bluuebunny/crossref_metadata_2025_split huggingface dataset:
Regulation of the pentose phosphate pathway by an androgen receptor–mTOR-mediated mechanism and its role in prostate cancer cell growth
Authors: Tsouko E , Khan A S , White M A , Han J J , Shi Y , Merchant F A , Sharpe M A , Xin L , Frigo D E 
Published: May 2014

AbstractCancer cells display an increased demand for glucose. Therefore, identifying the specific aspects of glucose metabolism that are involved in the pathogenesis of cancer may uncover novel therapeutic nodes. Recently, there has been a renewed interest in the role of the pentose phosphate pathway in cancer. This metabolic pathway is advantageous for rapidly growing cells because it provides nucleotide precursors and helps regenerate the reducing agent NADPH, which can contribute to reactive oxygen species (ROS) scavenging. Correspondingly, clinical data suggest glucose-6-phosphate dehydrogenase (G6PD), the rate-limiting enzyme of the pentose phosphate pathway, is upregulated in prostate cancer. We hypothesized that androgen receptor (AR) signaling, which plays an essential role in the disease, mediated prostate cancer cell growth in part by increasing flux through the pentose phosphate pathway. Here, we determined that G6PD, NADPH and ribose synthesis were all increased by AR signaling. Further, this process was necessary to modulate ROS levels. Pharmacological or molecular inhibition of G6PD abolished these effects and blocked androgen-mediated cell growth. Mechanistically, regulation of G6PD via AR in both hormone-sensitive and castration-resistant models of prostate cancer was abolished following rapamycin treatment, indicating that AR increased flux through the pentose phosphate pathway by the mammalian target of rapamycin (mTOR)-mediated upregulation of G6PD. Accordingly, in two separate mouse models of Pten deletion/elevated mTOR signaling, Pb-Cre;Ptenf/f and K8-CreERT2;Ptenf/f, G6PD levels correlated with prostate cancer progression in vivo. Importantly, G6PD levels remained high during progression to castration-resistant prostate cancer. Taken together, our data suggest that AR signaling can promote prostate cancer through the upregulation of G6PD and therefore, the flux of sugars through the pentose phosphate pathway. Hence, these findings support a vital role for other metabolic pathways (that is, not glycolysis) in prostate cancer cell growth and maintenance.
Novel hybrid artificial neural network based autopicking workflow for passive seismic data
Authors: Maity Debotyam , Aminzadeh Fred , Karrenbach Martin 
Published: May 2014

ABSTRACTMicroseismic monitoring is an increasingly common geophysical tool to monitor the changes in the subsurface. Autopicking involving phase arrival detection is a common element in microseismic data processing schemes and is necessary for accurate estimation of event locations as well as other workflows such as tomographic or moment tensor inversion, etc. The quality of first arrival picking is dependent on the actual seismic waveform, which in turn is related to the near surface and subsurface structure, source type, noise conditions, environmental factors, and monitoring array design, etc. We have developed a new hybrid autopicking workflow which makes use of multiple derived attributes from the seismic data and combines them within an artificial neural network framework. An evolutionary algorithm scheme is used as the network training algorithm. The autopicker has been tested and its applicability has been validated using a synthetically modelled seismic source, with promising results. In this work, we share the basic workflow and different attributes that have been tested with this algorithm for a synthetic data set to provide a framework for independent implementation, use and validation. We also compare the results obtained using the new neural network based autopicking routine with very robust contemporary autopicking algorithms in use within the industry.
On the use of microtremors for hydrocarbon detection
Authors: Vesnaver A. , Da Col F. , Jervis M. , Kaka S.I. , Nieto D. 
Published: May 2014

