bluuebunny/crossref_metadata_2025 huggingface dataset:
The influence of ENSO on South American precipitation during austral summer and autumn in observations and models
Authors: Tedeschi Renata G. , Collins Matthew
Published: May 2015

South American precipitation is observed to respond differently to different types of El Niño Southern Oscillation (ENSO) events, such as those in which the main signal in sea surface temperature (SST) occurs either in the eastern equatorial Pacific or central equatorial Pacific. This study investigates how Coupled Model Intercomparison Project Phase 5 (CMIP5) models represent different types of ENSO and how they represent teleconnections to South American precipitation. It is found that the CMIP5 models can represent the basic structure of SST anomalies that occur during different types of ENSO events and these are described using simple SST indices. Most of the CMIP5 models can reproduce the correct sign of precipitation anomalies in northeast South America during austral summer and autumn, in cases where the observed teleconnections are relatively strong. The same is also true of north South America in austral summer. In the east and southeast regions of South America, many models fail to reproduce the correct sign during both Canonical and Modoki/Central Pacific/Warm Pool ENSO events. The precipitation composites in Atmospheric Model Intercomparison Project (AMIP) models tend to agree with their CMIP5 counterparts, so we conclude that the errors in teleconnections are not principally driven by mean SST biases. Precipitation teleconnections in the northern regions are shown to be linked to variations in the Walker circulation in models, with the exception of that in north South America during March–May. During March–May, composite precipitation in southeast South America is related to wave trains emanating from the equator.
Chicken surimi fortified by omega‐3 fatty acid addition: manufacturing and quality properties
Authors: Wang Hao‐Lun , Chou Chung‐Hsi , Yu Yu‐Shan , Hsu Chin‐Lin , Wang Sheng‐Yao , Ko Yi‐Feng , Chen Yi‐Chen
Published: May 2015

BACKGROUND

The meat of spent hens is hard to use owing to its small amount and poor quality. A washing process to remove sarcoplasmic proteins and other impurities can prolong the shelf life of surimi‐like products. Owing to the benefits of omega‐3 polyunsaturated fatty acids (ω‐3 PUFAs), functional foods fortified with ω‐3 PUFAs are increasingly being marketed. Hence, in this study, ω‐3 FA‐fortified chicken surimi was manufactured, and how to ameliorate its lipid peroxidation during frozen storage was investigated.

RESULTS

A 0.10% (w/v) solution of sodium chloride (NaCl) instead of distilled water in the third washing step decreased (P < 0.05) myofibrillar protein loss and moisture content of spent hen breast protein recoveries. Oil droplets in fish, flaxseed or soybean oil‐added chicken surimi were well distributed. Moreover, flaxseed oil addition increased (P < 0.05) total ω‐3 FAs and ω‐3/ω‐6 FA ratio, while only fish oil provided long‐chain PUFAs. Oil addition decreased (P < 0.05) hardness and gumminess of chicken surimi, while flaxseed oil resulted in more (P < 0.05) yellow surimi than fish and soybean oil. Fish oil‐added samples showed higher (P < 0.05) lipid oxidation than flaxseed or soybean oil‐added samples under −15 to −10 °C storage, but α‐tocopherol addition ameliorated it.

CONCLUSION

A novel semi‐manufactured chicken surimi product with nutritional benefits could be developed by fortification with fish or flaxseed oil. © 2015 Society of Chemical Industry
What young people want from their diabetes team: developing a patient reported experience measure (PREM) for young people with type 1 diabetes
Authors: Girling Isabella , Day Emma , Fazakerley Kate , Gray Tat , Hindmarsh Peter , Musgrove Neil , Rahman Shakeel , Trevelyan Nicola , Warner Justin , Christie Deborah
Published: May 2015

The objectives of this study were: to explore whether a patient reported experience measure (PREM) questionnaire for carers reflected aspects of the clinic experience important to young people; and to develop a PREM for young people with type 1 diabetes (T1D) to measure their clinic experience.

A cross‐sectional study design and focus groups were used. Questions from a PREM for carers and four open‐ended questions were incorporated into a semi‐structured interview administered to 77 young people with T1D across four paediatric diabetes clinics.

Eighty‐two percent of young people rated help in managing high and low blood glucose as the most important aspect of their clinic experience. All items identified by parents as important were rated important by over two‐thirds of young people, with the exception of ‘How important is it to be seen on your own?’ (40% rated this as important). Thematic analysis identified two superordinate themes: learning new information, and age appropriate structure and communication. Exemplary quotations from each theme were converted into questions and reviewed by six young people using cognitive interviewing. The final question set was reviewed by the National Paediatric Diabetes Audit PREM working group. The PREM was distributed to 177 paediatric diabetes units in England and Wales for completion between September 2012 and January 2013.

Exploring what is important for a young person about their clinic experience has supported the construction of a paediatric‐centred measure. The young person PREM creates opportunities for improvement in care to help diabetes teams listen to patients and work with them to provide the best possible service. Copyright © 2015 John Wiley & Sons.
Life goals in patients with cancer: a systematic review of the literature
Authors: Hullmann Stephanie E. , Robb Sheri L. , Rand Kevin L.
Published: May 2015

Objective

Purposes of this systematic review of life goal research in cancer patients were to (1) identify life goal characteristics and processes being examined, (2) describe instruments used to assess life goal constructs, (3) identify theoretical models being used to guide research, and (4) summarize what is known about the impact of the cancer experience on life goal characteristics, processes, and psychological outcomes.

