bluuebunny/crossref_metadata_2025_split huggingface dataset:
Predation risk shapes the use of conflicting personal risk and social safety information in guppies
Authors: Feyten Laurence E A , Crane Adam L , Ramnarine Indar W , Brown Grant E 
Published: July 2021

Abstract
When faced with uncertainty, animals can benefit from using multiple sources of information in order to make an optimal decision. However, information sources (e.g., social and personal cues) may conflict, while also varying in acquisition cost and reliability. Here, we assessed behavioral decisions of Trinidadian guppies (Poecilia reticulata), in situ, when presented with conflicting social and personal information about predation risk. We positioned foraging arenas within high- and low-predation streams, where guppies were exposed to a personal cue in the form of conspecific alarm cues (a known indicator of risk), a novel cue, or a control. At the same time, a conspecific shoal (a social safety cue) was either present or absent. When social safety was absent, guppies in both populations showed typical avoidance responses towards alarm cues, and high-predation guppies showed their typical avoidance of novel cues (i.e., neophobia). However, the presence of social safety cues was persuasive, overriding the neophobia of high-predation guppies and emboldening low-predation guppies to ignore alarm cues. Our experiment is one of the first to empirically assess the use of safety and risk cues in prey and suggests a threshold level of ambient risk which dictates the use of conflicting social and personal information.
Reviewing and assessing existing meta-analysis models and tools
Authors: Makinde Funmilayo L , Tchamga Milaine S S , Jafali James , Fatumo Segun , Chimusa Emile R , Mulder Nicola , Mazandu Gaston K 
Published: July 2021

AbstractOver the past few years, meta-analysis has become popular among biomedical researchers for detecting biomarkers across multiple cohort studies with increased predictive power. Combining datasets from different sources increases sample size, thus overcoming the issue related to limited sample size from each individual study and boosting the predictive power. This leads to an increased likelihood of more accurately predicting differentially expressed genes/proteins or significant biomarkers underlying the biological condition of interest. Currently, several meta-analysis methods and tools exist, each having its own strengths and limitations. In this paper, we survey existing meta-analysis methods, and assess the performance of different methods based on results from different datasets as well as assessment from prior knowledge of each method. This provides a reference summary of meta-analysis models and tools, which helps to guide end-users on the choice of appropriate models or tools for given types of datasets and enables developers to consider current advances when planning the development of new meta-analysis models and more practical integrative tools.
Learning to SMILES: BAN-based strategies to improve latent representation learning from molecules
Authors: Wu Cheng-Kun , Zhang Xiao-Chen , Yang Zhi-Jiang , Lu Ai-Ping , Hou Ting-Jun , Cao Dong-Sheng 
Published: July 2021

Abstract
Computational methods have become indispensable tools to accelerate the drug discovery process and alleviate the excessive dependence on time-consuming and labor-intensive experiments. Traditional feature-engineering approaches heavily rely on expert knowledge to devise useful features, which could be costly and sometimes biased. The emerging deep learning (DL) methods deliver a data-driven method to automatically learn expressive representations from complex raw data. Inspired by this, researchers have attempted to apply various deep neural network models to simplified molecular input line entry specification (SMILES) strings, which contain all the composition and structure information of molecules. However, current models usually suffer from the scarcity of labeled data. This results in a low generalization ability of SMILES-based DL models, which prevents them from competing with the state-of-the-art computational methods. In this study, we utilized the BiLSTM (bidirectional long short term merory) attention network (BAN) in which we employed a novel multi-step attention mechanism to facilitate the extracting of key features from the SMILES strings. Meanwhile, SMILES enumeration was utilized as a data augmentation method in the training phase to substantially increase the number of labeled data and enlarge the probability of mining more patterns from complex SMILES. We again took advantage of SMILES enumeration in the prediction phase to rectify model prediction bias and provide a more accurate prediction. Combined with the BAN model, our strategies can greatly improve the performance of latent features learned from SMILES strings. In 11 canonical absorption, distribution, metabolism, excretion and toxicity-related tasks, our method outperformed the state-of-the-art approaches.
Predicting potential small molecule–miRNA associations based on bounded nuclear norm regularization
Authors: Chen Xing , Zhou Chi , Wang Chun-Chun , Zhao Yan 
Published: July 2021

