bluuebunny/crossref_metadata_2025_split huggingface dataset:
A novel multiplex-protein array for serum diagnostics of colon cancer: a case–control study
Authors: Bünger Stefanie , Haug Ulrike , Kelly Maria , Posorski Nicole , Klempt-Giessing Katja , Cartwright Andrew , Fitzgerald Stephen P , Toner Vicki , McAleer Damien , Gemoll Timo , Laubert Tilman , Büning Jürgen , Fellermann Klaus , Bruch Hans-Peter , Roblick Uwe J , Brenner Hermann , von Eggeling Ferdinand , Habermann Jens K 
Published: September 2012

Abstract

Background
More than 1.2 million new cases of colorectal cancer are reported each year worldwide. Despite actual screening programs, about 50% of the patients are diagnosed at advanced tumor stages presenting poor prognosis. Innovative screening tools could aid the detection at early stages and allow curative treatment interventions.

Methods
A nine target multiplex serum protein biochip was generated and evaluated using a training- and validation-set of 317 highly standardized, liquid nitrogen preserved serum samples comprising controls, adenomas, and colon cancers.

Results
Serum levels of CEA, IL-8, VEGF, S100A11, MCSF, C3adesArg, CD26, and CRP showed significant differences between cases and controls. The largest areas under the receiver operating characteristics curve were observed for CEA, IL-8, and CRP. At threshold levels yielding 90% specificity, sensitivities for CEA, IL-8 and CRP were 26%, 22%, and 17%, respectively. The most promising marker combinations were CEA + IL-8 reaching 37% sensitivity at 83% specificity and CEA + CRP with 35% sensitivity at 81% specificity. In an independent validation set CEA + IL-8 reached 47% sensitivity at 86% specificity while CEA + CRP obtained 39% sensitivity at 86% specificity. Early carcinomas were detected with 33% sensitivity for CEA + IL-8 and 28% for CEA + CRP.

Conclusions
Apart from CEA, IL-8, and CRP, the screening value of additional blood markers and the potential advantage of combining serum biochip testing with fecal occult blood testing needs to be studied. Multiplex biochip array technology utilizing serum samples offers an innovative approach to colorectal cancer screening.
Investigation of volatile organic biomarkers derived from Plasmodium falciparum in vitro
Authors: Wong Rina PM , Flematti Gavin R , Davis Timothy ME 
Published: September 2012

Abstract

Background
There remains a need for techniques that improve the sensitive detection of viable Plasmodium falciparum as part of diagnosis and therapeutic monitoring in clinical studies and usual-care management of malaria infections. A non-invasive breath test based on P. falciparum- associated specific volatile organic compounds (VOCs) could fill this gap and provide insights into parasite metabolism and pathogenicity. The aim of this study was to determine whether VOCs are present in the headspace above in vitro P. falciparum cultures.

Methods
A novel, custom-designed apparatus was developed to enable efficient headspace sampling of infected and non-infected cultures. Conditions were optimized to support cultures of high parasitaemia (>20%) to improve the potential detection of parasite-specific VOCs. A number of techniques for VOC analysis were investigated including solid phase micro-extraction using two different polarity fibres, and purge and trap/thermal desorption, each coupled to gas chromatography–mass spectrometry. Each experiment and analysis method was performed at least on two occasions. VOCs were identified by comparing their mass spectra against commercial mass spectral libraries.

Results
No unique malarial-specific VOCs could be detected relative to those in the control red blood cell cultures. This could reflect sequestration of VOCs into cell membranes and/or culture media but solvent extractions of supernatants and cell lysates using hexane, dichloromethane and ethyl acetate also showed no obvious difference compared to control non-parasitized cultures.

Conclusions
Future in vivo studies analysing the breath of patients with severe malaria who are harbouring a parasite biomass that is significantly greater than achievable in vitro may yet reveal specific clinically-useful volatile chemical biomarkers.
Some results on fixed points of asymptotically strict quasi-ϕ-pseudocontractions in the intermediate sense
Authors: Qin Xiaolong , Wang Lin , Kang Shin Min 
Published: September 2012

Abstract
In this paper, a new nonlinear mapping, asymptotically strict quasi-ϕ-pseudocontraction in the intermediate sense, is introduced. Projection algorithms are considered for the mapping. Strong convergence theorems for fixed points of the mapping are established based on projection algorithms in a real Banach space.

