bluuebunny/crossref_metadata_2025 huggingface dataset:
Highly Satisfied Total Knee Arthroplasty Patients Display a Wide Range of Soft Tissue Balance
Authors: McAuliffe Michael J. , O'Connor Patrick B. , Major Lisa J. , Garg Gautam , Whitehouse Sarah L. , Crawford Ross W.
Published: February 2019

Soft tissue balancing while crucial for a successful total knee arthroplasty (TKA) is incompletely defined and the subject of broad recommendations. We analyzed 69 unilateral computer-assisted surgery posterior stabilized (PS) TKA subjects who postoperatively scored ≥36 out of a possible 40 points on the satisfaction section of the American Knee Society score (2011). We examined a range of postoperative coronal plane laxity parameters and the correlation between preoperative and postoperative laxity. Total postoperative coronal laxity arcs at maximum extension and 20 degrees of flexion varied between 2 and 12 and 3 and 13 degrees, respectively. Depending on the position of measurement, medial laxity was between 0.5 and 9.5 degrees and lateral laxity between 1 and 12 degrees. The change in laxity between maximum extension and 90 degrees of flexion demonstrated a range of 7 degrees medially and 12 degrees laterally. The total coronal arc of movement did not affect functional outcomes. A moderate correlation of 0.452 and 0.424 was seen between initial and postoperative total coronal laxity arcs in maximum extension and 20 degrees of flexion, respectively. The individual variability for each measured parameter within our cohort demonstrates TKA satisfaction is not as simple as producing a narrow range of coronal laxity parameters and that as with many body systems considerable variation is still consistent with excellent function. Our findings help to define acceptable balance parameters for PS TKA. It does not appear necessary to closely match postoperative laxity to that present preoperatively.
Radiation-induced micro-structures as ground states of a Swift-Hohenberg energy functional
Authors: Simeone D. , Thorogood G. J. , Murphy G. L. , Forestier A. , Garcia P. , Luneville L.
Published: February 2019

We demonstrate that the Swift-Hohenberg functional, which is used to describe patterning observed in out of equilibrium systems such as diblock copolymers, Rayleigh-Benard convection, and thin film magnetic garnets, can be applied to radiation-induced patterns that occur in non-miscible alloys. By comparing ground states obtained from the minimization of this functional and a 2D numerical simulation performed on an irradiated AgCu material, which is the archetype of a non-miscible alloy, we show that the Swift-Hohenberg functional provides all possible patterns generated under irradiation and the solubility limits of radiation-induced precipitates in these patterns. To rationalize the formation of these radiation-induced patterns, we propose a generic “pseudophase diagram” that relies not only on the irradiation flux and temperature but also on the overall composition of the alloy. Tuning this overall composition offers the opportunity to tailor new materials with various micro-structures overcoming the limitation of the equilibrium phase diagram.
Effects of the shape of an inverted flag on its flapping dynamics
Authors: Park Jeong Woo , Ryu Jaeha , Sung Hyung Jin
Published: February 2019

The flapping motion of inverted flags with various shapes in a uniform flow was simulated by using the immersed boundary method. The shapes of the flags were characterized in terms of the shape ratio (S = WT/WL), i.e., the ratio of the trailing edge width (WT) to the leading edge width (WL). To explore the effects of varying S on the flapping dynamics of inverted flags, the peak-to-peak amplitude (A/L) and the Strouhal number (St) were determined as functions of the bending rigidity (0.1 ≤ γ ≤ 0.3) and the shape ratio (0.5 ≤ S ≤ 2). The vortical structures behind the inverted flag were visualized by using the Q-criterion to elucidate the vortex dynamics. The hydrodynamic forces exerted on each inverted flag were analyzed to find the correlation between its kinematics and vortex formation during the flapping period of the inverted flag. The strain energy (Es) stored in the inverted flag and the ratio (R) of the conversion of flow kinetic energy to strain energy were also determined. Finally, we explored the effects of varying the shape ratio S′ = WT/WL while keeping the trailing edge width constant (WT = 1) instead of the area of the inverted flag. The Strouhal number is maximized at S′ = 1. The conversion ratio of S′ = 2 is 2.5% higher than that of S′ = 1.
Ellipticity conditions for the extended MHD Grad-Shafranov-Bernoulli equilibrium equations
Authors: Kaltsas D. A. , Throumoulopoulos G. N. , Morrison P. J.
Published: February 2019

In this study, we find the points of transition between elliptic and hyperbolic regimes for the axisymmetric extended magnetohydrodynamic (MHD) equilibrium equations. The ellipticity condition is expressed via a single inequality but is more involved than the corresponding two-fluid ones due to the imposition of the quasineutrality condition and is also more complicated than the Hall MHD ellipticity condition, due to electron inertia. In fact, the inclusion of electron inertia is responsible for peculiar results; namely, even the static equilibrium equations can become hyperbolic.
Dense granular flow of mixtures of spheres and dumbbells down a rough inclined plane: Segregation and rheology
Authors: Mandal Sandip , Khakhar D. V.
Published: February 2019

