bluuebunny/crossref_metadata_2025 huggingface dataset:
Comparative membrane proteome analysis of three Borrelia species
Authors: Gesslbauer Bernd , Poljak Albina , Handwerker Claudia , Schüler Wolfgang , Schwendenwein Daniel , Weber Corinna , Lundberg Urban , Meinke Andreas , Kungl Andreas J.
Published: April 2012

The versatility of the surface of Borrelia, the causative agent of Lyme borreliosis, is very important in host–pathogen interactions allowing bacteria to survive in ticks and to persist in a mammalian environment. To identify the surface proteome of Borrelia, we have performed a large comparative proteomic analysis on the three most important pathogenic Borrelia species, namely B. burgdorferi (strain B31), B. afzelii (strain K78), and B. garinii (strain PBi). Isolation of membrane proteins was performed by using three different approaches: (i) a detergent‐based fractionation of outer membrane proteins; (ii) a trypsin‐based partial shedding of outer cell surface proteins; (iii) biotinylation of membrane proteins and preparation of the biotin‐labelled fraction using streptavidin. Proteins derived from the detergent‐based fractionation were further sub‐fractionated by heparin affinity chromatography since heparin‐like molecules play an important role for microbial entry into human cells. All isolated proteins were analysed using either a gel‐based liquid chromatography (LC)‐MS/MS technique or by two‐dimensional (2D)‐LC‐MS/MS resulting in the identification of 286 unique proteins. Ninety seven of these were found in all three Borrelia species, representing potential targets for a broad coverage vaccine for the prevention of Lyme borreliosis caused by the different Borrelia species.
Separation of kallikrein 6 glycoprotein subpopulations in biological fluids by anion‐exchange chromatography coupled to ELISA and identification by mass spectrometry
Authors: Kuzmanov Uros , Smith Christopher R. , Batruch Ihor , Soosaipillai Antoninus , Diamandis Anastasia , Diamandis Eleftherios P.
Published: April 2012

Kallikrein 6 (KLK6) has been shown to be aberrantly glycosylated in ovarian cancer. Here, we report a novel HPLC anion exchange method, coupled to a KLK6‐specific ELISA, capable of differentiating KLK6 glycoform subgroups in biological fluids. Biological fluids were fractionated using anion exchange and resulting fractions were analyzed for KLK6 content by ELISA producing a four‐peak elution profile. Using this assay, the KLK6 elution profile and distribution across peaks of a set (n = 7) of ovarian cancer patient matched serum and ascites fluid samples was found to be different than the profile of serum and cerebrospinal fluid (CSF) of normal individuals (n = 7). Glycosylation patterns of recombinant KLK6 (rKLK6) were characterized using tandem mass spectrometry (MS/MS), and found to consist of a highly heterogeneous KLK6 population. This protein was found to contain all of the four diagnostic KLK6 peaks present in the previously assayed biological fluids. The rKLK6 glycoform composition of each peak was assessed by lectin affinity and MS/MS based glycopeptide quantification by product ion monitoring. The combined results showed an increase in terminal alpha 2–6 linked sialic acid in the N‐glycans found on KLK6 from ovarian cancer serum and ascites, as opposed to CSF and serum of normal individuals.
A proteogenomic approach to map the proteome of an unsequenced pathogen – Leishmania donovani
Authors: Pawar Harsh , Sahasrabuddhe Nandini A. , Renuse Santosh , Keerthikumar Shivakumar , Sharma Jyoti , Kumar Ghantasala. S. Sameer , Venugopal Abhilash , Sekhar Nirujogi Raja , Kelkar Dhanashree S. , Nemade Harshal , Khobragade Sweta N. , Muthusamy Babylakshmi , Kandasamy Kumaran , Harsha H. C. , Chaerkady Raghothama , Patole Milind S. , Pandey Akhilesh
Published: April 2012

Visceral leishmaniasis or kala azar is the most severe form of leishmaniasis and is caused by the protozoan parasite Leishmania donovani. There is no published report on L. donovani genome sequence available till date, although the genome sequences of three related Leishmania species are already available. Thus, we took a proteogenomic approach to identify proteins from two different life stages of L. donovani. From our analysis of the promastigote (insect) and amastigote (human) stages of L. donovani, we identified a total of 22322 unique peptides from a homology‐based search against proteins from three Leishmania species. These peptides were assigned to 3711 proteins in L. infantum, 3287 proteins in L. major, and 2433 proteins in L. braziliensis. Of the 3711 L. donovani proteins that were identified, the expression of 1387 proteins was detectable in both life stages of the parasite, while 901 and 1423 proteins were identified only in promastigotes and amastigotes life stages, respectively. In addition, we also identified 13 N‐terminally and one C‐terminally extended proteins based on the proteomic data search against the six‐frame translated genome of the three related Leishmania species. Here, we report results from proteomic profiling of L. donovani, an organism with an unsequenced genome.
jmzReader: A Java parser library to process and visualize multiple text and XML‐based mass spectrometry data formats
Authors: Griss Johannes , Reisinger Florian , Hermjakob Henning , Vizcaíno Juan Antonio
Published: April 2012

