bluuebunny/crossref_metadata_2025 huggingface dataset:
Tn
6450
, a Novel Multidrug Resistance Transposon Characterized in a Proteus mirabilis Isolate from Chicken in China
Authors: Chen Yan-Peng , Lei Chang-Wei , Kong Ling-Han , Zeng Jin-Xin , Zhang Xiu-Zhong , Liu Bi-Hui , Li Yi , Xiang Rong , Wang Yong-Xiang , Chen Dan-Yu , Zhang An-Yun , Wang Hong-Ning
Published: January 2018

A novel 65.8-kb multidrug resistance transposon, designated Tn
6450
, was characterized in a
Proteus mirabilis
isolate from chicken in China. Tn
6450
contains 18 different antimicrobial resistance genes, including cephalosporinase gene
bla
DHA-1
and fluoroquinolone resistance genes
qnrA1
and
aac(6
′
)-Ib-cr
. It carries a class 1/2 hybrid integron composed of
intI2
and a 3′ conserved segment of the class 1 integron. Tn
6450
is derived from Tn
7
via acquisition of new mobile elements and resistance genes.
Trypanosoma cruzi Produces the Specialized Proresolving Mediators Resolvin D1, Resolvin D5, and Resolvin E2
Authors: Colas Romain A. , Ashton Anthony W. , Mukherjee Shankar , Dalli Jesmond , Akide-Ndunge Oscar B. , Huang Huan , Desruisseaux Mahalia S. , Guan Fangxia , Jelicks Linda A. , Matos dos Santos Fabiane , Nagajyothi Jyothi , Zingman Michael A. , Reyes Jinet , Weiss Louis M. , Serhan Charles N. , Tanowitz Herbert B.
Published: January 2018

Trypanosoma cruzi
is a protozoan parasite that causes Chagas disease (CD). CD is a persistent, lifelong infection affecting many organs, most notably the heart, where it may result in acute myocarditis and chronic cardiomyopathy. The pathological features include myocardial inflammation and fibrosis. In the Brazil strain-infected CD-1 mouse, which recapitulates many of the features of human infection, we found increased plasma levels of resolvin D1 (RvD1), a specialized proresolving mediator of inflammation, during both the acute and chronic phases of infection (>100 days postinfection) as determined by enzyme-linked immunosorbent assay (ELISA). Additionally, ELISA on lysates of trypomastigotes of both strains Tulahuen and Brazil revealed elevated levels of RvD1 compared with lysates of cultured epimastigotes of
T. cruzi
, tachyzoites of
Toxoplasma gondii
, trypomastigotes of
Trypanosoma brucei
, cultured L
6
E
9
myoblasts, and culture medium containing no cells. Lysates of
T. cruzi
-infected myoblasts also displayed increased levels of RvD1. Lipid mediator metabolomics confirmed that the trypomastigotes of
T. cruzi
produced RvD1, RvD5, and RvE2, which have been demonstrated to modulate the host response to bacterial infections. Plasma RvD1 levels may be both host and parasite derived. Since
T. cruzi
synthesizes specialized proresolving mediators of inflammation, as well as proinflammatory eicosanoids, such as thromboxane A
2
, one may speculate that by using these lipid mediators to modulate its microenvironment, the parasite is able to survive.
Bacteriophages of the Urinary Microbiome
Authors: Miller-Ensminger Taylor , Garretto Andrea , Brenner Jonathon , Thomas-White Krystal , Zambom Adriano , Wolfe Alan J. , Putonti Catherine
Published: January 2018

Bacterial viruses (bacteriophages) play a significant role in microbial community dynamics. Within the human gastrointestinal tract, for instance, associations among bacteriophages (phages), microbiota stability, and human health have been discovered. In contrast to the gastrointestinal tract, the phages associated with the urinary microbiota are largely unknown. Preliminary metagenomic surveys of the urinary virome indicate a rich diversity of novel lytic phage sequences at an abundance far outnumbering that of eukaryotic viruses. These surveys, however, exclude the lysogenic phages residing within the bacteria of the bladder. To characterize this phage population, we examined 181 genomes representative of the phylogenetic diversity of bacterial species within the female urinary microbiota and found 457 phage sequences, 226 of which were predicted with high confidence. Phages were prevalent within the bladder bacteria: 86% of the genomes examined contained at least one phage sequence. Most of these phages are novel, exhibiting no discernible sequence homology to sequences in public data repositories. The presence of phages with substantial sequence similarity within the microbiota of different women supports the existence of a core community of phages within the bladder. Furthermore, the observed variation between the phage populations of women with and without overactive bladder symptoms suggests that phages may contribute to urinary health. To complement our bioinformatic analyses, viable phages were cultivated from the bacterial isolates for characterization; a novel coliphage was isolated, which is obligately lytic in the laboratory strain
Escherichia coli
C. Sequencing of bacterial genomes facilitates a comprehensive cataloguing of the urinary virome and reveals phage-host interactions.