We study the flow of equal-volume binary granular mixtures of spheres and dumbbells with different aspect ratios down a rough inclined plane, using the discrete element method. We consider two types of mixtures—in the first type the particles of the two species have equal volume but different aspect ratios and in the second type they have variable volumes and aspect ratios. We also use mixtures of spheres of two different sizes (spheres-spheres) with the same volume ratios as in the mixtures of the second type, as the base case. Based on the study of Guillard, Forterre, and Pouliquen [“Scaling laws for segregation forces in dense sheared granular flows,” J. Fluid Mech. 807, R1–R11 (2016)], the inclination angle of the base for each mixture is adjusted and maintained at a high value to yield the same pressure and shear stress gradients for all mixtures and a high effective friction (μ) for each. This ensures that the segregation force and resulting extent of segregation depend only the size and shape of the particles. The species with larger effective size, computed in terms of the geometric mean diameter, floats up in all cases and the dynamics of the segregation process for all the mixtures are reported. The concentration profiles of the species at a steady state agree well with the predictions of a continuum theory. The extent of segregation is shown to be dependent only on the ratio of geometric mean diameters, irrespective of the type of mixture. The μ − I and ϕ − I scaling relations, where I is the inertial number and ϕ is the solid volume fraction, extended to the case of mixtures, are shown to describe the rheology for all the cases.
On the induced azimuthal electric field in the current drive of an odd-parity rotating magnetic field
Authors: Shi Peiyun , Ren Baoming , Zhu Guanghui , Luo Ming , Zheng Jian , Sun Xuan
Published: February 2019

The azimuthal electric field Eθω, which is induced by the axial oscillating magnetic field Bzω of the odd-parity Rotating Magnetic Field (RMF) scheme, is experimentally found to play an important role in driving the toroidal plasma current. In the odd-parity RMF scheme, Eθω at the middle plane of the field reversed configuration can generate the so-called punctuated betatron-orbital electrons to drive the toroidal current in addition to the current driven by the transverse component of RMF Brω, whereas Brω is the only driving mechanism in the even-parity scheme. In this work, Eθω (or Bzω) and Brω are each studied to account for different current driving mechanisms. We report that Eθω accounts for the more efficient current driving in our experiments.
Eley Rideal recombination of hydrogen atoms on Cu(111): Quantitative role of electronic excitation in cross sections and product distributions
Authors: Chen Jialu , Zhou Xueyao , Jiang Bin
Published: February 2019

Eley-Rideal (ER) reaction between a projectile and an adsorbate at a gas-surface interface represents many interesting dynamic features. Electron-hole pairs (EHPs) could play an important role in this process, given the interaction between the accelerated incident atom/molecule and the surface electrons. Here, we examine the EHP effects in a benchmark ER reaction of an impinging H/D atom and pre-covered D/H atoms on Cu(111) by ab initio molecular dynamics simulations. It is found that energy dissipation to EHPs lowers the reaction cross sections by ∼1/3, mainly due to the suppression of the hot atom mechanism, but has a minor effect on rotational distributions, leading to quantitative agreement with experimental data. More interestingly, electronic excitation is responsible for the isotopic effect in translational energy distributions, but probably not for that in angular distributions. Our results highlight the specific role of electronic excitation in detailed dynamic quantities in the ER process.
Relationships and cladistic analysis of Roquettea with description of two new species and notes about evolution of stylus in Cosmetidae (Opiliones, Grassatores)
Authors: Medrano Miguel , Kury Adriano B.
Published: February 2019

The phylogeny of the genus Roquettea Mello-Leitão, 1931 and its position in Discosomaticinae are investigated. The monophyly of an expanded Roquettea is for the first time tested and corroborated. The internal relations of Roquettea are elucidated by means of a morphological maximum parsimony cladistic analysis. Synapomorphies for the genus include: pedipalpal tibia forming long lobe projected anteriorly; supranumerary ventral plate macroseta grouped with macrosetae C; penis ventral plate projections and stylus with beak. New characters are proposed for the Cosmetidae species and genera, and special focus is placed on the finer study of the glans complex, with a fresh proposal of homology for its constituent parts and their evolution in the light of the topology proposed here. Roquettea bubalina, sp. nov. and Roquettea troguloides, sp. nov. are described respectively from the Brazilian states of Mato Grosso and Pará. Both species present unique dorsal protuberances and unusual ocularia. New material of previously described species of Roquettea is available, increasing our knowledge on the genus. The following new semaphoronts are described and illustrated: β male of R. carajas Kury & Ferreira, 2012; females of R. decioi Kury, 2013, R. taurina Ferreira & Kury, 2010 and of R. jalapensis Ferreira & Kury, 2010. An emended diagnosis and an identification key are provided for the species of Roquettea including all known semaphoronts.
The unusual case of the widely distributed fiddler crab Minuca rapax (Smith, 1870) from the western Atlantic: an exemplary polytypic species
Authors: Thurman C. L. , Hopkins M. J. , Brase A. L. , Shih H.-T.
Published: February 2019