ABSTRACTThe link of spectral anomalies of microtremors to underlying hydrocarbon reservoirs is very controversial, as field experiments support both positive and negative opinions, and there is not a solid theory supporting this work hypothesis. We conducted field tests at different sites, with and without oil and gas presence, to add new experimental data to the ongoing studies. Microtremor information may become repeatable (and so physically meaningful) only when the observation duration exceeds a few days, but even in this case, factors such as topography and active faults may severely bias the signal.Ocean waves impinging the coasts provide natural background noise, which stands out clearly when the observation time exceeds a dozen days or so, in such a way that human noise is stacked out statistically over time.Microtremors recorded in (relatively) deep wells may provide useful information about ongoing production in a reservoir, and may link well data and seismic surveys, as their interferometric analysis can provide information comparable to Vertical Seismic Profiles.
Enhancing the Global Ocean Observing System to meet evidence based needs for the ecosystem‐based management of coastal ecosystem services
Authors: Malone Thomas C. , DiGiacomo Paul M. , Gonçalves Emanuel , Knap Anthony H. , Talaue‐McManus Liana , de Mora Stephen , Muelbert Jose 
Published: May 2014

AbstractEcosystem‐based approaches (EBAs) to managing anthropogenic pressures on ecosystems, adapting to changes in ecosystem states (indicators of ecosystem health), and mitigating the impacts of state changes on ecosystem services are needed for sustainable development. EBAs are informed by integrated ecosystem assessments (IEAs) that must be compiled and updated frequently for EBAs to be effective. Frequently updated IEAs depend on the sustained provision of data and information on pressures, state changes, and impacts of state changes on services. Nowhere is this truer than in the coastal zone, where people and ecosystem services are concentrated and where anthropogenic pressures converge. This study identifies the essential indicator variables required for the sustained provision of frequently updated IEAs, and offers an approach to establishing a global network of coastal observations within the framework of the Global Ocean Observing System. The need for and challenges of capacity‐building are highlighted, and examples are given of current programmes that could contribute to the implementation of a coastal ocean observing system of systems on a global scale. This illustrates the need for new approaches to ocean governance that can achieve coordinated integration of existing programmes and technologies as a first step towards this goal.
De novo assembly and comparative analysis of the Ceratodon purpureus transcriptome
Authors: Szövényi Péter , Perroud Pierre‐François , Symeonidi Aikaterini , Stevenson Sean , Quatrano Ralph S. , Rensing Stefan A. , Cuming Andrew C. , McDaniel Stuart F. 
Published: May 2014

AbstractThe bryophytes are a morphologically and ecologically diverse group of plants that have recently emerged as major model systems for a variety of biological processes. In particular, the genome sequence of the moss, Physcomitrella patens, has significantly enhanced our understanding of the evolution of developmental processes in land plants. However, to fully explore the diversity within bryophytes, we need additional genomic resources. Here, we describe analyses of the transcriptomes of a male and a female isolate of the moss, Ceratodon purpureus, generated using the 454 FLX technology. Comparative analyses between C. purpureus and P. patens indicated that this strategy generated nearly complete coverage of the protonemal transcriptome. An analysis of the overlap in gene sets between C. purpureus and P. patens provides new insights into the evolution of gene family composition across the land plants. In spite of the overall transcriptomic similarity between the two species, Ka/Ks analysis of P. patens and C. purpureus suggests considerable physiological and developmental divergence. Additionally, while the codon usage was very similar between these two mosses, C. purpureus genes showed a slightly greater codon usage bias than P. patens genes potentially because of the contrasting mating system of the two species. Finally, we found evidence of a genome doubling ~65–76 MYA that likely coincided with the contemporaneous polyploidy event inferred for P. patens but postdates the divergence of P. patens and C. purpureus. The powerful laboratory tools now available for C. purpureus will enable the research community to fully exploit these genomic resources.
The effects of mice on stoats in southern beech forests
Authors: Veale A. J. , McMurtrie P. , Edge K.‐A. , Clout M. N. 
Published: May 2014

