bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evaluation of interparticle interactions between magnetic nanoparticles using first order reversal curves and Weiss temperature
Authors: Mamiya H , Furukawa I , Huaman J L Cuya , Suzuki K , Miyamura H , Jeyadevan B 
Published: March 2021

Abstract
Two conventional methods for evaluating interparticle magnetic interactions are applied to magnetic nanoparticle assemblies with various interparticle distances that are controlled by a silica coating. According to Weiss temperatures derived from superparamagnetic response analysis, the mean values of the interparticle magnetic interactions are relatively small and seem to be independent of the interparticle distance. The interaction fields in the first-order reversal curve diagram for narrow interparticle distances are widely distributed. However, the interaction fields disappear when the interparticle distance is sufficiently large. Analysis of these two contrasting results indicates that ferromagnetic-like and antiferromagnetic-like magnetic couplings coexist and cancel each other, as in atomic spin glasses.
Distinct vegetation response to drying and wetting trends across an aridity threshold
Authors: Zhao Wei , Yu Xiubo , Liu Yu , Xu Li , Chen Zhi , Li Shenggong 
Published: March 2021

Abstract
Aridity regulates the terrestrial ecosystem productivity in water-limited regions. The aridity index (AI) is often defined as the ratio of annual precipitation to annual potential evapotranspiration. However, how the drying and wetting influence the vegetation response and its characteristic along aridity gradient remains unclear. Here, we examined trends of the AI and normalized difference vegetation index (NDVI) in the drylands of East Asia from 1982 to 2015, which denoted the drying and wetting trends and vegetation response, respectively. The results show that the variability in land area and AI from 1982–2015 was lower in the whole dryland than its subtypes including hyper-arid, arid, semi-arid, and dry sub-humid regions. Drying and wetting trends were observed in each AI interval along a spatial aridity gradient. Wetting trends are prevalent owing to their area and magnitude were twice those of drying trends. Spatial variation of aridity shaped the pattern of trends in vegetation response to drying and wetting trends; drier regions had smaller and narrower ranges of variation in NDVI trends relative to wetter regions. A shift in AI trends and NDVI trends along the spatial aridity gradient occurred at 0.4 of AI. Distinct patterns of vegetation response to aridity change were observed across the aridity threshold, and the transition region was identified in the studied drylands. The results suggest that changes in the subtypes might be masked by the entire drylands and then leading to failure in recognizing the transformation of the subtypes. This implies that terrestrial carbon storage variability prediction should consider the spatial aridity changes to avoid the uncertainties due to the divergent vegetation response to AI trends at different aridity levels.
Seven steps to reliable cyclic voltammetry measurements for the determination of double layer capacitance
Authors: Morales Dulce M , Risch Marcel 
Published: March 2021

Abstract
Discovery of electrocatalytic materials for high-performance energy conversion and storage applications relies on the adequate characterization of their intrinsic activity, which is currently hindered by the dearth of a protocol for consistent and precise determination of double layer capacitance (C
DL). Herein, we propose a seven-step method that aims to determine C
DL reliably by scan rate-dependent cyclic voltammetry considering aspects that strongly influence the outcome of the analysis, including (a) selection of a suitable measuring window, (b) the uncompensated resistance, (c) optimization of measuring settings, (d) data acquisition, (e) selection of data suitable for analysis, (f) extraction of the desired information, and (g) validation of the results. To illustrate the proposed method, two systems were studied: a resistor–capacitor electric circuit, and a glassy carbon disk in an electrochemical cell. With these studies, it is demonstrated that when any of the mentioned steps of the procedure are neglected, substantial deviations of the results are observed with misestimations as large as 61% in the case of the investigated electrochemical system. Moreover, we propose allometric regression as a more suitable model than linear regression for the determination of C
DL for both the ideal and the non-ideal systems investigated. We stress the importance of assessing the accuracy of not only highly specialized electrochemical methods, but also of those that are well-known and commonly used as it is the case of the voltammetric methods. The procedure proposed herein is not limited to the determination of C
DL, but can be effectively applied to any other analysis that aims to deliver quantitative results via voltammetric methods, which is crucial for the study of kinetic and diffusion phenomena in electrochemical systems.
Efficient hyperparameter tuning for kernel ridge regression with Bayesian optimization
Authors: Stuke Annika , Rinke Patrick , Todorović Milica 
Published: March 2021