A classic dilemma in taxonomy is distinguishing intraspecific from interspecific variation. In order to better comprehend the process of divergence and speciation, we examine morphological, genetic, developmental and behavioural variation among related fiddler crab populations from eastern North America, the Caribbean and South America. We chose geographically remote populations that appear related to Minuca rapax (Smith, 1870). First, using females from across the range of the species, we use geometric morphometric techniques to identify regional differences in carapace shape. Second, in the northern portion of the range, the Caribbean into the Gulf of Mexico, we report variation in the relationship between corporal size and cheliped length in males. Third, we examine the major components of the courtship waves produced by males from several locations in the western Gulf of Mexico. Fourth, we compare the structure of the gastric mill between different populations in the Gulf of Mexico, the Caribbean and the Atlantic Ocean. And, fifth, we use mitochondrial 16S rDNA and cytochrome oxidase subunit I as genetic markers to define the phylogeographic relationship among specimens from more than 20 populations. From these studies, we find discrete, distinct populations across the original range of the species. In particular, populations in the northern Gulf of Mexico appear to represent a lineage that has resulted from limited gene flow and sustained selection pressures. On the basis of the observed degree of divergence, it is apparent that some separated populations in M. rapax should be recognised as evolutionary significant units. The geographic range of these populations is consistent with the historical range for Minuca virens (Salmon & Atsaides, 1968), a putative species that otherwise cannot be consistently distinguished from M. rapax based on discrete external morphological characters. This study provides evidence for M. virens as an emergent but possibly not completely isolated subclade of the M. rapax species complex.
Analysing morphological variation of appendages and labrum in 10 species of Heterocypris Claus, 1893 (Podocopida : Cyprididae) with additional description of Heterocypris exigua
Authors: Karan-Žnidaršič Tamara , Vujić Vukica , Baltanás Ángel
Published: February 2019

Natural selection can lead to speciation, but its effects depend on amount of morphological variation within populations. In Ostracoda, the appendages enclosed within the calcified carapace are less influenced by environmental conditions in comparison with carapace valves. Here, we explored morphological variation of appendages and labrum in cosmopolitan genus Heterocypris, investigating the species occurring in Europe. With the aim to overcome taxonomical problems, both traditional and geometric morphometrics were applied. The relative lengths were analysed by one-way ANOVA and post-hoc tests to determine interspecific variation and sexual dimorphism. Significant traits were further analysed by Canonical Variate Analysis separately for males and females as segment width/length ratios and relative length of claws and setae ratios. Landmark-based geometric morphometrics were applied to analyse shape variation of the labrum and traits of the maxillular palp. From this, a new perspective on morphological variation within this genus emerged. Relative measurements of the second segment of the maxillular palp, and relative lengths of the natatory setae were found to be the characters that contribute most to discrimination among Heterocypris species. The most important discriminant traits in females are the relative lengths of the G2 and G1 claws. Heterocypris exigua is additionally described, as all findings demonstrated that this is the most distinctive species, the most similar to H. gevgelica. In conclusion, we found that in comparison with maxillular palp and other analysed characters, labrum traits showed as more reliable and deserve more attention in descriptions of new species.
Modelling the fire propagation from the fuel bed to the lower canopy of ornamental species used in wildland–urban interfaces
Authors: Terrei L. , Lamorlette A. , Ganteaume A.
Published: February 2019

South-eastern France is strongly affected by wildfires mostly occurring in the wildland–urban interfaces (WUIs). A WUI fire is often initiated in dead surface fuel, then can propagate to shrubs and trees when the lower canopy is close to (or touches) the ground. Whereas a previous study assessed the fire propagation from the fuel bed to the lower canopy of different species used as ornamental vegetation in this region, the objectives of the current work consisted of checking if the modelling of this fire propagation was possible using WFDS (Wildland–Urban Interface Fire Dynamical Simulator) in comparing experimental and modelling results. Experimental and modelling constraints (i.e. branch geometric definition, branch motion due to convection) showed differences in some of the recorded data (such as time to ignition, ignition temperature, mass loss and maximum temperature), but comparisons of variation in mass loss and temperature over time showed that modelling the fire propagation at the scale of a branch was possible if the branch fuel-moisture content remained lower than 25%. For both experiments and modelling, the ranking of species according to their branch flammability highlighted identical groups of species.
Recoil-induced ultrafast molecular rotation probed by dynamical rotational Doppler effect
Authors: Céolin Denis , Liu Ji-Cai , Vaz da Cruz Vinícius , Ågren Hans , Journel Loïc , Guillemin Renaud , Marchenko Tatiana , Kushawaha Rajesh K. , Piancastelli Maria Novella , Püttner Ralph , Simon Marc , Gel’mukhanov Faris
Published: February 2019

Observing and controlling molecular motion and in particular rotation are fundamental topics in physics and chemistry. To initiate ultrafast rotation, one needs a way to transfer a large angular momentum to the molecule. As a showcase, this was performed by hard X-ray C1s ionization of carbon monoxide accompanied by spinning up the molecule via the recoil “kick” of the emitted fast photoelectron. To visualize this molecular motion, we use the dynamical rotational Doppler effect and an X-ray “pump-probe” device offered by nature itself: the recoil-induced ultrafast rotation is probed by subsequent Auger electron emission. The time information in our experiment originates from the natural delay between the C1s photoionization initiating the rotation and the ejection of the Auger electron. From a more general point of view, time-resolved measurements can be performed in two ways: either to vary the “delay” time as in conventional time-resolved pump-probe spectroscopy and use the dynamics given by the system, or to keep constant delay time and manipulate the dynamics. Since in our experiment we cannot change the delay time given by the core-hole lifetime