IMPORTANCE
Bacteriophages are abundant within the human body. However, while some niches have been well surveyed, the phage population within the urinary microbiome is largely unknown. Our study is the first survey of the lysogenic phage population within the urinary microbiota. Most notably, the abundance of prophage exceeds that of the bacteria. Furthermore, many of the prophage sequences identified exhibited no recognizable sequence homology to sequences in data repositories. This suggests a rich diversity of uncharacterized phage species present in the bladder. Additionally, we observed a variation in the abundances of phages between bacteria isolated from asymptomatic “healthy” individuals and those with urinary symptoms, thus suggesting that, like phages within the gut, phages within the bladder may contribute to urinary health.
An Autoimmune Disease-Associated Risk Variant in the
TNFAIP3
Gene Plays a Protective Role in Brucellosis That Is Mediated by the NF-κB Signaling Pathway
Authors: Lou Lixin , Bao Wanguo , Liu Xianjun , Song Hongxiao , Wang Yang , Zhang Kaiyu , Gao Wenjing , Li Haijun , Tu Zhengkun , Wang Shaofeng
Published: January 2018

Naturally occurring functional variants (rs148314165 and rs200820567, collectively referred to as TT>A) reduce the expression of the tumor necrosis factor alpha-induced protein 3 (
TNFAIP3
) gene, a negative regulator of NF-κB signaling, and predispose individuals to autoimmune disease. In this analysis, we conducted a genetic association study of the TT>A variants in 1,209 controls and 150 patients with brucellosis, an infectious disease, and further assessed the role of the variants in brucellosis. Our data demonstrated that the TT>A variants were correlated with cases of brucellosis (
P
= 0.002; odds ratio [OR] = 0.34) and with individuals who had a positive serum agglutination test (SAT) result (titer of >1/160) (
P
= 4.2 × 10
−6
; OR = 0.23). A functional study demonstrated that brucellosis patients carrying the protective allele (A) showed significantly lower expression levels of the TNFAIP3 gene in their peripheral blood mononuclear cells and showed increased NF-κB signaling. Monocytes from individuals carrying the A allele that were stimulated with
Brucella abortus
had lower mRNA levels of TNFAIP3 and produced more interleukin-10 (IL-10), IL-6, and IL-1β than those from TT allele carriers. These data showed that autoimmune disease-associated risk variants, TT>A, of the TNFAIP3 locus play a protective role in the pathogenesis of brucellosis. Our findings suggest that a disruption of the normal function of the TNFAIP3 gene might serve as a therapeutic target for the treatment of brucellosis.
Advancing Our Understanding of Protective Maternal Immunity as a Guide for Development of Vaccines To Reduce Congenital Cytomegalovirus Infections
Authors: Permar Sallie R. , Schleiss Mark R. , Plotkin Stanley A.
Published: January 2018

Human cytomegalovirus (HCMV) is the most common congenitally transmitted pathogen worldwide, impacting an estimated 1 million newborns annually. Congenital HCMV (cCMV) infection is a major global contributor to long-term neurologic deficits, including deafness, microcephaly, and neurodevelopmental delay, as well as to fetal loss and occasional infant mortality. Accordingly, design of a maternal vaccine to prevent cCMV continues to be a top public health priority. Nevertheless, we remain without a licensed vaccine. Maternal immunity provides partial protection, as the risk of vertical HCMV transmission from chronically infected mothers is reduced compared to settings in which the mother is newly infected during pregnancy. Therefore, an understanding of the maternal immune correlates of protection against cCMV is critical to informing design of an efficacious maternal vaccine. Although vaccine development is being assiduously pursued by a large number of pharmaceutical manufacturers, biotechnology organizations, and academic researchers, some pessimism has been expressed regarding the issue of whether a vaccine to protect against cCMV is possible. This pessimism is based on observations that natural immunity is not completely protective against maternal reinfection and congenital transmission. However, we assert that optimism regarding vaccine development is indeed justified, on the basis of accruing evidence of immune correlates of protection—readily achievable by vaccination—that are associated with reduced transmission of HCMV to the fetus in seronegative women. In light of the substantial burden on society conferred by cCMV infection, even a modest reduction in the occurrence of this fetal disease is an important public health goal and justifies aggressive clinical evaluation of vaccines currently in the pipeline.
Identification of Poxvirus Genome Uncoating and DNA Replication Factors with Mutually Redundant Roles
Authors: Liu Baoming , Panda Debasis , Mendez-Rios Jorge D. , Ganesan Sundar , Wyatt Linda S. , Moss Bernard
Published: January 2018

Genome uncoating is essential for replication of most viruses. For poxviruses, the process is divided into two stages: removal of the envelope, allowing early gene expression, and breaching of the core wall, allowing DNA release, replication, and late gene expression. Subsequent studies showed that the host proteasome and the viral D5 protein, which has an essential role in DNA replication, are required for vaccinia virus (VACV) genome uncoating. In a search for additional VACV uncoating proteins, we noted a report that described a defect in DNA replication and late expression when the gene encoding a 68-kDa ankyrin repeat/F-box protein (68k-ank), associated with the cellular SCF (Skp1, cullin1, F-box-containing complex) ubiquitin ligase complex, was deleted from the attenuated modified vaccinia virus Ankara (MVA). Here we showed that the 68k-ank deletion mutant exhibited diminished genome uncoating, formation of DNA prereplication sites, and degradation of viral cores as well as an additional, independent defect in DNA synthesis. Deletion of the 68k-ank homolog of VACV strain WR, however, was without effect, suggesting the existence of compensating genes. By inserting VACV genes into an MVA 68k-ank deletion mutant, we discovered that M2, a member of the poxvirus immune evasion (PIE) domain superfamily and a regulator of NF-κB, and C5, a member of the BTB/Kelch superfamily associated with cullin-3-based ligase complexes, independently rescued the 68k-ank deletion phenotype. Thus, poxvirus uncoating and DNA replication are intertwined processes involving at least three viral proteins with mutually redundant functions in addition to D5.

