bluuebunny/crossref_metadata_2025 huggingface dataset:
Fast and reliable method of conductive carbon nanotube-probe fabrication for scanning probe microscopy
Authors: Dremov Vyacheslav , Fedoseev Vitaly , Fedorov Pavel , Grebenko Artem
Published: May 2015

We demonstrate the procedure of scanning probe microscopy (SPM) conductive probe fabrication with a single multi-walled carbon nanotube (MWNT) on a silicon cantilever pyramid. The nanotube bundle reliably attached to the metal-covered pyramid is formed using dielectrophoresis technique from the MWNT suspension. It is shown that the dimpled aluminum sample can be used both for shortening/modification of the nanotube bundle by applying pulse voltage between the probe and the sample and for controlling the probe shape via atomic force microscopy imaging the sample. Carbon nanotube attached to cantilever covered with noble metal is suitable for SPM imaging in such modulation regimes as capacitance contrast microscopy, Kelvin probe microscopy, and scanning gate microscopy. The majority of such probes are conductive with conductivity not degrading within hours of SPM imaging.
Self-folding graphene-polymer bilayers
Authors: Deng Tao , Yoon ChangKyu , Jin Qianru , Li Mingen , Liu Zewen , Gracias David H.
Published: May 2015

In order to incorporate the extraordinary intrinsic thermal, electrical, mechanical, and optical properties of graphene with three dimensional (3D) flexible substrates, we introduce a solvent-driven self-folding approach using graphene-polymer bilayers. A polymer (SU-8) film was spin coated atop chemically vapor deposited graphene films on wafer substrates and graphene-polymer bilayers were patterned with or without metal electrodes using photolithography, thin film deposition, and etching. After patterning, the bilayers were released from the substrates and they self-folded to form fully integrated, curved, and folded structures. In contrast to planar graphene sensors on rigid substrates, we assembled curved and folded sensors that are flexible and they feature smaller form factors due to their 3D geometry and large surface areas due to their multiple rolled architectures. We believe that this approach could be used to assemble a range of high performance 3D electronic and optical devices of relevance to sensing, diagnostics, wearables, and energy harvesting.
Shielding in ungated field emitter arrays
Authors: Harris J. R. , Jensen K. L. , Shiffler D. A. , Petillo J. J.
Published: May 2015

Cathodes consisting of arrays of high aspect ratio field emitters are of great interest as sources of electron beams for vacuum electronic devices. The desire for high currents and current densities drives the cathode designer towards a denser array, but for ungated emitters, denser arrays also lead to increased shielding, in which the field enhancement factor β of each emitter is reduced due to the presence of the other emitters in the array. To facilitate the study of these arrays, we have developed a method for modeling high aspect ratio emitters using tapered dipole line charges. This method can be used to investigate proximity effects from similar emitters an arbitrary distance away and is much less computationally demanding than competing simulation approaches. Here, we introduce this method and use it to study shielding as a function of array geometry. Emitters with aspect ratios of 102–104 are modeled, and the shielding-induced reduction in β is considered as a function of tip-to-tip spacing for emitter pairs and for large arrays with triangular and square unit cells. Shielding is found to be negligible when the emitter spacing is greater than the emitter height for the two-emitter array, or about 2.5 times the emitter height in the large arrays, in agreement with previously published results. Because the onset of shielding occurs at virtually the same emitter spacing in the square and triangular arrays, the triangular array is preferred for its higher emitter density at a given emitter spacing. The primary contribution to shielding in large arrays is found to come from emitters within a distance of three times the unit cell spacing for both square and triangular arrays.
Large electrocaloric effect in lead-free K0.5Na0.5NbO3-SrTiO3 ceramics
Authors: Koruza J. , Rožič B. , Cordoyiannis G. , Malič B. , Kutnjak Z.
Published: May 2015

The electrocaloric effect (ECE), i.e., the adiabatic temperature change ΔTEC, of the lead-free relaxor ferroelectric 0.85K0.5Na0.5NbO3-0.15SrTiO3 (KNN-STO) ceramics is investigated. The ECE data obtained by a direct method show the existence of a large ECE near the temperature of the dielectric permittivity maximum. Due to the high break-down electric field, a large ΔTEC exceeding 1.2 K at 300 K and 1.9 K at 340 K was observed at 159 kV/cm in a broad temperature range of 80 K. Such a high ECE response near the room temperature is comparable to that found in lead-based ceramic materials, thus making KNN-STO a strong candidate to replace lead-based materials in future electrocaloric applications.
Evaluating the efficacy of a topical anaesthetic formulation and ketoprofen, alone and in combination, on the pain sensitivity of dehorning wounds in Holstein-Friesian calves
Authors: Espinoza Crystal A. , McCarthy Dominique , White Peter J. , Windsor Peter A. , Lomax Sabrina H.
Published: May 2015

