom-up) and cognitive/perceptual (top-down) information as they orchestrate communication across cortical columns. It has been inferred, based on intracellular recordings from juvenile animals, that supragranular neurons are electrically mature by the fourth postnatal week. However, the dynamics of the neuronal integration in adulthood is largely unknown. Electrophysiological characterization of the active properties of these neurons throughout adulthood will help to address the biophysical and computational principles of the neuronal integration.

Findings
Here, we provide a database of whole-cell intracellular recordings from 315 neurons located in the supragranular layers (L2/3) of the primary somatosensory cortex in adult mice (9–45 weeks old) from both sexes (females, N = 195; males, N = 120). Data include 361 somatic current-clamp (CC) and 476 voltage-clamp (VC) experiments, recorded using a step-and-hold protocol (CC, N = 257; VC, N = 46), frozen noise injections (CC, N = 104) and triangular voltage sweeps (VC, 10 (N = 132), 50 (N = 146) and 100 ms (N = 152)), from regular spiking (N = 169) and fast-spiking neurons (N = 66).

Conclusions
The data can be used to systematically study the properties of somatic integration and the principles of action potential generation across sexes and across electrically characterized neuronal classes in adulthood. Understanding the principles of the somatic transformation of postsynaptic potentials into action potentials will shed light onto the computational principles of intracellular information transfer in single neurons and information processing in neuronal networks, helping to recreate neuronal functions in artificial systems.
The Effect of Teacher's Aides in the Classroom: Evidence from a Randomized Trial
Authors: Andersen Simon Calmar , Beuchert Louise , Nielsen Helena Skyt , Thomsen Mette Kjærgaard 
Published: December 2018

Abstract
Teacher's aides are used worldwide, in various school systems, although, there is no strong evidence of their impact on student outcomes. We use a randomized trial to challenge this state of evidence. We randomly allocate 105 schools to two types of treatments—aides with or without a teaching degree—compared to a control group. Both types of aides have positive impacts on test scores and the effects are persistent over time for disadvantaged students. Exploratory analyses of mechanisms suggest that a teacher's aide is not just a class-size reduction, but especially impactful when sharing instructional responsibility for the classroom.
The peregrinations of porcelain
Authors: Clark Leah R 
Published: December 2018

Abstract
The Medici of Florence have long been acknowledged as possessing the largest collection of Chinese porcelain in the fifteenth century, but this article reveals that in fact Eleonora d’Aragona, Duchess of Ferrara had the largest such collection in Italy at this time. In fifteenth-century Europe, porcelain came not directly from China but rather through trade and diplomacy with foreign courts, so that its peregrinations gave rise to entangled histories and reception. Taking porcelain as a case-study, it is argued here that examining collecting through the lens of trade and diplomacy provides new interpretations of – and demands new approaches to – the history of collecting.
Reflectivity degradation of the Subaru Telescope primary mirror
Authors: Okita Hirofumi , Hayashi Saeko S , Takato Naruhisa 
Published: December 2018

Abstract
The reflectivity degradation of a telescope’s mirrors is broadly known; however, due to lack of suitable instrumentation, it has not been sufficiently studied. To overcome this situation, we developed a portable spectrophotometer named the “Subaru Portable Spectrophotometer” (SPS) to measure the absolute spectral reflectivity in-situ for a large optical component, such as a telescope’s primary mirror. The reflectivity of the Subaru telescope primary mirror was measured with SPS right before its eighth coating, and it showed larger degradation at shorter wavelength. Since then, the reflectivity degradation has been monitored with SPS. To explain the wavelength-dependence of the reflectivity degradation, we developed a two-factor model of a simple achromatic loss and scattering. The two-factor model shows an excellent match to real degradation. The time evolution of the achromatic loss and scattering are shown, and these are about 2.3% achromatic loss per year, and the color-dependent loss from root-mean-square (rms) surface roughness, which is the cause of scattering, increases from an initial small roughness after coating by about 40 Å per year. From these results, we extrapolated the model to a long-elapsed time to estimate the reflectivity in the future. The reflectivity of the Subaru Telescope primary mirror is expected to decrease about 22% at 400 nm by 1200 days after coating, and by 10% at 950 nm. We deduced the most efficient coating frequency of the Subaru Telescope primary mirror that maximizes the number of photons that can be acquired, and it is once every three years.
Evaluating the Medial Longitudinal Arch of the Foot: Correlations, Reliability, and Accuracy in People With a Low Arch
Authors: Zuil-Escobar Juan C , Martínez-Cepa Carmen B , Martín-Urrialde Jose A , Gómez-Conesa Antonia 
Published: December 2018

