bluuebunny/crossref_metadata_2025_split huggingface dataset:
Subsoil-potassium depletion accounts for the nutrient budget in high-potassium agricultural soils
Authors: Correndo Adrian A. , Rubio Gerardo , García Fernando O. , Ciampitti Ignacio A. 
Published: June 2021

AbstractContinuous potassium (K) removal without replenishment is progressively mining Argentinean soils. Our goals were to evaluate the sensitivity of soil-K to K budgets, quantify soil-K changes over time along the soil profile, and identify soil variables that regulate soil-K depletion. Four on-farm trials under two crop rotations including maize, wheat and soybean were evaluated. Three treatments were compared: (1) control (no fertilizer applied); (2) application of nitrogen, phosphorus, and sulfur fertilizers -NPS-; and (3) pristine condition. After nine years, crops removed from 258 to 556 kg K ha−1. Only two sites showed a decline in the exchangeable-K levels at 0–20 cm but unrelated to K budget. Topsoil exchangeable-K levels under agriculture resulted 48% lower than their pristine conditions, although still above response levels. Both soil exchangeable-K and slowly-exchangeable K vertical distribution patterns (0–100 cm) displayed substantial depletion relative to pristine conditions, mainly concentrated at subsoil (20–100 cm), with 55–83% for exchangeable-K, and 74–95% for slowly-exchangeable-K. Higher pristine levels of exchangeable-K and slowly-exchangeable-K and lower clay and silt contents resulted in higher soil-K depletion. Soil K management guidelines should consider both topsoil and subsoil nutrient status and variables related to soil K buffer capacity.
Good prediction of treatment responses to neoadjuvant chemoradiotherapy for esophageal cancer based on preoperative inflammatory status and tumor glucose metabolism
Authors: Li Chuan , Lin Jing-Wei , Yeh Hui-Ling , Chuang Cheng-Yen , Chen Chien-Chih 
Published: June 2021

AbstractTo develop a tool for predicting pathologic complete response (pCR) after neoadjuvant chemoradiotherapy (neoCRT) in patients with esophageal cancer by combining inflammatory status and tumor glucose metabolic activity. This study included 127 patients with locally advanced esophageal cancer who had received neoCRT followed by esophagectomy from 2007 to 2016. We collected their neutrophil–lymphocyte ratio (NLR) and standardized uptake value (SUV) obtained from fluorodeoxyglucose positron emission tomography (PET/CT) before and after neoCRT. Univariate and multivariate logistic regression analyses were performed to identify potential predictive factors for pCR. Sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV) of predictors were calculated. Between pCR and non-pCR groups, there were no statistically significant differences in patient characteristics, such as sex, age, site, and clinical T/N stage. Multivariate analyses identified four independent predictors for pCR, including pre-OP NLR < 5.4 [OR 11.179; 95% CI 8.385–13.495; p = 0.003], NLR change (ΔNLR) < 3 [OR 4.891; 95% CI 2.274–9.180; p = 0.005], changes in SUV (ΔSUV) > 7.2 [OR 3.033; 95% CI 1.354–6.791; p = 0.007], and SUV changes ratio (ΔSUV ratio) > 58% [OR 3.585; 95% CI 1.576–8.152; p = 0.002]. ΔNLR had the highest accuracy and NPV (84.3% and 90.3%, respectively). Combined factors of ΔNLR < 3 and ΔSUV ratio > 58% had the best PPV for pCR (84.8%). Inflammatory status (ΔNLR) and tumor glucose metabolic activity (ΔSUV ratio), when considered together, constitute a promising low-invasive tool with high efficacy for prediction of treatment response before surgery.
Covid-19 diagnosis by combining RT-PCR and pseudo-convolutional machines to characterize virus sequences
Authors: Gomes Juliana Carneiro , Masood Aras Ismael , Silva Leandro Honorato de S. , da Cruz Ferreira Janderson Romário B. , Freire Júnior Agostinho Antônio , Rocha Allana Laís dos Santos , de Oliveira Letícia Castro Portela , da Silva Nathália Regina Cauás , Fernandes Bruno José Torres , dos Santos Wellington Pinheiro 
Published: June 2021

