bluuebunny/crossref_metadata_2025 huggingface dataset:
Validation of aggregated risks models
Authors: Dacorogna Michel , Elbahtouri Laila , Kratz Marie
Published: December 2017

Validation of risk models is required by regulators and demanded by management and shareholders. Those models rely in practice heavily on Monte Carlo (MC) simulations. Given their complexity, the convergence of the MC algorithm is difficult to prove mathematically. To circumvent this problem and nevertheless explore the conditions of convergence, we suggest an analytical approach. Considering standard models, we compute, via mixing techniques, closed form formulas for risk measures as Value-at-Risk (VaR) VaR or Tail Value-at-Risk (TVaR) TVaR on a portfolio of risks, and consequently for the associated diversification benefit. The numerical convergence of MC simulations of those various quantities is then tested against their analytical evaluations. The speed of convergence appears to depend on the fatness of the tail of the marginal distributions; the higher the tail index, the faster the convergence. We also explore the behaviour of the diversification benefit with various dependence structures and marginals (heavy and light tails). As expected, it varies heavily with the type of dependence between aggregated risks. The diversification benefit is also studied as a function of the risk measure, VaR or TVaR.
The crisis of detention and the politics of denial in Latin America
Authors: Hathazy Paul , Müller Markus-Michael
Published: December 2017

This article assesses the causes of the crisis of detention in Latin America. It is argued that this crisis, which manifests itself in overpopulation of the region's prison systems, deficient infrastructure, prison informality and violence propelled ultimately by political processes, is mostly related to, on the one hand, disastrous human rights conditions inside Latin American prisons, and on other, the political denial of these conditions. This denial produces a state of institutional abandonment that is preserved by the interests of politicians and bureaucrats, who are engaged in denying prison violence and human rights abuses while simultaneously calling for more punishment and imprisonment.
The effect of adverse intrauterine conditions, early childhood growth and famine exposure on age at menopause: a systematic review
Authors: Sadrzadeh S. , Verschuuren M. , Schoonmade L. J. , Lambalk C. B. , Painter R. C.
Published: December 2017

When the follicle reserve, which is developed solely during the fetal period, is depleted, women enter menopause. Intrauterine and childhood adverse conditions might affect the ovarian capacity by influencing follicle production in the first trimester, limiting the initial follicle pool or mediate an accelerated follicular loss thereafter. To investigate if adverse early life influences result in younger age at menopause, the following online databases were systematically searched: PubMed, EMBASE, CINHAL (EBSCO) and Cochrane library (Wiley) up to 1 January 2017. Eligibility, data extraction and quality assessment was independently performed by two researchers. A total of 5278 studies were identified, 11 studies were deemed eligible and included. Nine were cohort studies, 1 case–control study and 1 twin study. Due to the diversity of reported data and risk estimates we were unable to pool data or perform meta-analysis on pooled data. Prenatal and childhood exposure to famine was significantly associated to an earlier age at menopause in three studies. Mean differences in age at menopause varied from 4 months up to 1.7 years between famine exposed and unexposed women. Three studies described a significant association between a low weight at ages 1 or 2 and a younger age at menopause. A younger age at menopause was associated with a higher weight at birth in only one study and with a high ponderal index, a measure for fatness at birth in another study. None of the nine studies reporting on low birth weight and age at natural menopause find a significant association.
Contrasting patterns of genome-level diversity across distinct co-occurring bacterial populations
Authors: Garcia Sarahi L , Stevens Sarah L R , Crary Benjamin , Martinez-Garcia Manuel , Stepanauskas Ramunas , Woyke Tanja , Tringe Susannah G , Andersson Siv G E , Bertilsson Stefan , Malmstrom Rex R , McMahon Katherine D
Published: December 2017

To understand the forces driving differentiation and diversification in wild bacterial populations, we must be able to delineate and track ecologically relevant units through space and time. Mapping metagenomic sequences to reference genomes derived from the same environment can reveal genetic heterogeneity within populations, and in some cases, be used to identify boundaries between genetically similar, but ecologically distinct, populations. Here we examine population-level heterogeneity within abundant and ubiquitous freshwater bacterial groups such as the acI Actinobacteria and LD12 Alphaproteobacteria (the freshwater sister clade to the marine SAR11) using 33 single-cell genomes and a 5-year metagenomic time series. The single-cell genomes grouped into 15 monophyletic clusters (termed “tribes”) that share at least 97.9% 16S rRNA identity. Distinct populations were identified within most tribes based on the patterns of metagenomic read recruitments to single-cell genomes representing these tribes. Genetically distinct populations within tribes of the acI Actinobacterial lineage living in the same lake had different seasonal abundance patterns, suggesting these populations were also ecologically distinct. In contrast, sympatric LD12 populations were less genetically differentiated. This suggests that within one lake, some freshwater lineages harbor genetically discrete (but still closely related) and ecologically distinct populations, while other lineages are composed of less differentiated populations with overlapping niches. Our results point at an interplay of evolutionary and ecological forces acting on these communities that can be observed in real time.
Diazotroph diversity and nitrogen fixation in the coral Stylophora pistillata from the Great Barrier Reef
Authors: Lesser Michael P , Morrow Kathleen M , Pankey Sabrina M , Noonan Sam H C
Published: December 2017

