bluuebunny/crossref_metadata_2025 huggingface dataset:
Annual Cycle Dampening and the Decrease Predictability of Water Level Fluctuations in a Dam-Regulated Neotropical Floodplain
Authors: Zanon Jaques Everton
Published: October 2019

The flood pulse concept refers to seasonal variations in river water level and is the driving force in river-floodplain systems that ‘responsible for the existence, productivity and interactions’ of these system’s biota. This seasonal variation is inherent to river-floodplain systems and establishes a natural pattern of these ecosystems that has frequently been observed in nature. One particular river-floodplain system of interest is the Upper Parana River and its floodplain, whose upstream contains a reservoir cascade that caused profound alterations on its flooding regime by having diminished flood magnitude, but increased its frequency. In this study, I sought to explore the flood pulse condition in the Upper Paraná River Floodplain by using a set of state-of-the-art spectral and non-linear analyses and a time series of water level fluctuations (1968-2017) from this system. I divided the data into four periods: i) natural regime period, ii) transitional period, iii) dam cascade period, and iv) Primavera’s dam period. Spectral analysis demonstrated a decrease in the annual cycle amplitude, reflected in its power spectrum, which means a weakening in the difference between flood and drought events. Additionally, nonlinear dynamical analysis revealed a less deterministic and predicable behavior leading to more erratic fluctuations jeopardizing the temporal heterogeneity of that system.
Study on the efficacy of dsRNAs with increasing length in RNAi-based silencing of the Fusarium CYP51 genes
Authors: Höfle L , Shrestha A , Werner B , Jelonek L , Koch A
Published: October 2019

Previously, we have demonstrated that transgenic Arabidopsis and barley plants, expressing a 791 nucleotide (nt) dsRNA (CYP3RNA) that targets all three CYP51 genes (FgCYP51A, FgCYP51B, FgCYP51C) in Fusarium graminearum (Fg), inhibited fungal infection via a process designated as host-induced gene silencing (HIGS). More recently, we have shown that spray applications of CYP3RNA also protect barley from fungal infection via a process termed spray-induced gene silencing (SIGS). Thus, RNAi technology may have the potential to revolutionize plant protection in agriculture. Therefore, successful field application will require optimization of RNAi design necessary to maximize the efficacy of the RNA silencing construct for making RNAi-based strategies a realistic and sustainable approach.

Previous studies indicate that silencing is correlated with the number of siRNAs generated from a dsRNA precursor. To prove the hypothesis that silencing efficiency is correlated with the number of siRNAs processed out of the dsRNA precursor, we tested in a HIGS and SIGS approach dsRNA precursors of increasing length ranging from 400 nt to 1500 nt to assess gene silencing efficiency of individual FgCYP51 genes. Concerning HIGS-mediated disease control, we found that there is no significant correlation between the length of the dsRNA precursor and the reduction of Fg infection on CYP51-dsRNA expressing Arabidopsis plants. Importantly and in clear contrast to HIGS, we measured a decrease in SIGS-mediated Fg disease resistance that significantly correlates with the length of the dsRNA construct that was sprayed, indicating that the size of the dsRNA interferes with a sufficient uptake of dsRNAs by the fungus.
A High-throughput Screening Method to Identify Proteins Involved in Unfolded Protein Response Signaling in Plants
Authors: Alcântara André , Seitner Denise , Navarrete Fernando , Djamei Armin
Published: October 2019

Background

The unfolded protein response (UPR) is a highly conserved process in eukaryotic organisms that plays a crucial role in adaptation and development. While the most ubiquitous components of this pathway have been characterized, current efforts are focused on identifying and characterizing other UPR factors that play a role in specific conditions, such as developmental changes, abiotic cues, and biotic interactions. Considering the central role of protein secretion in plant pathogen interactions, there has also been a recent focus on understanding how pathogens manipulate their host’s UPR to facilitate infection.

Results

We developed a high-throughput screening assay to identify proteins that interfere with UPR signalingin planta. A set of 35 genes from a library of secreted proteins from the maize pathogenUstilago maydiswere transiently co-expressed with a reporter construct that upregulates enhanced yellow fluorescent protein (eYFP) expression upon UPR stress inNicotiana benthamianaplants. After UPR stress induction, leaf discs were placed in 96 well plates and eYFP expression was measured. This allowed us to identify a previously undescribed fungal protein that inhibits plant UPR signaling, which was then confirmed using the classical but more laborious qRT-PCR method.

Conclusions

We have established a rapid and reliable fluorescence-based method to identify heterologously expressed proteins involved in UPR stress in plants. This system can be used for initial screens with libraries of proteins and potentially other molecules to identify candidates for further validation and characterization.
Multi-cancer analysis of clonality and the timing of systemic spread in paired primary tumors and metastases
Authors: Hu Zheng , Li Zan , Ma Zhicheng , Curtis Christina
Published: October 2019

