bluuebunny/crossref_metadata_2025_split huggingface dataset:
Improved Secondary Analysis of Linked Data: A Framework and an Illustration
Authors: Chambers Ray , Diniz da Silva Andrea 
Published: June 2019

SummaryApplications that use linked data are now part of mainstream social science research, though they generally do not take linkage error into consideration. Solutions that correct for the bias caused by these errors have been proposed but are not yet embedded in the various analysis procedures in common use. Secondary analyses based on linked data can therefore be potentially misleading. We review some recent approaches to non-deterministic data linkage together with a framework for secondary analysis of the linked data which makes use of paradata produced by the linkage process to correct this bias. We also describe a new method for secondary analysis of linked data that builds on this framework and show how it can be used for estimation of a set of domain means based on linked data. We then illustrate this approach via an empirical study based on record linkage of agricultural producers in four states of Brazil aimed at producing estimates of agricultural output by industry. Our study considers register-to-register linkage as well as sample-to-register linkage, and we show results for the traditional Fellegi–Sunter approach to record linkage as well as for a newer linkage procedure based on the use of classification trees and bagging.
A deep learning approach for rooftop geocoding
Authors: Yin Zhengcong , Ma Andong , Goldberg Daniel W. 
Published: June 2019

AbstractGeocoding has become a routine task for many research investigations to conduct spatial analysis. However, the output quality of geocoding systems is found to impact the conclusions of subsequent studies that employ this workflow. The published development of geocoding systems has been limited to the same set of interpolation methods and reference data sets for quite some time. We introduce a novel geocoding approach utilizing object detection on remotely sensed imagery based on a deep learning framework to generate rooftop geocoding output. This allows geocoding systems to use and output exact building locations without employing typical geocoding interpolation methods or being completely limited by the availability of reference data sets. The utility of the proposed approach is demonstrated over a sample of 22,481 addresses resulting in significant spatial error reduction and match rates comparable to typical geocoding methods. For different land‐use types, our approach performs better on low‐density residential and commercial addresses than on high‐density residential addresses. With appropriate model setup and training, the proposed approach can be extended to search different object locations and to generate new address and point‐of‐interest reference data sets.
Spatial optimization for land acquisition problems: A review of models, solution methods, and GIS support
Authors: Xiao Ningchuan , Murray Alan T. 
Published: June 2019

AbstractThis article reviews the interdisciplinary research field of spatial optimization for land acquisition problems. We start with a theoretical framework to identify three categories of spatial optimization models: problems with aspatial constraints, location models, and problems with topological constraints. Exact, heuristic, and metaheuristic approaches to solving these problems are critically discussed. Tools that are available in commercial and open‐source GIS packages are reviewed from four aspects. We first survey the off‐the‐shelf support and then the development environments in these packages. A case study of the one‐center problem is used to illustrate the computational performance of different solution methods. Finally the advantages and disadvantages of current GIS data models are discussed. The article concludes with challenges and future directions for solving spatial optimization problems for land acquisition.
Real‐time quantitative PCR‐based detection of Coxiella burnetii in unpasteurized cow's milk sold for human consumption
Authors: de Souza Ribeiro Mioni Mateus , Ribeiro Bruna Letícia Devidé , Peres Marina Gea , Teixeira Wanderson Sirley Reis , Pelícia Vanessa Cristina , Motta Rodrigo Garcia , Labruna Marcelo Bahia , Ribeiro Márcio Garcia , Sidi‐Boumedine Karim , Megid Jane 
Published: June 2019

AbstractCoxiella burnetii is a zoonotic pathogen with a worldwide distribution that is responsible for Q fever in humans. It is a highly infectious bacterium that can be transmitted from cattle to humans through the consumption of unpasteurized milk. We report the molecular identification of C. burnetii in raw cow's milk being sold directly for human consumption in Brazil without official inspection or pasteurization. One hundred and twelve samples of raw milk were analysed by real‐time quantitative PCR (qPCR), and C. burnetii was detected in 3.57% (4/112) of the samples at a concentration ranging from 125 to 404 bacteria per millilitre. The identification of this zoonotic pathogen in raw milk sold directly for human consumption is a public health concern since C. burnetii can be transmitted through the oral route. This result indicates that health education and other preventive measures should be officially implemented in Brazil to prevent the spread of infection. To our knowledge, this is the first qPCR‐based detection of C. burnetii in raw milk samples from cows sold in Brazil that do not undergo official inspection or pasteurization.
Energy Expenditure Equation Choice: Effects on Cycling Efficiency and its Reliability
Authors: Bossi Arthur H. , Timmerman Wouter P. , Hopker James G. 
Published: June 2019