Diazotrophs, both Bacteria and Archaea, capable of fixing nitrogen (N2), are present in the tissues and mucous, of corals and can supplement the coral holobiont nitrogen budget with fixed nitrogen (N) in the form of ammonia (NH3). Stylophora pistillata from Heron Island on the Great Barrier Reef collected at 5 and 15 m, and experimentally manipulated in the laboratory, showed that the rates of net photosynthesis, steady state quantum yields of photosystem II (PSII) fluorescence (∆Fv/Fm′) and calcification varied based on irradiance as expected. Rates of N2 fixation were, however, invariant across treatments while the amount of fixed N contributing to Symbiodinium spp. N demand is irradiance dependent. Additionally, both the Symbiodinium and diazotrophic communities are significantly different based on depth, and novel Cluster V nifH gene phylotypes, which are not known to fix nitrogen, were recovered. A functional analysis using PICRUSt also showed that shallow corals were enriched in genes involved in nitrogen metabolism, and N2 fixation specifically. Corals have evolved a number of strategies to derive nitrogen from organic (e.g., heterotrophic feeding) and inorganic sources (e.g., N2 fixation) to maintain critical pathways such as protein synthesis to succeed ecologically in nitrogen-limited habitats.
Andean mountain building and magmatic arc migration driven by subduction-induced whole mantle flow
Authors: Schellart W. P.
Published: December 2017

Subduction along the western margin of South America has been active since the Jurassic, but Andean orogeny started in the middle Cretaceous and was preceded by backarc extension in the Jurassic-Early Cretaceous. The timing and sequence of these events has remained unexplained. Here I present a four-dimensional buoyancy-driven whole-mantle subduction model implying that the ~200 Myr geological evolution can be attributed to sinking of a wide slab into a layered mantle, where upper-mantle wide-slab subduction causes backarc extension, while whole-mantle (upper+lower) wide-slab subduction drives Andean orogeny. The model reproduces the maximum shortening and crustal thickness observed in the Central Andes and their progressive northward and southward decrease. The subduction evolution coincides with a 29° decrease in slab dip angle, explaining ~200 km of Jurassic-present eastward migration of the Central Andean magmatic arc. Such arc migration negates proposed long-term subduction erosion and continental destruction, but is consistent with long-term crustal growth.
Tree co-occurrence and transcriptomic response to drought
Authors: Swenson Nathan G. , Iida Yoshiko , Howe Robert , Wolf Amy , Umaña María Natalia , Petprakob Krittika , Turner Benjamin L. , Ma Keping
Published: December 2017

The distribution and co-occurrence of species are partly the outcome of their interactions with environmental drivers. Drought is a key driver related to the distribution of plant species. Drought events continue to increase in frequency and severity and identifying those aspects of plant function that are related to drought is critical. Here, we perform a community-level analysis of gene expression in relation to experimental drought and relate the similarity in gene set enrichment across species to their natural co-occurrence. Species with similar gene set enrichment in response to experimental drought tend to non-randomly co-occur in a natural stand. We demonstrate that similarity in the transcriptomic response of species to drought is a significantly better indicator of natural co-occurrence than measures of functional trait similarity and phylogenetic relatedness and that transcriptomics has the capacity to greatly enhance ecological investigations of species distributions and community structure.
Serendipity and strategy in rapid innovation
Authors: Fink T. M. A. , Reeves M. , Palma R. , Farr R. S.
Published: December 2017

Innovation is to organizations what evolution is to organisms: it is how organizations adapt to environmental change and improve. Yet despite advances in our understanding of evolution, what drives innovation remains elusive. On the one hand, organizations invest heavily in systematic strategies to accelerate innovation. On the other, historical analysis and individual experience suggest that serendipity plays a significant role. To unify these perspectives, we analysed the mathematics of innovation as a search for designs across a universe of component building blocks. We tested our insights using data from language, gastronomy and technology. By measuring the number of makeable designs as we acquire components, we observed that the relative usefulness of different components can cross over time. When these crossovers are unanticipated, they appear to be the result of serendipity. But when we can predict crossovers in advance, they offer opportunities to strategically increase the growth of the product space.
Induced unconventional superconductivity on the surface states of Bi2Te3 topological insulator
Authors: Charpentier Sophie , Galletti Luca , Kunakova Gunta , Arpaia Riccardo , Song Yuxin , Baghdadi Reza , Wang Shu Min , Kalaboukhov Alexei , Olsson Eva , Tafuri Francesco , Golubev Dmitry , Linder Jacob , Bauch Thilo , Lombardi Floriana
Published: December 2017