Methods

We conducted this systematic review using MEDLINE, PubMed, CINAHL, and PsycINFO databases. Inclusion criteria were as follows: (1) published between 1993 and 2014, (2) English language, (3) cancer patient population, and (4) original research articles that assessed life goal characteristics and/or goal processes. One hundred ninety‐seven articles were screened and 27 included in the final review.

Results

Seven life goal characteristics and seven life goal processes were identified, and less than half of studies investigated associations between goal characteristics and processes. Conceptual definitions were not provided for about half of the identified life goal constructs. Studies used both validated and author‐developed instruments to assess goal constructs. Twenty‐four different theoretical models were identified, with self‐regulation theory most frequently cited. Overall, the literature suggests that cancer impacts patients' life goal characteristics and processes, and life goal disturbance is related to poorer psychological outcomes.

Conclusions

The impact of the cancer experience on life goals is an important and emerging area of research that would benefit from conceptual and theoretical clarity and measurement consistency. Copyright © 2015 John Wiley & Sons, Ltd.
Electrical penetration graph technique as a tool to monitor the early stages of aphid resistance to insecticides
Authors: Garzo Elisa , Moreno Aranzazu , Hernando Sara , Mariño Vera , Torne María , Santamaria Estrella , Díaz Isabel , Fereres Alberto
Published: May 2015

BACKGROUND

Sulfoxaflor, a new insecticide from the sulfoximine chemical family, and imidacloprid, a widely used neonicotinoid insecticide, were tested to assess the susceptibility and feeding behaviour of two populations of Myzus persicae: Mp61, which exhibited target‐site R81T resistance to neonicotinoids, and Mp1989, a laboratory clone maintained since 1989 as a susceptible reference.

RESULTS

The imidacloprid LC50 value for Mp61 was 16 times higher than for Mp1989, showing a moderate level of resistance. Sulfoxaflor LC50 values for Mp61 and Mp1989 were much closer. The probing behaviour, as assessed by electrical penetration graphs (EPGs), of both populations was clearly altered by sulfoxaflor, which reduced the ability of aphids to find and feed from the phloem. The feeding behaviour of the susceptible Mp1989 population was much more severely affected than the moderately resistant Mp61 population on imidacloprid‐treated plants. PCR assays of both aphid populations followed by DNA sequencing identified differences between populations in the point mutation in the β‐subunit of the nicotinic acetylcholine receptor linked to the resistant gene against the neonicotinoid insecticide.

CONCLUSIONS

Sulfoxaflor provoked feeding cessation more rapidly than imidacloprid in both aphid populations. Sharp differences in feeding behaviour were detected between the susceptible and the moderately resistant neonicotinoid‐resistant aphid populations. The EPG technique can be used as a useful tool to give new insights into the functional effects of new chemical compounds and for early detection of low to moderate levels of resistance of sap‐feeding insects to insecticides. The potential of this technique was validated by molecular analysis of the R81T mutation target site. © 2015 Society of Chemical Industry
Taxonomic relationships of pollens from matrix‐assisted laser desorption/ionization time‐of‐flight mass spectrometry data using multivariate statistics
Authors: Seifert Stephan , Weidner Steffen M. , Panne Ulrich , Kneipp Janina
Published: May 2015

Rationale

Matrix‐assisted laser desorption/ionization mass spectrometry (MALDI‐MS) has been suggested as a promising tool for the investigation of pollen, but the usefulness of this approach for classification and identification of pollen species has to be proven by an application to samples of varying taxonomic relations.

Method

MALDI‐MS in combination with hierarchical cluster analysis (HCA) and principal component analysis (PCA) was used to delineate taxonomic relations between plants based on pollen biochemistry. To assess the robustness of the approach, pollen of 74 species of the plant orders Fagales and Coniferales were probed.

Results

Discrimination at the levels of plant order and genus were achieved using the whole spectral range. In many cases, different species of the same genus could be distinguished. The sources of the spectral/chemical differences at the genus level can be understood using PCA. Specifically, typical mass regions for exact genus detection were identified.

Conclusions

Our results indicate that the chemical information represented by MALDI‐TOFMS data is useful for reconstructing taxonomic relationships and is complementary to other chemical information on pollen from other spectroscopic data. Copyright © 2015 John Wiley & Sons, Ltd.
Letting Go of Stand‐Alone Technology
Authors: Calvert Heather
Published: May 2015

With the nationwide focus on increasing students understanding and use of technology, many teachers are beginning to incorporate a variety of technology into small group rotations. However, the use of technology during these rotations often does not require students to use higher level thinking or problem solving skills. By eliminating the ‘technology station' and instead providing students the chance to use technology to complete learning tasks at every work station, teachers can prepare students to be 21st century learners.
Keep your office afloat despite declining state revenues
Authors: Hope Joan
Published: May 2015

BALTIMORE, MD. — If you are the registrar at a public institution, you have probably felt the impact of cuts in state funding on your institution and your office. And you've heard about the challenges students face as a growing part of funding the institution comes from tuition and fees. But you still need to provide quality services and good customer service to students. How do you do it?
Review complexities of disclosing directory information, §99.37, Part 3
Authors: Rainsberger Richard
Published: May 2015

