bluuebunny/crossref_metadata_2025_split huggingface dataset:
What Research Institutions Can Do to Foster Research Integrity
Authors: Bouter Lex 
Published: January 2020

AbstractIn many countries attention for fostering research integrity started with a misconduct case that got a lot of media exposure. But there is an emerging consensus that questionable research practices are more harmful due to their high prevalence. QRPs have in common that they can help to make study results more exciting, more positive and more statistically significant. That makes them tempting to engage in. Research institutions have the duty to empower their research staff to steer away from QRPs and to explain how they realize that in a Research Integrity Promotion Plan. Avoiding perverse incentives in assessing researchers for career advancement is an important element in that plan. Research institutions, funding agencies and journals should make their research integrity policies as evidence-based as possible. The dilemmas and distractions researchers face are real and universal. We owe it to society to collaborate and to do our utmost best to prevent QRPs and to foster research integrity.
Diagnostic performance of a computer-assisted diagnostic system: sensitivity of BONENAVI for bone scintigraphy in patients with disseminated skeletal metastasis is not so high
Authors: Koizumi Mitsuru , Motegi Kazuki , Koyama Masamichi , Ishiyama Mitsutomi , Togawa Takashi , Makino Tomoko , Arisaka Yukiko , Terauchi Takashi 
Published: January 2020

Abstract
Purpose
Bone scintigraphy (BS) of disseminated skeletal metastasis is sometimes misinterpreted as normal. The use of computer-assisted diagnosis (CAD) may resolve this problem. We investigated the performance of a CAD system, BONENAVI, in the diagnosis of disseminated skeletal metastasis.

Methods
Cases of disseminated skeletal metastasis were selected from a BS log. These patients’ BSs were analyzed by BONENAVI to obtain an artificial neural network (ANN) and bone scan index (BSI). Clinical features (type of primary cancer, CT type, and BS type) were compared with the BONENAVI (ANN and BSI) results. The BS findings (diffuse increased axial skeleton uptake, inhomogeneity of uptake, proximal extremity contrast, and degree of renal uptake) and ANN or BSI were evaluated. Then, negative ANN patients were presented.

Results
Fifty-four patients were diagnosed as having disseminated skeletal metastasis. Regarding the primary cancers, 12 had prostate cancer, 16 gastric cancers, 16 breast cancers, and 10 miscellaneous cancers. Total sensitivity of ANN (≥ 0.5) was 76% (41/54). ANN values correlated with the BS type among clinical features. Diffuse increased axial skeleton uptake was mostly correlated with ANN of the BS findings.

Conclusion
The BONENAVI CAD system was partially helpful in diagnosing disseminated skeletal metastasis, but the sensitivity of BONENAVI was not sufficient and underestimated the disseminated skeletal metastasis. Further improvement of this CAD system is necessary to improve the detectability of disseminated skeletal metastasis.
CFD analysis and field observation of tool erosion caused by abrasive waterjet fracturing
Authors: Sheng Mao , Huang Zhong-Wei , Tian Shou-Ceng , Zhang Yi , Gao Shi-Wang , Jia Yun-Peng 
Published: January 2020

AbstractAbrasive waterjet (AWJ) fracturing has become an accepted horizontal multistage stimulation technique due to its flexibility and high efficiency of extensive fracture placement. The downhole tool failure of AWJ fracturing becomes an issue in the massive hydraulic fracturing because of high velocity and proppant erosion. This paper proposed a 3D computational fluid dynamics (CFD)-based erosion model by considering high-velocity waterjet impact, proppant shear erosion, and specific inner structure of hydra-jet tool body. The discrete phase approach was used to track the proppant transport and its concentration distribution. Field observation provides strong evidence of erosion patterns and mechanisms obtained from CFD simulation. The results show that the erosion rate has a space dependence in the inner wall of the tool body. The severe erosion areas are primarily located at the entries of the nozzle. Evident erosion patterns are found including a ‘Rabbit’s ear’ erosion at the upper-layer nozzles and a half bottom loop erosion at the lower-layer nozzles. Erosion mechanisms attribute to high flow velocity at the entry of nozzles and the inertia force of proppant. Sensitivity analysis demonstrates that the pumping rate is a primary factor contributing to erosion intensity.
Control and Ownership of Neuroprosthetic Speech
Authors: Maslen Hannah , Rainey Stephen 
Published: January 2020

