bluuebunny/crossref_metadata_2025 huggingface dataset:
Plasmon-induced transparency in ring-bar meta-atom
Authors: Huang Wan-Xia , Zhu Cun-Yuan , Wang Mao-Sheng , Li Kuan-Guo , Shi Jian-Ping , Zhang Fa-Bao
Published: March 2018

We introduce an approach for constructing a scalable metamaterial structure, which is composed of a ring and a bar in a unit cell, and supports singular plasmon-induced transparency. The composite multilayered structure consists of coupled meta-atom with bright modes and dark modes interacting through the introduction of structural asymmetry, which involves the displacement of the bar from the center of the ring. The splitting and merging of the absorption peaks is observed with the change in asymmetric degree. In addition, coupled-mode theory with a two-mode and two-port model is introduced to explain the observed novel spectral feature. The results provide a reference for further application to optoelectronic devices.
Nonlinear dynamics of resonant electrons interacting with coherent Langmuir waves
Authors: Tobita Miwa , Omura Yoshiharu
Published: March 2018

We study the nonlinear dynamics of resonant particles interacting with coherent waves in space plasmas. Magnetospheric plasma waves such as whistler-mode chorus, electromagnetic ion cyclotron waves, and hiss emissions contain coherent wave structures with various discrete frequencies. Although these waves are electromagnetic, their interaction with resonant particles can be approximated by equations of motion for a charged particle in a one-dimensional electrostatic wave. The equations are expressed in the form of nonlinear pendulum equations. We perform test particle simulations of electrons in an electrostatic model with Langmuir waves and a non-oscillatory electric field. We solve equations of motion and study the dynamics of particles with different values of inhomogeneity factor S defined as a ratio of the non-oscillatory electric field intensity to the wave amplitude. The simulation results demonstrate deceleration/acceleration, thermalization, and trapping of particles through resonance with a single wave, two waves, and multiple waves. For two-wave and multiple-wave cases, we describe the wave-particle interaction as either coherent or incoherent based on the probability of nonlinear trapping.
Quantitative evaluation of the piezoelectric response of unpoled ferroelectric ceramics from elastic and dielectric measurements: Tetragonal BaTiO3
Authors: Cordero F.
Published: March 2018

A method is proposed for evaluating the potential piezoelectric response, that a ferroelectric material would exhibit after full poling, from elastic and dielectric measurements of the unpoled ceramic material. The method is based on the observation that the softening in a ferroelectric phase with respect to the paraelectric phase is of piezoelectric origin, and is tested on BaTiO3. The angular averages of the piezoelectric softening in unpoled ceramics are calculated for ferroelectric phases of different symmetries. The expression of the orientational average with the piezoelectric and dielectric constants of single crystal tetragonal BaTiO3 from the literature reproduces well the softening of the Young's modulus of unpoled ceramic BaTiO3, after a correction for the porosity. The agreement is good in the temperature region sufficiently far from the Curie temperature and from the transition to the orthorhombic phase, where the effect of fluctuations should be negligible, but deviations are found outside this region, and possible reasons for this are discussed. This validates the determination of the piezoelectric response by means of purely elastic measurements on unpoled samples. The method is indirect and, for quantitative assessments, requires the knowledge of the dielectric tensor. On the other hand, it does not require poling of the sample, and therefore is insensitive to inaccuracies from incomplete poling, and can even be used with materials that cannot be poled, for example, due to excessive electrical conductivity. While the proposed example of the Young's modulus of a ceramic provides an orientational average of all the single crystal piezoelectric constants, a Resonant Ultrasound Spectroscopy measurement of a single unpoled ceramic sample through the ferroelectric transition can in principle measure all the piezoelectric constants, together with the elastic ones.
Thermally conductive tough flexible elastomers as composite of slide-ring materials and surface modified boron nitride particles via plasma in solution
Authors: Goto Taku , Iida Masaki , Tan Helen , Liu Chang , Mayumi Koichi , Maeda Rina , Kitahara Koichi , Hatakeyama Kazuto , Ito Tsuyohito , Shimizu Yoshiki , Yokoyama Hideaki , Kimura Kaoru , Ito Kohzo , Hakuta Yukiya , Terashima Kazuo
Published: March 2018

We have developed a thermally conductive flexible elastomer as a composite material with slide-ring (SR) materials and boron nitride (BN) particles surface-modified via plasma in solution. This composite shows excellent properties as a flexible insulator for thermal management. Surface modification of BN particles using plasma in solution increases the tensile strength, extension ratio at break, toughness, and rubber characteristics of the composites, compared to SR and non-modified BN, while the Young's modulus values are identical. Furthermore, the thermal conductivity also improved as a result of plasma surface modification.
A thermodynamic potential, energy storage performances, and electrocaloric effects of Ba1-xSrxTiO3 single crystals
Authors: Huang Y. H. , Wang J. J , Yang T. N. , Wu Y. J. , Chen X. M. , Chen L. Q.
Published: March 2018