The aim of this study was to investigate the effect of a topically applied local anaesthetic and the non-steroidal anti-inflammatory drug ketoprofen, alone and in combination, on the pain sensitivity response of calves to dehorning (mean age 2.2 months). Calves were randomly allocated and blocked by age to one of four groups. Groups were: scoop dehorning (D, n = 8), scoop dehorning + i.m. administration of 3 mg/kg ketoprofen (DK, n = 8), scoop dehorning + application of topical anaesthetic (DTA, n = 7) and scoop dehorning + application of topical anaesthetic and i.m. administration of ketoprofen (DKTA, n = 7). A pressure algometer was used to determine the mechanical nociceptive threshold (MNT), being the pressure (kg/f) at which calves withdrew from the stimulus. Measurements were taken before dehorning and at 1 min, 1, 2, 5 and 24 h post-dehorning at both the cut skin edge of the wound and the peri-wound area. The effect of treatment changed over time (P < 0.001). MNT was highest before treatment (MNT = 5.03 kg/f) and tended to decrease over time (MNT = 1.16 kg/f 24 h post-treatment). Overall, D calves exhibited the lowest MNT with an average of 1.77 kg/f. DTA calves had the highest MNT (3.89 kg/f), followed closely by DKTA calves (3.24 kg/f). DK calves exhibited an intermediate MNT of 2.61 kg/f. MNT of the cut skin edge was generally lower than that of the peri-wound area (2.01 vs 3.81 kg/f, respectively, P = 0.02).The topical anaesthetic formulation significantly reduced the pain sensitivity of dehorning wounds. There was no observed enhanced analgesic effect with addition of ketoprofen. The cut skin edge was more sensitive to pressure than the peri-wound area.
‘Kids in the Kitchen’ impact evaluation: engaging primary school students in preparing fruit and vegetables for their own consumption
Authors: Ritchie Barbara , O'Hara Lily , Taylor Jane
Published: May 2015

Issue addressed

Children's fruit and vegetable (FV) consumption in Australia is below levels recommended for optimal growth, development and health.

Methods

‘Kids in the Kitchen’ is a classroom‐based program that engages students in preparing FV. Impact evaluation was conducted with students from Grade 1 (around 6 years old) and Grade 5 (around 11 years old) who participated in the program. A questionnaire was used to collect pre‐ and post‐program data on knowledge, attitudes and consumption of FV, FV preparation skills and environmental supports for FV consumption. A skill audit was also conducted for Grade 1 students.

Results

Study participants (n = 118) included 70 Grade 1 and 48 Grade 5 students. There was an increase in the median number of fruits correctly identified (from 14 to 16), tried (from 14 to 16) and liked (from 10.5 to 12; P = 0.0001 for all changes). The median number of vegetables correctly identified increased from 10 to 12 (P = 0.0001), but there was no change in the number of vegetables tried or liked. The proportion of participants who rated their skills in using a knife to prepare FV as ‘not really that good’ decreased by 15%, from 42% to 27% (P = 0.04). Grade 1 participants' skills in cutting, grating and peeling improved (P = 0.0001 for all changes).

Conclusions

If children are involved in the preparation of FV, they are more likely to correctly identify them, try them, like them and eat them.
Diversity and abundance of epibiota on invasive and native estuarine gastropods depend on substratum and salinity
Authors: Thyrring Jakob , Thomsen Mads Solgaard , Brunbjerg Ane Kirstine , Wernberg Thomas
Published: May 2015

Our understanding of variation in epibiota communities remains incomplete. This study relates such variability to multiple concurrent environmental factors. Specifically we determined the relative importance of salinity, depth, wave exposure, habitat and ‘shell type’ (shell type combined species, size, morphology and mobility traits) for community structure of sessile epibiota on gastropods in the Swan River Estuary, Australia. We quantified distribution, biofouling patterns, and detailed epibiota community structures on gastropod species in the estuary – the native Nassarius pauperatus and Bedeva paiva and the invasive Batillaria australis. The invasive Batillaria was much more abundant, and more biofouled, than any of the native species, thereby supporting orders of magnitude more epibiota in the estuary. Generalised linear models were used to partition variation in richness and abundance of epibiota among the above listed factors. Of the five factors were only shell type and salinity significant in 9 of 14 models. These results highlight (1) that a single invasive species can alter epibiota communities on a large system-wide scale, (2) an overwhelming importance of shell type and salinity in explaining estuarine epibiota communities, and (3) that additional environmental factors need to be included in future studies to improve predictive models of distribution for epibiota communities.
Estimating Trout Abundance with Cataraft-Mounted Dual-Frequency Identification Sonar: a Comparison with Drift Diving
Authors: Hayes John W. , Hay Joe , Maxwell Iain , Quarterman Aaron
Published: May 2015

We investigated the potential of dual-frequency identification sonar (DIDSON) deployed from a drifting cataraft for estimating abundance in rivers of Brown Trout Salmo trutta larger than 20 cm. We compared triplicate trout density estimates made by DIDSON with drift-diving density estimates in three reaches of a clear-water river in New Zealand. DIDSON density estimates were much lower (∼22% of drift-dive estimates, range = 7–33%) and less precise than drift-dive estimates (DIDSON CV = 0.13–0.47; drift diving CV = 0.15–0.17). Variation in detecting fish in the DIDSON field survey contributed substantially more (95%) to DIDSON count variability than did fish detection in the image files. Highest precision with DIDSON was achieved in the reach with the least shallow habitat and most uniform channel. Fewer person-hours were required to undertake the field component of DIDSON surveys than the drift dives (5 versus 8.3 h), but the substantial time spent on image review (3.3 h) made DIDSON surveys 34% more costly than drift dives in terms of overall effort. Despite observed shortcomings, cataraft-mounted DIDSON has utility as a noninvasive survey method for estimating abundance of large (>20-cm) fish, particularly in situations where turbidity is too high for visual counting methods to be effective.