AbstractThe Covid-19 pandemic, a disease transmitted by the SARS-CoV-2 virus, has already caused the infection of more than 120 million people, of which 70 million have been recovered, while 3 million people have died. The high speed of infection has led to the rapid depletion of public health resources in most countries. RT-PCR is Covid-19’s reference diagnostic method. In this work we propose a new technique for representing DNA sequences: they are divided into smaller sequences with overlap in a pseudo-convolutional approach and represented by co-occurrence matrices. This technique eliminates multiple sequence alignment. Through the proposed method, it is possible to identify virus sequences from a large database: 347,363 virus DNA sequences from 24 virus families and SARS-CoV-2. When comparing SARS-CoV-2 with virus families with similar symptoms, we obtained$$0.97 \pm 0.03$$0.97±0.03for sensitivity and$$0.9919 \pm 0.0005$$0.9919±0.0005for specificity with MLP classifier and 30% overlap. When SARS-CoV-2 is compared to other coronaviruses and healthy human DNA sequences, we obtained$$0.99 \pm 0.01$$0.99±0.01for sensitivity and$$0.9986 \pm 0.0002$$0.9986±0.0002for specificity with MLP and 50% overlap. Therefore, the molecular diagnosis of Covid-19 can be optimized by combining RT-PCR and our pseudo-convolutional method to identify DNA sequences for SARS-CoV-2 with greater specificity and sensitivity.
Influence of InP coupling cavity on Fano resonance of sub wavelength MIM waveguide
Authors: Ban Shihao , Liu Huangqing , Xiao Shifang , Mao Jingjing , Luo Jie 
Published: June 2021

AbstractIn this paper, influence of InP coupling cavity on Fano resonance of sub wavelength MIM waveguide was studied by FDTD. It was observed that the resonant wavelengths of mode mj (j = 1, 2, 3) were closely related with the height H2 of InP coupling cavity. In addition, before and after the addition of air cavity, the relative farfield intensities I was a function of height H2. Therefore, InP as discrete state could be used as the filling dielectrics of Fano resonance in the MIM waveguide.
Contingency and determinism in the evolution of bird song sound frequency
Authors: Friis Jakob I. , Dabelsteen Torben , Cardoso Gonçalo C. 
Published: June 2021

AbstractSexual signals are archetypes of contingent evolution: hyper-diverse across species, often evolving fast and in unpredictable directions. It is unclear to which extent their evolutionary unpredictability weakens deterministic evolution, or takes place bounded by deterministic patterns of trait evolution. We compared the evolution of sound frequency in sexual signals (advertisement songs) and non-sexual social signals (calls) across > 500 genera of the crown songbird families. Contrary to the acoustic adaptation hypothesis, we found no evidence that forest species used lower sound frequencies in songs or calls. Consistent with contingent evolution in song, we found lower phylogenetic signal for the sound frequency of songs than calls, which suggests faster and less predictable evolution, and found unpredictable direction of evolution in lineages with longer songs, which presumably experience stronger sexual selection on song. Nonetheless, the most important deterministic pattern of sound frequency evolution—its negative association with body size—was stronger in songs than calls. This can be explained by songs being longer-range signals than most calls, and thus using sound frequencies that animals of a given size produce best at high amplitude. Results indicate that sexual selection can increase aspects of evolutionary contingency while strengthening, rather than weakening, deterministic patterns of evolution.
Tarsal morphology of ischyromyid rodents from the middle Eocene of China gives an insight into the group’s diversity in Central Asia
Authors: Fostowicz-Frelik Łucja , López-Torres Sergi , Li Qian 
Published: June 2021

AbstractIschyromyids are a group of large rodents with the earliest fossil record known from the late Paleocene (Clarkforkian) of North America; they are considered the earliest fossil representatives of Rodentia of modern aspect. Ischyromyids dominated early Paleogene small-mammal assemblages of North America and in the latest Paleocene migrated to western Europe and to Asia; in the latter they survived only to the beginning of the late Eocene, but were never abundant. Here we describe for the first time the calcanei of ischyromyids from the early middle Eocene of the Erlian Basin in Nei Mongol, northern China. These calcanei document the existence of three species. The morphology of the studied tarsal bones overall suggests ambulatory locomotion for these animals (‘slow cursors’), similar to that of the coypu and porcupines, but one form shows more marked cursorial capabilities. These differences show that Chinese ischyromyids, although rare, had attained greater taxonomic diversity by the middle Eocene in Nei Mongol than estimated from dental remains. We also address the question of the morphological and ecological divergence of these ischyromyids in relation to their North American counterparts, as well as the issue of a direct dispersal route from North America to Asia in the early Eocene.
Learning from crowds in digital pathology using scalable variational Gaussian processes
Authors: López-Pérez Miguel , Amgad Mohamed , Morales-Álvarez Pablo , Ruiz Pablo , Cooper Lee A. D. , Molina Rafael , Katsaggelos Aggelos K. 
Published: June 2021

