bluuebunny/crossref_metadata_2025 huggingface dataset:
Isothiocyanate‐rich Moringa oleifera extract reduces weight gain, insulin resistance, and hepatic gluconeogenesis in mice
Authors: Waterman Carrie , Rojas‐Silva Patricio , Tumer Tugba Boyunegmez , Kuhn Peter , Richard Allison J. , Wicks Shawna , Stephens Jacqueline M. , Wang Zhong , Mynatt Randy , Cefalu William , Raskin Ilya
Published: January 2015

Scope

Moringa oleifera (moringa) is tropical plant traditionally used as an antidiabetic food. It produces structurally unique and chemically stable moringa isothiocyanates (MICs) that were evaluated for their therapeutic use in vivo.

Methods and results

C57BL/6L mice fed very high fat diet (VHFD) supplemented with 5% moringa concentrate (MC, delivering 66 mg/kg/d of MICs) accumulated fat mass, had improved glucose tolerance and insulin signaling, and did not develop fatty liver disease compared to VHFD‐fed mice. MC‐fed group also had reduced plasma insulin, leptin, resistin, cholesterol, IL‐1β, TNFα, and lower hepatic glucose‐6‐phosphatase (G6P) expression. In hepatoma cells, MC and MICs at low micromolar concentrations inhibited gluconeogenesis and G6P expression. MICs and MC effects on lipolysis in vitro and on thermogenic and lipolytic genes in adipose tissue in vivo argued these are not likely primary targets for the anti‐obesity and anti‐diabetic effects observed.

Conclusion

Data suggest that MICs are the main anti‐obesity and anti‐diabetic bioactives of MC, and that they exert their effects by inhibiting rate‐limiting steps in liver gluconeogenesis resulting in direct or indirect increase in insulin signaling and sensitivity. These conclusions suggest that MC may be an effective dietary food for the prevention and treatment of obesity and type 2 diabetes.
Can proteomics‐based diagnostics aid clinical psychiatry?
Authors: Filiou Michaela D.
Published: January 2015

Despite major advances in infrastructure and instrumentation, proteomics‐driven translational applications have not yet yielded the results that the scientific community has envisaged. In this viewpoint, the perspective of proteomics‐based diagnostics in the field of clinical psychiatry is explored. The challenges that proteomics faces in the context of translational approaches are outlined and directions toward a successful clinical implementation are provided. Additional challenges that psychiatric disorders pose for clinical proteomics are highlighted and the potential of proteomics‐based, blood tests for psychiatric disorders is being assessed. Proteomics offers a valuable toolkit for clinical translation that needs to be handled in a pragmatic manner and with realistic expectations.
Eco‐Friendly Countermeasures for Enlarged Basins Erosion
Authors: Pagliara S. , Palermo M. , Das R.
Published: January 2015

Eco‐friendly hydraulic structures (such as block ramps, rock weirs and stepped gabion weir) are generally made of rocks placed in two or more layers on a sloped bed. They are usually used in mountainous rivers to control sediment transport. The downstream stilling basin plays an important role in terms of both energy dissipation and erosion control. In addition, a correct design of the downstream stilling basin can create an optimal habitat for fish species in the river. Therefore, in the present work, an attempt was made to control the scour depth downstream of a block ramp using rock structures. In particular, the analysis was focused on scour characteristics in the presence of a protected and enlarged downstream channel. Namely, an abrupt symmetrically enlarged channel was simulated downstream of block ramps. Eco‐friendly protection structures, such as rock sills, were tested to limit the erosive process. Rock sills were placed transversally at different longitudinal and vertical positions in the stilling basin and scour morphology variations were investigated. Experiments were carried out for two different ratios of the width of the channel to the width of the ramp and three different ramp slopes. Several scour morphologies were distinguished and classified. In addition, empirical relationships were derived, by which it is possible to estimate the main scour geometry characteristics. Copyright © 2015 John Wiley & Sons, Ltd.
Spawning Migration of Wild and Supplementary Stocked Landlocked Atlantic Salmon (Salmo Salar)
Authors: Hagelin A. , Calles O. , Greenberg L. , Piccolo J. , Bergman E.
Published: January 2015

Upstream migration by adult salmonids is impeded by dams in many regulated rivers, as is the case for landlocked Atlantic salmon, Salmo salar, in the River Klarälven, Sweden. There, the salmon cannot reach the spawning grounds due to the presence of eight dams. Hence, hatchery‐reared smolts are released downstream of the dams, and upstream migrating spawners are caught in a trap at the lowermost dam before transported by truck to the spawning grounds past the dams. To identify the spawning grounds and compare the behavior of wild and hatchery‐reared Atlantic salmon during upstream migration and spawning, 34 wild and 28 hatchery‐reared, radio‐tagged Atlantic salmon were followed during their spawning migration from August to October 2011. Half (50%) of the hatchery fish, but only 11,8% of the wild fish ended up as fallbacks, i.e. they migrated past the first downstream power station, and did not spawn. A significantly higher proportion (21.4%) of hatchery‐ reared salmon moved in an erratic way, with several up and down stream movements, when compared to the wild salmon (5.9%). When looking at the salmon that stayed in the river (exc. fallbacks), wild individuals exhibited a holding behavior (little or no movements before presumed spawning) more often (86.7%) than the reared ones (50%). The wild salmon also held position (and presumably spawned) for longer time (25.4 days) than the reared salmon (16.1 days). Reared salmon held position, on average, 10 km further upstream than wild salmon, passing the presumed best‐quality spawning habitat. The migration speed (average 17.4 km/day) between two logger stations did not differ between wild and reared fish or between sexes. Our results suggest that the reproductive success of hatchery‐reared Atlantic salmon is relatively low and their capacity as supplementary spawners to the wild population in the Klarälven, is probably small. Copyright © 2015 John Wiley & Sons, Ltd.
Education, communication, and science in the public sphere
Authors: Feinstein Noah Weeth
Published: January 2015