A thermodynamic potential for Ba1-xSrxTiO3 solid solutions is developed, and the corresponding thermodynamic properties of Ba1-xSrxTiO3 single crystals are calculated. The predicted temperature-composition phase diagram from the thermodynamic potential agrees well with the experimental measurements. Based on this potential, the energy storage performances and electrocaloric effects of Ba1-xSrxTiO3 single crystals are obtained using the phase-field method. It is found that there is an optimal Sr concentration which maximizes the discharged energy density of a Ba1-xSrxTiO3 single crystal under an applied electric field. The electrocaloric effects of Ba0.8Sr0.2TiO3, Ba0.7Sr0.3TiO3, Ba0.6Sr0.4TiO3, and Ba0.5Sr0.5TiO3 single crystals are also predicted, from which the corresponding optimal temperatures are identified.
Cluster formation of network-modifier cations in cesium silicate glasses
Authors: Jardón-Álvarez Daniel , Sanders Kevin J. , Phyo Pyae , Baltisberger Jay H. , Grandinetti Philip J.
Published: March 2018

Natural abundance 29Si two-dimensional magic-angle flipping (2D MAF) NMR spectra were measured in a series of ten cesium silicate glass compositions xCs2O·(1 − x)SiO2, where x is 0.067, 0.113, 0.175, 0.179, 0.218, 0.234, 0.263, 0.298, 0.31, and 0.36. The Q3 shielding anisotropy decreases with increasing Cs content—interpreted as an increase in the non-bridging oxygen (NBO) bond length from increasing Cs coordination (clustering) around the NBO. The 29Si 2D MAF spectra for four glass compositions x = 0.218, 0.234, 0.263, 0.298 exhibit a second co-existing and distinctly smaller shielding anisotropy corresponding to a significantly longer Si–NBO length arising from a higher degree of Cs clustering around the NBO. This second Q3 site appears at a Cs2O mole fraction close to the critical mole fraction of x = 0.24 associated with the percolation threshold of non-bridging oxygen in random close packing of oxygen, thus suggesting that the longer Si–NBO length is associated with an infinite size spanning cluster while the sites with larger anisotropies are associated with shorter Si–NBO lengths and belong to finite size clusters. The equilibrium constant of the Q3 disproportionation reaction was determined as k3 = 0.005, indicating a Qn anionic species distribution close to a binary model as expected for a low field strength modifier such as cesium. It is also found that evolution of the isotropic Q4 and line shapes with increasing Cs content are consistent with a random connectivity model between Qn of differing number of bridging oxygen, n.
Selective area growth of InGaN-based nanocolumn LED crystals on AlN/Si substrates useful for integrated μ-LED fabrication
Authors: Yamano Koji , Kishino Katsumi
Published: March 2018

Triangular-lattice nanopillar-array templates with a lattice constant of 280 nm and with AlN disks on top of the underlying Si pillars were prepared on 2-in. AlN/Si substrates through nanoimprint lithography and dry etching. Regularly arranged GaN nanocolumn arrays with a 220-nm diameter were grown on the templates to fabricate wide-area emission InGaN/GaN nanocolumn light emitting diodes (LEDs). An LED chip with an Indium Tin Oxide (ITO) electrode with an area of 3 × 4 mm2 operated at a current of 100 mA emitted blue-green light (504 nm in wavelength) from the entire surface of the large emission area.
Skyrmion states in thin confined polygonal nanostructures
Authors: Pepper Ryan Alexander , Beg Marijan , Cortés-Ortuño David , Kluyver Thomas , Bisotti Marc-Antonio , Carey Rebecca , Vousden Mark , Albert Maximilian , Wang Weiwei , Hovorka Ondrej , Fangohr Hans
Published: March 2018

Recent studies have demonstrated that skyrmionic states can be the ground state in thin-film FeGe disk nanostructures in the absence of a stabilising applied magnetic field. In this work, we advance this understanding by investigating to what extent this stabilisation of skyrmionic structures through confinement exists in geometries that do not match the cylindrical symmetry of the skyrmion—such as squares and triangles. Using simulation, we show that skyrmionic states can form the ground state for a range of system sizes in both triangular and square-shaped FeGe nanostructures of 10 nm thickness in the absence of an applied field. We further provide data to assist in the experimental verification of our prediction; to imitate an experiment where the system is saturated with a strong applied field before the field is removed, we compute the time evolution and show the final equilibrium configuration of magnetization fields, starting from a uniform alignment.
Long-term urban carbon dioxide observations reveal spatial and temporal dynamics related to urban characteristics and growth
Authors: Mitchell Logan E. , Lin John C. , Bowling David R. , Pataki Diane E. , Strong Courtenay , Schauer Andrew J. , Bares Ryan , Bush Susan E. , Stephens Britton B. , Mendoza Daniel , Mallia Derek , Holland Lacey , Gurney Kevin R. , Ehleringer James R.
Published: March 2018

Significance

Recent efforts to reduce greenhouse gas emissions have focused on cities due to intensive emissions, viable policy levers, and interested stakeholders. Atmospheric observations can be used to independently evaluate emissions, but suitable networks are sparse. We present a unique decadal record of atmospheric CO
2
from five sites with contrasting urban characteristics that show divergent trends in CO
2
emissions across a city. Comparison with population growth reveals a nonlinear relationship that may reflect how urban form affects CO
2
emissions. Four state-of-the-art global-scale emission inventories capture the nonlinear relationship with population density but not the divergent long-term trends across the city. This demonstrates that CO
2
monitoring networks can provide insight into urban carbon cycle processes and provide policy-relevant information to urban stakeholders.
Uranium isotope evidence for two episodes of deoxygenation during Oceanic Anoxic Event 2
Authors: Clarkson Matthew O. , Stirling Claudine H. , Jenkyns Hugh C. , Dickson Alexander J. , Porcelli Don , Moy Christopher M. , Pogge von Strandmann Philip A. E. , Cooke Ilsa R. , Lenton Timothy M.
Published: March 2018

