bluuebunny/crossref_metadata_2025_split huggingface dataset:
Attosecond soft X-ray high harmonic generation
Authors: Johnson Allan S. , Avni Timur , Larsen Esben W. , Austin Dane R. , Marangos Jon P. 
Published: April 2019

High harmonic generation (HHG) of an intense laser pulse is a highly nonlinear optical phenomenon that provides the only proven source of tabletop attosecond pulses, and it is the key technology in attosecond science. Recent developments in high-intensity infrared lasers have extended HHG beyond its traditional domain of the XUV spectral range (10–150 eV) into the soft X-ray regime (150 eV to 3 keV), allowing the compactness, stability and sub-femtosecond duration of HHG to be combined with the atomic site specificity and electronic/structural sensitivity of X-ray spectroscopy. HHG in the soft X-ray spectral region has significant differences from HHG in the XUV, which necessitate new approaches to generating and characterizing attosecond pulses. Here, we examine the challenges and opportunities of soft X-ray HHG, and we use simulations to examine the optimal generating conditions for the development of high-flux, attosecond-duration pulses in the soft X-ray spectral range.
This article is part of the theme issue ‘Measurement of ultrafast electronic and structural dynamics with X-rays’.
Optical control, selection and analysis of population dynamics in ultrafast protein X-ray crystallography
Authors: Hutchison Christopher D. M. , van Thor Jasper J. 
Published: April 2019

Ultrafast pump-probe X-ray crystallography has now been established at X-ray free electron lasers that operate at hard X-ray energies. We discuss the performance and development of current applications in terms of the available data quality and sensitivity to detect and analyse structural dynamics. A discussion of technical capabilities expected at future high repetition rate applications as well as future non-collinear multi-pulse schemes focuses on the possibility to advance the technique to the practical application of the X-ray crystallographic equivalent of an impulse time-domain Raman measurement of vibrational coherence. Furthermore, we present calculations of the magnitude of population differences and distributions prepared with ultrafast optical pumping of single crystals in the typical serial femtosecond crystallography geometry, which are developed for the general uniaxial and biaxial cases. The results present opportunities for polarization resolved anisotropic X-ray diffraction analysis of photochemical populations for the ultrafast time domain.
This article is part of the theme issue ‘Measurement of ultrafast electronic and structural dynamics with X-rays’.
On the limits of observing motion in time-resolved X-ray scattering
Authors: Ware Matthew R. , Glownia James M. , Natan Adi , Cryan James P. , Bucksbaum Philip H. 
Published: April 2019

Limits on the ability of time-resolved X-ray scattering (TRXS) to observe harmonic motion of amplitude,
A
and frequency,
ω
0
, about an equilibrium position,
R
0
, are considered. Experimental results from a TRXS experiment at the LINAC Coherent Light Source are compared to classical and quantum theories that demonstrate a fundamental limitation on the ability to observe the amplitude of motion. These comparisons demonstrate dual limits on the spatial resolution through
Q
max
and the temporal resolution through
ω
max
for observing the amplitude of motion. In the limit where
ω
max
≈
ω
0
, the smallest observable amplitude of motion is
A
= 2
π
/
Q
max
. In the limit where
ω
max
≥2
ω
0
,
A
≤2
π
/
Q
max
is observable provided there are sufficient statistics.

This article is part of the theme issue ‘Measurement of ultrafast electronic and structural dynamics with X-rays’.
Compounding the disturbance: Family forest owner reactions to invasive forest insects
Authors: Markowski-Lindsay Marla , Borsuk Mark E. , Butler Brett J. , Duveneck Matthew J. , Holt Jonathan , Kittredge David B. , Laflower Danelle , MacLean Meghan Graham , Orwig David , Thompson Jonathan R. 
Published: March 2019

AbstractInvasive forest insect and pathogens (FIP) are having significant, direct, adverse impacts. Interactions between FIPs and forest owners have the potential to create ecosystem impacts that compound direct impacts. We assessed family forest owners’ responses to numerous contingent behavior, FIP-outbreak scenarios in the northeastern U.S. based on FIP outbreak attributes. Sixty-two percent of scenario responses (n=2,752) reflected a harvest intent as a result of FIPs; 84% of respondents (n=688) would consider harvesting in at least one of the four hypothetical scenarios presented to them. Harvest intention increased with greater FIP-related tree mortality and decreased with delayed total tree mortality. Owners with larger holdings, who had previously harvested forest products, and live on their forestland had greater intentions to harvest in response to FIPs. Results suggest that FIPs could transform the regional harvest regime with socio-ecological impacts that are distinct from those caused by FIPs or harvesting alone.
Oriented basement membrane fibrils provide a memory for F-actin planar polarization via the Dystrophin-Dystroglycan complex during tissue elongation
Authors: Campos Fabiana Cerqueira , Dennis Cynthia , Alégot Hervé , Fritsch Cornelia , Isabella Adam , Pouchin Pierre , Bardot Olivier , Horne-Badovinac Sally , Mirouse Vincent 
Published: March 2019