AbstractImplantable brain-computer interfaces (BCIs) are being developed to restore speech capacity for those who are unable to speak. Patients with locked-in syndrome or amyotrophic lateral sclerosis could be able to use covert speech – vividly imagining saying something without actual vocalisation – to trigger neural controlled systems capable of synthesising speech. User control has been identified as particularly pressing for this type of BCI. The incorporation of machine learning and statistical language models into the decoding process introduces a contribution to (or ‘shaping of’) the output that is beyond the user’s control. Whilst this type of ‘shared control’ of BCI action is not unique to speech BCIs, the automated shaping of what a user ‘says’ has a particularly acute ethical dimension, which may differ from parallel concerns surrounding automation in movement BCIs. This paper provides an analysis of the control afforded to the user of a speech BCI of the sort under development, as well as the relationships between accuracy, control, and the user’s ownership of the speech produced. Through comparing speech BCIs with BCIs for movement, we argue that, whilst goal selection is the more significant locus of control for the user of a movement BCI, control over process will be more significant for the user of the speech BCI. The design of the speech BCI may therefore have to trade off some possible efficiency gains afforded by automation in order to preserve sufficient guidance control necessary for users to express themselves in ways they prefer. We consider the implications for the speech BCI user’s responsibility for produced outputs and their ownership of token outputs. We argue that these are distinct assessments. Ownership of synthetic speech concerns whether the content of the output sufficiently represents the user, rather than their morally relevant, causal role in producing that output.
Identifying viruses from metagenomic data using deep learning
Authors: Ren Jie , Song Kai , Deng Chao , Ahlgren Nathan A. , Fuhrman Jed A. , Li Yi , Xie Xiaohui , Poplin Ryan , Sun Fengzhu 
Published: January 2020

BackgroundThe recent development of metagenomic sequencing makes it possible to massively sequence microbial genomes including viral genomes without the need for laboratory culture. Existing reference‐based and gene homology‐based methods are not efficient in identifying unknown viruses or short viral sequences from metagenomic data.MethodsHere we developed a reference‐free and alignment‐free machine learning method, DeepVirFinder, for identifying viral sequences in metagenomic data using deep learning.ResultsTrained based on sequences from viral RefSeq discovered before May 2015, and evaluated on those discovered after that date, DeepVirFinder outperformed the state‐of‐the‐art method VirFinder at all contig lengths, achieving AUROC 0.93, 0.95, 0.97, and 0.98 for 300, 500, 1000, and 3000 bp sequences respectively. Enlarging the training data with additional millions of purified viral sequences from metavirome samples further improved the accuracy for identifying virus groups that are under‐represented. Applying DeepVirFinder to real human gut metagenomic samples, we identified 51,138 viral sequences belonging to 175 bins in patients with colorectal carcinoma (CRC). Ten bins were found associated with the cancer status, suggesting viruses may play important roles in CRC.ConclusionsPowered by deep learning and high throughput sequencing metagenomic data, DeepVirFinder significantly improved the accuracy of viral identification and will assist the study of viruses in the era of metagenomics.
Machine Learning to Analyze Single-Case Data: A Proof of Concept
Authors: Lanovaz Marc J. , Giannakakos Antonia R. , Destras Océane 
Published: January 2020

AbstractVisual analysis is the most commonly used method for interpreting data from single-case designs, but levels of interrater agreement remain a concern. Although structured aids to visual analysis such as the dual-criteria (DC) method may increase interrater agreement, the accuracy of the analyses may still benefit from improvements. Thus, the purpose of our study was to (a) examine correspondence between visual analysis and models derived from different machine learning algorithms, and (b) compare the accuracy, Type I error rate and power of each of our models with those produced by the DC method. We trained our models on a previously published dataset and then conducted analyses on both nonsimulated and simulated graphs. All our models derived from machine learning algorithms matched the interpretation of the visual analysts more frequently than the DC method. Furthermore, the machine learning algorithms outperformed the DC method on accuracy, Type I error rate, and power. Our results support the somewhat unorthodox proposition that behavior analysts may use machine learning algorithms to supplement their visual analysis of single-case data, but more research is needed to examine the potential benefits and drawbacks of such an approach.
Social and economic flows across multimodal transportation networks in the Greater Tokyo Area
Authors: Bramson Aaron , Hori Megumi , Zha Bingran , Inamoto Hirohisa 
Published: January 2020

