bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genomic and phenotypic characterization of in vitro-generated Chlamydia trachomatis recombinants
Authors: Jeffrey Brendan M , Suchland Robert J , Eriksen Steven G , Sandoz Kelsi M , Rockey Daniel D 
Published: June 2013

Abstract

Background
Pre-genomic and post-genomic studies demonstrate that chlamydiae actively recombine in vitro and in vivo, although the molecular and cellular biology of this process is not well understood. In this study, we determined the genome sequence of twelve Chlamydia trachomatis recombinants that were generated in vitro under antibiotic selection. These strains were used to explore the process of recombination in Chlamydia spp., including analysis of candidate recombination hotspots, and to correlate known C. trachomatis in vitro phenotypes with parental phenotypes and genotypes.

Results
Each of the 190 examined recombination events was the product of homologous recombination, and no candidate targeting motifs were identified at recombination sites. There was a single deletion event in one recombinant progeny that resulted in the removal of 17.1 kilobases between two rRNA operons. There was no evidence for preference for any specific region of the chromosome for recombination, and analyses of a total of over 200 individual recombination events do not provide any support for recombination hotspots in vitro. Two measurable phenotypes were analyzed in these studies. First, the efficiency of attachment to host cells in the absence of centrifugation was examined, and this property segregated to regions of the chromosome that carry the polymorphic membrane protein (Pmp) genes. Second, the formation of secondary inclusions within cells varied among recombinant progeny, but this did not cleanly segregate to specific regions of the chromosome.

Conclusions
These experiments examined the process of recombination in C. trachomatis and identified tools that can be used to associate phenotype with genotype in recombinant progeny. There were no data supporting the hypothesis that particular nucleotide sequences are preferentially used for recombination in vitro. Selected phenotypes can be segregated by analysis of recombination, and this technology may be useful in preliminary analysis of the relationship of genetic variation to phenotypic variation in the chlamydiae.
Hedgehog signaling regulates hypoxia induced epithelial to mesenchymal transition and invasion in pancreatic cancer cells via a ligand-independent manner
Authors: Lei Jianjun , Ma Jiguang , Ma Qingyong , Li Xuqi , Liu Han , Xu Qinhong , Duan Wanxing , Sun Qing , Xu Jun , Wu Zheng , Wu Erxi 
Published: June 2013

Abstract

Background
Hypoxia plays a vital role in cancer epithelial to mesenchymal transition (EMT) and invasion. However, it is not quite clear how hypoxia may contribute to these events. Here we investigate the role of Hedgehog (Hh) signaling in hypoxia induced pancreatic cancer EMT and invasion.

Methods
Pancreatic cancer cells were cultured under controlled hypoxia conditions (3% O2) or normoxic conditions. HIF-1α siRNA, cyclopamine (a SMO antagonist) and GLI1 siRNA were used to inhibit HIF-1α transcription or Hh signaling activation. The effect of hypoxia and Hh signaling on cancer cell EMT and invasion were evaluated by Quantitative real-time PCR analysis, Western blot analysis and invasion assay.

Results
Here, we show that non-canonical Hh signaling is required as an important role to switch on hypoxia-induced EMT and invasion in pancreatic cancer cells. Moreover, our data demonstrate hypoxia induces EMT process as well as invasion, and activates the non-canonical Hh pathway without affecting sonic hedgehog homolog (SHH) expression. Moreover, these effects are reversible upon HIF-1α siRNA interference with unchanged SHH and patched1 (PTCH1) level. Furthermore, our data demonstrate that hypoxia induced invasion and EMT process are effectively inhibited by Smoothened (SMO) antagonist cyclopamine and GLI1 siRNA. In addition, GLI1 interference inhibited EMT progress with significantly suppressed vimentin expression, whereas inhibition of SMO through cyclopamine could not reduce vimentin level. This data indicate that hypoxia could trigger other factors (such as TGF-β, KRAS or RTK) bypassing SMO to activate GLI1 directly.