Received September 22, 2014; accepted January 8, 2015
Agonistic Behavior among Three Stocked Trout Species
Authors: Hafen Konrad , Budy Phaedra
Published: May 2015

The popularity of reservoirs to support sport fisheries has led to the stocking of species that did not co-evolve, creating novel reservoir fish communities. In Utah, the Bear Lake strain of Bonneville Cutthroat Trout Oncorhynchus clarkii utah and tiger trout (female Brown Trout Salmo trutta × male Brook Trout Salvelinus fontinalis) are being more frequently added to a traditional stocking regimen consisting primarily of Rainbow Trout O. mykiss. Interactions between these three predatory species are not well understood, and studies evaluating community interactions have raised concern for an overall decrease of trout condition. To evaluate the potential for negative interactions among these species, we tested aggression in laboratory aquaria using three-species and pairwise combinations at three densities. Treatments were replicated before and after feeding. During the three-species trials Rainbow Trout initiated 24.8 times more aggressive interactions than Cutthroat Trout and 10.2 times more aggressive interactions than tiger trout, and tiger trout exhibited slightly (1.9 times) more aggressive initiations than Cutthroat Trout. There was no significant difference in behavior before versus after feeding for any species, and no indication of increased aggression at higher densities. Although Rainbow Trout in aquaria may benefit from their bold, aggressive behavior, given observations of decreased relative survival in the field, these benefits may be outweighed in reservoirs, possibly through unnecessary energy expenditure and exposure to predators.

Received October 1, 2014; accepted January 27, 2015
Carbon tetrachloride-induced hepatic and renal damages in rat: inhibitory effects of cacao polyphenol
Authors: Suzuki Koichiro , Nakagawa Kiyotaka , Yamamoto Takayuki , Miyazawa Taiki , Kimura Fumiko , Kamei Masanori , Miyazawa Teruo
Published: May 2015

Here, we investigated the protective effect of cacao polyphenol extract (CPE) on carbon tetrachloride (CCl4)-induced hepato-renal oxidative stress in rats. Rats were administered CPE for 7 days and then received intraperitoneal injection of CCl4. Two hours after injection, we found that CCl4 treatment significantly increased biochemical injury markers, lipid peroxides (phosphatidylcholine hydroperoxide (PCOOH) and malondialdehyde (MDA)) and decreased glutathione peroxidase activity in kidney rather than liver, suggesting that kidney is more vulnerable to oxidative stress under the present experimental conditions. CPE supplementation significantly reduced these changes, indicating that this compound has antioxidant properties against CCl4-induced oxidative stress. An inhibitory effect of CPE on CCl4-induced CYP2E1 mRNA degradation may provide an explanation for CPE antioxidant property. Together, these results provide quantitative evidence of the in vivo antioxidant properties of CPE, especially in terms of PCOOH and MDA levels in the kidneys of CCl4-treated rats.
P-body assembly requires DDX6 repression complexes rather than decay or Ataxin2/2L complexes
Authors: Ayache Jessica , Bénard Marianne , Ernoult-Lange Michèle , Minshall Nicola , Standart Nancy , Kress Michel , Weil Dominique
Published: May 2015

P-bodies are cytoplasmic ribonucleoprotein granules involved in posttranscriptional regulation. DDX6 is a key component of their assembly in human cells. This DEAD-box RNA helicase is known to be associated with various complexes, including the decapping complex, the CPEB repression complex, RISC, and the CCR4/NOT complex. To understand which DDX6 complexes are required for P-body assembly, we analyzed the DDX6 interactome using the tandem-affinity purification methodology coupled to mass spectrometry. Three complexes were prominent: the decapping complex, a CPEB-like complex, and an Ataxin2/Ataxin2L complex. The exon junction complex was also found, suggesting DDX6 binding to newly exported mRNAs. Finally, some DDX6 was associated with polysomes, as previously reported in yeast. Despite its high enrichment in P-bodies, most DDX6 is localized out of P-bodies. Of the three complexes, only the decapping and CPEB-like complexes were recruited into P-bodies. Investigation of P-body assembly in various conditions allowed us to distinguish required proteins from those that are dispensable or participate only in specific conditions. Three proteins were required in all tested conditions: DDX6, 4E-T, and LSM14A. These results reveal the variety of pathways of P-body assembly, which all nevertheless share three key factors connecting P-body assembly to repression.
Protein degradation corrects for imbalanced subunit stoichiometry in OST complex assembly
Authors: Mueller Susanne , Wahlander Asa , Selevsek Nathalie , Otto Claudia , Ngwa Elsy Mankah , Poljak Kristina , Frey Alexander D. , Aebi Markus , Gauss Robert
Published: May 2015

Protein degradation is essential for cellular homeostasis. We developed a sensitive approach to examining protein degradation rates in Saccharomyces cerevisiae by coupling a SILAC approach to selected reaction monitoring (SRM) mass spectrometry. Combined with genetic tools, this analysis made it possible to study the assembly of the oligosaccharyl transferase complex. The ER-associated degradation machinery compensated for disturbed homeostasis of complex components by degradation of subunits in excess. On a larger scale, protein degradation in the ER was found to be a minor factor in the regulation of protein homeostasis in exponentially growing cells, but ERAD became relevant when the gene dosage was affected, as demonstrated in heterozygous diploid cells. Hence the alleviation of fitness defects due to abnormal gene copy numbers might be an important function of protein degradation.
Identification of lamin B–regulated chromatin regions based on chromatin landscapes
Authors: Zheng Xiaobin , Kim Youngjo , Zheng Yixian
Published: May 2015