AbstractWe model the flow of human capital and resources across multimodal transportation networks throughout the Greater Tokyo Area. Our transportation networks include trains, buses, and roads integrated with a walking network among a geographically grounded hexagonal grid and connecting nodes of different modes. The hexagonal grid holds data on both the working population and number of jobs from which we built probability distributions for the origins and destinations of commuting trips. Using both the network simplex method and stochastically generated origin-destination trips we estimate the population flows necessary to satisfy this demand. Rather than micro-simulations of actual commuting patterns, congestion, or route planning, our approach aims to uncover patterns in the aggregate flow of human resources to and from economic opportunities. We describe the details of the socioeconomic data, network generation, and the results of our exploratory analysis, then discuss the implications of these findings for transportation usage and future work.
Effect of Sieving on Ex Situ Soil Respiration of Soils from Three Land Use Types
Authors: Adekanmbi Adetunji Alex , Shaw Liz J. , Sizmur Tom 
Published: January 2020

AbstractThis study aims to investigate the effect of sieving on ex situ soil respiration (CO2 flux) measurements from different land use types. We collected soils (0–10 cm) from arable, grassland and woodland sites, allocated them to either sieved (4-mm mesh, freshly sieved) or intact core treatments and incubated them in gas-tight jars for 40 days at 10 °C. Headspace gas was collected on days 1, 3, 17, 24, 31 and 38 and CO2 analysed. Our results showed that sieving (4 mm) did not significantly influence soil respiration measurements, probably because micro aggregates (< 0.25 mm) remain intact after sieving. However, soils collected from grassland soil released more CO2 compared with those collected from woodland and arable soils, irrespective of sieving treatments. The higher CO2 from grassland soil compared with woodland and arable soils was attributed to the differences in the water holding capacity and the quantity and stoichiometry of the organic matter between the three soils. We conclude that soils sieved prior to ex situ respiration experiments provide realistic respiration measurements. This finding lends support to soil scientists planning a sampling strategy that better represents the inhomogeneity of field conditions by pooling, homogenising and sieving samples, without fear of obtaining unrepresentative CO2 flux measurements caused by the disruption of soil architecture.
Enhancement of Amorphous Silica Dissolution by Interaction with Six-Membered Ring Heterocyclic Compounds
Authors: Kawano Motoharu , Hwang Jinyeon 
Published: January 2020

AbstractSix-membered ring heterocyclic compounds are widely present in the Earth's surface environments as biological organic molecules composed of soil organic matter including plant and microbial residues, while little is known about their effect on the dissolution of silicate minerals including amorphous silica. To evaluate the effect of these biological molecules on amorphous silica dissolution, dissolution experiments were carried out by the flow-through method using 0.1 g of amorphous silica and 0.1 mM NaCl electrolyte solutions containing 0.0, 0.1, 1.0, or 10.0 mM of the heterocyclic compounds, piperidine (pK = 11.12), pyridine (pK = 5.25), or pyridazine (pK = 2.33), at a pH of 6, 5, or 4. Additionally, adsorption experiments of the compounds on the amorphous silica surface were performed to confirm the adsorption affinity for the amorphous silica surface. The results demonstrated that these heterocyclic compounds enhance the dissolution rate of amorphous silica in the following order: piperidine > pyridine > pyridazine. When 10.0 mM solutions were used, the heterocyclic compounds enhanced greatly the dissolution rate up to enhancement factors of 6.0 to ~14.8, 5.0 to ~14.0, and 1.0 to ~2.6 through an interaction of piperidine, pyridine, and pyridazine, respectively, in the pH range of approximately 6 to ~ 4. The adsorption experiments indicated that the heterocyclic compounds exhibited significant adsorption affinity for the amorphous silica surface as follows: piperidine > pyridine > pyridazine, which was consistent with the order of their effects on the dissolution enhancement. The geochemical calculation revealed that this order of enhancement was in good agreement with the concentrations of cationic species of heterocyclic compounds at corresponding pH conditions. Consequently, the enhancement of amorphous silica dissolution is likely to be influenced by the electrostatic complexation of the cationic species of the heterocyclic compounds with the negative >SiO– sites on the amorphous silica surface.
Sea-ice freeboard and thickness in the Ross Sea from airborne (IceBridge 2013) and satellite (ICESat 2003–2008) observations
Authors: Tian Liuxi , Xie Hongjie , Ackley Stephen F. , Tang Jiakui , Mestas-Nuñez Alberto M. , Wang Xianwei 
Published: January 2020

