bluuebunny/crossref_metadata_2025_split huggingface dataset:
NMR Structure Determination for Oligonucleotides
Authors: Spring‐Connell Alexander M. , Evich Marina , Germann Markus W. 
Published: April 2018

AbstractNMR spectroscopy is a versatile tool for determining the structure and dynamics of nucleic acids under solution conditions. In this unit, we provide an overview and detail of the experiments and methods used in our laboratory to determine the structure of oligonucleotides at natural abundance, thus limiting our approach to 1H, 13C, and 31P NMR techniques. Isotopic labeling is heavily used in RNA NMR studies, however, labeling of DNA is still less common and, if modified nucleotides are investigated, is exceptionally expensive or not feasible. Each method described here is extensively documented and annotated with tips and observations to facilitate their application. Sections are devoted to sample preparation, NMR experiments and setup, resonance assignment, structure generation protocols, evaluation, tips that may be useful, and software sources. © 2018 by John Wiley & Sons, Inc.
Absolute Quantitation of Plant Proteins
Authors: Ahsan Nagib , Wilson Rashaun S. , Thelen Jay J. 
Published: April 2018

AbstractAmong targeted proteomic techniques, AQUA‐MRM is considered as one of the most reliable for accurate protein quantitation. This method displays high sensitivity, specificity, and reproducibility compared to many common biochemical techniques by coupling the use of unique, heavy‐labeled peptide standards and triple‐quadrupole mass spectrometry. However, there are several important steps that are required for successful development and validation of a robust AQUA‐MRM assay. The following protocol outlines and details the key steps necessary for plant sample preparation as well as AQUA‐MRM development and validation, specifically for absolute quantitation of plant proteins in vivo. © 2018 by John Wiley & Sons, Inc.
In Vitro Enzyme Assays for JmjC‐Domain‐Containing Lysine Histone Demethylases (JmjC‐KDMs)
Authors: Tarhonskaya Hanna , Tumber Anthony , Kawamura Akane , Schofield Christopher J. 
Published: April 2018

AbstractHistone modifications, including lysine methylation marks on histone tails, modulate the accessibility of genes for transcription. Changes in histone tail methylation patterns can cause transcriptional activation or repression. The dynamic regulation of lysine methylation patterns is enabled by two distinct groups of enzymes: histone methyltransferases (KMTs) and demethylases (KDMs). The Jumonji C (JmjC) domain–containing lysine histone demethylases (JmjC‐KDMs) alter the methylation levels of histone tails by removing tri‐, di‐, or mono‐methylation marks. Because JmjC‐KDMs activities are dysfunctional in cancer and other clinical conditions, they are targets for drug discovery. Efforts are underway to develop high‐throughput assays capable of identifying selective, small‐molecule inhibitors of KDMs. Detailed in this unit are protocols for mass spectrometry–based and formaldehyde dehydrogenase–coupled enzyme‐based assays that can be used to identify inhibitors of JmjC‐KDMs. © 2018 by John Wiley & Sons, Inc.
Fuzzy logic–based jamming detection algorithm for cluster‐based wireless sensor network
Authors: Vijayakumar K. P. , Ganeshkumar P. , Anandaraj M. , Selvaraj K. , Sivakumar P. 
Published: April 2018

SummaryIn this paper, a fuzzy logic–based jamming detection algorithm (FLJDA) is proposed to detect the presence of jamming in downstream data communication for cluster‐based wireless sensor networks. The proposed FLJDA keeps an eye on the existing nodes and new node to determine their behavior by applying fuzzy logic on measured jamming detection metrics. To monitor the behavior of the nodes, the FLJDA computes the jamming detection metrics, namely, packet delivery ratio and received signal strength indicator. The major features of this paper are the following: (1) The jamming detection algorithm is specifically implemented for downstream data communication, (2) cluster head estimates jamming detection metrics for detecting the jamming unlike the existing algorithms where individual nodes explicitly collect the jamming detection metrics, and (3) the proposed algorithm optimizes the jamming detection metrics on the basis of fuzzy logic unlike the existing approaches, which uses merely jamming detection threshold alone for jamming detection. The simulation results of the proposed system provide the true detection ratio as high as 99.89%.
A model for virtual network embedding using Artificial Bee Colony
Authors: Pathak Isha , Tripathi Atul , Vidyarthi Deo Prakash 
Published: April 2018