Abstract
Machine learning methods usually depend on internal parameters—so called hyperparameters—that need to be optimized for best performance. Such optimization poses a burden on machine learning practitioners, requiring expert knowledge, intuition or computationally demanding brute-force parameter searches. We here assess three different hyperparameter selection methods: grid search, random search and an efficient automated optimization technique based on Bayesian optimization (BO). We apply these methods to a machine learning problem based on kernel ridge regression in computational chemistry. Two different descriptors are employed to represent the atomic structure of organic molecules, one of which introduces its own set of hyperparameters to the method. We identify optimal hyperparameter configurations and infer entire prediction error landscapes in hyperparameter space that serve as visual guides for the hyperparameter performance. We further demonstrate that for an increasing number of hyperparameters, BO and random search become significantly more efficient in computational time than an exhaustive grid search, while delivering an equivalent or even better accuracy.
Keratin 17 Is a Novel Cytologic Biomarker for Urothelial Carcinoma Diagnosis
Authors: Babu Sruthi , Kim Nam W , Wu Maoxin , Chan Ina , Escobar-Hoyos Luisa F , Shroyer Kenneth R 
Published: March 2021

Abstract

Objectives
The microscopic features of urine cytology specimens are subjective and may not reliably distinguish between benign urothelial cells and low-grade urothelial carcinoma (UC). Prior studies demonstrated that keratin 17 (K17) detection in biopsies is highly sensitive for UC. The current study aimed to define K17 diagnostic test performance for initial screening and detect recurrent UC in urine specimens.

Methods
K17 was detected by immunocytochemistry (ICC) in consecutively collected urine specimens (2018-2019). A qualitative score for the K17 test was determined in 81 samples (discovery cohort) and validated in 98 samples (validation cohort). K17 sensitivity and specificity were analyzed in both cohorts across all grades of UC.

Results
Based on the discovery cohort, the presence of 5 or more K17 immunoreactive urothelial cells (area under the curve = 0.90; P &lt; .001) was the optimal threshold to define a K17-positive test. The sensitivity of the K17 ICC test for biopsy-confirmed UC was 35 of 36 (97%) and 18 of 21 (86%) in the discovery and validation cohorts, respectively. K17 was positive in 16 of 19 (84%) specimens with biopsy-confirmed low-grade UC and in 34 of 34 (100%) of specimens with high-grade UC.

Conclusions
K17 ICC is a highly sensitive diagnostic test for initial screening and detection of recurrence across all grades of UC.
Adjustment for Disease Severity in the Test-Negative Study Design
Authors: Ciocănea-Teodorescu Iuliana , Nason Martha , Sjölander Arvid , Gabriel Erin E 
Published: March 2021

Abstract
The test-negative study design is often used to estimate vaccine effectiveness in influenza studies, but it has also been proposed in the context of other infectious diseases, such as cholera, dengue, or Ebola. It was introduced as a variation of the case-control design, in an attempt to reduce confounding bias due to health-care–seeking behavior, and has quickly gained popularity because of its logistic advantages. However, examination of the directed acyclic graphs that describe the test-negative design reveals that without strong assumptions, the estimated odds ratio derived under this sampling mechanism is not collapsible over the selection variable, such that the results obtained for the sampled individuals cannot be generalized to the whole population. In this paper, we show that adjustment for severity of disease can reduce this bias and, under certain assumptions, makes it possible to unbiasedly estimate a causal odds ratio. We support our findings with extensive simulations and discuss them in the context of recently published cholera test-negative studies of the effectiveness of cholera vaccines.
Polypharmacy side-effect prediction with enhanced interpretability based on graph feature attention network
Authors: Bang Sunjoo , Jhee Jong Ho , Shin Hyunjung 
Published: March 2021

Abstract

Motivation
Polypharmacy side effects should be carefully considered for new drug development. However, considering all the complex drug–drug interactions that cause polypharmacy side effects is challenging. Recently, graph neural network (GNN) models have handled these complex interactions successfully and shown great predictive performance. Nevertheless, the GNN models have difficulty providing intelligible factors of the prediction for biomedical and pharmaceutical domain experts.