Lamins, the major structural components of the nuclear lamina (NL) found beneath the nuclear envelope, are known to interact with most of the nuclear peripheral chromatin in metazoan cells. Although NL–chromatin associations correlate with a repressive chromatin state, the role of lamins in tethering chromatin to NL and how such tether influences gene expression have remained challenging to decipher. Studies suggest that NL proteins regulate chromatin in a context-dependent manner. Therefore understanding the context of chromatin states based on genomic features, including chromatin–NL interactions, is important to the study of lamins and other NL proteins. By modeling genome organization based on combinatorial patterns of chromatin association with lamin B1, core histone modification, and core and linker histone occupancy, we report six distinct large chromatin landscapes, referred to as histone lamin landscapes (HiLands)-red (R), -orange (O), -yellow (Y), -green (G), -blue (B), and -purple (P), in mouse embryonic stem cells (mESCs). This HiLands model demarcates the previously mapped lamin-associated chromatin domains (LADs) into two HiLands, HiLands-B and HiLands-P, which are similar to facultative and constitutive heterochromatins, respectively. Deletion of B-type lamins in mESCs caused a reduced interaction between regions of HiLands-B and NL as measured by emerin–chromatin interaction. Our findings reveal the importance of analyzing specific chromatin types when studying the function of NL proteins in chromatin tether and regulation.
Russian Approaches to International Law
Authors: Mälksoo Lauri
Published: May 2015

This book examines Russian approaches to international law from three different yet closely interconnected perspectives: history, theory, and recent state practice. The study uses comparative international law as a starting point and argues that in order to understand post-Soviet Russia’s state and scholarly approaches to international law, one should take into account the history of ideas in Russia. To some extent, Russian understandings of international law differ from what is considered the mainstream in the West. One specific feature of this work is that it goes inside the language of international law as it is spoken and discussed in post-Soviet Russia, especially the scholarly literature in the Russian language, and relates this literature to the history of international law as discipline in Russia. Recent state practice such as the annexation of Crimea in 2014, Russia’s record in the UN SC, the European Court of Human Rights, investor-state arbitration, and the creation of the Eurasian Economic Union are laid out and discussed in the context of increasingly popular ‘civilizational’ ideas, i.e. the claim that Russia is a unique civilization and not part of Europe understood as the West. The implications of this claim for the future of international law, its universality and regionalism are discussed. This study concludes the author’s five-year work on ERC-funded grant that enabled him to attend international law conferences in Russia and other CIS countries, as well as get access to relevant sources that often cannot be so easily accessed in the West.
Inductive Inference
Authors: Gilboa Itzhak , Samuelson Larry , Schmeidler David
Published: May 2015

This chapter focuses on case-based reasoning. It offers an axiomatic approach to the following problem: given a database of observations, how should different eventualities be ranked? The approach is complementary to the Bayesian approach at two levels: first, it may offer an alternative model of prediction, when the information available to the predictor is not easily translated to the language of a prior probability. Second, the approach may describe how a prior is generated. The chapter is organized as follows. Section 2 presents the formal model and the main results. Section 3 discusses the relationship to kernel methods and to maximum likelihood rankings. Section 4 presents a critical discussion of the axioms, outlining their scope of application. Finally, Section 5 briefly discusses alternative interpretations of the model, and, in particular, relates it to case‐based decision theory.
The Sleeping Beauty Awakens Late: An Absolute Prohibition with Many Buts
Authors: Dembour Marie-Bénédicte
Published: May 2015

This chapter focuses on Soering v. the United Kingdom, which concerned the State of Virginia in the United States’ request for the extradition of a young German national, to be put on trial for murder. The case affirmed the obligation under Article 3 of the European Convention on Human Rights (ECHR) for a contracting state not to send a person to a place where this person might be subjected to torture or inhuman and degrading treatment or punishment. The chapter questions why Soering, rather than Vilvarajah v. the United Kingdom which had been previously lodged by a number of failed asylum seekers from Sri Lanka, became the leading case in Article 3 return cases. It also identifies the regrettable seeds—from a human rights perspective—which the Cruz Varas v. Sweden judgment, of the same period, planted, with effects discernible up to this day.
Domestic Asylum Procedures Aside: Scrutinising Strasbourg’s ‘Scrutiny’
Authors: Dembour Marie-Bénédicte
Published: May 2015

This chapter analyses the M.S.S. v. Belgium and Greece judgment of 2011, which called into question a central piece of the Common European Asylum System put in place by the European Union. It argues that the Court was ready to allow migrants to be returned to circumstances of serious adversity, including in Afghanistan. This is in part because the Court requires an impossibly high level of documentation before accepting that a situation is such that individuals should not be returned to a place of adversity.
Plasmonic Effects in Metal-Semiconductor Nanostructures
Authors: Toropov Alexey A. , Shubina Tatiana V.
Published: May 2015