In the 1920s, John Dewey and Walter Lippmann both wrote important books examining whether the public was capable of playing a constructive role in policy, particularly when specialized knowledge was involved. This essay uses the Lippmann–Dewey debate to identify new challenges for science education and to explore the relationship between science education and science communication. It argues that science education can help foster democracy in ways that embody Habermas' ideal of the public sphere, but only if we as a field pay more attention to (1) the non‐scientific frames and narratives that people use to interpret news about science, (2) the “second shaping” of scientific facts by the media, and (3) emerging platforms for public engagement. © 2015 Wiley Periodicals, Inc. J Res Sci Teach 52:145–163, 2015.
Creating Heroic Readers With Comic Books and Graphic Novels
Authors: Arneson Jason
Published: January 2015

View From the Chalkboard essays share readers' reflections on teaching experiences, advice for new teachers, and perspectives on current issues.
Triacylglycerol Composition Profiling and Comparison of High‐Oleic and Normal Peanut Oils
Authors: Dong X. Y. , Zhong J. , Wei F. , Lv X. , Wu L. , Lei Y. , Liao B. S. , Quek S. Y. , Chen H.
Published: January 2015

Oilseed plants produce huge amounts of fatty acids (FA) stored as triacylglycerols (TAG) in seeds that give a great variation in their composition. The variety and content of TAG directly affect the nutrition and function of lipids. TAG composition of 12 high‐oleic and normal peanut oil samples were profiled by two‐dimensional liquid chromatography (2D LC) coupled with atmospheric pressure chemical ionization mass spectrometry (APCI‐MS). The statistical evaluation of the TAG profiles determined was conducted on the basis of multidimensional data matrix using Principal Component Analysis (PCA). The technique enabled the differentiation of high‐oleic oils from normal peanut oils—as results illustrated TAG of high‐oleic peanut oil were clearly different from those of normal peanut oils. High‐oleic and normal peanut oils had different profiles mainly in the contents of OOO, OPO and POL. This finding provided theoretical foundation for detecting the adulteration of edible oils and analyzing the nutrition and function of high‐oleic peanut oils.
High-uptake areas on positron emission tomography with the hypoxic radiotracer 18F-FRP170 in glioblastomas include regions retaining proliferative activity under hypoxia
Authors: Beppu Takaaki , Sasaki Toshiaki , Terasaki Kazunori , Saura Hiroaki , Mtsuura Hideki , Ogasawara Kuniaki , Sasaki Makoto , Ehara Shigeru , Iwata Ren , Takai Yoshihiro
Published: January 2015

Objective

The aim was to evaluate the proliferative activity of high-uptake areas on positron emission tomography (PET) with the hypoxic cell radiotracer, 1-(2-[18F]fluoro-1-[hydroxymethyl]ethoxy)methyl-2-nitroimidazole (FRP170).

Methods

Thirteen patients with glioblastoma underwent FRP170 PET before tumor resection. During surgery, tumor specimens were stereotaxically obtained from regions corresponding to high (high-uptake areas, HUAs) and relatively low (low-uptake areas, LUAs) accumulation of FRP170. We compared immunohistochemical staining for Ki-67 and hypoxia-inducible factor (HIF)-1α between HUA and LUA.

Results

HIF-1α index was significantly higher in HUAs than in LUAs. In contrast, mean Ki-67 indices did not differ significantly between HUAs and LUAs.

Conclusions

Findings for HIF-1α index clearly indicated that HUAs on FRP170 PET represented hypoxic regions in glioblastoma. However, findings of Ki-67 index suggest that HUAs on FRP170 PET include regions retaining proliferative activity regardless of tissue hypoxia.
Adolescent online romantic relationship initiation: Differences by sexual and gender identification
Authors: Korchmaros Josephine D. , Ybarra Michele L. , Mitchell Kimberly J.
Published: January 2015

Data from the national Teen Health and Technology Study of adolescents 13–18 years old (N = 5091) were used to examine online formation of romantic relationships. Results show that lesbian, gay, bisexual, transgender, and queer (LGBTQ) and non‐LGBTQ adolescents similarly were most likely to have met their most recent boy/girlfriend in the past 12 months at school. However, they differed on many characteristics of romantic relationship initiation, including the extent to which they initiated romantic relationships online. LGBTQ and non‐LGBTQ adolescents also differed on level of offline access to potential partners, offline popularity, and numerous other factors possibly related to online relationship initiation (e.g., Internet use and demographic factors). Even after adjusting for differences in these factors, LGBTQ adolescents were more likely than non‐LGBTQ adolescents to find boy/girlfriends online in the past 12 months. The results support the rich‐get‐richer hypothesis as well as the social compensation hypothesis.
The Wonderful World of the Windpipe: A Review of Central Airway Anatomy and Pathology
Authors: Lawrence David A. , Branson Brittany , Oliva Isabel , Rubinowitz Ami
Published: January 2015

A variety of pathologic processes can involve the central airways. Abnormalities may either diffusely or focally involve the tracheal or mainstem bronchial walls. Diseases that diffusely involve the tracheal wall can be subclassified as sparing the membranous trachea or circumferentially involving the tracheal wall. Focal diseases of the trachea and mainstem bronchi include benign and malignant causes. Additionally, congenital and acquired morphologic abnormalities of the trachea will be reviewed.
GAPDH binders as potential drugs for the therapy of polyglutamine diseases: Design of a new screening assay
Authors: Lazarev Vladimir F. , Benken Konstantin A. , Semenyuk Pavel I. , Sarantseva Svetlana V. , Bolshakova Olga I. , Mikhaylova Elena R. , Muronetz Vladimir I. , Guzhova Irina V. , Margulis Boris A.
Published: January 2015