Metastasis is the primary cause of cancer-related deaths, but the natural history, clonal evolution and impact of treatment are poorly understood. We analyzed exome sequencing data from 457 paired primary tumor and metastatic samples from 136 breast, colorectal and lung cancer patients, including untreated (n=99) and treated (n=100) metastatic tumors. Treated metastases often harbored private ‘driver’ mutations whereas untreated metastases did not, suggesting that treatment promotes clonal evolution. Polyclonal seeding was common in untreated lymph node metastases (n=17/29, 59%) and distant metastases (n=20/70, 29%), but less frequent in treated distant metastases (n=9/94, 10%). The low number of metastasis-private clonal mutations is consistent with early metastatic seeding, which we estimated commonly occurred 2-4 years prior to diagnosis across these cancers. Further, these data suggest that the natural course of metastasis is selectively relaxed relative to early tumor development and that metastasis-private mutations are not drivers of cancer spread but instead associated with drug resistance.
Modular protein-oligonucleotide signal exchange
Authors: Agrawal Deepak K.
Published: October 2019

The ability to detect a protein selectively and produce a predicted signal in real time is a long-lasting engineering challenge in the field of biochemistry. Such a mechanism typically requires a sensing module to recognize the input protein and a translation module to produce a programmable output signal that reflects the concentration of the input. Here we present a generic biomolecular reaction process that exchanges the concentration of an input protein with a DNA oligonucleotide. This approach uses the unique characteristic of DNA oligonucleotide aptamer that can either bind to a specific protein or to a complementary DNA oligonucleotide reversibly. We then pass the information of the protein concentration to the output signal through DNA strand displacement reactions. Using this strategy, we design and characterize four different exchange processes that can produce modular DNA oligonucleotides in response to different proteins such as clinically important human α-thrombin and vascular endothelial growth factor (VEGF). These exchange processes are capable of real time sensing and are modular such that they can be used for concurrent detection of different proteins with well-defined input-output characteristics. The novelty and simplicity of our approach encourage to develop advanced biochemical systems for point-of-care testing of infectious diseases and treatments.
Wolbachiamanipulates host pre-imaginal learning in a parasitoid wasp
Authors: Abroon Pouria , Ashori Ahmad , Duplouy Anne , Farahani Hossein Kishani
Published: October 2019

The Hopkin’s host-selection principle (HHSP) suggests that organisms at higher trophic levels demonstrate a preference for the host species on which they developed during larval stage. Although investigated in many herbivorous and predatory insects, the HHSP has, to our knowledge, never been tested in the context of insects hosting selfish endosymbiotic passengers such as the maternally inherited bacteriumWolbachia pipientis. Here, we investigate the effect ofWolbachiainfection on host pre-imaginal learning in the parasitoid waspTrichogramma brassicae(Hymenoptera: Trichogrammatidae). We compare host-choice inWolbachia-infected and uninfected adult female parasitoids after rearing them on two different Lepidopteran hosts, namely the flour mothEphestia kuehniellaZeller (Lepidoptera: Pyralidae) or the grain mothSitotroga cerealella(Lep.: Gelechiidae). We show that inT. brassicae, Wolbachiaaffect the pre-imaginal learning ability of female wasps.Wolbachiainfected wasps do not show any host preference and easily switch hosts in the laboratory, while uninfected wasps significantly prefer to lay eggs on the host species they developed on. We discuss how the facilitation of a generalist strategy byWolbachiamay allowT. brassicaeto escape intraspecific competition with their uninfected counterparts, and may have important evolutionary consequences for the host and its symbionts.
Intrinsic Buffer Hydroxyl Radical Dosimetry Using Tris(Hydroxymethyl)Aminomethane
Authors: Roush Addison E. , Riaz Mohammad , Misra Sandeep K. , Weinberger Scot R. , Sharp Joshua S.
Published: October 2019

Fast Photochemical Oxidation of Proteins (FPOP) is a powerful covalent labeling tool that uses hydroxyl radicals generated by laser flash photolysis of hydrogen peroxide to footprint protein surfaces. Because radical production varies with many experimental parameters, hydroxyl radical dosimeters have been introduced to track the effective radical dosage experienced by the protein analyte. FPOP experiments performed using adenine optical radical dosimetry containing protein in Tris buffer demonstrated unusual dosimetry behavior. We have investigated the behavior of Tris under oxidative conditions in detail. We find that Tris can act as a novel gain-of-signal optical hydroxyl radical dosimeter in FPOP experiments. This new dosimeter is also amenable to inline real-time monitoring thereby allowing real-time adjustments to compensate for differences in samples for their quenching ability.
Role of the central junction in folding topology of the protein-free human U2-U6 snRNA complex analyzed by time-resolved FRET
Authors: Chu Huong , Greenbaum Nancy L.
Published: October 2019

Intron removal during splicing of precursor pre-mRNA requires assembly of spliceosomal small nuclear (sn)RNAs into catalytically competent conformations to promote two transesterification reactions. U2 and U6 snRNA are the only snRNAs directly implicated in pre-mRNA splicing catalysis, but rearrangement and remodeling steps prior to catalysis require numerous proteins. Previous studies have shown that the protein-free U2-U6 snRNA complex adopts two conformations characterized by four and three helices surrounding a central junction in equilibrium. To analyze the role of the central junction in positioning the two helices critical for formation of the active site, we used ensemble time-resolved fluorescence resonance energy transfer to measure distances between fluorophores at selected locations in constructs representing the protein-free human U2-U6 snRNA complex. Data describing four angles in the four-helix conformer suggest the complex adopts a tetrahedral geometry; addition of Mg2+results in shortening of the distances between neighboring helices, indicating compaction of the complex around the junction. In contrast, the three-helix conformer shows a closer approach between the two helices bearing critical elements, but addition of Mg2+widens the distance between these stems. Presence of Mg2+also enhances the steady state fraction of the three-helix conformer found to be active in spliceosomes. Although the central junction assumes a significant role in orienting helices, in neither conformer, with or without Mg2+, are the critical helices positioned sufficiently close to favor interaction, implying that a major role of spliceosomal remodeling proteins is to overcome such distances to create and stabilize a catalytically active fold.
Topology of the U12-U6atac snRNA complex of the minor spliceosome and binding by NTC-related protein RBM22
Authors: Ciavarella Joanna , Perea William , Greenbaum Nancy L.
Published: October 2019