This book offers an up-to-date overview of the growing trends in the field of solid state physics known as plasmonics. Initially, plasmonics was concerned with the study of resonant interactions of light with various metal structures. In recent years, however, the emphasis has shifted towards investigation of more sophisticated nanostructures involving not only metals but also semiconductors. The combination of strong surface plasmon resonances inherent to conducting structures with high responsivity of semiconductors to external electromagnetic fields have opened new exciting pathways to control light in ultra-compact geometries. The purpose of the book is to give a general view of electromagnetic and quantum phenomena taking place in metal-semiconductor plasmonic structures, ranging from basic physical theories to practical engineering applications, such as plasmonic nanolasers, plasmon-enhanced light-emitting diodes and solar cells, plasmonic emitters of quantum light, and advanced plasmonic devices operating in infrared and terahertz domains. The list of topics also includes achievement of the strong coupling regime in plasmonic cavities with both organic and inorganic semiconductors and preservation of the non-classical statistics of photons by propagating surface plasmon polaritons.
Bayesian Mechanism Design
Authors: Tilman Börgers , Daniel Krähmer , Roland Strausz
Published: May 2015

This chapter begins by applying general insights from the theory of incentive compatibility to the design of Bayesian incentive-compatible mechanisms when private signals are independent. It then moves on to study the case of correlated private signals and proves Cremer and McLean’s famous result on full surplus extraction in this case. The implications of this paradoxical result for the theory of mechanism are also discussed.
Trans-species learning of cellular signaling systems with bimodal deep belief networks
Authors: Chen Lujia , Cai Chunhui , Chen Vicky , Lu Xinghua
Published: May 2015

Motivation: Model organisms play critical roles in biomedical research of human diseases and drug development. An imperative task is to translate information/knowledge acquired from model organisms to humans. In this study, we address a trans-species learning problem: predicting human cell responses to diverse stimuli, based on the responses of rat cells treated with the same stimuli.

Results: We hypothesized that rat and human cells share a common signal-encoding mechanism but employ different proteins to transmit signals, and we developed a bimodal deep belief network and a semi-restricted bimodal deep belief network to represent the common encoding mechanism and perform trans-species learning. These ‘deep learning’ models include hierarchically organized latent variables capable of capturing the statistical structures in the observed proteomic data in a distributed fashion. The results show that the models significantly outperform two current state-of-the-art classification algorithms. Our study demonstrated the potential of using deep hierarchical models to simulate cellular signaling systems.

Availability and implementation: The software is available at the following URL: http://pubreview.dbmi.pitt.edu/TransSpeciesDeepLearning/. The data are available through SBV IMPROVER website, https://www.sbvimprover.com/challenge-2/overview, upon publication of the report by the organizers.

Contact: xinghua@pitt.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
ABC: a tool to identify SNVs causing allele-specific transcription factor binding from ChIP-Seq experiments
Authors: Bailey Swneke D. , Virtanen Carl , Haibe-Kains Benjamin , Lupien Mathieu
Published: May 2015

Motivation: Detection of allelic imbalances in ChIP-Seq reads is a powerful approach to identify functional non-coding single nucleotide variants (SNVs), either polymorphisms or mutations, which modulate the affinity of transcription factors for chromatin. We present ABC, a computational tool that identifies allele-specific binding of transcription factors from aligned ChIP-Seq reads at heterozygous SNVs. ABC controls for potential false positives resulting from biases introduced by the use of short sequencing reads in ChIP-Seq and can efficiently process a large number of heterozygous SNVs.

Results: ABC successfully identifies previously characterized functional SNVs, such as the rs4784227 breast cancer risk associated SNP that modulates the affinity of FOXA1 for the chromatin.

Availability and implementation: The code is open-source under an Artistic-2.0 license and versioned on GitHub (https://github.com/mlupien/ABC/). ABC is written in PERL and can be run on any platform with both PERL (≥5.18.1) and R (≥3.1.1) installed. The script requires the PERL Statistics::R module.

Contact:  mlupien@uhnres.utoronto.ca

Supplementary information:  Supplementary data are available at Bioinformatics online.
Impact of Preoperative Environmental Enrichment on Prevention of Development of Cognitive Impairment following Abdominal Surgery in a Rat Model
Authors: Kawano Takashi , Eguchi Satoru , Iwata Hideki , Tamura Takahiko , Kumagai Naoko , Yokoyama Masataka
Published: May 2015

AbstractAbstract

Anesthesia and surgery were associated with memory deficits, microglial activation, and elaboration of inflammatory cytokines in aged, but not young, animals. Preoperative environmental enrichment attenuated cognitive deficits and cytokine production in the brain. The data suggest that preoperative environmental enrichment can mitigate the adverse effects of anesthesia and surgery on postoperative cognitive function.

Supplemental Digital Content is available in the text.

Background:

Sustained neuroinflammation may contribute to the pathogenesis of postoperative cognitive dysfunction (POCD). Here, the authors evaluated the preventive effect of preoperative environmental enrichment (PEE) on the development of neuroinflammation and concomitant POCD in a rat abdominal surgery model.

Methods:

Young and aged rats were assigned to one of four groups using a 2 × 2 experimental design: PEE versus sedentary condition for 14 days, by abdominal surgery versus anesthesia alone (n = 8 in each group). After a 7-day postsurgical recovery period, cognitive function was assessed using a novel object recognition test, followed by measurement of hippocampal levels of proinflammatory cytokines. Under identical conditions, microglia were isolated from the hippocampus for assessment of cytokine response to lipopolysaccharide.