Method
A novel approach, graph feature attention network (GFAN), is presented for interpretable prediction of polypharmacy side effects by emphasizing target genes differently. To artificially simulate polypharmacy situations, where two different drugs are taken together, we formulated a node classification problem by using the concept of line graph in graph theory.

Results
Experiments with benchmark datasets validated interpretability of the GFAN and demonstrated competitive performance with the graph attention network in a previous work. And the specific cases in the polypharmacy side-effect prediction experiments showed that the GFAN model is capable of very sensitively extracting the target genes for each side-effect prediction.

Availability and implementation
https://github.com/SunjooBang/Polypharmacy-side-effect-prediction.
ExperimentSubset: an R package to manage subsets of Bioconductor Experiment objects
Authors: Sarfraz Irzam , Asif Muhammad , Campbell Joshua D 
Published: March 2021

Abstract

Motivation
R Experiment objects such as the SummarizedExperiment or SingleCellExperiment are data containers for storing one or more matrix-like assays along with associated row and column data. These objects have been used to facilitate the storage and analysis of high-throughput genomic data generated from technologies such as single-cell RNA sequencing. One common computational task in many genomics analysis workflows is to perform subsetting of the data matrix before applying down-stream analytical methods. For example, one may need to subset the columns of the assay matrix to exclude poor-quality samples or subset the rows of the matrix to select the most variable features. Traditionally, a second object is created that contains the desired subset of assay from the original object. However, this approach is inefficient as it requires the creation of an additional object containing a copy of the original assay and leads to challenges with data provenance.

Results
To overcome these challenges, we developed an R package called ExperimentSubset, which is a data container that implements classes for efficient storage and streamlined retrieval of assays that have been subsetted by rows and/or columns. These classes are able to inherently provide data provenance by maintaining the relationship between the subsetted and parent assays. We demonstrate the utility of this package on a single-cell RNA-seq dataset by storing and retrieving subsets at different stages of the analysis while maintaining a lower memory footprint. Overall, the ExperimentSubset is a flexible container for the efficient management of subsets.

Availability and implementation
ExperimentSubset package is available at Bioconductor: https://bioconductor.org/packages/ExperimentSubset/ and Github: https://github.com/campbio/ExperimentSubset.

Supplementary information
Supplementary data are available at Bioinformatics online.
Zp4 is completely dispensable for fertility in female rats
Authors: Zeng Ming-Hua , Wang Yan , Huang Hua-Lin , Quan Ru-Ping , Yang Jun-Ting , Guo Dan , Sun Ying , Lv Chao , Li Tian-Ying , Wang Le , Tan Hang-Jin , Long Pan-Pan , Deng Hong-Wen , Xiao Hong-Mei 
Published: March 2021

Abstract
Zona pellucida (ZP), which is composed of at most four extracellular glycoproteins (ZP1, ZP2, ZP3, and ZP4) in mammals, shelters the oocytes and is vital in female fertility. Several studies have identified the indispensable roles of ZP1–3 in maintaining normal female fertility. However, the understanding of ZP4 is still very poor because only one study on ZP4-associated infertility performed in rabbits has been reported up to date. Here we investigated the function of mammalian Zp4 by creating a knockout (KO) rat strain (Zp4−/− rat) using CRISPR–Cas9-mediated DNA-editing method. The influence of Zp4 KO on ZP morphology and some pivotal processes of reproduction, including oogenesis, ovulation, fertilization, and pup production, were studied using periodic acid–Schiff’s staining, superovulation, in vitro fertilization, and natural mating. The ZP morphology in Zp4−/− rats was normal, and none of these pivotal processes was affected. This study renewed the knowledge of mammalian Zp4 by suggesting that Zp4 was completely dispensable for female fertility.
The extreme capsule and aphasia: proof-of-concept of a new way relating structure to neurological symptoms
Authors: Martinez Oeckel Ariane , Rijntjes Michel , Glauche Volkmar , Kümmerer Dorothee , Kaller Christoph P , Egger Karl , Weiller Cornelius 
Published: March 2021