τ

, we use the second option and control the rotational speed by changing the kinetic energy of the photoelectron. The recoil-induced rotational dynamics controlled in such a way is observed as a photon energy-dependent asymmetry of the Auger line shape, in full agreement with theory. This asymmetry is explained by a significant change of the molecular orientation during the core-hole lifetime, which is comparable with the rotational period.
Structural basis for HOCl recognition and regulation mechanisms of HypT, a hypochlorite-specific transcriptional regulator
Authors: Jo Inseong , Kim Dajeong , No Taehoon , Hong Seokho , Ahn Jinsook , Ryu Sangryeol , Ha Nam-Chul
Published: February 2019

Hypochlorous acid (HOCl) is generated in the immune system to kill microorganisms. In
Escherichia coli
, a hypochlorite-specific transcription regulator, HypT, has been characterized. HypT belongs to the LysR-type transcriptional regulator (LTTR) family that contains a DNA-binding domain (DBD) and a regulatory domain (RD). Here, we identified a
hypT
gene from
Salmonella enterica
serovar Typhimurium and determined crystal structures of the full-length HypT protein and the RD. The full-length structure reveals a type of tetrameric assembly in the LTTR family. Based on HOCl-bound and oxidation-mimicking structures, we identified a HOCl-driven methionine oxidation mechanism, in which the bound HOCl oxidizes a conserved methionine residue lining the putative ligand-binding site in the RD. Furthermore, we proposed a molecular model for the oxidized HypT, where methionine oxidation by HOCl results in a conformational change of the RD, inducing a counter rotation of the DBD dimers. Target genes that are regulated by HypT and their roles in
Salmonella
were also investigated. DNase I footprinting experiments revealed a DNA segment containing two pseudopalindromic motifs that are separated by ∼100 bp, suggesting that only the oxidized structure makes a concomitant binding, forming a DNA loop. An understanding of the HypT-mediated mechanism would be helpful for controlling many pathogenic bacteria by counteracting bacterial HOCl defense mechanisms.
Interpreting contemporary trends in atmospheric methane
Authors: Turner Alexander J. , Frankenberg Christian , Kort Eric A.
Published: February 2019

Atmospheric methane plays a major role in controlling climate, yet contemporary methane trends (1982–2017) have defied explanation with numerous, often conflicting, hypotheses proposed in the literature. Specifically, atmospheric observations of methane from 1982 to 2017 have exhibited periods of both increasing concentrations (from 1982 to 2000 and from 2007 to 2017) and stabilization (from 2000 to 2007). Explanations for the increases and stabilization have invoked changes in tropical wetlands, livestock, fossil fuels, biomass burning, and the methane sink. Contradictions in these hypotheses arise because our current observational network cannot unambiguously link recent methane variations to specific sources. This raises some fundamental questions: (i) What do we know about sources, sinks, and underlying processes driving observed trends in atmospheric methane? (ii) How will global methane respond to changes in anthropogenic emissions? And (iii), What future observations could help resolve changes in the methane budget? To address these questions, we discuss potential drivers of atmospheric methane abundances over the last four decades in light of various observational constraints as well as process-based knowledge. While uncertainties in the methane budget exist, they should not detract from the potential of methane emissions mitigation strategies. We show that net-zero cost emission reductions can lead to a declining atmospheric burden, but can take three decades to stabilize. Moving forward, we make recommendations for observations to better constrain contemporary trends in atmospheric methane and to provide mitigation support.
Grammar of protein domain architectures
Authors: Yu Lijia , Tanwar Deepak Kumar , Penha Emanuel Diego S. , Wolf Yuri I. , Koonin Eugene V. , Basu Malay Kumar
Published: February 2019

From an abstract, informational perspective, protein domains appear analogous to words in natural languages in which the rules of word association are dictated by linguistic rules, or grammar. Such rules exist for protein domains as well, because only a small fraction of all possible domain combinations is viable in evolution. We employ a popular linguistic technique,
n
-gram analysis, to probe the “proteome grammar”—that is, the rules of association of domains that generate various domain architectures of proteins. Comparison of the complexity measures of “protein languages” in major branches of life shows that the relative entropy difference (information gain) between the observed domain architectures and random domain combinations is highly conserved in evolution and is close to being a universal constant, at ∼1.2 bits. Substantial deviations from this constant are observed in only two major groups of organisms: a subset of Archaea that appears to be cells simplified to the limit, and animals that display extreme complexity. We also identify the
n-
grams that represent signatures of the major branches of cellular life. The results of this analysis bolster the analogy between genomes and natural language and show that a “quasi-universal grammar” underlies the evolution of domain architectures in all divisions of cellular life. The nearly universal value of information gain by the domain architectures could reflect the minimum complexity of signal processing that is required to maintain a functioning cell.
HCMV trimer- and pentamer-specific antibodies synergize for virus neutralization but do not correlate with congenital transmission
Authors: Vanarsdall Adam L. , Chin Andrea L. , Liu Jing , Jardetzky Theodore S. , Mudd James O. , Orloff Susan L. , Streblow Daniel , Mussi-Pinhata Marisa M. , Yamamoto Aparecida Y. , Duarte Geraldo , Britt William J. , Johnson David C.
Published: February 2019