SummaryIn a network virtualization environment, a significant research problem is that of virtual network embedding. As the network virtualization system is distributed in nature, an effective solution on how to optimally embed a dynamically generated virtual network request on the substrate networks that are owned and managed by multiple infrastructure providers needs proper attention. The problem is computationally hard, and therefore, many approaches, implying heuristics/meta‐heuristics, have been applied for the same. A meta‐heuristic, Artificial Bee Colony algorithm is getting popular due to its robustness toward complex problem solving. A novel approach based on Artificial Bee Colony to address the dynamic virtual network embedding problem in a multiple infrastructure provider scenario is proposed in this work. Bee population is initialized by using a greedy heuristic in which the number of substrate networks together with virtual network requests constructs a bee. Generated solution, in the population, is improvised by using greedy selection that explores a local search method adopted by the bees. In greedy selection, the new candidate source is memorized by the bee if its fitness is better than the fitness of the existing source. The performance study of the proposed model is done by simulation over various metrics such as embedding cost, embedding time, and acceptance ratio. A comparative study is conducted with other nature‐inspired virtual network embedding algorithms on these metrics. The findings affirm that the proposed virtual network embedding approach performs well and produces better results.
The Evaluator, the Arts, and Functional Skepticism
Authors: Jenkins David 
Published: April 2018

AbstractDavid Jenkins traces his education as an escape from the coalfields of Wales and his mother's religion toward a haphazard career in evaluation based on literary approaches to curriculum criticism and celebrating the exercise of judgment in the teeth of uncertainty. See the interview document here: http://onlinelibrary.wiley.com/wol1/doi/10.1002/ev.20294/suppinfo. Read only. This should not be used in any form without explicit permission from the author.
Blending Rationality and Intuition
Authors: Fitzpatrick Jody 
Published: April 2018

AbstractJody Fitzpatrick gives examples of her father's influence on her learning to be rational and her mother's examples of emotion and intuition. Jody has found ways to include both values in her personal life, with greater emphasis on the rational search for evidence in her professional work both as a professor and as an evaluator. See the interview document here: http://onlinelibrary.wiley.com/wol1/doi/10.1002/ev.20296/suppinfo. Read only. This should not be used in any form without explicit permission from the author.
The Dialog Between Internal and External Evaluation
Authors: Nevo David 
Published: April 2018

AbstractDavid Nevo relates how his father and rabbi taught him by their examples the importance of appropriate external evaluations to help others learn to make responsible internal/self‐evaluations. He notes how the tension between internal and external evaluation has continued to influence his approach to educational evaluation and how he continues to seek ways to combine them appropriately. See the interview document here: http://onlinelibrary.wiley.com/wol1/doi/10.1002/ev.20306/suppinfo. Read only. This should not be used in any form without explicit permission from the author.
Jurassic ca. 160 Ma crustal remelting and Paleoproterozoic intrusive rock residues in the Liaodong Peninsula, East China: Evidence from in situ zircon U–Pb dating and Lu–Hf isotopic analysis
Authors: Gu Yu‐Chao , Chen Ren‐Yi , Li Dong‐Tao , Yang Jia‐Lin , Yang Feng‐Chao , Jia Hong‐Xiang , Dick Jeffrey , Hu Qing‐Hai , Ju Nan , Cao Jie 
Published: April 2018