AbstractIntroduced stoats (Mustela erminea) are important invasive predators in southern beech (Nothofagus sp.) forests in New Zealand. In these forests, one of their primary prey species – introduced house mice (Mus musculus), fluctuate dramatically between years, driven by the irregular heavy seed‐fall (masting) of the beech trees. We examined the effects of mice on stoats in this system by comparing the weights, age structure and population densities of stoats caught on two large islands in Fiordland, New Zealand – one that has mice (Resolution Island) and one that does not (Secretary Island). On Resolution Island, the stoat population showed a history of recruitment spikes and troughs linked to beech masting, whereas the Secretary Island population had more constant recruitment, indicating that rodents are probably the primary cause for the ‘boom and bust’ population cycle of stoats in beech forests. Resolutions Island stoats were 10% heavier on average than Secretary Island stoats, supporting the hypothesis that the availability of larger prey (mice verses wētā) leads to larger stoats. Beech masting years on this island were also correlated with a higher weight for stoats born in the year of the masting event. The detailed demographic information on the stoat populations of these two islands supports previously suggested interactions among mice, stoats and beech masting. These interactions may have important consequences for the endemic species that interact with fluctuating populations of mice and stoats.
Contemporary Biological Anthropology in 2013: Integrative, Connected, and Relevant
Authors: MacKinnon Katherine C. 
Published: May 2014

ABSTRACT2013 was a remarkable year in biological anthropology. From perplexing fossil hominin discoveries to revealing genome analyses, discussions of ethics in the field, and the continuing public dissemination of our work, we grappled with many issues both within and outside the academy. Here I explore some of these major accomplishments across four main themes: (1) new hominin finds and resulting consideration of the complex landscapes across which our various ancestors lived, adapted, and possibly interbred; (2) recent news from (nonhuman) primate evolution and contemporary primatological practice; (3) the demonstrated relevance of biological anthropology to anthropology with examples from integrative biocultural and ethnoprimatological approaches that move beyond dated subfield constraints; and (4) the value of social media and engagement of the public.
Effect of diquafosol ophthalmic solution on the optical quality of the eyes in patients with aqueous‐deficient dry eye
Authors: Koh Shizuka , Maeda Naoyuki , Ikeda Chikako , Oie Yoshinori , Soma Takeshi , Tsujikawa Motokazu , Watanabe Hitoshi , Nishida Kohji 
Published: May 2014

AbstractPurposeTo investigate the short‐ and long‐term effects of diquafosol ophthalmic solution on the optical quality of the eyes in patients with aqueous‐deficient dry eye.MethodsSixteen eyes in 16 patients with mild or moderate aqueous‐deficient dry eye were treated with 3% diquafosol ophthalmic solution. Ocular higher‐order aberrations (HOAs) were measured with a wavefront sensor before and at 15 min after diquafosol instillation at the baseline visit and at 4 weeks after treatment initiation. Dry eye symptoms, tear break‐up time (BUT), corneal/conjunctival fluorescein staining and Schirmer's test were also evaluated before and after treatment with diquafosol.ResultsTreatment with diquafosol ophthalmic solution significantly improved dry eye symptoms, corneal staining and BUT. Compared with mean total HOAs at baseline (0.180 ± 0.06 μm), those at 4 weeks after treatment significantly decreased (0.148 ± 0.039 μm; p = 0.035), whereas those 15 min after diquafosol instillation at the baseline visit did not change significantly (0.170 ± 0.049 μm; p = 0.279).ConclusionsAlthough no significant change in HOAs was observed as a short‐term effect of a single‐drop instillation of diquafosol, long‐term use of diquafosol to treat aqueous‐deficient dry eye reduced HOAs as well as improved corneal epithelial damage and tear film stability.
Use of a combination formulation of bismuth, metronidazole and tetracycline with omeprazole as a rescue therapy for eradication of Helicobacter pylori
Authors: Delchier J. C. , Malfertheiner P. , Thieroff‐Ekerdt R. 
Published: May 2014