AbstractThe volume of labeled data is often the primary determinant of success in developing machine learning algorithms. This has increased interest in methods for leveraging crowds to scale data labeling efforts, and methods to learn from noisy crowd-sourced labels. The need to scale labeling is acute but particularly challenging in medical applications like pathology, due to the expertise required to generate quality labels and the limited availability of qualified experts. In this paper we investigate the application of Scalable Variational Gaussian Processes for Crowdsourcing (SVGPCR) in digital pathology. We compare SVGPCR with other crowdsourcing methods using a large multi-rater dataset where pathologists, pathology residents, and medical students annotated tissue regions breast cancer. Our study shows that SVGPCR is competitive with equivalent methods trained using gold-standard pathologist generated labels, and that SVGPCR meets or exceeds the performance of other crowdsourcing methods based on deep learning. We also show how SVGPCR can effectively learn the class-conditional reliabilities of individual annotators and demonstrate that Gaussian-process classifiers have comparable performance to similar deep learning methods. These results suggest that SVGPCR can meaningfully engage non-experts in pathology labeling tasks, and that the class-conditional reliabilities estimated by SVGPCR may assist in matching annotators to tasks where they perform well.
Metabolic syndrome in women with previous gestational diabetes
Authors: Kaiser Karsten , Nielsen Michael Festersen , Kallfa Ervin , Dubietyte Greta , Lauszus Finn Friis 
Published: June 2021

AbstractTo evaluate the incidence and timing of the diagnosis of metabolic syndrome in a cohort of Danish women after a pregnancy with gestational diabetes (GDM) to estimate the optimum time for preventative actions in relation to metabolic syndrome (MetS). In this follow-up study, 435 women were included from a consecutive cohort with prior history of GDM. Data on dyslipidemia, hypertension and other cardiovascular disorders (CVD) were extracted from the electronic patient journal. Any antidiabetic, cardiovascular and cholesterol-lowering medicine was ascertained in the national prescription database. Similarly, any blood test taken was evaluated. We defined a patient having MetS if the criteria of the WHO based definition of diabetes or impaired glucose regulation were met. Further, we added as alternative for glucose intolerance, a glycosylated hemoglobin (HbA1c) > 44 mmol/mol or the former level ≥ 6.5%. Further, dyslipidemia, lipid lowering medications, BMI > 30 kg/m2 or antihypertensive treatment were used. For MetS outcome, diagnosis or medication for CVD was registered. All women were followed for median 5.7 years (range 0; 9). The incidence of MetS was 28%. Thirteen percent of these qualified already within one year after pregnancy for the diagnosis of MetS. Postpartum MetS was detected after a median of 3 years (range 0; 7 years); further, 36 (8%) had been diagnosed with manifest diabetes after pregnancy. The diagnosis of postpartum MetS was strongly associated with the prevalence of manifest diabetes. Six years after pregnancy the rate of metabolic syndrome was more than tripled (25 vs. 89%, no DM vs manifest DM, RR: 6.7; 95% CI 2.7–17, p < 0.001). At 40 years the MetS rate nearly tripled if manifest DM was diagnosed (26 vs. 78%, no DM vs. manifest DM, RR: 3.3, 95% CI 1.8–6, p < 0.001). We found that GDM and later on manifest DM in women increase the risk of metabolic syndrome. There seems to be a window of opportunity before the early thirties where it would be especially beneficial to begin preventive efforts in women with GDM.
Three novel quantum-inspired swarm optimization algorithms using different bounded potential fields
Authors: Alvarez-Alvarado Manuel S. , Alban-Chacón Francisco E. , Lamilla-Rubio Erick A. , Rodríguez-Gallegos Carlos D. , Velásquez Washington 
Published: June 2021