IMPORTANCE
Poxviruses comprise a family of large DNA viruses that infect vertebrates and invertebrates and cause diseases of medical and zoological importance. Poxviruses, unlike most other DNA viruses, replicate in the cytoplasm, and their large genomes usually encode 200 or more proteins with diverse functions. About 90 genes may be essential for chordopoxvirus replication based either on their conservation or individual gene deletion studies. However, this number may underestimate the true number of essential functions because of redundancy. Here we show that any one of three seemingly unrelated and individually nonessential proteins is required for the incompletely understood processes of genome uncoating and DNA replication, an example of synthetic lethality. Thus, poxviruses appear to have a complex genetic interaction network that has not been fully appreciated and which will require multifactor deletion screens to assess.
Tracking brain damage in progressive supranuclear palsy: a longitudinal MRI study
Authors: Agosta Federica , Caso Francesca , Ječmenica-Lukić Milica , Petrović Igor N , Valsasina Paola , Meani Alessandro , Copetti Massimiliano , Kostić Vladimir S , Filippi Massimo
Published: January 2018

Objectives

In this prospective, longitudinal, multiparametric MRI study, we investigated clinical as well as brain grey matter and white matter (WM) regional changes in patients with progressive supranuclear palsy-Richardson’s syndrome (PSP-RS).

Methods

Twenty-one patients with PSP-RS were evaluated at baseline relative to 36 healthy controls and after a mean follow-up of 1.4 years with clinical rating scales, neuropsychological tests and MRI scans.

Results

Relative to controls, patients with PSP-RS showed at baseline a typical pattern of brain damage, including midbrain atrophy, frontal cortical thinning and widespread WM involvement of the main infratentorial and supratentorial tracts that exceeded cortical damage. Longitudinal study showed that PSP-RS exhibited no further changes in cortical thinning, which remained relatively focal, while midbrain atrophy and WM damage significantly progressed. Corpus callosum and frontal WM tract changes correlated with the progression of both disease severity and behavioural dysfunction.

Conclusions

This study demonstrated the feasibility of carrying out longitudinal diffusion tensor MRI in patients with PSP-RS and its sensitivity to identifying the progression of pathology. Longitudinal midbrain volume loss and WM changes are associated with PSP disease course.
Spatial linkages between geomorphic and hydraulic conditions and invertebrate drift characteristics in a small mountain stream
Authors: Cienciala Piotr , Hassan Marwan A.
Published: January 2018

Although invertebrate drift plays a fundamental role in river ecosystems, spatial linkages between its characteristics and hydrogeomorphic conditions remain poorly understood. This study, conducted in a small stream in British Columbia, provides insight into such relationships. Most notably, drift concentration was positively correlated with bed scour, and mean body size was negatively correlated with bed fill. Although correlational design precludes inference regarding mechanisms, these results are consistent with protracted effects of flood-related bed disturbances on spatial pattern of drift characteristics under low flow conditions. We detected no robust associations between drift and flow characteristics that could not be explained by bed disturbances. Because of high spatial variability, drift characteristics were statistically distinct only in few habitat types. Compared with middepth, invertebrate drift concentration was higher near water surface, and mean body size was larger near the bed. Mean body size was also statistically smaller in riffle–pool transitions, which experienced largest bed fill. Possible legacy effects of bed disturbances could have broader implications for drift-related energy and nutrient fluxes in river corridors and for quantitative drift models.
Living on a catfish: nested occupation of ectosymbiotic chironomids on host body
Authors: Dala-Corte Renato B. , Melo Adriano S.
Published: January 2018

Symbiotic species often have preferential attachment sites on their host body and thus some sites may only be occupied if the supposed best sites are already occupied. Alternatively, colonization may be similar in all sites, but removal may differ among them. Both mechanisms might generate a nested pattern. Moreover, the host size can alter the quality of the site for symbiotic occupation; for instance, by increasing the area and anchorage structures or reducing removal. We predicted that the spatial distribution of the ectosymbiotic chironomid Ichthyocladius lilianae Mendes, Andersen and Sæther, 2004 on their host, the armored catfish Pareiorhaphis hypselurus (Pereira and Reis, 2002), would present a nested pattern with regards to body-part preference and variation according to host size. We found that (i) suboptimal sites on the host body were usually only occupied by a symbiont when the optimal sites were already occupied and (ii) sites occupied by larvae on small host body surface were a subset of the sites occupied on large hosts. Our results indicate a nested distribution, yet the mechanisms generating this pattern are unclear. One possibility is that symbionts have preferential sites for attachment on the host body surface and compete for these sites. As an alternative, symbionts may present no preference and colonize equally all sites, but they remain attached to sites that offer better resources or protection from removal.
Impacts of hypoxia on estuarine macroinvertebrate assemblages across a regional nutrient gradient
Authors: Coffin Michael R.S. , Courtenay Simon C. , Knysh Kyle M. , Pater Christina C. , van den Heuvel Michael R.
Published: January 2018