The Liaodong Peninsula is an important component of the eastern North China Craton which underwent a transition from an orogenic stage to extension and lithospheric thinning in the Mesozoic era. This transition resulted in large‐scale magmatism and gold mineralization. In this paper, we report findings on Paleoproterozoic intrusive rock residues in the Mesozoic Wulong pluton. To analyse the chronology, magma source, and petrogenetic relationships between the Mesozoic and Paleoproterozoic intrusives, we performed SHRIMP U–Pb isotopic dating and in situ micro‐area Lu–Hf isotopic analysis of zircons. The results show that the crystallization age of the large‐scale Mesozoic intrusive rock is 158 ± 2 Ma, which is in the Late Jurassic. The εHf(t) values of the zircons are between −29.3 and −22.1, and their tDM2 values are between 2,606 and 3,064 Ma, which indicates that the magma source of materials is the Archean supracrust. The zircons of the Paleoproterozoic intrusive rock residues have a typical core–mantle–rim texture. The cores of the zircons have an age range from 1,851 to 2,528 Ma, εHf(t) from −12.2 to +4.0, and tDM2 between 2,519 and 3,437 Ma, reflecting characteristics of multiple sources for the inherited zircons. The mantles of the zircons have an upper intercept age of 1,862 ± 13 Ma, εHf(t) values between −11.9 and −2.2, and tDM2 between 2,644 and 3,241 Ma representing the age of the source rocks. The new growth rims of the zircons have a concordia age of 157.1 ± 2.2 Ma, εHf(t) values from −30.8 to −26.1, and tDM2 between 2,852 and 3,150 Ma representing the metamorphic recrystallization age and characteristics of the upper crustal magma source. The findings of this work suggest that the Wulong pluton, which occupies a large area in the Liaodong Peninsula, recrystallized from Paleoproterozoic granites that were affected by Late Jurassic (ca. 160 Ma) crustal remelting. The incompletely remolten residues are the direct result of the delamination and remelting during the Mesozoic era of Palaeoproterozoic intrusive rocks in the northern margin of the eastern North China Craton.
The Purchased Patient Advocate
Authors: Elliott Carl 
Published: April 2018

AbstractThirty years ago, the only people drug companies thought worth buying were doctors and politicians. But the ground began to shift in the 1980s, when HIV/AIDS activists showed everyone how powerful patient advocates could be. It didn't hurt that many advocates were so strapped for money that they could be purchased at bargain prices. Today over 80 percent of patient advocacy groups accept money from the pharmaceutical industry, and the testimony of marginalized patients carries such cultural power that drug companies like Sprout Pharmaceuticals are willing to fake grassroots patient movements. Whether you see this change as a victory for patients or a cautionary tale of institutional corruption depends on how deeply committed you are to the idea that free markets represent our best hope for the future of medicine. Count Sharon Batt as one of the skeptics. Her superb new book, Health Advocacy, Inc.: How Pharmaceutical Funding Changed the Breast Cancer Movement, is a deep scholarly account of the way that pharmaceutical funding has warped the patient advocacy movement into a tool for medical capitalism. Taking the Canadian breast cancer movement as a case study, Batt uses extensive interviews, scholarly resources, and her personal history to explore the struggles faced by patient advocates as they decide whether industry funding is necessary to keep their organizations afloat.
Impact of oncogene panel results on surgical management of cytologically indeterminate thyroid nodules
Authors: Valderrabano Pablo , Khazai Laila , Thompson Zachary J. , Leon Marino E. , Otto Kristen J. , Hallanger‐Johnson Julie E. , Wadsworth J. Trad , Chung Christine H. , Centeno Barbara A. , McIver Bryan 
Published: April 2018

AbstractBackgroundThe impact of oncogene panel results on the surgical management of indeterminate thyroid nodules (ITNs) is currently unknown.MethodsSurgical management of 649 patients consecutively evaluated from October 2008 to April 2016 with a single nodule biopsied and indeterminate cytology (193 evaluated with and 456 without oncogene panels) was assessed and compared. Histological features of 629 consecutively resected ITNs (164 evaluated with and 465 without oncogene panels) were also characterized and compared.ResultsOncogene panel evaluation was associated with higher rates of total thyroidectomy (45% vs 28%; P = .006), and central lymph node dissection (19% vs 12%; P = .03) without increasing the yield of malignancy or decreasing the rate of completion thyroidectomy. Most malignancies (64%), including 83% of those with driver mutation identified, were low‐risk cancers for which a lobectomy could have been sufficient initial treatment.ConclusionCurrent oncogene panel results seem insufficient to guide the surgical extent of solitary ITNs.
Decoupling the effects of deforestation and climate variability in the Tapajós river basin in the Brazilian Amazon
Authors: Arias Mauricio E. , Lee Eunjee , Farinosi Fabio , Pereira Fabio F. , Moorcroft Paul R. 
Published: April 2018