Results:

In the sedentary group, aged, but not young, rats receiving surgery showed memory deficits (novel object preference during testing phase of 54.6 ± 7.8% vs. 76.9 ± 11.3% in nonsurgery group, P < 0.05) and increased hippocampal levels of cytokines compared with nonsurgical rats. PEE had no effects on novel object preference in nonsurgery animals (78.6 ± 10.7%), whereas it attenuated surgery-induced impairment of novel object preference (70.9 ± 15.0%, P < 0.05 vs. sedentary/surgery group) as well as increase of cytokine levels in hippocampus. Furthermore, upon ex vivo stimulation with lipopolysaccharide, cytokines release from hippocampal microglia isolated from aged rats before intervention was significantly higher in comparison with young rats. PEE resulted in reduction of these age-related microglial phenotypic changes.

Conclusions:

PEE could prevent the development of neuroinflammation and related POCD in aged rats by reversion of a proinflammatory phenotype of hippocampal microglia.
Cost-effectiveness of Lumbar Epidural Steroid Injections
Authors: Carreon Leah Y. , Bratcher Kelly R. , Ammous Farah , Glassman Steven D.
Published: May 2015

Study Design.

Longitudinal cohort.

Objective.

To determine the cost per quality-adjusted life-year for lumbar epidural steroid injections (LESI).

Summary of Background Data.

Despite being a widely performed procedure, there are few studies evaluating the cost-effectiveness of LESIs.

Methods.

Patients who had received LESI between June 2012 and July 2013 with EuroQOL-5D (EQ-5D) scores available before and after LESIs but before any surgical intervention were identified. Costs were calculated on the basis of the Medicare Fee Schedule multiplied by the number of LESIs received between the 2 clinic visits. Quality-adjusted life-years (QALYs) were calculated using the EQ-5D.

Results.

Of 421 patients who had pre-LESI EQ-5D data, 323 (77%) had post-LESI data available; 200 females, 123 males, mean age: 59.2 ± 14.2 years. Cost per LESI was $608, with most patients receiving 3 LESIs for more than 1 year (range: 1–6 yr). Mean QALY gained was 0.005. One hundred forty-five patients (45%) had a QALY gain (mean = 0.117) at a cost of $62,175 per QALY gained; 127 patients (40%) had a loss in QALY (mean = −0.120) and 51 patients (15%) had no change in QALY. Fourteen of the 145 patients who improved, and 29 of the 178 patients who did not, have medical comorbidities that precluded surgery. Thirty-two (22%) of 131 patients without medical comorbidities who improved and 57 (32%) of 149 patients without medical comorbidities who did not improve subsequently had undergone surgery (P = 0.015).

Conclusion.

LESI may not be cost-effective in patients with lumbar degenerative disorders. For the 145 patients who improved, cost per QALY gained was acceptable at $62,175. However, for the 178 patients with no gain or a loss in QALY, the economics are not reportable with a cost per QALY gained being theoretically infinite. Further studies are needed to identify specific patient populations who will benefit from LESI because the economic viability of LESI requires improved patient selection.

Level of Evidence: 2
Atypical Testicular Torsion
Authors: Güneş Mustafa , Umul Mehmet , Altok Muammer
Published: May 2015

Testicular torsion is a common important urological emergency. Testicles usually undergo various degrees of rotation in a medial (inward) direction. Manual detorsion is a critical maneuver, allowing to prevent testis viability in patients with delay to get into the operation room. Testis torsion rarely occurs in lateral direction. It is important for patients undergoing manual detorsion. Hereby, we present a case of atypical lateral (outward) torsion who performed preoperative manual derotation.
Penetrating Cardiac Nail Gun Injury in a Child
Authors: Kulaylat Afif N. , Chesnut Charles H. , Patel Sunil , Rocourt Dorothy V. , Clark Joseph B.
Published: May 2015

Nail gun injuries primarily occur in the extremities of adult males as a consequence of accidental occupational trauma. Such injury involving the thorax is much less common, and penetrating cardiac injury secondary to pneumatic nail gun discharge is rare. Although potentially lethal, most cases with cardiac trauma are survivable with expedient surgical intervention. Despite improvements in engineered safety mechanisms, the incidence of nail gun injuries has risen as use of the devices has increased. The widespread availability of these tools to nonprofessional consumers exposes a broader population to the potential hazards associated with these devices. We describe the presentation and successful management of the first reported case of penetrating cardiac nail gun injury in a young child.
Simulating droplet motion on virtual leaf surfaces
Authors: Mayo Lisa C. , McCue Scott W. , Moroney Timothy J. , Forster W. Alison , Kempthorne Daryl M. , Belward John A. , Turner Ian W.
Published: May 2015