Purpose:There are several published equations to calculate energy expenditure (EE) from gas exchanges. The authors assessed whether using different EE equations would affect gross efficiency (GE) estimates and their reliability.Methods:Eleven male and 3 female cyclists (age 33 [10] y; height: 178 [11] cm; body mass: 76.0 [15.1] kg; maximal oxygen uptake: 51.4 [5.1] mL·kg−1·min−1; peak power output: 4.69 [0.45] W·kg−1) completed 5 visits to the laboratory on separate occasions. In the first visit, participants completed a maximal ramp test to characterize their physiological profile. In visits 2 to 5, participants performed 4 identical submaximal exercise trials to assess GE and its reliability. Each trial included three 7-minute bouts at 60%, 70%, and 80% of the gas exchange threshold. EE was calculated with 4 equations by Péronnet and Massicotte, Lusk, Brouwer, and Garby and Astrup.Results:All 4 EE equations produced GE estimates that differed from each other (allP < .001). Reliability parameters were only affected when the typical error was expressed in absolute GE units, suggesting a negligible effect—related to the magnitude of GE produced by each EE equation. The mean coefficient of variation for GE across different exercise intensities and calculation methods was 4.2%.Conclusions:Although changing the EE equation does not affect GE reliability, exercise scientists and coaches should be aware that different EE equations produce different GE estimates. Researchers are advised to share their raw data to allow for GE recalculation, enabling comparison between previous and future studies.
Positive Relations Between Vision and Posture in the Fixation Task Performed Upright
Authors: Bonnet Cédrick T. 
Published: June 2019

In an upright stance, individuals sway in unpredictable ways. Their eyes also move in unpredictable ways in fixation tasks. The objective of this study was to analyze visual functions, postural control, and cognitive involvement in stationary gaze. A total of 14 healthy young adults performed a fixation task and a free-viewing task (three trials per task, 45 s per trial). As expected, the results showed many (n = 32) significant positive Pearson correlation coefficients between the eye and center of pressure/body (head, neck, and lower back) movements in the fixation task. In the free-viewing task, the correlations were nonsignificant. Only 3 of the 32 significant correlations (9.4%) were significantly related to cognitive involvement (measured with a subjective questionnaire). These results indirectly strengthened the validity of the synergistic model of postural control.
Understanding people who self-referred in an emergency department with primary care problems during office hours: a qualitative interview study at a Daytime General Practice Cooperative in two hospitals in The Hague, The Netherlands
Authors: Minderhout Rosa Naomi , Venema Pien , Vos Hedwig M M , Kant Jojanneke , Bruijnzeels Marc Abraham , Numans Mattijs E 
Published: June 2019

ObjectiveTo provide insight into the motives for hospital self-referral during office hours and the barriers deterring general practitioner (GP) consultation with a primary care request.SettingPeople who self-referred at a Daytime General Practice Cooperative (GPC) in two hospitals in The Hague, The Netherlands.ParticipantsA total of 44 people who self-referred were interviewed in two hospitals. The average age of interviewees was 35 years (range 19 months to 83 years), a parent of a young patient was interviewed, but the age of patients is shown here. There were more male patients (66%) than female patients (34%). Patients were recruited using a sampling method after triage. Triage was the responsibility of an emergency department (ED) nurse in one hospital and of a GP in the other. Those excluded from participation included (a) children under the age of 18 years and not accompanied by a parent or legal guardian, (b) foreign patients not resident in the Netherlands, (c) patients unable to communicate in Dutch or English and (d) patients directly referred to the ED after triage by the GP (in one hospital).ResultsPeople who self-referred generally reported several motives for going to the hospital directly. Information and awareness factors played an important role, often related to a lack of information regarding where to go with a medical complaint. Furthermore, many people who self-referred mentioned hospital facilities, convenience and perceived medical necessity as motivational factors. Barriers deterring a visit to the own GP were mainly logistical, including not being registered with a GP, the GP was too far away, poor GP telephone accessibility or a waiting list for an appointment.ConclusionInformation and awareness factors contribute to misperceptions among people who self-referred concerning the complaint, the GP and the hospital. As a range of motivational factors are involved, there is no straightforward solution. However, better dissemination of information might alleviate misconceptions and contribute to providing the right care to the right patient in the right setting.
How could NHS change management agents learn from corporate innovation strategy to deliver services more effectively?
Authors: Mezher Sermed , Sajid Muhammad 
Published: June 2019