Significance

Past “Oceanic Anoxic Events” (OAEs) represent important carbon cycle perturbations that offer the opportunity to study Earth’s response to extreme climate warming. A fundamental limitation for understanding OAEs is quantifying the timing and total extent of ocean anoxia. We present a quantitative account of global redox conditions for OAE 2 (∼94 million years ago), using a high-resolution record of uranium isotopes combined with a biogeochemical model. We present new evidence for two discrete intervals of globally extensive anoxia that were coupled to enhanced terrestrial weathering, within the typically defined OAE interval. These anoxic intervals were separated by ocean reoxygenation and the temporary recovery of the carbon cycle.
BRICHOS domain of Bri2 inhibits islet amyloid polypeptide (IAPP) fibril formation and toxicity in human beta cells
Authors: Oskarsson Marie E. , Hermansson Erik , Wang Ye , Welsh Nils , Presto Jenny , Johansson Jan , Westermark Gunilla T.
Published: March 2018

Significance

Accumulation of islet amyloid polypeptide (IAPP)-containing amyloid fibrils is the main pathological finding in pancreatic islets in type 2 diabetes. The formation of these IAPP amyloid fibrils is considered toxic and may constitute a major cause for the loss of insulin-producing beta cells. The protein domain BRICHOS is present in several different proproteins and possesses antiamyloid chaperone activity. This study demonstrates expression of the BRICHOS-containing protein Bri2 in human pancreatic beta cells and its colocalization with IAPP. The Bri2 BRICHOS domain effectively prevents IAPP from forming fibrils and protects cells from the toxicity associated with IAPP fibrillation. It is concluded that the Bri2 BRICHOS domain may act as an endogenous inhibitor of IAPP amyloid formation in pancreatic beta cells.
Biogeographical disparity in the functional diversity and redundancy of corals
Authors: McWilliam Mike , Hoogenboom Mia O. , Baird Andrew H. , Kuo Chao-Yang , Madin Joshua S. , Hughes Terry P.
Published: March 2018

Significance

The wide variety of functional trait combinations among the world’s coral faunas can be represented by just a few dimensions of variation. The diversity of coral traits among these dimensions is consistently high along Pacific and Indian Ocean diversity gradients, despite a threefold decline in species richness (from approximately 600 to 200 species). Functional redundancy, defined as multiple species sharing similar arrays of traits, is highest in the central Indo-Pacific biodiversity hotspot. While these Indo-Pacific provinces are globally important reserves of coral reef resilience and function, peripheral species-poor regions are potentially more vulnerable to functional collapse, as indicated by a critical lack of redundancy among species and the reduced capacity for similar species to respond differently to chronic or acute stressors.
MERS coronaviruses from camels in Africa exhibit region-dependent genetic diversity
Authors: Chu Daniel K. W. , Hui Kenrie P. Y. , Perera Ranawaka A. P. M. , Miguel Eve , Niemeyer Daniela , Zhao Jincun , Channappanavar Rudragouda , Dudas Gytis , Oladipo Jamiu O. , Traoré Amadou , Fassi-Fihri Ouafaa , Ali Abraham , Demissié Getnet F. , Muth Doreen , Chan Michael C. W. , Nicholls John M. , Meyerholz David K. , Kuranga Sulyman A. , Mamo Gezahegne , Zhou Ziqi , So Ray T. Y. , Hemida Maged G. , Webby Richard J. , Roger Francois , Rambaut Andrew , Poon Leo L. M. , Perlman Stanley , Drosten Christian , Chevalier Veronique , Peiris Malik
Published: March 2018

Significance

Middle East respiratory syndrome (MERS) is a zoonotic disease of global health concern, and dromedary camels are the source of human infection. Although Africa has the largest number of dromedary camels, and MERS-coronavirus (MERS-CoV) is endemic in these camels, locally acquired zoonotic MERS is not reported from Africa. However, little is known of the genetic or phenotypic characterization of MERS-CoV from Africa. In this study we characterize MERS-CoV from Burkina Faso, Nigeria, Morocco, and Ethiopia. We demonstrate viral genetic and phenotypic differences in viruses from West Africa, which may be relevant to differences in zoonotic potential, highlighting the need for studies of MERS-CoV at the animal–human interface.
Near-atomic cryo-EM imaging of a small protein displayed on a designed scaffolding system
Authors: Liu Yuxi , Gonen Shane , Gonen Tamir , Yeates Todd O.
Published: March 2018

Significance

New electron microscopy (EM) methods are making it possible to view the structures of large proteins and nucleic acid complexes at atomic detail, but the methods are difficult to apply to molecules smaller than approximately 50 kDa, which is larger than the size of the average protein in the cell. The present work demonstrates that a protein much smaller than that limit can be successfully visualized when it is attached to a large protein scaffold designed to hold 12 copies of the attached protein in symmetric and rigidly defined orientations. The small protein chosen for attachment and visualization can be modified to bind to other diverse proteins, opening a new avenue for imaging cellular proteins by cryo-EM.
Protein homology model refinement by large-scale energy optimization
Authors: Park Hahnbeom , Ovchinnikov Sergey , Kim David E. , DiMaio Frank , Baker David
Published: March 2018