§99.37 What conditions apply to disclosing directory information? …
Prepare young leaders to be successful
Authors: Hope Joan
Published: May 2015

BALTIMORE, MD. — Are you ever the youngest person in the room at important campus meetings? Do you have young staff members who have the potential to become leaders?
Collaborate to provide comprehensive support, boost retention
Authors: Hope Joan
Published: May 2015

When students appear to be struggling, faculty members often suggest tutoring or other academic resources. But what if the student is hungry? What if she is being evicted from her apartment?
Development of a cutting force prediction model based on brittle fracture for carbon fiber reinforced polymers for rotary ultrasonic drilling
Authors: Yuan Songmei , Zhang Chong , Amin Muhammad , Fan Huitao , Liu Ming
Published: May 2015

Carbon fiber reinforced polymers (CFRP) T700 have got increasing demand in the aerospace industry due to their high specific strength, specific stiffness, and other unique properties. Due to their inhomogeneous, anisotropic, and thermal properties, it is challenging to achieve desired accuracy and to avoid from delamination, chip-off, cracking, and burning especially in the drilling process. The cutting force is the critical parameter which is required to minimize in order to drill a hole with better accuracy and minimize defects. In this research, the brittle fracture approach was adopted and a cutting force model was developed for CFRP-T700 based on the rotary ultrasonic drilling (RUD) process. The experimental RUD was carried out on CFRP-T700 material and found that the feed rate and spindle speed are two main parameters that affect the cutting force in RUD. The cutting force data obtained from the model and experimental setup were then analyzed and found that there is small variation even below 10 % (max value of variation is 8.5 % and the average value is 0.49 %) between simulated and measured values. So, the developed cutting force model was validated and found robust. Also, it was found that with four times increase of feed rate, there is also an increase of material removal rate (MRR) four times with the decrease in the cutting force. Moreover, this model will be much helpful to keep cutting force within limits through the optimal set of parameters as feed rate and spindle speed without extensive experimentation of such costly materials.
Retinal microvascular network attenuation in Alzheimer's disease
Authors: Williams Michael A. , McGowan Amy J. , Cardwell Chris R. , Cheung Carol Y. , Craig David , Passmore Peter , Silvestri Giuliana , Maxwell Alexander P. , McKay Gareth J.
Published: May 2015

Introduction

Cerebral small‐vessel disease has been implicated in the development of Alzheimer's disease (AD). The retinal microvasculature enables the noninvasive visualization and evaluation of the systemic microcirculation. We evaluated retinal microvascular parameters in a case‐control study of AD patients and cognitively normal controls.

Methods

Retinal images were computationally analyzed and quantitative retinal parameters (caliber, fractal dimension, tortuosity, and bifurcation) measured. Regression models were used to compute odds ratios (OR) and confidence intervals (CI) for AD with adjustment for confounders.

Results

Retinal images were available in 213 AD participants and 294 cognitively normal controls. Persons with lower venular fractal dimension (OR per standard deviation [SD] increase, 0.77 [CI: 0.62–0.97]) and lower arteriolar tortuosity (OR per SD increase, 0.78 [CI: 0.63–0.97]) were more likely to have AD after appropriate adjustment.

Discussion

Patients with AD have a sparser retinal microvascular network and retinal microvascular variation may represent similar pathophysiological events within the cerebral microvasculature of patients with AD.
Astrocytic β1‐integrin affects cellular composition of murine blood brain barrier in the cerebral cortex
Authors: Venkatesan Charu , Birch Derin , Peng Chian‐yu , Kessler John A.
Published: May 2015

The blood brain barrier (BBB) is composed of endothelial cells, astrocytes, and pericytes and maintains functional homeostasis by regulating transport of ions, fluid and cells between blood and neural tissue. The cellular and molecular pathways that contribute to the formation of the BBB in the developing brain have not been fully deciphered. β1‐integrin (β1‐itg) within endothelial cells is known to play a critical role in vasculogenesis. However, the role of astrocytic β1‐itg in BBB development is not known. Our study used a mouse glial fibrillary acidic protein (GFAP)‐cre transgenic line to selectively ablate β1‐itg within astrocytes. We found that deletion of astrocytic β1‐itg had a striking effect on the different cell types that form the BBB. Mutant mice had a decreased density of aquaporin‐4 immunoreactivity within the perivascular astrocytic end‐feet. We also found decreases in immunoreactivity for vimentin and CD‐31 within endothelial cells. These changes were not accompanied by functional changes in BBB under physiological conditions as assessed by extravasation of large and small molecular weight molecules. However, mutant mice had an increased incidence of severe cystic injury in response to neonatal hypoxia. Our findings show that astrocytic β1‐itg has an important role in defining cellular properties of the blood brain barrier in the cerebral cortex.
Permanent cardiac pacing in a patient with persistent left superior vena cava and concomitant agenesis of the right‐sided superior vena cava
Authors: Hassine M. , Hamdi S. , Chniti G. , Boussaada M. , Bouchehda N. , Mahjoub M. , Ben Hamda K. , Betbout F. , Maatouk F. , Gamra H.
Published: May 2015