Topological superconductivity is central to a variety of novel phenomena involving the interplay between topologically ordered phases and broken-symmetry states. The key ingredient is an unconventional order parameter, with an orbital component containing a chiral p
x
 + ip
y
wave term. Here we present phase-sensitive measurements, based on the quantum interference in nanoscale Josephson junctions, realized by using Bi2Te3 topological insulator. We demonstrate that the induced superconductivity is unconventional and consistent with a sign-changing order parameter, such as a chiral p
x
 + ip
y
component. The magnetic field pattern of the junctions shows a dip at zero externally applied magnetic field, which is an incontrovertible signature of the simultaneous existence of 0 and π coupling within the junction, inherent to a non trivial order parameter phase. The nano-textured morphology of the Bi2Te3 flakes, and the dramatic role played by thermal strain are the surprising key factors for the display of an unconventional induced order parameter.
Input-dependent regulation of excitability controls dendritic maturation in somatosensory thalamocortical neurons
Authors: Frangeul Laura , Kehayas Vassilis , Sanchez-Mut Jose V. , Fièvre Sabine , Krishna-K K. , Pouchelon Gabrielle , Telley Ludovic , Bellone Camilla , Holtmaat Anthony , Gräff Johannes , Macklis Jeffrey D. , Jabaudon Denis
Published: December 2017

Input from the sensory organs is required to pattern neurons into topographical maps during development. Dendritic complexity critically determines this patterning process; yet, how signals from the periphery act to control dendritic maturation is unclear. Here, using genetic and surgical manipulations of sensory input in mouse somatosensory thalamocortical neurons, we show that membrane excitability is a critical component of dendritic development. Using a combination of genetic approaches, we find that ablation of N-methyl-d-aspartate (NMDA) receptors during postnatal development leads to epigenetic repression of Kv1.1-type potassium channels, increased excitability, and impaired dendritic maturation. Lesions to whisker input pathways had similar effects. Overexpression of Kv1.1 was sufficient to enable dendritic maturation in the absence of sensory input. Thus, Kv1.1 acts to tune neuronal excitability and maintain it within a physiological range, allowing dendritic maturation to proceed. Together, these results reveal an input-dependent control over neuronal excitability and dendritic complexity in the development and plasticity of sensory pathways.
The dynamic dimer structure of the chaperone Trigger Factor
Authors: Morgado Leonor , Burmann Björn M. , Sharpe Timothy , Mazur Adam , Hiller Sebastian
Published: December 2017

The chaperone Trigger Factor (TF) from Escherichia coli forms a dimer at cellular concentrations. While the monomer structure of TF is well known, the spatial arrangement of this dimeric chaperone storage form has remained unclear. Here, we determine its structure by a combination of high-resolution NMR spectroscopy and biophysical methods. TF forms a symmetric head-to-tail dimer, where the ribosome binding domain is in contact with the substrate binding domain, while the peptidyl-prolyl isomerase domain contributes only slightly to the dimer affinity. The dimer structure is highly dynamic, with the two ribosome binding domains populating a conformational ensemble in the center. These dynamics result from intermolecular in trans interactions of the TF client-binding site with the ribosome binding domain, which is conformationally frustrated in the absence of the ribosome. The avidity in the dimer structure explains how the dimeric state of TF can be monomerized also by weakly interacting clients.
Bioinspired graphene membrane with temperature tunable channels for water gating and molecular separation
Authors: Liu Jingchong , Wang Nü , Yu Li-Juan , Karton Amir , Li Wen , Zhang Weixia , Guo Fengyun , Hou Lanlan , Cheng Qunfeng , Jiang Lei , Weitz David A. , Zhao Yong
Published: December 2017

Smart regulation of substance permeability through porous membranes is highly desirable for membrane applications. Inspired by the stomatal closure feature of plant leaves at relatively high temperature, here we report a nano-gating membrane with a negative temperature-response coefficient that is capable of tunable water gating and precise small molecule separation. The membrane is composed of poly(N-isopropylacrylamide) covalently bound to graphene oxide via free-radical polymerization. By virtue of the temperature tunable lamellar spaces of the graphene oxide nanosheets, the water permeance of the membrane could be reversibly regulated with a high gating ratio. Moreover, the space tunability endows the membrane with the capability of gradually separating multiple molecules of different sizes. This nano-gating membrane expands the scope of temperature-responsive membranes and has great potential applications in smart gating systems and molecular separation.
RAN translation at C9orf72-associated repeat expansions is selectively enhanced by the integrated stress response
Authors: Green Katelyn M. , Glineburg M. Rebecca , Kearse Michael G. , Flores Brittany N. , Linsalata Alexander E. , Fedak Stephen J. , Goldstrohm Aaron C. , Barmada Sami J. , Todd Peter K.
Published: December 2017

Repeat-associated non-AUG (RAN) translation allows for unconventional initiation at disease-causing repeat expansions. As RAN translation contributes to pathogenesis in multiple neurodegenerative disorders, determining its mechanistic underpinnings may inform therapeutic development. Here we analyze RAN translation at G4C2 repeat expansions that cause C9orf72-associated amyotrophic lateral sclerosis and frontotemporal dementia (C9RAN) and at CGG repeats that cause fragile X-associated tremor/ataxia syndrome. We find that C9RAN translation initiates through a cap- and eIF4A-dependent mechanism that utilizes a CUG start codon. C9RAN and CGG RAN are both selectively enhanced by integrated stress response (ISR) activation. ISR-enhanced RAN translation requires an eIF2α phosphorylation-dependent alteration in start codon fidelity. In parallel, both CGG and G4C2 repeats trigger phosphorylated-eIF2α-dependent stress granule formation and global translational suppression. These findings support a model whereby repeat expansions elicit cellular stress conditions that favor RAN translation of toxic proteins, creating a potential feed-forward loop that contributes to neurodegeneration.
Tuning the interactions between chiral plasmonic films and living cells
Authors: Zhao Xueli , Xu Liguang , Sun Maozhong , Ma Wei , Wu Xiaoling , Xu Chuanlai , Kuang Hua
Published: December 2017

