bluuebunny/crossref_metadata_2025 huggingface dataset:
Bi-global stability analysis in curvilinear coordinates
Authors: Wang Jinchun , Ziadé Paul , Huang Guoping , Sullivan Pierre E.
Published: October 2019

A method is developed to solve biglobal stability functions in curvilinear systems which avoids reshaping of the airfoil or remapping the disturbance flow fields. As well, the biglobal stability functions for calculation in a curvilinear system are derived. The instability features of the flow over a NACA (National Advisory Committee for Aeronautics) 0025 airfoil at two different angles of attack, corresponding to a flow with a separation bubble and a fully separated flow, are investigated at a chord-based Reynolds number of 100 000. The most unstable mode was found to be related to the wake instability, with a dimensionless frequency close to one. For the flow with a separation bubble, there is an instability plateau in the dimensionless frequency ranging from 2 to 5.5. After the plateau and for an increasing dimensionless frequency, the growth rate of the most unstable mode decreases. For a fully separated flow, the plateau is narrower than that for the flow with a separation bubble. After the plateau, with an increased dimensionless frequency, the growth rate of the most unstable mode decreases and then increases once again. The growth rate of the upstream shear layer instability was found to be larger than that of the downstream shear layer instability.
Characterization of heterogeneous InP-on-Si optical modulators operating between 77 K and room temperature
Authors: Pintus Paolo , Zhang Zeyu , Pinna Sergio , Tran Minh A. , Jain Aditya , Kennedy MJ , Ranzani Leonardo , Soltani Mohammad , Bowers John E.
Published: October 2019

Heterogeneous integration of InP modulators on a silicon photonic platform, fabricated by bonding III–V wafer on patterned silicon waveguides, are proved to work between 77 K and 295 K. The performance of modulators based on the Franz-Keldysh effect (bulk) and the quantum confined Stark effect (quantum-well) is investigated for wavelengths ranging within 1460 nm–1580 nm. The bulk modulator is preferred when operating over a wide range of temperatures. The demonstration of such integrated optical components at low temperatures is especially attractive for applications that demand massive data communication between cryogenic and room temperatures requiring photonic interconnect, as well as applications with extreme environmental conditions, such as outer space exploration.
Current-reversal operation for a single-parameter electron pump by control of semiconductor-based cryo-switch gate potentials
Authors: Yu Byeong-Sung , Kim Bum-Kyu , Park Suk-In , Song Jindong , Choi Hyung-Kook , Cho Sung-Un , Kim Ju-Jin , Kim Wan-Seop , Kim Nam , Bae Myung-Ho
Published: October 2019

The reversal technique in electrical measurements has been generally used to obtain a genuine value of an interesting physical quantity without unwanted signal offset. In the present work, we developed a novel cryo-switch made of electrical gates on GaAs heterostructure and demonstrate the current-reversal operation for a single-parameter electron pump. In precision measurements, we confirmed that the current values in reversal (i.e., approximately ±12.817 pA) being generated by the electron pump at T = 4.2 K agree well with each other in the deviation and uncertainty levels for various exit gate voltages. We also show that the accuracy level evaluated via the difference between the currents reversed was consistent with the unipolar measurements. Consequently, the measurement uncertainty was improved by a factor of two with the same measurement cycle number because of enhancement of signal-to-noise ratio.
Highly mobile carriers in a candidate of quasi-two-dimensional topological semimetal AuTe2Br
Authors: Wang Zeji , Cheng Shuyu , Chang Tay-Rong , Ma Wenlong , Xu Xitong , Zhou Huibin , Wang Guangqiang , Gui Xin , Zhu Haipeng , Zhu Zhen , Zheng Hao , Jia Jinfeng , Wang Junfeng , Xie Weiwei , Jia Shuang
Published: October 2019

We report the crystal and electronic structures of a noncentrosymmetric quasi-two-dimensional (2D) candidate of topological semimetal AuTe2Br. The Fermi surface of this layered compound consists of 2D-like, topological trivial electron and nontrivial hole pockets, which host a Dirac cone along the kz direction. Our transport measurements on the single crystals show highly anisotropic, compensated low-density electrons and holes, both of which exhibit ultrahigh mobility at a level of 105 cm2 V−1 s−1 at low temperature. The highly mobile, compensated carriers lead a nonsaturated, parabolic magnetoresistance as large as 3 × 105 in single-crystalline AuTe2Br in a magnetic field up to 58 T.
Mechanism of Si doping in plasma assisted MBE growth of β-Ga2O3
Authors: Kalarickal Nidhin Kurian , Xia Zhanbo , McGlone Joe , Krishnamoorthy Sriram , Moore Wyatt , Brenner Mark , Arehart Aaron R. , Ringel Steven A. , Rajan Siddharth
Published: October 2019