BackgroundThe National Health Service (NHS) is facing the most difficult time in history. Public satisfaction rates are falling, waiting times are rising and along with bed occupancy, staff morale is of major concern. With progressively worsening performance nationwide, undoubtedly, a large number of implemented changes are underperforming. To understand the aetiology of this, it is essential to compare NHS service change methodology with successful changes in other sectors; potentially boosting success in future projects.Objectives/MethodsTo discover NHS and Corporate innovation projects of comparable complexity, environmental difficulty and scale; for comparison of strategy based on leadership theory.ResultsFour case studies matching selection criteria were found from each sector. A total of 16 comparisons were made with Grupo Santander’s UK entry and the NHS ‘Making It Better’ programme selected as most comparable. Grupo Santander unified three failing institutions with legacies dating back to 1849, moving from worst bank to the group’s most profitable region in 8 years. The ‘Making It Better’ programme consolidated 12 maternal and neonatal centres to 8 after 2 failed prior attempts, costing £125 million over 12 years. Dissecting the two projects using primarily Rogers’ Diffusion of Innovation Model revealed deficiencies in healthcare stakeholder communication, unaddressed patient concerns and outcome measure collection. The latter is of paramount importance as it remains unclear whether drivers for change were addressed.ConclusionsWith projects of comparable complexity, the corporate sector serves as an underutilised source of learning for NHS change management agents. Further study is required to determine whether the deficiencies identified are endemically lacking from NHS innovations.
Does internet-accessed STI (e-STI) testing increase testing uptake for chlamydia and other STIs among a young population who have never tested? Secondary analyses of data from a randomised controlled trial
Authors: Wilson Emma , Leyrat Clémence , Baraitser Paula , Free Caroline 
Published: June 2019

ObjectivesTo assess the effectiveness of an internet-accessed STI (e-STI) testing and results service on testing uptake among young adults (16–30 years) who have never tested for STIs in London, England.MethodsWe conducted secondary analyses on data from a randomised controlled trial. In the trial, participants were randomly allocated to receive a text message with the web link of an e-STI testing and results service (intervention group) or a text message with the link of a website listing the locations, contact details and websites of seven local sexual health clinics (control group). We analysed a subsample of 528 trial participants who reported never testing for STIs at baseline. Outcomes were self-reported STI testing at 6 weeks, verified by patient record checks, and time from randomisation to completion of an STI test.ResultsUptake of STI testing among ‘never testers’ almost doubled. At 6 weeks, 45.3% of the intervention completed at least one test (chlamydia, gonorrhoea, syphilis and HIV), compared with 24.1% of the control (relative risk [RR] 1.88, 95% CI 1.47 to 2.40, p<0.001). For chlamydia and gonorrhoea testing combined, uptake was 44.3% in the intervention versus 24.1% in controls (RR 1.84, 95% CI 1.44 to 2.36, p<0.001). The intervention reduced time to any STI test (restricted mean survival time: 29.0 days vs 36.3 days, p<0.001) at a time horizon of 42 days.Conclusions e-STI testing increased uptake of STI testing and reduced time to test among a young population of ‘never testers’ recruited in community settings. Although encouraging, questions remain on how best to manage the additional demand generated by e-STI testing in a challenging funding environment. Larger studies are required to assess the effects later in the cascade of care, including STI diagnoses and cases treated.
Regional spatial variability of root-zone soil moisture in arid regions and the driving factors — a case study of Xinjiang, China
Authors: Li Xiangdong , Shao Ming’an , Zhao Chunlei , Liu Tong , Jia Xiaoxu , Ma Changkun 
Published: June 2019