In this study, we examined the effects of dissolved oxygen, via metrics based on hourly measurements, and other environmental variables on invertebrate assemblages in estuaries spanning a gradient of nutrient loading and geography in the southern Gulf of St. Lawrence, Canada. Upper areas (15–25 practical salinity units (PSU)) of 13 estuaries that were dominated by either seagrass ( Zostera marina Linnaeus, 1753) or macroalgae ( Ulva spp. Linnaeus, 1753) were sampled from June to September 2013. Macroinvertebrate assemblages from Z. marina were found to be distinct from Ulva assemblages for both epifauna and infauna. Small snails dominated each vegetation type, specifically cerithids in Z. marina and hydrobids in Ulva. Although Z. marina had higher species richness, approximately 70% of species were common to both habitats. Faunal communities differed among estuaries with large, within-estuary, temporal variance only observed at Ulva sites impacted by hypoxia and particularly at sites with long water residence time. Indeed, abundances varied by several orders of magnitude in Ulva ranging from zero to thousands of macroinvertebrates. There was a strong negative correlation between hypoxic or anoxic water, 48 h prior to sampling, with relative abundances of amphipods, and a positive correlation with the relative abundances of snails. As one of the first studies to use high-frequency oxygen monitoring, this study revealed probable impacts and the transient nature of hypoxia in eutrophication.
A Multi-Fidelity Model Approach for Simultaneous Scheduling of Machines and Vehicles in Flexible Manufacturing Systems
Authors: Lin James T. , Chiu Chun-Chih , Huang Edward , Chen Hung-Ming
Published: January 2018

Driven by sensor technologies and Internet of Things, massive real-time data from highly interconnected devices are available, which enables the improvement of decision-making quality. Scheduling of such production systems can be challenging as it must incorporate the latest data and be able to re-plan quickly. In this research, a multi-fidelity model for simultaneous scheduling problem of machines and vehicles at flexible manufacturing system has been proposed. In order to improve the computational efficiency, we extend the framework, called multi-fidelity optimization with ordinal transformation and optimal sampling, with combining with the K-means method. The proposed framework enables the benefits of both fast and inexpensive low-fidelity models with accurate but more expensive high-fidelity models. Results show that this approach can significantly decrease computational cost compared with other algorithms in the literature.
Editorial to the Special Issue Information Integration for Innovative Design and Smart Manufacturing
Authors: Peruzzini Margherita , Stjepandić Josip
Published: January 2018

Information integration is one of the key features to foster innovative design approaches and to enable smart manufacturing in modern companies. Future manufacturing will be more automated, more digitalized, but also more flexible, distributed, networked and collaborative. As a consequence, information integration approaches are necessary to support companies to be innovative and profitable. The issue collects valuable examples of how collaborative approaches and interdisciplinary actions can benefit companies, from new idea co-creation to smart enterprise management, from intelligent data analysis to flexible decision-making, from smart management of business relationships to reconfigurable manufacturing automation.
Prolonged dynamic support from the Icelandic plume of the NE Atlantic margin
Authors: Hardman Jonathon P. A. , Schofield Nick , Jolley David W. , Holford Simon P. , Hartley Adrian J. , Morse Stephen , Underhill John R. , Watson Douglas A. , Zimmer Eva H.
Published: January 2018

Sedimentary basins affected by hotspots often contain records of uplift and subsidence within coeval stratigraphic successions. The subsidence history can contain measurable perturbations in ancient palaeogeographies that can help constrain the duration of dynamic support. At
c.
56 Ma the NE Atlantic experienced uplift related to the Iceland mantle plume. Within the Faroe–Shetland Basin, we document the stratigraphic record of subsidence following plume uplift, through integration of regional seismic datasets and well data. Subsidence following plume uplift is recorded by mapping the southward migration of palaeocoastlines throughout the early Eocene of the Faroe–Shetland Basin. We find that after initial uplift over 0.5 myr, subsidence was inhibited for 0.45 myr. Coeval with initiation of rifting in the North Atlantic, at 54.9 Ma, a
c.
0.9 myr period of accelerated subsidence occurred, recorded by migration of the coastline by
c.
80 km inland. We attribute these events to a prolonged period (2 myr) of dynamic support from the Iceland plume terminated by rapid loss of dynamic support coeval with rifting in the NE Atlantic at 54.9 Ma. Our results suggest that palaeogeographical analysis is a powerful tool in constraining the duration of dynamic support in basins affected by mantle plumes.
The provenance of the Devonian Old Red Sandstone of the Dingle Peninsula, SW Ireland; the earliest record of Laurentian and peri-Gondwanan sediment mixing in Ireland
Authors: Fairey Brenton J. , Kerrison Aidan , Meere Patrick A. , Mulchrone Kieran F. , Hofmann Mandy , Gärtner Andreas , Sonntag Benita-Lisette , Linnemann Ulf , Kuiper Klaudia F. , Ennis Meg , Mark Chris , Cogné Nathan , Chew David
Published: January 2018

The Lower Old Red Sandstone in southern Ireland is hosted in the Early Devonian Dingle Basin, which lies immediately south of the Iapetus Suture on the Dingle Peninsula, County Kerry. The basin developed as a post-Caledonian pull-apart structure prior to Acadian deformation, which in turn was followed by end-Carboniferous Variscan deformation. Detrital zircon U–Th–Pb geochronology is complemented by mica Ar–Ar and apatite U–Pb geochronology to gain a comprehensive understanding of the provenance of the Lower Devonian Lower Old Red Sandstone of the Dingle Basin and assess contributions of major tectonic components (e.g. Laurentia, Ganderia). Sedimentary rocks in the Lower Old Red Sandstone have similar detrital zircon age distributions, which are dominated by
c.
1.2 Ga zircons as well as late Neoproterozoic grains. This indicates a dominant contribution of detritus of Laurentian affinity as well as contributions from westerly and southerly derived Ganderian detritus. Caledonian uplift of the area north of the Iapetus Suture would have facilitated a large contribution of (peri-)Laurentian material. The Upper Old Red Sandstone on the Dingle Peninsula has a distinctly different detrital zircon character including few late Neoproterozoic zircons and abundant zircons of
c.
1.05 Ga age, indicating sediment derivation only from Laurentia and no recycling from the Lower Old Red Sandstone.