A curvilinear thin film model is used to simulate the motion of droplets on a virtual leaf surface, with a view to better understand the retention of agricultural sprays on plants. The governing model, adapted from Roy
et al.
(2002
J. Fluid Mech.
454, 235–261 (
doi:10.1017/S0022112001007133
)) with the addition of a disjoining pressure term, describes the gravity- and curvature-driven flow of a small droplet on a complex substrate: a cotton leaf reconstructed from digitized scan data. Coalescence is the key mechanism behind spray coating of foliage, and our simulations demonstrate that various experimentally observed coalescence behaviours can be reproduced qualitatively. By varying the contact angle over the domain, we also demonstrate that the presence of a chemical defect can act as an obstacle to the droplet's path, causing break-up. In simulations on the virtual leaf, it is found that the movement of a typical spray size droplet is driven almost exclusively by substrate curvature gradients. It is not until droplet mass is sufficiently increased via coalescence that gravity becomes the dominating force.
GenoWAP: Post-GWAS Prioritization Through Integrated Analysis of Genomic Functional Annotation
Authors: Lu Qiongshi , Yao Xinwei , Hu Yiming , Zhao Hongyu
Published: May 2015

Genome-wide association study (GWAS) has been a great success in the past decade. However, significant challenges still remain in both identifying new risk loci and interpreting results. Bonferroni-corrected significance level is known to be conservative, leading to insufficient statistical power when the effect size is moderate at risk locus. Complex structure of linkage disequilibrium also makes it challenging to separate causal variants from nonfunctional ones in large haplotype blocks. We describe GenoWAP, a post-GWAS prioritization method that integrates genomic functional annotation and GWAS test statistics. The effectiveness of GenoWAP is demonstrated through its applications to Crohn’s disease and schizophrenia using the largest studies available, where highly ranked loci show substantially stronger signals in the whole dataset after prioritization based on a subset of samples. At the single nucleotide polymorphism (SNP) level, top ranked SNPs after prioritization have both higher replication rates and consistently stronger enrichment of eQTLs. Within each risk locus, GenoWAP is also able to distinguish functional sites from groups of correlated SNPs. GenoWAP is freely available on the web at http://genocanyon.med.yale.edu/GenoWAP
Topologically associating domains and their long-range contacts are established during early G1 coincident with the establishment of the replication-timing program
Authors: Dileep Vishnu , Ay Ferhat , Sima Jiao , Vera Daniel L. , Noble William S. , Gilbert David M.
Published: May 2015

Mammalian genomes are partitioned into domains that replicate in a defined temporal order. These domains can replicate at similar times in all cell types (constitutive) or at cell type-specific times (developmental). Genome-wide chromatin conformation capture (Hi-C) has revealed sub-megabase topologically associating domains (TADs), which are the structural counterparts of replication domains. Hi-C also segregates inter-TAD contacts into defined 3D spatial compartments that align precisely to genome-wide replication timing profiles. Determinants of the replication-timing program are re-established during early G1 phase of each cell cycle and lost in G2 phase, but it is not known when TAD structure and inter-TAD contacts are re-established after their elimination during mitosis. Here, we use multiplexed 4C-seq to study dynamic changes in chromatin organization during early G1. We find that both establishment of TADs and their compartmentalization occur during early G1, within the same time frame as establishment of the replication-timing program. Once established, this 3D organization is preserved either after withdrawal into quiescence or for the remainder of interphase including G2 phase, implying 3D structure is not sufficient to maintain replication timing. Finally, we find that developmental domains are less well compartmentalized than constitutive domains and display chromatin properties that distinguish them from early and late constitutive domains. Overall, this study uncovers a strong connection between chromatin re-organization during G1, establishment of replication timing, and its developmental control.
X-ray diffraction method for determination of interplanar spacing and temperature distribution in crystals under an external temperature gradient
Authors: Kocharyan V. R. , Gogolev A. S. , Movsisyan A. E. , Beybutyan A. H. , Khlopuzyan S. G. , Aloyan L. R.
Published: May 2015

An X-ray diffraction method is developed for the determination of the distribution of temperature and interplanar spacing in a single-crystal plate. In particular, the temperature and the interplanar spacing differences in two different parts of a quartz single crystal of X-cut are experimentally determined depending on the value of the temperature gradient applied perpendicularly to the reflecting atomic planes (10\bar 11). The temperature distribution along the direction perpendicular to the reflecting atomic planes (10\bar 11) and the interplanar spacing distribution of atomic planes (10\bar 11) are determined as well.
Fast synthesis and refinement of the atomic pair distribution function
Authors: Coelho A. A. , Chater P. A. , Kern A.
Published: May 2015

A fast method for calculating the atomic pair distribution function is described in the context of performing refinements of structural models. Central to the speed of synthesis is the approximation of Gaussian functions of varying full widths at half-maximum using a narrower Gaussian with a fixed full width at half-maximum. The initial Gaussians are first laid down as delta functions which are then convoluted with the narrower Gaussian to form the final pattern. The net result is an algorithm, which has been included in the Rietveld refinement computer program TOPAS, that synthesizes and refines structural parameters a factor of 300–1000 times faster than alternative algorithms/programs, with speed advantages increasing as the number of atomic pairs increases.
Large field of view X-ray microscopy with asymmetric bent crystals and a laboratory source
Authors: Cusatis Cesar
Published: May 2015

In microscopy, there is a trade-off between the magnification and a workable field of view (FOV). In this paper, bent asymmetric diffraction wafers were used with a conventional X-ray source to accept high divergence and increase the FOV of a two-dimensional X-ray microscope. An FOV of 5 mm with 20× magnification was realized with two independent wafers in a thermomechanically stable setup. Using the knife-edge method, a resolution of 2.5 µm was measured in one dimension. The FOV of such a system is limited by the sizes of the wafers, and the magnification is limited only by the critical angle of external reflection.
Magnetite nanoparticles for nonradionuclide brachytherapy
Authors: Safronov Victor , Sozontov Evgeny , Polikarpov Mikhail
Published: May 2015