Soil moisture is a key element of the hydrological cycle, and it significantly impacts the surface water and energy fluxes. However, a knowledge gap exists on the spatial variability of root-zone soil moisture at the regional scale in arid and hyperarid regions. Thus, soil moisture measurements at 142 sites were taken in Xinjiang (northwest China), and the relationships between soil moisture and 19 environmental factors were analyzed. The results showed that both absolute gravitational soil water content (SWC) and relative extractable water (REW) increased with increasing soil depth in the 0–100 cm soil profile. It generally decreased in the order of cropland > forestland > grassland > shrubland > bare land. Semivariograms suggested that SWC had moderate spatial dependence over a large range of 473–558 km, and REW was more randomly distributed at the regional scale in Xinjiang. Redundancy analysis suggested that environmental factors could explain 47.5%–50.9% of the variability of soil moisture, which was more strongly driven by land surface factors (p < 0.01) than by climatic factors (p > 0.05). Soil properties and other local variables explained, respectively, 40.7% and 32.3% of the variability of soil moisture in the 0–100 cm soil profile. Soil properties independently accounted for 12.8% and 28.1% of the variability in soil moisture in the 0–50 and 50–100 cm soil layers, respectively. Soil texture, field capacity, wilting point, organic carbon, bulk density, land use, and normalized difference vegetation index were the dominant factors influencing soil moisture variations.
The limit shapes of midpoint polygons in ℝ3
Authors: Wang Chao , Wang Zhongzi 
Published: June 2019

For a polygon in the [Formula: see text]-dimensional Euclidean space, we give two kinds of normalizations of its [Formula: see text]th midpoint polygon by a homothetic transformation and an affine transformation, respectively. As [Formula: see text] goes to infinity, the normalizations will approach “regular” polygons inscribed in an ellipse and a generalized Lissajous curve, respectively, where the curves may be degenerate. The most interesting case is when [Formula: see text], where polygons with all its [Formula: see text]th midpoint polygons knotted are discovered and discussed. Such polygonal knots can be seen as a discrete version of the Lissajous knots.
An ERG Enhancer–Based Reporter Identifies Leukemia Cells with Elevated Leukemogenic Potential Driven by ERG-USP9X Feed-Forward Regulation
Authors: Aqaqe Nasma , Yassin Muhammad , Yassin Abed Alkader , Ershaid Nour , Katz-Even Chen , Zipin-Roitman Adi , Kugler Eitan , Lechman Eric R. , Gan Olga I. , Mitchell Amanda , Dick John E. , Izraeli Shai , Milyavsky Michael 
Published: June 2019

Abstract

Acute leukemia is a rapidly progressing blood cancer with low survival rates. Unfavorable prognosis is attributed to insufficiently characterized subpopulations of leukemia stem cells (LSC) that drive chemoresistance and leukemia relapse. Here we utilized a genetic reporter that assesses stemness to enrich and functionally characterize LSCs. We observed heterogeneous activity of the ERG+85 enhancer–based fluorescent reporter in human leukemias. Cells with high reporter activity (tagBFPHigh) exhibited elevated expression of stemness and chemoresistance genes and demonstrated increased clonogenicity and resistance to chemo- and radiotherapy as compared with their tagBFPNeg counterparts. The tagBFPHigh fraction was capable of regenerating the original cellular heterogeneity and demonstrated increased invasive ability. Moreover, the tagBFPHigh fraction was enriched for leukemia-initiating cells in a xenograft assay. We identified the ubiquitin hydrolase USP9X as a novel ERG transcriptional target that sustains ERG+85–positive cells by controlling ERG ubiquitination. Therapeutic targeting of USP9X led to preferential inhibition of the ERG-dependent leukemias. Collectively, these results characterize human leukemia cell functional heterogeneity and suggest that targeting ERG via USP9X inhibition may be a potential treatment strategy in patients with leukemia.