Splicing of precursor messenger RNA is catalyzed by the spliceosome, a dynamic ribonucleoprotein assembly composed of five small nuclear (sn)RNAs and >100 proteins. RNA components catalyze the two transesterification reactions, but proteins perform critical roles in assembly and rearrangement. The catalytic core comprises a paired complex involving U2 and U6 snRNAs for the major form of the spliceosome and U12 and U6atac snRNAs for the minor variant (~0.3% of all spliceosomes in higher eukaryotes); the latter performs identical chemistry, despite limited sequence conservation outside key catalytic elements, and lack of the multi-stem central junction found in the U2-U6 snRNA complex. Here we use solution NMR techniques to show that base pairing patterns of the U12-U6atac snRNA complex of both human and Arabidopsis share key elements with the major spliceosome’s U2-U6 snRNA complex; probing of the single-stranded segment opposing termini of the snRNAs indicates elongation in this region in place of the stacked base pairs at the base of the U6 intramolecular stem loop in the U2-U6 snRNA complex. Binding affinity of RBM22, a protein implicated in remodeling human U2-U6 snRNA prior to catalysis, to U12-U6atac was analyzed by electrophoretic mobility shift assays in which we monitored migration of both protein and RNA components in the same gel. Results indicate that RBM22 binds the U2-U6 and U12-U6atac snRNA complexes specifically and with Kd = 3.5 µM and 8.2 µM, respectively. Similar affinity between RBM22 and each RNA complex suggests that the protein performs the same role in both spliceosomes.
finFindR: Computer-assisted Recognition and Identification of Bottlenose Dolphin Photos in R
Authors: Thompson Jaime W. , Zero Victoria H. , Schwacke Lori H. , Speakman Todd R. , Quigley Brian M. , Morey Jeanine S. M. , McDonald Trent L.
Published: October 2019

Photographic identification is an essential research and management tool for studying population size and dynamics of common bottlenose dolphins (Tursiops truncatus). Photographic identification involves recognizing individuals based on unique dorsal fin markings. Manual identification of dolphins, while successful, is labor-intensive and time-consuming. To shorten processing times, we developed a series of neural networks that finds fins, assesses their unique characteristics, and matches them to an existing catalog.

Our software, finFindR, shortens photo-ID processing times by autonomously finding and isolating (i.e., “cropping”) dolphin fins in raw field photographs, tracing the trailing edge of fins in cropped images, and producing a sorted list of likely identities from a catalog of known individuals. The program then presents users with the top 50 most likely matching identities, allowing users to view side-by-side image pairs and make final identity determinations.

During testing on two sets of novel images, finFindR placed the correct individual in the first position of its ordered list in 88% (238/272 and 354/400) of test cases. finFindR placed the correct identity among the top 10 ranked images in 94% of test cases, and among the top 50 ranked images in 97% of test cases. Hence, if a match does not exist in the first 50 images of finFindR’s ordered list, researchers can be almost certain (~97%) that a match does not exist in the entire catalog.

During a head-to-head blind test of the human-only and finFindR-assisted matching methods, two experienced photo-ID technicians both achieved 97% correct identification of identities when matched against a catalog containing over 2,000 known individuals. However, the manual-only technician examined 124 images on average before making a match, while the technician using finFindR examined only 10 images on average before finding a match.

We conclude that finFindR will facilitate equal or improved match accuracy while greatly reducing the number of examined photos. The faster matches, automated detection, and automated cropping afforded by finFindR will greatly reduce typical photo-ID processing times.
Diversification of a cryptic radiation, a closer look at Madagascar’s recently recognized bird family
Authors: Younger Jane L. , Block Nicholas L. , Raherilalao Marie J. , Maddox J. Dylan , Wacker Kristen S. , Kyriazis Christopher C. , Goodman Steven M. , Reddy Sushma
Published: October 2019

Despite its status as a global biodiversity hotspot there is still much to be discovered about the birds of Madagascar, including a full accounting of species-level diversity and the avifauna’s origins. The Bernieridae is a Malagasy endemic family that went unrecognized by science for decades and unnamed until 2010. This cryptic family has long represented a missing piece of the puzzle of the avian tree of life. We present the first comprehensive phylogeny of Bernieridae in order to examine its diversification history on Madagascar and its place within Passeriformes. In light of recent discoveries of cryptic species-level diversity in Madagascar’s vertebrate fauna, we used broad geographic sampling and integrative taxonomic methods to investigate the potential for cryptic lineages within every known species of the Bernieridae. Our approach combines phylogenomics using ∼4500 loci of ultraconserved elements (UCEs), genetic clustering of thousands of single nucleotide polymorphisms (SNPs), and statistical analysis of morphological variation. These methods yielded the discovery of two unrecognized species in the previously monotypic genusBernieria, along with new insights into patterns of fine-scale endemism in Madagascar’s humid forests. Our phylogenomic analyses provide conclusive support for Donacobiidae and Bernieridae as sister families, a biogeographically intriguing result given that the former is restricted to the Neotropics. We found a significant decline in the rate of speciation over time on Madagascar, consistent with a model of adaptive radiation. Bernieridae therefore joins the Vangidae as a second avian adaptive radiation on the island of Madagascar. These insights into the evolution of Bernieridae represent a step forward in understanding the origins and diversity of Madagascar’s endemic avifauna.
Polyjet 3D printing of tissue-mimicking materials: how well can 3D printed synthetic myocardium replicate mechanical properties of organic myocardium?
Authors: Severseike Leah , Lee Vania , Brandon Taycia , Bakken Chris , Bhatia Varun
Published: October 2019