We report on the origin of high Si flux observed during the use of Si as a doping source in plasma assisted MBE growth of β-Ga2O3. We show on the basis of secondary ion mass spectroscopy analysis that Si flux is not limited by the vapor pressure of Si but by the formation of volatile SiO. The low sublimation energy of SiO leads to a weak dependence of the SiO flux of Si cell temperature and a strong dependence on the background oxygen pressure. Extended exposure to activated oxygen results in reduction of SiO flux due to the formation of SiO2 on the Si surface. The work reported provides key understanding for incorporating Si into future oxide-based semiconductor heterostructure and device MBE growth.
Topological nodal lines and hybrid Weyl nodes in YCoC2
Authors: Xu Yuanfeng , Gu Yueqiang , Zhang Tiantian , Fang Chen , Fang Zhong , Sheng Xian-Lei , Weng Hongming
Published: October 2019

Based on first-principles calculations and effective model analysis, we propose that the noncentrosymmetric superconductor YCoC2 in normal state is a topological semimetal. In the absence of spin-orbit coupling (SOC), it can host two intersecting nodal rings protected by two mirror planes, respectively. One ring is composed of type-I nodes, where the two crossing bands have opposite slope sign in their dispersions. The other ring consists of both type-I and type-II nodes (the slope signs of the two bands are the same in certain direction). In the presence of SOC, the former nodal ring is gapped totally while the latter one evolves into ten pairs of Weyl nodes, with two of them being type-I and eight being type-II. The type-II Weyl nodes are further classified into two kinds with different velocity matrices when described in Weyl equation near the nodes. Fermi arcs from topological surface states are observed in the surface projected energy dispersions. It is notable that YCoC2 has been reported as a superconductor with a critical temperature Tc of 4.2 K. This makes it very attractive since including superconducting into a topological semimetal state might result in topological superconductivity and be used to synthesize Majorana zero modes.
Optical response of Te-based monolayer materials from first principles
Authors: Hu Jie , Xiong Wen , Cai Congzhong , Wang Jianwei , Li Junjun , Xie Yiqun , Wang Yin
Published: October 2019

Using density functional theory combined with nonequilibrium Green's function, the photocurrent induced by the photogalvanic effect of two phases of Te-based monolayer materials is calculated along both their zigzag and armchair directions under the irradiation of the linearly polarized light. Results show that the photocurrent has a sinusoidal shape with regard to the polarization angle of the light at all simulated bias voltages for different photon energies. A photocurrent peak for α-Te and β-Te is at the photon energy of around 1.4 and 1.8 eV, respectively. Furthermore, for α-Te the phase of the photocurrent vs the polarization angle curve reserves when the photon energy increases, while for β-Te the phase remains unchanged in our simulated photon energy range. The different optical responses of the two phases of Te-based monolayer materials along different directions make them have potential applications in various aspects of optoelectronics.
Dynamic Leidenfrost behaviors of different fluid drops on superheated surface: Scaling for vapor film thickness
Authors: Park Junseok , Kim Dong Eok
Published: October 2019

For an impact drop on a superheated surface, the dynamic Leidenfrost temperature, TLF, depends on several parameters such as impact velocity, vapor layer thickness, and thermophysical properties of the fluids. In this letter, we derived a scaling formula for TLF using the well-known balance relation between the pressures exerted by drop impact and evaporated vapor flow. As the TLF scale intrinsically requires estimating the vapor film thickness δv, it should be scaled based on the consideration of relevant physics postulated on the impact drop and evaporated vapor. Thus, for proper scaling of δv, we considered the drop–vapor interface deformation by drop inertial and surface tension forces during initial impact of drop. Results showed that δv could be scaled with drop diameter D0 and Weber number We. For drops with low We (<10), δv scaled to ∼D0We−1/4 and ∼D0We−2/5 for drops with higher We. The explicit scale for TLF agreed well with present experimental data.
Coherent spin transport through a six-coordinate FeN6 spin-crossover complex with two different spin configurations
Authors: Gu Yue , Huang Jing , Hu Yu-jie , Li Qun-xiang
Published: October 2019

Due to the magnetic bistability, single-molecule spin-crossover (SCO) complexes have been considered to be the most promising building blocks for molecular spintronic devices. Here, we explore the SCO behavior and coherent spin transport properties of a six-coordinate FeN6 complex with the low-spin (LS) and high-spin (HS) states by performing extensive first-principles calculations combined with non-equilibrium Green’s function technique. Theoretical results show that the LS↔HS spin transition via changing the metal-ligand bond lengths can be realized by external stimuli, such as under light radiation in experiments. According to the calculated zero-bias transmission coefficients and density of states as well as the I-V curves under small bias voltages of FeN6 SCO complex with the LS and HS states sandwiched between two Au electrodes, we find that the examined molecular junction can act as a molecular switch, tuning from the OFF (LS) state to the ON (HS) state. Moreover, the spin-down electrons govern the current of the HS molecular junction, and this observed perfect spin-filtering effect is not sensitive to the detailed anchoring structure. These theoretical findings highlight this examined six-coordinate FeN6 SCO complex for potential applications in molecular spintronics.
He aha te mea nui o te ao? He tāngata! (What is the most important thing in the world? It is people!)
Authors: Masters-Awatere Bridgette , Rarere Moana , Gilbert Rewa , Manuel Carey , Scott Nina
Published: October 2019

