bluuebunny/crossref_metadata_2025_split huggingface dataset:
Integrative survival analysis of breast cancer with gene expression and DNA methylation data
Authors: Bichindaritz Isabelle , Liu Guanghui , Bartlett Christopher 
Published: March 2021

Abstract

Motivation
Integrative multi-feature fusion analysis on biomedical data has gained much attention recently. In breast cancer, existing studies have demonstrated that combining genomic mRNA data and DNA methylation data can better stratify cancer patients with distinct prognosis than using single signature. However, those existing methods are simply combining these gene features in series and have ignored the correlations between separate omics dimensions over time.

Results
In the present study, we propose an adaptive multi-task learning method, which combines the Cox loss task with the ordinal loss task, for survival prediction of breast cancer patients using multi-modal learning instead of performing survival analysis on each feature dataset. First, we use local maximum quasi-clique merging (lmQCM) algorithm to reduce the mRNA and methylation feature dimensions and extract cluster eigengenes respectively. Then, we add an auxiliary ordinal loss to the original Cox model to improve the ability to optimize the learning process in training and regularization. The auxiliary loss helps to reduce the vanishing gradient problem for earlier layers and helps to decrease the loss of the primary task. Meanwhile, we use an adaptive weights approach to multi-task learning which weighs multiple loss functions by considering the homoscedastic uncertainty of each task. Finally, we build an ordinal cox hazards model for survival analysis and use long short-term memory (LSTM) method to predict patients’ survival risk. We use the cross-validation method and the concordance index (C-index) for assessing the prediction effect. Stringent cross-verification testing processes for the benchmark dataset and two additional datasets demonstrate that the developed approach is effective, achieving very competitive performance with existing approaches.

Availability and implementation
https://github.com/bhioswego/ML_ordCOX.
Quantitative proteomics identifies FOLR1 to drive sorafenib resistance via activating autophagy in hepatocellular carcinoma cells
Authors: Chu Hongwei , Wu Changqing , Zhao Qun , Sun Rui , Yang Kuo , Zhao Baofeng , Liu Yang , Liang Zhen , Zhong Shijun , Zhang Lihua , Zhang Yukui 
Published: March 2021

AbstractSorafenib is commonly used to treat advanced human hepatocellular carcinoma (HCC). However, clinical efficacy has been limited by drug resistance. In this study, we used label-free quantitative proteomic analysis to systematically investigate the underlying mechanisms of sorafenib resistance in HCC cells. A total of 1709 proteins were confidently quantified. Among them, 89 were differentially expressed and highly enriched in the processes of cell–cell adhesion, negative regulation of apoptosis, response to drug and metabolic processes involving in sorafenib resistance. Notably, folate receptor α (FOLR1) was found to be significantly upregulated in resistant HCC cells. In addition, in vitro studies showed that overexpression of FOLR1 decreased the sensitivity of HCC cells to sorafenib, whereas siRNA-directed knockdown of FOLR1 increased the sensitivity of HCC cells to sorafenib. Immunoprecipitation-mass spectrometry analysis suggested a strong link between FOLR1 and autophagy-related proteins. Further biological experiments found that FOLR1-related sorafenib resistance was accompanied by the activation of autophagy, whereas inhibition of autophagy significantly reduced FOLR1-induced cell resistance. These results suggest the driving role of FOLR1 in HCC resistance to sorafenib, which may be exerted through FOLR1-induced autophagy. Therefore, this study may provide new insights into understanding the mechanism of sorafenib resistance.
Biodiesel production by the electrocatalytic process: a review
Authors: Thangaraj Baskar , Solomon Pravin Raj 
Published: March 2021

Abstract
Biodiesel—an impressive alternative fuel with favourable physico-chemical properties having environmental benefits—is prepared from vegetable oil. However, the cost is one of the main hurdles in commercializing it. Its production by conventional transesterification processes needs high ambient temperature and a specialized catalyst. Due to the multifaceted adversities of many of the catalysts, there is active consideration for an electrocatalytic process that does not require elevated temperature. In addition, an electrocatalytic process is carried out in the presence or absence of a catalyst or co-solvent. In this review, various parameters such as electrolysis voltage, stirring rate, electrode type, water content, co-solvent type, reaction temperature, reaction duration, oil-to-methanol molar ratio and concentration of NaCl affecting the electrocatalytic transesterification process are presented.
Salvage Therapy with Sofosbuvir/Velpatasvir/Voxilaprevir in DAA-experienced Patients: Results from a Prospective Canadian Registry
Authors: Onofrio Fernanda Q , Cooper Curtis , Borgia Sergio M , Vachon Marie-Louise , Ramji Alnoor , Lilly Leslie B , Wong Alexander , Booth Joshua , Sattar Izza , Morales Heidy , Lee Samuel , Conway Brian , Feld Jordan J 
Published: March 2021