SummaryBackgroundHelicobacter pylori infection occurs in children and adults worldwide. Standard triple therapy of omeprazole, amoxicillin and clarithromycin (OAC) may not be optimal.AimTo evaluate quadruple therapy with bismuth subcitrate potassium, metronidazole and tetracycline hydrochloride, given with omeprazole in H. pylori infected subjects who failed previous OAC eradication therapy.MethodsThis was a multicenter, open‐label, single‐arm, multinational study. Helicobacter pylori‐positive subjects who had failed ≥1 previous course of OAC therapy with or without up to three supplemental treatments in the previous year. Subjects were treated for 10 days with a combination formulation containing bismuth subcitrate potassium 140 mg, tetracycline hydrochloride 125 mg, and metronidazole 125 mg, three capsules four times daily (q.d.s.), and omeprazole 20 mg twice daily (b.d.). The primary endpoint was H. pylori eradication rate defined as one negative 13C‐urea breath test ≥28 days post‐treatment.ResultsHelicobacter pylori eradication rates ranged from 93.2% to 93.8% in the intent‐to‐treat population (n = 49), and from 94.7% to 95.0% in the PP population (n = 40). No clinically meaningful differences were observed when analysed by country. Metronidazole resistance was observed in 16/49 (32.7%) subjects and clarithromycin resistance in 31/49 (63.3%) subjects. Thirty‐three subjects (67.3%) reported 87 adverse events, and only one (2%) discontinued the study for an adverse event.ConclusionsA quadruple regimen of bismuth, metronidazole and tetracycline plus omeprazole produces a high eradication rate in subjects previously failing H. pylori eradication regimens. This bismuth‐based regimen offers an effective option as rescue therapy.
Development and validation of a 3ABC antibody ELISA in Australia for foot and mouth disease
Authors: Colling A , Morrissy C , Barr J , Meehan G , Wright L , Goff W , Gleeson LJ , van der Heide B , Riddell S , Yu M , Eagles D , Lunt R , Khounsy S , Than Long Ngo , Phong Vu Pham , Than Phuong Nguyen , Tung Nguyen , Linchongsubongkoch W , Hammond J , Johnson M , Johnson WO , Unger H , Daniels P , Crowther JR 
Published: May 2014

ObjectiveTo measure the diagnostic performance of an Australian‐developed ELISA for the detection of antibodies against the non‐structural proteins (NSP) 3ABC of the foot and mouth disease (FMD) virus.DesignTest development and validation study.MethodsThe diagnostic specificity was determined using 2535 sera from naïve animals and 1112 sera from vaccinated animals. Diagnostic sensitivity was calculated from the data for 995 sera from experimentally and field‐infected animals from FMD‐endemic countries in South East Asia. A commercial ELISA detecting antibodies against FMD virus NSP was used as the reference test to establish relative sensitivity and specificity. Bayesian latent class analysis was performed to corroborate results. The diagnostic window and rate of detection were determined at different times using sera from cattle, sheep and pigs before and after infection, and after vaccination and subsequent infection. Repeatability and reproducibility data were established.ResultsAt 35% test cut‐off, the 3ABC ELISA had an overall diagnostic sensitivity of 91.5% and diagnostic specificity of 96.4%. The diagnostic sensitivity in vaccinated and subsequently infected cattle was 68.4% and diagnostic specificity in vaccinated cattle was 98.0%.ConclusionsThe 3ABC ELISA identified field and experimentally infected animals, as well as vaccinated and subsequently infected animals. Diagnostic sensitivity and specificity estimates for other FMD NSP tests are comparable with the results obtained in this study. This NSP ELISA was found to be ‘fit for purpose’ as a screening assay at the herd level to detect viral infection and also to substantiate absence of infection.
Cognitive styles and clinical correlates of childhood abuse in bipolar disorder
Authors: Perich Tania , Mitchell Philip B , Loo Colleen , Hadzi‐Pavlovic Dusan , Roberts Gloria , Green Melissa , Frankland Andrew , Lau Phoebe , Corry Justine 
Published: May 2014