This paper highlights the importance of people as a central factor in improving health for Māori (Indigenous people of New Zealand). How whānau (family) relationships, connections, values and inspiration are integral to achieving Indigenous health goals is explained. Descriptions of how community researchers, healthcare staff, consumers and academics worked together to design interventions for two health services (in the Waikato and Bay of Plenty regions) is included. Through highlighting the experiences of health consumers, the potential for future interventions to reduce the advancement of pre-diabetes among whānau is described. Evidence from the study interviews reinforces the importance of whānau and whakapapa (heritage) as enabling factors for Indigenous people to improve health. Specifically, the positive effect of whānau enhancing activities that support peoples’ aspirations of tino rangatiratanga (self-determination) in their lives when engaging with health care has been observed. This study highlights the many positives that have emerged, and offers an opportunity for taking primary health to the next level by placing whānau alongside Indigenous primary care providers at the centre of change strategies.
The mean gauges in bimetric relativity
Authors: Torsello Francesco
Published: October 2019

The choice of gauge in numerical relativity is crucial in avoiding coordinate and curvature singularities. In addition, the gauge can affect the well-posedness of the system. In this work, we consider the mean gauges, established with respect to the geometric mean metric

in bimetric relativity. We consider three gauge conditions widely used in numerical relativity, and compute them with respect to the geometric mean: The

gauge condition and the maximal slicing for the lapse function of

, and the

-driver gauge condition for the shift vector of

. In addition, in the bimetric covariant BSSN formalism, there are other arbitrary choices to be made before evolving the system. We show that it is possible to make them by using the geometric mean metric, which is determined dynamically by the system, rather than using an arbitrary external metric, as in general relativity. These choices represent opportunities to recast the system in a well-posed form.
Study of lateral density distributions of Cherenkov photons in extensive air showers at primary energy 50 GeV and above
Authors: Das Prity Rekha , Boruah Kalyanee
Published: October 2019

An EAS (extensive air shower) refers to the cascade of secondary particles created from the interactions of high energy primary cosmic ray particles with the air nuclei and subsequent decay of the particles produced. Ultra-relativistic secondary charged particles in the atmosphere produce Cherenkov radiation, which may be detected by ground based detector array. Such an array, HAGAR (High Altitude GAmma Ray) experiment is operating at Hanle, Ladakh, at an energy threshold of about 100 GeV, which will be lowered to 50 GeV using MACE telescope. We have studied the simulations of the distribution patterns of lateral density of Cherenkov photons generated in EAS for different primary particles (γ, p) incident with the fixed primary energy 50 GeV and these are compared with those of 100 GeV showers using the standard CORSIKA code. From our study it has been found that, for all primary particles, the variation of lateral density distribution of Cherenkov photons almost obey the functional relation, ρch
(r) = ρ0 e(−βr). The steepness of the lateral distribution function is found to depend on the primary mass composition. Further a prominent hump is observed in the lateral distribution for gamma shower only.
Farmer adaptation to reduced groundwater availability
Authors: Running Katrina , Burnham Morey , Wardropper Chloe , Ma Zhao , Hawes Jason , du Bray Margaret V
Published: October 2019

The sustainability of agriculture in the American West depends on the capacity of farmers to adapt to water resource constraints. Most US studies of agricultural adaptations measure farmers’ willingness to adopt various water use reduction strategies, meaning we have little empirical data on which strategies farmers implement and how these decisions impact their farms. We use survey data from 265 farmers in southeastern Idaho who, beginning in 2016, were required to cut annual groundwater withdrawals by 4%–20% to identify (1) the adaptation practices farmers implemented; (2) how reported crop yields and farm income were impacted; and (3) how adaptation practices varied by farm and farmer characteristics. We found the most commonly used adaptations were reduced spending, installation of more efficient irrigation systems or less frequent watering, and changing crop rotations. Farmers reported losing on average 7.6% of their yield and 8.4% of their income over the first two years of the water cuts. We found no systematic variation based on specific farm or farmer characteristics. Drawing on these results and prior research, we present a typology of adaptation categories intended to inform future research, allow comparisons to adaptation strategies elsewhere, and assist policymakers in designing effective policy interventions.
4D biofabrication of skeletal muscle microtissues
Authors: Apsite Indra , Uribe Juan Manuel , Posada Andrés Fernando , Rosenfeldt Sabine , Salehi Sahar , Ionov Leonid
Published: October 2019

Skeletal muscle is one of the most abundant tissues in the body. Although it has a relatively good regeneration capacity, it cannot heal in the case of disease or severe damage. Many current tissue engineering strategies fall short due to the complex structure of skeletal muscle. Biofabrication techniques have emerged as a popular set of methods for increasing the complexity of tissue-like constructs. In this paper, 4D biofabrication technique is introduced for fabrication of the skeletal muscle microtissues. To this end, a bilayer scaffold consisting of a layer of anisotropic methacrylated alginate fibers (AA-MA) and aligned polycaprolactone (PCL) fibers were fabricated using electrospinning and later induced to self-fold to encapsulate myoblasts. Bilayer mats undergo shape-transformation in an aqueous buffer, a process that depends on their overall thickness, the thickness of each layer and the geometry of the mat. Proper selection of these parameters allowed fabrication of scroll-like tubes encapsulating myoblasts. The myoblasts were shown to align along the axis of the anisotropic PCL fibers and further differentiated into aligned myotubes that contracted under electrical stimulation. Overall the significance of this approach is in the fabrication of hollow tubular constructs that can be further developed for the formation of a vascularized and functional muscle.
Constitutive expression of a fluorescent protein reports the size of live human cells
Authors: Berenson Daniel F. , Zatulovskiy Evgeny , Xie Shicong , Skotheim Jan M.
Published: October 2019