Persistent left superior vena cava (PLSVC) can be incidentally detected during pacemaker implantation from the left pectoral side. Optimal site pacing is technically difficult, and lead stability of the right ventricle (RV) can lead to such a situation. We describe a case of successful single‐chamber pacemaker implantation in a 76‐year‐old woman with a PLSVC and concomitant agenesis of the right‐sided superior vena cava, after failed attempts with the conventional procedure. The pacemaker had been working well after 12 months of follow‐up.
Comparison of the effects of bepridil and aprindine for the prevention of atrial fibrillation after cardiac and aortic surgery: A prospective randomized study
Authors: Ozawa Mahito , Komatsu Takashi , Sato Yoshihiro , Kunugita Fusanori , Tachibana Hideaki , Tashiro Atsushi , Okabayashi Hitoshi , Nakamura Motoyuki
Published: May 2015

Background

Approximately one‐third of the patients undergoing cardiovascular surgery reportedly experience paroxysmal atrial fibrillation (AF) during the postoperative period. However, the usefulness of antiarrhythmic drugs for preventing postoperative AF recurrence in the Japanese population has not been extensively studied.

Methods

From a total of 118 patients who developed postoperative paroxysmal AF between April 2009 and March 2011, 72 patients (45 men, mean age 68±8 years) requiring treatment for postoperative AF due to symptoms lasting ≥30 min were enrolled to prospectively investigate the efficacy of oral bepridil (100 mg/day, n=37) or aprindine (40 mg/day, n=35).

Result

The AF recurrence‐free survival rates at 1, 3, 7, and 14 days were 100%, 94%, 57%, and 49%, respectively, in the aprindine group, and 100%, 97%, 86%, and 76%, respectively, in the bepridil group (P=0.028, aprindine vs. bepridil).

Conclusion

Bepridil, at a fixed dose of 100 mg/day, was considered to be more effective than a routine dose of aprindine for the prevention of postoperative AF recurrence.
Watchdogs or guard dogs: Do anti-corruption agencies need strong teeth?
Authors: Kuris Gabriel
Published: May 2015

Anti-corruption advocates worldwide deride “toothless” anti-corruption agencies and demand agencies “with teeth,” meaning strong law enforcement powers. However, there are drawbacks to such powers. This paper draws from the documented experiences of dozens of anti-corruption agencies worldwide to show that law enforcement powers are not determinative of agency effectiveness, nor are they always helpful. Rather, both “guard dog” agencies, which use law-enforcement powers to address crimes of corruption directly, and “watchdog” agencies, which merely uncover and report corruption issues, face unique challenges and constraints. An anti-corruption agency's powers may influence its strategic response to its operating environment, but ultimately are less critical to corruption reduction than other factors such as independence, political will, and the reliability of partner institutions.
Austrostigmidium, a new austral genus of lichenicolous fungi close to rock-inhabiting meristematic fungi in Teratosphaeriaceae
Authors: Pérez-Ortega Sergio , Garrido-Benavent Isaac , De Los Ríos Asunción
Published: May 2015

The new genus of lichenicolous fungi Austrostigmidium is described from Antarctica and Tierra del Fuego (Chile). It is characterized by the presence of black pseudothecia, pseudoparaphyses, fissitunicate, I−, KI− asci and 3-septate hyaline ascospores. So far, the only known species grows on Mastodia tessellata (Verrucariales, Eurotiomycetes). The new genus is compared with anatomically close genera. Based on nuLSU and nuSSU markers we inferred its phylogenetic relationships and found that it belongs to the family Teratosphaeriaceae (Capnodiales, Dothideomycetes) and is closely related to rock-inhabiting fungal species, as well as to the hyphomycetous lichenicolous fungus Xanthoriicola. Finally, the host-parasite interface has been analyzed by means of transmission electron microscopy and fluorescence microscopy in order to describe the interactions among the new fungus and the symbionts forming the host lichen.
Passions of the Intellect: A Study of Polemics
Authors: Dorschel Andreas
Published: May 2015

Polemics are a sort of critique typically suffused with inimical emotions and passions. But how are these emotions and passions to be construed? Neither authorial expression nor actual arousal properly account for their role in polemics. Rather, the polemicist must stage an unequal battle between a polemical self and the polemical target vis-à-vis an anticipated audience, skilfully handling, through his or her words, the emotions ascribed to each of them.
Three Temperature Regimes in Superconducting Photon Detectors: Quantum, Thermal and Multiple Phase-Slips as Generators of Dark Counts
Authors: Murphy Andrew , Semenov Alexander , Korneev Alexander , Korneeva Yulia , Gol’tsman Gregory , Bezryadin Alexey
Published: May 2015

We perform measurements of the switching current distributions of three w ≈ 120 nm wide, 4 nm thick NbN superconducting strips which are used for single-photon detectors. These strips are much wider than the diameter of the vortex cores, so they are classified as quasi-two-dimensional (quasi-2D). We discover evidence of macroscopic quantum tunneling by observing the saturation of the standard deviation of the switching distributions at temperatures around 2 K. We analyze our results using the Kurkijärvi-Garg model and find that the escape temperature also saturates at low temperatures, confirming that at sufficiently low temperatures, macroscopic quantum tunneling is possible in quasi-2D strips and can contribute to dark counts observed in single photon detectors. At the highest temperatures the system enters a multiple phase-slip regime. In this range single phase-slips are unable to produce dark counts and the fluctuations in the switching current are reduced.
Fluorometric assay for phenotypic differentiation of drug-resistant HIV mutants
Authors: Zhu Qinchang , Yu Zhiqiang , Kabashima Tsutomu , Yin Sheng , Dragusha Shpend , El-Mahdy Ahmed F. M. , Ejupi Valon , Shibata Takayuki , Kai Masaaki
Published: May 2015