ObjectivesIn a relatively small number of previous studies, childhood abuse has been found to be associated with more severe symptom course, earlier onset, greater comorbidity, and greater suicidality in those diagnosed with bipolar disorder. There have been no prior reports looking for any association between childhood abuse and cognitive style. This study aimed to examine the relationship between cognitive factors, such as response styles to depressed mood and dysfunctional attitudes, clinical features, and childhood physical and sexual abuse in this population.MethodsA total of 157 adult participants diagnosed with DSM‐IV bipolar disorder I or II were assessed on clinical features of this condition and measures of childhood sexual and physical abuse. Participants also completed self‐report questionnaires covering areas such as symptom measures of depression, anxiety and stress, dysfunctional attitudes, and response styles to depressed mood.ResultsSeventy‐four participants (37%) reported having experienced either sexual or physical abuse. Those who reported physical or sexual abuse were significantly more likely to report self‐harm or suicidal behaviors and showed higher stress scores. Specifically, those who reported sexual abuse were more likely to have simple phobias, to have attempted suicide, and to have had more hospitalizations for depression. After controlling for current mood severity, there were no significant differences on the self‐report cognitive style measures for those who reported childhood sexual or physical abuse compared to those who did not report abuse.ConclusionsCognitive styles were not found to be associated with childhood sexual or physical abuse in participants with bipolar disorder. Stress may be important to target in psychological interventions, whilst special attention should also be paid to those with a history of sexual abuse given the greater likelihood of suicide attempt.
Immune dysfunction in bipolar disorder and suicide risk: is there an association between peripheral corticotropin‐releasing hormone and interleukin‐1β?
Authors: Monfrim Xênia , Gazal Marta , De Leon Pâmela B , Quevedo Luciana , Souza Luciano D , Jansen Karen , Oses Jean P , Pinheiro Ricardo T , Silva Ricardo A , Lara Diogo R , Ghisleni Gabriele , Spessato Barbara , Kaster Manuella P 
Published: May 2014

ObjectiveThe aim of the present study was to investigate the relationship between peripheral levels of corticotropin‐releasing hormone (CRH) and interleukin‐1β (IL‐1β) in individuals with bipolar disorder (BD) with and without suicide risk (SR), and controls.MethodsA total of 120 young adults (40 controls, 40 subjects with BD without SR, and 40 subjects with BD with SR) were enrolled from a population‐based study carried out in the city of Pelotas, Brazil. BD and SR were assessed through the Mini International Neuropsychiatric Interview (MINI 5.0), and peripheral markers were evaluated by enzyme‐linked immunosorbent assay (ELISA).ResultsLevels of CRH were significantly lower both in subjects with BD without SR (p = 0.04) and subjects with BD with SR (p = 0.02) when compared to controls. However, levels of IL‐1β were increased in subjects with BD with SR (p = 0.05) when compared to controls. Sociodemographic and clinical variables, current mood episode, and use of psychiatric medications were not associated with changes in these markers. No correlation was found between peripheral levels of CRH and IL‐1β (p = 0.60) in the population or in the BD with SR group (p = 0.88).ConclusionsThese results suggest that peripheral mechanisms linking stress hormones and the immune system might be critical patterns involved in suicidal behavior associated with BD.
PackMerger: A 3D Print Volume Optimizer
Authors: Vanek J. , Galicia J. A. Garcia , Benes B. , Měch R. , Carr N. , Stava O. , Miller G. S. 
Published: May 2014

AbstractWe propose an optimization framework for 3D printing that seeks to save printing time and the support material required to print 3D shapes. Three‐dimensional printing technology is rapidly maturing and may revolutionize how we manufacture objects. The total cost of printing, however, is governed by numerous factors which include not only the price of the printer but also the amount of material and time to fabricate the shape. Our PackMerger framework converts the input 3D watertight mesh into a shell by hollowing its inner parts. The shell is then divided into segments. The location of splits is controlled based on several parameters, including the size of the connection areas or volume of each segment. The pieces are then tightly packed using optimization. The optimization attempts to minimize the amount of support material and the bounding box volume of the packed segments while keeping the number of segments minimal. The final packed configuration can be printed with substantial time and material savings, while also allowing printing of objects that would not fit into the printer volume. We have tested our system on three different printers and it shows a reduction of 5–30% of the printing time while simultaneously saving 15–65% of the support material. The optimization time was approximately 1 min. Once the segments are printed, they need to be assembled.