Abstract

Background
The medial longitudinal arch of the foot is a variable structure, and a decrease in its height could affect several functions and increase the risk of injuries in the lower limbs. There are many different techniques for evaluating it.

Objective
The objective of this study was to evaluate the correlations of the Navicular Drop Test, several footprint parameters, and the Foot Posture Index-6 in people with a low medial longitudinal arch. Intrarater reliability and interrater reliability were also estimated.

Design
This was a repeated-measures, observational descriptive study.

Methods
Seventy-one participants (53.5% women; mean age = 24.13 years; SD = 3.41) were included. All of the parameters were collected from the dominant foot. The correlation coefficients were calculated. The reliability was also calculated using the intraclass correlation coefficient, 95% CI, and kappa coefficient.

Results
Statistically significant correlations were obtained between the Navicular Drop Test and the footprint parameters, with r absolute values ranging from 0.722 to 0.788. The Navicular Drop Test and the Foot Posture Index-6 showed an excellent correlation (Spearman correlation coefficient = 0.8), and good correlations (Spearman correlation coefficient = |0.663–0.703|) were obtained between the footprint parameters and the Foot Posture Index-6. Excellent intrarater reliability and interrater reliability were obtained for all of the parameters.

Limitations
Radiographic parameters, the gold standard for evaluating the medial longitudinal arch height, were not used. In addition, the results of this research cannot be generalized to people with normal and high medial longitudinal arches.

Conclusions
In participants with a low medial longitudinal arch, the Navicular Drop Test showed significant correlations with footprint parameters; correlations were good for the arch angle and Chippaux-Smirnak Index, and excellent for the Staheli Index. The Foot Posture Index-6 showed an excellent correlation with the Navicular Drop Test and a good correlation with the footprint parameters evaluated. All of the parameters showed high reliability.
Fall Prevalence and Contributors to the Likelihood of Falling in Persons With Upper Limb Loss
Authors: Major Matthew J 
Published: December 2018

Abstract

Background
Arms are important for locomotor stability and preventing falls by controlling whole-body angular momentum, redirecting the body's center of mass, and providing support to arrest descent. Hence, upper limb loss (ULL) can increase fall risk. However, the prevalence of falls and factors that influence fall risk have not previously been reported for people with ULL.

Objective
This study quantified fall prevalence in persons with ULL at or proximal to the wrist and identified clinical factors that contributed to the likelihood of falling.

Design
This was a cross-sectional study.

Methods
Factors including body and health characteristics, activity level, fall history, prosthesis use, and balance confidence were determined for persons with ULL proximal to the wrist using an online survey. Logistic regression analyses assessed the contribution of these factors to the classification of fallers (≥2 falls in previous year) and nonfallers.

Results
A percentage (28.6%) of participants (n = 105) reported experiencing 2 or more falls in the past year. The regression model (R2 = 0.473) correctly classified 84.5% of cases and indicated that increased likelihood of falling was significantly influenced by reduced balance confidence, use of upper limb prostheses, and reduced physical capabilities.

Limitations
Data were collected online from a convenience sample, and fall classification was based on retrospective data.