Proteins with long polyglutamine repeats form a complex with glyceraldehyde‐3‐phosphate dehydrogenase (GAPDH), which enhances aggregation and cytotoxicity in models of Huntington disease. The aim of this study was to develop a novel assay for the screening of anti‐aggregation compounds with a focus on the aggregation‐promoting capacity of GAPDH. The assay includes a pure Q58 polyglutamine fragment, GAPDH, and a transglutaminase that links the two proteins. The feasibility of the new assay was verified using two GAPDH binders, hydroxynonenal and −(−)deprenyl, and the benzothiazole derivative PGL‐135 which exhibits anti‐aggregation effect. All three substances were shown to reduce aggregation and cytotoxicity in the cell and in the fly model of Spinocerebellar ataxia.
Sinomenine alleviates mechanical hypersensitivity in mice with experimentally induced rheumatoid arthritis
Authors: Gao Tianle , Shi Tiansheng , Wiesenfeld-Hallin Zsuzsanna , Svensson Camilla I. , Xu Xiao-Jun
Published: January 2015

Background and aims

We have previously reported that sinomenine, an alkaloid isolated from the root of the plant Sinomenium acutum, had antinociceptive effect in rodent models of acute inflammatory or neuropathic pain. As a traditional medicine, sinomenine is used in China to treat rheumatoid arthritis (RA).

Methods

In the present study, we evaluated the potential antinociceptive effect of sinomenine in a mouse model of RA, collagen type II antibody (CII Ab) induced arthritis (CAIA) after acute and chronic administration.

Results

As single administration, sinomenine at 40 or 80 mg/kg significantly reduced mechanical hypersensitivity both at the time of peak joint inflammation (days 11–19 after CII Ab injection) or during the post-inflammatory phase (days 35–54). No tolerance to the effect of 80 mg/kg sinomenine was observed during repeated injection twice a day for 5 days from day 11 to day 19 or from day 49 to day 53 after CII Ab injection in CAIA mice.

Conclusions

We have shown that sinomenine is effective in alleviating localized and spread hypersensitivities in CAIA mice both during acute inflammation and in post-inflammatory phase. Further, repeated sinomenine administration has elevated the baseline mechanical threshold without producing tolerance.

Implications

Sinomenine may be clinically useful to treat chronic pain in RA, including wide-spread pain which appears to be a difficult clinical problem despite the improvement in the acute treatment of RA by disease modifying agents.
Was ist ästhetische Bildung?
Authors: Scheurle Christoph
Published: January 2015

Ästhetische Erfahrungen sind ubiquitär. Sie lassen sich überall machen und haben mit Kunst zunächst nichts zu tun. Fragen Sie nur einfach einmal jemanden in Neapel nach einer Straße und ergötzen Sie sich an der Erklärung. Bei der ästhetischen Erfahrung geht es um den Kollaps jener Kategorien, in denen wir Welt wahrnehmen. Gute Kunst nötigt uns, all den Schemata auf den Grund zu gehen, mit denen wir wie selbstverständlich operieren. (Buergel, 2004 S. 374)
Lehrkräfte an Kranken- und Altenpflegeschulen
Authors: Lauxen Oliver , Slotala Lukas
Published: January 2015

Die Situation der Lehrkräfte an deutschen Pflegeschulen ist bisher kaum beleuchtet. Im Rahmen eines regelmäßigen Pflegearbeitsmarktmonitorings im Bundesland Hessen sind Daten zur aktuellen Situation sowie zum zukünftigen Bedarf an Lehrkräften in den Kranken- und Altenpflegeschulen erhoben worden. Im Artikel werden die Qualifikationsstruktur der derzeit beschäftigten Lehrkräfte sowie der aktuelle und zukünftige Bedarf beschrieben. Die Ergebnisse deuten auf einen zunehmenden Bedarf an akademisch qualifizierten Pflegepädagoginnen und -pädagogen hin.
Negative Differential Resistance and Spin-Filtering Effects in Zigzag Graphene Nanoribbons with Nitrogen-Vacancy Defects
Authors: Xu Ting , Huang Jing , Li Qun-xiang
Published: January 2015

We explore the electronic and transport properties of zigzag graphene nanoribbons (GNRs) with nitrogen-vacancy defects by performing fully self-consistent spin-polarized density functional theory calculations combined with non-equilibrium Green's function technique. We observe robust negative differential resistance (NDR) effect in all examined molecular junctions. Through analyzing the calculated electronic structures and the bias-dependent transmission coefficients, we find that the narrow density of states of electrodes and the bias-dependent effective coupling between the central molecular orbitals and the electrode subbands are responsible for the observed NDR phenomenon. In addition, the obvious difference of the transmission spectra of two spin channels is observed in some bias ranges, which leads to the near perfect spin-filtering effect. These theoretical findings imply that GNRs with nitrogen-vacancy defects hold great potential for building molecular devices.
Effect of Surface Dangling Bonds and Molecular Passivation on Doped GaAs Nanowires
Authors: Cui Jian-gong , Zhang Xia , Huang Yong-qing , Ren Xiao-min
Published: January 2015