SummaryHow extracellular matrix participates to tissue morphogenesis is still an open question. In theDrosophilaovarian follicle, it has been proposed that after Fat2-dependent planar polarization of the follicle cell basal domain, oriented basement membrane (BM) fibrils and F-actin stress fibers constrain follicle growth, promoting its axial elongation. However, the relationship between BM fibrils and stress fibers and their respective impact on elongation are unclear. We found that Dystroglycan (Dg) and Dystrophin (Dys) are involved in BM fibril deposition. Moreover, they orient stress fibers, by acting locally and in parallel to Fat2. Nonetheless, Dg-Dys complex-mediated cell autonomous control of F-actin fibers orientation relies on the previous BM fibril deposition, indicating two distinct but interdependent functions. Thus, the Dg-Dys complex works as a critical organizer of the epithelial basal domain, regulating both F-actin and BM. Furthermore, BM fibrils act as a persistent cue for the orientation of stress fibers that are the main effector of elongation.
Controlling Heterogeneity and Increasing Titer from Riboswitch-RegulatedBacillus subtilisSpores for Time-Delayed Protein Expression Applications
Authors: Tamiev Denis , Lantz Alyssa , Vezeau Grace , Salis Howard , Reuel Nigel F. 
Published: March 2019

AbstractSporulated cells have potential as time-delayed expression chassis of proteins for applications such as ‘on-demand’ biologics production, whole cell biosensors, or oral vaccines. However, the desired attributes of high expression rates and low product variances are difficult to maintain from germinated spores. In this work we study the effect of an integratingvs.theta replicating plasmid in a wild-typeBacillus subtilisand two PolY mutants. The cells were engineered to produce a fluorescent reporter protein (RFP) under the control of a riboswitch activated by theophylline. This allowed for greater sensitivity to point mutations. The fluorescence and cell growth curves were fit with a custom kinetic model and a peak kinetic rate (LKPmax) was extracted for each clonal population (n = 30 for all cell, vector, and growth combinations). Plasmid based expression yields higher (8.7x) expression rates due to an increased copy number of the expression cassette (10x over integrated). The variance of LKPmaxvalues increased 2.07x after sporulation for the wild type strain. This increase in variance from sporulation is very similar to what is observed with UV exposure. This effect can be partially mitigated by the use of PolY knockouts observed in suspended cell growths and adherent biofilms.
A toolset of constitutive promoters for metabolic engineering ofRhodosporidium toruloides
Authors: Nora Luísa Czamanski , Wehrs Maren , Kim Joonhoon , Cheng Jan-Fang , Tarver Angela , Simmons Blake A. , Magnuson Jon , Harmon-Smith Miranda , Silva-Rocha Rafael , Gladden John M. , Mukhopadhyay Aindrila , Skerker Jeffrey M. , Kirby James 
Published: March 2019

ABSTRACTBackgroundRhodosporidium toruloidesis a promising host for the production of bioproducts from lignocellulosic biomass. A key prerequisite for efficient pathway engineering is the availability of robust genetic tools and resources. However, there is a lack of characterized promoters to drive expression of heterologous genes for strain engineering inR. toruloides.ResultsOur data describes a set of nativeR. toruloidespromoters, characterized over time in four different media commonly used for cultivation of this yeast. The promoter sequences were selected using transcriptional analysis and several of them were found to drive expression bidirectionally. We measured promoter expression strength by flow cytometry using a dual fluorescent reporter system. From these analyses, we found a total of 20 constitutive promoters (12 monodirectional and 8 bidirectional) of potential value for genetic engineering ofR. toruloides.ConclusionsWe present a list of robust and constitutive, native promoters to facilitate genetic engineering ofR. toruloides.This set of thoroughly characterized promoters significantly expands the range of engineering tools available for this yeast and can be applied in future metabolic engineering studies.
Immortalization of different breast epithelial cell types results in distinct mitochondrial mutagenesis
Authors: Kwon Sujin , Kim Susan S. , Nebeck Howard E. , Ahn Eun Hyun 
Published: March 2019