Conclusions
Our findings suggest that Hh signaling modulates hypoxia induced pancreatic cancer EMT and invasion in a ligand-independent manner. Thus, Hh signaling may represent a promising therapeutic target for preventing pancreatic cancer progression.
Single view-based 3D face reconstruction robust to self-occlusion
Authors: Lee Youn Joo , Lee Sung Joo , Park Kang Ryoung , Jo Jaeik , Kim Jaihie 
Published: June 2013

Abstract
State-of-the-art 3D morphable model (3DMM) is used widely for 3D face reconstruction based on a single image. However, this method has a high computational cost, and hence, a simplified 3D morphable model (S3DMM) was proposed as an alternative. Unlike the original 3DMM, S3DMM uses only a sparse 3D facial shape, and therefore, it incurs a lower computational cost. However, this method is vulnerable to self-occlusion due to head rotation. Therefore, we propose a solution to the self-occlusion problem in S3DMM-based 3D face reconstruction.
This research is novel compared with previous works, in the following three respects. First, self-occlusion of the input face is detected automatically by estimating the head pose using a cylindrical head model. Second, a 3D model fitting scheme is designed based on selected visible facial feature points, which facilitates 3D face reconstruction without any effect from self-occlusion. Third, the reconstruction performance is enhanced by using the estimated pose as the initial pose parameter during the 3D model fitting process.
The experimental results showed that the self-occlusion detection had high accuracy and our proposed method delivered a noticeable improvement in the 3D face reconstruction performance compared with previous methods.
Spontaneous Temperature Control Using Reversible Spectroscopic Responses of PNIPAM-coated Gold Nanorods
Authors: Shimoda Kohei , Fujigaya Tsuyohiko , Nakashima Naotoshi , Niidome Yasuro 
Published: June 2013

Abstract
Poly(N-isopropylacrylamide) (PNIPAM) was coated on gold nanorods (NRs) without forming aggregates. The PNIPAM-coated NRs (PNIPAM-NRs) formed aggregates at higher temperature than the lower critical solution temperature (LCST) of the PNIPAM layers. The aggregation showed reversible spectroscopic responses under repeated temperature cycles. When a PNIPAM-NR solution was irradiated with near-infrared (near-IR) light, the temperature increased and aggregates formed showing broad and weak surface plasmon bands. The spectroscopic responses in near-IR work as a negative feedback for heating a photoirradiated nanorod solution. The feedback offers spontaneous temperature control of the photoirradiated solution at the LCST of PNIPAM.
Leucippus and Democritus on Like to Like and ou mallon
Authors: Andrew Gregory 
Published: June 2013

Abstract The central issue for this paper is whether for Leucippus and Democritus, 1 the like to like principle, which is critical to cosmos formation once a vortex forms, operates outside of the vortices. Should we consider like to like in the early atomists to be akin to a ‘fundamental force’, with a universal application, as some commentators have suggested?3 Or should we rather consider it to be a sorting effect generated by certain types of motion, occurring only when those types of motion occur? As a matter of detail this is interesting in itself and it also bears on several important interpretive issues for Leucippus and Democritus. What are the intrinsic properties of atoms, if any, beyond their size and shape? Is the initial formation of a vortex a matter of necessity or a matter of chance? Is what happens in a cosmos a matter of necessity or chance? Although not immediately obvious, this will also raise issues concerning to what extent Leucippus and Democritus are committed to the principle of sufficient reason. I will argue that there are good theoretical and textual reasons to believe that like to like occurs only in the vortices. I will also argue that just as there are no preferred sizes and shapes for atoms for Leucippus and Democritus, no preferred distribution of the atoms in the void and there are no preferred times or places for vortex/cosmos formation either. This I suggest gives Leucippus and Democritus a coherent and interesting position relative to Parmenides. Where Parmenides denies multiplicity and raises sufficient reason issues about the time and place of cosmos formation, Leucippus and Democritus assert multiplicity but without preferred shapes and sizes of atoms and cosmogony without preferred times and places of cosmos formation. Of importance here will be an interesting paradox in cosmogony - if we begin with a uniform entity or uniform distribution of entities how does a non-uniform state such as a cosmos arise, while if we begin with a non-uniform entity or non-uniform distribution of entities how do we explain this non-uniformity?
The Effect of Water-Induced Stress To Enhance Hydrocarbon Recovery in Shale Reservoirs
Authors: Fakcharoenphol Perapon , Charoenwongsa Sarinya , Kazemi Hossein , Wu Yu-Shu 
Published: June 2013