MSC:47H09, 47J05, 47J25.
Comment on ‘Fixed point theorems for contraction mappings in modular metric spaces, Fixed Point Theory and Applications, doi:10.1186/1687-1812-2011-93, 20 pages’
Authors: Dehghan H , Eshaghi Gordji M , Ebadian A 
Published: September 2012

Abstract
In this paper, we provide an example to show that some results obtained in [Mongkolkeha et al. in Fixed Point Theory Appl. 2011, doi:10.1186/1687-1812-2011-93] are not valid.

MSC:47H09, 47H10.
A pragmatic cluster randomized controlled trial of early intervention for chronic obstructive pulmonary disease by practice nurse-general practitioner teams: Study Protocol
Authors: Bunker Jeremy M , Reddel Helen K , Dennis Sarah M , Middleton Sandy , Van Schayck CP , Crockett Alan J , Hasan Iqbal , Hermiz Oshana , Vagholkar Sanjyot , Marks Guy B , Zwar Nicholas A 
Published: September 2012

Abstract

Background
Chronic Obstructive Pulmonary Disease (COPD) is a leading cause of disability, hospitalization, and premature mortality. General practice is well placed to diagnose and manage COPD, but there is a significant gap between evidence and current practice, with a low level of awareness and implementation of clinical practice guidelines. Under-diagnosis of COPD is a world-wide problem, limiting the benefit that could potentially be achieved through early intervention strategies such as smoking cessation, dietary advice, and exercise. General practice is moving towards more structured chronic disease management, and the increasing involvement of practice nurses in delivering chronic care.

Design
A pragmatic cluster randomised trial will test the hypothesis that intervention by a practice nurse-general practitioner (GP) team leads to improved health-related quality of life and greater adherence with clinical practice guidelines for patients with newly-diagnosed COPD, compared with usual care. Forty general practices in greater metropolitan Sydney Australia will be recruited to identify patients at risk of COPD and invite them to attend a case finding appointment. Practices will be randomised to deliver either practice nurse-GP partnership care, or usual care, to patients newly-diagnosed with COPD.
The active intervention will involve the practice nurse and GP working in partnership with the patient in developing and implementing a care plan involving (as appropriate), smoking cessation, immunisation, pulmonary rehabilitation, medication review, assessment and correction of inhaler technique, nutritional advice, management of psycho-social issues, patient education, and management of co-morbidities.
The primary outcome measure is health-related quality of life, assessed with the St George’s Respiratory Questionnaire 12 months after diagnosis. Secondary outcome measures include validated disease-specific and general health related quality of life measures, smoking and immunisation status, medications, inhaler technique, and lung function. Outcomes will be assessed by project officers blinded to patients’ randomization groups.

Discussion
This study will use proven case-finding methods to identify patients with undiagnosed COPD in general practice, where improved care has the potential for substantial benefit in health and healthcare utilization. The study provides the capacity to trial a new model of team-based assessment and management of newly diagnosed COPD in Australian primary care.

Trial registration
ACTRN12610000592044\
The effects of high dose and highly fractionated radiation on distraction osteogenesis in the murine mandible
Authors: Monson Laura A , Cavaliere Christi M , Deshpande Sagar S , Ayzengart Alexander L , Buchman Steven R 
Published: September 2012