Anatomical 3-D printing has potential for many uses in education, research and development, implant training, and procedure planning. Conventionally, the material properties of 3D printed anatomical models have often been similar only in form and not in mechanical response compared to biological tissue. The new Digital Anatomy material from Stratasys utilizes composite printed materials to more closely mimic the mechanical properties of tissue. Work was done to evaluate Digital Anatomy myocardium under axial loading for comparison with porcine myocardium regarding puncture, compliance, suturing, and cutting performance.

In general, the Digital Anatomy myocardium showed promising comparisons to porcine myocardium. For compliance testing, the Digital Anatomy was either within the same range as the porcine myocardium or stiffer. Specifically, for use conditions involving higher stress concentrations or smaller displacements, Digital Anatomy was stiffer. Digital Anatomy did not perform as strongly as porcine myocardium when evaluating suture and cutting properties. The suture tore through the printed material more easily and had higher friction forces both during needle insertion and cutting. Despite these differences, the new Digital Anatomy myocardium material was much closer to the compliance of real tissue than other 3D printed materials. Furthermore, unlike biological tissue, Digital Anatomy provided repeatability of results. For tests such as cyclic compression, the material showed less than two percent variation in results between trials and between parts, resulting in lower variability than tissue. Despite some limitations, the myocardium Digital Anatomy material can be used to configure structures with similar mechanical properties to porcine myocardium in a repeatable manner, making this a valuable research tool.
Rod-cone signal interference in the retina shapes perception in primates
Authors: Songco-Aguas Adree , Grimes William N , Rieke Fred
Published: October 2019

Linking the activity of neurons, circuits and synapses to human behavior is a fundamental goal of neuroscience. Meeting this goal is challenging, in part because behavior, particularly perception, often masks the complexity of the underlying neural circuits, and in part because of the significant behavioral differences between primates and animals like mice and flies in which genetic manipulations are relatively common. Here we relate circuit-level processing of rod and cone signals in the non-human primate retina to a known break in the normal seamlessness of human vision – a surprising inability to see high contrast flickering lights under specific conditions. We use electrophysiological recordings and perceptual experiments to identify key mechanisms that shape the retinal integration of rod- and cone-generated retinal signals. We incorporate these mechanistic insights into a predictive model that accurately captures the cancellation of rod- and cone-mediated responses and can explain the perceptual insensitivity to flicker.
Crystal structures of two dimeric nickel diphenylacetate complexes
Authors: Nikiforov A. A. , Blinou D. O. , Dubrov E. N. , Panina N. S. , Ponyaev A. I. , Gurzhiy V. V. , Eremin A. V. , Fischer A. I.
Published: October 2019

In the crystal structures of the title compounds, namely μ-aqua-κ2
O:O-di-μ-diphenylacetato-κ4
O:O′-bis[(diphenylacetato-κO)bis(pyridine-κN)nickel(II)], [Ni2(C14H11O2)4(C5H5N)4(H2O)] (1) and μ-aqua-κ2
O:O-di-μ-diphenylacetato-κ4
O:O′-bis[(2,2′-bipyridine-κ2
N,N′)(diphenylacetato-κO)nickel(II)]–acetonitrile–diphenylacetic acid (1/2.5/1), [Ni2(C14H11O2)4(C10H8N2)2(H2O)]·2.5CH3CN·C14H12O2 (2), the complex units are stabilized by a variety of intra- and intermolecular hydrogen bonds, as well as C—H...π and π–π contacts between the aromatic systems of the pyridine, dipyridyl and diphenylacetate ligands. Despite the fact that the diphenylacetate ligand is sterically bulky, this does not interfere with the formation of the described aqua-bridged dimeric core, even with a 2,2′-bipyridine ligand, which has a strong chelating effect.
Crystal structure, Hirshfeld surface analysis and DFT studies of ethyl 2-{4-[(2-ethoxy-2-oxoethyl)(phenyl)carbamoyl]-2-oxo-1,2-dihydroquinolin-1-yl}acetate
Authors: Filali Baba Yassir , Hayani Sonia , Hökelek Tuncer , Kaur Manpreet , Jasinski Jerry , Sebbar Nada Kheira , Kandri Rodi Youssef
Published: October 2019