Significance

Protein structure refinement by direct global energy optimization has been a longstanding challenge in computational structural biology due to limitations in both energy function accuracy and conformational sampling. This manuscript demonstrates that with recent advances in both areas, refinement can significantly improve protein comparative models based on structures of distant homologues.
Enzymatic reconstitution of ribosomal peptide backbone thioamidation
Authors: Mahanta Nilkamal , Liu Andi , Dong Shihui , Nair Satish K. , Mitchell Douglas A.
Published: March 2018

Significance

Thioamidation as a posttranslational modification is exceptionally rare, with only one protein example known (methyl-coenzyme M reductase, MCR), as well as a few ribosomal natural products. The genes involved in MCR thioamidation have recently been elucidated, but the enzymes have yet to be characterized. Herein, we report the in vitro reconstitution and substrate preferences of peptidic thioamidation using peptides and enzymes derived from methanogenic archaea. We demonstrate that MCR thioamidation requires an ATP-dependent YcaO enzyme and a sulfide source. Our results shed light on the biosynthesis of other thioamide-containing compounds, which bioinformatics surveys predict to be considerably more numerous than currently appreciated, thus laying a foundation for assigning biological functions for this posttranslational modification.
Antidepression action of BDNF requires and is mimicked by Gαi1/3 expression in the hippocampus
Authors: Marshall John , Zhou Xiao-zhong , Chen Gang , Yang Su-qing , Li Ya , Wang Yin , Zhang Zhi-qing , Jiang Qin , Birnbaumer Lutz , Cao Cong
Published: March 2018

Significance

Heterotrimeric Gαi proteins are known to transduce G protein-coupled receptor signals. We have identified a role for Gαi proteins in mediating brain-derived neurotrophic factor (BDNF)–tropomyosin-related kinase B (TrkB) signaling. BDNF dysfunction contributes to the pathophysiology of depression. In a stress model of depression Gαi1 and Gαi3 proteins are downregulated in the hippocampus, a limbic structure associated with major depressive disorder. We show that Gαi1/Gαi3 proteins are required for TrkB downstream signaling, and knockout mice exhibited severe depressive behaviors with decreased dendritic morphology. Established stress-induced depressive behavior is corrected by intrahippocampal expression of Gαi3. These results demonstrate that heterotrimeric Gαi1 and Gαi3 proteins are essential for TrkB signaling and that disruption of Gαi1 or Gαi3 function could contribute to depressive behaviors.
Primary cilia sensitize endothelial cells to BMP and prevent excessive vascular regression
Authors: Vion Anne-Clémence , Alt Silvanus , Klaus-Bergmann Alexandra , Szymborska Anna , Zheng Tuyu , Perovic Tijana , Hammoutene Adel , Oliveira Marta Bastos , Bartels-Klein Eireen , Hollfinger Irene , Rautou Pierre-Emmanuel , Bernabeu Miguel O. , Gerhardt Holger
Published: March 2018

Blood flow shapes vascular networks by orchestrating endothelial cell behavior and function. How endothelial cells read and interpret flow-derived signals is poorly understood. Here, we show that endothelial cells in the developing mouse retina form and use luminal primary cilia to stabilize vessel connections selectively in parts of the remodeling vascular plexus experiencing low and intermediate shear stress. Inducible genetic deletion of the essential cilia component intraflagellar transport protein 88 (IFT88) in endothelial cells caused premature and random vessel regression without affecting proliferation, cell cycle progression, or apoptosis. IFT88 mutant cells lacking primary cilia displayed reduced polarization against blood flow, selectively at low and intermediate flow levels, and have a stronger migratory behavior. Molecularly, we identify that primary cilia endow endothelial cells with strongly enhanced sensitivity to bone morphogenic protein 9 (BMP9), selectively under low flow. We propose that BMP9 signaling cooperates with the primary cilia at low flow to keep immature vessels open before high shear stress–mediated remodeling.
3. The Rape of Lucrece
Authors: Post Jonathan F. S.
Published: March 2018

‘The Rape of Lucrece’ considers the range of sources—and their particular emphases—that Shakespeare may have drawn on when writing his poem, published in 1594: Livy’s Roman civic history; Ovid’s lures of the emotions; and Chaucer’s Lucrece as the exemplary, loyal wife. Shakespeare broadened, deepened, and updated the known outlines of the story, selecting and expanding what he needed to fit the stylistic and thematic needs of the poem and the expectations of its readers. The result is a profoundly thoughtful poem, exploring the psyches of both villain and victim in greater depth and concentration than even his experience in the theatre had yet allowed.
4. On first looking into Shakespeare’s Sonnets
Authors: Post Jonathan F. S.
Published: March 2018

Shakespeare’s Sonnets are generally regarded as the finest collection of sonnets in the English language, and ‘On first looking into Shakespeare’s Sonnets’ seeks to offer yet one more perspective on why this is so. It outlines some of the puzzles and problems linked to the date of authorship and structure of the Sonnets; describes the sonnet form, comparing Shakespeare’s sonnet structure with that of Spenser; and considers some of the Sonnets in more depth, including Sonnet 116, the great ‘marriage’ poem. It is also noted that the Sonnets raise many ‘contemporary’ issues: matters of homosexual desire and transsexuality, of gender and racial stereotyping, of temptation and sexual addiction.
1. What is a mammal?
Authors: Kemp T. S.
Published: March 2018