Designing chiral materials to manipulate the biological activities of cells has been an important area not only in chemistry and material science, but also in cell biology and biomedicine. Here, we introduce monolayer plasmonic chiral Au nanoparticle (NP) films modified withl- ord-penicillamine (Pen) to be developed for cell growth, differentiation, and retrieval. The monolayer films display high chiroptical activity, with circular dichroism values of 3.5 mdeg at 550 nm and 26.8 mdeg at 775 nm. Thel-Pen-NP films accelerate cell proliferation, whereas thed-Pen-NP films have the opposite effect. Remote irradiation with light is chosen to noninvasively collect the cells. The results demonstrate that left circularly polarized light improves the efficiency of cell detachment up to 91.2% forl-Pen-NP films. These findings will facilitate the development of cell culture in biomedical application and help to understand natural homochirality.
Scaling of Yu-Shiba-Rusinov energies in the weak-coupling Kondo regime
Authors: Hatter Nino , Heinrich Benjamin W. , Rolf Daniela , Franke Katharina J.
Published: December 2017

The competition of the free-spin state of a paramagnetic impurity on a superconductor with its screened counterpart is characterized by the energy scale of Kondo screening compared to the superconducting pairing energy Δ. When the experimental temperature suppresses Kondo screening, but preserves superconductivity, i.e., when Δ/kB > T > TK (kB is Boltzmann’s constant and TK the Kondo temperature), this description fails. Here, we explore this temperature range in a set of manganese phthalocyanine molecules decorated with ammonia on Pb(111). We show that these molecules suffice the required energy conditions by exhibiting weak-coupling Kondo resonances. We correlate the Yu-Shiba-Rusinov bound states energy inside the superconducting gap with the intensity of the Kondo resonance. The observed correlation follows the expectations for a classical spin on a superconductor. This finding is important in view of many theoretical predictions using a classical spin model, in particular for the description of Majorana bound states in magnetic nanostructures on superconducting substrates.
A control analysis perspective on Katz centrality
Authors: Sharkey Kieran J.
Published: December 2017

Methods for efficiently controlling dynamics propagated on networks are usually based on identifying the most influential nodes. Knowledge of these nodes can be used for the targeted control of dynamics such as epidemics, or for modifying biochemical pathways relating to diseases. Similarly they are valuable for identifying points of failure to increase network resilience in, for example, social support networks and logistics networks. Many measures, often termed ‘centrality’, have been constructed to achieve these aims. Here we consider Katz centrality and provide a new interpretation as a steady-state solution to continuous-time dynamics. This enables us to implement a sensitivity analysis which is similar to metabolic control analysis used in the analysis of biochemical pathways. The results yield a centrality which quantifies, for each node, the net impact of its absence from the network. It also has the desirable property of requiring a node with a high centrality to play a central role in propagating the dynamics of the system by having the capacity to both receive flux from others and then to pass it on. This new perspective on Katz centrality is important for a more comprehensive analysis of directed networks.
Conserved Gene Microsynteny Unveils Functional Interaction Between Protein Disulfide Isomerase and Rho Guanine-Dissociation Inhibitor Families
Authors: Moretti Ana I. S. , Pavanelli Jessyca C. , Nolasco Patrícia , Leisegang Matthias S. , Tanaka Leonardo Y. , Fernandes Carolina G. , Wosniak João , Kajihara Daniela , Dias Matheus H. , Fernandes Denise C. , Jo Hanjoong , Tran Ngoc-Vinh , Ebersberger Ingo , Brandes Ralf P. , Bonatto Diego , Laurindo Francisco R. M.
Published: December 2017

Protein disulfide isomerases (PDIs) support endoplasmic reticulum redox protein folding and cell-surface thiol-redox control of thrombosis and vascular remodeling. The family prototype PDIA1 regulates NADPH oxidase signaling and cytoskeleton organization, however the related underlying mechanisms are unclear. Here we show that genes encoding human PDIA1 and its two paralogs PDIA8 and PDIA2 are each flanked by genes encoding Rho guanine-dissociation inhibitors (GDI), known regulators of RhoGTPases/cytoskeleton. Evolutionary histories of these three microsyntenic regions reveal their emergence by two successive duplication events of a primordial gene pair in the last common vertebrate ancestor. The arrangement, however, is substantially older, detectable in echinoderms, nematodes, and cnidarians. Thus, PDI/RhoGDI pairing in the same transcription orientation emerged early in animal evolution and has been largely maintained. PDI/RhoGDI pairs are embedded into conserved genomic regions displaying common cis-regulatory elements. Analysis of gene expression datasets supports evidence for PDI/RhoGDI coexpression in developmental/inflammatory contexts. PDIA1/RhoGDIα were co-induced in endothelial cells upon CRISP-R-promoted transcription activation of each pair component, and also in mouse arterial intima during flow-induced remodeling. We provide evidence for physical interaction between both proteins. These data support strong functional links between PDI and RhoGDI families, which likely maintained PDI/RhoGDI microsynteny along > 800-million years of evolution.
Ground-state cooling of a mechanical oscillator in a hybrid optomechanical system including an atomic ensemble
Authors: Zeng Wei , Nie Wenjie , Li Ling , Chen Aixi
Published: December 2017