The title compound, C24H24N2O6, consists of ethyl 2-(1,2,3,4-tetrahydro-2-oxoquinolin-1-yl)acetate and 4-[(2-ethoxy-2-oxoethyl)(phenyl)carbomoyl] units, where the oxoquinoline unit is almost planar and the acetate substituent is nearly perpendicular to its mean plane. In the crystal, C—HOxqn...OEthxand C—HPhyl...OCarbx(Oxqn = oxoquinolin, Ethx = ethoxy, Phyl = phenyl and Carbx = carboxylate) weak hydrogen bonds link the molecules into a three-dimensional network sturucture. A π–π interaction between the constituent rings of the oxoquinoline unit, with a centroid–centroid distance of 3.675 (1) Å may further stabilize the structure. Both terminal ethyl groups are disordered over two sets of sites. The ratios of the refined occupanies are 0.821 (8):0.179 (8) and 0.651 (18):0.349 (18). The Hirshfeld surface analysis of the crystal structure indicates that the most important contributions for the crystal packing are from H...H (53.9%), H...O/O...H (28.5%) and H...C/C...H (11.8%) interactions. Weak intermolecular hydrogen-bond interactions and van der Waals interactions are the dominant interactions in the crystal packing. Density functional theory (DFT) geometric optimized structures at the B3LYP/6-311G(d,p) level are compared with the experimentally determined molecular structure in the solid state. The HOMO–LUMO molecular orbital behaviour was elucidated to determine the energy gap.
Different packing motifs mediated by weak interactions and polymorphism in the crystal structures of five 2-(benzylidene)benzosuberone derivatives
Authors: Seaman Lewis S. , Costa Cristiane F. da , Souza Marcus V. N. de , Wardell Solange M. S. V. , Wardell James L. , Harrison William T. A.
Published: October 2019

The syntheses and crystal structures of five 2-benzylidene-1-benzosuberone [1-benzosuberone is 6,7,8,9-tetrahydro-5H-benzo[7]annulen-5-one] derivatives,viz.2-(4-methoxybenzylidene)-1-benzosuberone, C19H18O2, (I), 2-(4-ethoxybenzylidene)-1-benzosuberone, C20H20O2, (II), 2-(4-benzylbenzylidene)-1-benzosuberone, C25H22O2, (III), 2-(4-chlorobenzylidene)-1-benzosuberone, C18H15ClO, (IV) and 2-(4-cyanobenzylidene)-1-benzosuberone, C19H15NO, (V), are described. The conformations of the benzosuberone fused six- plus seven-membered ring fragments are very similar in each case, but the dihedral angles between the fused benzene ring and the pendant benzene ring differ somewhat, with values of 23.79 (3) for (I), 24.60 (4) for (II), 33.72 (4) for (III), 29.93 (8) for (IV) and 21.81 (7)° for (V). Key features of the packing include pairwise C—H...O hydrogen bonds for (II) and (IV), and pairwise C—H...N hydrogen bonds for (V), which generate inversion dimers in each case. The packing for (I) and (III) feature C—H...O hydrogen bonds, which lead to [010] and [100] chains, respectively. Weak C—H...π interactions consolidate the structures and weak aromatic π–π stacking is seen in (II) [centroid–centroid separation = 3.8414 (7) Å] and (III) [3.9475 (7) Å]. A polymorph of (I) crystallized from a different solvent has been reported previously [Dimmocket al.(1999)J. Med. Chem.42, 1358–1366] in the same space group but with a packing motif based on inversion dimers resembling that seen in (IV) in the present study. The Hirshfeld surfaces and fingerprint plots for (I) and its polymorph are compared and structural features of the 2-benzylidene-1-benzosuberone family of phases are surveyed.
The `super acid' BF3H2O stabilized by 1,4-dioxane: new preparative aspects and the crystal structure of BF3H2O·C4H8O2
Authors: Barthen Peter , Frank Walter
Published: October 2019

Highly Brønsted-acidic boron trifluoride monohydrate, a widely used `super acid-catalyst', is a colourless fuming liquid that releases BF3 at room temperature. Compared to the liquid components, i.e. boron trifluoride monohydrate and 1,4-dioxane, their 1:1 adduct, BF3H2O·C4H8O2, is a solid with pronounced thermal stability (m.p. 401–403 K). The crystal structure of the long-time-stable easy-to-handle and weighable compound is reported along with new preparative aspects and the results of 1H, 11B, 13C and 19F spectroscopic investigations, particularly documenting its high Brønsted acidity in acetonitrile solution. The remarkable stability of solid BF3H2O·C4H8O2 is attributed to the chain structure established by O—H...O hydrogen bonds of exceptional strength {O2...H1—O1 [O...O = 2.534 (3) Å] and O1—H1...O3i [2.539 (3) Å] in the concatenating unit >O2...H1—O1—H2...O3i<}, taking into account the molecular (non-ionic) character of the structural moieties. Indirectly, this structural feature documents the outstanding acidification of the H2O molecule bound to BF3 and reflects the super acid nature of BF3H2O. In detail, the C
2
2(7) zigzag chain system of hydrogen bonding in the title structure is characterized by the double hydrogen-bond donor and double (κO,κO′) hydrogen-bond acceptor functionality of the aqua ligand and dioxane molecule, respectively, the almost equal strength of both hydrogen bonds, the approximatety linear arrangement of the dioxane O atoms and the two neighbouring water O atoms. Furthermore, the approximately planar arrangement of B, F and O atoms in sheets perpendicular to the c axis of the orthorhombic unit cell is a characteristic structural feature.
SAD phasing of XFEL data depends critically on the error model
Authors: Brewster Aaron S. , Bhowmick Asmit , Bolotovsky Robert , Mendez Derek , Zwart Petrus H. , Sauter Nicholas K.
Published: October 2019