Supplementary material:
The full detrital U–Pb zircon and apatite analytical dataset and the revised detrital mica age dataset are available at
https://doi.org/10.6084/m9.figshare.c.3971862
GeoBurst+
Authors: Zhang Chao , Lei Dongming , Yuan Quan , Zhuang Honglei , Kaplan Lance , Wang Shaowen , Han Jiawei
Published: January 2018

The real-time discovery of local events (e.g., protests, disasters) has been widely recognized as a fundamental socioeconomic task. Recent studies have demonstrated that the geo-tagged tweet stream serves as an unprecedentedly valuable source for local event detection. Nevertheless, how to effectively extract local events from massive geo-tagged tweet streams in real time remains challenging. To bridge the gap, we propose a method for effective and real-time local event detection from geo-tagged tweet streams. Our method, named G
eo
B
urst+
, first leverages a novel cross-modal authority measure to identify several pivots in the query window. Such pivots reveal different geo-topical activities and naturally attract similar tweets to form candidate events. G
eo
B
urst+
further summarizes the continuous stream and compares the candidates against the historical summaries to pinpoint truly interesting local events. Better still, as the query window shifts, G
eo
B
urst+
is capable of updating the event list with little time cost, thus achieving continuous monitoring of the stream. We used crowdsourcing to evaluate G
eo
B
urst+
on two million-scale datasets and found it significantly more effective than existing methods while being orders of magnitude faster.
Simulating Urban Pedestrian Crowds of Different Cultures
Authors: Kaminka Gal A. , Fridman Natalie
Published: January 2018

Models of crowd dynamics are critically important for urban planning and management. They support analysis, facilitate qualitative and quantitative predictions, and synthesize behaviors for simulations. One promising approach to crowd modeling relies on micro-level agent-based simulations, where the interactions of simulated individual agents in the crowd result in macro-level crowd dynamics which are the object of study. This article reports on an agent-based model of urban pedestrian crowds, where
culture is explicitly modeled
. We extend an established agent-based social agent model, inspired by social psychology, to account for individual cultural attributes discussed in social science literature. We then embed the model in a simulation of pedestrians and explore the resulting macro-level crowd behaviors, such as pedestrian flow, lane changes rate, and so on. We validate the model by quantitatively comparing the simulation results to the pedestrian dynamics in movies of human crowds in five different countries: Iraq, Israel, England, Canada, and France. We conclude that the model can faithfully replicate urban pedestrians in different cultures. Encouraged by these results, we explore simulations of mixed-culture pedestrian crowds.
Computational Design of Transforming Pop-up Books
Authors: Xiao Nan , Zhu Zhe , Martin Ralph R. , Xu Kun , Lu Jia-Ming , Hu Shi-Min
Published: January 2018

We present the first computational tool to help ordinary users create
transforming pop-up
books. In each transforming pop-up, when the user pulls a tab, an initial flat two-dimensional (2D) pattern, i.e., a 2D shape with a superimposed picture, such as an airplane, turns into a new 2D pattern, such as a robot. Given the two 2D patterns, our approach automatically computes a 3D pop-up mechanism that transforms one pattern into the other; it also outputs a design blueprint, allowing the user to easily make the final model. We also present a theoretical analysis of basic transformation mechanisms; combining these basic mechanisms allows more flexibility of final designs. Using our approach, inexperienced users can create models in a short time; previously, even experienced artists often took weeks to manually create them. We demonstrate our method on a variety of real-world examples.
Appearance Modeling via Proxy-to-Image Alignment
Authors: Huang Hui , Xie Ke , Ma Lin , Lischinski Dani , Gong Minglun , Tong Xin , Cohen-Or Daniel
Published: January 2018

Endowing 3D objects with realistic surface appearance is a challenging and time-demanding task, as real-world surfaces typically exhibit a plethora of spatially variant geometric and photometric detail. Not surprisingly, computer artists commonly use images of real-world objects as an inspiration and a reference for their digital creations. However, despite two decades of research on image-based modeling, there are still no tools available for automatically extracting the detailed appearance (microgeometry and texture) of a 3D surface from a single image. In this article, we present a novel user-assisted approach for quickly and easily extracting a nonparametric appearance model from a single photograph of a reference object.