‘What is a mammal?’ considers the diverse range of animals of varying forms, lifestyles, and habitats that make up the Class Mammalia. Despite the diversity, these animals share key characteristics: they have a single bone in the lower jaw; three little, sound-conducting ear bones; a very large forebrain; a permanently warm body and a high energy-expenditure level; and females have mammary glands for feeding milk to their young. The c.5,500 species of mammals alive today fall into three very unequal groups: the monotremes found in Australasia; the marsupials found in Australasia and South America; and the placentals, of which there are 5,000 species classified into twenty Orders.
5. Carnivorous mammals
Authors: Kemp T. S.
Published: March 2018

‘Carnivorous mammals’ considers the various carnivorous mammals that have evolved from the common ancestor of all modern mammals—the small, nocturnal, insectivorous mammal. Several mammals still follow this mode of life today: the placental shrews, moles, and hedgehogs; the tenrecs of Madagascar; and many of the opossums of South America and Australia. These have sharp, pointed incisors and canines for capturing prey, followed by sharp-crested premolar and molar teeth. The evolution of a small, insectivorous ancestor into larger bodied, predaceous mammals required relatively few anatomical changes, the main adaptations being for capture of its prey—by stealth hunting by solitary animals or pack hunting by organized social groups.
7. Diggers and burrowers
Authors: Kemp T. S.
Published: March 2018

‘Diggers and burrowers’ considers mammals at the opposite extreme to the high-speed running ungulate mammals. It describes mammals with short, powerfully built legs that bear large feet equipped with strong, blunt claws. When the limb muscles contract, they move the limb relatively slowly but powerfully, and so a large force is applied to the ground. Most of these animals are adapted for digging burrows to live in and find underground food such as beetle larvae or plant rhizomes. Examples are moles and mole-rats. With aardvarks, pangolins, and anteaters, the limbs are adapted for digging into extremely hard ant and termite nests, when particularly powerful muscles and claws are needed.
10. Primates
Authors: Kemp T. S.
Published: March 2018

‘Primates’ considers how a group of small, rather insignificant, tree-dwelling mammals living 60 mya eventually evolved the highest level of expression of the mammalian characteristic of adaptable behaviour by means of a large brain. It first discusses lemurs, lorises, bush babies, and tarsiers. It then describes the differences between New World and Old World monkeys, part of the Anthropoidea, which started their separate evolutionary journeys around 30 mya. Finally, it considers the rest of the Anthropoidea—the lesser apes (gibbons) and the great apes (orang-utans, chimpanzees, gorillas, and humans). The two most important new adaptations to evolve in humans are bipedalism and a huge brain.
11. Humans and mammals: the past and the future
Authors: Kemp T. S.
Published: March 2018

From the very start of the spread of humans, the world’s mammals have been irreversibly, and mostly detrimentally, affected through direct exploitation for food and for skins to make clothes and shelter. Our domestication of certain mammal species has also had a huge impact on the rest of the world’s mammalian fauna, and indeed on its whole biota. ‘Humans and mammals: the past and the future’ considers how human activity has caused the latest megafaunal extinction and looks at the future crisis facing many mammalian species. A quarter of mammalian species are, today, faced with severe population decreases that may result in extinction. What can be done to conserve them?
Agricultural Extension and Technology Adoption for Food Security: Evidence from Uganda
Authors: Pan Yao , Smith Stephen C , Sulaiman Munshi
Published: March 2018

We evaluate causal impacts of a large‐scale agricultural extension program for smallholder women farmers on technology adoption and food security in Uganda through a regression discontinuity design that exploits an arbitrary distance‐to‐branch threshold for village program eligibility. We find eligible farmers used better basic cultivation methods, achieved improved food security. Given minimal changes in adoption of relatively expensive inputs, we attribute these gains to improved cultivation methods that require low upfront monetary investment. Farmers also modified their shock‐coping methods. These results highlight the role of information and training in boosting agricultural productivity among poor farmers and, indirectly, improving food security.
Estimating the Productivity Impacts of Technology Adoption in the Presence of Misclassification
Authors: Wossen Tesfamicheal , Abdoulaye Tahirou , Alene Arega , Nguimkeu Pierre , Feleke Shiferaw , Rabbi Ismail Y. , Haile Mekbib G. , Manyong Victor
Published: March 2018

This article examines the impact that misreporting adoption status has on the identification and estimation of causal effects on productivity. In particular, by comparing measurement error‐ridden self‐reported adoption data with measurement‐error‐free DNA‐fingerprinted adoption data, we investigate the extent to which such errors bias the causal effects of adoption on productivity. Taking DNA‐fingerprinted adoption data as a benchmark, we find 25% “false negatives” and 10% “false positives” in farmers’ responses. Our results show that misreporting of adoption status is not exogenous to household characteristics, and produces a bias of about 22 percentage points in the productivity impact of adoption. Ignoring inherent behavioral adjustments of farmers based on perceived adoption status has a bias of 13 percentage points. The results of this article underscore the crucial role that correct measurement of adoption plays in designing policy interventions that address constraints to technology adoption in agriculture.
FasParser2: a graphical platform for batch manipulation of tremendous amount of sequence data
Authors: Sun Yan-Bo
Published: March 2018

FasParser is a graphical platform for manipulating sequences and alignments in a batch mode. It is particularly useful for biologists handling large datasets of sequences, even without an experience in programming. Here, I present an updated version ‘FasParser2’, featuring numerous improvements with sets of novel functions that can facilitate sequence manipulation. Its main additional features include (i) re-designed graphical interface which greatly improves its capability for batch processing, (ii) a trimming function to strip poorly-aligned regions in multiple sequence alignments, (iii) a series of functions that can identify as well as remove ‘bad’ sequence (either too short or too divergent sequences), (iv) an Editor tool for viewing and editing of biological sequences and (v) interfaces (with other programs) for detection of positive selection as well as primer design.