We investigate dynamical properties and the ground-state cooling of a mechanical oscillator in an optomechanical system coupling with an atomic ensemble. In this hybrid optomechanical system, an atomic ensemble which consists of two-level atoms couples with the cavity field. Here we consider the case where the atomic ensemble is in higher excitation. Studies show that the atom-field coupling strength can obviously influence the cooling process, and we can achieve the ground-state cooling of the mechanical oscillator by choosing the appropriate physical parameters of the system. Our cooling mechanism has potential applications in quantum information processing and procession measurement.
Utilization of blood by-products: An in silico and experimental combined study for BSA usage
Authors: Arrutia Fátima , Fernández Rebeca , Menéndez Carlos , González Ulises A. , Riera Francisco A.
Published: December 2017

In order to exploit industrial discards, protein enzymatic hydrolysis is a currently popular methodology for obtaining bioactive peptides. However, once released, most promising peptides have to be selected from the mixture. In this work, the suitability of pepsin (EC 3.4.23.1) to hydrolyse serum albumin in order to obtain bioactive peptides was assessed. Then, a suitable process to obtain best separation of bioactive peptides was evaluated, using polyethersulfone membranes at different pH values. Serum albumin was easily hydrolysed by pepsin, reaching a DH value of the 65.64 ± 1.57% of the maximum possible. A 23.25% of the identified peptides possessed high bioactivity scores (greater than 0.5), and one of them had reported bioactivity (LLL). Charge mechanisms always predominated over the sieve effect, and best transmission was accomplished at pH values close to the peptides isoelectric points. Basic and neutral peptides with the highest scores were always the most transmitted. Membrane material had greater influence than NMWCO in determining peptide transmission. In order to obtain purified fractions rich in peptides with high bioactivity scores from serum albumin, polyethersulfone membranes (applicable to industrial scale) of 5 kDa MWCO should be used at basic pH values after pepsin digestion.
Author Correction: Temperature dependence of protein-water interactions in a gated yeast aquaporin
Authors: Aponte-Santamaría Camilo , Fischer Gerhard , Båth Petra , Neutze Richard , de Groot Bert L.
Published: December 2017

A correction to this article has been published and is linked from the HTML version of this paper. The error has been fixed in the paper.
Publisher Correction: Method to Reduce Long-lived Fission Products by Nuclear Transmutations with Fast Spectrum Reactors
Authors: Chiba Satoshi , Wakabayashi Toshio , Tachi Yoshiaki , Takaki Naoyuki , Terashima Atsunori , Okumura Shin , Yoshida Tadashi
Published: December 2017

A correction to this article has been published and is linked from the HTML version of this paper. The error has been fixed in the paper.
The Irish DNA Atlas: Revealing Fine-Scale Population Structure and History within Ireland
Authors: Gilbert Edmund , O’Reilly Seamus , Merrigan Michael , McGettigan Darren , Molloy Anne M. , Brody Lawrence C. , Bodmer Walter , Hutnik Katarzyna , Ennis Sean , Lawson Daniel J. , Wilson James F. , Cavalleri Gianpiero L.
Published: December 2017

The extent of population structure within Ireland is largely unknown, as is the impact of historical migrations. Here we illustrate fine-scale genetic structure across Ireland that follows geographic boundaries and present evidence of admixture events into Ireland. Utilising the ‘Irish DNA Atlas’, a cohort (n = 194) of Irish individuals with four generations of ancestry linked to specific regions in Ireland, in combination with 2,039 individuals from the Peoples of the British Isles dataset, we show that the Irish population can be divided in 10 distinct geographically stratified genetic clusters; seven of ‘Gaelic’ Irish ancestry, and three of shared Irish-British ancestry. In addition we observe a major genetic barrier to the north of Ireland in Ulster. Using a reference of 6,760 European individuals and two ancient Irish genomes, we demonstrate high levels of North-West French-like and West Norwegian-like ancestry within Ireland. We show that that our ‘Gaelic’ Irish clusters present homogenous levels of ancient Irish ancestries. We additionally detect admixture events that provide evidence of Norse-Viking gene flow into Ireland, and reflect the Ulster Plantations. Our work informs both on Irish history, as well as the study of Mendelian and complex disease genetics involving populations of Irish ancestry.
A highly printable and biocompatible hydrogel composite for direct printing of soft and perfusable vasculature-like structures
Authors: Suntornnond Ratima , Tan Edgar Yong Sheng , An Jia , Chua Chee Kai
Published: November 2017

Vascularization is one major obstacle in bioprinting and tissue engineering. In order to create thick tissues or organs that can function like original body parts, the presence of a perfusable vascular system is essential. However, it is challenging to bioprint a hydrogel-based three-dimensional vasculature-like structure in a single step. In this paper, we report a new hydrogel-based composite that offers impressive printability, shape integrity, and biocompatibility for 3D bioprinting of a perfusable complex vasculature-like structure. The hydrogel composite can be used on a non-liquid platform and is printable at human body temperature. Moreover, the hydrogel composite supports both cell proliferation and cell differentiation. Our results represent a potentially new vascularization strategy for 3D bioprinting and tissue engineering.
Impact of model calibration on cost-effectiveness analysis of cervical cancer prevention
Authors: Moriña David , de Sanjosé Silvia , Diaz Mireia
Published: December 2017