Conclusions
Falls in persons with ULL are prevalent, suggesting that clinicians should use screening methods to identify at-risk individuals. Balance confidence, use of upper limb prostheses, and perceived physical capabilities could be useful screening metrics. Research is warranted to better understand the factors that underlie fall risk in persons with ULL and the efficacy of therapeutic interventions capable of mitigating fall risk.
Cumulative Prospect Theory, Option Returns, and the Variance Premium
Authors: Baele Lieven , Driessen Joost , Ebert Sebastian , Londono Juan M , Spalt Oliver G 
Published: December 2018

Abstract
We develop a tractable equilibrium asset pricing model with cumulative prospect theory (CPT) preferences. Using GMM on a sample of U.S. equity index option returns, we show that by introducing a single common probability weighting parameter for both tails of the return distribution, the CPT model can simultaneously generate the otherwise puzzlingly low returns on both out-of-the-money put and out-of-the-money call options as well as the high observed variance premium. In a dynamic setting, probability weighting and time-varying equity return volatility combine to match the observed time-series pattern of the variance premium.
Received May 30, 2017; editorial decision August 10, 2018 by Editor Andrew Karolyi.
Heritable Phytohormone Profiles of Poplar Genotypes Vary in Resistance to a Galling Aphid
Authors: Body Mélanie J. A. , Zinkgraf Matthew S. , Whitham Thomas G. , Lin Chung-Ho , Richardson Ryan A. , Appel Heidi M. , Schultz Jack C. 
Published: December 2018

Insect galls are highly specialized structures arising from atypical development of plant tissue induced by insects. Galls provide the insect enhanced nutrition and protection against natural enemies and environmental stresses. Galls are essentially plant organs formed by an intimate biochemical interaction between the gall-inducing insect and its host plant. Because galls are plant organs, their development is likely to be governed by phytohormones involved in normal organogenesis. We characterized concentrations of both growth and defensive phytohormones in ungalled control leaves and galls induced by the aphid Pemphigus betae on narrowleaf cottonwood Populus angustifolia that differ genotypically in resistance to this insect. We found that susceptible trees differed from resistant trees in constitutive concentrations of both growth and defense phytohormones. Susceptible trees were characterized by significantly higher constitutive cytokinin concentrations in leaves, significantly greater ability of aphids to elicit cytokinin increases, and significantly lower constitutive defense phytohormone concentrations than observed in resistant trees. Phytohormone concentrations in both constitutive and induced responses in galled leaves exhibited high broad-sense heritability that, respectively, ranged from 0.39 to 0.93 and from 0.28 to 0.66, suggesting that selection can act upon these traits and that they might vary across the landscape. Increased cytokinin concentrations may facilitate forming strong photosynthate sinks in the galls, a requirement for galling insect success. By characterizing for the first time the changes in 15 phytohormones belonging to five different classes, this study offers a better overview of the signaling alteration occurring in galls that has likely been important for their ecology and evolution.[Formula: see text] Copyright © 2019 The Author(s). This is an open-access article distributed under the CC BY-NC-ND 4.0 International license .
Comparative Evaluation of LAMP, qPCR, Conventional PCR, and ELISA to DetectRalstonia solanacearumin Kenyan Potato Fields
Authors: Okiro Lilian A. , Tancos Matthew A. , Nyanjom Steven G. , Smart Christine D. , Parker Monica L. 
Published: December 2018

Bacterial wilt caused by Ralstonia solanacearum is considered among the most damaging diseases of potato in Sub-Saharan Africa and the most significant biotic constraint of potato production alongside late blight. Unlike late blight, which can be managed by chemical means, R. solanacearum can only be managed through cultural methods and clean seed. Laboratory testing to certify seed before planting is required to confirm the absence of the pathogen in Kenya. A loop-mediated isothermal amplification (LAMP) assay was developed using the UDP-(3-O-acyl)-N-acetylglucosamine deacetylase gene (IpxC) to screen seed potato for R. solanacearum strains. The assay was assessed using DNA extracted from R. solanacearum and other soil and potato pathogens to demonstrate specificity and sensitivity. The LAMP assay was validated using field samples from different potato growing regions of Kenya collected over two growing seasons and compared with established nucleic acid and protein-based assays. The IpxC LAMP assay was found to be specific and sensitive to R. solanacearum, detecting as low as 2.5 pg/µl of R. solanacearum DNA. Of the 47 potentially infected field samples collected, both IpxC LAMP and quantitative polymerase chain reaction (PCR) detected R. solanacearum DNA in 90% of the samples, followed by conventional PCR (86%) and ELISA (75%). This IpxC LAMP assay is a promising diagnostic tool to rapidly screen for R. solanacearum in seed potato with high sensitivity in Kenya.[Formula: see text] Copyright © 2019 The Author(s). This is an open access article distributed under the CC BY 4.0 International license .
Examining Disparities in Route of Surgery and Postoperative Complications in Black Race and Hysterectomy
Authors: Alexander Amy L. , Strohl Anna E. , Rieder Stephanie , Holl Jane , Barber Emma L. 
Published: December 2018

OBJECTIVE:
To estimate the associations among race, route of hysterectomy, and postoperative complications among women undergoing hysterectomy for benign indications.