Abstract
Mounting evidence has demonstrated the significance of taking microRNAs (miRNAs) as the target of small molecule (SM) drugs for disease treatment. Given the fact that exploring new SM–miRNA associations through biological experiments is extremely expensive, several computing models have been constructed to reveal the possible SM–miRNA associations. Here, we built a computing model of Bounded Nuclear Norm Regularization for SM–miRNA Associations prediction (BNNRSMMA). Specifically, we first constructed a heterogeneous SM–miRNA network utilizing miRNA similarity, SM similarity, confirmed SM–miRNA associations and defined a matrix to represent the heterogeneous network. Then, we constructed a model to complete this matrix by minimizing its nuclear norm. The Alternating Direction Method of Multipliers was adopted to minimize the nuclear norm and obtain predicted scores. The main innovation lies in two aspects. During completion, we limited all elements of the matrix within the interval of (0,1) to make sure they have practical significance. Besides, instead of strictly fitting all known elements, a regularization term was incorporated to tolerate the noise in integrated similarities. Furthermore, four kinds of cross-validations on two datasets and two types of case studies were performed to evaluate the predictive performance of BNNRSMMA. Finally, BNNRSMMA attained areas under the curve of 0.9822 (0.8433), 0.9793 (0.8852), 0.8253 (0.7350) and 0.9758 ± 0.0029 (0.8759 ± 0.0041) under global leave-one-out cross-validation (LOOCV), miRNA-fixed LOOCV, SM-fixed LOOCV and 5-fold cross-validation based on Dataset 1(Dataset 2), respectively. With regard to case studies, plenty of predicted associations have been verified by experimental literatures. All these results confirmed that BNNRSMMA is a reliable tool for inferring associations.
Alpha-Band Phase Modulates Bottom-up Feature Processing
Authors: Jia Jianrong , Fan Ying , Luo Huan 
Published: July 2021

AbstractRecent studies reveal that attention operates in a rhythmic manner, that is, sampling each location or feature alternatively over time. However, most evidence derives from top-down tasks, and it remains elusive whether bottom-up processing also entails dynamic coordination. Here, we developed a novel feature processing paradigm and combined time-resolved behavioral measurements and electroencephalogram (EEG) recordings to address the question. Specifically, a salient color in a multicolor display serves as a noninformative cue to capture attention and presumably reset the oscillations of feature processing. We then measured the behavioral performance of a probe stimulus associated with either high- or low-salient color at varied temporal lags after the cue. First, the behavioral results (i.e., reaction time) display an alpha-band (~8 Hz) profile with a consistent phase lag between high- and low-salient conditions. Second, simultaneous EEG recordings show that behavioral performance is modulated by the phase of alpha-band neural oscillation at the onset of the probes. Finally, high- and low-salient probes are associated with distinct preferred phases of alpha-band neural oscillations. Taken together, our behavioral and neural results convergingly support a central function of alpha-band rhythms in feature processing, that is, features with varied saliency levels are processed at different phases of alpha neural oscillations.
Epidemiology and Risk of Coronavirus Disease 2019 Among Travelers at Airport and Port Quarantine Stations Across Japan: A Nationwide Descriptive Analysis and an Individually Matched Case-Control Study
Authors: Tsuboi Motoyuki , Hachiya Masahiko , Ohtsu Hiroshi , Akashi Hidechika , Miyoshi Chiaki , Umeda Tamami 
Published: July 2021

Abstract

Background
The epidemiology and risk of coronavirus disease 2019 (COVID-19) among travelers at international borders remain unclear.

Methods
We conducted descriptive and individually matched case-control studies using a nationwide register for COVID-19 testing of travelers from 3 August to 31 October 2020 at airport/port quarantine stations across Japan. Case patients, defined as travelers positive for COVID-19 on arrival, were individually matched with 4 controls for arrival date and airport or port. We assessed associations between test positivity and traveler characteristics using conditional logistic regression analysis.