AbstractBased on the behavior of the quantum particles, it is possible to formulate mathematical expressions to develop metaheuristic search optimization algorithms. This paper presents three novel quantum-inspired algorithms, which scenario is a particle swarm that is excited by a Lorentz, Rosen–Morse, and Coulomb-like square root potential fields, respectively. To show the computational efficacy of the proposed optimization techniques, the paper presents a comparative study with the classical particle swarm optimization (PSO), genetic algorithm (GA), and firefly algorithm (FFA). The algorithms are used to solve 24 benchmark functions that are categorized by unimodal, multimodal, and fixed-dimension multimodal. As a finding, the algorithm inspired in the Lorentz potential field presents the most balanced computational performance in terms of exploitation (accuracy and precision), exploration (convergence speed and acceleration), and simulation time compared to the algorithms previously mentioned. A deeper analysis reveals that a strong potential field inside a well with weak asymptotic behavior leads to better exploitation and exploration attributes for unimodal, multimodal, and fixed-multimodal functions.
Mortality and microbial diversity after allogeneic hematopoietic stem cell transplantation: secondary analysis of a randomized nutritional intervention trial
Authors: Skaarud Kristin J. , Hov Johannes R. , Hansen Simen H. , Kummen Martin , Valeur Jørgen , Seljeflot Ingebjørg , Bye Asta , Paulsen Vemund , Lundin Knut E. A. , Trøseid Marius , Tjønnfjord Geir E. , Iversen Per Ole 
Published: June 2021

AbstractGut mucosal barrier injury is common following allogeneic hematopoietic stem cell transplantation (allo-HSCT) and associated with poor clinical outcomes. Diet is critical for microbial diversity, but whether nutritional support affects microbiota and outcome after allo-HSCT is unknown. We present a secondary analysis of a randomized controlled nutritional intervention trial during allo-HSCT. We investigated if the intervention influenced gut microbiota, short-chain fatty acids (SCFAs), and markers of gut barrier functions, and if these parameters were associated with clinical outcomes. Fecal specimens were available from 47 recipients, and subjected to 16S rRNA gene sequencing. We found no significant differences between the intervention group and controls in investigated parameters. We observed a major depletion of microbiota, SCFAs, and altered markers of gut barrier function from baseline to 3 weeks post-transplant. One-year mortality was significantly higher in patients with lower diversity at 3 weeks post-HSCT, but not related to diversity at baseline. The relative abundance of Blautia genus at 3 weeks was higher in survivors. Fecal propionic acid was associated with survival. Markers of gut barrier functions were less strongly associated with clinical outcomes. Possibly, other strategies than dietary intervention are needed to prevent negative effects of gut microbiota and clinical outcomes after allo-HSCT.ClinicalTrials.gov (NCT01181076).
Reproducibility of CT-based radiomic features against image resampling and perturbations for tumour and healthy kidney in renal cancer patients
Authors: Mottola Margherita , Ursprung Stephan , Rundo Leonardo , Sanchez Lorena Escudero , Klatte Tobias , Mendichovszky Iosif , Stewart Grant D , Sala Evis , Bevilacqua Alessandro 
Published: June 2021

AbstractComputed Tomography (CT) is widely used in oncology for morphological evaluation and diagnosis, commonly through visual assessments, often exploiting semi-automatic tools as well. Well-established automatic methods for quantitative imaging offer the opportunity to enrich the radiologist interpretation with a large number of radiomic features, which need to be highly reproducible to be used reliably in clinical practice. This study investigates feature reproducibility against noise, varying resolutions and segmentations (achieved by perturbing the regions of interest), in a CT dataset with heterogeneous voxel size of 98 renal cell carcinomas (RCCs) and 93 contralateral normal kidneys (CK). In particular, first order (FO) and second order texture features based on both 2D and 3D grey level co-occurrence matrices (GLCMs) were considered. Moreover, this study carries out a comparative analysis of three of the most commonly used interpolation methods, which need to be selected before any resampling procedure. Results showed that the Lanczos interpolation is the most effective at preserving original information in resampling, where the median slice resolution coupled with the native slice spacing allows the best reproducibility, with 94.6% and 87.7% of features, in RCC and CK, respectively. GLCMs show their maximum reproducibility when used at short distances.
Working memory load reduces corticospinal suppression to former go and trained no-go cues
Authors: Tran Dominic M. D. , Nicholson William G. , Harris Justin A. , Harris Irina M. , Livesey Evan J. 
Published: June 2021