Convenient drug-resistance testing of viral mutants is indispensable to effective treatment of viral infection. We developed a novel fluorometric assay for phenotypic differentiation of drug-resistant mutants of human immunodeficiency virus-I protease (HIV-PR) which uses enzymatic and peptide-specific fluorescence (FL) reactions and high-performance liquid chromatography (HPLC) of three HIV-PR substrates. This assay protocol enables use of non-purified enzyme sources and multiple substrates for the enzymatic reaction. In this study, susceptibility of HIV mutations to drugs was evaluated by selective formation of three FL products after the enzymatic HIV-PR reaction. This proof-of-concept study indicates that the present HPLC-FL method could be an alternative to current phenotypic assays for the evaluation of HIV drug resistance.
Eutectic Nano-Droplet Template Injection into Bulk Silicon to Construct Porous Frameworks with Concomitant Conformal Coating as Anodes for Li-Ion Batteries
Authors: Qu Fei , Li Chilin , Wang Zumin , Wen Yuren , Richter Gunther , Strunk Horst P.
Published: May 2015

Building porosity in monolithic materials is highly desired to design 3D electrodes, however ex-situ introduction or in-situ generation of nano-scale sacrificial template is still a great challenge. Here Al-Si eutectic droplet templates are uniformly injected into bulk Si through Al-induced solid-solid convection to construct a highly porous Si framework. This process is concomitant with process-inherent conformal coating of ion-conductive oxide. Such an all-in-one method has generated a (continuously processed) high-capacity Si anode integrating longevity and stable electrolyte-anode diaphragm for Li-ion batteries (e.g. a reversible capacity as large as ~1800 mAh/g or ~350 μAh/cm2-μm with a CE of ~99% at 0.1 C after long-term 400 cycles).
Neurocognitive dysfunction and pharmacological intervention using guanfacine in a rhesus macaque model of self-injurious behavior
Authors: Freeman Z T , Rice K A , Soto P L , Pate K A M , Weed M R , Ator N A , DeLeon I G , Wong D F , Zhou Y , Mankowski J L , Zink M C , Adams R J , Hutchinson E K
Published: May 2015

Self-injurious behavior (SIB) is a common comorbidity of psychiatric disorders but there is a dearth of information about neurological mechanisms underlying the behavior, and few animal models exist. SIB in humans is characterized by any intentional self-directed behavior that leads to wounds, whereas in macaques it is not always accompanied by wounds. We describe a cohort of rhesus macaques displaying SIB as adults, in which changes within the central nervous system were associated with the SIB. In these macaques, increases in central nervous system striatal dopamine (DA) receptor binding (BPND) measured by positron emission tomography (PET) [11C]raclopride imaging correlated with severity of wounding (rs=0.662, P=0.014). Furthermore, utilizing standardized cognitive function tests, we showed that impulsivity (stop signal reaction time, SSRT) and deficits in attentional set shifting (intra-/extradimensional shift) were correlated with increased severity of SIB (rs=0.563, P=0.045 and rs=0.692, P=0.009, respectively). We also tested the efficacy of guanfacine, an α2A adrenergic agonist that acts to improve postsynaptic transmission of neuronal impulses, in reducing SIB. A subset of these animals were enrolled in a randomized experimenter-blinded study that demonstrated guanfacine decreased the severity of wounding in treated animals compared with vehicle-only-treated controls (P=0.043), with residual beneficial effects seen for several weeks after cessation of therapy. Animals with the highest severity of SIB that received guanfacine also showed the most significant improvement (rs=−0.761, P=0.009). The elevated PET BPND was likely due to low intrasynaptic DA, which in turn may have been improved by guanfacine. With underlying physiology potentially representative of the human condition and the ability to affect outcome measures of disease using pharmacotherapy, this model represents a unique opportunity to further our understanding of the biology and treatment of SIB in both animals and humans.
Polyvinyl alcohol/polysaccharide hydrogel graft materials for arsenic and heavy metal removal
Authors: Chowdhury Md. Najmul Kabir , Ismail Ahmad Fauzi , Beg Mohammad Dalour Hossen , Hegde Gurumurthy , Gohari Rasool Jamshidi
Published: May 2015

Polyvinyl alcohol/polysaccharide hydrogel formation ((A)–(C)) and metallic species adsorption ((D)) for water treatment.
Tuning the optoelectronic properties of core-substituted naphthalene diimides by the selective conversion of imides to monothioimides
Authors: Etheridge F. S. , Fernando R. , Golen J. A. , Rheingold A. L. , Sauve G.
Published: May 2015