The extraction process requires a user-provided proxy, whose geometry roughly approximates that of the object in the image. Since the proxy is just a rough approximation, it is necessary to align and deform it so as to match the reference object. The main contribution of this work is a novel technique to perform such an alignment, which enables accurate joint recovery of geometric detail and reflectance. The correlations between the recovered geometry at various scales and the spatially varying reflectance constitute a nonparametric appearance model. Once extracted, the appearance model may then be applied to various 3D shapes, whose large-scale geometry may differ considerably from that of the original reference object. Thus, our approach makes it possible to construct an appearance library, allowing users to easily enrich detail-less 3D shapes with realistic geometric detail and surface texture.
Assembly of COPI and COPII Vesicular Coat Proteins on Membranes
Authors: Béthune Julien , Wieland Felix T.
Published: January 2018

In eukaryotes, distinct transport vesicles functionally connect various intracellular compartments. These carriers mediate transport of membranes for the biogenesis and maintenance of organelles, secretion of cargo proteins and peptides, and uptake of cargo into the cell. Transport vesicles have distinct protein coats that assemble on a donor membrane where they can select cargo and curve the membrane to form a bud. A multitude of structural elements of coat proteins have been solved by X-ray crystallography. More recently, the architectures of the COPI and COPII coats were elucidated in context with their membrane by cryo-electron tomography. Here, we describe insights gained from the structures of these two coat lattices and discuss the resulting functional implications.
Transient stretch induces cytoskeletal fluidization through the severing action of cofilin
Authors: Lan Bo , Krishnan Ramaswamy , Park Chan Yong , Watanabe Rodrigo A. , Panganiban Ronald , Butler James P. , Lu Quan , Cole William C. , Fredberg Jeffrey J.
Published: January 2018

With every deep inspiration (DI) or sigh, the airway wall stretches, as do the airway smooth muscle cells in the airway wall. In response, the airway smooth muscle cell undergoes rapid stretch-induced cytoskeletal fluidization. As a molecular mechanism underlying the cytoskeletal fluidization response, we demonstrate a key role for the actin-severing protein cofilin. Using primary human airway smooth muscle cells, we simulated a DI by imposing a transient stretch of physiological magnitude and duration. We used traction microscopy to measure the resulting changes in contractile forces. After a transient stretch, cofilin-knockdown cells exhibited a 29 ± 5% decrease in contractile force compared with prestretch conditions. By contrast, control cells exhibited a 67 ± 6% decrease ( P < 0.05, knockdown vs. control). Consistent with these contractile force changes with transient stretch, actin filaments in cofilin-knockdown cells remained largely intact, whereas actin filaments in control cells were rapidly disrupted. Furthermore, in cofilin-knockdown cells, contractile force at baseline was higher and rate of remodeling poststretch was slower than in control cells. Additionally, the severing action of cofilin was restricted to the release phase of the transient stretch. We conclude that the actin-severing activity of cofilin is an important factor in stretch-induced cytoskeletal fluidization and may account for an appreciable part of the bronchodilatory effects of a DI.
Distinct niches within the extracellular matrix dictate fibroblast function in (cell free) 3D lung tissue cultures
Authors: Burgstaller Gerald , Sengupta Arunima , Vierkotten Sarah , Preissler Gerhard , Lindner Michael , Behr Jürgen , Königshoff Melanie , Eickelberg Oliver
Published: January 2018

Cues from the extracellular matrix (ECM) and their functional interplay with cells play pivotal roles for development, tissue repair, and disease. However, the precise nature of this interplay remains elusive. We used an innovative 3D cell culture ECM model by decellularizing 300-µm-thick ex vivo lung tissue scaffolds (d3D-LTCs) derived from diseased and healthy mouse lungs, which widely mimics the native (patho)physiological in vivo ECM microenvironment. We successfully repopulated all d3D-LTCs with primary human and murine fibroblasts, and moreover, we demonstrated that the cells also populated the innermost core regions of the d3D-LTCs in a real 3D fashion. The engrafted fibroblasts revealed a striking functional plasticity, depending on their localization in distinct ECM niches of the d3D-LTCs, affecting the cells’ tissue engraftment, cellular migration rates, cell morphologies, and protein expression and phosphorylation levels. Surprisingly, we also observed fibroblasts that were homing to the lung scaffold’s interstitium as well as fibroblasts that were invading fibrotic areas. To date, the functional nature and even the existence of 3D cell matrix adhesions in vivo as well as in 3D culture models is still unclear and controversial. Here, we show that attachment of fibroblasts to the d3D-LTCs evidently occurred via focal adhesions, thus advocating for a relevant functional role in vivo. Furthermore, we found that protein levels of talin, paxillin, and zyxin and phosphorylation levels of paxillin Y118, as well as the migration-relevant small GTPases RhoA, Rac, and CDC42, were significantly reduced compared with their attachment to 2D plastic dishes. In summary, our results strikingly indicate that inherent physical or compositional characteristics of the ECM act as instructive cues altering the functional behavior of engrafted cells. Thus, d3D-LTCs might aid to obtain more realistic data in vitro, with a high relevance for drug discovery and mechanistic studies alike.
Neonatal hyperoxia depletes pulmonary vein cardiomyocytes in adult mice via mitochondrial oxidation
Authors: Yee Min , Cohen Ethan David , Domm William , Porter George A. , McDavid Andrew N. , O’Reilly Michael A.
Published: January 2018