AbstractThe ability of irradiated tissue to support bony growth remains poorly defined, although there are anecdotal cases reported showing mixed results for the use of mandibular distraction osteogenesis after radiation for head and neck cancer. Many of these reports lack objective measures that would allow adequate analysis of outcomes or efficacy. The purpose of this experiment was to utilize a rat model of mandibular distraction osteogenesis after high dose and highly fractionated radiation therapy and to evaluate and quantify distracted bone formation under these conditions. Male Sprague–Dawley rats underwent 12 fractions of external beam radiation (48 Gray) of the left mandible. Following a two week recovery period, an external frame distractor was applied and gradual distraction of the mandible was performed. Tissue was harvested after a twenty-eight day consolidation period. Gross, radiologic and histological evaluations were undertaken. Those animals subjected to pre-operative radiation showed severe attenuation of bone formation including bone atrophy, incomplete bridging of the distraction gap, and gross bony defects or non-union. Although physical lengthening was achieved, the irradiated bone consistently demonstrated marked damaging effects on the normal process of distraction osteogenesis. This murine model has provided reliable evidence of the injurious effects of high dose radiation on bone repair and regeneration in distraction osteogenesis utilizing accurate and reproducible metrics. These results can now be used to assist in the development of therapies directed at mitigating the adverse consequences of radiation on the regeneration of bone and to optimize distraction osteogenesis so it can be successfully applied to post-oncologic reconstruction.
Efficient procedures for the numerical simulation of mid-size RNA kinetics
Authors: Aviram Iddo , Veltman Ilia , Churkin Alexander , Barash Danny 
Published: September 2012

Abstract

Motivation
Methods for simulating the kinetic folding of RNAs by numerically solving the chemical master equation have been developed since the late 90's, notably the programs Kinfold and Treekin with Barriers that are available in the Vienna RNA package. Our goal is to formulate extensions to the algorithms used, starting from the Gillespie algorithm, that will allow numerical simulations of mid-size (~ 60–150 nt) RNA kinetics in some practical cases where numerous distributions of folding times are desired. These extensions can contribute to analyses and predictions of RNA folding in biologically significant problems.

Results
By describing in a particular way the reduction of numerical simulations of RNA folding kinetics into the Gillespie stochastic simulation algorithm for chemical reactions, it is possible to formulate extensions to the basic algorithm that will exploit memoization and parallelism for efficient computations. These can be used to advance forward from the small examples demonstrated to larger examples of biological interest.

Software
The implementation that is described and used for the Gillespie algorithm is freely available by contacting the authors, noting that the efficient procedures suggested may also be applicable along with Vienna's Kinfold.
The pretreatment of corn stover with Gloeophyllum trabeum KU-41 for enzymatic hydrolysis
Authors: Gao Ziqing , Mori Toshio , Kondo Ryuichiro 
Published: September 2012

Abstract

Background
Pretreatment is an essential step in the enzymatic hydrolysis of biomass for bio-ethanol production. The dominant concern in this step is how to decrease the high cost of pretreatment while achieving a high sugar yield. Fungal pretreatment of biomass was previously reported to be effective, with the advantage of having a low energy requirement and requiring no application of additional chemicals. In this work, Gloeophyllum trabeum KU-41 was chosen for corn stover pretreatment through screening with 40 strains of wood-rot fungi. The objective of the current work is to find out which characteristics of corn stover pretreated with G. trabeum KU-41 determine the pretreatment method to be successful and worthwhile to apply. This will be done by determining the lignin content, structural carbohydrate, cellulose crystallinity, initial adsorption capacity of cellulase and specific surface area of pretreated corn stover.

Results
The content of xylan in pretreated corn stover was decreased by 43% in comparison to the untreated corn stover. The initial cellulase adsorption capacity and the specific surface area of corn stover pretreated with G. trabeum were increased by 7.0- and 2.5-fold, respectively. Also there was little increase in the cellulose crystallinity of pretreated corn stover.

Conclusion

G. trabeum has an efficient degradation system, and the results indicated that the conversion of cellulose to glucose increases as the accessibility of cellulose increases due to the partial removal of xylan and the structure breakage of the cell wall. This pretreatment method can be further explored as an alternative to the thermochemical pretreatment method.
Evaluation of the efficacy of topically administered imidacloprid + pyriproxyfen and orally administered spinosad against cat fleas (Ctenocephalides felis): Impact of treated dogs on flea life stages in a simulated home environment
Authors: Ross Douglas H , Arther Robert G , von Simson Cristiano , Doyle Veronica , Dryden Michael W 
Published: September 2012

Abstract

Background
Cat fleas, Ctenocephalides felis, are one of the most common ectoparasites infesting dogs and their environments. This study evaluated the efficacy of imidacloprid + pyriproxyfen (PPF) (Advantage® II for Dogs) and spinosad (Comfortis®) against established C. felis populations in dogs’ simulated home environments.