Cell size is important for cell physiology because it sets the geometric scale of organelles and biosynthesis. A number of methods exist to measure different aspects of cell size, but each has significant drawbacks. Here, we present an alternative method to measure the size of single human cells using a nuclear localized fluorescent protein expressed from a constitutive promoter. We validate this method by comparing it to several established cell size measurement strategies, including flow cytometry optical scatter, total protein dyes, and quantitative phase microscopy. We directly compare our fluorescent protein measurement with the commonly used measurement of nuclear volume and show that our measurements are more robust and less dependent on image segmentation. We apply our method to examine how cell size impacts the cell division cycle and reaffirm that there is a negative correlation between size at cell birth and G1 duration. Importantly, combining our size reporter with fluorescent labeling of a different protein in a different color channel allows measurement of concentration dynamics using simple wide-field fluorescence imaging. Thus, we expect our method will be of use to researchers interested in how dynamically changing protein concentrations control cell fates.
Multivalent electrostatic microtubule interactions of synthetic peptides are sufficient to mimic advanced MAP-like behavior
Authors: Drechsler Hauke , Xu Yong , Geyer Veikko F. , Zhang Yixin , Diez Stefan
Published: October 2019

Microtubule-associated proteins (MAPs) are a functionally highly diverse class of proteins that help to adjust the shape and function of the microtubule cytoskeleton in space and time. For this purpose, MAPs structurally support microtubules, modulate their dynamic instability, or regulate the activity of associated molecular motors. The microtubule-binding domains of MAPs are structurally divergent, but often depend on electrostatic interactions with the negatively charged surface of the microtubule. This suggests that the surface exposure of positive charges rather than a certain structural fold is sufficient for a protein to associate with microtubules. Consistently, positively charged artificial objects have been shown to associate with microtubules and to diffuse along their lattice. Natural MAPs, however, show a more sophisticated functionality beyond lattice-diffusion. Here, we asked whether basic electrostatic interactions are sufficient to also support advanced MAP functionality. To test this hypothesis, we studied simple positively charged peptide sequences for the occurrence of typical MAP-like behavior. We found that a multivalent peptide construct featuring four lysine-alanine heptarepeats (starPEG-(KA7)4)—but not its monovalent KA7-subunits—show advanced, biologically relevant MAP-like behavior: starPEG-(KA7)4 binds microtubules in the low nanomolar range, diffuses along their lattice with the ability to switch between intersecting microtubules, and tracks depolymerizing microtubule ends. Further, starPEG-(KA7)4 promotes microtubule nucleation and growth, mediates depolymerization coupled pulling at plus ends, and bundles microtubules without significantly interfering with other proteins on the microtubule lattice (as exemplified by the motor kinesin-1). Our results show that positive charges and multivalency are sufficient to mimic advanced MAP-like behavior.
Cross-activity of honeybee queen mandibular pheromone in bumblebees provides evidence for sensory exploitation
Authors: Princen Sarah A , Van Oystaeyen Annette , Petit Clément , van Zweden Jelle S , Wenseleers Tom
Published: October 2019

The evolutionary origin of queen pheromones (QPs), which regulate reproductive division of labor in insect societies, has been explained by two evolutionary scenarios: the sender-precursor hypothesis and the sensory exploitation hypothesis. These scenarios differ in terms of whether the signaling system was built on preadaptations on the part of either the sender queens or the receiver workers. While some social insect QPs—such as cuticular hydrocarbons—were likely derived from ancestral fertility cues and evolved according to the former theory, the honeybee’s queen mandibular pheromone (QMP) has been suggested to act directly on preexisting gene-regulatory networks linked with reproduction. This is evidenced by the fact that QMP has been shown to also inhibit ovary activation in fruit flies, thereby implying exploitation of conserved physiological pathways. To verify whether QMP has similar effects on more closely related eusocial species, we here tested for QMP cross-activity in the bumblebee Bombus terrestris. Interestingly, we found that the non-native QMP blend significantly inhibited egg laying in both worker and queen bumblebees and caused accompanying shifts in ovary activation. The native bumblebee QP pentacosane, by contrast, only inhibited the reproduction of the workers. Overall, these findings support the hypothesis that honeybee QMP likely evolved via a route of sensory exploitation. We argue that such exploitation could allow social insect queens to produce compounds that manipulate the workers to remain sterile, but that a major hurdle would be that the queens themselves would have to be immune to such compounds.
DRUDIT: web-based DRUgs DIscovery Tools to design small molecules as modulators of biological targets
Authors: Lauria Antonino , Mannino Salvatore , Gentile Carla , Mannino Giuseppe , Martorana Annamaria , Peri Daniele
Published: October 2019

Motivation

New in silico tools to predict biological affinities for input structures are presented. The tools are implemented in the DRUDIT (DRUgs DIscovery Tools) web service. The DRUDIT biological finder module is based on molecular descriptors that are calculated by the MOLDESTO (MOLecular DEScriptors TOol) software module developed by the same authors, which is able to calculate more than one thousand molecular descriptors. At this stage, DRUDIT includes 250 biological targets, but new external targets can be added. This feature extends the application scope of DRUDIT to several fields. Moreover, two more functions are implemented: the multi- and on/off-target tasks. These tools applied to input structures allow for predicting the polypharmacology and evaluating the collateral effects.