AbstractDifferent phenotypes of normal cells might influence genetic profiles, epigenetic profiles, and tumorigenicities of their transformed derivatives. In this study, we investigated whether the whole mitochondrial genome of immortalized cells can be attributed to different phenotypes (stem vs non-stem) of their normal epithelial cell originators. To accurately determine mutations, we employed Duplex Sequencing, which exhibits the lowest error rates among currently available DNA sequencing methods. Our results indicate that the vast majority of observed mutations of the whole mitochondrial DNA occur at low-frequency (rare mutations). The most prevalent rare mutation types are C→T/G→A and A→G/T→C transitions. Frequencies and spectra of homoplasmic point mutations are virtually identical between stem cell-derived immortalized (SV1) cells and non-stem cell-derived immortalized (SV22) cells, verifying that both cell types were derived from the same woman. However, frequencies of rare point mutations are significantly lower in SV1 cells (5.79×10-5) than in SV22 cells (1.16×10-4). Additionally, the predicted pathogenicity for rare mutations in the mitochondrial tRNA genes is significantly lower (by 2.5-fold) in SV1 cells than in SV22 cells. Our findings suggest that the immortalization of normal cells with stem cell features leads to decreased mitochondrial mutagenesis, particularly in noncoding RNA regions. The mutation spectra and mutations specific to stem cell-derived immortalized cells (vs non-stem cell derived) have implications in characterizing heterogeneity of tumors and understanding the role of mitochondrial mutations in immortalization and transformation of human cells.
Mitochondrial dynamics and mitophagy are necessary for proper invasive growth in Rice Blast
Authors: Kou Yanjun , He Yunlong , Qiu Jiehua , Yazhou Shu , Yang Fan , Deng YiZhen , Naqvi Naweed I. 
Published: March 2019

SUMMARYMagnaporthe oryzaecauses Blast disease, which is one of the most devastating infections in rice and several important cereal crops.M. oryzaeneeds to coordinate gene regulation, morphological changes, nutrient acquisition, and host evasion, in order to invade and proliferate within the plant tissues. Thus far, the molecular mechanisms underlying the regulation of invasive growthin plantahave remained largely unknown. We identified a precise filamentous-punctate-filamentous cycle in mitochondrial morphology duringMagnaporthe-Rice interaction. Interestingly, loss of either the mitochondrial fusion (MoFzo1) or fission (MoDnm1) machinery, or inhibition of mitochondrial fission using Mdivi-1 caused significant reduction inM. oryzaepathogenicity. Furthermore, exogenous carbon source(s) but not antioxidant treatment delayed such mitochondrial dynamics/transition during invasive growth. Such nutrient-based regulation of organellar dynamics preceded MoAtg24-mediated mitophagy, which was found to be essential for proper biotrophic development and invasive growthin planta. We propose that precise mitochondrial dynamics and mitophagy occur during the transition from biotrophy to necrotrophy, and are required for proper induction and establishment of the blast disease in rice.
Ultrasound- and microbubble-mediated targeted delivery of therapeutic microRNA-loaded nanocarriers to deep liver and kidney tissues in pigs
Authors: Di Ianni Tommaso , Bose Rajendran J.C. , Sukumar Uday K. , Bachawal Sunitha , Wang Huaijun , Telichko Arsenii , Herickhoff Carl D. , Robinson Elise , Baker Sam , Vilches-Moure José G. , Felt Stephen A. , Gambhir Sanjiv S. , Paulmurugan Ramasamy , Dahl Jeremy D. 
Published: March 2019