AbstractNASA's Operation IceBridge mission flew over the Ross Sea, Antarctica (20 and 27 November 2013) and collected data with Airborne Topographic Mapper (ATM) and Digital Mapping System (DMS). Using the DMS and reflectivity of ATM L1B, leads are detected to define local sea level height. The total freeboard is then obtained and converted to ice thickness. The estimated mean sea-ice thickness values are found to be in the 0.48–0.99 m range. Along the N-S track, sea ice was thinner southward rather than northward of the fluxgate, resulting in two peaks of modal thickness: 0.35 m (south) and 0.7 m (north). This supports that new ice produced in coastal polynyas is transported northward by katabatic winds off the ice-shelf. The lowest (2%) elevation method used for freeboard retrieval for ICESat is also tested for ATM data. It is found that the lowest elevation method tends to overestimate freeboard, but mean values are less affected than mode values. Using mean thickness values of ICESat and ATM along the ‘fluxgate’, separating the shelf from the deep ocean, the exported ice volume at this ‘fluxgate’ is found to be higher during the ICESat years (2003–2008) than during the IceBridge year (2013).
‘Are we losing touch?’ Mainstream parties' failure to represent their voters on immigration and its electoral consequences
Authors: Brady David W. , Ferejohn John A. , Paparo Aldo 
Published: January 2020

AbstractIn many advanced democracies, mainstream political parties have been disrupted either by the rise of new (populist) parties or by hostile takeovers. In this article we argue that immigration attitudes have had a powerful impact on the strategic environment of political parties and leaders. We show, based on evidence from a comparative study conducted by YouGov in spring of 2015, that immigration attitudes had, by that time, driven a wedge between mainstream parties – those that regularly play a role in government – and their partisans. This ‘immigration gap’ opened up enormous space for new political movements to form, either inside existing parties or outside. Furthermore, we show that the representation gap on immigration issues is a relevant predictor of vote choice, so that parties are particularly likely to lose votes when they are more distant from their supporters on immigration.
The association between milk consumption and the metabolic syndrome: a cross-sectional study of the residents of Suzhou, China and a meta-analysis
Authors: Hidayat Khemayanto , Yu Lu-Gang , Yang Jin-Rong , Zhang Xue-Ying , Zhou Hui , Shi Yu-Jie , Liu Biao , Qin Li-Qiang 
Published: January 2020