Supplemental oxygen given to preterm infants has been associated with permanently altering postnatal lung development. Now that these individuals are reaching adulthood, there is growing concern that early life oxygen exposure may also promote cardiovascular disease through poorly understood mechanisms. We previously reported that adult mice exposed to 100% oxygen between postnatal days 0 and 4 develop pulmonary hypertension, defined pathologically by capillary rarefaction, dilation of arterioles and veins, cardiac failure, and a reduced lifespan. Here, Affymetrix Gene Arrays are used to identify early transcriptional changes that take place in the lung before pulmonary capillary rarefaction. We discovered neonatal hyperoxia reduced expression of cardiac muscle genes, including those involved in contraction, calcium signaling, mitochondrial respiration, and vasodilation. Quantitative RT-PCR, immunohistochemistry, and genetic lineage mapping using Myh6CreER; Rosa26RmT/mG mice revealed this reflected loss of pulmonary vein cardiomyocytes. The greatest loss of cadiomyocytes was seen within the lung followed by a graded loss beginning at the hilum and extending into the left atrium. Loss of these cells was seen by 2 wk of age in mice exposed to ≥80% oxygen and was attributed, in part, to reduced proliferation. Administering mitoTEMPO, a scavenger of mitochondrial superoxide during neonatal hyperoxia prevented loss of these cells. Since pulmonary vein cardiomyocytes help pump oxygen-rich blood out of the lung, their early loss following neonatal hyperoxia may contribute to cardiovascular disease seen in these mice, and perhaps in people who were born preterm.
Deletion of estrogen receptor α in skeletal muscle results in impaired contractility in female mice
Authors: Collins Brittany C. , Mader Tara L. , Cabelka Christine A. , Iñigo Melissa R. , Spangenburg Espen E. , Lowe Dawn A.
Published: January 2018

Estradiol deficiency in females can result in skeletal muscle strength loss, and treatment with estradiol mitigates the loss. There are three primary estrogen receptors (ERs), and estradiol elicits effects through these receptors in various tissues. Ubiquitous ERα-knockout mice exhibit numerous biological disorders, but little is known regarding the specific role of ERα in skeletal muscle contractile function. The purpose of this study was to determine the impact of skeletal muscle-specific ERα deletion on contractile function, hypothesizing that ERα is a main receptor through which estradiol affects muscle strength in females. Deletion of ERα specifically in skeletal muscle (skmERαKO) did not affect body mass compared with wild-type littermates (skmERαWT) until 26 wk of age, at which time body mass of skmERαKO mice began to increase disproportionally. Overall, skmERαKO mice had low strength demonstrated in multiple muscles and by several contractile parameters. Isolated extensor digitorum longus muscles from skmERαKO mice produced 16% less eccentric and 16–26% less submaximal and maximal isometric force, and isolated soleus muscles were more fatigable, with impaired force recovery relative to skmERαWT mice. In vivo maximal torque productions by plantarflexors and dorsiflexors were 16% and 12% lower in skmERαKO than skmERαWT mice, and skmERαKO muscles had low phosphorylation of myosin regulatory light chain. Plantarflexors also generated 21–32% less power, submaximal isometric and peak concentric torques. Data support the hypothesis that ablation of ERα in skeletal muscle results in muscle weakness, suggesting that the beneficial effects of estradiol on muscle strength are receptor mediated through ERα.

NEW & NOTEWORTHY We comprehensively measured in vitro and in vivo skeletal muscle contractility in female estrogen receptor α (ERα) skeletal muscle-specific knockout mice and report that force generation is impaired across multiple parameters. These results support the hypothesis that a primary mechanism through which estradiol elicits its effects on strength is mediated by ERα. Evidence is presented that estradiol signaling through ERα appears to modulate force at the molecular level via posttranslational modifications of myosin regulatory light chain.
Atrial Repolarization Waves (Ta) Mimicking Inferior Wall ST Segment Elevation Myocardial Infarction in a Patient with Ectopic Atrial Rhythm
Authors: Manne Janaki Rami Reddy
Published: January 2018

We present a case of atrial repolarization waves from an ectopic atrial rhythm mimicking inferior ST segment elevation myocardial infarction in a 78-year-old male patient who presented with left sided chest wall and shoulder pain. His ischemic workup was negative, and the ST elevations completely resolved upon the resumption of sinus rhythm before discharge.
Protein Kinase G Induces an Immune Response in Cows Exposed toMycobacterium aviumSubsp.paratuberculosis
Authors: Bach Horacio , Richard-Greenblatt Melissa , Bach Eviatar , Chaffer Marcelo , Lai Wanika , Keefe Greg , Begg Douglas J.
Published: January 2018

To establish infection, pathogens secrete virulence factors, such as protein kinases and phosphatases, to modulate the signal transduction pathways used by host cells to initiate immune response. The protein MAP3893c is annotated in the genome sequence ofMycobacterium aviumsubspeciesparatuberculosis(MAP), the causative agent of Johne’s disease, as the serine/threonine protein kinase G (PknG). In this work, we report that PknG is a functional kinase that is secreted within macrophages at early stages of infection. The antigen is able to induce an immune response from cattle exposed to MAP in the form of interferon gamma production after stimulation of whole blood with PknG. These findings suggest that PknG may contribute to the pathogenesis of MAP by phosphorylating macrophage signalling and/or adaptor molecules as observed with other pathogenic mycobacterial species.
Bundle Pricing Decisions for Fresh Products with Quality Deterioration
Authors: Fang Yan , Jiang Yiping , Han Xingxing
Published: January 2018