We here present the jmzReader library: a collection of Java application programming interfaces (APIs) to parse the most commonly used peak list and XML‐based mass spectrometry (MS) data formats: DTA, MS2, MGF, PKL, mzXML, mzData, and mzML (based on the already existing API jmzML). The library is optimized to be used in conjunction with mzIdentML, the recently released standard data format for reporting protein and peptide identifications, developed by the HUPO proteomics standards initiative (PSI). mzIdentML files do not contain spectra data but contain references to different kinds of external MS data files. As a key functionality, all parsers implement a common interface that supports the various methods used by mzIdentML to reference external spectra. Thus, when developing software for mzIdentML, programmers no longer have to support multiple MS data file formats but only this one interface. The library (which includes a viewer) is open source and, together with detailed documentation, can be downloaded from http://code.google.com/p/jmzreader/.
Early intervention services in psychiatry: the right stuff?
Authors: Mortimer Ann
Published: April 2012

Early intervention aims to prevent progression to psychosis in young at‐risk patients; however, in reality, patients referred to early intervention services are a heterogeneous group and more can be achieved by creating a sound formulation for each patient in order to understand their individual needs, argues Professor Mortimer.
Rehabilitation for multiple sclerosis: bridging the gaps
Authors: Greener Mark
Published: April 2012

There is increasing evidence that neuropsychological rehabilitation reduces cognitive symptoms in multiple sclerosis (MS). However, a national report by the Royal College of Physicians suggests that many MS patients are still experiencing difficulty accessing neurological rehabilitation services.
Identifying and reducing the risk of antipsychotic drug interactions
Authors: Bleakley Stephen
Published: April 2012

In this review, Stephen Bleakley, Registrar of the College of Mental Health Pharmacy, provides a summary of the principal interactions associated with antipsychotic drugs and discusses strategies to help reduce the risk of such interactions.
A qualitative and quantitative post‐mortem analysis: Studying free‐radical initiation processes via soft ionization mass spectrometry
Authors: Voll Dominik , Junkers Tanja , Barner‐Kowollik Christopher
Published: April 2012

The current article contains a review of the electrospray ionization‐mass spectrometry characterization of polymers prepared via thermal‐ and photoinitiation processes. The used analysis method permits direct access to detailed endgroup information. For a qualitative and quantitative endgroup analysis, sophisticated methods have been developed which provide a detailed image of the incorporation propensity of thermally as well as photolytically generated radicals at the polymer chain termini. Such a post‐mortem analysis of polymeric materials specifically allows for the quantification of the ability of radical fragments to initiate polymerization processes. Herein, the most recent progress in the field of mass spectrometric radical reactivity mapping is outlined and open questions as well as future directions are discussed. © 2012 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem, 2012
Controllable glycosylation of polyphosphazene via radical thiol–yne click chemistry
Authors: Ren Ning , Huang Xiao‐Jun , Huang Xu , Qian Yue‐Cheng , Wang Cang , Xu Zhi‐Kang
Published: April 2012

We describe a versatile approach to synthesize glycosylated polyphosphazenes with controllable density of glycosyl groups. These glycopolymers have been synthesized by the nucleophilic substitution of poly(dichlorophosphazene) with propargylamine and subsequent “thiol–yne” click reaction between poly[di(propargylamine)phosphazene] and 2,3,4,6‐tetra‐O‐acetyl‐1‐thio‐β‐D‐glucopyranose (SH‐GlcAc4). The polymers were characterized with FTIR and 1H NMR. We found that the high steric hindrance of SH‐GlcAc4 plays a key role in the overall reaction process, and ∼55% of the alkyne groups participate in the “thiol–yne” click reaction. About 8% of the alkyne groups convert to alkene groups at the end of click reaction. The substitution of alkyne/alkane mixture was conducted to reduce the alkyne density in the side groups of polyphosphazenes and minimize the influences of this steric effect. Mixed‐substituent polyphosphazene was synthesized with 2:3 ratio of alkyne and alkane. In this case, almost no alkyne group remains after the “thiol–yne” click reaction, and thus the glycosylated polyphosphazene is able to form into micelles through self‐assembly process. © 2012 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem, 2012
Polymerization shrinkage of (meth)acrylate determined by reflective laser beam scanning
Authors: Jian Yu , He Yong , Jiang Tongzhou , Li Chunguang , Yang Wantai , Nie Jun
Published: April 2012

The real‐time study of the shrinkage during UV‐curing of (meth)acrylate monomers is limited due to the very fast curing rate, their thin sample geometry (<100 μm), and low viscosity. We report a reflective laser scanning system for direct measurement of UV‐curing shrinkage. A low‐power laser beam at a wavelength of 650 nm, different from the polymerization wavelength (395 nm), was used. This noncontact method of measurement makes it possible to analyze the thin liquid monomer with a very low shrinkage (measuring accuracy 0.02 μm), and very fast curing rate (fast sampling speed of 50 KHz). Eight different kinds of UV monomers were tested using 2–5 mg specimens, and the shrinkage process was examined. The results proved that this new method was accurate and precise, and could be applied to different kinds of (meth)acrylates. Furthermore, the shrinkage capability of acrylic double bonds was determined as 23.98 mL/mol using this novel method. © 2012 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys, 2012
Prostasomes are heterogeneous regarding size and appearance but affiliated to one DNA‐containing exosome family
Authors: Ronquist Göran K. , Larsson Anders , Stavreus‐Evers Anneli , Ronquist Gunnar
Published: April 2012

BACKGROUND

Prostate acinar epithelial cells release microvesicles (prostasomes) that possess pleiotropic biological effects relevant for successful fertilization. Prostasomes are formed in a similar way as exosomes but are heterogeneous as regards size and appearance. Like exosomes they are thought to be mediators of intercellular communication.