AbstractIn this study, we designed and validated a platform for ultrasound (US) and microbubble (MB)-mediated delivery of FDA-approved pegylated poly lactic-co-glycolic acid (PLGA) nanoparticles (NPs) loaded with anticancer microRNAs (miRNAs) to deep tissues in a pig model. Small RNAs have the ability to reprogram tumor cells and sensitize them to clinically used chemotherapy. However, to overcome their short intravascular circulation half-life and achieve controlled and sustained release into tumor cells, anticancer miRNAs need to be encapsulated into NPs. Moreover, focused US combined with gas-filled MBs provides a safe and noninvasive way to improve the permeability of tumor vasculature and increase the delivery efficiency of drug-loaded nanocarriers. A single handheld, curvilinear US array was used in this study for image-guidance and therapy with clinical-grade SonoVue MBs. First, we validated the platform on phantoms to optimize the MB cavitation dose based on acoustic parameters, including peak negative pressure, pulse length, and pulse repetition frequency. We then tested the system in vivo by delivering PLGA-NPs co-loaded with antisense-miRNA-21 and antisense-miRNA-10b in pig liver and kidney. Enhanced miRNA delivery was observed (1.9- to 3.7-fold increase) as a result of the US-MB treatment compared to untreated control regions. Additionally, we used highly fluorescent semiconducting polymer nanoparticles (SPNs) co-delivered with miRNA-loaded PLGA-NPs to visually assess NP delivery. Fluorescent microscopy of SPNs confirmed NP extravasation and showed the presence of particles in the extravascular compartment. Hematoxylin and eosin staining of treated tissues did not reveal tissue damage. The results presented in this manuscript suggest that enhanced delivery of miRNA-loaded NPs to target regions in deep organs is feasible in large animal models using the proposed platform.
Single cell transcriptomics identifies master regulators of neurodegeneration in SOD1 ALS motor neurons
Authors: Namboori Seema C. , Thomas Patricia , Ames Ryan , Hawkins Sophie , Garrett Lawrence O. , Willis Craig R. G. , Rosa Alessandro , Stanton Lawrence W. , Bhinge Akshay 
Published: March 2019

AbstractBackgroundBulk RNA-Seq has been extensively utilized to investigate the molecular changes accompanying motor neuron degeneration in Amyotrophic Lateral Sclerosis (ALS). However, due to the heterogeneity and degenerating phenotype of the neurons, it has proved difficult to assign specific changes to neuronal subtypes and identify which factors drive these changes. Consequently, we have utilized single cell transcriptomics of degenerating motor neurons derived from ALS patients to uncover key transcriptional drivers of dysfunctional pathways.ResultsSingle cell analysis of spinal neuronal cultures derived from SOD1 E100G ALS and isogenic iPSCs allowed us to classify cells into neural subtypes including motor neurons and interneurons. Differential expression analysis between disease and control motor neurons revealed downregulation of genes involved in synaptic structure, neuronal cytoskeleton, mitochondrial function and autophagy. Interestingly, interneurons did not show similar suppression of these homeostatic functions. Single cell expression data enabled us to derive a context-specific transcriptional network relevant to ALS neurons. Master regulator analysis based on this network identified core transcriptional factors driving the ALS MN gene dysregulation. Specifically, we identified activation of SMAD2, a downstream mediator of the TGF-β signalling pathway as a potential driving factor of ALS motor neuron degeneration. Our phenotypic analysis further confirmed that an activated TGF-β signalling is major driver of motor neuron loss in SOD1 ALS. Importantly, expression analysis of TGFβ target genes and computational analysis of publicly available datasets indicates that activation of TGFβ signalling may be a common mechanism shared between SOD1, FUS and sporadic ALS.ConclusionsOur results demonstrate the utility of single cell transcriptomics in mapping disease-relevant gene regulatory networks driving neurodegeneration in ALS motor neurons. We find that ALS-associated mutant SOD1 targets transcriptional networks that perturb motor neuron homeostasis.
Multi-Trait Improvement by Predicting Genetic Correlations in Breeding Crosses
Authors: Neyhart Jeffrey L. , Lorenz Aaron J. , Smith Kevin P. 
Published: March 2019

ABSTRACTThe many quantitative traits of interest to plant breeders are often genetically correlated, which can complicate progress from selection. Improving multiple traits may be enhanced by identifying parent combinations – an important breeding step – that will deliver more favorable genetic correlations (rG). Modeling the segregation of genomewide markers with estimated effects may be one method of predictingrGin a cross, but this approach remains untested. Our objectives were to: (i) use simulations to assess the accuracy of genomewide predictions ofrGand the long-term response to selection when selecting crosses on the basis of such predictions; and (ii) empirically measure the ability to predict genetic correlations using data from a barley (Hordeum vulgareL.) breeding program. Using simulations, we found that the accuracy to predictrGwas generally moderate and influenced by trait heritability, population size, and genetic correlation architecture (i.e. pleiotropy or linkage disequilibrium). Among 26 barley breeding populations, the empirical prediction accuracy ofrGwas low (−0.012) to moderate (0.42), depending on trait complexity. Within a simulated plant breeding program employing indirect selection, choosing crosses based on predictedrGincreased multi-trait genetic gain by 11-27% compared to selection on the predicted cross mean. Importantly, when the starting genetic correlation was negative, such cross selection mitigated or prevented an unfavorable response in the trait under indirect selection. Prioritizing crosses based on predicted genetic correlation can be a feasible and effective method of improving unfavorably correlated traits in breeding programs.
Urban ecology of arboviral mosquito vectors along the Kenyan coast
Authors: Karisa Jonathan , Muriu Simon , Omuoyo Donwilliams , Karia Boniface , Nyamwaya Doris , Rono Martin , Warimwe George , Mwangangi Joseph , Mbogo Charles 
Published: March 2019