Results

The applications described in the article show that DRUDIT is able to predict a single biological target, to identify similarities among biological targets, and to discriminate different target isoforms. The main advantages of DRUDIT for the scientific community lie in its ease of use by worldwide scientists and the possibility to be used also without specific, and often expensive, hardware and software. In fact, it is fully accessible through the WWW from any device to perform calculations. Just a click or a tap can start tasks to predict biological properties for new compounds or repurpose drugs, lead compounds, or unsuccessful compounds. To date, DRUDIT is supported by four servers each able to execute 8 jobs simultaneously.

Availability and implementation

The web service is accessible at the www.drudit.com URL and its use is free of charge.

Supplementary information

Supplementary data are available at Bioinformatics online.
CCR2 mediates the adverse effects of LPS in the pregnant mouse
Authors: Hua Renyi , Edey Lydia F , O’Dea Kieran P , Howe Laura , Herbert Bronwen R , Cheng Weiwei , Zheng Xia , MacIntyre David A , Bennett Philip R , Takata Masao , Johnson Mark R
Published: October 2019

In our earlier work, we found that intrauterine (i.u.) and intraperitoneal (i.p.) injection of LPS (10-μg serotype 0111:B4) induced preterm labor (PTL) with high pup mortality, marked systemic inflammatory response and hypotension. Here, we used both i.u. and i.p. LPS models in pregnant wild-type (wt) and CCR2 knockout (CCR2−/−) mice on E16 to investigate the role played by the CCL2/CCR2 system in the response to LPS.

Basally, lower numbers of monocytes and macrophages and higher numbers of neutrophils were found in the myometrium, placenta, and blood of CCR2−/− vs. wt mice. After i.u. LPS, parturition occurred at 14 h in both groups of mice. At 7 h post-injection, 70% of wt pups were dead vs. 10% of CCR2−/− pups, but at delivery 100% of wt and 90% of CCR2−/− pups were dead. Myometrial and placental monocytes and macrophages were generally lower in CCR2−/− mice, but this was less consistent in the circulation, lung, and liver. At 7 h post-LPS, myometrial ERK activation was greater and JNK and p65 lower and the mRNA levels of chemokines were higher and of inflammatory cytokines lower in CCR2−/− vs. wt mice. Pup brain and placental inflammation were similar. Using the IP LPS model, we found that all measures of arterial pressure increased in CCR2−/− but declined in wt mice.

These data suggest that the CCL2/CCR2 system plays a critical role in the cardiovascular response to LPS and contributes to pup death but does not influence the onset of inflammation-induced PTL.
On semiparametric estimation of a path-specific effect in the presence of mediator-outcome confounding
Authors: Miles C H , Shpitser I , Kanki P , Meloni S , Tchetgen Tchetgen E J
Published: October 2019

Path-specific effects constitute a broad class of mediated effects from an exposure to an outcome via one or more causal pathways along a set of intermediate variables. Most of the literature concerning estimation of mediated effects has focused on parametric models, with stringent assumptions regarding unmeasured confounding. We consider semiparametric inference of a path-specific effect when these assumptions are relaxed. In particular, we develop a suite of semiparametric estimators for the effect along a pathway through a mediator, but not through an exposure-induced confounder of that mediator. These estimators have different robustness properties, as each depends on different parts of the likelihood of the observed data. One estimator is locally semiparametric efficient and multiply robust. The latter property implies that machine learning can be used to estimate nuisance functions. We demonstrate these properties, as well as finite-sample properties of all the estimators, in a simulation study. We apply our method to an HIV study, in which we estimate the effect comparing two drug treatments on a patient’s average log CD4 count mediated by the patient’s level of adherence, but not by previous experience of toxicity, which is clearly affected by which treatment the patient is assigned to and may confound the effect of the patient’s level of adherence on their virologic outcome.
Complex Evolutionary Origins of Specialized Metabolite Gene Cluster Diversity among the Plant Pathogenic Fungi of the Fusarium graminearum Species Complex
Authors: Tralamazza Sabina Moser , Rocha Liliana Oliveira , Oggenfuss Ursula , Corrêa Benedito , Croll Daniel
Published: October 2019