We have investigated the effect of surface dangling bonds and molecular passivation on the doping of GaAs nanowires by first-principles calculations. Results show that the positively charged surface dangling bond on Ga atom is the most stable defect for both ultrathin and large size GaAs nanowires. It can form the trap centers of holes and then prefer to capture the holes from p-type doping. Thus it could obviously reduce the efficiency of the p-type doping. We also found that the NO2 molecule is electronegative enough to capture the unpaired electrons of surface dangling bonds, which is an ideal passivation material for the Zn-doped GaAs nanowires.
Effect of Magnetic Field on Properties of AuPt Particles Magneto-electrodeposited on Carbon Paper
Authors: Zhang Jin-qiu , Li Da , Chen Miao-miao , An Mao-zhong , Yang Pei-xia , Wang Peng
Published: January 2015

AuPt nano particles are bi-functional catalysts for oxygen reduction reaction and oxygen evolution reaction that takes place on air electrodes in lithium air batteries. In this work, magnetic field was applied during electrodeposition for the preparation of AuPt particles. With the increase of the magnetic flux density under constant current density, the grain size decreases from ∼1 μm to 200 nm and the activity of the AuPt catalyst increases. The magnetic field orienting vertically to the electric field has a promotion effect on increasing the catalytic ability of AuPt/carbon electrode. By pulse plating, the grain size decreases to about 100 nm. By adjusting parameters of the electric field and the magnetic field, controllable in situ preparation of AuPt catalyst with various morphology and catalytic activity can be achieved.
Electrochemical Behavior and Specific Capacitance of Polyaniline/Silver Nanoparticle/Multi-walled Carbon Nanotube Composites
Authors: Li Jia , Zhang Di , Guo Jin-bao , Wei Jie
Published: January 2015

In this work, we fabricated the polyaniline/silver nanoparticle/multi-walled carbon nanotube (PANI/Ag/MWCNT) composites by in situ polymerization of aniline on the wall of Ag/MWCNTs with different aniline to Ag/MWCNT mass ratios. The chemical structure of the ternary composites was characterized by Fourier transform infrared spectroscopy, X-ray diffraction, and X-ray photoelectron spectroscopy. Scanning electron microscope and high-resolution transmission electron microscopy were used to observe the morphology of the ternary composites. The results showed that the polyaniline PANI layer was prepared successfully and it covered Ag/MWCNTs completely. In addition, Ag nanoparticles between the MWCNT core and the PANI layer existed in the form of elemental crystal, which could contribute to the electrochemical performance of the composites. Then we prepared the composite electrodes and studied their electrochemical behaviors in 1 mol/L KOH. It was found that these composite electrodes had very low impedance, and exhibited lower resistance, higher electrochemical activity, and better cyclic stability compared with pure PANI electrode. Particularly, when the mass ratio of aniline to Ag/MWCNTs was 5:5, the composite electrode displayed a small equivalent series resistance (0.23 Ω) and low interfacial charge transfer resistance (<0.25 Ω), as well as 160 F/g of the maximum specific capacitance at a current density of 0.25 A/g in KOH solution. We could conclude that the composite material had potential applications as cathode materials for lithium batteries and supercapacitors.
A Soviet West: nationhood, regionalism, and empire in the annexed western borderlands
Authors: Risch William
Published: January 2015

This article considers the role the Soviet Union's western borderlands annexed during World War II played in the evolution of Soviet politics of empire. Using the Baltic Republics and Western Ukraine as case studies, it argues that Sovietization had a profound impact on these borderlands, integrating them into a larger Soviet polity. However, guerrilla warfare and Soviet policy-making indirectly led to these regions becoming perceived as more Western and nationalist than other parts of the Soviet Union. The Baltic Republics and Western Ukraine differed in their engagement with the Western capitalist world. Different experiences of World War II and late Stalinism and contacts with the West ultimately led to this region becoming Soviet, yet different from the rest of the Soviet Union. While the Soviet West was far from uniform, perceived differences between it and the rest of the Soviet Union justified claims at the end of the 1980s that the Soviet Union was an empire rather than a family of nations.
“Serbs” in Bela krajina: a (deliberately) forgotten minority?
Authors: Bešter Romana , Komac Miran , Medvešek Mojca , Pirc Janez
Published: January 2015

There are three constitutionally recognized national/ethnic minorities in Slovenia: the Italians, the Hungarians and the Roma. In addition, there are other ethnic groups that could perhaps be considered as “autochthonous” national minorities in line with Slovenia's understanding of this concept. Among them is a small community of “Serbs” – the successors of the Uskoks living in Bela krajina, a border region of Slovenia. In this article we present results of a field research that focused on the following question: Can the “Serb” community in Bela krajina be considered a national minority? On the basis of the objective facts, it could be said that the “Serbs” in four Bela krajina villages are a potential national minority, but with regard to their modest social vitality and the fact that they do not express their desire for minority status, the realization of special minority protection is questionable.
Plant photosynthesis phenomics data quality control
Authors: Xu Lei , Cruz Jeffrey A. , Savage Linda J , Kramer David M. , Chen Jin
Published: January 2015

Motivation: Plant phenomics, the collection of large-scale plant phenotype data, is growing exponentially. The resources have become essential component of modern plant science. Such complex datasets are critical for understanding the mechanisms governing energy intake and storage in plants, and this is essential for improving crop productivity. However, a major issue facing these efforts is the determination of the quality of phenotypic data. Automated methods are needed to identify and characterize alterations caused by system errors, all of which are difficult to remove in the data collection step and distinguish them from more interesting cases of altered biological responses.

Results: As a step towards solving this problem, we have developed a coarse-to-refined model called dynamic filter to identify abnormalities in plant photosynthesis phenotype data by comparing light responses of photosynthesis using a simplified kinetic model of photosynthesis. Dynamic filter employs an expectation-maximization process to adjust the kinetic model in coarse and refined regions to identify both abnormalities and biological outliers. The experimental results show that our algorithm can effectively identify most of the abnormalities in both real and synthetic datasets.