ABSTRACTBackgroundThe emergence and re-emergence of arboviral infections particularly Chikungunya, dengue hemorrhagic fever, rift valley fever, and yellow fever in humans around the world threatens global health and security. The purpose of this study was to determine the urban ecology of the common arboviral mosquito vectors in urban Coastal Kenya areas.Materials and MethodsThe current study was conducted in urban settings of Kilifi and Mombasa counties in coastal Kenya in 2016 to 2017. Adult mosquitoes were collected both indoors and outdoors by CDC light traps and BG-Sentinel traps respectively. All blood fed mosquitoes were tested for blood meal sources by an Enzyme Linked Immunosorbent Assay (ELISA). Mosquito larvae were collected using standard dippers and pipettes. Egg survivorship in dry soil was evaluated by collecting of soil samples from dry potential breeding habitats, watering them for hatching and rearing of the eventual larvae to adults. Mosquitoes were screened forFlavivirus, Alphavirus,andPhlebovirusarboviruses using Reverse Transcriptase quantitative Polymerase Chain Reaction (RT qPCR).ResultsA total of 3,264 adult mosquitoes belonging to ten species ofCulex, AedesandAnopheleswere collected. Overall, the predominant species wereCx. quinquefasciatus72.4% (n=2,364) andAe. aegypti,25.7%, (n=838). A total of 415 breeding habitat types were identified indoors (n=317) and outdoors (n=98). The most productive habitat types in both indoors and outdoors were: assorted small containers, water tanks, drainages, drums and jericans. Overall, 62% (n=18) of the soil samples collected from the two sites (Kilifi and Malindi) were positive for larvae which were used as proxy to measure the presence of eggs. The mosquitoes had high preference for human blood (29.81%) and chicken (3.73%) but none had fed on either goat or bovine. Of 259 mosquitoes tested for viral infection, 11.6% were positive forflavivirusonly.ConclusionDomestic and peri-domestic containers were identified to be the key breeding areas of arboviral vectors. Therefore, efforts should be put in place targeting the productive habitat types.
Chronic corticosterone administration induces negative valence and impairs positive valence behaviors in mice
Authors: Dieterich Andrew , Srivastava Prachi , Sharif Aitesam , Stech Karina , Samuels Benjamin A. 
Published: March 2019

AbstractBehavioral approaches utilizing rodents to study mood disorders have focused primarily on negative valence behaviors associated with potential threat (anxiety). However, for disorders such as depression, positive valence behaviors that assess reward processing may be more translationally-valid and predictive of antidepressant treatment outcome. Chronic corticosterone (CORT) administration is a well-validated pharmacological stressor that increases negative valence behaviors (David et al., 2009; Gourley et al., 2008a,b; Gourley et al., 2012; Olausson et al., 2013). However, whether chronic stress paradigms such as CORT administration also lead to deficits in positive valence behaviors remains unclear. We treated male C57BL/6J mice with chronic CORT and assessed both negative and positive valence behaviors. We found that CORT induced negative valence behaviors associated with anxiety in the open field and NSF. Interestingly, CORT also impaired instrumental acquisition, reduced sensitivity to a devalued outcome, reduced breakpoint in progressive ratio, and impaired performance in probabilistic reversal learning. Taken together, these results demonstrate that chronic CORT administration at the same dosage both induces negative valence behaviors associated with anxiety and impairs positive valence behaviors associated with reward processing. These data suggest that CORT administration is a useful experimental system for preclinical approaches to studying stress-induced mood disorders.Significance StatementChronic exposure to stress can precipitate mood disorders such as anxiety and depression. However, most studies focus on the effects of chronic stress on increasing negative affect behaviors. Elucidating how chronic stress impacts translationally-valid positive valence behaviors is less studied. Here, we show that chronic pharmacological stress induces negative affect behaviors associates with anxiety and impairs reward-related, positive valence behaviors in mice.