Molecules with a low optical gap and high electron affinity were obtained via selective thionation of the distal carbonyls of 2,6-dialkylamino core-substituted naphthalene diimide.
4-Nitro-2,1,3-benzoxadiazole derivatives as potential fluorescent sigma receptor probes
Authors: Schininà Barbara , Martorana Andrea , Colabufo Nicola Antonio , Contino Marialessandra , Niso Mauro , Perrone Maria Grazia , De Guidi Guido , Catalfo Alfio , Rappazzo Giancarlo , Zuccarello Elisa , Prezzavento Orazio , Amata Emanuele , Rescifina Antonio , Marrazzo Agostino
Published: May 2015

New fluorescent derivatives forσreceptors were designed and synthesized.
Interactions between fluid and fibers in a turbulent backward-facing step flow
Authors: Capone Alessandro , Romano Giovanni Paolo
Published: May 2015

In this work, a turbulent backward-facing step flow at Reynolds number ReH = 17 520, laden with rod-like particles, is investigated by means of particle image velocimetry. Particle loadings tested are within 0.02% and 0.05% volume fractions; thus, the suspensions may be considered as dilute. The high spatial resolution allows the identification of fiber orientation within the flow, so that mutual interactions between phases can be investigated by considering flow modifications and phenomena related to preferential concentration and orientation of fibers. Fibers’ concentration data show a moderate trend to accumulate at the channel centreline, whereas orientation data display a strong preferential orientation of fibers. Specifically, the local fibers’ orientation is correlated to the flow field in terms of mean flow direction and plane of maximum shear. The occurrence of a symmetrical orientation profile with respect to the channel centre-line is reported as well as the tendency to recover such profile downstream of the step.
Molecular dynamics insight to phase transition in n-alkanes with carbon nanofillers
Authors: Rastogi Monisha , Vaish Rahul
Published: May 2015

The present work aims to investigate the phase transition, dispersion and diffusion behavior of nanocomposites of carbon nanotube (CNT) and straight chain alkanes. These materials are potential candidates for organic phase change materials(PCMs) and have attracted flurry of research recently. Accurate experimental evaluation of the mass, thermal and transport properties of such composites is both difficult as well as economically taxing. Additionally it is crucial to understand the factors that results in modification or enhancement of their characteristic at atomic or molecular level. Classical molecular dynamics approach has been extended to elucidate the same. Bulk atomistic models have been generated and subjected to rigorous multistage equilibration. To reaffirm the approach, both canonical and constant-temperature, constant- pressure ensembles were employed to simulate the models under consideration. Explicit determination of kinetic, potential, non-bond and total energy assisted in understanding the enhanced thermal and transport property of the nanocomposites from molecular point of view. Crucial parameters including mean square displacement and simulated self diffusion coefficient precisely define the balance of the thermodynamic and hydrodynamic interactions. Radial distribution function also reflected the density variation, strength and mobility of the nanocomposites. It is expected that CNT functionalization could improve the dispersion within n-alkane matrix. This would further ameliorate the mass and thermal properties of the composite. Additionally, the determined density was in good agreement with experimental data. Thus, molecular dynamics can be utilized as a high throughput technique for theoretical investigation of nanocomposites PCMs.
Acetogenesis from H2plus CO2and nitrogen fixation by an endosymbiotic spirochete of a termite-gut cellulolytic protist
Authors: Ohkuma Moriya , Noda Satoko , Hattori Satoshi , Iida Toshiya , Yuki Masahiro , Starns David , Inoue Jun-ichi , Darby Alistair C. , Hongoh Yuichi
Published: May 2015

Symbiotic associations of cellulolytic eukaryotic protists and diverse bacteria are common in the gut microbial communities of termites. Besides cellulose degradation by the gut protists, reductive acetogenesis from H2plus CO2and nitrogen fixation by gut bacteria play crucial roles in the host termites’ nutrition by contributing to the energy demand of termites and supplying nitrogen poor in their diet, respectively. Fractionation of these activities and the identification of key genes from the gut community of the wood-feeding termiteHodotermopsis sjoestedtirevealed that substantial activities in the gut—nearly 60% of reductive acetogenesis and almost exclusively for nitrogen fixation—were uniquely attributed to the endosymbiotic bacteria of the cellulolytic protist in the genusEucomonympha. The rod-shaped endosymbionts were surprisingly identified as a spirochete species in the genusTreponema, which usually exhibits a characteristic spiral morphology. The endosymbionts likely use H2produced by the protist for these dual functions. Although H2is known to inhibit nitrogen fixation in some bacteria, it seemed to rather stimulate this important mutualistic process. In addition, the single-cell genome analyses revealed the endosymbiont's potentials of the utilization of sugars for its energy requirement, and of the biosynthesis of valuable nutrients such as amino acids from the fixed nitrogen. These metabolic interactions are suitable for the dual functions of the endosymbiont and reconcile its substantial contributions in the gut.
Classical conditioning of analgesic and hyperalgesic pain responses without conscious awareness
Authors: Jensen Karin , Kirsch Irving , Odmalm Sara , Kaptchuk Ted J. , Ingvar Martin
Published: May 2015

Significance

It is unclear to what extent new learning can take place outside of conscious awareness. In the present study, we used psychophysical measures and classical conditioning to establish whether psychologically mediated analgesic and hyperalgesic responses could be acquired by unseen (subliminally presented) stimuli. Our study demonstrates that analgesia and hyperalgesia can be learned without conscious awareness, suggesting that higher-order cognitive processes may be affected by implicit learning mechanisms.
Substrate-binding domain conformational dynamics mediate Hsp70 allostery
Authors: Zhuravleva Anastasia , Gierasch Lila M.
Published: May 2015