Summary
Waterflooding has been an effective improved-oil-recovery (IOR) process for several decades. However, stress induced by waterflooding has not been well studied or documented. Water injection typically increases reservoir pressure and decreases reservoir temperature. The increase in reservoir pressure and decrease in reservoir temperature synergistically reduce the effective stress. Because of such decrease in stress, existing healed natural fractures can be reactivated and/or new fractures can be created. Similar effects can enhance hydrocarbon recovery in shale reservoirs.
In this paper, we calculated the magnitude of water-injection-induced stress with a coupled flow/geomechanics model. To evaluate the effect of water injection in the Bakken, a numerical-simulation study for a sector model was carried out. Stress changes caused by the volume created by the hydraulic fracture, water injection, and oil production were calculated. The Hoek-Brown failure criterion was used to compute rock-failure potential.
Our numerical results for a waterflooding example show that during water injection, the synergistic effects of reservoir cooling and pore-pressure increase significantly promote rock failure, potentially reactivating healed natural macrofractures and/or creating new macrofractures, especially near an injector. The rock cooling can create small microfractures on the surface of the matrix blocks. In shale oil reservoirs, the numerical experiments indicate that stress changes during water injection can improve oil recovery by opening some of the old macrofractures and creating new small microfractures on the surface of the matrix blocks to promote shallow water invasion into the rock matrix. Furthermore, the new microfractures provide additional interface area between macrofractures and matrix to improve oil drainage when using surfactant and CO2 enhanced-oil-recovery techniques. These positive effects are particularly important farther away from the immediate vicinity of the hydraulic fracture, which is where much of the undrained oil resides.
Stability of three commonly compounded extemporaneous enrofloxacin suspensions for oral administration to exotic animals
Authors: Petritz Olivia A. , Guzman David Sanchez-Migallon , Wiebe Valerie J. , Papich Mark G. 
Published: June 2013

Abstract
Objective—To evaluate the stability of 3 extemporaneous oral suspensions of enrofloxacin mixed with readily available flavoring vehicles when stored at room temperature (approx 22°C).
Design—Evaluation study.
Samples—3 commonly compounded oral suspensions of enrofloxacin.
Procedures—On day 0, commercially available enrofloxacin tablets were compounded with a mixture of distilled water and corn syrup (formulation A) or cherry syrup (formulation B) flavoring vehicles to create suspensions with a nominal enrofloxacin concentration of 22.95 mg/mL, and 2.27% enrofloxacin injectable solution was compounded with a liquid sweetener (formulation C) to create a suspension with a nominal enrofloxacin concentration of 11.35 mg/mL. Preparations were stored in amber-colored vials at room temperature for 56 days. For each preparation, the enrofloxacin concentration was evaluated with high-performance liquid chromatography at prespecified intervals during the study. The pH, odor, and consistency for all suspensions were recorded at the start and completion of the study.
Results—Relative to the nominal enrofloxacin concentration, the enrofloxacin concentration strength ranged from 95.80% to 100.69% for formulation A, 108.44% to 111.06% for formulation B, and 100.99% to 103.28% for formulation C. A mild pH increase was detected in all 3 suspensions during the study.
Conclusions and Clinical Relevance—Results indicated that, when stored in amber-colored vials at room temperature for 56 days, the enrofloxacin concentration strength in all 3 formulations was retained within acceptance criteria of 90% to 110%. Subjectively, cherry syrup flavoring was better at masking the smell and taste of enrofloxacin than were the other mixing vehicles.
Outcomes of Pregnancies Fathered by Solid-Organ Transplant Recipients Exposed to Mycophenolic Acid Products
Authors: Jones Alyssa , Clary Megan J. , McDermott Erin , Coscia Lisa A. , Constantinescu Serban , Moritz Michael J. , Armenti Vincent T. 
Published: June 2013

Context In women, exposure to mycophenolic acid products during pregnancy results in an increase in both miscarriages and birth defects in the live born. Objective To describe the outcomes of pregnancies fathered by transplant recipients who were being maintained on mycophenolic acid products at the estimated time of conception and compare these pregnancies with pregnancies in the general population. Methods Data were collected by the National Transplantation Pregnancy Registry via questionnaires, telephone interviews, and medical records. Results One hundred fifty-two male transplant recipients with exposure to mycophenolic acid products fathered 205 pregnancies (208 outcomes, including 3 pairs of twins). Pregnancy outcomes included 194 live births with a prematurity rate of 10.8%, 14 spontaneous abortions, and no therapeutic abortions or stillbirths. Among the live births, 6 malformations were reported, for an incidence of 3.1%. No pattern of malformations was identified. Conclusion The outcomes of pregnancies fathered by transplant recipients treated with mycophenolic acid products appear similar to outcomes in the general population.
Tunable Assembly of sp3 Cross‐Linked 3D Graphene Monoliths: A First‐Principles Prediction
Authors: Jiang Xue , Zhao Jijun , Li Yan‐Ling , Ahuja Rajeev 
Published: June 2013