Abstract
We present anatomy-based symptom-lesion mapping to assess the association between lesions of tracts in the extreme capsule and aphasia. The study cohort consisted of 123 patients with acute left-hemispheric stroke without a lesion of language-related cortical areas of the Stanford atlas of functional regions of interest. On templates generated through global fibre tractography, lesions of the extreme capsule and of the arcuate fascicle were quantified and correlated with the occurrence of aphasia (n = 18) as defined by the Token Test. More than 15% damage of the slice plane through the extreme capsule was a strong independent predictor of aphasia in stroke patients, odds ratio 16.37, 95% confidence interval: 3.11–86.16, P &lt; 0.01. In contrast, stroke lesions of &gt;15% in the arcuate fascicle were not associated with aphasia. Our results support the relevance of a ventral pathway in the language network running through the extreme capsule.
Daily activity rhythms, chronotypes, and risk-taking behavior in the signal crayfish
Authors: Sbragaglia Valerio , Breithaupt Thomas 
Published: March 2021

AbstractConsistent inter-individual differences in daily activity rhythms (i.e., chronotypes) can have ecological consequences in determining access to food resources and avoidance of predators. The most common measure to characterize chronotypes in animals as well as humans is the onset of activity (i.e., early or late chronotypes). However, daily activity rhythms may also differ in the relative amount of activity displayed at particular time periods. Moreover, chronotypes may also be linked to other consistent inter-individual differences in behavior (i.e., personality), such as the propensity to take risks. Here, we used the signal crayfish Pacifastacus leniusculus to test the presence of chronotypes and risk-taking personality traits and a potential behavioral syndrome between these traits. We first exposed crayfish to 5 days of light–darkness to measure daily activity rhythms and then we applied a visual predator-simulating stimulus in 2 different contexts (neutral and food). Our results showed consistent (i.e., across 5 days) inter-individual differences in the relative nocturnal activity displayed in the early and middle, but not in the late part of darkness hours. Moreover, while crayfish displayed inter-individual differences in risk-taking behavior, these were not found to be consistent across 2 contexts. Therefore, we were not able to formally test a behavioral syndrome between these 2 traits. In conclusion, our study provides the first evidence of chronotypes in the relative amount of activity displayed at particular time periods. This could be a valuable information for applied ecological aspects related to the signal crayfish, which is a major invasive species of freshwater ecosystems.
Utilization of sacubitril/valsartan in patients with heart failure with reduced ejection fraction: real-world data from the ARIADNE registry
Authors: Zeymer Uwe , Clark Andrew L , Barrios Vivencio , Damy Thibaud , Drożdż Jaroslaw , Fonseca Candida , Lund Lars H , Kalus Stefanie , Ferber Philippe C , Hussain Rizwan I , Koch Cornelia , Maggioni Aldo P 
Published: March 2021

Abstract

Aims
To compare baseline characteristics of patients with heart failure with reduced ejection fraction (HFrEF) initiated on sacubitril/valsartan compared with patients continued on conventional heart failure (HF)-treatment in a European out-patient setting.

Methods and results
Between July 2016 and July 2019, ARIADNE enrolled 8787 outpatients aged ≥18 years with HFrEF from 17 European countries. Choice of therapy was solely at the investigators’ discretion. In total, 4173 patients were on conventional HF-treatment (non-S/V group), while 4614 patients were on sacubitril/valsartan either at enrolment or started sacubitril/valsartan within 1 month of enrolment (S/V group). Of these, 2108 patients started sacubitril/valsartan treatment ±1 month around enrolment [restricted S/V (rS/V) group]. The average age of the patients was 68 years. Patients on S/V were more likely to have New York Heart Association (NYHA) class III or IV symptoms (50.3%, 44.6%, 32.1% in rS/V, S/V, and non-S/V, respectively) and had lower left ventricular ejection fraction (LVEF; 32.3%, 32.7%, and 35.4% in rS/V, S/V, and non-S/V, respectively; P &lt; 0.0001). The most frequently received HF treatments were angiotensin-converting enzyme inhibitor/angiotensin receptor blocker (ACEI/ARB; ∼84% in non-S/V), followed by β-blockers (∼80%) and mineralocorticoid receptor antagonists (MRAs; 53%). The use of triple HF therapy (ACEI/ARB/angiotensin receptor neprilysin inhibitor with β-blockers and MRA) was higher in the S/V groups than non-S/V group (48.2%, 48.2%, and 40.2% in rS/V, S/V, and non-S/V, respectively).