Methods
Thirty Beagle dogs were randomly assigned to three groups of 10 dogs each and treated twice (Study Days 0 and 28) with imidacloprid + PPF, spinosad tablets, or a negative control (untreated). Dogs were housed individually in controlled simulated home environments capable of supporting the flea life cycle. Flea infestations were established in these environments by infesting each dog with 100 adult cat fleas on Study Days −21, -16 and 1. The impact of the treatments on fleas in the dogs’ environments were assessed by collecting floor mat samples from each simulated home environment, incubating them for 32 days, and counting the number of emerging adult fleas. On Study Days 7, 14, 21, 28, 35, 42, 49 and 56, after collection of the cocoa matting samples, each dog was infested with an additional 5 ± 1 fleas to maintain the environmental infestations. Flea comb counts on dogs were conducted on Study Days 0 (pretreatment) and 63.

Results
From Study Days 7–28, flea infestations in the imidacloprid + PPF environments were significantly lower (p < 0.03) than those in the spinosad environments. Following the second treatment, flea infestations in all the imidacloprid + PPF environments fell to zero for the remainder of the study. In contrast, flea infestations persisted in some of the spinosad environments through the study’s end.
On Study Day 63 all 10 dogs treated with imidacloprid + PPF were flea free, while only one of the 10 spinosad treated dogs was flea free. Flea counts on the other 9 spinosad treated dogs ranged from 3 to 46 fleas/dog (geometric mean = 8.6). A mean of 405 adult fleas/animal were recovered from the control dogs on Study Day 63.

Conclusion
Flea infestations in environments of dogs treated with imidacloprid + PPF declined more rapidly than in those containing dogs treated with spinosad. Flea infestations were completely eliminated by Study Day 56 in environments of dogs treated with imidacloprid + PPF, but persisted through the study’s end in some of environments of dogs treated with spinosad.
Functional analysis of transcription factor binding sites in human promoters
Authors: Whitfield Troy W , Wang Jie , Collins Patrick J , Partridge E Christopher , Aldred Shelley Force , Trinklein Nathan D , Myers Richard M , Weng Zhiping 
Published: September 2012

Abstract
Background
The binding of transcription factors to specific locations in the genome is integral to the orchestration of transcriptional regulation in cells. To characterize transcription factor binding site function on a large scale, we predicted and mutagenized 455 binding sites in human promoters. We carried out functional tests on these sites in four different immortalized human cell lines using transient transfections with a luciferase reporter assay, primarily for the transcription factors CTCF, GABP, GATA2, E2F, STAT, and YY1.

Results
In each cell line, between 36% and 49% of binding sites made a functional contribution to the promoter activity; the overall rate for observing function in any of the cell lines was 70%. Transcription factor binding resulted in transcriptional repression in more than a third of functional sites. When compared with predicted binding sites whose function was not experimentally verified, the functional binding sites had higher conservation and were located closer to transcriptional start sites (TSSs). Among functional sites, repressive sites tended to be located further from TSSs than were activating sites. Our data provide significant insight into the functional characteristics of YY1 binding sites, most notably the detection of distinct activating and repressing classes of YY1 binding sites. Repressing sites were located closer to, and often overlapped with, translational start sites and presented a distinctive variation on the canonical YY1 binding motif.

Conclusions
The genomic properties that we found to associate with functional TF binding sites on promoters -- conservation, TSS proximity, motifs and their variations -- point the way to improved accuracy in future TFBS predictions.
Seismic reflection profiling of the Pyhäsalmi VHMS-deposit: A complementary approach to the deep base metal exploration in Finland
Authors: Heinonen Suvi , Imaña Marcello , Snyder David B. , Kukkonen Ilmo T. , Heikkinen Pekka J. 
Published: September 2012