AbstractBackgroundDespite the current highly effective therapies with direct-acting antiviral agents (DAAs), some patients with chronic hepatitis C virus (HCV) infection still do not achieve sustained virological response (SVR) and require retreatment. Sofosbuvir/velpatasvir/voxilaprevir (SVV) is recommended as the first-line retreatment option for most patients. The aim of this study was to evaluate the efficacy of SVV as salvage therapy after at least one course of DAA.MethodsData were collected on all HCV-infected patients who failed DAAs and were prescribed SVV from a prospective Canadian registry (CANUHC) including 17 sites across Canada. Factors associated with failure to achieve SVR with SVV therapy and the utility of RAS testing and ribavirin use were evaluated.ResultsA total of 128 patients received SVV after non-SVR with DAA treatment: 80% male, median age 57.5 (31–86), 44% cirrhotic, and 17 patients post liver transplant. First line regimens included: sofosbuvir/velpatasvir (27.3%), sofosbuvir/ledipasvir (26.5%), grazoprevir/elbasvir (12.5%), other (33.5%). Ribavirin was added to SVV in 26 patients due to past sofosbuvir/velpatasvir use (n = 8), complex resistance associated substitution profiles (n = 16) and/or cirrhosis (n = 9). Overall SVR rate was 96% (123/128). Of 35 patients who previously failed sofosbuvir/velpatasvir, 31 (88.5%) achieved SVR compared to 92 of 93 (99%) among those receiving any other regimen (P = .01).ConclusionsSimilar to reports from phase 3 clinical trials, SVV proved highly effective as salvage therapy for patients who failed a previous DAA therapy. Those who failed SVV had at least 2 of the following factors: genotype 3, presence of cirrhosis, past liver transplantation, past exposure to sofosbuvir/velpatasvir and/or complex resistance profiles.
Antibody and Antigen Prevalence as Indicators of Ongoing Transmission or Elimination of Visceral Leishmaniasis: A Modeling Study
Authors: Coffeng Luc E , Le Rutte Epke A , Munoz Johanna , Adams Emily , de Vlas Sake J 
Published: March 2021

Abstract

Background
Control of visceral leishmaniasis (VL) on the Indian subcontinent has been highly successful. Control efforts such as indoor residual spraying and active case detection will be scaled down or even halted over the coming years. We explored how after scale-down, potential recurrence of VL cases may be predicted based on population-based surveys of antibody or antigenemia prevalence.

Methods
Using a stochastic age-structured transmission model of VL, we predicted trends in case incidence and biomarker prevalence over time after scaling down control efforts when the target of 3 successive years without VL cases has been achieved. Next, we correlated biomarker prevalence with the occurrence of new VL cases within 10 years of scale-down.

Results
Occurrence of at least 1 new VL case in a population of 10 000 was highly correlated with the seroprevalence and antigenemia prevalence at the moment of scale-down, or 1 or 2 years afterward. Receiver operating characteristic curves indicated that biomarker prevalence in adults provided the most predictive information, and seroprevalence was a more informative predictor of new VL cases than antigenemia prevalence. Thresholds for biomarker prevalence to predict occurrence of new VL cases with high certainty were robust to variation in precontrol endemicity.

Conclusions
The risk of recrudescence of VL after scaling down control efforts can be monitored and mitigated by means of population-based surveys. Our findings highlight that rapid point-of-care diagnostic tools to assess (preferably) seroprevalence or (otherwise) antigenemia in the general population could be a key ingredient of sustainable VL control.
2-Nonanone is a Critical Pheromone Component for Cerambycid Beetle Species Native to North and South America
Authors: Silva Weliton D , Hanks Lawrence M , Mongold-Diers Judith A , Grommes Anna C , Bento José Maurício S , Millar Jocelyn G 
Published: March 2021