Significance

Human cytomegalovirus (HCMV) causes severe morbidity and mortality in immunocompromised patients and is the most commonly transmitted virus that causes developmental defects in the fetus. Currently, there is no licensed HCMV vaccine available, and prior efforts using attenuated viruses and subunit vaccines were not successful. Recently, there has been intense interest in the HCMV pentamer glycoprotein as a component of vaccines. Here, we show that transplant patients’ and pregnant mothers’ sera contain neutralizing antibodies specific for the pentamer and also for a second HCMV glycoprotein, the trimer, which is essential for HCMV entry into cells. Trimer- and pentamer-specific antibodies acted synergistically to neutralize virus and block cell–cell spread. These observations will have major implications for the future of HCMV vaccine development.
Therapeutic targeting of HER2–CB
2
R heteromers in HER2-positive breast cancer
Authors: Blasco-Benito Sandra , Moreno Estefanía , Seijo-Vila Marta , Tundidor Isabel , Andradas Clara , Caffarel María M. , Caro-Villalobos Miriam , Urigüen Leyre , Diez-Alarcia Rebeca , Moreno-Bueno Gema , Hernández Lucía , Manso Luis , Homar-Ruano Patricia , McCormick Peter J. , Bibic Lucka , Bernadó-Morales Cristina , Arribas Joaquín , Canals Meritxell , Casadó Vicent , Canela Enric I. , Guzmán Manuel , Pérez-Gómez Eduardo , Sánchez Cristina
Published: February 2019

Significance

There is a subtype of breast cancer characterized by the overexpression of the oncogene HER2. Although most patients with this diagnosis benefit from HER2-targeted treatments, some do not respond to these therapies and others develop resistance with time. New tools are therefore warranted for the treatment of this patient population, and for early identification of those individuals at a higher risk of developing innate or acquired resistance to current treatments. Here, we show that HER2 forms heteromer complexes with the cannabinoid receptor CB
2
R, the expression of these structures correlates with poor patient prognosis, and their disruption promotes antitumor responses. Collectively, our results support HER2–CB
2
R heteromers as new therapeutic targets and prognostic tools in HER2+ breast cancer.
Visualizing the iron atom exchange front in the Fe(II)-catalyzed recrystallization of goethite by atom probe tomography
Authors: Taylor Sandra D. , Liu Jia , Zhang Xin , Arey Bruce W. , Kovarik Libor , Schreiber Daniel K. , Perea Daniel E. , Rosso Kevin M.
Published: February 2019

Significance

The bioavailability of iron in the environment, and coupled metals, nutrients, and contaminants, depends on the stability of common Fe(III) minerals such as goethite (FeOOH) and hematite (Fe
2
O
3
). At redox boundaries, iron isotopic tracer studies suggest that interaction with aqueous Fe(II) creates dynamic conditions of atom exchange (AE). However, mechanistic models have not advanced beyond speculation, because of the challenges of mapping AE fronts recorded in isotopic distributions in individual nanoscale crystallites. Here we demonstrate successful use of 3D atom probe tomography for this purpose. The penetration depth, spatial heterogeneity, and ties to mineral defects are visualized, helping constrain mechanistic models and setting a precedent for detailed interrogation of iron redox cycling in the environment.
Machine-learning approach to the design of OSDAs for zeolite beta
Authors: Daeyaert Frits , Ye Fengdan , Deem Michael W.
Published: February 2019

Significance

Zeolite beta is one of the top-six zeolites of commercial interest. It has been synthesized through the use of a number of organic structure directing agents (OSDAs). Pure zeolite beta A has not yet been synthesized, nor has chiral zeolite beta A. We here report a machine-learning strategy to aid the computational design of chemically synthesizable OSDAs for zeolite beta A. The use of machine learning speeds up the computation by a factor of 350. Through de novo materials design runs, a total of 3,062 promising OSDAs were identified, and 469 OSDAs were computed to stabilize the structure of zeolite beta A better than known compounds.
Molecular basis for autoinhibition of RIAM regulated by FAK in integrin activation
Authors: Chang Yu-Chung , Su Wenjuan , Cho Eun-ah , Zhang Hao , Huang Qingqiu , Philips Mark R. , Wu Jinhua
Published: February 2019

RAP1-interacting adapter molecule (RIAM) mediates RAP1-induced integrin activation. The RAS-association (RA) segment of the RA-PH module of RIAM interacts with GTP-bound RAP1 and phosphoinositol 4,5 bisphosphate but this interaction is inhibited by the N-terminal segment of RIAM. Here we report the structural basis for the autoinhibition of RIAM by an intramolecular interaction between the IN region (aa 27–93) and the RA-PH module. We solved the crystal structure of IN-RA-PH to a resolution of 2.4-Å. The structure reveals that the IN segment associates with the RA segment and thereby suppresses RIAM:RAP1 association. This autoinhibitory configuration of RIAM can be released by phosphorylation at Tyr45 in the IN segment. Specific inhibitors of focal adhesion kinase (FAK) blocked phosphorylation of Tyr45, inhibited stimulated translocation of RIAM to the plasma membrane, and inhibited integrin-mediated cell adhesion in a Tyr45-dependent fashion. Our results reveal an unusual regulatory mechanism in small GTPase signaling by which the effector molecule is autoinhibited for GTPase interaction, and a modality of integrin activation at the level of RIAM through a FAK-mediated feedforward mechanism that involves reversal of autoinhibition by a tyrosine kinase associated with integrin signaling.
Adaptation of precision agriculture to root crops (sugar beet and potato).
Authors: Mahmood S. A. , Murdoch A. J.
Published: February 2019