Availability and implementation: Software available at www.msu.edu/%7Ejinchen/DynamicFilter

Contact:  jinchen@msu.edu or kramerd8@cns.msu.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
ASSIGN: context-specific genomic profiling of multiple heterogeneous biological pathways
Authors: Shen Ying , Rahman Mumtahena , Piccolo Stephen R. , Gusenleitner Daniel , El-Chaar Nader N. , Cheng Luis , Monti Stefano , Bild Andrea H. , Johnson W. Evan
Published: January 2015

Motivation: Although gene-expression signature-based biomarkers are often developed for clinical diagnosis, many promising signatures fail to replicate during validation. One major challenge is that biological samples used to generate and validate the signature are often from heterogeneous biological contexts—controlled or in vitro samples may be used to generate the signature, but patient samples may be used for validation. In addition, systematic technical biases from multiple genome-profiling platforms often mask true biological variation. Addressing such challenges will enable us to better elucidate disease mechanisms and provide improved guidance for personalized therapeutics.

Results: Here, we present a pathway profiling toolkit, Adaptive Signature Selection and InteGratioN (ASSIGN), which enables robust and context-specific pathway analyses by efficiently capturing pathway activity in heterogeneous sets of samples and across profiling technologies. The ASSIGN framework is based on a flexible Bayesian factor analysis approach that allows for simultaneous profiling of multiple correlated pathways and for the adaptation of pathway signatures into specific disease. We demonstrate the robustness and versatility of ASSIGN in estimating pathway activity in simulated data, cell lines perturbed pathways and in primary tissues samples including The Cancer Genome Atlas breast carcinoma samples and liver samples exposed to genotoxic carcinogens.

Availability and implementation: Software for our approach is available for download at: http://www.bioconductor.org/packages/release/bioc/html/ASSIGN.html and https://github.com/wevanjohnson/ASSIGN .

Contact : andreab@genetics.utah.edu or wej@bu.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
CypRules: a rule-based P450 inhibition prediction server
Authors: Shao Chi-Yu , Su Bo-Han , Tu Yi-Shu , Lin Chieh , Lin Olivia A. , Tseng Yufeng J.
Published: January 2015

Summary: Cytochrome P450 (CYPs) are the major enzymes involved in drug metabolism and bioactivation. Inhibition models were constructed for five of the most popular enzymes from the CYP superfamily in human liver. The five enzymes chosen for this study, namely CYP1A2, CYP2D6, CYP2C19, CYP2C9 and CYP3A4, account for 90% of the xenobiotic and drug metabolism in human body. CYP enzymes can be inhibited or induced by various drugs or chemical compounds. In this work, a rule-based CYP inhibition prediction online server, CypRules, was created based on predictive models generated by the rule-based C5.0 algorithm. CypRules can predict and provide structural rulesets for CYP inhibition for each compound uploaded to the server. Capable of fast execution performance, it can be used for virtual high-throughput screening (VHTS) of a large set of testing compounds.

Availability and implementation:  CypRules is freely accessible at http://cyprules.cmdm.tw/ and models, descriptor and program files for all compounds are publically available at http://cyprules.cmdm.tw/sources/sources.rar .

Contact:  yjtseng@csie.ntu.edu.tw

Supplementary information:  Supplementary data are available at Bioinformatics online.
Analysis of marine mammal bycatch in the Uruguayan pelagic longline fishery operating in the Southwestern Atlantic Ocean
Authors: Passadore Cecilia , Domingo Andrés , Secchi Eduardo R.
Published: January 2015

Bycatch is one of the main causes of human-caused mortality and population decline of many marine mammals. Monitoring bycatch is the first step to understand the impact of the fisheries on the species affected. Understanding how the interaction between marine mammals and fishing operations varies in space and time, and how it is influenced by environmental variables, is essential for designing mitigation strategies to reduce bycatch mortality. In this paper, we use data gathered by scientific observers and a fishing skipper to analyse marine mammals bycatch by the Uruguayan pelagic longline fishery operating in the Southwestern Atlantic Ocean from 1996 to 2007. The total bycatch per unit effort (Bcpue) was 0.0150 marine mammals/1000 hooks and the highest values (∼0.2) were recorded between 37°–38°S and 49°–51°W. Total cetacean Bcpue during the study period was low (0.0051 cetacean/1000 hooks) and occurred between 32°–37°S and 46°–54°W. Generalized additive models showed that cetaceans' bycatch was mainly affected by the depth, sea surface temperature, and season. Although cetaceans were captured year-round, the highest values were registered in spring months, most bycatch events occurred over the continental slope (median = 619 m) and in waters with a median temperature of 19.7°C. The bycatch of pinnipeds was influenced by depth, location, and season. Pinniped bycatch occurred mainly in winter, in waters ranging from 80 to 5000 m of depth (median = 2366 m) between 34°–37°S (median = 35.9°S) and 54°–49°W (median = 51.8°W). The spatial analysis showed that most bycatch events occurred within the Brazil–Malvinas Confluence zone, an area of high productivity where the pelagic longline fleet concentrates its fishing effort and where marine mammals probably concentrate to feed.
Discard mortality rates in the Bering Sea snow crab, Chionoecetes opilio, fishery
Authors: Urban J. Daniel
Published: January 2015