Results
Overall, 157 507 travelers arriving from 146 countries/areas at 17 quarantine stations across Japan were tested for COVID-19. The percentage of test positivity during the study period was 0.35%. In the case-control study, with 536 case patients and 2144 controls, we found evidence of lower test positivity in travelers aged 3–19 years, female travelers, and travel corridor users (adjusted odds ratio [95% confidence interval], 0.36 [.22–.60], 0.71 [.56–.89], and 0.48 [.30–.77], respectively), whereas higher positivity was associated with arrival from South-East Asia (1.88 [1.33–2.65]) or lower-middle- or low-income countries (2.46 [1.69–3.58] and 7.25 [2.22–23.66], respectively), any symptom (4.08 [1.43–11.65]), and nasopharyngeal compared with saliva sampling (2.75 [1.85–4.09]). A higher 14-day average incidence in the countries of stay was also associated with higher test positivity (1.64 [1.16–2.33] and 3.13 [1.88–5.23] for those from countries and areas where the 14-day average incidence was from 10 to &lt;100 and ≥100 cases per million, respectively).

Conclusions
These findings justify travel restrictions based on the epidemic situation in countries of stay, although underestimation of the epidemic in lower-income countries should be considered. A strict travel corridor could also reduce the risk of COVID-19 importation.
Reintervention rates following bioprosthetic surgical aortic valve replacement—a Danish Nationwide Cohort Study
Authors: Schmiegelow Michelle D S , Elming Hanne , Sibilitz Kirstine L , Bruun Niels E , Carranza Christian L , Dahl Jordi S , Fosbøl Emil , Køber Lars , Torp-Pedersen Christian , Schmiegelow Søren S 
Published: July 2021

Abstract

OBJECTIVES
Updated European guidelines recommend annual echocardiographic evaluation after bioprosthetic surgical aortic valve replacement (bio-SAVR). Given the increased demand on health care resources, only clinically relevant controls can be prioritized. We therefore aimed to explore reintervention rates following bio-SAVR.

METHODS
From the nationwide Danish Register of Surgical Procedures, we identified all patients ≥40 years with isolated bio-SAVR ± concomitant coronary artery bypass graft surgery (CABG) during 2000–2016. In 90-day reintervention-free survivors, we assessed aortic valve reintervention rates (primary outcome) and all-cause mortality rates (secondary outcome) at 1, 3 and 5 years with total follow-up until 31 December 2017 and further estimated annual theoretical echocardiographic control visits.

RESULTS
In 10 518 patients with bio-SAVR (+CABG 39.7%), we observed low reintervention rates at 1, 3 and 5 years, but with high rates of all-cause mortality; i.e. 5-year reintervention rate of 3.7/1000 person-years (≤1.5%) and 5-year mortality rate of 21.7/1000 person-years. Accounting for the competing risk of death, 5-year rates were inversely related to age group and remained relatively low across all age categories but increased gradually in the long term. A significant proportion of reinterventions were presumed due to infectious endocarditis (48% at 3 years, 37% at 5 years). With annual transthoracic echocardiography, the theoretical ratio of echocardiographies per reintervention in the first 5 years was 248, and 425 when endocarditis events were excluded.

CONCLUSION
Reintervention rates within the first 5 years following bio-SAVR were relatively rare, and with a substantial number due to endocarditis.
Strong host-specific selection and over-dominance characterize arbuscular mycorrhizal fungal root colonizers of coastal sand dune plants of the Mediterranean region
Authors: Tsiknia M , Skiada V , Ipsilantis I , Vasileiadis S , Kavroulakis N , Genitsaris S , Papadopoulou K K , Hart M , Klironomos J , Karpouzas D G , Ehaliotis C 
Published: July 2021