Fungal genomes encode highly organized gene clusters that underlie the production of specialized (or secondary) metabolites. Gene clusters encode key functions to exploit plant hosts or environmental niches. Promiscuous exchange among species and frequent reconfigurations make gene clusters some of the most dynamic elements of fungal genomes. Despite evidence for high diversity in gene cluster content among closely related strains, the microevolutionary processes driving gene cluster gain, loss, and neofunctionalization are largely unknown. We analyzed the Fusarium graminearum species complex (FGSC) composed of plant pathogens producing potent mycotoxins and causing Fusarium head blight on cereals. We de novo assembled genomes of previously uncharacterized FGSC members (two strains of F. austroamericanum, F. cortaderiae, and F. meridionale). Our analyses of 8 species of the FGSC in addition to 15 other Fusarium species identified a pangenome of 54 gene clusters within FGSC. We found that multiple independent losses were a key factor generating extant cluster diversity within the FGSC and the Fusarium genus. We identified a modular gene cluster conserved among distantly related fungi, which was likely reconfigured to encode different functions. We also found strong evidence that a rare cluster in FGSC was gained through an ancient horizontal transfer between bacteria and fungi. Chromosomal rearrangements underlying cluster loss were often complex and were likely facilitated by an enrichment in specific transposable elements. Our findings identify important transitory stages in the birth and death process of specialized metabolism gene clusters among very closely related species.
Yes, no, maybe so: the importance of cognitive interviewing to enhance structured surveys on respectful maternity care in northern India
Authors: Scott Kerry , Gharai Dipanwita , Sharma Manjula , Choudhury Namrata , Mishra Bibha , Chamberlain Sara , LeFevre Amnesty
Published: October 2019

Quantitative survey findings are important in measuring health-related phenomena, including on sensitive topics such as respectful maternity care (RMC). But how well do survey results truly capture respondent experiences and opinions? Quantitative tool development and piloting often involve translating questions from other settings and assessing the mechanics of implementation, which fails to deeply explore how respondents understand survey questions and response options. To address this gap, we conducted cognitive interviews on survey questions (n = 88) adapted from validated RMC instruments used in Ethiopia, Kenya and elsewhere in India. Cognitive interviews with rural women (n = 21) in Madhya Pradesh, India involved asking the respondent the survey question, recording her response, then interviewing her about what the question and response options meant to her. We analysed the interviews to revise the tool and identify question failures, which we grouped into six areas: issues with sequencing, length and sensitivity; problematic response options; inappropriate vocabulary; temporal and spatial confusion; accessing different cognitive domains; and failure to resonate with the respondent’s worldview and reality. Although women tended to provide initial answers to the survey questions, cognitive interviews revealed widespread mismatch between respondent interpretation and question intent. Likert scale response options were generally incomprehensible and questions involving hypothetical scenarios could be interpreted in unexpected ways. Many key terms and concepts from the international RMC literature did not translate well and showed low resonance with respondents, including consent and being involved in decisions about one’s care. This study highlights the threat to data quality and the validity of findings when translating quantitative surveys between languages and cultures and showcases the value of cognitive interviews in identifying question failures. While survey tool revision can address many of these issues, further critical discussion is needed on the use of standardized questions to assess the same domains across contexts.
Different in vivo impact of Dynamin 2 mutations implicated in Charcot-Marie-Tooth neuropathy or Centronuclear Myopathy
Authors: Muñoz Xènia Massana , Buono Suzie , Koebel Pascale , Laporte Jocelyn , Cowling Belinda S
Published: October 2019

Dynamin 2 (DNM2) is a ubiquitously expressed GTPase implicated in many cellular functions such as membrane trafficking and cytoskeleton regulation. Dominant mutations in DNM2 result in tissue specific diseases affecting peripheral nerves (Charcot-Marie-Tooth neuropathy, CMT) or skeletal muscles (Centronuclear myopathy, CNM). However, the reason for this tissue specificity is unknown, and it remains unclear if these diseases share a common pathomechanism. To compare the disease pathophysiological mechanisms in skeletal muscle, we exogenously expressed wild-type DNM2 (WT-DNM2), the DNM2-CMT mutation K562E, or DNM2-CNM mutations R465W and S619L causing adult and neonatal forms respectively, by intramuscular adeno-associated virus (AAV) injections. All muscles expressing exogenous WT-DNM2 and CNM or CMT mutations exhibited reduced muscle force. However, only expression of CNM mutations and WT-DNM2 correlated with CNM-like histopathological hallmarks of nuclei centralization and reduced fiber size. The extent of alterations correlated with clinical severity in patients. Ultrastructural and immunofluorescence analyses highlighted defects of the triads, mitochondria and costameres as major causes of the CNM phenotype. Despite the reduction in force upon expression of the DNM2-CMT mutation, muscle histology and ultrastructure were almost normal. However, the neuromuscular junction was affected in all DNM2 injected muscles, with the DNM2-CMT mutation inducing the most severe alterations, potentially explaining the reduction in force observed with this mutant. In conclusion, expression of WT and CNM mutants recreate a CNM-like phenotype, suggesting CNM mutations are gain-of-function. Histological, ultrastructural and molecular analyses pointed to key pathways uncovering the different pathomechanisms involved in centronuclear myopathy or Charcot-Marie-Tooth neuropathy linked to DNM2 mutations.
Histopathological Mimics of Inflammatory Bowel Disease
Authors: Schofield John B , Haboubi Najib
Published: October 2019

This review article discusses the challenges of making a firm histopathological diagnosis of inflammatory bowel disease (IBD) on biopsy and resection material and the importance of its distinction from a range of other inflammatory and infective conditions that may closely mimic IBD.