Availability and implementation

The compiled Windows binary is freely available at https://github.com/Sun-Yanbo/FasParser/releases.
PWMScan: a fast tool for scanning entire genomes with a position-specific weight matrix
Authors: Ambrosini Giovanna , Groux Romain , Bucher Philipp
Published: March 2018

Transcription factors regulate gene expression by binding to specific short DNA sequences of 5–20 bp to regulate the rate of transcription of genetic information from DNA to messenger RNA. We present PWMScan, a fast web-based tool to scan server-resident genomes for matches to a user-supplied PWM or transcription factor binding site model from a public database.

Availability and implementation

The web server and source code are available at http://ccg.vital-it.ch/pwmscan and https://sourceforge.net/projects/pwmscan, respectively.

Supplementary information

Supplementary data are available at Bioinformatics online.
Development and Validation of the Nursing Home Minimum Data Set 3.0 Mortality Risk Score (MRS3)
Authors: Thomas Kali S , Ogarek Jessica A , Teno Joan M , Gozalo Pedro L , Mor Vincent
Published: March 2018

Background

To develop a score to predict mortality using the Minimum Data Set 3.0 (MDS 3.0) that can be readily calculated from items collected during nursing home (NH) residents’ admission assessments.

Participants

We developed a training cohort of Medicare beneficiaries newly admitted to United States NHs during 2012 (N = 1,426,815) and a testing cohort from 2013 (N = 1,160,964).

Methods

Data came from the MDS 3.0 assessments linked to the Medicare Beneficiary Summary File. Using the training dataset, we developed a composite MDS 3.0 Mortality Risk Score (MRS3) consisting of 17 clinical items and patients’ age groups based on their relation to 30-day mortality. We assessed the calibration and discrimination of the MRS3 in predicting 30- and 60-day mortality and compared its performance to the Charlson Comorbidity Index and the clinician’s assessment of 6-month prognosis measured at admission.

Results

The 30- and 60-day mortality rates for the testing population were 2.8% and 5.6%, respectively. Results from logistic regression models suggest that the MRS3 performed well in predicting death within 30 and 60 days (C-Statistics of 0.744 [95% confidence limit (CL) = 0.741, 0.747] and 0.709 [95% CL = 0.706, 0.711], respectively). The MRS3 was a superior predictor of mortality compared to the Charlson Comorbidity Index (C-statistics of 0.611 [95% CL = 0.607, 0.615] and 0.608 [95% CL = 0.605, 0.610]) and the clinicians’ assessments of patients’ 6-month prognoses (C-statistics of 0.543 [95% CL = 0.542, 0.545] and 0.528 [95% CL = 0.527, 0.529]).

Conclusions

The MRS3 is a good predictor of mortality and can be useful in guiding decision-making, informing plans of care, and adjusting for patients’ risk of mortality.
Age and Gender Differences in Social Network Composition and Social Support Among Older Rural South Africans: Findings From the HAALSI Study
Authors: Harling Guy , Morris Katherine Ann , Manderson Lenore , Perkins Jessica M , Berkman Lisa F
Published: March 2018

Objectives

Drawing on the “Health and Aging in Africa: A Longitudinal Study of an INDEPTH community in South Africa” (HAALSI) baseline survey, we present data on older adults’ social networks and receipt of social support in rural South Africa. We examine how age and gender differences in social network characteristics matched with patterns predicted by theories of choice- and constraint-based network contraction in older adults.

Method

We used regression analysis on data for 5,059 South African adults aged 40 and older.

Results

Older respondents reported fewer important social contacts and less frequent communication than their middle-aged peers, largely due to fewer nonkin connections. Network size difference between older and younger respondents was greater for women than for men. These gender and age differences were explicable by much higher levels of widowhood among older women compared to younger women and older men. There was no evidence for employment-related network contraction or selective retention of emotionally supportive ties.

Discussion

Marriage-related structural constraints impacted on older women’s social networks in rural South Africa, but did not explain choice-based network contraction. These findings suggest that many older women in rural Africa, a growing population, may have an unmet need for social support.
Reorganized Force Control in Elbow Pain Patients During Isometric Wrist Extension
Authors: Mista Christian A. , Monterde Sonia , Inglés Montserrat , Salvat Isabel , Graven-Nielsen Thomas
Published: March 2018

Introduction:

Reorganized force control may be an important adaptation following painful traumas. In this study, force control adaptations were assessed in elbow pain patients. Increasing the contraction demand may overcome pain interference on the motor control and as such act as an internal control. It was hypothesized that elbow pain patients compared with controls would present greater change in the direction of force when increasing the demand of the motor task.