AbstractOne of the biggest challenges in graphene applications is how one can fabricate 3D architectures comprising graphene sheets in which the resulting architectures have inherited graphene's excellent intrinsic properties but have overcome its shortcomings. Two series of 3D graphene monoliths (GMs) using zigzag or armchair graphene nanoribbons as building blocks and sp3 carbon chains as junction nodes are constructued, and calculations based on first principles are performed in order to predict their mechanical and electronic properties. The perfect match between sp2 nanoribbons and sp3 linkers results in favorable energy and mechanical/dynamic stability. Owing to their tailored motifs, wine‐rack‐like pores, and rigid sp3 linkers, these GMs possess high surface areas, appreciable mechanical strength, and tunable band gaps. Negative linear compressibilities in a wide range are found for the zigzag GMs. By solving the problems of zero gap and dimensionality of graphene sheets simultaneously, these GMs offer a viable strategy towards many applications, e.g., microelectronic devices, energy storage, molecular sieves, sensitive pressure detectors, and telecommunication line systems.
Facts and myths of antibacterial properties of silk
Authors: Kaur Jasjeet , Rajkhowa Rangam , Afrin Tarannum , Tsuzuki Takuya , Wang Xungai 
Published: June 2013

ABSTRACTSilk cocoons provide protection to silkworm from biotic and abiotic hazards during the immobile pupal phase of the lifecycle of silkworms. Protection is particularly important for the wild silk cocoons reared in an open and harsh environment. To understand whether some of the cocoon components resist growth of microorganisms, in vitro studies were performed using gram negative bacteria Escherichia coli (E. coli) to investigate antibacterial properties of silk fiber, silk gum, and calcium oxalate crystals embedded inside some cocoons. The results show that the previously reported antibacterial properties of silk cocoons are actually due to residues of chemicals used to isolate/purify cocoon elements, and properly isolated silk fiber, gum, and embedded crystals free from such residues do not have inherent resistance to E. coli. This study removes the uncertainty created by previous studies over the presence of antibacterial properties of silk cocoons, particularly the silk gum and sericin. © 2013 Wiley Periodicals, Inc. Biopolymers 101: 237–245, 2014.
Water scaffolding in collagen: Implications on protein dynamics as revealed by solid‐state NMR
Authors: Aliev Abil E. , Courtier‐Murias Denis 
Published: June 2013

ABSTRACTSolid‐state NMR studies of collagen samples of various origins confirm that the amplitude of collagen backbone and sidechain motions increases significantly on increasing the water content. This conclusion is supported by the changes observed in three different NMR observables: (i) the linewidth dependence on the1H decoupling frequency; (ii)13C CSA changes for the peptide carbonyl groups, and (iii) dephasing rates of1H‐13C dipolar couplings. In particular, a nearly threefold increase in motional amplitudes of the backbone librations about C‐Cαor N‐Cαbonds was found on increasing the added water content up to 47 wt%D2O. On the basis of the frequencies of NMR observables involved, the timescale of the protein motions dependent on the added water content is estimated to be of the order of microseconds. This estimate agrees with that from wideline T21H NMR measurements. Also, our wideline1H NMR measurements revealed that the timescale of the microsecond motions in proteins reduces significantly on increasing the added water content, i.e., an ∼15‐fold increase in protein motional frequencies is observed on increasing the added water content to 45 wt% D2O. The observed changes in collagen dynamics is attributed to the increase in water translational diffusion on increasing the amount of added water, which leads to more frequent “bound water/free water” exchange on the protein surface, accompanied by the breakage and formation of new hydrogen bonds with polar functionalities of protein. © 2013 Wiley Periodicals, Inc. Biopolymers 101: 246–256, 2014.
Localization of the Contacts Between Kenyon Cells and Aminergic Neurons in the Drosophila melanogaster Brain Using SplitGFP Reconstitution
Authors: Pech Ulrike , Pooryasin Atefeh , Birman Serge , Fiala André 
Published: June 2013