A nonlinear least-squares method for refining a parametric expression describing the estimated errors of reflection intensities in serial crystallographic (SX) data is presented. This approach, which is similar to that used in the rotation method of crystallographic data collection at synchrotrons, propagates error estimates from photon-counting statistics to the merged data. Here, it is demonstrated that the application of this approach to SX data provides better SAD phasing ability, enabling the autobuilding of a protein structure that had previously failed to be built. Estimating the error in the merged reflection intensities requires the understanding and propagation of all of the sources of error arising from the measurements. One type of error, which is well understood, is the counting error introduced when the detector counts X-ray photons. Thus, if other types of random errors (such as readout noise) as well as uncertainties in systematic corrections (such as from X-ray attenuation) are completely understood, they can be propagated along with the counting error, as appropriate. In practice, most software packages propagate as much error as they know how to model and then include error-adjustment terms that scale the error estimates until they explain the variance among the measurements. If this is performed carefully, then during SAD phasing likelihood-based approaches can make optimal use of these error estimates, increasing the chance of a successful structure solution. In serial crystallography, SAD phasing has remained challenging, with the few examples of de novo protein structure solution each requiring many thousands of diffraction patterns. Here, the effects of different methods of treating the error estimates are estimated and it is shown that using a parametric approach that includes terms proportional to the known experimental uncertainty, the reflection intensity and the squared reflection intensity to improve the error estimates can allow SAD phasing even from weak zinc anomalous signal.
Structure of Sonic Hedgehog protein in complex with zinc(II) and magnesium(II) reveals ion-coordination plasticity relevant to peptide drug design
Authors: Bonn-Breach Rachel , Gu Yu , Jenkins Jermaine , Fasan Rudi , Wedekind Joseph
Published: October 2019

The Hedgehog pathway is an essential cell-signaling paradigm implicated in cancer tumorigenesis and the developmental disorder holoprosencephaly, making it an attractive target for therapeutic design. The N-terminal domain of the Sonic Hedgehog protein (Shh-N) is the essential signaling molecule in the Hedgehog pathway. In this role Shh-N interacts with its cognate membrane receptor Patched, as well as the regulatory proteins HHIP and CDO, by utilizing interfaces harboring one or more divalent ions. Here, the crystal structure of human Shh-N is presented at 1.43 Å resolution, representing a landmark in the characterization of this protein. The structure reveals that the conserved Zn2+-binding site adopts an atypical octahedral coordination geometry, whereas an adjacent binding site, normally occupied by binuclear Ca2+, has been supplanted by a single octahedrally bound Mg2+. Both divalent sites are compared with those in previous Shh-N structures, which demonstrates a significant degree of plasticity of the Shh-N protein in terms of divalent ion binding. The presence of a high Mg2+ concentration in the crystallization medium appears to have influenced metal loading at both metal ion-binding sites. These observations have technical and design implications for efforts focused on the development of inhibitors that target Shh-N-mediated protein–protein interactions.
CO2intensity and GDP per capita
Authors: Hannesson Rögnvaldur
Published: October 2019

Purpose

To investigate whether CO2intensity falls at a diminishing rate as countries grow richer.

Design/methodology/approach

Regression of CO2intensity on the gross domestic product (GDP) per capita, including squared and cubic terms, for a panel of countries and individual countries.

Findings

CO2intensity falls at a diminishing rate as countries grow richer.

Originality/value

Many studies have found that CO2intensity falls with GDP per capita, but whether it does so at a diminishing rate has not been investigated. This result suggests that structural changes in GDP (more services) as countries get richer will provide little or no help toward decarbonization. It is shown that the extraction of minerals critical for industrial production has increased on par with real GDP. This could explain why CO2emissions fall at a diminishing rate.
Interdisciplinary treatment of family violence in traumatized refugee families
Authors: Dalgaard Nina Thorup , Thøgersen Marie Høgh , Montgomery Edith
Published: October 2019

Purpose

The purpose of this paper is to explore the defining characteristics of an interdisciplinary culturally sensitive approach to family therapy with traumatized refugee families affected by family violence. Furthermore, the paper aims to explore the mechanisms of change as seen from the perspective of the therapists.

Design/methodology/approach

Based on qualitative analysis of semi-structured interviews with therapists working in an interdisciplinary team as well as observations of treatment conferences, the study identified the ways in which therapists perceive the challenges faced by their patients, the ways in which positive change is facilitated within therapy and the characteristics of a culturally sensitive interdisciplinary approach to family therapy with traumatized refugee families.

Findings

The study identified a number of defining characteristics of the treatment model, which includes the interdisciplinary approach, treatment objectives and concrete interventions targeting these objectives.

Originality/value

Through a theoretically informed critical analysis of the data, the present study examined the defining characteristics of the treatment model as well as the mechanisms of change as perceived by the therapists.
Comparison of STL skull models produced using open-source software versus commercial software
Authors: Abdullah Johari Yap , Abdullah Abdul Manaf , Hadi Helmi , Husein Adam , Rajion Zainul Ahmad
Published: October 2019

Purpose

This paper aims to compare the automatic segmentation of medical data and conversion to stereolithography (STL) skull models using open-source software versus commercial software.

Design/methodology/approach

Both open-source and commercial software used automatic segmentation and post-processing of the data without user intervention, thus avoiding human error. Detailed steps were provided for comparisons and easier to be repeated by other researchers. The results of segmentation, which were converted to STL format were compared using geometric analysis.