Sugar beet (
Beta vulgaris
) meets about 30% of the global demand for sucrose while potato (
Solanum tuberosum
) is the world's fourth staple food crop contributing to a significant proportion of global food needs. As world population increases, increasing the yields of these crops sustainably is important, providing it is not to the detriment of the environment and farm profitability. Despite its potential contribution towards sustainable intensification, few farmers have adopted precision agriculture (PA) approaches in these crops. This paper reviews and discusses the scope and challenges of implementing PA in sugar beet and potato. The main challenges identified are: the general paucity of yield maps especially for sugar beet; the difficulty of detecting the underground yield components of root crops by remote sensing; the ability of root crops to absorb water and nutrients from deep in the soil; and changes in the EU support to sugar beet farmers. The crops are, however, grown in large areas, mostly in developed countries that have more access to PA techniques and technologies, so that there is a good scope for adaptation. For example, existing PA techniques of weed control, nutrient management and irrigation could be adapted for root crops. Future research should focus on overcoming these challenges, evaluate commercial application of PA techniques to root crops and examine the possibility of early detection of crop stress.
Lymnaeid snails hosts of
Fasciola hepatica
and
Fasciola gigantica
(Trematoda: Digenea): a worldwide review.
Authors: Vázquez A. A. , Alda P. , Lounnas M. , Sabourin E. , Alba A. , Pointier J. P. , Hurtrez-Boussès S.
Published: February 2019

Fasciolosis is a snail-borne disease, causing serious public and veterinary health problems worldwide. This disease is produced by infection with
Fasciola hepatica
or
Fasciola gigantica
through the consumption of vegetables or water contaminated with the parasite's metacercarial cysts. Both species of liver flukes are transmitted worldwide by small freshwater snails of the family Lymnaeidae. A global account on the species that are actually or may act as potential hosts of
Fasciola
spp., compiling particular research on their geographical distribution and susceptibility, is needed as a helpful tool in the understanding of fasciolosis transmission, and therefore in the control and prevention programmes of the disease. We have gathered here a comprehensive review of those lymnaeid species that are known to transmit the parasites in the field or that have been experimentally tested. We aim to bring forward the main intermediate hosts by regions in order to facilitate the understanding of worldwide transmission.
Altered multi‐muscle coordination patterns in habitual forefoot runners during a prolonged, exhaustive run
Authors: Jewell Carl , Hamill Joseph , von Tscharner Vinzenz , Boyer Katherine A.
Published: February 2019

Introduction: In response to fatigue during an exhaustive treadmill run, forefoot runner's muscles must adapt to maintain their pace. From a neuromuscular control perspective, certain muscles may not be able to sustain the force to meet the run's demands; thus, there may be alternative muscle coordination in the lower extremity that allows for continued running for an extended period of time. The aim of this study was to quantify the change in muscle coordination during a prolonged run in forefoot runners.

Methods: Thirteen forefoot runners performed exhaustive treadmill runs (mean duration: 15.4 ± 2.2 min). The muscle coordination of seven lower extremity muscles was quantified using a high‐resolution time–frequency analysis together with a pattern recognition algorithm.

Results: The mean EMG intensity for the lateral and medial gastrocnemius muscles decreased with the run (p = 0.02; 0.06). The weight factors of the second principal pattern decrease by 128.01% by the end of run (p = 0.05, Cohen's d = 0.42) representing a relatively greater biceps femoris activation in midstance but smaller midstance rectus femoris, vastus medialis, triceps surae, and tibialis anterior activation.

Discussion: These results suggest that forefoot runners cannot sustain plantar flexor activation throughout an exhaustive run and change their muscle coordination strategy as a compensation. Understanding the underlying compensation mechanisms humans use to cope with fatigue will help to inform training modalities to enhance these late stage muscle activation strategies for athletes with the goal of improving performance and reducing injury.
Heterochromatic foci and transcriptional repression by an unstructured MET-2/SETDB1 co-factor LIN-65
Authors: Delaney Colin E. , Methot Stephen P. , Guidi Micol , Katic Iskra , Gasser Susan M. , Padeken Jan
Published: February 2019