Abstract
An increasing body of evidence indicates that cerambycid beetles native to different continents may share pheromone components, suggesting that these compounds arose as pheromone components early in the evolution of the family. Here, we describe the identification and field testing of the pheromone blends of two species in the subfamily Cerambycinae that share 2-nonanone as an important component of their male-produced aggregation-sex pheromones, the South American Stizocera consobrina Gounelle (tribe Elaphidiini) and the North American Heterachthes quadrimaculatus Haldeman (tribe Neoibidionini). Along with 2-nonanone, males of S. consobrina also produce 1-(1H-pyrrol-2-yl)-1,2-propanedione, whereas males of H. quadrimaculatus produce 10-methyldodecanol. Field bioassays conducted in Brazil (targeting S. consobrina) and Illinois (targeting H. quadrimaculatus) demonstrated that adults of both species were attracted only by the blends of both their pheromone components, and not to the individual components. The use of the pyrrole as a critical component for the former species is further evidence that this compound is a common pheromone structure among cerambycines in different biogeographical regions of the world.
Educational interventions using a primer and motivational interviewing: randomized clinical trial
Authors: Sabino Leidiane Minervina M de , Ferreira Ádria Marcela V , Mendes Elizamar Regina R , Melo Emanuella S J , Penha Jardeliny C , Lima Kamila F , Nascimento Ludmila A do , Lima Francisca Elisângela T , Melo Regina Claúdia de , de Almeida Paulo César , Barbosa Lorena P 
Published: March 2021

Abstract

Background
Many educational technologies have been used to promote the health of the population. Thus, the objective was to assess the effect of using an individual educational primer along with the Brief Motivational Interviewing (BMI) for increasing maternal self-efficacy for preventing childhood diarrhoea.

Methods
Randomized clinical trial, conducted in Fortaleza/Ceará—Brazil, composed of 181 mothers and/or guardians of children under five years, who were randomized into three groups: experimental group A (EG A)—who read the primer, experimental group B (EG B)—application of the primer and BMI and the control group (CG). The participants’ assessment was based on the Maternal Self-Efficacy Scale for Preventing Childhood Diarrhoea and the diarrhoea Investigation Form at the beginning of the intervention and then 30 and 60 days after the first contact with the participants.

Results
There were 60 participants in EG A and CG and 61 in EG B. It was noted a greater incidence of participants with high self-efficacy in EG B after applying the technologies. All groups manifested diarrhoea among children after the interventions, although with a lower number in EG B, one-month post-intervention (P = 0.025).

Conclusions
The combined use of the primer and the BMI contributed significantly over time to increase maternal self-efficacy in preventing childhood diarrhoea and reduce cases of this disease.
Characterizing the culturable surface microbiomes of diverse marine animals
Authors: Keller Abigail G , Apprill Amy , Lebaron Philippe , Robbins Jooke , Romano Tracy A , Overton Ellysia , Rong Yuying , Yuan Ruiyi , Pollara Scott , Whalen Kristen E 
Published: March 2021

ABSTRACT
Biofilm-forming bacteria have the potential to contribute to the health, physiology, behavior and ecology of the host and serve as its first line of defense against adverse conditions in the environment. While metabarcoding and metagenomic information furthers our understanding of microbiome composition, fewer studies use cultured samples to study the diverse interactions among the host and its microbiome, as cultured representatives are often lacking. This study examines the surface microbiomes cultured from three shallow-water coral species and two whale species. These unique marine animals place strong selective pressures on their microbial symbionts and contain members under similar environmental and anthropogenic stress. We developed an intense cultivation procedure, utilizing a suite of culture conditions targeting a rich assortment of biofilm-forming microorganisms. We identified 592 microbial isolates contained within 15 bacterial orders representing 50 bacterial genera, and two fungal species. Culturable bacteria from coral and whale samples paralleled taxonomic groups identified in culture-independent surveys, including 29% of all bacterial genera identified in the Megaptera novaeangliae skin microbiome through culture-independent methods. This microbial repository provides raw material and biological input for more nuanced studies which can explore how members of the microbiome both shape their micro-niche and impact host fitness.
Multiphenomenology explosion monitoring (MultiPEM): a general framework for data interpretation and yield estimation
Authors: Williams Brian J , Brug W Patrick , Casleton Emily M , Syracuse Ellen M , Blom Philip S , Meierbachtol Collin S , Stead Richard J , MacLeod Gordon A , Bauer Amy L , Shao Xuan-Min , Anderson Dale N 
Published: March 2021