Fish and invertebrates that are unintentionally captured during commercial fishing operations and then released back into the ocean suffer mortality at unknown rates, introducing uncertainty into the fishery management process. Attempts have been made to quantify discard mortality rates using reflex action mortality predictors or RAMP which use the presence or absence of a suite of reflexes to predict discard mortality. This method was applied to snow crab, Chionoecetes opilio, during the 2010–2012 fisheries in the Bering Sea. Discard mortality in the fishery is currently assumed to be 50% in stock assessment models, but that rate is not based on empirical data and is widely recognized to be in need of refinement. Over 19 000 crab were evaluated using the RAMP method. The estimated discard mortality rate was 4.5% (s.d. = 0.812), significantly below the rate used in stock assessment models. Predicted discard mortality rates from the 2010 to 2012 study were strongly correlated with the air temperature at the St Paul Island airport in the Pribilof Islands. Using this relationship, the discard mortality rate from 1991 to 2011 was estimated at 4.8% (s.d. = 1.08).
Targeted Trapping of Mosquito Vectors in the Chesapeake Bay Area of Maryland
Authors: Shone Scott M. , Glass Gregory E. , Norris Douglas E.
Published: January 2015

Most adult mosquito surveillance in Maryland is performed using dry ice-baited or unbaited Centers for Disease Control (CDC) miniature light traps suspended ≈1.5 m above the ground. However, standardized trapping methods may miss mosquito species involved in disease transmission cycles. During a 2-yr study, the effectiveness of the olfactory attractant 1-octen-3-ol alone and in combination with carbon dioxide was evaluated for collecting mosquito vector species. In addition, trap heights were examined to determine the optimal vertical placement to target various species. We evaluated the results during the second year by targeting selected species by using various habitat–height–bait combinations. Although Culex erraticus Dyar & Knab and Anopheles quadrimaculatus Say were not successfully targeted, Culex salinarius Coquillett, Aedes vexans Meigen, Anopheles bradleyi/crucians King, Coquillettidia perturbans Walker, Aedes sollicitans Walker, and Aedes taeniorhynchus Wiedemann were preferentially captured using targeted trapping schemes.
Borrelia lusitaniae and Spotted Fever Group Rickettsiae in Ixodes ricinus (Acari: Ixodidae) in Tuscany, Central Italy
Authors: Bertolotti Luigi , Tomassone Laura , Tramuta Clara , Grego Elena , Amore Giuseppina , Ambrogi Cecilia , Nebbia Patrizia , Mannelli Alessandro
Published: January 2015

Prevalence of infection by Borrelia burgdorferi s.l. and spotted fever group (SFG) rickettsiae was estimated in host-seeking ticks in an area in Tuscany, central Italy, where Lyme borreliosis was reported in a forestry worker. B. burgdorferi s.l. was identified by polymerase chain reaction in 16.7% (95% CI = 10.3, 24.8) of Ixodes ricinus (L.) nymphs and 39.6% (95% CI = 26.5, 54.0) of adults. Borrelia lusitaniae accounted for 82.9% of positive samples, followed by Borrelia garinii (9.8%), Borrelia afzelii (2.4%), and Borrelia burgdorferi s.s. (2.4%). One Rhipicephalus spp. adult was infected with B. garinii (prevalence = 8.3%; 95% CI = 0.21, 38.5). Prevalence of infection by SFG rickettsiae was 38.5% (95% CI = 26.7, 51.4) in I. ricinus nymphs, 34.6% (95% CI = 22.0, 49.1) in I. ricinus adults, and 50% (95% CI = 21.1, 78.9) in Rhipicephalus spp. adults. Phylogenetic analysis showed the similarity of B. lusitaniae strains that were identified in this study and of a strain that was previously isolated from a human patient in Portugal. Results of this study confirm the dominance of B. lusitaniae in areas in the Mediterranean basin and the infection by SFG rickettsiae in I. ricinus.
Population Dynamics of Malaria Vectors in Western Kenya Highlands
Authors: Ndenga Bryson , Githeko Andrew , Omukunda Elizabeth , Munyekenye Godwil , Atieli Harrysonne , Wamai Peter , Mbogo Charles , Minakawa Noboru , Zhou Goufa , Yan Guiyun
Published: January 2015

Studies were carried out at three sites in the highlands of western Kenya (Iguhu and Mbale in Kakamega and Vihiga districts, respectively, and Marani in Kisii district) and at one site in the western Kenya lowlands (Kombewa in Kisumu district) to determine the spatial-temporal dynamics of malaria vectors and intensity of malaria transmission from June 2003 to June 2004. At the highland sites, Anopheles gambiae Giles predominated, constituting >80% of the vector species, whereas An. funestus Giles made up <20%. In contrast, at the lowland site, An. funestus made up 68% of the vector species. The mean annual indoor resting densities of An. gambiae at Iguhu were 5.0 female mosquitoes per house per night, 14.2- and 26.3-fold greater than those at Mbale and Marani. During the main transmission season, the indoor resting densities of An. gambiae increased 4.1-, 10.1-, and 5.0-fold over the dry season period in Iguhu, Mbale, and Marani, respectively. The estimated annual entomological inoculation rate (EIR) at Iguhu was 16.6 infectious bites per person per year (ib/p/yr), 1.1 at Mbale, and 0.4 at Marani. This suggests high spatial variation in vector abundance and malaria transmission intensity. At the lowland site, Kombewa, the total annual EIR was 31.1 ib/p/yr and the indoor resting densities during the transmission season increased 7.1-fold in An. funestus and 18.5-fold in An. gambiae sensu lato over the dry season. The low level of transmission in the highlands suggests that it may be disrupted by vector control methods such as residual spraying.
Electroantennogram and Behavioral Responses of Culex quinquefasciatus (Diptera: Culicidae) Females to Chemicals Found in Human Skin Emanations
Authors: Puri Sarika N. , Mendki M. J. , Sukumaran D. , Ganesan K. , Prakash Shri , Sekhar K.
Published: January 2015