How to sell fresh products quickly to decrease the storage cost and to meet customer quality requirement is of vital importance in the food supply chain. Bundling fresh products is an efficient strategy to promote sales and reduce storage pressure of retailers. In this paper, we consider the bundle pricing decisions for homogeneous fresh products with quality deterioration. The value of fresh products with quality deterioration is approximated as an exponential function based on which customer’s reservation prices are calculated. A nonlinear mixed integer programming model is used to formulate the bundle pricing problem for fresh products. By adding auxiliary decision variables, this model is converted into a mixed integer linear program. Numerical experiments and sensitive analysis are conducted to provide managerial insights for bundling fresh products with quality deterioration.
Principal Eigenvalues of a Second-Order Difference Operator with Sign-Changing Weight and Its Applications
Authors: Ma Ruyun , Xu Man , Long Yan
Published: January 2018

Let T>2 be an integer and T={1,2,…,T}. We show the existence of the principal eigenvalues of linear periodic eigenvalue problem -Δ2u(j-1)+q(j)u(j)=λg(j)u(j),  j∈T, u(0)=u(T),  u(1)=u(T+1), and we determine the sign of the corresponding eigenfunctions, where λ is a parameter, q(j)≥0 and q(j)≢0 in T, and the weight function g changes its sign in T. As an application of our spectrum results, we use the global bifurcation theory to study the existence of positive solutions for the corresponding nonlinear problem.
Autotransplantation and Orthodontic Treatment after Maxillary Central Incisor Region Trauma: A 13-Year Follow-Up Case Report Study
Authors: Piroozmand Farzad , Hessari Hossein , Shirazi Mohsen , Khazaei Pegah
Published: January 2018

The anterior maxilla is the most prone region to the trauma during childhood, and tooth loss sometimes happens due to trauma. Replacing the missing teeth has always been one of the dentists’ challenges in children and adolescents, since their dentofacial growth is not complete. Autotransplantation of mandibular premolars with two-thirds or three-quarters of root formation provides the best prognosis for the tooth survival. This case report describes the management of a 10-year-old boy suffering a severe dental injury who received the autotransplantation of the premolars from mandible to restore the space caused by trauma in maxillary central incisor region and a 13-year follow-up of the autotransplantation.
MCM-41-Accelerated PWA Catalysis of Friedel-Crafts Reaction of Indoles and Isatins
Authors: Xing Liuzhuang , Hui YongHai , Yang Jinghui , Xing Xuejian , Hou Yadong , Wu Yang , Fan Kui , Wang Wei
Published: January 2018

Ordered mesoporous siliceous material has been identified as one of the key elements of the catalysis concept. Here we report an efficient Friedel-Crafts reaction of indoles with isatins catalyzed by PWA/MCM-41, which got the di(indolyl)indolin-2-ones derivatives with high yield. Moreover, the catalysts were characterized by XRD and SEM/EDS, the EDS spectrum indicated that the catalyst used in this reaction also contains tungsten, and the proposed mechanism for the synthesis of 3,3-di(indolyl)indolin-2-ones was also discussed. Finally, the catalyst can be reused repeatedly for several times without obvious loss of activity.
Criterion-Related Validity of a Simple Muscle Strength Test to Assess Whole Body Muscle Strength in Chinese Children Aged 10 to 12 Years
Authors: Yin Liqin , Tang Changfa , Tao Xia
Published: January 2018

Objective. To study the criterion-related validity of simple muscle strength test (SMST) indicators and assess whole body muscle strength in Chinese children aged 10 to 12 years old.Methods. Two hundred and forty children were equally divided into four groups in different genders and residences. The SMST indicators (hand-grip, knee bent push-up, back muscle strength, sit-up, leg muscle strength, and standing long jump) were tested. We set up the total level of the whole-body muscle strength (Ftotal) through testing isokinetic muscle strength of the six joints’ flexion and extension movements. Pearson correlation analyses were used to analyze the correlation between the SMST indicators and theFtotal.Results.(1)Leg muscle strength and back muscle strength demonstrated the highest validity scores. Sit-ups, hand grip, and standing long jump demonstrated the lowest validity scores.(2)Leg muscle strength had the highest validity for males, but back muscle strength had the highest validity for females.Conclusions. Back muscle strength and leg muscle strength can give the highest validity of assessing whole body muscle strength, and also has higher validity in both the urban and rural children. For urban children, but not rural, the knee bent push-up also has a high validity indicator.
Polymorphisms in the Osteopontin Are Associated with Susceptibility to Ankylosing Spondylitis in a Han Chinese Population
Authors: Li Juyi , Cai Yi , Wang Zhongjing , Deng Aiping , Yang Guoliang
Published: January 2018

The aim of this study was to investigate whether osteopontin(OPN)variants are associated with susceptibility to ankylosing spondylitis (AS) in a Chinese population. Polymorphisms at the 9175th position in exon 7 ofOPNand rs17524488 were genotyped using direct sequencing in 186 unrelated AS patients and 188 ethnically matched healthy controls. Serum concentration of OPN was measured by enzyme-linked immunosorbent assay (ELISA) in all participants. AS patients displayed significantly higher OPN serum levels than the controls (P<001). A heterozygous, novel 9175 T>A in exon 7 of theOPNgene was found in this study. In healthy controls, subjects carrying the rs17524488 G/G genotype of theOPNdisplay significantly higher OPN serum levels than the GG/GG genotype (P<0.05). Plasma OPN level is implicated as an early diagnostic marker of AS. The novel 9175th- (exon 7) position polymorphism ofOPNand rs17524488 were related to susceptibility to AS in a Chinese population, the rs17524488 G/G genotype may be involved in the pathogenesis of AS, and the precise molecular mechanism underlying the influence ofOPNpolymorphisms on the development of AS remains to be determined in the further prospective studies.