Conclusion
In this large multinational HFrEF registry, patients receiving sacubitril/valsartan tended to be younger with lower LVEF and higher NYHA class. Fewer than half of the patients received triple HF therapy.
Sarcopenic Obesity and Amino Acids: Concord Health and Ageing in Men Project
Authors: Le Couteur David G , Handelsman David J , Stanaway Fiona , Waite Louise M , Blyth Fiona M , Naganathan Vasi , Cumming Robert G , Hirani Vasant 
Published: March 2021

Abstract
Although characteristic changes in amino acid concentrations occur in obesity and sarcopenia, amino acids concentrations have not been reported in sarcopenic obesity. We studied n = 831 men aged 75 years and older from the 5-year follow-up of the Concord Health and Ageing in Men Project. Sarcopenia was defined using the Foundation of the National Institutes of Health criteria and obesity was defined as &gt;30% fat mass. There were 31 men (3.7%) who had sarcopenic obesity. Branched chain amino acids were elevated in the obese (but not sarcopenic) group (n = 348) but reduced in both the sarcopenic (but not obese) (n = 44) and the sarcopenic obese groups. Apart from this, most of the amino acid concentrations were between those for the obese and the sarcopenic groups. Yet despite low concentrations of branched chain amino acids, the sarcopenic obese group had indications of insulin resistance and diabetes mellitus (fasting glucose and insulin concentrations, homeostatic model assessment, and percentage of participants taking diabetes medications) that were similar to the obese group. In summary, sarcopenic obese participants did not have a unique amino acid signature. In obesity, elevated branched chain amino acids are not a prerequisite for insulin resistance and diabetes if obesity is associated with sarcopenia.
Risk of Nursing Home Use Among Older Americans: The Impact of Psychiatric History and Trajectories of Cognitive Function
Authors: Brown Maria T , Mutambudzi Miriam 
Published: March 2021

Abstract

Objectives
Mental illness and cognitive functioning may be independently associated with nursing home use. We investigated the strength of the association between baseline (1998) psychiatric history, 8-year cognitive function trajectories, and prospective incidence of nursing home use over a 10-year period while accounting for relevant covariates in U.S. adults aged 65 and older. We hypothesized that self-reported baseline history of psychiatric, emotional, or nervous problems would be associated with a greater risk of nursing home use and that cognition trajectories with the greatest decline would be associated with a subsequent higher risk of nursing home use.

Methods
We used 8 waves (1998–2016) of Health and Retirement Study data for adults aged 65 years and older. Latent class mixture modeling identified 4 distinct cognitive function trajectory classes (1998–2006): low-declining, medium-declining, medium-stable, and high-declining. Participants from the 1998 wave (N = 5,628) were classified into these 4 classes. Competing risks regression analysis modeled the subhazard ratio of nursing home use between 2006 and 2016 as a function of baseline psychiatric history and cognitive function trajectories.

Results
Psychiatric history was independently associated with greater risk of nursing home use (subhazard ratio [SHR] 1.26, 95% confidence interval [CI] 1.06–1.51, p &lt; .01), net the effects of life course variables. Furthermore, “low-declining” (SHR 2.255, 95% CI 1.70–2.99, p &lt; .001) and “medium-declining” (2.103, 95% CI 1.69–2.61, p &lt; .001) trajectories predicted increased risk of nursing home use.

Discussion
Evidence of these associations can be used to educate policymakers and providers about the need for appropriate psychiatric training for staff in community-based and residential long-term care programs.