Abstract
Sand dunes of the Mediterranean region constitute drought-stressed, low-fertility ecosystems. Arbuscular mycorrhizal fungi (AMF) are regarded as key components of their biota, that contribute to plant host adaptation and fitness. However, AMF community assembly rules in the roots of the psammophilous plants of coastal sand dunes have not been investigated. We studied the root colonizing AMF communities of four characteristic native plants of eastern Mediterranean coastal foredunes, in nine locations in Greece. Host specificity (plant identity) was the major driver of AMF community assembly in the plant roots, while geographical distance between locations was not related to differences in the AMF communities. Additionally, colonizer AMF communities were characterized by overdominance of a single OTU which was remarkably host-specific among locations. Wider dissimilarity in AMF communities was observed in small and disturbed (SD) sites compared to large and undisturbed (LU) sites, a trait that may be attributed to relaxed environmental filtering and facilitated AMF dispersal/immigration in SD sites from surrounding habitats. Overall, our results indicate that the assembly of root-colonizing AMF communities in the eastern Mediterranean sand dunes is characterized by strong biotic filtering (host identity), suggesting that co-adaptation processes may be more pronounced than previously proposed, under extreme environmental conditions.
Utilization of ethanol for itaconic acid biosynthesis by engineered Saccharomyces cerevisiae
Authors: Xu Yaying , Li Zhimin 
Published: July 2021

ABSTRACT
In Saccharomyces cerevisiae, ethanol can serve as both a carbon source and NADH donor for the production of acetyl-CoA derivatives. Here we investigated the metabolic regulation of ethanol utilization for itaconic acid production by S. cerevisiae. To understand the interconnection between the TCA cycle and the glyoxylate pathway, mitochondrial membrane transporter proteins SFC1, YHM2, CTP1, DIC1 and MPC1 were knocked out and results showed that SFC1 functions as an important entrance of the glyoxylate pathway into the TCA cycle, and YHM2 is helpful to IA production but not the primary pathway for citric acid supply. To decrease the accumulation of acetic acid, the major ADP/ATP carrier of the mitochondrial inner membrane, AAC2, was upregulated and determined to accelerate ethanol utilization and itaconic acid production. RNA sequencing results showed that AAC2 overexpression enhanced IA titer by upregulating the ethanol-acetyl-CoA pathway and NADH oxidase in the mitochondrial membrane. RNA-seq analysis also suggested that aconitase ACO1 may be a rate-limiting step of IA production. However, the expression of exogenous aconitase didn't increase IA production but enhanced the rate of ethanol utilization and decreased cell growth.
Gradient-boosted equivalent sources
Authors: Soler Santiago R , Uieda Leonardo 
Published: July 2021

SUMMARY
The equivalent source technique is a powerful and widely used method for processing gravity and magnetic data. Nevertheless, its major drawback is the large computational cost in terms of processing time and computer memory. We present two techniques for reducing the computational cost of equivalent source processing: block-averaging source locations and the gradient-boosted equivalent source algorithm. Through block-averaging, we reduce the number of source coefficients that must be estimated while retaining the minimum desired resolution in the final processed data. With the gradient-boosting method, we estimate the sources coefficients in small batches along overlapping windows, allowing us to reduce the computer memory requirements arbitrarily to conform to the constraints of the available hardware. We show that the combination of block-averaging and gradient-boosted equivalent sources is capable of producing accurate interpolations through tests against synthetic data. Moreover, we demonstrate the feasibility of our method by gridding a gravity data set covering Australia with over 1.7 million observations using a modest personal computer.
Spinal cord injury during selective cerebral perfusion and segmental artery occlusion: an experimental study
Authors: Honkanen Hannu-Pekka , Mustonen Caius , Tuominen Hannu , Kiviluoma Kai , Anttila Vesa , Juvonen Tatu 
Published: July 2021

Abstract OBJECTIVESSince selective cerebral perfusion (SCP) has been used in aortic arch surgical procedures, the core temperature during lower body circulatory arrest (LBCA) has been steadily rising. Simultaneously, the use of a frozen elephant trunk (FET) graft has been increasing. The safe period of LBCA in relation to spinal cord ischaemic tolerance in combination with segmental artery occlusion by the FET procedure has not been defined.METHODSSixteen pigs were assigned to undergo 65 (n = 10) or 90 min (n = 6) of SCP at 28°C with LBCA in combination with occlusion of the 8 uppermost segmental arteries in the thoracic (Th) aorta (15–20 cm FET, Th8-level). The follow-up period consisted of a 6-h intensive period and a 5-day observation period. Near-infrared spectroscopy of the collateral network was used to determine spinal cord oxygenation. The neurological status of the patients was evaluated daily, and the brain and the spinal cord were harvested for a histopathological analysis.RESULTSFive out of 6 pigs after 90 min and 1 out of 10 pigs after 65 min of LBCA died within 48 h of multiorgan failure. Of the survivors in the 65-min group, 6 out of 9 had paraparesis/paraplegia; the remaining 3 reached normal function. The lone survivor after 90 min of LBCA was paraplegic. Nadir near-infrared spectroscopy of the collateral network values at Th8 and Th10 were 34 (±5) and 39 (±4), and they were reached within 35 min of SCP in both groups.CONCLUSIONSAn extended FET graft with LBCA and SCP durations &gt;65 min at 28°C results in a poor outcome.
Potential test-negative design study bias in outbreak settings: application to Ebola vaccination in Democratic Republic of Congo
Authors: Pearson Carl A B , Edmunds W John , Hladish Thomas J , Eggo Rosalind M 
Published: July 2021