Findings

STL skull models produced using open-source software are comparable with the one produced using commercial software. A comparison of STL skull model produced using InVesalius with STL skull model produced using MIMICS resulted in an average dice similarity coefficient (DSC) of 97.6 ± 0.04 per cent and Hausdorff distance (HD) of 0.01 ± 0.005 mm. Inter-rater study for repeatability on MIMICS software yielded an average DSC of 100 per cent and HD of 0.

Social implications

The application of open-source software will benefit the small research institutions or hospitals to produce and virtualise three-dimensional model of the skulls for teaching or clinical purposes without having to purchase expensive commercial software. It is also easily reproduceable by other researchers.

Originality/value

This study is one of the first comparative evaluations of an open-source software with propriety commercial software in producing accurate STL skull models. Inaccurate STL models can lead to inaccurate pre-operative planning or unfit implant.
Gametophytic competition games among relatives: When does spatial structure select for facilitativeness or competitiveness in pollination?
Authors: Iritani Ryosuke
Published: October 2019

Determining whether pollination occurs competitively or rather facilitatively among co‐flowering plants is a central question in plant reproductive ecology. Kobayashi [2018;Journal of Ecology107: 1433–1438] theoretically investigated the scenario in which intraspecific pollen tube competition (male–male competition) can lead to regulation of population growth due to reduced female success.

Kobayashi (2018) showed that evolutionary dynamics in intraspecific pollen tube competition can reduce female success and consequently generate negative density‐dependence of population growth, which allows for numerous species to coexist in a spatially subdivided metacommunity. Kobayashi (2018) hypothesized that trait evolution driven by sexual selection may maintain biodiversity.

However, the models proposed by Kobayashi (2018) allow for the assumptions to be relaxed; he assumed: (i) fully global seed dispersal (instead of limited dispersal, albeit the spatial subdivision), (ii) fully local pollination (i.e., pollination occurred exclusively within patches), (iii) selfing rate was exactly proportionate (i.e., pollen grains distributed equally among all individuals within a patch, irrespective of their parental origins), (iv) haploid mode of inheritance, and most importantly, (v) each individual was mutually competitive, rather than facilitative for pollination.

Here, I extend the models of Kobayashi (2018) and show that when I relax assumptions (i)–(v), facilitativeness, as opposed to competitiveness, is more likely to be favoured by selection. The present results are attributed to kin selection in gametopythic competition among relatives in spatially subdivided populations.

If facilitativeness for pollination is favoured by kin selection, then the premise that the evolution of pollen traits can generate negative density‐dependence does not necessarily follow. I also discuss the potential mechanisms by which pollen phenotypes can either strengthen or attenuate intraspecific and interspecific competition.
Dynamic and synergistic influences of air temperature and rainfall on general flowering in a Bornean lowland tropical forest
Authors: Ushio Masayuki , Osada Yutaka , Kumagai Tomo'omi , Kume Tomonori , Pungga Runi anak Sylvester , Nakashizuka Tohru , Itioka Takao , Sakai Shoko
Published: October 2019

Supra‐annually synchronized flowering events occurring in tropical forests in Southeast Asia, known as general flowering (GF), are “spectacular and mysterious” forest events. Recently, studies that combined novel molecular techniques and model‐based theoretical approaches suggested that cool temperature and drought synergistically drove GF. Although these advanced our understanding of GF, it is still difficult to know whether the individual‐based molecular measurements and model‐based mathematical representations reasonably well capture the complex and dynamic GF processes at the community level. In the present study, we collected a 17‐year set of community‐wide phenology data from Lambir Hills National Park in Borneo, Malaysia, and analyzed it using a model‐free approach, empirical dynamic modeling (EDM), which does not rely on specific assumptions about the underlying mechanisms, to overcome and complement the previous limitations. We found that GF in the region is driven synergistically, not independently, by cool air temperature and drought, which is consistent with the previous studies. More importantly, our model‐free approach showed for the first time that effects of cumulative meteorological variables on GF changed over time. The time‐varying influences of meteorological variables on GF imply that the relationship between GF and meteorological variables might be influenced by other factors such as plant/soil nutrient resource dynamics. Our study provides a novel insight about the mechanism underlying the spectacular tropical forest event GF, and future studies integrating advanced mathematical/statistical frameworks, long‐term and large spatial scale ecosystem monitoring and molecular phenology data are promising for achieving better understanding and forecasting of GF events in Southeast Asia.
Preferential catabolism of the (S)‐enantiomer of the herbicide napropamide mediated by the enantioselective amidohydrolase SnaH and the dioxygenase Snpd in Sphingobium sp. strain B2
Authors: Huang Junwei , Chen Dian , Jiang Jiandong
Published: October 2019