Significance:
This study couples a novel experimental tool with state-of-the-art approaches to delineate molecular mechanisms underlying stem cell-related characteristics in leukemia cells.
Genetic Ablation of the Cystine Transporter xCT in PDAC Cells Inhibits mTORC1, Growth, Survival, and Tumor Formation via Nutrient and Oxidative Stresses
Authors: Daher Boutaina , Parks Scott K. , Durivault Jerome , Cormerais Yann , Baidarjad Hanane , Tambutte Eric , Pouysségur Jacques , Vučetić Milica 
Published: June 2019

Abstract

Although chemoresistance remains a primary challenge in the treatment of pancreatic ductal adenocarcinoma (PDAC), exploiting oxidative stress might offer novel therapeutic clues. Here we explored the potential of targeting cystine/glutamate exchanger (SLC7A11/xCT), which contributes to the maintenance of intracellular glutathione (GSH). Genomic disruption of xCT via CRISPR-Cas9 was achieved in two PDAC cell lines, MiaPaCa-2 and Capan-2, and xCT-KO clones were cultivated in the presence of N-acetylcysteine. Although several cystine/cysteine transporters have been identified, our findings demonstrate that, in vitro, xCT plays the major role in intracellular cysteine balance and GSH biosynthesis. As a consequence, both xCT-KO cell lines exhibited amino acid stress with activation of GCN2 and subsequent induction of ATF4, inhibition of mTORC1, proliferation arrest, and cell death. Tumor xenograft growth was delayed but not suppressed in xCT-KO cells, which indicated both the key role of xCT and also the presence of additional mechanisms for cysteine homeostasis in vivo. Moreover, rapid depletion of intracellular GSH in xCT-KO cells led to accumulation of lipid peroxides and cell swelling. These two hallmarks of ferroptotic cell death were prevented by vitamin E or iron chelation. Finally, in vitro pharmacologic inhibition of xCT by low concentrations of erastin phenocopied xCT-KO and potentiated the cytotoxic effects of both gemcitabine and cisplatin in PDAC cell lines. In conclusion, our findings strongly support that inhibition of xCT, by its dual induction of nutritional and oxidative cellular stresses, has great potential as an anticancer strategy.

Significance:
The cystine/glutamate exchanger xCT is essential for amino acid and redox homeostasis and its inhibition has potential for anticancer therapy by inducing ferroptosis.
Identifying Candidate Druggable Targets in Canine Cancer Cell Lines Using Whole-Exome Sequencing
Authors: Das Sunetra , Idate Rupa , Cronise Kathryn E. , Gustafson Daniel L. , Duval Dawn L. 
Published: June 2019

AbstractCancer cell culture has been a backbone in cancer research, in which analysis of human cell line mutational profiles often correlates with oncogene addiction and drug sensitivity. We have conducted whole-exome sequence analyses on 33 canine cancer cell lines from 10 cancer types to identify somatic variants that contribute to pathogenesis and therapeutic sensitivity. A total of 66,344 somatic variants were identified. Mutational load ranged from 15.79 to 129.37 per Mb, and 13.2% of variants were located in protein-coding regions (PCR) of 5,085 genes. PCR somatic variants were identified in 232 genes listed in the Cancer Gene Census (COSMIC). Cross-referencing variants with human driving mutations on cBioPortal identified 61 variants as candidate cancer drivers in 30 cell lines. The most frequently mutated cancer driver was TP53 (15 mutations in 12 cell lines). No drivers were identified in three cell lines. We identified 501 non-COSMIC genes with PCR variants that functionally annotate with COSMIC genes. These genes frequently mapped to the KEGG MAPK and PI3K–AKT pathways. We evaluated the cell lines for ERK1/2 and AKT(S473) phosphorylation and sensitivity to the MEK1/2 inhibitor, trametinib. Twelve of the 33 cell lines were trametinib-sensitive (IC50 &lt; 32 nmol/L), all 12 exhibited constitutive or serum-activated ERK1/2 phosphorylation, and 8 carried MAPK pathway cancer driver variants: NF1(2), BRAF(3), N/KRAS(3). This functionally annotated database of canine cell line variants will inform hypothesis-driven preclinical research to support the use of companion animals in clinical trials to test novel combination therapies.