Markov chain models are commonly used to simulate the natural history of human papillomavirus infection and subsequent cervical lesions with the aim of predicting future benefits of health interventions. Developing and calibrating these models entails making a number of critical decisions that will influence the ability of the model to reflect real conditions and predict future situations. Accuracy of selected inputs and calibration procedures are two of the crucial aspects for model performance and understanding their influence is essential, especially when involves policy decisions. The aim of this work is to assess the health and economic impact on cervical cancer prevention strategies currently under discussion according to the most common methods of model calibration combined with different accuracy degree of initial inputs. Model results show large differences on the goodness of fit and cost-effectiveness outcomes depending on the calibration approach used, and these variations may affect health policy decisions. Our findings strengthen the importance of obtaining good calibrated probability matrices to get reliable health and cost outcomes, and are directly generalizable to any cost-effectiveness analysis based on Markov chain models.
Biotrophy-necrotrophy switch in pathogen evoke differential response in resistant and susceptible sesame involving multiple signaling pathways at different phases
Authors: Chowdhury Supriyo , Basu Arpita , Kundu Surekha
Published: December 2017

Infection stages of charcoal rot fungus Macrophomina phaseolina in sesame revealed for the first time a transition from biotrophy via BNS (biotrophy-to-necrotrophy switch) to necrotrophy as confirmed by transcriptional studies. Microscopy using normal and GFP-expressing pathogen showed typical constricted thick intercellular bitrophic hyphae which gave rise to thin intracellular necrotrophic hyphae during BNS and this stage was delayed in a resistant host. Results also show that as the pathogen switched its strategy of infection, the host tailored its defense strategy to meet the changing situation. Less ROS accumulation, upregulation of ROS signaling genes and higher antioxidant enzyme activities post BNS resulted in resistance. There was greater accumulation of secondary metabolites and upregulation of secondary metabolite-related genes after BNS. A total of twenty genes functioning in different aspects of plant defense that were monitored over a time course during the changing infection phases showed a coordinated response. Experiments using phytohormone priming and phytohormone inhibitors showed that resistance resulted from activation of JA-ET signaling pathway. Most importantly this defense response was more prompt in the resistant than the susceptible host indicating that a resistant host makes different choices from a susceptible host during infection which ultimately influences the severity of the disease.
Cytokines and chemokines measured in dried SLA-stimulated whole blood spots for asymptomatic Leishmania infantum and Leishmania donovani infection
Authors: Ibarra-Meneses A. V. , Mondal D. , Alvar J. , Moreno J. , Carrillo E.
Published: December 2017

Whole blood stimulation with soluble Leishmania antigen (SLA), followed by plasma cytokine and chemokine determination, provides means of detecting subjects with asymptomatic Leishmania infection. This work examines the potential of Protein Saver 903 cards for the storage and transport of SLA-stimulated dried plasma spot samples. Blood was collected from asymptomatic and negative control subjects living in a Leishmania infantum- (Spain) and Leishmania donovani-endemic area (Bangladesh). After SLA-stimulation, three types of sample were prepared: frozen liquid plasma (−20 °C), and plasma dropped onto Protein Saver cards kept at −20 °C (DPS-FZ), and at ambient temperature (DPS-AT). The concentrations of IFN-γ, IL-2, CXCL10, CXCL9, CCL2 and CXCL8 in the thawed liquid plasma (TLP), DPS-FZ and DPS-AT samples were then determined. Strong correlations were seen between the TLP and DPS-FZ/AT samples for all the studied cytokines/chemokines in both the L. infantum and L. donovani areas. Protein Saver 903 cards would therefore appear to allow for the transport of SLA-stimulated plasma samples by courier at ambient temperature. The CXCL10 and CXCL9 detectable in these plasma spots provided robust markers for identifying asymptomatic subjects from both endemic areas. This easy procedure opens up new possibilities for field studies in resource-limited settings, which could help in Leishmania control.
Dissecting the Genetic Basis of Local Adaptation in Soybean
Authors: Bandillo Nonoy B. , Anderson Justin E. , Kantar Michael B. , Stupar Robert M. , Specht James E. , Graef George L. , Lorenz Aaron J.
Published: December 2017

Soybean (Glycine max) is the most widely grown oilseed in the world and is an important source of protein for both humans and livestock. Soybean is widely adapted to both temperate and tropical regions, but a changing climate demands a better understanding of adaptation to specific environmental conditions. Here, we explore genetic variation in a collection of 3,012 georeferenced, locally adapted landraces from a broad geographical range to help elucidate the genetic basis of local adaptation. We used geographic origin, environmental data and dense genome-wide SNP data to perform an environmental association analysis and discover loci displaying steep gradients in allele frequency across geographical distance and between landrace and modern cultivars. Our combined application of methods in environmental association mapping and detection of selection targets provide a better understanding of how geography and selection may have shaped genetic variation among soybean landraces. Moreover, we identified several important candidate genes related to drought and heat stress, and revealed important genomic regions possibly involved in the geographic divergence of soybean.
Genome-wide and gene-based association mapping for rice eating and cooking characteristics and protein content
Authors: Wang Xiaoqian , Pang Yunlong , Zhang Jian , Wu Zhichao , Chen Kai , Ali Jauhar , Ye Guoyou , Xu Jianlong , Li Zhikang
Published: December 2017