Significance

Heat shock protein 70 (Hsp70) molecular chaperones help maintain protein homeostasis. Hsp70 functions require regulated promiscuous binding and release of a wide range of protein substrates. ATP binding to the Hsp70 nucleotide-binding domain (NBD) regulates the affinity and kinetics of substrate binding to their substrate-binding domain (SBD). Our work sought deeper understanding of the role of conformational dynamics for allosteric signaling in Hsp70s: The SBD undergoes a seesaw-like conformational change from a high substrate affinity state to one with lower substrate affinity, and we show that this conformational change results in drastic changes in conformational flexibility for the SBD that are essential for efficient substrate binding and release. These insights will help efforts to use Hsp70s as therapeutic targets.
Seq2pathway: an R/Bioconductor package for pathway analysis of next-generation sequencing data
Authors: Wang Bin , Cunningham John M. , (Holly) Yang Xinan
Published: May 2015

Summary: Seq2pathway is an R/Python wrapper for pathway (or functional gene-set) analysis of genomic loci, adapted for advances in genome research. Seq2pathway associates the biological significance of genomic loci with their target transcripts and then summarizes the quantified values on the gene-level into pathway scores. It is designed to isolate systematic disturbances and common biological underpinnings from next-generation sequencing (NGS) data. Seq2pathway offers Bioconductor users enhanced capability in discovering collective pathway effects caused by both coding genes and cis-regulation of non-coding elements.

Availability and implementation: The package is freely available at http://www.bioconductor.org/packages/release/bioc/html/seq2pathway.html.

Contact: xyang2@uchicago.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
CoRegNet: reconstruction and integrated analysis of co-regulatory networks
Authors: Nicolle Rémy , Radvanyi François , Elati Mohamed
Published: May 2015

CoRegNet is an R/Bioconductor package to analyze large-scale transcriptomic data by highlighting sets of co-regulators. Based on a transcriptomic dataset, CoRegNet can be used to: reconstruct a large-scale co-regulatory network, integrate regulation evidences such as transcription factor binding sites and ChIP data, estimate sample-specific regulator activity, identify cooperative transcription factors and analyze the sample-specific combinations of active regulators through an interactive visualization tool. In this study CoRegNet was used to identify driver regulators of bladder cancer.

Availability: CoRegNet is available at http://bioconductor.org/packages/CoRegNet

Contact:  remy.nicolle@issb.genopole.fr or mohamed.elati@issb.genopole.fr

Supplementary inform  a  tion:  Supplementary data are available at Bioinformatics online.
Likelihood-based complex trait association testing for arbitrary depth sequencing data
Authors: Yan Song , Yuan Shuai , Xu Zheng , Zhang Baqun , Zhang Bo , Kang Guolian , Byrnes Andrea , Li Yun
Published: May 2015

Summary: In next generation sequencing (NGS)-based genetic studies, researchers typically perform genotype calling first and then apply standard genotype-based methods for association testing. However, such a two-step approach ignores genotype calling uncertainty in the association testing step and may incur power loss and/or inflated type-I error. In the recent literature, a few robust and efficient likelihood based methods including both likelihood ratio test (LRT) and score test have been proposed to carry out association testing without intermediate genotype calling. These methods take genotype calling uncertainty into account by directly incorporating genotype likelihood function (GLF) of NGS data into association analysis. However, existing LRT methods are computationally demanding or do not allow covariate adjustment; while existing score tests are not applicable to markers with low minor allele frequency (MAF). We provide an LRT allowing flexible covariate adjustment, develop a statistically more powerful score test and propose a combination strategy (UNC combo) to leverage the advantages of both tests. We have carried out extensive simulations to evaluate the performance of our proposed LRT and score test. Simulations and real data analysis demonstrate the advantages of our proposed combination strategy: it offers a satisfactory trade-off in terms of computational efficiency, applicability (accommodating both common variants and variants with low MAF) and statistical power, particularly for the analysis of quantitative trait where the power gain can be up to ∼60% when the causal variant is of low frequency (MAF < 0.01).

Availability and implementation: UNC combo and the associated R files, including documentation, examples, are available at http://www.unc.edu/∼yunmli/UNCcombo/

Contact:  yunli@med.unc.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
WGE: a CRISPR database for genome engineering
Authors: Hodgkins Alex , Farne Anna , Perera Sajith , Grego Tiago , Parry-Smith David J. , Skarnes William C. , Iyer Vivek
Published: May 2015

Summary: The rapid development of CRISPR-Cas9 mediated genome editing techniques has given rise to a number of online and stand-alone tools to find and score CRISPR sites for whole genomes. Here we describe the Wellcome Trust Sanger Institute Genome Editing database (WGE), which uses novel methods to compute, visualize and select optimal CRISPR sites in a genome browser environment. The WGE database currently stores single and paired CRISPR sites and pre-calculated off-target information for CRISPRs located in the mouse and human exomes. Scoring and display of off-target sites is simple, and intuitive, and filters can be applied to identify high-quality CRISPR sites rapidly. WGE also provides a tool for the design and display of gene targeting vectors in the same genome browser, along with gene models, protein translation and variation tracks. WGE is open, extensible and can be set up to compute and present CRISPR sites for any genome.