METHODS

We prepared seminal prostasomes in accordance with the prevailing protocol for exosome preparation including passage through a 0.2 µm filter and centrifugation in a sucrose gradient.

RESULTS

We compared the “filterable prostasomes” with those trapped on the filter (“nonfilterable prostasomes”) and, qualitatively, no conspicuous differences were apparent regarding ultrastructure and SDS–PAGE banding pattern. Moreover, both types of prostasomes contained DNA fragments and Western blot revealed presence of prostate specific membrane antigen (PSMA), CD38, and annexin A1.

CONCLUSIONS

Reasonably, prostasomes could be included in the exosome family and be regarded as one entity containing chromosomal DNA. Prostate 72:1736–1745, 2012. © 2012 Wiley Periodicals, Inc.
Aerosol delivery of trail pheromone disrupts the foraging of the red imported fire ant, Solenopsis invicta
Authors: Suckling David Maxwell , Stringer Lloyd D , Corn Joshua E , Bunn Barry , El‐Sayed Ashraf M , Vander Meer Robert K
Published: April 2012

BACKGROUND: The fire ant, Solenopsis invicta, is one of the most aggressive and invasive species in the world. The trail pheromone Z,E‐α‐farnesene (91% purity) was prepared, and disruption of worker trail orientation was tested using an ethanol‐based aerosol formulation presenting a single puff of this compound by airbrush and compressed air. Trail‐following behaviour was recorded by overhead webcam and ants digitised before and after presentation of the aerosol treatment at four rates (1.6, 16, 160 and 1600 ng cm−2).

RESULTS: Ants preferred 110 ng cm−1 over 11, 1.1 and 0.11 ng cm−1 for trail following. Within seconds of presentation of 1600 ng cm−2, the highest dose tested, trail disruption was observed. Disruption was evident as reduced arrival success and reduction in the trail integrity statistic (r2), as well as increased deviation from the trail (deg). The distribution of walking track angles was also flattened.

CONCLUSIONS: The feasibility of using aerosol for delivery of trail pheromone was demonstrated, but the need for high purity combined with the difficulty of commercial supply makes this technique impractical. However, the commercial production of Z,E‐α‐farnesene of high purity by industrial biotechnology or from (E)‐nerolidol may be possible in future, which would facilitate further development of trail pheromone disruption of S. invicta. Copyright © 2012 Society of Chemical Industry
Insect growth regulators as potential insecticides to control olive fruit fly (Bactrocera oleae Rossi): insect toxicity bioassays and molecular docking approach
Authors: Bengochea Paloma , Christiaens Olivier , Amor Fermín , Viñuela Elisa , Rougé Pierre , Medina Pilar , Smagghe Guy
Published: April 2012

BACKGROUND: Olive fruit fly, Bactrocera oleae (Rossi), is a key pest in olive orchards, causing serious economic damage. To date, the pest has already developed resistance to the insecticides commonly applied to control it. Thus, in searching for new products for an accurate resistance management programme, targeting the ecdysone receptor (EcR) might provide alternative compounds for use in such programmes.

RESULTS: Residual contact and oral exposure in the laboratory of B. oleae adults to the dibenzoylhydrazine‐based compounds methoxyfenozide, tebufenozide and RH‐5849 showed different results. Methoxyfenozide and tebufenozide did not provoke any negative effects on the adults, but RH‐5849 killed 98‐100% of the treated insects 15 days after treatment. The ligand‐binding domain (LBD) of the EcR of B. oleae (BoEcR‐LBD) was sequenced, and a homology protein model was constructed. Owing to a restricted extent of the ligand‐binding cavity of the BoEcR‐LBD, docking experiments with the three tested insecticides showed a severe steric clash in the case of methoxyfenozide and tebufenozide, while this was not the case with RH‐5849.

CONCLUSION: IGR molecules similar to the RH‐5849 molecule, and different from methoxyfenozide and tebufenozide, might have potential in controlling this pest. Copyright © 2012 Society of Chemical Industry
Fertility control of rodent pests: a review of the inhibitory effects of plant extracts on ovarian function
Authors: Tran Tung Thanh , Hinds Lyn A
Published: April 2012

BACKGROUND: Plant extracts can inhibit fertility by adversely affecting, directly or indirectly, reproductive processes ranging from gonadal function and development to gestation. This review focuses on plant extracts that disrupt ovarian function in rodents.

RESULTS: Extracts from at least 40 plant species exert some of their disruptive reproductive effects at the ovarian level. Of those, 13 plants induce a reduction in the number and type of ovarian follicles and also cause disruption to the oestrous cycle. Their effects are short term and reversible once treatment ceases.