Methods:

Elbow pain patients (n=19) and asymptomatic participants (n=21) performed isometric wrist extensions at 5% to 70% of maximum voluntary contraction. Pressure pain thresholds were recorded at the lateral epicondyle and tibialis anterior muscle. Contraction force was recorded using a 3-directional force transducer. Participants performed contractions according to visual feedback of the task-related force intensity (main direction of wrist extension) and another set of contractions with feedback of the 3 force directions. Going from the simple to the detailed force feedback will increase the demand of the motor task. Force steadiness in all 3 dimensions and force directions were extracted.

Results:

Compared with controls, elbow pain patients presented lower pressure pain thresholds at both sites (P<0.05). Force steadiness was not significantly different between groups or feedback methods. The change in force direction when providing simple visual feedback in contrast with feedback of all force components at all contraction levels was greater for patients compared with controls (P<0.05).

Conclusion:

The larger change in force direction in pain patients implies redistribution of loads across the arm as an associated effect of pain.
Intramedullary Percutaneous Fixation of Extra-Articular Proximal and Middle Phalanx Fractures
Authors: Jovanovic Nebojsa , Aldlyami Ehab , Saraj Basem , FM Seidam Mohamed , Badawi Hamed , Shaat Ahmed , Alawadi Khalid , Dodakundi Chaitanya
Published: March 2018

Multiple methods have been described for treating unstable proximal and middle phalangeal fractures. Irrespective of using an open or closed technique of fixation, stiffness and extensor lag at the proximal/distal interphalangeal joint almost always occur. This issue can be avoided by allowing the patients to mobilize the fingers out of plaster or splint as early as possible from the day of surgery. We describe a technique of intramedullary percutaneous fixation of extra-articular proximal and middle phalanx fractures allowing immediate mobilization of fingers, concurrent stabilization with progressive healing and thus preventing such complications.
Stony Hard Skin During Early Infancy
Authors: Bachour Julien , Ghandour Fatmeh , Ammoury Alfred
Published: March 2018

Stiff skin syndrome is a rare disease causing stony hard induration of skin usually in early childhood. We report a case of 12 years old boy who presented to our clinic with biopsy showing adipocyte entrapment which we believe is an unrecognized key pathological finding in diagnosis of this entity.
Genomic survey of Clostridium difficile reservoirs in the East of England implicates environmental contamination of wastewater treatment plants by clinical lineages
Authors: Moradigaravand Danesh , Gouliouris Theodore , Ludden Catherine , Reuter Sandra , Jamrozy Dorota , Blane Beth , Naydenova Plamena , Judge Kim , H. Aliyu Sani , F. Hadjirin Nazreen , A. Holmes Mark , Török Estée , M. Brown Nicholas , Parkhill Julian , Peacock Sharon
Published: March 2018

There is growing evidence that patients with Clostridiumdifficile-associated diarrhoea often acquire their infecting strain before hospital admission. Wastewater is known to be a potential source of surface water that is contaminated with C. difficile spores. Here, we describe a study that used genome sequencing to compare C. difficile isolated from multiple wastewater treatment plants across the East of England and from patients with clinical disease at a major hospital in the same region. We confirmed that C. difficile from 65 patients were highly diverse and that most cases were not linked to other active cases in the hospital. In total, 186 C. difficile isolates were isolated from effluent water obtained from 18 municipal treatment plants at the point of release into the environment. Whole genome comparisons of clinical and environmental isolates demonstrated highly related populations, and confirmed extensive release of toxigenic C. difficile into surface waters. An analysis based on multilocus sequence types (STs) identified 19 distinct STs in the clinical collection and 38 STs in the wastewater collection, with 13 of 44 STs common to both clinical and wastewater collections. Furthermore, we identified five pairs of highly similar isolates (≤2 SNPs different in the core genome) in clinical and wastewater collections. Strategies to control community acquisition should consider the need for bacterial control of treated wastewater.
fastp: an ultra-fast all-in-one FASTQ preprocessor
Authors: Chen Shifu , Zhou Yanqing , Chen Yaru , Gu Jia
Published: March 2018

Motivation

Quality control and preprocessing of FASTQ files are essential to providing clean data for downstream analysis. Traditionally, a different tool is used for each operation, such as quality control, adapter trimming, and quality filtering. These tools are often insufficiently fast as most are developed using high-level programming languages (e.g., Python and Java) and provide limited multi-threading support. Reading and loading data multiple times also renders preprocessing slow and I/O inefficient.

Results

We developed fastp as an ultra-fast FASTQ preprocessor with useful quality control and data-filtering features. It can perform quality control, adapter trimming, quality filtering, per-read quality cutting, and many other operations with a single scan of the FASTQ data. It also supports unique molecular identifier preprocessing, poly tail trimming, output splitting, and base correction for paired-end data. It can automatically detect adapters for single-end and paired-end FASTQ data. This tool is developed in C++ and has multi-threading support. Based on our evaluation, fastp is 2–5 times faster than other FASTQ preprocessing tools such as Trimmomatic or Cutadapt despite performing far more operations than similar tools.