Rice eating and cooking quality and protein content (PC) are important properties affecting consumers’ preferences, nutrition and health. Linkage QTL mapping and association studies are usually applied to genetically dissect related traits, which could be further facilitated by high density SNP markers and gene annotation based on reference genome to rapid identify candidate genes associated with interested traits. Here, we carried out an association study for apparent amylose content (AC), gel consistency (GC), gelatinization temperature (GT) and PC evaluated in two environments using a diverse panel of 258 accessions from 3 K Rice Genome Project. Wide phenotypic variations were observed in this panel. Genome-wide association study using 22,488 high quality SNPs identified 19 QTL affecting the four traits. Combining gene-based association study and haplotype analyses plus functional annotation allowed us to shortlist nine candidate genes for four important QTL regions affecting AC, GC and GT, including two cloned genes (Wx and ALK), and seven novels. The research suggested that GWAS and gene-based association analysis followed by haplotype analysis is an effective way to detect candidate genes. The identified genes and QTL provided valuable sources for future functional characterization and genetic improvement of rice eating and cooking quality and PC.
Prediction of genomic breeding values using new computing strategies for the implementation of MixP
Authors: Dong Linsong , Fang Ming , Wang Zhiyong
Published: December 2017

MixP is an implementation that uses the Pareto principle to perform genomic prediction. This study was designed to develop two new computing strategies: one strategy for nonMCMC-based MixP (FMixP), and the other one for MCMC-based MixP (MMixP). The difference is that MMixP can estimate variances of SNP effects and the probability that a SNP has a large variance, but FMixP cannot. Simulated data from an international workshop and real data on large yellow croaker were used as the materials for the study. Four Bayesian methods, BayesA, BayesCπ, MMixP and FMixP, were used to compare the predictive results. The results show that BayesCπ, MMixP and FMixP perform better than BayesA for the simulated data, but all methods have very similar predictive abilities for the large yellow croaker. However, FMixP is computationally significantly faster than the MCMC-based methods. Our research may have a potential for the future applications in genomic prediction.
Functional analysis of human intrafusal fiber innervation by human γ-motoneurons
Authors: Colón A. , Guo X. , Akanda N. , Cai Y. , Hickman J. J.
Published: December 2017

Investigation of neuromuscular deficits and diseases such as SMA, as well as for next generation prosthetics, utilizing in vitro phenotypic models would benefit from the development of a functional neuromuscular reflex arc. The neuromuscular reflex arc is the system that integrates the proprioceptive information for muscle length and activity (sensory afferent), to modify motoneuron output to achieve graded muscle contraction (actuation efferent). The sensory portion of the arc is composed of proprioceptive sensory neurons and the muscle spindle, which is embedded in the muscle tissue and composed of intrafusal fibers. The gamma motoneurons (γ-MNs) that innervate these fibers regulate the intrafusal fiber’s stretch so that they retain proper tension and sensitivity during muscle contraction or relaxation. This mechanism is in place to maintain the sensitivity of proprioception during dynamic muscle activity and to prevent muscular damage. In this study, a co-culture system was developed for innervation of intrafusal fibers by human γ-MNs and demonstrated by morphological and immunocytochemical analysis, then validated by functional electrophysiological evaluation. This human-based fusimotor model and its incorporation into the reflex arc allows for a more accurate recapitulation of neuromuscular function for applications in disease investigations, drug discovery, prosthetic design and neuropathic pain investigations.
Reconfigurable Yagi-Uda antenna based on a silicon reflector with a solid-state plasma
Authors: Kim Da-Jin , Park Jang-Soon , Kim Cheol Ho , Hur Jae , Kim Choong-Ki , Cho Young-Kyun , Ko Jun-Bong , Park Bonghyuk , Kim Dongho , Choi Yang-Kyu
Published: December 2017

This paper describes the fabrication and characterization of a reconfigurable Yagi-Uda antenna based on a silicon reflector with a solid-state plasma. The silicon reflector, composed of serially connected p-i-n diodes, forms a highly dense solid-state plasma by injecting electrons and holes into the intrinsic region. When this plasma silicon reflector is turned on, the front-realized gain of the antenna increases by more than 2 dBi beyond 5.3 GHz. To achieve the large gain increment, the structure of the antenna is carefully designed with the aid of semiconductor device simulation and antenna simulation. By using an aluminum nitride (AlN) substrate with high thermal conductivity, self-heating effects from the high forward current in the p-i-n diode are efficiently suppressed. By comparing the antenna simulation data and the measurement data, we estimated the conductivity of the plasma silicon reflector in the on-state to be between 104 and 105 S/m. With these figures, silicon material with its technology is an attractive tunable material for a reconfigurable antenna, which has attracted substantial interest from many areas, such as internet of things (IoT) applications, wireless network security, cognitive radio, and mobile and satellite communications as well as from multiple-input-multiple-output (MIMO) systems.
Numerical value biases sound localization
Authors: Golob Edward J. , Lewald Jörg , Getzmann Stephan , Mock Jeffrey R.
Published: December 2017

