bluuebunny/crossref_metadata_2025_split huggingface dataset:
Outcomes of very high‐risk prostate cancer after radical prostatectomy: Validation study from 3 centers
Authors: Sundi Debasish , Tosoian Jeffrey J. , Nyame Yaw A. , Alam Ridwan , Achim Mary , Reichard Chad A. , Li Jianbo , Wilkins Lamont , Schwen Zeyad , Han Misop , Davis John W. , Klein Eric A. , Schaeffer Edward M. , Stephenson Andrew J. , Ross Ashley E. , Chapin Brian F. 
Published: November 2018

BackgroundAmong men with localized high‐risk prostate cancer (PCa), patients who meet very high‐risk (VHR) criteria have been shown to experience worse outcomes after radical prostatectomy (RP) in a previous study. Variations of VHR criteria have been suggested to be prognostic in other single‐center cohorts, but multicenter outcomes validating VHR criteria have not been described. This study was designed to validate VHR criteria for identifying which PCa patients are at greatest risk for cancer progression.MethodsPatients with high‐risk PCa undergoing RP (2005‐2015) at 3 tertiary centers were pooled. The outcomes of men with VHR PCa were compared with the outcomes of those who did not meet VHR criteria. The high‐risk criteria were a clinical stage of T3 to T4, a prostate‐specific antigen level > 20 ng/mL, or a biopsy Gleason grade sum of 8 to 10. The VHR criteria were multiple high‐risk features, >4 biopsy cores with a Gleason grade sum of 8 to 10, or primary Gleason grade pattern 5. Biochemical recurrence, metastasis (METS), and cancer‐specific mortality (CSM) were assessed with competing risks regressions. Overall mortality was assessed with Cox survival models.ResultsAmong 1981 patients with high‐risk PCa, men with VHR PCa (n = 602) had adverse pathologic outcomes: 37% versus 25% for positive margins and 37% versus 15% for positive lymph nodes (P <  .001 for both comparisons). Patients with VHR PCa also had higher adjusted hazard ratios for METS (2.78; 95% confidence interval [CI], 2.08‐3.72), CSM (6.77; 95% CI, 2.91‐15.7), and overall mortality (2.44; 95% CI, 1.56‐3.80; P <  .001 for all comparisons).ConclusionsIn a validation study of patients who underwent treatment for high‐risk PCa, VHR criteria were strongly associated with adverse pathologic and oncologic outcomes.
Good Citizenship Made Easy: A Step‐by‐Step Guide to Submitting RNA‐Seq Data to NCBI
Authors: Feindt Wiebke , Oppenheim Sara J. , DeSalle Robert , Mehr Shaadi 
Published: November 2018

AbstractThe analysis of transcriptome data from non‐model organisms contributes to our understanding of diverse aspects of evolutionary biology, including developmental processes, speciation, adaptation, and extinction. Underlying this diversity is one shared feature, the generation of enormous amounts of sequence data. Data availability requirements in most journals oblige researchers to make their raw transcriptome data publicly available, and the databases housed at the National Center for Biotechnology Information (NCBI) are a popular choice for data deposition. Unfortunately, the successful submission of raw sequences to the Sequence Read Archive (SRA) and transcriptome assemblies to the Transcriptome Shotgun Assembly (TSA) can be challenging for novice users, significantly delaying data availability and publication. Here we present two comprehensive protocols for submitting RNA‐Seq data to NCBI databases, accompanied by an easy‐to‐use website that facilitates the timely submission of data by researchers of any experience level. © 2018 by John Wiley & Sons, Inc.
Alchemist: An Apache Spark ⇔ MPI interface
Authors: Gittens Alex , Rothauge Kai , Wang Shusen , Mahoney Michael W. , Kottalam Jey , Gerhardt Lisa , Prabhat  , Ringenburg Michael , Maschhoff Kristyn 
Published: November 2018