In many cases, the diagnosis of ulcerative colitis or Crohn's disease is straightforward, especially when patients have a typical presentation and characteristic histopathological features. Knowledge of the full clinical history is very important, particularly past and recent medical history, drug history, foreign travel, or known contact with individuals with specific infection. Discussion of all cases of suspected IBD within a multidisciplinary team meeting is required to ensure that clinical, radiological, and pathological features can be correlated.

Mimics of IBD can be divided into 4 categories: 1) those due to specific infection, 2) those due to a specific localized inflammatory process, 3) those due to iatrogenic causes, and 4) other rarer causes. Accurate diagnosis of IBD and exclusion of these mimics are crucial for patient management. Once a diagnosis of IBD has been proffered by a pathologist, it is very difficult to “undiagnose” the condition when an alternative diagnosis or “mimic” has been subsequently identified. The histological diagnosis of each of these IBD mimics is discussed in detail, with guidance on how to avoid the pitfall of missing these sometimes very subtle and “difficult to diagnose” conditions.
Online Surveillance, Censorship, and Encryption in Academia
Authors: Tanczer Leonie Maria , Deibert Ronald J , Bigo Didier , Franklin M I , Melgaço Lucas , Lyon David , Kazansky Becky , Milan Stefania
Published: October 2019

The Internet and digital technologies have become indispensable in academia. A world without email, search engines, and online databases is practically unthinkable. Yet, in this time of digital dependence, the academy barely demonstrates an appetite to reflect upon the new challenges that digital technologies have brought to the scholarly profession. This forum's inspiration was a roundtable discussion at the 2017 International Studies Association Annual Convention, where many of the forum authors agreed on the need for critical debate about the effects of online surveillance and censorship techniques on scholarship. This forum contains five critiques regarding our digitized infrastructures, datafied institutions, mercenary corporations, exploitative academic platforms, and insecure online practices. Together, this unique collection of articles contributes to the research on academic freedom and helps to frame the analysis of the neoliberal higher education sector, the surveillance practices that students and staff encounter, and the growing necessity to improve our “digital hygiene.”
Inclusion of Borderlanders in Border Management in Africa: Toward an Emancipatory Framework for the Study and Management of African Borders
Authors: Hlovor Ishmael Kwabla
Published: October 2019

African borderlands are sites where the state, borderlanders, criminal groups, and other groups compete and cooperate to achieve diverse interests. They are also zones of competing perspectives on security. However, current border security policies and practices operate within a restrictive neorealist theoretical paradigm with the state as the referent object of security thereby ignoring other perspectives on security. The vulnerabilities of borderlanders and the role of the border as a source of livelihood demand new ways of thinking about African borders in order to incorporate these major stakeholders into the bordering process. Although the adoption of the African Union's integrated border management strategy holds the potential to reconcile the needs of borderlanders with the objectives of the state, it remains within the restrictive neorealist framework. This paper argues that an emancipatory security theory provides an appropriate framework to understand African borders and borderlands. This theory holds the key for enhancing the security of African borders by reconciling the needs of borderlanders with the objectives of state security, and thereby making people and communities the referent objects of security. However, the failure of the theory to engage with the concept of power limits its usefulness.
The Production of Legitimacy: Race and Gender in Peacebuilding Praxis
Authors: Smith Sarah
Published: October 2019

Peace operations have increasingly sought to demonstrate their legitimacy in the face of critiques that characterize them as top-down impositions with limited impact and which entail a host of unintended consequences. Each book under review explores in depth the institutional consignment and attribution of legitimacy to certain spaces, actors, and bodies, which can serve to confirm and embed hierarchical relations of power. Von Billerbeck delineates the ambivalence with which “local ownership” is deployed in peace operations, closing down knowledge exchange rather than presenting opportunity. Shepherd builds on similar insights and argues that gendered logics and power inform the conceptualization and deployment of “local” and “civil society” and thus the (relative) lack of legitimacy afforded to these spaces. This essay seeks to develop from these insights further, drawing especially on postcolonial and critical race theory to demonstrate how race and racism structure the production and use of such categories, in both peace operation practice and international relations more broadly.
Bismarck’s Health Insurance and the Mortality Decline
Authors: Bauernschuster Stefan , Driva Anastasia , Hornung Erik
Published: October 2019

We study the impact of social health insurance on mortality. Using the introduction of compulsory health insurance in the German Empire in 1884 as a natural experiment, we estimate difference-in-differences and regional fixed effects models exploiting variation in eligibility for insurance across occupations. Our findings suggest that Bismarck’s health insurance generated a significant mortality reduction. Despite the absence of antibiotics and most vaccines, we find the results to be largely driven by a decline of deaths from infectious diseases. Further evidence suggests that statutory access to well-trained doctors was an elementary channel. This finding may be explained by insurance fund physicians transmitting new knowledge on infectious disease prevention.
Acute appendicitis in Amyand’s hernia: ultrasound findings and histopathology correlation. A case report
Authors: Ornelas-Cortinas Gerardo E , Cantu-Gonzalez Juan R , Enríquez-Rodriguez Rolando , Montemayor-Martinez Alberto , Negreros-Osuna Adrian , Cortinas-Gonzalez Julio C , Gloria-Juarez Luis O , Guerra-Leal Jesus D
Published: October 2019