AbstractEnvironmental cues associated with an action can prime the motor system, decreasing response times and activating motor regions of the brain. However, when task goals change, the same responses to former go-associated cues are no longer required and motor priming needs to be inhibited to avoid unwanted behavioural errors. The present study tested whether the inhibition of motor system activity to presentations of former go cues is reliant on top-down, goal-directed cognitive control processes using a working memory (WM) load manipulation. Applying transcranial magnetic stimulation over the primary motor cortex to measure motor system activity during a Go/No-go task, we found that under low WM, corticospinal excitability was suppressed to former go and trained no-go cues relative to control cues. Under high WM, the cortical suppression to former go cues was reduced, suggesting that the underlying mechanism required executive control. Unexpectedly, we found a similar result for trained no-go cues and showed in a second experiment that the corticospinal suppression and WM effects were unrelated to local inhibitory function as indexed by short-interval intracortical inhibition. Our findings reveal that the interaction between former response cues and WM is complex and we discuss possible explanations of our findings in relation to models of response inhibition.
Vulnerability to climate change of a microendemic lizard species from the central Andes
Authors: Laspiur A. , Santos J. C. , Medina S. M. , Pizarro J. E. , Sanabria E. A. , Sinervo B. , Ibargüengoytía N. R. 
Published: June 2021

AbstractGiven the rapid loss of biodiversity as consequence of climate change, greater knowledge of ecophysiological and natural history traits are crucial to determine which environmental factors induce stress and drive the decline of threatened species. Liolaemus montanezi (Liolaemidae), a xeric-adapted lizard occurring only in a small geographic range in west-central Argentina, constitutes an excellent model for studies on the threats of climate change on such microendemic species. We describe field data on activity patterns, use of microhabitat, behavioral thermoregulation, and physiology to produce species distribution models (SDMs) based on climate and ecophysiological data. Liolaemus montanezi inhabits a thermally harsh environment which remarkably impacts their activity and thermoregulation. The species shows a daily bimodal pattern of activity and mostly occupies shaded microenvironments. Although the individuals thermoregulate at body temperatures below their thermal preference they avoid high-temperature microenvironments probably to avoid overheating. The population currently persists because of the important role of the habitat physiognomy and not because of niche tracking, seemingly prevented by major rivers that form boundaries of their geographic range. We found evidence of habitat opportunities in the current range and adjacent areas that will likely remain suitable to the year 2070, reinforcing the relevance of the river floodplain for the species’ avoidance of extinction.
Interannual variability of the frequency of MJO phases and its association with two types of ENSO
Authors: Dasgupta Panini , Roxy M. K. , Chattopadhyay Rajib , Naidu C. V. , Metya Abirlal 
Published: June 2021

AbstractIn this study, we reexamine the effect of two types of El Niño Southern Oscillation (ENSO) modes on Madden Julian Oscillation (MJO) activity in terms of the frequency of MJO phases. Evaluating all-season data, we identify two dominant zonal patterns of MJO frequency exhibiting prominent interannual variability. These patterns are structurally similar to the Wheeler and Hendon (Mon. Weather Rev. 132:1917–1932, 2004) RMM1 and RMM2 spatial patterns. The first pattern explains a higher frequency of MJO activity over the Maritime Continent and a lower frequency over the central Pacific Ocean and the western Indian Ocean, or vice versa. The second pattern is associated with a higher frequency of MJO active days over the eastern Indian Ocean and a lower frequency over the western Pacific, or vice versa. We find that these two types of MJO frequency patterns are related to the central Pacific and eastern Pacific ENSO modes. From the positive to the negative ENSO (central Pacific or eastern Pacific) phases, the respective MJO frequency patterns change their sign. The MJO frequency patterns are the lag response of the underlying ocean state. The coupling between ocean and atmosphere is exceedingly complex. The first MJO frequency pattern is most prominent during the negative central-Pacific (CP-type) ENSO phases (specifically during September–November and December-February seasons). The second MJO frequency pattern is most evident during the positive eastern-Pacific (EP-type) ENSO phases (specifically during March–May, June–August and September–November). Different zonal circulation patterns during CP-type and EP-type ENSO phases alter the mean moisture distribution throughout the tropics. The horizontal convergence of mean background moisture through intraseasonal winds are responsible for the MJO frequency anomalies during the two types of ENSO phases. The results here show how the MJO activity gets modulated on a regional scale in the presence of two types of ENSO events and can be useful in anticipating the seasonal MJO conditions from a predicted ENSO state.