SummaryThe Apache Spark framework for distributed computation is popular in the data analytics community due to its ease of use, but its MapReduce‐style programming model can incur significant overheads when performing computations that do not map directly onto this model. One way to mitigate these costs is to off‐load computations onto MPI codes. In recent work, we introduced Alchemist, a system for the analysis of large‐scale data sets. Alchemist calls MPI‐based libraries from within Spark applications, and it has minimal coding, communication, and memory overheads. In particular, Alchemist allows users to retain the productivity benefits of working within the Spark software ecosystem without sacrificing performance efficiency in linear algebra, machine learning, and other related computations. In this paper, we discuss the motivation behind the development of Alchemist, and we provide a detailed overview of its design and usage. We also demonstrate the efficiency of our approach on medium‐to‐large data sets, using some standard linear algebra operations, namely, matrix multiplication and the truncated singular value decomposition of a dense matrix, and we compare the performance of Spark with that of Spark+Alchemist. These computations are run on the NERSC supercomputer Cori Phase 1, a Cray XC40.
Navigating tensions in a cross‐sector social partnership: How a convener drives change for sustainability
Authors: van Hille Iteke , de Bakker Frank G.A. , Ferguson Julie E. , Groenewegen Peter 
Published: November 2018

AbstractIn this paper, we study conveners' work in establishing change towards sustainability through cross‐sector social partnerships (CSSPs). Applying a paradox lens, we offer a new perspective on tensions in CSSPs: These are not hurdles or challenges to overcome in order to reach success but endure throughout the entire CSSP process. This insight changes the role of the convener, who no longer has to overcome but has to navigate tension. We focus on two tensions related to the convener role: the convener as leader but without formal authority over CSSP‐partners and the convener as both stakeholder and (neutral) facilitator in the process. Through a case study on a CSSP in the Dutch timber sector, we explain how a convener (Forest Stewardship Council Netherlands) responded to these tensions over time. We add to literatures on CSSPs and convening by outlining the relevance of a paradox perspective in this domain.
Deep ultraviolet lasers for flow cytometry
Authors: Telford William , Georges Thierry , Miller Clint , Voluer Pascal 
Published: November 2018

AbstractModern flow cytometers require multiple laser wavelengths to excite the wide variety of fluorescent probes now available for high‐dimensional analysis. Ultraviolet (UV) lasers (typically solid state 355 nm) have become a critical excitation source for the Brilliant Ultraviolet (BUV) series of polymer fluorochromes. The BUV dyes have pushed the number of fluorescent probes available for simultaneous analysis to nearly 30, allowing an unprecedented level of precision for immune cell analysis. However, immunologists are already seeking analyze more than 30 simultaneous parameters, requiring both new fluorochromes and corresponding laser wavelengths. A group of polymer dyes requiring deep ultraviolet (UV) excitation (~280–300 nm) is currently under development, allowing the expansion of high‐dimensional cytometry beyond the current 30 color limit. In this study, we evaluated a newly available laser emitting at 280 nm as a possible laser source for exciting these dyes. Since deep UV polymer dyes are not yet available, we used quantum nanoparticles (Qdots) as a surrogate probe to assess the utility of this laser wavelength for flow cytometry. Deep UV laser light was found to excite Qdots as well as traditional UV sources. Deep UV 280 nm did not excite BUV dyes well, suggesting that BUV and deep UV polymers will be spectrally compatible with low crossbeam spillover issues. Deep UV excitation did excite considerable autofluorescence in the violet to blue range, a limitation that will need to guide deep UV fluorochrome development. A deep UV 280 nm laser may therefore be the next essential wavelength for high‐dimensional flow cytometry. © 2018 International Society for Advancement of Cytometry
Spatial variation in throughfall, soil, and plant water isotopes in a temperate forest
Authors: Goldsmith Gregory R. , Allen Scott T. , Braun Sabine , Engbersen Nadine , González‐Quijano Clara R. , Kirchner James W. , Siegwolf Rolf T.W. 
Published: November 2018

AbstractStudies of stable isotopes of water in the environment have been fundamental to advancing our understanding of how water moves through the soil–plant–atmosphere continuum; however, much of this research focuses on how water isotopes vary in time, rather than in space. We examined the spatial variation in the δ18O and δ2H of throughfall and bulk soil water, as well as branch xylem and bulk leaf water of Picea abies (Norway spruce) and Fagus sylvatica (beech), in a 1‐ha forest plot in the northern Alps of Switzerland. Means and ranges of water isotope ratios varied considerably among throughfall, soil, and xylem samples. Soil water isotope ratios were often poorly explained by soil characteristics and often not predictable from proximal samples. Branch xylem water isotope values varied less than either soil water or bulk leaf water. The isotopic range observed within an individual tree crown was often similar to that observed among different crowns. As a result of the heterogeneity in isotope ratios, inferences about the depth of plant root water uptake drawn from a two end‐member mixing model were highly sensitive to the soil sampling location. Our results clearly demonstrate that studies using water isotopes to infer root water uptake must explicitly consider how to characterize soil water, incorporating measures of both vertical and lateral variations. By accounting for this spatial variation and the processes that shape it, we can improve the application of water isotopes to studies of plant ecophysiology, ecohydrology, soil hydrology, and palaeoclimatology.
Moonlight enhances growth in larval fish
Authors: Shima Jeffrey S. , Swearer Stephen E. 
Published: November 2018