METHODS:
A cohort study was performed. All patients undergoing hysterectomy for benign indications, recorded in the National Surgical Quality Improvement Program and its targeted hysterectomy file in 2015, were identified. The primary exposure was patient race. The primary outcome was route of hysterectomy and the secondary outcome was postoperative complication. Associations were examined using both bivariable tests and logistic regression.

RESULTS:
Of 15,136 women who underwent hysterectomy for benign indications, 75% were white and 25% were black. Black women were more likely to undergo an open hysterectomy than white women (50.1% vs 22.9%; odds ratio [OR] 3.36, 95% CI 3.11–3.64). Black women had larger uteri (median 262 g vs 123 g; 60.7% vs 25.6% with uterus greater than 250 g), more prior pelvic surgery (58.5% vs 53.2%), and higher body mass indices (32.7 vs 30.4). After adjusting for these and other clinical factors, black women remained more likely to undergo an open hysterectomy (adjusted OR 2.02, 95% CI 1.85–2.20). Black women experienced more major complications than white women (4.1% vs 2.3%; P<.001) and more minor complications (11.4% vs 6.7%; OR 1.78, P<.001). Again these disparities persisted with adjustment (major adjusted OR 1.56, 95% CI 1.25–1.95; minor adjusted OR 1.27, 95% CI 1.11–1.47).

CONCLUSIONS:
Black women undergo a higher proportion of open hysterectomy and experience more major and minor postoperative complications. These differences persisted even after adjusting for confounding medical, surgical, and gynecologic factors.
Amnioinfusion Compared With No Intervention in Women With Second-Trimester Rupture of Membranes
Authors: van Kempen Liselotte E. M. , van Teeffelen Augustinus S. , de Ruigh Annemijn A. , Oepkes Dick , Haak Monique C. , van Leeuwen Elisabeth , Woiski Mallory , Porath Martina M. , Bax Caroline J. , van Wassenaer-Leemhuis Aleid G. , Mulder Antonius L. , van der Ham David P. , Willekes Christine , Franssen Maureen T. , Derks Jan B. , Schuit Ewoud , Mol Ben W. , Pajkrt Eva 
Published: December 2018

OBJECTIVE:
To assess the effectiveness of amnioinfusion in women with second-trimester preterm prelabor rupture of membranes.

METHODS:
We performed a nationwide, multicenter, open-label, randomized controlled trial, the PPROM: Expectant Management versus Induction of Labor-III (PPROMEXIL-III) trial, in women with singleton pregnancies and preterm prelabor rupture of membranes at 16 0/7 to 24 0/7 weeks of gestation with oligohydramnios (single deepest pocket less than 20 mm). Participants were allocated to transabdominal amnioinfusion or no intervention in a one-to-one ratio by a web-based system. If the single deepest pocket was less than 20 mm on follow-up visits, amnioinfusion was repeated weekly until 28 0/7 weeks of gestation. The primary outcome was perinatal mortality. We needed 56 women to show a reduction in perinatal mortality from 70% to 35% (β error 0.20, two-sided α error 0.05).

RESULTS:
Between June 15, 2012, and January 13, 2016, we randomized 28 women to amnioinfusion and 28 to no intervention. One woman was enrolled before the trial registration date (June 19, 2012). Perinatal mortality rates were 18 of 28 (64%) in the amnioinfusion group vs 21 of 28 (75%) in the no intervention group (relative risk 0.86, 95% CI 0.60–1.22, P=.39).

CONCLUSION:
In women with second-trimester preterm prelabor rupture of membranes and oligohydramnios, we found no reduction in perinatal mortality after amnioinfusion.

CLINICAL TRIAL REGISTRATION:
NTR Dutch Trial Register, NTR3492.