AbstractTropical river basins are experiencing major hydrological alterations as a result of climate variability and deforestation. These drivers of flow changes are often difficult to isolate in large basins based on either observations or experiments; however, combining these methods with numerical models can help identify the contribution of climate and deforestation to hydrological alterations. This paper presents a study carried out in the Tapajόs River (Brazil), a 477,000 km2 basin in South‐eastern Amazonia, in which we analysed the role of annual land cover change on daily river flows. Analysis of observed spatial and temporal trends in rainfall, forest cover, and river flow metrics for 1976 to 2008 indicates a significant shortening of the wet season and reduction in river flows through most of the basin despite no significant trend in annual precipitation. Coincident with seasonal trends over the past 4 decades, over 35% of the original forest (140,000 out of 400,000 km2) was cleared. In order to determine the effects of land clearing and rainfall variability to trends in river flows, we conducted hindcast simulations with ED2 + R, a terrestrial biosphere model incorporating fine scale ecosystem heterogeneity arising from annual land‐use change and linked to a flow routing scheme. The simulations indicated basin‐wide increases in dry season flows caused by land cover transitions beginning in the early 1990s when forest cover dropped to 80% of its original extent. Simulations of historical potential vegetation in the absence of land cover transitions indicate that reduction in rainfall during the dry season (mean of −9 mm per month) would have had an opposite and larger magnitude effect than deforestation (maximum of +4 mm/month), leading to the overall net negative trend in river flows. In light of the expected increase in future climate variability and water infrastructure development in the Amazon and other tropical basins, this study presents an approach for analysing how multiple drivers of change are altering regional hydrology and water resources management.
Pressured HIV testing “in the name of love”: a mixed methods analysis of pressured HIV testing among men who have sex with men in China
Authors: Ong Jason J , Wu Dan , Huang Wenting , Fu Hongyun , Desmond Nicola , Ma Wei , Kang Dianmin , Liao Meizhen , Marley Gifty , Wei Chongyi , Tang Weiming , Liu Chuncheng , Zhang Ye , Pan Stephen W , Yang Bin , Yang Ligang , Huang Shujie , Tucker Joseph D 
Published: April 2018

AbstractIntroductionHIV testing has rapidly expanded into diverse, decentralized settings. While increasing accessibility to HIV testing is beneficial, it may lead to unintended consequences such as being pressured to test. We examined the frequency, correlates and contexts of pressured HIV testing among Chinese men who have sex with men (MSM) using mixed methods.MethodsWe conducted an online survey of MSM (N = 1044) in May 2017. Pressured HIV testing was defined as being forced to test for HIV. We conducted logistic regression analysis to determine the associations between pressured HIV testing and socio‐demographic and sexual behavioural factors. Follow‐up interviews (n = 17) were conducted with men who reported pressured testing and we analysed qualitative data using a thematic analysis approach.ResultsNinety‐six men (9.2%) reported experiencing pressure to test for HIV. Regular male sex partners were the most common source of pressure (61%, 59/96), and the most common form of pressure was a threat to end a relationship with the one who was being pressured (39%, 37/96). We found a higher risk of pressured testing in men who had only used HIV self‐testing compared to men who had never self‐tested (AOR 2.39 (95%CI: 1.38 to 4.14)). However, this relationship was only significant among men with low education (AOR 5.88 (95% CI: 1.92 to 17.99)) and not among men with high education (AOR 1.62 (95% CI: 0.85 to 3.10)). After pressured testing, about half of men subsequently tested for HIV (55%, 53/96) without pressure – none reported being diagnosed with HIV. Consistent with this finding, qualitative data suggest that perceptions of pressure existed on a continuum and depended on the relationship status of the one who pressured them. Although being pressured to test was accompanied by negative feelings, men who were pressured into testing often changed their attitude towards HIV testing, testing behaviours, sexual behaviours and relationship with the one who pressured them to test.ConclusionPressured HIV testing was reported among Chinese MSM, especially from men with low education levels and men who received HIV self‐testing. However, in some circumstances, pressure to test helped MSM in several ways, challenging our understanding of the role of agency in the setting of HIV testing.
A time‐motion study of cardiovascular disease risk factor screening integrated into HIV clinic visits in Swaziland
Authors: Palma Anton M , Rabkin Miriam , Simelane Samkelo , Gachuhi Averie B , McNairy Margaret L , Nuwagaba‐Biribonwoha Harriet , Bongomin Pido , Okello Velephi N , Bitchong Raymond A , El‐Sadr Wafaa M 
Published: April 2018