SUMMARYAn underground nuclear explosion (UNE) couples mechanical energy into crustal rock, which propagates as seismic and acoustic waves. These different physical phenomena transport, by different pathways, to standoff detectors at varying distances. The transport pathways attenuate the original signal but in different ways. Enabled by correct statistical weighting, signal attenuation models can be used to combine these disparate sensor data to estimate the yield of an UNE. Contemporaneous statistical models, used in yield estimation, can be improved with an advanced partition of error for these physical signal propagation models. We present an advanced multivariate approach to error modelling of multiphenomenology physical signatures. In addition to measurement error, our error model represents physical model biases as random with a physics-based covariance structure. To illustrate this proposed framework, we demonstrate the estimation of explosion yield using openly available seismic and acoustic data from chemical single-point explosions.
Longitudinal Assessment of Anti-Severe Acute Respiratory Syndrome Coronavirus 2 Immune Responses for Six Months Based on the Clinical Severity of Coronavirus Disease 2019
Authors: Noh Ji Yun , Kwak Jeong-Eun , Yang Jeong-Sun , Hwang Soon Young , Yoon Jin Gu , Seong Hye , Hyun Hakjun , Lim Chae Seung , Yoon Soo-Young , Ryou Jungsang , Lee Joo-Yeon , Kim Sung-Soon , Park Su-Hyung , Cheong Hee Jin , Kim Woo Joo , Shin Eui-Cheol , Song Joon Young 
Published: March 2021

Abstract

Background
There is insufficient data on the longevity of immunity acquired after severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection.

Methods
We aimed to evaluate the duration of SARS-CoV-2-specific humoral and cellular immunity according to the clinical severity of coronavirus disease 2019 (COVID-19). The study population comprised asymptomatic (n = 14), symptomatic/nonpneumonic (n = 42), and pneumonic (n = 41) patients.

Results
The anti-SARS-CoV-2 immunoglobulin class G and neutralizing antibody (NAb) titers lasted until 6 months after diagnosis, with positivity rates of 66.7% and 86.9%, respectively. Older age, prolonged viral shedding, and accompanying pneumonia were more frequently found in patients with sustained humoral immunity. Severe acute respiratory syndrome coronavirus 2-specific T-cell response was strongly observed in pneumonic patients and prominent in individuals with sustained humoral immunity.

Conclusions
In conclusion, most (&gt;85%) patients carry NAb until 6 months after diagnosis of SARS-CoV-2 infection, providing insights for establishing vaccination strategies against COVID-19.
Antimicrobial resistance during the COVID-19 pandemic: the missing patient perspective
Authors: Dahal Deepa , Sundar Swarna , Kullar Ravina , Milevska-Kostova Neda , Dindial Karen 
Published: March 2021

Abstract
While the use of antibiotics for secondary infections in COVID-19 has been described in scientific literature and guidelines have been issued for their appropriate use, the importance of listening to patients in a systematic manner has often been overlooked. To highlight this issue, we spoke with patients about their experiences with antibiotics as treatment for COVID-19 and their understanding of antimicrobial resistance (AMR). We found that there is a general lack of awareness of the risks of AMR, and even when patients are knowledgeable, fear of COVID-19 and pressure from healthcare providers often override considerations for appropriate use. We present case examples of three patients’ experiences and provide recommendations for health systems, healthcare providers, and patients or caregivers on actions they can each take to reduce the risk of AMR during and beyond the COVID-19 pandemic. We also share ways that the patient community can be empowered to provide their voices to decision-making on both COVID-19 treatment protocols and prescriptions of antibiotics.
Performance of an Advanced Interferon-Gamma Release Assay forMycobacterium tuberculosisDetection
Authors: Altawallbeh Ghaith , Gabrielson Deanna , Peters Jennifer M , Killeen Anthony A 
Published: March 2021