CONCLUSIONS: Protection of plant extracts to prevent their degradation before uptake in the gastrointestinal tract could enhance short‐term efficacy but would not enhance the longevity of their effects. Identification and further testing of the specific chemicals responsible for reproductive effects would be beneficial. The adoption of a standard protocol for treatment and assessment of the inhibitory effects of potential control agents on reproductive function in rodents is essential. Treatment with higher concentrations of extracts in conjunction with other extracts or with other chemosterilants could have potential complementary effects and lead to more rapid and permanent changes in ovarian function. An orally delivered agent(s) that causes major depletion of all follicle types, and particularly of non‐regenerating primordial follicles, could be an ideal fertility control product and serve as an additional tool for population control of pest rodents. © 2012 Society of Chemical Industry
A waste of ethics: the unjustified disposal of unused medicines
Authors: Humphreys Stephen
Published: April 2012

The author explains why he believes that the disposal of unused medicines is an instance of ethics beings used to serve an unethical purpose and that their redistribution could realise substantial savings for the NHS. Copyright © 2012 Wiley Interface Ltd
Management of type 2 diabetes: how and when to initiate insulin
Authors: Mostafa Samiul , Lawrence Ian
Published: April 2012

The natural history of type 2 diabetes is to ultimately require insulin for optimal glycaemic control. Here, the authors discuss when to initiate insulin and the recommended insulin options. Copyright © 2012 Wiley Interface Ltd
Rifaximin: unabsorbed oral antibiotic for travellers' diarrhoea
Authors: Chaplin Steve , Baburajan Bijay
Published: April 2012

Rifaximin (Xifaxanta) is a new orally administered antibiotic licensed for the treatment of noninvasive travellers' diarrhoea. In our New products review, Steve Chaplin presents the data relating to its efficacy and adverse events and Dr Bijay Baburajan discusses its place in treatment of traveller's diarrhoea. Copyright © 2012 Wiley Interface Ltd
Time evolution of dense multigraph limits under edge‐conservative preferential attachment dynamics
Authors: Ráth Balázs
Published: April 2012

We define the edge reconnecting model, a random multigraph evolving in time. At each time step we change one endpoint of a uniformly chosen edge: the new endpoint is chosen by linear preferential attachment. We consider a sequence of edge reconnecting models where the sequence of initial multigraphs is convergent in a sense which is a natural generalization of the notion of convergence of dense graph sequences, defined by Lovász and Szegedy (J. Combin. Theory Ser B 96 (2006) 933–957). We investigate how the limit object evolves under the edge reconnecting dynamics if we rescale time properly: we give the complete characterization of the time evolution of the limit object from its initial state up to the stationary state, which is described in the companion paper (Ráth and Szakács, in press). In our proofs we use the theory of exchangeable arrays, queuing and diffusion processes. The number of parallel edges and the degrees evolve on different timescales and because of this the model exhibits subaging. © 2012 Wiley Periodicals, Inc. Random Struct. Alg., 2012
A partially reconstructed previous Gmail session by live digital evidences investigation through volatile data acquisition
Authors: Chu Hai‐Cheng , Yang Szu‐Wei , Park Jong Hyuk
Published: April 2012

The essence of this paper is to illustrate live data acquisition within the random access memory of a notebook trying to utilize the collected digital evidences in order to partially reconstruct previous Gmail session, which could be probative digital evidence in a court of law. The proposed framework is essentially crucial for the investigation of certain related cybercrimes on the basis of the digital breadcrumb trails being professionally disclosed and appropriately handled. Without loss of generality, the volatile data would vanish forever when the power of the computing devices is no longer sustainable. This research pinpoints the imminent threat of IT savvy cyber criminals and the corresponding counter procedures used to crack criminal cases if web‐based e‐mail utilities are essentially involved. This paper is focused on the prevalent e‐mail utility, Gmail, as the research subject. At last, live digital evidence acquisition must be accurately fulfilled before the seizure of the computing devices in the crime scene to avoid irreversible investigation procedures which mean the digital evidences could be deleted, resulting in the loss of probative evidence. Copyright © 2012 John Wiley & Sons, Ltd.
Nonparametric multistate representations of survival and longitudinal data with measurement error
Authors: Hu Bo , Li Liang , Wang Xiaofeng , Greene Tom
Published: April 2012

This paper proposes a nonparametric procedure to describe the progression of longitudinal cohorts over time from a population averaged perspective, leading to multistate probability curves with the states defined jointly by survival and longitudinal outcomes measured with error. To account for the challenges of informative dropout and nonlinear shapes of the longitudinal trajectories, we apply a bias corrected penalized spline regression to estimate the unobserved longitudinal trajectory for each subject. We then estimate the multistate probability curves on the basis of the survival data and the estimated longitudinal trajectories. We further use simulation‐extrapolation method to reduce the estimation bias caused by the randomness of the estimated trajectories. We develop a bootstrap test to compare multistate probability curves between groups. We present theoretical justification of the estimation procedure along with a simulation study to demonstrate finite sample performance. We illustrate the procedure by data from the African American Study of Kidney Disease and Hypertension, and it can be widely applied in longitudinal studies. Copyright © 2012 John Wiley & Sons, Ltd.
The legacy of climategate: revitalizing or undermining climate science and policy?
Authors: Grundmann Reiner
Published: April 2012

The release of emails from a server at the University of East Anglia's Climate Research Unit (CRU) in November 2009 and the following climategate controversy have become a topic for interpretation in the social sciences. This article picks out some of the most visible social science comments on the affair for discussion. These comments are compared to an account of what can be seen as problematic practices by climate scientists. There is general agreement in these comments that climate science needs more openness and transparency. But when evaluating climategate a variety of responses is seen, ranging from the apologetic to the highly critical, even condemning the practices in question. It is argued that reluctance to critically examine the climategate affair, including suspect practices of scientists, has to do with the nature of the debate which is highly politicized. A call is made for more reflection on this case which should not be closed off because of political expediency. WIREs Clim Change 2012 doi: 10.1002/wcc.166