Abstract

Background
Infectious disease outbreaks present unique challenges to study designs for vaccine evaluation. Test-negative design (TND) studies have previously been used to estimate vaccine effectiveness and have been proposed for Ebola virus disease (EVD) vaccines. However, there are key differences in how cases and controls are recruited during outbreaks and pandemics of novel pathogens, whcih have implications for the reliability of effectiveness estimates using this design.

Methods
We use a modelling approach to quantify TND bias for a prophylactic vaccine under varying study and epidemiological scenarios. Our model accounts for heterogeneity in vaccine distribution and for two potential routes to testing and recruitment into the study: self-reporting and contact-tracing. We derive conventional and hybrid TND estimators for this model and suggest ways to translate public health response data into the parameters of the model.

Results
Using a conventional TND study, our model finds biases in vaccine effectiveness estimates. Bias arises due to differential recruitment from self-reporting and contact-tracing, and due to clustering of vaccination. We estimate the degree of bias when recruitment route is not available, and propose a study design to eliminate the bias if recruitment route is recorded.

Conclusions
Hybrid TND studies can resolve the design bias with conventional TND studies applied to outbreak and pandemic response testing data, if those efforts collect individuals’ routes to testing. Without route to testing, other epidemiological data will be required to estimate the magnitude of potential bias in a conventional TND study. Since these studies may need to be conducted retrospectively, public health responses should obtain these data, and generic protocols for outbreak and pandemic response studies should emphasize the need to record routes to testing.
Home Medicines Review and frailty among community-dwelling older women
Authors: Thiruchelvam Kaeshaelya , Byles Julie , Hasan Syed Shahzad , Egan Nicholas , Kairuz Therese 
Published: July 2021

Abstract

Objectives
Home Medicines Reviews (HMRs) can optimize medications for frail older adults. This study aimed to determine the use of HMRs according to frailty status and the association between frailty and use of HMRs.

Methods
The study included 9139 female participants enrolled in the Australian Longitudinal Study on Women’s Health from 2003 (aged 77–82 years) to 2017 (aged 91–96 years). Generalized estimating equations (GEEs) using log-binomial regressions were used to determine associations using repeated measures on individuals over time.

Key findings
The majority of participants in the study remained non-frail and did not receive HMRs from 2003 [7116 (77.86%)] to 2017 [1240 (71.31%)]. The use of HMRs was low in both groups with 33 (1.68%; 95% CI, 1.16 to 2.36) frail and 64 (0.89%; 95% CI, 0.69 to 1.14) non-frail participants receiving HMRs in 2003; by 2017, 19 (4.19%; 95% CI, 2.54 to 6.46) frail and 45 (3.50%; 95% CI, 2.57 to 4.66) non-frail participants received HMRs. Frailty was not associated with receiving a HMR (RR 1.06; 95% CI, 0.95 to 1.20), although for every 1-year increase, participants were 10% more likely to receive a HMR (RR 1.10; 95% CI, 1.09 to 1.11). Participants with continuous polypharmacy, ≥4 chronic diseases, &gt;4 general practitioner visits and Department of Veterans Affairs coverage were more likely to receive a HMR.

Conclusions
Despite the proven value of HMRs for frail older people, HMRs were not used for most frail and non-frail community-dwelling women in this study. Reasons for low use of the service should be explored, with interventions to raise awareness of the benefits of the service.