AbstractThe association between milk consumption and the metabolic syndrome remains inconclusive, and data from Chinese populations are scarce. We conducted a cross-sectional study to investigate the association between milk consumption and the metabolic syndrome and its components among the residents of Suzhou Industrial Park, Suzhou, China. A total of 5149 participants were included in the final analysis. A logistic regression model was applied to estimate the OR and 95 % CI for the prevalence of the metabolic syndrome and its components according to milk consumption. In addition, the results of our study were further meta-analysed with other published observational studies to quantify the association between the highestv. lowest categories of milk consumption and the metabolic syndrome and its components. There was no significant difference in the odds of having the metabolic syndrome between milk consumers and non-milk consumers (OR 0·86, 95 % CI 0·73, 1·01). However, milk consumers had lower odds of having elevated waist circumference (OR 0·78, 95 % CI 0·67, 0·92), elevated TAG (OR 0·83, 95 % CI 0·70, 0·99) and elevated blood pressure (OR 0·85, 95 % CI 0·73, 0·99). When the results were pooled together with other published studies, higher milk consumption was inversely associated with the risk of the metabolic syndrome (relative risk 0·80, 95 % CI 0·72, 0·88) and its components (except elevated fasting blood glucose); however, these results should be treated with caution as high heterogeneity was observed. In summary, the currently available evidence from observational studies suggests that higher milk consumption may be inversely associated with the metabolic syndrome.
Daily intake of non-fried potato does not affect markers of glycaemia and is associated with better diet quality compared with refined grains: a randomised, crossover study in healthy adults
Authors: Johnston E. A. , Petersen K. S. , Kris-Etherton P. M. 
Published: January 2020

AbstractEpidemiological studies suggest that consumption of potatoes is associated with increased risk of cardiometabolic diseases. However, few clinical trials have empirically tested this. The aim of this single-blind, randomised, crossover study was to evaluate the effect of daily potato consumption, compared with refined grains, on risk factors for cardiometabolic diseases. It was hypothesised that no difference in cardiometabolic endpoints would be detected between conditions, but diet quality would improve with potato consumption. Healthy participants on self-selected diets received one potato-based side dish or one refined grain-based side dish daily, for 4 weeks, separated by a minimum 2-week break. Dishes were isoenergetic, carbohydrate-matched and prepared without excess saturated fat or Na. Participants were instructed to consume the side dish with a meal in place of carbohydrates habitually consumed. Lipids/lipoproteins, markers of glycaemic control, blood pressure, weight and pulse wave velocity were measured at baseline and condition endpoints. Diet quality was calculated, based on 24-h recalls, using the Healthy Eating Index (HEI)-2015. Fifty adults (female n 34; age 40 (sd 13) years; BMI 24·5 (sd 3·6) kg/m2) completed the present study. No between-condition differences were detected for fasting plasma glucose (–0·05 mmol/l, 95 % CI –0·14, 0·04; P = 0·15), the primary outcome or any other outcomes. Compared with refined grains, the HEI-2015 score (3·5, 95 % CI 0·6, 6·4; P = 0·01), K (547 mg, 95 % CI 331, 764, P < 0·001) and fibre (2·4 g, 95 % CI 0·6, 4·2, P = 0·01) were higher following the potato condition. Consuming non-fried potatoes resulted in higher diet quality, K and fibre intake, without adversely affecting cardiometabolic risk.
Partial replacement of nitrogen fertilization with legumes in tropical pasture overseeded with temperate species for the production of steers
Authors: Schmitz G. R. , Paris W. , Biesek R. R. , Costa O. A. D. , Mafioletti R. D. , Umezaki A. M. , Menezes L. F. G. 
Published: January 2020

AbstractUsing legumes in forage mixes can help decrease the use of nitrogen fertilizers and possibly increase the nutritive value of pasture. The aim of the current study was to determine animal production and behavioural and ingestion parameters by evaluating the production and nutritive value of Aruana grass (Panicum maximum‘Aruana’) intercropped with forage peanut (Arachis pintoi‘Amarillo’) or fertilized with nitrogen. The treatments were N200 (200 kg N/ha per season – summer and winter), 100N + PE (100 kg N/ha per season plus pasture mixture with forage peanut) and N100 (100 kg N/ha per season). The presence of forage peanut in the pasture did not replace nitrogen fertilization as the pasture fertilized with 200 kg of nitrogen had a greater leaf/stem ratio (0.66v.0.54), stocking rate (2600v.2290 kg live weight/ha), average daily gain (0.880v.0.700 kg/day) and live weight gain (LWG) (652v.468 kg/ha) during summer. During winter, no effect of increased nitrogen fertilization on pasture and animal production was observed. In the total study period (summer + winter), a greater LWG (897v.741 kg/ha) occurred when a higher quantity of nitrogen (N200) was placed in the pasture compared to the insertion of forage peanuts in the system.