This article is categorized under:

Social Status of Climate Change Knowledge > Knowledge and Practice
The legacy of climategate: undermining or revitalizing climate science and policy?
Authors: Maibach Edward , Leiserowitz Anthony , Cobb Sara , Shank Michael , Cobb Kim M. , Gulledge Jay
Published: April 2012

In mid‐November 2009, emails were removed without authorization from a University of East Anglia server and posted to the internet; within 24 h an international scandal was born—alleging fraud by leading climate scientists—which almost immediately became known as climategate. Multiple investigations concluded that no fraud or scientific misconduct had occurred. Despite the exonerations, however, the email controversy has had impacts, both negative and positive. On the negative side, a small minority of the American public and a somewhat larger minority of American TV news professionals—mostly political conservatives—indicated that the controversy made them more certain that climate change is not happening, and undermined their trust in climate scientists. Conservative organizations and politicians continue to cite the controversy in justifying their opposition to government action on climate change. On the positive side, the controversy impressed upon the climate science community the need for improved communication and public engagement efforts, and many individuals and organizations have begun to address these needs. It also reminded the climate science community of the importance of transparency, data availability, and strong quality assurance procedures, stimulating many organizations to review their data management practices. Although it is too soon to gauge the lasting legacy of the controversy, if the climate science community takes it as an opportunity to improve its already high standards of scientific conduct—as well as improve its less well‐developed approach to public engagement—the long‐term prognosis is good. WIREs Clim Change 2012 doi: 10.1002/wcc.168

This article is categorized under:

Social Status of Climate Change Knowledge > Knowledge and Practice
Climate and history: a critical review of historical climatology and climate change historiography
Authors: Carey Mark
Published: April 2012

This paper provides a critical analysis of recent climate history (or historical climatology) scholarship. It identifies four key subfields in this historiography of climate change. First, it examines scholarship on climate reconstructions that use a variety of innovative historical sources to document past climatic conditions. Second, it analyzes scholarship on social impacts and responses to climate change. This literature is prolific with significant attention given to climatic variability and climatic or weather‐related disasters. Third, the paper discusses research on the uses and abuses of climate knowledge, such as innovations in meteorology and climatology as well as ways that Western climate knowledge helped justify colonialism and perpetuate racism. Fourth, the paper examines research on cultural constructions and perceptions of climate. This includes analysis of diverse climatic understandings and climate narratives that have varied across time and space. While the climate historiography is steadily expanding and constantly probing new areas, this paper contends that the field overall would benefit from a stronger emphasis on social history to examine race, class, and gender in climate history while also focusing on how social relations and power dynamics affect human–climate interactions. Additionally, it argues that the uncovering of more diverse climate meanings and narratives, partly through better social history, could both enrich the historiography and contribute to today's broader discussions about global climate change in the past and future. WIREs Clim Change 2012 doi: 10.1002/wcc.171

This article is categorized under:

Climate, History, Society, Culture > Disciplinary Perspectives
Bayesian estimation for target tracking: part I, general concepts
Authors: Haug A.J.
Published: April 2012

This is the first part of a three‐part article examining methods for Bayesian estimation and tracking. This first part presents the general theory of Bayesian estimation where we show that Bayesian estimation methods can be divided into two very general classes: the first class where the observation conditioned posterior densities are propagated in time through a predictor/corrector method; and the second class where the first two moments are propagated in time, with state and observation moment prediction steps followed by state moment update steps that use the latest observations. We show how the moment propagation method leads to very general linear and extended Kalman filters that are applicable to non‐Gaussian densities that meet several restrictions.

In Part 2 of this article we will show that for Gaussian densities, with the expansion of all nonlinear functions in polynomials, the moment propagation method leads to several well‐known Kalman filter methods. In Part 3, we will show that approximating a density by a set of Monte Carlo samples leads to particle filter methods, where the posterior density is propagated in time and moment integrals are approximated by sample moments. WIREs Comput Stat 2012 doi: 10.1002/wics.1211

This article is categorized under:

Statistical and Graphical Methods of Data Analysis > Bayesian Methods and Theory
Mining high‐throughput screens for cancer drug targets—lessons from yeast chemical‐genomic profiling and synthetic lethality
Authors: Heiskanen Marja A. , Aittokallio Tero
Published: April 2012

The recent decrease in the rate that new cancer therapies are being translated into clinical use is mainly due to the lack of therapeutic efficacy and clinical safety or toxicology of the candidate drug compounds. An important prerequisite for the development of safe and effective chemical compounds is the identification of their cellular targets. High‐throughput screening is increasingly being used to test new drug compounds and to infer their cellular targets, but these quantitative screens result in high‐dimensional datasets with many inherent sources of noise. We review here the state‐of‐the‐art statistical scoring approaches used in the prediction of drug–target interactions, and illustrate their operation using publicly available data from yeast chemical‐genomic profiling studies. The real data examples underscore the need for developing more advanced data mining approaches for extracting the full information from the high‐throughput screens. A particular medical application stems from the concept of synthetic lethality in cancer and how it could open up new opportunities for personalized cancer therapies. © 2012 Wiley Periodicals, Inc.