ABSTRACTThe mushroom body of the insect brain represents a neuronal circuit involved in the control of adaptive behavior, e.g., associative learning. Its function relies on the modulation of Kenyon cell activity or synaptic transmitter release by biogenic amines, e.g., octopamine, dopamine, or serotonin. Therefore, for a comprehensive understanding of the mushroom body, it is of interest not only to determine which modulatory neurons interact with Kenyon cells but also to pinpoint where exactly in the mushroom body they do so. To accomplish the latter, we made use of the GRASP technique and created transgenic Drosophila melanogaster that carry one part of a membrane‐bound splitGFP in Kenyon cells, along with a cytosolic red fluorescent marker. The second part of the splitGFP is expressed in distinct neuronal populations using cell‐specific Gal4 drivers. GFP is reconstituted only if these neurons interact with Kenyon cells in close proximity, which, in combination with two‐photon microscopy, provides a very high spatial resolution. We characterize spatially and microstructurally distinct contact regions between Kenyon cells and dopaminergic, serotonergic, and octopaminergic/tyraminergic neurons in all subdivisions of the mushroom body. Subpopulations of dopaminergic neurons contact complementary lobe regions densely. Octopaminergic/tyraminergic neurons contact Kenyon cells sparsely and are restricted mainly to the calyx, the α′‐lobes, and the γ‐lobes. Contacts of Kenyon cells with serotonergic neurons are heterogeneously distributed over the entire mushroom body. In summary, the technique enables us to localize precisely a segmentation of the mushroom body by differential contacts with aminergic neurons. J. Comp. Neurol. 521:3992–4026, 2013. © 2013 Wiley Periodicals, Inc.
Application of mercury isotopes for tracing trophic transfer and internal distribution of mercury in marine fish feeding experiments
Authors: Kwon Sae Yun , Blum Joel D. , Chirby Michelle A. , Chesney Edward J. 
Published: June 2013

Abstract

Feeding experiments were performed to investigate mercury (Hg) isotope fractionation during trophic transfer and internal distribution of total Hg (THg) in marine fish on exposure to natural seafood. Young-of-the-year amberjack (Seriola dumerili) were fed with either blackfin tuna (Thunnus atlanticus; 2647 ng/g THg) or brown shrimp (Farfantepenaeus aztecus; 25.1 ng/g THg) for 80 d or 50 d, respectively, and dissected for muscle, liver, kidney, brain, and blood. After 30 d of tuna consumption, Hg isotopes (δ202Hg and Δ199Hg) of the amberjack organs shifted to the tuna value (δ202Hg = 0.55‰, Δ199Hg = 1.54‰,), demonstrating the absence of Hg isotope fractionation. When amberjack were fed a shrimp diet, there was an initial mixing of the amberjack organs toward the shrimp value (δ202Hg = −0.48‰, Δ199Hg = 0.32‰), followed by a cessation of further shifts in Δ199Hg and a small shift in δ202Hg. The failure of Δ199Hg to reach the shrimp value can be attributed to a reduction in Hg bioaccumulation from shrimp resulting from feeding inhibition and the δ202Hg shift can be attributed to a small internal fractionation during excretion. Given that the feeding rate and Hg concentration of the diet can influence internal Hg isotope distribution, these parameters must be considered in biosentinel fish studies. Environ Toxicol Chem 2013;32:2322–2330. © 2013 SETAC
Ambient noise cross‐correlation observations of fundamental and higher‐mode Rayleigh wave propagation governed by basement resonance
Authors: Savage Martha K. , Lin Fan‐Chi , Townend John 
Published: June 2013

AbstractMeasurement of basement seismic resonance frequencies can elucidate shallow velocity structure, an important factor in earthquake hazard estimation. Ambient noise cross correlation, which is well‐suited to studying shallow earth structure, is commonly used to analyze fundamental‐mode Rayleigh waves and, increasingly, Love waves. Here we show via multicomponent ambient noise cross correlation that the basement resonance frequency in the Canterbury region of New Zealand can be straightforwardly determined based on the horizontal to vertical amplitude ratio (H/V ratio) of the first higher‐mode Rayleigh waves. At periods of 1–3 s, the first higher‐mode is evident on the radial‐radial cross‐correlation functions but almost absent in the vertical‐vertical cross‐correlation functions, implying longitudinal motion and a high H/V ratio. A one‐dimensional regional velocity model incorporating a ~ 1.5 km‐thick sedimentary layer fits both the observed H/V ratio and Rayleigh wave group velocity. Similar analysis may enable resonance characteristics of other sedimentary basins to be determined.