Availability and Implementation

The open-source code and corresponding instructions are available at https://github.com/OpenGene/fastp

Contact

chen@haplox.com
Examining consumer attitudes toward genetically modified and organic foods
Authors: Larson Ronald B.
Published: March 2018

Purpose

The purpose of this paper is to examine consumer attitudes toward genetically modified (GM) and organic foods with a broader list of control variables that includes green attitudes, impulsive purchasing, concerns about privacy, religiosity, birth order, and political preferences.

Design/methodology/approach

US internet panelists were asked about their preferences for purchasing non-GM produce, non-GM cereal, and organic products even if they cost a little more. They were also asked if genetically engineered foods are safe to consume. Responses to these four questions were dependent variables in binary logistic regressions. The sample size was 725 adults.

Findings

Attitudes toward non-GM produce and non-GM cereal were linked with different variables. Green attitudes were positively linked with non-GM and organic food attitudes. Impulsive purchases, a religiosity factor, and a privacy concern factor were linked with non-GM but not organic food attitudes. Social desirability bias was also significant. The genetically engineered food model identified some unique linkages with the control variables, suggesting that these terms may not improve consumer confidence with food.

Originality/value

New measures and several variables that researchers independently found to be significant were tested together in models and found to be linked with organic and non-GM food attitudes. Some expected relationships were not found. The results provide better profiles of consumers who have strong attitudes toward GM and organic foods.
How entrepreneurs’Zhong-yongthinking improves new venture performance
Authors: Ma Cuiping , Liu Hefu , Gu Jibao , Dou Junsheng
Published: March 2018

Purpose

The purpose of this paper is to focus on the cultural cognition of ChineseZhong-yongthinking, which is deeply rooted in Chinese Confucius culture, and to examine how entrepreneurs’Zhong-yongthinking is related to new venture performance throughguanxinetwork, and also examine how environmental turbulence affects the influencing mechanism.

Design/methodology/approach

This paper follows an empirical design. Data are collected from a survey administered to entrepreneurs in new ventures of China. Regression analysis is used to test the hypothesis.

Findings

Results show that entrepreneurs’Zhong-yongthinking is positively related toguanxiand new venture performance, andguanximediates the relationship between entrepreneurs’Zhong-yongthinking and new venture performance. In addition, environmental turbulence moderates the relationship between entrepreneurs’Zhong-yongthinking andguanxisuch that the relationship is stronger under higher technological turbulence or lower market turbulence.

Research limitations/implications

This research uses cross-sectional data, so causal conclusions cannot be made. In addition, more moderators should be considered.

Practical implications

The present study enriches the understanding of how entrepreneurs’Zhong-yongthinking affects new ventures, which helps entrepreneur understand how to strategize according to external environment and develop what kind of cognitive style to deal with complex situation of their own venture.

Originality/value

This study is a pioneer in exploring non-Western cognitive style–Zhong-yongthinking in entrepreneurial context. It not only enriches the understanding of how Chinese wisdom affects organizational strategy and organizational performance but also advances the cognition research in the field of entrepreneurship.
Communicating medication risk to cardiovascular patients in Qatar
Authors: Wilbur Kerry , Sahal Arwa , Elgaily Dina
Published: March 2018

Purpose

Patient safety is gaining prominence in health professional curricula. Patient safety must be complemented by teaching and skill development in practice settings. The purpose of this paper is to explore how experienced pharmacists identify, prioritize and communicate adverse drug effects to patients.

Design/methodology/approach

A focus group discussion was conducted with cardiology pharmacy specialists working in a Doha hospital, Qatar. The topic guide sought to explore participants’ views, experiences and approaches to educating patients regarding specific cardiovascular therapy safety and tolerability. Discussions were audio-recorded and transcribed verbatim. Data were coded and organized around identified themes and sub-themes. Working theories were developed by the three authors based on relevant topic characteristics associated with the means in which pharmacists prioritize and choose adverse effect information to communicate to patients.

Findings

Nine pharmacists participated in the discussion. The specific adverse effects prioritized were consistent with the reported highest prevalence. Concepts and connections to three main themes described how pharmacists further tailored patient counseling: potential adverse effects and their perceived importance; patient encounter; and cultural factors. Pharmacists relied on initial patient dialogue to judge an individual’s needs and capabilities to digest safety information, and drew heavily upon experience with other counseling encounters to further prioritize this information, processes dependent upon development and accessing exemplar cases.

Originality/value

The findings underscore practical experience as a critical instructional element of undergraduate health professional patient safety curricula and for developing associated clinical reasoning.
Determining total CEO compensation of selected US public companies
Authors: Rahman Matiur , Mustafa Muhammad
Published: March 2018

Purpose

The purpose of this paper is to explore the effects of total assets, stock performances, CEOs’ tenures, ages, and board sizes on total CEO compensations of 249 publicly listed US companies over a nine-year period from 2004-2012.

Design/methodology/approach

Pedroni’s panel cointegration, generalized method of moments, and dynamic ordinary least squares methodologies are applied.

Findings

All variables are non-stationary in log-levels. The findings show significant positive effects of total assets and stock performances on total CEO compensations. The effects of CEO’s tenure and age as well as board size on total CEO compensation deem negative. However, short-run net interactive feedback effects are generally positive with some exceptions.

Research limitations/implications

The above variables matter in rewarding the CEOs. They should be carefully weighed in for proper formulation of CEO compensation policy.

Originality/value

This paper applies relatively new econometric tools for a large panel data set. This work considers some new variables for determining CEO compensation in USA. The findings are relatively new with empirical originality.