The southern house mosquito, Culex quinquefasciatus Say (Diptera: Culicidae), is closely associated with humans and is a vector of filariasis. Use of semiochemicals for control of mosquitoes is a novel and potentially ecofriendly control approach. Human skin emanations are known to attract mosquitoes. In the current study, olfactory and behavioral responses of host-seeking female Cx. quinquefasciatus to various chemical components of human skin emanations (carboxylic acids, alcohols, and aldehydes) were evaluated separately at three doses (0.01, 0.1, and 1 μg) for electroantennogram (EAG) and three doses (0.1, 1, and 10 μg) for behavioral assay. Results of EAG studies indicated that all carboxylic acids elicited significant olfactory responses except tetradecanoic acid (C14) and octadecanoic acid (C18). In particular, hexanoic acid (C6) elicited a maximum, eight-fold olfactory response compared with the solvent control. Ethylene glycol and benzyl alcohol exhibited significant EAG and behavioral responses, whereas among aldehydes, nonanal elicited high EAG and behavioral responses, but only at all three doses tested compared with control. Some carboxylic acids elicited significant behavioral responses, attracting ≈75% of females tested toward chemical stimuli in a Y-tube olfactometer.
Heated Oligonucleotide Ligation Assay (HOLA): An Affordable Single Nucleotide Polymorphism Assay
Authors: Black W. C. , Gorrochotegui-escalante N. , Duteau N. M.
Published: January 2015

Most single nucleotide polymorphism (SNP) detection requires expensive equipment and reagents. The oligonucleotide ligation assay (OLA) is an inexpensive SNP assay that detects ligation between a biotinylated "allele-specific detector" and a 3′ fluorescein-labeled "reporter" oligonucleotide. No ligation occurs unless the 3′ detector nucleotide is complementary to the SNP nucleotide. The original OLA used chemical denaturation and neutralization. Heated OLA (HOLA) instead uses a thermal stable ligase and cycles of denaturing and hybridization for ligation and SNP detection. The cost per genotype is ≈US$1.25 with two-allele SNPs or ≈US$1.75 with three-allele SNPs. We illustrate the development of HOLA for SNP detection in the Early Trypsin and Abundant Trypsin loci in the mosquito Aedes aegypti (L.) and at the α  -glycerophosphate dehydrogenase locus in the mosquito Anopheles gambiae s.s.
Insecticide Resistance in Anopheles funestus (Diptera: Culicidae) from Mozambique
Authors: Casimiro S. , Coleman M. , Mohloai P. , Hemingway J. , Sharp B.
Published: January 2015

Malaria control in southern Mozambique is currently by indoor residual carbamate insecticide treatment, with pyrethroid-treated bed-nets distributed to pregnant women and children under five in northern Mozambique. The susceptibility of Anopheles funestus s.s. to pyrethroid, carbamate, organochlorine, and organophosphorus insecticides was determined by World Health Organization adult mosquito susceptibility tests at 19 localities in Mozambique, from March 2000 to July 2002. Biochemical assays were carried out on mosquitoes from the same families to detect shifts in the quantity or activity of enzyme families involved in insecticide detoxification. An. funestus from all localities remained fully susceptible to DDT and the organophosphorus insecticide malathion. A high level of pyrethroid resistance was detected in An. funestus populations in southern Mozambique. An. funestus outside Maputo province were still susceptible to pyrethroids. An. funestus from six localities also were resistant to carbamate insecticides propoxur and bendiocarb. Both pyrethroid and carbamate resistance occurred in five of these six localities. Mosquitoes from five of the localities with elevated p450 estimates, compared with the insecticide-susceptible Durban strain, were pyrethroid-resistant. The only exception to this trend was Mozal, which had elevated p450 estimates but full pyrethroid susceptibility by bioassay. The lack of cross-resistance between pyrethroids and DDT in Mozambican An. funestus suggests that a kdr-type target site resistance mechanism has not been selected. Low levels of insecticide-insensitive acetylcholinesterase, the target site for carbamates and organophosphates, were found in all populations tested. The high level of metabolically based pyrethroid resistance has implications for current malaria control programs in Mozambique.
Horizontal Transfer of Shiga Toxin and Antibiotic Resistance Genes Among Escherichia coli Strains in House Fly (Diptera: Muscidae) Gut
Authors: Petridis M. , Bagdasarian M. , Waldor M. K. , Walker E.
Published: January 2015

Whether the house fly, Musca domestica L., gut is a permissive environment for horizontal transfer of antibiotic resistance and virulence genes between strains of Escherichia coli is not known. House flies were immobilized and force fed suspensions of defined, donor strains of E. coli containing chloramphenicol resistance genes on a plasmid, or lysogenic, bacteriophage-born Shiga toxin gene stx1 (bacteriophage H-19B::Ap1). Recipient strains were E. coli lacking these mobile elements and genes but having rifampicin as a selectable marker. Plasmid transfer occurred at rates of 10−2 per donor cell in the fly midgut and 10−3 in the fly crop after 1 h of incubation postfeeding. Bacteriophage transfer rate was ≈10−6 per donor cell without induction, but induction with mitomycin C increased rates of transfer to 10−2 per donor cell. These findings show that genes encoding antibiotic resistance or toxins will transfer horizontally among bacteria in the house fly gut via plasmid transfer or phage transduction. The house fly gut may provide a favorable environment for the evolution and emergence of pathogenic bacterial strains through acquisition of antibiotic resistance genes or virulence factors.
Glossina Proteolytic Lectin Does Not Require a Carbohydrate Moiety for Enzymatic or Trypanosome-Transforming Activities
Authors: Amin Daniel N. , Kamita Shizuo G. , Muluvi Geoffrey M. , Machuka Jesse , Hammock Bruce D. , Osir Ellie O.
Published: January 2015