Amyand’s hernia is an uncommon form of inguinal hernia. It represents <1% of all hernias and its complication with appendicitis is still rarer with 0.1–0.13% being reported. A 78-year-old woman was taken to the emergency room with pain in the right groin. The patient was assessed by ultrasound with the clinical suspicion of an inguinal hernia. We present the ultrasonographic features of appendicitis within an inguinal hernia sac. A tubular image that terminated in a blind-ended tip in the longitudinal plane and a target image on the cross-sectional plane were consistent with the sonographically demonstrated appendix. The diagnosis of Amyand’s hernia is difficult in the clinical setting. The patient is frequently referred to surgery with the diagnosis of an incarcerated hernia. Ultrasound is a good imaging modality that detects and characterizes this uncommon condition.
Tools for Selecting Working Correlation Structures When Using Weighted GEE to Model Longitudinal Survey Data
Authors: Westgate Philip M , West Brady T
Published: October 2019

Weighted generalized estimating equations (GEEs) are popular for the marginal analysis of longitudinal survey data. This popularity is due to the ability of these estimating equations to provide consistent regression parameter estimates and corresponding standard error estimates as long as the population mean and survey weights are correctly specified. Although the data analyst must incorporate a working correlation structure within the weighted GEEs, this structure need not be correctly specified. However, accurate modeling of this structure has the potential to improve regression parameter estimation (i.e., reduce standard errors) and therefore, the selection of a working correlation structure for use within GEEs has received considerable attention in standard longitudinal data analysis settings. In this article, we describe how correlation selection criteria can be extended for use with weighted GEE in the context of analyzing longitudinal survey data. Importantly, we provide and demonstrate an R function that we have created for such analyses. Furthermore, we discuss correlation selection in the context of using existing software that does not have this explicit capability. The methods are demonstrated via the use of data from a real survey in which we are interested in the mean number of falls that elderly individuals in a specific subpopulation experience over time.
On physical interpretations of the reference transit radius of gas-giant exoplanets
Authors: Heng Kevin
Published: October 2019

Two theoretical quandaries involving transmission spectra of gas-giant exoplanets are elucidated. When computing the transit radius as a function of wavelength, one needs to specify a reference transit radius corresponding to a reference pressure. Mathematically, the reference transit radius is a constant of integration that originates from evaluating an integral for the transit depth. Physically, its interpretation has been debated in the literature. Jordán & Espinoza suggested that the optical depth is discontinuous across, and infinite below, the reference transit radius. Bétrémieux & Swain interpreted the spherical surface located at the reference transit radius to represent the boundary associated with an opaque cloud deck. It is demonstrated that continuous functions for the optical depth may be found. The optical depth below and at the reference transit radius need not take on special or divergent values. In the limit of a spatially uniform grey cloud with constant opacity, the transit chord with optical depth of the order of unity mimics the presence of a ‘cloud top’. While the surface located at the reference pressure may mimic the presence of grey clouds, it is more natural to include the effects of these clouds as part of the opacity function because the cloud opacity may be computed from first principles. It is unclear how this mimicry extends to non-grey clouds comprising small particles.
Revisiting the statistical isotropy of GRB sky distribution
Authors: Andrade Uendert , Bengaly Carlos A P , Alcaniz Jailson S , Capozziello Salvatore
Published: October 2019

The assumption of homogeneity and isotropy on large scales is one of the main hypotheses of the standard cosmology. In this paper, we test the hypothesis of isotropy from the two-point angular correlation function of 2626 gamma-ray bursts (GRB) of the FERMI GRB catalogue. We show that the uncertainties in the GRB positions induce spurious anisotropic signals in their sky distribution. However, when such uncertainties are taken into account no significant evidence against the large-scale statistical isotropy is found. This result remains valid even for the sky distribution of short-lived GRB, contrarily to previous reports.
Adapting a solid accretion scenario for migrating planets in fargo3d
Authors: DePaula L A , Michtchenko T A , Sousa-Silva P A
Published: October 2019

In this work, we adapt a module for planetary formation within the hydrodynamic code fargo3d. Planetary formation is modelled by a solid core accretion scenario, with the core growing in oligarchic regime. The initial superficial density of planetesimals is proportional to the initial superficial density of gas in the disc. We include a numerical approach to describe the evolution of the eccentricity and the inclination of planetesimals during the formation. This approach impacts directly on the accretion rate of solids. When the core reaches a critical mass, gas accretion begins, following the original fargo scheme adapted to the fargo3d code. To exemplify how the module for planetary formation can be used, we investigate the migration of a planet in a 2D, locally isothermal gas disc with a prescribed accretion rate, analysing the time-scale involved in the planetary migration process along with the time-scale for planetary formation. The analysis reveals that the mass of the nucleus must be close to its critical value when crossing the ice line to avoid the planet’s fall into the stellar envelope. This will allow enough time for the planet to initiate runaway gas accretion, leading to a rapid mass increase and entering type II planetary migration.