The segregation of the genome into accessible euchromatin and histone H3K9-methylated heterochromatin helps silence repetitive elements and tissue-specific genes. In Caenorhabditis elegans, MET-2, the homologue of mammalian SETDB1, catalyzes H3K9me1 and me2, yet like SETDB1, its regulation is enigmatic. Contrary to the cytosolic enrichment of overexpressed MET-2, we show that endogenous MET-2 is nuclear throughout development, forming perinuclear foci in a cell cycle–dependent manner. Mass spectrometry identified two cofactors that bind MET-2: LIN-65, a highly unstructured protein, and ARLE-14, a conserved GTPase effector. All three factors colocalize in heterochromatic foci. Ablation of lin-65, but not arle-14, mislocalizes and destabilizes MET-2, resulting in decreased H3K9 dimethylation, dispersion of heterochromatic foci, and derepression of MET-2 targets. Mutation of met-2 or lin-65 also disrupts the perinuclear anchoring of genomic heterochromatin. Loss of LIN-65, like that of MET-2, compromises temperature stress resistance and germline integrity, which are both linked to promiscuous repeat transcription and gene expression.
Modernism and Asian American Writers
Authors: Clark Audrey Wu
Published: February 2019

In her pathbreaking book Asian American Panethnicity (1992), Yen Le Espiritu traces Asian American panethnicity to the Yellow Power movement of the civil rights era of the 1960s. Thereafter the political struggles of Chinese, Japanese, Korean, Indian, and Filipino Americans were documented in literature and studied in literary anthologies such as Frank Chin et al.’s Aiiieeeee! (1974) and David Hsin-Fu Wand’s Asian-American Heritage: An Anthology of Prose and Poetry (1974). However, early Asian American literature suggests that Asian American consciousness emerged earlier than the civil rights era. During the era of Chinese exclusion (1882–1943), Chinese American writers such as Lee Yan Phou, Sui Sin Far, and Onoto Watanna—Sui Sin Far’s sister, who wrote under a Japanese pseudonym—wrote about Chinese American and Japanese American experiences. The subsequent era of Japanese exclusion (1907–1945) brought about the modernist haiku poetry of Japanese American writers Yone Noguchi and Sadakichi Hartmann. Nevertheless, it wasn’t until the Popular Front era of the 1930s that various forms of panethnic and queer Asian American political consciousness emerged in the literature of Korean American writer Younghill Kang, Filipino American writers Carlos Bulosan (who mentions Kang in his novel, America Is In the Heart) and José García Villa, and Chinese American writer H. T. Tsiang.

The politically progressive Popular Front of the 1930s, together with the influence of experimental literary forms of high modernism from just a decade before, set the stage for the Asian American panethnicity and queer consciousness that are described in the works of Kang and Bulosan, and Villa and Tsiang, respectively. Kang’s autobiographical novels The Grass Roof (1931) and East Goes West: The Making of an Oriental Yankee (1937) and Bulosan’s novel, America Is in the Heart (1943) exhibit important thematic influences by T. S. Eliot’s The Waste Land and “The Love Song of J. Alfred Prufrock.” Likewise, Villa’s Have Come, Am Here (1942) and Tsiang’s novels The Hanging on Union Square (1935) and And China Has Hands (1937) demonstrate the influence of queer modernist Gertrude Stein. Just a few decades earlier, Yone Noguchi and Sadakichi Hartmann were both writing modernist haikus that responded to those of their friend Ezra Pound. However, without the language of political solidarity that the Popular Front provided, Noguchi’s and Hartmann’s politics, implicit in their poetry, remained overlooked by critics until the 1990s.
Journalism and Its Audience
Authors: Wahl-Jorgensen Karin , Kilby Allaina
Published: February 2019

The relationship between journalism and its audience has undergone significant transformations from the earliest newspapers in the 18th century to 21st-century digital news. The role of the audience (and journalists’ conceptions of it) has been shaped by economic, social, and technological developments. Though the participation of the audience has always been important to news organizations, it has taken very different forms across times, genres, and platforms. Early newspapers drew on letters from their publics as vital sources of information and opinion, while radio established a more intimate relationship with its audience through its mode of address. Though television news genres may not have emphasized audience engagement, research on the medium was heavily invested in understanding how it affected its audience.

The rise of the Internet as a platform for journalism has represented a significant turning point in several respects. First, it has challenged conventional hierarchies of news production and value by facilitating user-generated content and social media, enhancing opportunities for audience contributions. This presents new opportunities for engagement but also challenges journalists’ professional identities, compelling them to assert their authority and skill sets. Further, digital journalism has led to the rise of the quantified audience, leading to the increased role of metrics in driving the behavior of journalists. As the audience and its behavior are shifting, so are the practices of journalism. The two actors—journalists and audiences—remain interlocked in what may be a troubled marriage, but one which is structurally compelled to change and grow over time.
Aethicus Ister
Authors: Marone Paola
Published: February 2019

Aethicus Ister is the unknown author of the Cosmographia, a fictional world travelogue that probably belongs to the 7th to 8th centuries. This work, written in an abstruse Latin, makes use of a whole range of antique (the Bible, the Isidore’s Etymologies, the Pseudo-Augustine’s De mirabilibus sacrae scripturae, etc.) and medieval texts (the Apocalypse of Pseudo-Methodius, the Liber historiae Francorum, some Latin translations of the Alexander Romance, etc.). It is one of the most difficult and puzzling early medieval texts, and it has been the object of intense study since its earliest editions. According to a recent theory espoused by Herren, it could have been written c. 675–725 by a Frank with connexions to Ireland and, possibly, England.
The Future of Climate Epidemiology: Opportunities for Advancing Health Research in the Context of Climate Change
Authors: Anderson G Brooke , Barnes Elizabeth A , Bell Michelle L , Dominici Francesca
Published: February 2019