AbstractBackgroundThe LIAISON® QuantiFERON®-TB Gold Plus (QFT-Plus) assay, a fully automated chemiluminescence immunoassay (CLIA) system, has recently received FDA approval for the detection of interferon-γ (IFN-γ) on the LIAISON XL analyzer. Here, we evaluated the diagnostic performance of the LIAISON’s CLIA method in comparison to the widely used ELISA method using the Qiagen QuantiFERON-TB Gold Plus Blood Collection Tubes.MethodsHeparinized blood samples from 329 participants were categorized into 3 cohorts, including 15 with confirmed tuberculosis (TB) (active TB cohort), 129 non-TB (low-risk cohort), and 185 potential TB (mixed risk cohort). Samples were analyzed with both assays and results were interpreted according to the manufacturers’ criteria.ResultsThe LIAISON CLIA assay showed an overall agreement with the Qiagen ELISA assay in 13/14 (92.8%) samples among the active cohort, 93/95 (97.9%) among the low-risk cohort, with a Cohen’s kappa value of 0.76 and 0.74, respectively. Test results for 185 mixed risk cohort participants showed 97.8% agreement between the LIAISON and the Qiagen, with 17 positive, 163 negative, and 1 indeterminate. Four samples were discrepant; 3 of these were negative on the ELISA but positive on the CLIA assay.ConclusionOverall, the results were comparable (&gt;92% agreement) in our study cohorts. In addition, our mixed risk cohort results showed an excellent agreement of 0.88 (Cohen’s kappa value) between the 2 assays. These findings suggest that the automated LIAISON QFT-Plus assay has a comparable diagnostic performance to the Qiagen assay and can be used for latent TB infection (LTBI) diagnosis.
Evaluating the Biological Potential of Prodigiosin from Serratia Marcescens KH-001 Against Asian Citrus Psyllid
Authors: Hu Wei , Zheng Rongkun , Liao Yihong , Kuang Fan , Yang Zhaolan , Chen Tingtao , Zhang Ning 
Published: March 2021

Abstract
The insecticides of microbial origin may be promising biocontrol agents to control pests. In this study, a major metabolite was extracted and purified from Serratia marcescens KH-001 and identified as prodigiosin with a molecule weight of 324.2094, and our primary aim was to evaluate the effects of prodigiosin against Diaphorina citri Kuwayama (Hemiptera: Liviidae) in the laboratory and in the field. Toxicity of purified prodigiosin to nymphs increased with increasing temperature from 25 to 35°C. The laboratory experiment results observed inhibition effects of purified prodigiosin at LC50 on oviposition and egg hatch of D. citri at 30°C. Furthermore, adults that fed on citrus leaves treated with LC20 and LC50 solution of purified prodigiosin at 30°C excreted less honeydew (28–35%) compared with controls, suggesting moderate antifeedant activity of prodigiosin. The results of field experiment showed that 10% prodigiosin emulsifiable concentrate exhibited better control efficacy (70–100%) at three concentrations (100, 200, and 500 mg/liter) in July and August than in October. These data indicate that prodigiosin will be a highly effective compound for the control of D. citri depending on the prevailing temperature conditions and may become a commercially available product to be widely used in citrus orchards.
In the name of public health: misoprostol and the new criminalization of abortion in Brazil
Authors: Assis Mariana Prandini , Erdman Joanna N 
Published: March 2021

Abstract
This article explores the criminal regulation of misoprostol as a controlled drug in Brazil as a new form of abortion criminalization. A qualitative analysis of Brazilian case law shows how the courts use a public health rhetoric of unsafe abortion to criminalize the distribution of misoprostol in the informal sector. Rather than an invention of the local bench, this judicial rhetoric reflects global public health discourse and policy on unsafe abortion and the double life of misoprostol as both an essential medicine and a controlled drug. In contrast to previous studies, the article shows that abortion criminalization is not the cause, but rather the consequence of misoprostol’s double life. In the last section, it draws on an outlier judgment of the case law to chart a regulatory future for misoprostol and its supply in the informal sector as a site of harm reduction and safe abortion in public health policy.
The Impact of Social Distancing for COVID-19 Upon Diagnosis of Kawasaki Disease
Authors: Shulman Stanford , Geevarghese Bessey , Kim Kwang-Youn , Rowley Anne 
Published: March 2021

Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) mitigation policies have been associated with profound decreases in diagnoses of common childhood respiratory infections. A leading theory of etiology of Kawasaki disease (KD) is that it is triggered by presently unidentified ubiquitous respiratory agent. We document that mitigation policies instituted in mid-March 2020 were associated with strikingly fewer diagnoses of KD in April-December 2020 compared with the same period in the previous 8 years (P = .01), a &gt;67% decline. This finding supports the hypothesis that KD is caused by a respiratory-transmitted agent.