Speech recognition starts with representations of basic acoustic perceptual features and ends by categorizing the sound based on long-term memory for word meaning. However, little is known about whether the reverse pattern of lexical influences on basic perception can occur. We tested for a lexical influence on auditory spatial perception by having subjects make spatial judgments of number stimuli. Four experiments used pointing or left/right 2-alternative forced choice tasks to examine perceptual judgments of sound location as a function of digit magnitude (1–9). The main finding was that for stimuli presented near the median plane there was a linear left-to-right bias for localizing smaller-to-larger numbers. At lateral locations there was a central-eccentric location bias in the pointing task, and either a bias restricted to the smaller numbers (left side) or no significant number bias (right side). Prior number location also biased subsequent number judgments towards the opposite side. Findings support a lexical influence on auditory spatial perception, with a linear mapping near midline and more complex relations at lateral locations. Results may reflect coding of dedicated spatial channels, with two representing lateral positions in each hemispace, and the midline area represented by either their overlap or a separate third channel.
The genome sequence of Bipolaris cookei reveals mechanisms of pathogenesis underlying target leaf spot of sorghum
Authors: Zaccaron Alex Z. , Bluhm Burton H.
Published: December 2017

Bipolaris cookei (=Bipolaris sorghicola) causes target leaf spot, one of the most prevalent foliar diseases of sorghum. Little is known about the molecular basis of pathogenesis in B. cookei, in large part due to a paucity of resources for molecular genetics, such as a reference genome. Here, a draft genome sequence of B. cookei was obtained and analyzed. A hybrid assembly strategy utilizing Illumina and Pacific Biosciences sequencing technologies produced a draft nuclear genome of 36.1 Mb, organized into 321 scaffolds with L50 of 31 and N50 of 378 kb, from which 11,189 genes were predicted. Additionally, a finished mitochondrial genome sequence of 135,790 bp was obtained, which contained 75 predicted genes. Comparative genomics revealed that B. cookei possessed substantially fewer carbohydrate-active enzymes and secreted proteins than closely related Bipolaris species. Novel genes involved in secondary metabolism, including genes implicated in ophiobolin biosynthesis, were identified. Among 37 B. cookei genes induced during sorghum infection, one encodes a putative effector with a limited taxonomic distribution among plant pathogenic fungi. The draft genome sequence of B. cookei provided novel insights into target leaf spot of sorghum and is an important resource for future investigation.
A new method to evaluate floodwater for control/use in high-sediment rivers of Northwest China
Authors: Li Xungui
Published: December 2017

Evaluating the quantity of flood season floodwater that is difficult to control or use in rivers with high sediment concentration is an important part of water resource evaluation and floodwater resource utilisation. This study proposes a method coupling water quantity and quality to evaluate such floodwater. The method divides floodwater into floodwater that is difficult to control (‘difficult-controllable’) and floodwater that is controllable but difficult to use (‘controllable but difficult-use’). A case study of the Bajiazui Reservoir in the Jing River in China’s Loess Plateau is presented. The average annual quantity of difficult-controllable floodwater is 10.4 million m3. The annual mean quantity of the difficult-controllable/-use floodwater is 38.1 million m3. The majority of that amount (78.21%) comprised controllable but difficult-use floodwater. An analysis of 64 combinations of factors influencing the quantity of the difficult-controllable/-use floodwater shows that the sediment concentration of run-off is the primary factor influencing the difficult-controllable/-use floodwater. The reservoir’s maximum flood release capacity and floodwater rejection coefficient are the primary factors affecting the difficult-controllable and controllable but difficult-use floodwater, respectively. The new evaluation method is superior to traditional methods and is suitable for evaluating difficult-controllable/-use floodwater in high-sediment rivers.
Voluntary modulation of mental effort investment: an fMRI study
Authors: Khachouf Omar T. , Chen Gang , Duzzi Davide , Porro Carlo A. , Pagnoni Giuseppe
Published: December 2017

Mental effort is a common phenomenological construct deeply linked to volition and self-control. While it is often assumed that the amount of exertion invested in a task can be voluntarily regulated, the neural bases of such faculty and its behavioural effects are yet insufficiently understood. In this study, we investigated how the instructions to execute a demanding cognitive task either “with maximum exertion” or “as relaxed as possible” affected performance and brain activity. The maximum exertion condition, compared to relaxed execution, was associated with speeded motor responses without an accuracy trade-off, and an amplification of both task-related activations in dorsal frontoparietal and cerebellar regions, and task-related deactivations in default mode network (DMN) areas. Furthermore, the visual cue to engage maximum effort triggered an anticipatory widespread increase of activity in attentional, sensory and executive regions, with its peak in the brain stem reticular activating system. Across individuals, this surge of activity in the brain stem, but also in medial wall cortical regions projecting to the adrenal medulla, positively correlated with increases in heart rate, suggesting that the intention to willfully modulate invested effort involves mechanisms related to catecholaminergic transmission and a suppression of DMN activity in favor of externally-directed attentional processes.