In the coming decades, climate change is expected to dramatically affect communities worldwide, altering the patterns of many ambient exposures and disasters, including extreme temperatures, heat waves, wildfires, droughts, and floods. These exposures, in turn, can affect risks for a variety of human diseases and health outcomes. Climate epidemiology plays an important role in informing policy related to climate change and its threats to public health. Climate epidemiology leverages deep, integrated collaborations between epidemiologists and climate scientists to understand the current and potential future impacts of climate-related exposures on human health. A variety of recent and ongoing developments in climate science are creating new avenues for epidemiologic contributions. Here, we discuss the contributions of climate epidemiology and describe some key current research directions, including research to better characterize uncertainty in climate health projections. We end by outlining 3 developing areas of climate science that are creating opportunities for high-impact epidemiologic advances in the near future: 1) climate attribution studies, 2) subseasonal to seasonal forecasts, and 3) decadal predictions.
Discovering spurious links in multiplex networks based on interlayer relevance
Authors: Samei Zeynab , Jalili Mahdi
Published: February 2019

Many real-world complex systems can be better modelled as multiplex networks, where the same individuals develop connections in multiple layers. Examples include social networks between individuals on multiple social networking platforms, and transportation networks between cities based on air, rail and road networks. Accurately predicting spurious links in multiplex networks is a challenging issue. In this article, we show that one can effectively use interlayer information to build an algorithm for spurious link prediction. We propose a similarity index that combines intralayer similarity with interlayer relevance for the link prediction purpose. The proposed similarity index is used to rank the node pairs, and identify those that are likely to be spurious. Our experimental results show that the proposed metric is much more accurate than intralayer similarity measures in correctly predicting the spurious links. The proposed method is an unsupervised method and has low computation complexity, and thus can be effectively applied for spurious link prediction in large-scale networks.
Strengths and limitations of before–after–control–impact analysis for testing the effects of marine protected areas on managed populations
Authors: Kerr Lisa A , Kritzer Jacob P , Cadrin Steven X
Published: February 2019

Marine protected areas (MPAs) are a common management strategy for conserving marine resources, but it can be challenging to evaluate their effectiveness for meeting management objectives. Measuring the effectiveness of MPAs is particularly challenging in dynamic and changing environments where other management approaches are simultaneously implemented. Before–after–control–impact (BACI) analysis is a tool that offers a simple and robust design for evaluating complex effects. However, design and interpretation of a BACI analysis is not always straightforward. The goal of this study was to explore the potential for BACI to evaluate MPA performance in a system simultaneously impacted by other management measures and environmental change. We develop a typology of interpretations of BACI results based on the main and interaction effects of the model, categorized by the extent to which dynamics inside and outside of the MPA are independent. Furthermore, we examine how decisions about the spatial and temporal design of the study, and the focal species and response variables, can determine which outcomes from within the typology are evident through BACI applications to New England groundfish area closures. We identify strengths and limitations of the BACI approach and demonstrate that BACI is a valuable but imperfect tool for evaluating MPAs.
The Politics of Time in Colonial Bombay: Labor Patterns and Protest in Cotton Mills
Authors: Yıldız Hatice
Published: February 2019

This article examines the modes of time and work discipline that emerged through factory industry in colonial Bombay. Based on a wide range of archival sources, it shows that mechanized production did not invariably suggest a transition from task-based, irregular to clock-measured, rationally organized work patterns. Operating simultaneously within temporal orders constructed by the global economy, agriculture, family, and community, cotton mills combined new disciplinary practices with a flexible approach to labor. Gender, marital status, religion, skill, and position in the manufacturing chain influenced the pace and duration of work as well as subjective experiences of time at the factory. By maintaining the diversity and flexibility of time organization, mill owners could adjust production to fluctuations in market demand. At the same time, the strategy facilitated and obscured exploitation. As the industry grew, workers developed a language of resistance that emphasized the value of regular and standard work patterns defined with reference to clock hours and calendar days. In the factories of colonial Bombay, clocks were not just symbols of discipline and subjugation but also instruments of resistance and negotiation.
Distant viewing: analyzing large visual corpora
Authors: Arnold Taylor , Tilton Lauren
Published: February 2019

In this article we establish a methodological and theoretical framework for the study of large collections of visual materials. Our framework, distant viewing, is distinguished from other approaches by making explicit the interpretive nature of extracting semantic metadata from images. In other words, one must ‘view’ visual materials before studying them. We illustrate the need for the interpretive process of viewing by simultaneously drawing on theories of visual semiotics, photography, and computer vision. Two illustrative applications of the distant viewing framework to our own research are draw upon to explicate the potential and breadth of the approach. A study of television series shows how facial detection is used to compare the role of actors within the narrative arcs across two competing series. An analysis of the Farm Security Administration–Office of War Information corpus of documentary photography is used to establish how photographic style compared and differed amongst those photographers involved with the collection. We then aim to show how our framework engages with current methodological and theoretical conversations occurring within the digital humanities.