This article is categorized under:

Algorithmic Development > Biological Data Mining

Application Areas > Health Care
Raptor community composition in the Texas Southern High Plains lesser prairie‐chicken range
Authors: Behney Adam C. , Boal Clint W. , Whitlaw Heather A. , Lucia Duane R.
Published: April 2012

Predation can be a factor in preventing prey population growth and sustainability when prey populations are small and fragmented, and when predator density is unrelated to the density of the single prey species. We conducted monthly raptor surveys from February 2007 to May 2009 in adjacent areas of the Texas Southern High Plains (USA) that do and do not support lesser prairie‐chickens (Tympanuchus pallidicinctus), a candidate for protection under the Endangered Species Act. During the summer period corresponding to prairie‐chicken nesting and brood‐rearing, Swainson's hawks (Buteo swainsoni) were the most abundant raptor. During the lekking and overwintering period, the raptor community was diverse, with northern harriers (Circus cyaneus) being the most abundant species. Raptor abundance peaked during the early autumn and was lowest during the spring. Utility poles were a significant predictor of raptor density at survey points and Swainson's hawks and all raptors, pooled, were found in greater densities in non‐prairie‐chicken habitat dominated by mesquite (Prosopis glandulosa). Avian predation risk on prairie‐chickens, based on presence and abundance of raptors, appears to be greatest during winter when there is a more abundant and diverse raptor community, and in areas with utility poles. Published 2012. This article is a U.S. Government work and is in the public domain in the USA.
Synthesis and Reactivity of Mono‐, Di‐, and, Triiron Selenocarboxylate Complexes
Authors: El‐khateeb Mohammad , Weheabby Saddam , Jibril Ibrahim , Görls Helmar , Weigand Wolfgang
Published: April 2012

Treatment of the iron selenide (μ‐Se)[CpFe(CO)2]2with one equivalent of 1, 3, 5‐C6H3(COCl)3gave the organoiron selenocarboxylate complex CpFe(CO)2SeCO‐3, 5‐C6H3(COCl)2(1), which contains two free acid chloride groups. Complex1reacted with amines, thiols, and phenols to produce the corresponding amides CpFe(CO)2SeCO‐3, 5‐C6H3(CONR2)2(2), thioesters CpFe(CO)2SeCO‐3, 5‐C6H3(COSR)2(3), and aromatic esters CpFe(CO)2SeCO‐3, 5‐C6H3(CO2Ar)2(4), respectively. Complex1was converted into the diacid CpFe(CO)2SeCO‐3, 5‐C6H3(COOH)2(5) or the diamide CpFe(CO)2SeCO‐3, 5‐C6H3(CONH2)2(6) complexes by reactions with NaOH or NaNH2, respectively. The bis(seleno)‐1, 3‐(CpFe(CO)2SeCO)2‐5‐C6H3(COCl) (7) and tris(seleno)‐carboxylate 1, 3, 5‐(CpFe(CO)2SeCO)3C6H3(8) complexes were also prepared by controlled reaction of 1, 3, 5‐C6H3(COCl)3with the iron selenide (μ‐Se)[CpFe(CO)2]2. Complexes1–8were characterized by spectroscopic techniques (IR,1H‐NMR) and by elemental analysis as well. The X‐ray structures of CpFe(CO)2SeCO‐3, 5‐C6H3(COCl)2(1) and CpFe(CO)2SeCO‐3, 5‐C6H3(COSCH2Ph)2(3b) were determined.
Formation of Stable Rhodium η6‐Arene Complexes with Aniline Derivatives
Authors: Fischer Christian , König Anja , Drexler Hans‐Joachim , Heller Detlef
Published: April 2012

Three new, hitherto unknown, rhodium complexes with aniline and two of its derivatives (2, 6‐dimethylaniline and N‐methylaniline) are presented. All complexes have been characterized by X‐ray analysis.
Synthesis and Characterization of Alkaline and Alkaline Earth Salts of the Nitrotetrazolate‐2N‐oxide Anion
Authors: C. Härtel Martin A. , Klapötke Thomas M. , Piercey Davin G. , Stierstorfer Jörg
Published: April 2012

The oxidation of the 5‐nitrotetrazolate anion to its 2‐oxide (NTX) by Oxone® (2KHSO5·KHSO4·K2SO4) gives synthetic access to a new class of oxidizing coloring agents for pyrotechnical formulations. via aqueous ion metathesis reactions starting from the ammonium salt alkaline (Na, K, Rb, Cs) and alkaline earth metal salts (Ca, Sr, Ba) were prepared and characterized by 1H, 13C NMR, mass, Raman, and IR spectroscopy, elemental analysis and, where possible, by X‐ray diffraction (Na, K, Rb, Cs, Ba). The energetic properties were characterized with differential scanning calorimetry (DSC), impact and friction BAM tests and electrical spark sensitivity testing. 2N‐oxidation of the 5‐nitrotetrazolate anion is shown to effect positive oxygen balances ranging from 3.0–4.7 % and general improvement of safety properties under simultaneous reduction of desensitizing molar hydration water content in comparison to the non‐oxidized 5‐nitrotetrazolate salts.
LiCa3Si2N5 – A Lithium Nitridosilicate with a [Si2N5]7– Double‐Chain
Authors: Lupart Saskia , Schnick Wolfgang
Published: April 2012