In the Pyhäsalmi case study, the seismic data is used in direct targeting of shallowly dipping mineralized zones in a massive sulfide ore system that was deformed in complex fold interference structures under high-grade metamorphic conditions. The Pyhäsalmi volcanic-hosted massive sulfide (VHMS) deposit ([Formula: see text]) is located in a Proterozoic volcanic belt in central Finland. Acoustic impedance of Pyhäsalmi ore ([Formula: see text]) is distinct from the host rocks ([Formula: see text]), enabling its detection with seismic reflection methods. Drill-hole logging further indicates that the seismic imaging of a contact zone between mafic and felsic volcanic rocks possibly hosting additional mineralizations is plausible. Six seismic profiles showed discontinuous reflectors and complicated reflectivity patterns due to the complex geology. The most prominent reflective package at 1–2 km depth was produced by shallowly dipping contacts between interlayered felsic and mafic volcanic rocks. The topmost of these bright reflections coincides with high-grade zinc mineralization. Large acoustic impedances associated with the sulfide minerals locally enhanced the reflectivity of this topmost contact zone which could be mapped over a wide area using the seismic data. Seismic data enables extrapolation of the geologic model to where no drill-hole data exists; thus, seismic reflection profiling is an important method for defining new areas of interest for deep exploration.
Migration velocity analysis using traveltime wavefield tomography
Authors: Al-Saleh Saleh M. , Jiao Jianwu 
Published: September 2012

We introduce an integrated wave-equation technique for migration velocity analysis (MVA) that consists of three steps: (1) forming the extended data, (2) approximating the correct transmitted wavefield, and (3) using wavefield tomography to update the velocity model. In the first step, the crosscorrelation imaging condition is relaxed to produce other nonzero-lag common image gathers (CIG) that, combined, form a common image cube (CIC). Slicing the CIC at different crosscorrelation lags forms a series of CIGs. Flattened events will occur in the CIGs at a lag other than the zero-lag when an incorrect velocity model is used in the migration. In the second step, for each event on the CIG, we pick the focusing depth and crosscorrelation lag at which it is flattest. We then model a Green’s function by seeding a source at the focusing depth using one-way wave equation modeling, then shift the modeled wavefield with the focusing crosscorrelation lag. This process is repeated for the other primary events at different lateral and vertical positions. The result is a set of modeled data whose wavefield approximates the wavefield that would have been generated if the correct velocity model had been used to simulate these gathers. We then apply wavefield tomography on these data-driven modeled data to update the velocity model. Our inversion scheme is based on wave-equation traveltime tomography that can update the velocity model in the presence of large velocity errors and a complex environment. Tests on synthetic and real 2D seismic data confirm the method’s effectiveness in building velocity models in complex structural areas that have large lateral velocity variations.
3D reflection seismic imaging for open-pit mine planning and deep exploration in the Kevitsa Ni-Cu-PGE deposit, northern Finland
Authors: Malehmir Alireza , Juhlin Christopher , Wijns Chris , Urosevic Milovan , Valasti Petri , Koivisto Emilia 
Published: September 2012

A 3D reflection seismic survey was conducted over an area of about [Formula: see text] at the Kevitsa Ni-Cu-PGE (platinum group elements) orebody, northern Finland, where open-pit mining started in mid-2012. The principal objective of the survey was to image major fault and fracture zones at depth that may have an impact on the mine stability and safety. Mine planning would then take into account the geometry of these zones at Kevitsa. Processing results, using conventional prestack DMO and poststack migration methods, show gently dipping and steeply dipping reflections from depths of approximately 2 km to as shallow as 150–200 m. Many of the reflections are interpreted to originate from either fault systems or internal magmatic layering within the Kevitsa main intrusion. Further correlation between the surface seismic data and VSP data suggests that numerous faults are present in the imaged volume based upon time shifts or phase changes along horizontal to gently dipping reflections. Some of these faults cross the planned open-pit mine at depths of about 300–500 m, and are therefore critical for geotechnical planning. In terms of in-pit and near-mine exploration, the magmatic layering internal to the intrusion controls the distribution of the bulk of economic mineralization. The ability to image this magmatic layering could therefore guide future drilling, particularly by constraining the presumed lateral extents of the resource area. Exploration also will target discrete reflectors that potentially represent higher-grade sulfide mineralization.