The developmental cycle of the cyclically transmitted African trypanosome involves an obligatory passage through the tsetse fly, Glossina spp. This intricate relationship requires the presence of molecules within the insect vector, including a midgut lectin, that interact with the trypanosome. Recently, a gene encoding for a proteolytic lectin, with trypanosome-transforming activity, was isolated from a midgut cDNA library of Glossina fuscipes fuscipes Austen in our laboratory. Using the same approach, we have identified a similar gene from a midgut cDNA library of Glossina austeni (Newstead). The protein encoded by this gene was expressed in bacteria and a baculovirus-based expression system. The baculovirus-expressed lectin was found in the medium of baculovirus-infected Sf-21 cell cultures, indicating that the tsetse fly-derived signal peptide was recognized and cleaved by the Sf-21 cells. The baculovirus-expressed protein also was glycosylated despite the absence of classical O-linked and N-linked sugar attachment motifs. Both the baculovirus- and bacterium-expressed lectin proteins were shown to agglutinate trypanosomes and rabbit red blood cells in vitro. This agglutination was strongly inhibited by d-glucosamine. d-Glucosamine also inhibited the action of the authentic and recombinant lectins upon the chromogenic substrate Chromozym TRY. Interestingly, both baculovirus- and bacterium-expressed lectins showed no significant differences in terms of these activities, indicating that a sugar moiety is not essential for biological activity. Our results provide an important molecular tool for further characterization of Glossina proteolytic lectin.
Plasmodium Development in White-Eye (kh
w) and Transformed Strains (kh43) of Aedes aegypti (Diptera: Culicidae)
Authors: Beerntsen Brenda T. , LI Jianyong
Published: January 2015

Xanthurenic acid (XA) has been implicated as an inducer in vivo of exflagellation in Plasmodium spp. Consequently, the development of Plasmodium gallinaceum was assessed in a white-eye mosquito strain, kh  w, of Aedes aegypti (L.), which is deficient in XA because of a mutation of the gene encoding the enzyme kynurenine hydroxylase, and in a transformed line of kh  w mosquitoes that carry the wild-type cn  + gene of Drosophila melanogaster Meigen and express a functional enzyme necessary for XA production. Although XA was not detectable in kh  w mosquitoes by using high-pressure liquid chromatography with electrochemical detection, parasites were able to develop. Transformed kh  w mosquitoes failed to consistently support parasite development at higher prevalences and mean intensities than did the nontransformed kh  w lines, even though XA was detectable. These data suggest that factors other than XA may play a role in initiating Plasmodium development in vivo.
Transmission of Vesicular Stomatitis New Jersey Virus to Cattle by the Biting Midge Culicoides sonorensis (Diptera: Ceratopogonidae)
Authors: De Leon Adalberto A. Perez , Tabachnick Walter J.
Published: January 2015

Laboratory-reared Culicoides sonorensis Wirth & Jones were infected with vesicular stomatitis virus serotype New Jersey (family Rhabdoviridae, genus Vesiculovirus, VSNJV) through intrathoracic inoculation. After 10-d incubation at 25°C, these insects were allowed to blood feed on four steers. Two other steers were exposed to VSNJV through intralingual inoculation with 108 tissue culture infective dose50 VSNJV. All six steers became seropositive for VSNJV. The results demonstrate the ability of C. sonorensis to transmit VSNJV to livestock. Only the animals intralingually inoculated with VSNJV showed clinical signs in the form of vesicles at the site of inoculation. Uninfected C. sonorensis allowed to feed on the exposed animals did not become infected with VSNJV. Animals infected by C. sonorensis showed a slower antibody response compared with intralingually inoculated animals. This is probably because of different amounts of virus received via insect transmission and syringe inoculation. A significant difference was found in the serum acute-phase protein α-1-acid glycoprotein in animals that received VSNJV through C. sonorensis transmission. These animals had previously been exposed to insect attack in the field compared with intralingually inoculated animals and C. sonorensis-infected animals that had been protected from insect attack. The failure to observe clinical signs of vesicular stomatitis through transmission of VSNJV by C. sonorensis may explain widespread subclinical infections during vesicular stomatitis epidemics.
Evaluating Satellite Sensor-Derived Indices for Lyme Disease Risk Prediction
Authors: Rodgers Sarah E. , Mather Thomas N.
Published: January 2015

The wetness and greenness indices created using Landsat Thematic Mapper (TM) data from June 1995 and 1997 and July 2002 were tested for their ability to predict the location of sites with different levels of nymphal blacklegged tick, Ixodes scapularis Say, abundance in Rhode Island. In 1995, there were statistically significant differences in the mean of greenness and wetness indices between sites classified as low and moderate tick abundance areas (P = 0.005 and P = 0.041, respectively). In 1997, there also were statistically significant differences in the mean of the greenness and wetness indices, but these differences were between the grouping of low/moderate tick abundance and the high tick abundance category (P = 0.023 and P = 0.015, respectively). The same indices from the 2002 image were not significant predictors of tick abundance. It may be that Landsat TM-derived indices can be used to predict nymphal blacklegged tick abundance in years (e.g., 1995 and 1997) when tick abundance is lower than average but not in years when it is higher (e.g., 2002). Thus, it seems unlikely that these remotely sensed indices will be very useful for modeling nonperidomestic Lyme disease risk over a large region in Rhode Island.