The lithium nitridosilicate LiCa3Si2N5 was synthesized by the reaction of calcium with Si(NH)2 and Li3N in weld shut tantalum ampoules at 900 °C. The structure of LiCa3Si2N5 [space group C2/c, no. 15, a = 5.1454(10), b = 20.380(4), c = 10.357(2) Å, β = 91.24(3)°, wR2 = 0.1084, 863 data, 102 parameters] consists of [Si2N5]7– double‐chains including edge‐sharing tetrahedra. The lithium atoms in the crystal structure are situated in strands along the crystallographic b axis. Lattice energy calculations (MAPLE) and EDX measurements confirmed the electrostatic bonding interactions and the chemical composition. The 29Si and 7Li solid‐state MAS NMR spectroscopic investigations are reported.
Systems of Care: New Partnerships for Community Psychology
Authors: Cook James R. , Kilmer Ryan P.
Published: April 2012

For almost two decades, the federal government has supported the development of integrated models of mental health service delivery for children and families, known as systems of care (SOCs), that strive to be child‐centered, family‐focused, community‐based, and culturally competent. These efforts align well with the values and principles (e.g., empowerment, collaboration, strengths emphasis, focus on macro‐level social/system change) central to community psychology (CP; Kloos et al. in Community psychology, Cengage Learning, Belmont, 2012). Despite the convergence of many core values, CPs have historically been underrepresented in key roles in SOC initiatives. However, this has changed in recent years, with increasing examples of community psychology skills and principles applied to the development, implementation, and evaluation of SOCs. Because successful and sustainable implementation of SOCs requires community and system‐level change, and SOCs are increasingly being urged to adopt a stronger “public health” orientation (Miles et al. in A public health approach to children's mental health: a conceptual framework, Georgetown University Center for Child and Human Development, National Technical Assistance Center for Children's Mental Health, Washington, DC, 2010), there is great potential for CPs to play important roles in SOCs. This paper discusses opportunities and roles for CPs in SOCs in applied research and evaluation, community practice, and training.
Response of soil nematode community structure and diversity to long‐term land use in the black soil region in China
Authors: Pan Feng‐Juan , Xu Yan‐Li , McLaughlin Neil B. , Xue Allen G. , Yu Qing , Han Xiao‐Zeng , Liu Wei , Zhan Li‐Li , Zhao Dan , Li Chun‐Jie
Published: April 2012

Soil nematodes are sensitive to environmental changes and are used widely as indicators of soil conditions. The community structure and diversity of soil nematodes were studied in different long‐term land use regimes in the black soil area in Northeast China. The land use regimes were maintained for 22 years, and included crop land (CL), grass land (GL) and bare land (BL). Soil samples were taken throughout the growing season, and nematodes were extracted and identified. A total of 39 nematode genera with relative abundance over 0.1 % were identified.Heteroderawas the dominant genus in CL;Boleodoruswas the dominant genus in GL, andBoleodorus,EucephalobusandFilenchuswere the dominant genera in BL. Land use had a significant effect on abundance of all soil nematode tropic groups and ecological indices. Sampling time had an effect on soil nematode abundance, but only on three of the eight nematode ecological indices MI (maturity index of free‐living nematode), CI (channel index) and EI (enrichment index). SR (species richness index) was highest in GL where plant species diversity was also high. The CI was the highest in BL among three land uses, which means the soil food web dominated, with fungal decomposition channels in BL. Soil nematode community structure and diversity was shown to be an effective and informative tool for analyzing ecological aspects of land use in black soil regions. The data are inconclusive as to whether the effect of land use on soil nematode parameters is direct, or indirect via inducing changes in soil physicochemical properties.
Characterization of the Solvent Properties of Glycerol Using Inverse Gas Chromatography and Solubility Parameters
Authors: Vincent Joel D. , Srinivas Keerthi , King Jerry W.
Published: April 2012

The production of glycerol from the synthesis of biodiesel has led to a market surplus of this polyhydric alcohol and additional research to find new applications for this versatile chemical. This study involves the use of inverse gas chromatography (IGC) to characterize the solute–solvent interactions between glycerol and a homologous series of aliphatic alcohols, in which the latter components are at infinite dilution in the glycerol, which is the stationary phase contained in a packed GC column. The IGC experiments were conducted between 51.5 and 111 °C for the n‐alcohols ranging from methanol to n‐butanol. All of the n‐alcohol homologs exhibited positive deviations from Raoult's law as based on mole fraction activity coefficients values ranging from 1.86 to 14.4. The measured mole fraction activity coefficients of the alcoholic solutes in glycerol showed good agreement with literature values, and in some cases with those predicted using existing theoretical models. The mole fraction activity coefficients increased going from methanol to n‐butanol, reflecting the change in the alcohol's cohesive energy densities relative to that for glycerol. The total solubility parameter of glycerol calculated from IGC data was found to be 34.8 MPa1/2 which is in good agreement with that obtained using Hansen solubility parameter approach (31.6 MPa1/2). This data can be used to characterize the solvent properties of glycerol as well as to provide thermodynamic data for the removal of the alcoholic solutes from glycerol.
The Geography of Evolution and the Evolution of Geography
Authors: Lieberman Bruce S.
Published: April 2012

Insights into the geography of life have played a fundamental role in motivating major developments in evolutionary biology. The focus here is on outlining some of these major developments, specifically in the context of paleontology, by emphasizing the significance of geographic isolation and allopatric speciation, punctuated equilibria, and the Turnover Pulse Hypothesis to evolutionary theory. One of the major debates in evolution concerns the relative contributions of abiotic and biotic factors to macroevolution, and each one of these developments increasingly suggested that it was climatic and geologic factors, rather than competition, that played the primary role in motivating macroevolution. New technical developments, including in the area of Geographic Information Systems, allow continued detailed testing of the relative roles that biotic as opposed to abiotic factors play in causing evolution, and some of the work in this area will also be described.
Whither the New Great Game in Central Asia?
Authors: Blank Stephen
Published: April 2012