Availability and implementation: The WGE database is freely available at www.sanger.ac.uk/htgt/wge

Contact: vvi@sanger.ac.uk or skarnes@sanger.ac.uk

Supplementary information:  Supplementary data are available at Bioinformatics online.
Vert
Versus
Verre
: Vegetal Violence in Huysmans's
En Rade
Authors: Scott Hannah
Published: May 2015

In Joris-Karl Huysmans's 1887 novel
En rade
, Jacques Marles and his wife Louise, beset by financial troubles, flee Paris to find safe harbour in a dilapidated rural chateau. At first glance, this country setting seems to display all the stereotypical features of pastoral fantasy; however, Huysmans uses implicit urban rhetoric and imagery to create a wry subversion of the natural idyll. The comforts of nature are denied to the male subject as the countryside is stripped of its promise of escapism. This article examines, firstly, Huysmans's use of signifiers of urban unrest to turn nature's exuberance into a corollary for human, revolutionary violence. Secondly, it focuses specifically on glass and glass-breaking at the hands of an aggressive Mother Nature, evoking memories of urban destruction and Parisian civil strife. The association of nature with violence culminates in the invasion of the chateau and its looking glasses by green, the colour of nature, forcing this distressing natural world between man and his own narcissistic reflection. Huysmans reveals that the natural world is no more an ally than the unruly urban masses, and confronts the reader with the inexorable violence of vegetation.
A spatially resolved pressure-based approach to evaluate combined effects of human activities and management in marine ecosystems
Authors: Goodsir Freya , Bloomfield Helen J. , Judd Adrian D. , Kral Filip , Robinson Leonie A. , Knights Antony M.
Published: May 2015

Our oceans are heavily utilized by a wide variety of human activities that exert pressures which negatively impact marine ecosystems, occasionally leading to unsustainable rates of exploitation. A linkage framework approach can be used to make independent associations between sectors, activities, and the pressures they introduce. However, in reality, many different sectors and their associated activities overlap in time and space, potentially changing the severity of their impact as pressures combine, and undermine the efforts of environmental managers to mitigate the harmful effects of those activities. Here, we present a spatially resolved approach to assess the potential for combined effects using a linkage framework assessment. Using illustrative examples from the Northeast Atlantic, we show the likelihood of changes in pressure severity as a result of multiple overlapping activities. Management options to limit pressure introduction are explored and their benefit—measured as a reduction in the area of seabed impacted—assessed. In its simplest form, the approach can be used to develop potential precautionary management options in areas where data availability is poor and more comprehensive management measures where data are more widely available.
Mackerel predation on herring larvae during summer feeding in the Norwegian Sea
Authors: Skaret Georg , Bachiller Eneko , Langøy Herdis , Stenevik Erling K.
Published: May 2015

In the course of the past two decades, Atlantic mackerel, Scomber scombrus, have expanded their summer feeding distribution in the Norwegian Sea substantially, and now potentially overlap with pelagic larvae of Norwegian spring-spawning herring, Clupea harengus, as these drift northwards. Mackerel are known to be opportunistic predators, and the aim of this study was to evaluate mackerel predation in an area of overlap between mackerel and herring larvae, with particular focus on predation on herring larvae. In early June 2013, we followed a predefined transect in the expected core larvae distribution area on the Norwegian coastal shelf between about 66°N and 69°N. The transect was repeated twice, and samples of mackerel for stomach analyses and subsequent herring larvae samples were obtained at pre-defined stations. Mackerel were caught in all but one of the trawl hauls, but were hardly ever observed acoustically, suggesting that they were dispersed close to the surface throughout the study area. Herring larvae were caught in all samples. Calanoid copepods were the dominant prey of the mackerel, but 45% of the mackerel guts contained herring larvae, with a maximum of 225 larvae counted in a single gut. Both the frequency of guts containing herring larvae and the average amount of herring larvae increased in line with increasing abundance of larvae. On the other hand, no spatial correlation between mackerel abundance and herring larvae abundance was found at the station level. The results suggest that mackerel fed opportunistically on herring larvae, and that predation pressure therefore largely depends on the degree of overlap in time and space. Rough areal projections suggest that the mackerel would be capable of consuming the herring larvae present in the investigation area in 6–7 d, and that such predation therefore could have regulatory effects on stocks of Norwegian spring-spawning herring.
Accounting for Right Censoring in Interdependent Duration Analysis
Authors: Hays Jude C. , Schilling Emily U. , Boehmke Frederick J.
Published: May 2015

Duration data are often subject to various forms of censoring that require adaptations of the likelihood function to properly capture the data generating process, but existing spatial duration models do not yet account for these potential issues. Here, we develop a method to estimate spatial-lag duration models when the outcome suffers from right censoring, the most common form of censoring. We adapt Wei and Tanner's (1991) imputation algorithm for censored (non-spatial) regression data to models of spatially interdependent durations. The algorithm treats the unobserved duration outcomes as censored data and iterates between multiple imputation of the incomplete, that is, right censored, values and estimation of the spatial duration model using these imputed values. We explore the performance of an estimator for log-normal durations in the face of varying degrees of right censoring via Monte Carlo and provide empirical examples of its estimation by analyzing spatial dependence in states' entry dates into World War I.