Magnetite nanoparticles possess several properties that can make them useful for targeted delivery of radiation to tumors for the purpose of brachytherapy. Such particles are biodegradable and magnetic and can emit secondary radiation when irradiated by an external source. In this work, the dose distribution around a magnetite particle of 10 nm diameter being irradiated by monochromatic X-rays with energies in the range 4–60 keV is calculated.
X-ray structure of cyanide-bound bovine heart cytochromecoxidase in the fully oxidized state at 2.0 Å resolution
Authors: Yano Naomine , Muramoto Kazumasa , Mochizuki Masao , Shinzawa-Itoh Kyoko , Yamashita Eiki , Yoshikawa Shinya , Tsukihara Tomitake
Published: May 2015

The X-ray structure of cyanide-bound bovine heart cytochromecoxidase in the fully oxidized state was determined at 2.0 Å resolution. The structure reveals that the peroxide that bridges the two metals in the fully oxidized state is replaced by a cyanide ion bound in a nearly symmetric end-on fashion without significantly changing the protein conformation outside the two metal sites.
Crystallization and preliminary X-ray diffraction analysis of the CRISPR–Cas RNA-silencing Cmr complex
Authors: Osawa Takuo , Inanaga Hideko , Numata Tomoyuki
Published: May 2015

Clustered regularly interspaced short palindromic repeat (CRISPR)-derived RNA (crRNA) and CRISPR-associated (Cas) proteins constitute a prokaryotic adaptive immune system (CRISPR–Cas system) that targets and degrades invading genetic elements. The type III-B CRISPR–Cas Cmr complex, composed of the six Cas proteins (Cmr1–Cmr6) and a crRNA, captures and cleaves RNA complementary to the crRNA guide sequence. Here, a Cmr1-deficient functional Cmr (CmrΔ1) complex composed ofPyrococcus furiosusCmr2–Cmr3,Archaeoglobus fulgidusCmr4–Cmr5–Cmr6 and the 39-merP. furiosus7.01-crRNA was prepared. The CmrΔ1 complex was cocrystallized with single-stranded DNA (ssDNA) complementary to the crRNA guide by the vapour-diffusion method. The crystals diffracted to 2.1 Å resolution using synchrotron radiation at the Photon Factory. The crystals belonged to the triclinic space groupP1, with unit-cell parametersa= 75.5,b= 76.2,c= 139.2 Å, α = 90.3, β = 104.8, γ = 118.6°. The asymmetric unit of the crystals is expected to contain one CmrΔ1–ssDNA complex, with a Matthews coefficient of 2.03 Å3 Da−1and a solvent content of 39.5%.
Crystallization and preliminary crystallographic analysis of latent, active and recombinantly expressed aurone synthase, a polyphenol oxidase, fromCoreopsis grandiflora
Authors: Molitor Christian , Mauracher Stephan Gerhard , Rompel Annette
Published: May 2015

Aurone synthase (AUS), a member of a novel group of plant polyphenol oxidases (PPOs), catalyzes the oxidative conversion of chalcones to aurones. Two activecgAUS1 (41.6 kDa) forms that differed in the level of phosphorylation or sulfation as well as the latent precursor form (58.9 kDa) were purified from the petals ofCoreopsis grandiflora. The differing activecgAUS1 forms and the latentcgAUS1 as well as recombinantly expressed latentcgAUS1 were crystallized, resulting in six different crystal forms. The active forms crystallized in space groupsP212121andP1211 and diffracted to ∼1.65 Å resolution. Co-crystallization of activecgAUS1 with 1,4-resorcinol led to crystals belonging to space groupP3121. The crystals of latentcgAUS1 belonged to space groupP1211 and diffracted to 2.50 Å resolution. Co-crystallization of recombinantly expressed pro-AUS with the hexatungstotellurate(VI) salt Na6[TeW6O24] within the liquid–liquid phase separation zone significantly improved the quality of the crystals compared with crystals obtained without hexatungstotellurate(VI).
Purification, crystallization and preliminary X-ray diffraction analysis of 3-ketoacyl-CoA thiolase A1887 fromRalstonia eutrophaH16
Authors: Kim Jieun , Kim Kyung-Jin
Published: May 2015

The gene product of A1887 fromRalstonia eutropha(ReH16_A1887) has been annotated as a 3-ketoacyl-CoA thiolase, an enzyme that catalyzes the fourth step of β-oxidation degradative pathways by converting 3-ketoacyl-CoA to acyl-CoA.ReH16_A1887 was overexpressed and purified to homogeneity by affinity and size-exclusion chromatography. The degradative thiolase activity of the purifiedReH16_A1887 was measured and enzyme-kinetic parameters for the protein were obtained, withKm,Vmaxandkcatvalues of 158 µM, 32 mM min−1and 5 × 106 s−1, respectively. TheReH16_A1887 protein was crystallized in 17% PEG 8K, 0.1 MHEPES pH 7.0 at 293 K and a complete data set was collected to 1.4 Å resolution. The crystal belonged to space groupP43212, with unit-cell parametersa=b= 129.52,c= 114.13 Å, α = β = γ = 90°. The asymmetric unit contained two molecules, with a solvent content of 58.9%.