AbstractMoonlight mediates trophic interactions and shapes the evolution of life‐history strategies for nocturnal organisms. Reproductive cycles and important life‐history transitions for many marine organisms coincide with moon phases, but few studies consider the effects of moonlight on pelagic larvae at sea. We evaluated effects of moonlight on growth of pelagic larvae of a temperate reef fish using “master chronologies” of larval growth constructed from age‐independent daily increment widths recorded in otoliths of 321 individuals. We found that daily growth rates of fish larvae were enhanced by lunar illumination after controlling for the positive influence of temperature and the negative influence of cloud cover. Collectively, these results indicate that moonlight enhances growth rates of larval fish. This pattern is likely the result of moonlight's combined effects on foraging efficiency and suppression of diel migrations of mesopelagic predators, and has the potential to drive evolution of marine life histories.
Having it all? The implications of public health and environmental protection partnerships in the American states
Authors: Hopper JoyAnna S. 
Published: November 2018

AbstractTo save money and avoid redundancy, states may choose to combine complementary areas of policy implementation into a single bureaucratic agency or ministry. This is often the case with environmental protection, a policy area that is inarguably interdisciplinary in its aims and functions. A number of scholars have noted that the combination of policy mandates may lead to the neglect of certain agency functions, particularly when one of the mandates is regulatory whereas the other is nonregulatory in nature. However, what occurs when environmental protection is combined with a seemingly complementary and relevant policy area, such as public health? In this article, I argue that the combination of these policy areas will lead to the elevation of public health goals and preferences over those of environmental enforcement. Using the American states as a case, I find through interviews with environmental and public health employees, text analysis, and empirical analyses that public health functions and goals are prioritized within combined agencies. That prioritization leads to fewer punitive actions taken by the agencies during the regulatory process. Given the popularity of “multitask” agencies, it is imperative to understand how even the most convenient and reasonable combinations may affect day‐to‐day environmental protection efforts.
Corporate reporting and conservation realities: Understanding differences in what businesses say and do regarding biodiversity
Authors: Smith Thomas , Paavola Jouni , Holmes George 
Published: November 2018

AbstractBusinesses are increasingly called on to participate in tackling biodiversity loss, but the extent of corporate commitments to act is unclear. We have a limited understanding of differences in perceptions and actions regarding biodiversity across business sectors. Doubts also remain concerning the reliability of corporate reporting as a window into business involvement in biodiversity. This paper tackles these uncertainties by using formal corporate reporting and interviews with managers and stakeholders about actions regarding biodiversity as the evidence base. Taking the cases of forestry and salmon farming in Chile, it finds sectoral differences are influenced by distinct regulatory settings and forms of stakeholder engagement. Whilst reporting serves as a partial window into each sector, manager interviews and stakeholder accounts indicate firms in both sectors perceive biodiversity primarily as a reputational risk rather than a core responsibility. In both cases, businesses have used formal corporate reporting to mask negative impacts, and it has failed to leverage fundamental reform. The findings indicate that formal reporting can only ever play a partial role in understanding and motivating business action on biodiversity. Stakeholder views and the particularities of local contexts must be more clearly articulated to ensure businesses undertake substantive rather than symbolic action on their impacts. The paper concludes by reflecting on implications for Natural Capital reporting and identifies limitations and avenues for future research.
Factors influencing the use of opioids for breakthrough cancer pain: A secondary analysis of the IOPS‐MS study
Authors: Mercadante Sebastiano , Adile Claudio , Masedu Francesco , Marchetti Paolo , Costanzi Andrea , Aielli Federica 
Published: November 2018