AbstractIntroductionScreening of modifiable cardiovascular disease (CVD) risk factors is recommended but not routinely provided for HIV‐infected patients, especially in low‐resource settings. Potential concerns include limited staff time and low patient acceptability, but little empirical data exists. As part of a pilot study of screening in a large urban HIV clinic in Swaziland, we conducted a time‐motion study to assess the impact of screening on patient flow and HIV service delivery and exit interviews to assess patient acceptability.MethodsA convenience sample of patients ≥40 years of age attending routine HIV clinic visits was screened for hypertension, diabetes, hyperlipidemia and tobacco smoking. We observed HIV visits with and without screening and measured time spent on HIV and CVD risk factor screening activities. We compared screened and unscreened patients on total visit time and time spent receiving HIV services using Wilcoxon rank‐sum tests. A separate convenience sample of screened patients participated in exit interviews to assess their satisfaction with screening.ResultsWe observed 172 patient visits (122 with CVD risk factor screening and 50 without). Screening increased total visit time from a median (range) of 4 minutes (2 to 11) to 15 minutes (9 to 30) (p < 0.01). Time spent on HIV care was not affected: 4 (2 to 10) versus 4 (2 to 11) (p = 0.57). We recruited 126 patients for exit interviews, all of whom indicated that they would recommend screening to others.ConclusionProvision of CVD risk factor screening more than tripled the length of routine HIV clinic visits but did not reduce the time spent on HIV services. Programme managers need to take longer visit duration into account in order to effectively integrate CVD risk factor screening and counselling into HIV programmes.
Men who have sex with men more often chose daily than event‐driven use of pre‐exposure prophylaxis: baseline analysis of a demonstration study in Amsterdam
Authors: Hoornenborg Elske , Achterbergh Roel CA , van der Loeff Maarten F Schim , Davidovich Udi , van der Helm Jannie J , Hogewoning Arjan , van Duijnhoven Yvonne THP , Sonder Gerard JB , de Vries Henry JC , Prins Maria ,   the Amsterdam PrEP Project team in the HIV Transmission Elimination AMsterdam Initiative
Published: April 2018

AbstractIntroductionThe Amsterdam PrEP project is a prospective, open‐label demonstration study at a large sexually transmitted infection (STI) clinic. We examined the uptake of PrEP; the baseline characteristics of men who have sex with men (MSM) and transgender persons initiating PrEP; their choices of daily versus event‐driven PrEP and the determinants of these choices.MethodsFrom August 2015 through May 2016, enrolment took place at the STI clinic of the Public Health Service of Amsterdam, the Netherlands. MSM or transgender persons were eligible if they had at least one risk factor for HIV infection within the preceding six months. Participants were offered a choice between daily or event‐driven use of tenofovir/emtricitabine. Baseline data were analysed using descriptive statistics and multivariable analysis was employed to determine variables associated with daily versus event‐driven PrEP.ResultsOnline applications were submitted by 870 persons, of whom 587 were invited for a screening visit. Of them, 415 were screened for eligibility and 376 initiated PrEP. One quarter (103/376, 27%) chose event‐driven PrEP. Prevalence of bacterial STI was 19.0% and mean condomless anal sex (CAS) episodes in the preceding three months were 11. In multivariable analysis, older age (≥45 vs. ≤34, aOR 2.1, 95% CI 1.2 to 3.9), being involved in a steady relationship (aOR 1.7, 95% CI 1.0 to 2.7), no other daily medication use (aOR 0.6, 95% CI 0.3 to 0.9), and fewer episodes of CAS (per log increase aOR 0.7, 95% CI 0.6 to 0.9) were determinants for choosing event‐driven PrEP.DiscussionPrEP programmes are becoming one of the more important intervention strategies with the goal of reducing incident HIV‐infection and we were unable to accommodate many of the persons applying for this study. Offering a choice of dosing regimen to PrEP users may enable further personalization of HIV prevention strategies and enhance up‐take, adherence and cost‐effectiveness.ConclusionsThe majority of participants preferred daily versus event‐driven use. Within this majority, a high number of CAS episodes before PrEP initiation was reported and we observed a high prevalence of STI. Determinants of choosing event‐driven PrEP were older age, fewer CAS episodes, no other daily medication use, and involved in a steady relationship.