This paper represents an assessment of the present great game or new great game in Central Asia among the major external and internal political actors three. It finds that the game is probably intensifying and at the same time serves the purposes of Central Asian governments in helping them preserve domestic security. Thus the foreign rivalry serves multiple and paradoxical purposes. On the one hand states like Russia and China pursue great power aggrandizement and even neo-imperial policies there and on the other hand Central Asian states attach themselves to these countries in the hope of obtaining resources form them with which to augment their independence. At the same time as the United States announces its impending withdrawal from Afghanistan, it is already evident that the rivalry among the other major actors is heating up. Moscow is pursuing military bases the right to intervene in the domestic affairs of members of the CSTO and its customs union and China is strengthening its commercial primacy in the area. And while all this is occurring simultaneously we see concern over succession issues in several states, the possibility of something resembling the Arab spring occurring, an outcome that greatly alarms Russian, Chinese, and local leaders, and of course, the uncertain prognosis in Afghanistan. Thus the international competition within and around Central Asia is likely to intensify.
Fast versus slow onset of depressive episodes: A clinical criterion for subtyping patients with major depression
Authors: Hegerl U. , Mergl R. , Quail D. , Schneider E. , Strauß M. , Hundemer H.-P. , Linden M.
Published: April 2012

Purpose:

The speed of onset of depressive episodes is a clinical aspect of affective disorders that has not been sufficiently investigated. Thus, we aimed to explore whether patients with fast onset of the full-blown depressive symptomatology (≤ 7 days) differ from those with slow onset (> 7 days) with regard to demographic and clinical aspects.

Subjects and methods:

Data were obtained within an observational study conducted in outpatients with major depression who were treated with duloxetine (30–120 mg/day). Onset of depression (without any preceding critical life event) was fast in 416 (less than one week) and slower in 2220 patients.

Results:

Compared to patients with slow onset, those with fast onset of depression had more suicide attempts in the previous 12 months (2.7% versus 1.3%, P = 0.046) and less somatic comorbidity (61.7% versus 74.1%, P < 0.0001). In addition, they were slightly younger at onset of depression (mean ± SD 40.2 ± 14.6 versus 42.8 ± 14.2 years, P < 0.001) and used analgesics at baseline significantly less frequently (22.8% versus 33.4%, P < 0.0001).

Discussion and conclusion:

The speed of onset of depression has to be regarded as a relevant clinical characteristic in patients with unipolar depression.
Calmodulin regulates the translocation of Grb7 into the nucleus
Authors: García-Palmero Irene , Villalobo Antonio
Published: April 2012

We describe in this report the presence of a nuclear localization signal (NLS) overlapping the calmodulin‐binding domain (CaM‐BD) of the growth factor receptor bound protein 7 (Grb7). We show that deletion of the CaM‐BD of Grb7 prevents its nuclear localization, and that its Src homology 2 (SH2) domain might participate as well in the translocation process. Also, treating cells with the CaM antagonist N‐(6‐aminohexyl)‐5‐chloro‐1‐naphthalenesulfonamide (W‐7) enhances the presence of Grb7 in the nucleus. We propose that CaM inhibits the translocation of Grb7 to the nucleus after binding to its CaM‐BD and therefore occluding its overlapping NLS.
Live imaging of active fluorophore labelled Wnt proteins
Authors: Holzer Tatjana , Liffers Katrin , Rahm Karolin , Trageser Benjamin , Özbek Suat , Gradl Dietmar
Published: April 2012

Here, we have generated a Wnt2b–EGFP fusion protein that retains functionality in bona fide Wnt activity assays, although the secreted protein is rapidly cleaved by extracellular proteases. We can show with this new tool that Wnt2b–EGFP moves along the microtubules of Wnt producing cells and that this directed movement is essential for the secretion of active Wnt protein.
Professional Autonomy Reconsidered: The Case of Czech Medicine under State Socialism
Authors: Hoffman Lily M.
Published: April 2012

The opening of the formerly closed, state socialist societies of East Central Europe has provided the opportunity to bring new empirical evidence to bear upon models of profession-state relations developed in pluralist western societies. The classic view of Tocqueville and Durkheim has been that professions are an intermediary group linking individuals and the state. Although not always explicitly stated, this model served as the basis for scholarly work on the professions in the post-World War II period, where it (more or less) fit the image of a differentiated pluralist society. Most work on the professions was based on the Anglo-American case.

But even in the United States, state support was more central to maintaining professional authority than was originally thought. Without explicitly discarding the model, Freidson (1970) introduced a distinction between corporate and technical (clinical) autonomy that provided a way out of the paradox he identified, that both aspects of professional autonomy are protected by the state. Corporate autonomy refers to the political power of the organized profession to define the social and economic context of professional work, and clinical autonomy, to the control of decision making in the workplace. Testing his hypothesis on the United States, the United Kingdom, and the Soviet Union, Freidson argued that despite differing degrees of corporate autonomy, the medical profession retained clinical control of decision making, the core of professional autonomy, even in the extreme case of the former Soviet Union.