AbstractBackgroundControversies exist about the choice and the doses of opioid medication in breakthrough cancer pain (BTcP).MethodsThe aim was to assess factors influencing the use and the doses of opioids prescribed for BTcP. There was performed a secondary analysis of a national, multicentre study that involving 32 centres performed in patients having BTcP. Diagnosis of BTcP was based on a definite algorithm. Patients using opioids for background pain and for BTcP were selected. Average pain intensity and opioids used for background pain and BTcP, and adverse effects were assessed, as well as patient’s satisfaction and the grade of mucositis.ResultsThe analysis was performed in 2,771 patients. Opioid doses given for BTcP were significantly associated with those given for background pain. No relationship between adverse effects and the use and the doses of opioids used for BTcP was found. Drugs and doses were not correlated to the grade of oral mucositis. Nasal fentanyl preparations provided the fastest meaningful pain relief in comparison with other fentanyl transmucosal preparations or morphine preparations (P = 0.000). The majority of patients were satisfied with opioid medications given for BTcP. Only 2.8% of patients reported adverse effects related to opioid medication used for BTcP. Age and gender were independently associated with dosages of some fentanyl products.ConclusionsOpioids for BTcP were effective and safe in a large sample of cancer patients with different stages of disease. Doses of opioids proportional to doses used for background pain seem to guarantee both efficacy and safety.SignificanceThe use of opioids for breakthough cancer pain was effective and safe in a large sample of advanced cancer patients recruited in different stages of disease and settings. Doses of opioids proportional to opioid doses used for background analgesia, seem to guarantee both effectiveness and safety.
The relative efficacy of mindfulness versus distraction: The moderating role of attentional bias
Authors: Shires Alice , Sharpe Louise , Newton John Toby R. O. 
Published: November 2018

AbstractBackgroundThis study investigated whether the ability to disengage quickly from pain‐related stimuli moderated the relative efficacy of a mindfulness‐based intervention versus distraction in response to an experimental pain task.MethodsParticipants (n = 100) completed a dot probe task with eye tracking and were then randomized (2:2:1) to receive a mindfulness‐based interoceptive exposure task (MIET), distraction instructions or no instructions (control group) before engaging in the cold pressor test.ResultsParticipants who were allocated to the MIET condition reported a significantly higher pain threshold and distress than the distraction group, although not significantly higher than the control group. Those in the MIET group had improved tolerance compared to both the distraction and control groups. Difficulty disengaging from pain‐related stimuli, as measured by the duration of the first fixation on sensory words, was found to moderate the relative efficacy of mindfulness versus distraction in terms of pain threshold and distress, but not tolerance. Those with difficulty disengaging from sensory pain words benefited less from the MIET. Duration of first fixation on sensory and affective pain words were highly correlated, and duration of first fixation on affective pain words also moderated the relative efficacy of MIET and distraction on threshold, but not distress.ConclusionsThese results show that a single brief session of a mindfulness task was sufficient to change an acute pain experience in comparison with a distraction task, and that those who disengaged quickly from pain words benefited most.SignificanceThis study demonstrated the efficacy of a novel, exposure‐based mindfulness technique for pain tolerance and showed that those who disengaged easily from pain stimuli benefited most. This brief task could be clinically useful, particularly for those who are not overly focused on their pain symptoms.
Anti‐hypersensitive effect of angiotensin (1‐7) on streptozotocin‐induced diabetic neuropathic pain in mice
Authors: Ogata Yoshiki , Nemoto Wataru , Yamagata Ryota , Nakagawasai Osamu , Shimoyama Shuji , Furukawa Tomonori , Ueno Shinya , Tan‐No Koichi 
Published: November 2018