The (R)‐ and (S)‐enantiomers of the chiral herbicide napropamide (NAP) show different biological activities and ecotoxicities. These two enantiomers behave differently in the environment due to enantioselective catabolism by microorganisms. However, the molecular mechanisms underlying this enantioselective catabolism remain largely unknown. In this study, the genes (snaH and snpd) involved in the catabolism of NAP were cloned from Sphingobium sp. B2, which was capable of catabolizing both NAP enantiomers. Compared with (R)‐NAP, (S)‐NAP was much more rapidly transformed by the amidase SnaH, which initially cleaved the amide bonds of (S)/(R)‐NAP to form (S)/(R)‐2‐(1‐naphthalenyloxy)‐propanoic acid [(S)/(R)‐NP] and diethylamine. The α‐ketoglutarate‐dependent dioxygenase Snpd, showing strict stereoselectivity for (S)‐NP, further transformed (S)‐NP to 1‐naphthol and pyruvate. Molecular docking and site‐directed mutagenesis analyses revealed that when the (S)‐enantiomers of NAP and NP occupied the active sites, the distance between the ligand molecule and the coordination atom was shorter than that when the (R)‐enantiomers occupied the active sites, which facilitated formation of the transition state complex. This study enhances our understanding of the preferential catabolism of the (S)‐enantiomer of NAP on the molecular level.
Beyond trade creation: Preferential trade agreements and trade disputes
Authors: Li Tan , Qiu Larry D.
Published: October 2019

This study investigates the effects of preferential trade agreements (PTA) on bilateral trade disputes. We construct a unique and comprehensive dataset on inter‐country trade disputes from 1995 to 2007. The dataset covers 110 countries and 1,162 bilateral country‐pair trade disputes. Using this dataset in a gravity‐type model of trade dispute analysis, we find that countries belonging to the same PTA tend to experience fewer trade conflicts among themselves than with non‐member countries. By studying various types of PTA with different dispute settlement mechanisms, we further find that the dispute‐reducing effect only comes from PTA with specific provisions on dispute settlement mechanisms. Moreover, the effect is stronger if those PTA explicitly stipulate that members can also resolve their disputes via the WTO Dispute Settlement Body. However, having PTA that do not address how members should resolve their disputes may lead to more dispute initiations than in cases without PTA.
Discrimination in the United States: Experiences of Latinos
Authors: Findling Mary G. , Bleich Sara N. , Casey Logan S. , Blendon Robert J. , Benson John M. , Sayde Justin M. , Miller Carolyn
Published: October 2019

Objective

To examine experiences of racial/ethnic discrimination among Latinos in the United States, which broadly contribute to their poor health outcomes.

Data Source and Study Design

Data come from a nationally representative, probability‐based telephone survey including 803 Latinos and a comparison group of 902 non‐Hispanic white US adults, conducted January—April 2017.

Methods

We calculated the percent of Latinos reporting discrimination in several domains, including health care. We used logistic regression to compare the Latino‐white difference in odds of discrimination, and among Latinos only to examine variation by socioeconomic status and country of birth.

Principal Findings

One in five Latinos (20 percent) reported experiencing discrimination in clinical encounters, while 17 percent avoided seeking health care for themselves or family members due to anticipated discrimination. A notable share of Latinos also reported experiencing discrimination with employment (33 percent applying for jobs; 32 percent obtaining equal pay/promotions), housing (31 percent), and police interactions (27 percent). In adjusted models, Latinos had significantly higher odds than whites for reporting discrimination in health care visits (OR: 3.18, 95% CI: 1.61, 6.26) and across several other domains. Latinos with college degrees had significantly higher odds of reporting discrimination in multiple domains than those without college degrees, with few differences between foreign‐born and US‐born Latinos.

Conclusions

Latinos in the United States report experiencing widespread discrimination in health care and other areas of their lives, at significantly higher levels than whites. Being born in the United States and earning a college degree are not protective against discrimination, suggesting that further health and social policy efforts to eliminate discrimination are needed.
The Evolving Structure of Chinese R&D Funding and its Implications for the Productivity of Agricultural Biotechnology Research
Authors: Cai Jinyang , Chen Weiqiong , Huang Jikun , Hu Ruifa , Pray Carl E.
Published: October 2019

China’s research and development (R&D) policy has changed considerably over recent decades, and great changes occurred in 2006 when the main programme objective of China’s R&D changed from the 863 Programme and 973 Programme to the National Science and Technology Major Project. One topic that has drawn extensive attention is whether the investment reform improved R&D productivity in China. Using a unique panel dataset from 160 universities, this paper examines the effect of the investment reform on productivity improvement in China’s agricultural biotechnology sector. We use a panel count data model with a dynamic feedback mechanism to model the knowledge production process. Strong evidence indicates that the investment reform greatly contributes to knowledge output production in China’s agricultural biotechnology sector. We also find that the input quality is more important than the absolute quantity; human research capacity exhibits the greatest contribution to the output of patents; past knowledge accumulation helps produce more patents; and entry barriers to patent production exist in China’s agricultural biotechnology sector. Moreover, the patent explosion in China may have been largely caused by improvements in the human capital input quality.
Nonfatal Bites by a Sicklefin Lemon Shark Negaprion acutidens on a Surfer in Makemo Atoll (French Polynesia)
Authors: Clua Eric E. G. , Haguenauer Anne
Published: October 2019

Identifying the species and size of sharks responsible for biting humans is essential for developing strategies to prevent these incidents. Here, we use bite wound characteristics and genetic analysis of a tooth fragment extracted from the wounds to identify a sicklefin lemon shark Negaprion acutidens as the perpetrator of nonfatal bites on the legs of an adult male surfer at Makemo atoll (French Polynesia) in January 2018. The bite was superficial, and N. acutidens are fish predators not known to feed on large prey; hence, foraging is an unlikely explanation for this incident rather linked to territoriality. Lemon sharks are occasionally aggressive toward humans and are site attached with relatively small home ranges; hence, avoiding surfing in the area of a previous bite incident is recommended to decrease the risk of future injuries.