AbstractBackgroundWe have recently reported that the spinal angiotensin (Ang) converting enzyme (ACE)/Ang II/AT1 receptor axis and downstream p38 MAPK phosphorylation are activated in streptozotocin (STZ)‐induced diabetic mice and lead to tactile hypersensitivity. Moreover, our previous results suggested that the intrathecal (i.t.) administration of Ang (1‐7), an N‐terminal fragment of Ang II, may attenuate the Ang II‐induced nociceptive behaviour through the inhibition of p38 MAPK phosphorylation via Mas receptors. Here, we investigated whether the i.t. administration of Ang (1‐7) can attenuate STZ‐induced diabetic neuropathic pain.MethodsTactile and thermal hypersensitivities were determined using the von Frey filament and Hargreaves tests, respectively. The protein expression of ACE2, Mas receptors and phospho‐p38 MAPK was measured by western blotting. Spinal ACE2 activity was determined using ACE2 activity assay kit.ResultsThe i.t. administration of Ang (1‐7) significantly reduced the tactile and thermal hypersensitivities on day 14 after STZ injection, and these effects were significantly prevented by the Mas receptor antagonist A779. The expression of ACE2 and Mas receptors in the plasma membrane fraction of the lumbar dorsal spinal cord was both significantly decreased in STZ mice. Spinal ACE2 activity was also decreased while p38 MAPK phosphorylation was increased in the lumbar dorsal region of these mice. This phosphorylation was attenuated by the injection of Ang (1‐7), whose effect was reversed by A779.ConclusionsOur data demonstrate that Ang (1‐7) attenuates STZ‐induced diabetic neuropathic pain and that this occurs through a mechanism involving spinal Mas receptors and he inhibition of p38 MAPK phosphorylation.SignificanceThe ACE2/Ang (1‐7)/Mas receptor axis was down‐regulated in the spinal cord of STZ mice and the i.t. administration of Ang (1‐7) attenuated the STZ‐induced diabetic neuropathic pain via Mas receptors. Therefore, the activation of this axis could be an effective therapeutic target to alleviate the neuropathic pain in diabetic patients.
Physicochemical Characteristics of Polypyrrole/(Glucose oxidase)/(Prussian Blue)‐based Biosensor Modified with Ni‐ and Co‐Hexacyanoferrates
Authors: Rekertaitė Asta Inesė , Valiūnienė Aušra , Virbickas Povilas , Ramanavicius Arunas 
Published: November 2018

AbstractIn this work, three types of electrodes suitable for amperometric glucose biosensors were designed. One type of electrode was based on bio‐selective layer of polypyrrole/(glucose oxidase)/(Prussian Blue) (Ppy/GOx/PB) and it was used as a control electrode regarding to which electrochemical properties of two other types of electrodes were compared. During the formation of Prussian blue layers graphite electrodes were additionally modified by Ni‐hexacyanoferrate (NiHCF) and by Co‐hexacyanoferrate (CoHCF) in order to design Ppy/GOx/PB‐NiHCF and Ppy/GOx/PB‐CoHCF electrodes, respectively. Some physicochemical characteristics of all three types of electrodes were evaluated and compared. The Ppy/GOx/PB‐NiHCF electrode showed wider linear range of the calibration curve than Ppy/GOx/PB and Ppy/GOx/PB‐CoHCF electrodes. The effect of temperature on analytical performance of the Ppy/GOx/PB‐NiHCF based biosensor has been evaluated and activation energy of enzyme catalysed reaction has been calculated within the temperature range of 15 °C to 30 °C.
Disposable Amperometric Immunosensor for the Determination of the E‐Cadherin Tumor Suppressor Protein in Cancer Cells and Human Tissues
Authors: Muñoz‐San Martín Cristina , Pedrero María , Manuel de Villena F. Javier , Garranzo‐Asensio María , Rodríguez Nuria , Domínguez Gemma , Barderas Rodrigo , Campuzano Susana , Pingarrón José M. 
Published: November 2018

AbstractThis paper describes the results obtained in the development of the first electrochemical immunosensor described to date for the detection of E‐cadherin (E‐cad) protein, a relevant biomarker of prognosis and metastasis in cancer, based on the use of magnetic microcarriers (MBs) and amperometric transduction at screen‐printed carbon electrodes (SPCEs). Thus, the determination of E‐cad protein involved the use of two specific antibodies against this protein (one of them labelled with HRP) in a sandwich configuration onto HOOC‐MBs. The magnetic bioconjugates were captured onto SPCEs and the amperometric transduction was performed using the H2O2/hydroquinone (HQ) system. Under optimal conditions, this bioplatform demonstrated a wide linear concentration range (0.50–25 ng mL−1) and a detection limit as low as 0.16 ng mL−1, well below the optimal cut‐off level for the E‐cad protein (defined as 10,000 ng mL−1 for soluble E‐cad levels in serum). The developed sensor also showed a good reproducibility among measurements with seven different sensors constructed in the same manner (RSD, 5.4 %), stability for more than 15 days and good specificity towards other proteins commonly found on biological samples. The applicability of this simple handling bioplatform for the direct determination of this protein in cell lysates with different metastatic potential and extracts from paraffined‐embedded human colorectal cancer tissues of different grade were also demonstrated.