bluuebunny/crossref_metadata_2025_split huggingface dataset:
Research on RNA secondary structure predicting via bidirectional recurrent neural network
Authors: Lu Weizhong , Cao Yan , Wu Hongjie , Ding Yijie , Song Zhengwei , Zhang Yu , Fu Qiming , Li Haiou 
Published: September 2021

Abstract
Background
RNA secondary structure prediction is an important research content in the field of biological information. Predicting RNA secondary structure with pseudoknots has been proved to be an NP-hard problem. Traditional machine learning methods can not effectively apply protein sequence information with different sequence lengths to the prediction process due to the constraint of the self model when predicting the RNA secondary structure. In addition, there is a large difference between the number of paired bases and the number of unpaired bases in the RNA sequences, which means the problem of positive and negative sample imbalance is easy to make the model fall into a local optimum. To solve the above problems, this paper proposes a variable-length dynamic bidirectional Gated Recurrent Unit(VLDB GRU) model. The model can accept sequences with different lengths through the introduction of flag vector. The model can also make full use of the base information before and after the predicted base and can avoid losing part of the information due to truncation. Introducing a weight vector to predict the RNA training set by dynamically adjusting each base loss function solves the problem of balanced sample imbalance.

Results
The algorithm proposed in this paper is compared with the existing algorithms on five representative subsets of the data set RNA STRAND. The experimental results show that the accuracy and Matthews correlation coefficient of the method are improved by 4.7% and 11.4%, respectively.

Conclusions
The flag vector introduced allows the model to effectively use the information before and after the protein sequence; the introduced weight vector solves the problem of unbalanced sample balance. Compared with other algorithms, the LVDB GRU algorithm proposed in this paper has the best detection results.
Transcriptional responses to Fusarium oxysporum f. sp. lycopersici (Sacc.) Snyder & Hansen infection in three Colombian tomato cultivars
Authors: López Walter Ricardo , Garcia-Jaramillo Dora Janeth , Ceballos-Aguirre Nelson , Castaño-Zapata Jairo , Acuña-Zornosa Ricardo , Jovel Juan 
Published: September 2021

Abstract
Background
Fusarium oxysporum f. sp. lycopersici (Fol) is a compendium of pathogenic and non-pathogenic fungal strains. Pathogenic strains may cause vascular wilt disease and produce considerable losses in commercial tomato plots. To gain insight into the molecular mechanisms mediating resistance to Fol in tomato, the aim of our study was to characterize the transcriptional response of three cultivars (CT1, CT2 and IAC391) to a pathogenic (Fol-pt) and a non-pathogenic (Fo-npt) strain of Fo.

Results
All cultivars exhibited differentially expressed genes in response to each strain of the fungus at 36 h post-inoculation. For the pathogenic strain, CT1 deployed an apparent active defense response that included upregulation of WRKY transcription factors, an extracellular chitinase, and terpenoid-related genes, among others. In IAC391, differentially expressed genes included upregulated but mostly downregulated genes. Upregulated genes mapped to ethylene regulation, pathogenesis regulation and transcription regulation, while downregulated genes potentially impacted defense responses, lipid transport and metal ion binding. Finally, CT2 exhibited mostly downregulated genes upon Fol-pt infection. This included genes involved in transcription regulation, defense responses, and metal ion binding.

Conclusions
Results suggest that CT1 mounts a defense response against Fol-pt. IAC391 exhibits an intermediate phenotype whereby some defense response genes are activated, and others are suppressed. Finally, the transcriptional profile in the CT2 hints towards lower levels of resistance. Fo-npt also induced transcriptional changes in all cultivars, but to a lesser extent. Results of this study will support genetic breeding programs currently underway in the zone.
Circulatory trajectories after out-of-hospital cardiac arrest: a prospective cohort study
Authors: Langeland Halvor , Bergum Daniel , Nordseth Trond , Løberg Magnus , Skaug Thomas , Bjørnstad Knut , Gundersen Ørjan , Skjærvold Nils-Kristian , Klepstad Pål 
Published: September 2021

Abstract
Background
Circulatory
failure frequently occurs after out-of-hospital cardiac arrest (OHCA) and is part of post-cardiac arrest syndrome (PCAS). The aim of this study was to investigate circulatory disturbances in PCAS by assessing the circulatory trajectory during treatment in the intensive care unit (ICU).

Methods
This was a prospective single-center observational cohort study of patients after OHCA. Circulation was continuously and invasively monitored from the time of admission through the following five days. Every hour, patients were classified into one of three predefined circulatory states, yielding a longitudinal sequence of states for each patient. We used sequence analysis to describe the overall circulatory development and to identify clusters of patients with similar circulatory trajectories. We used ordered logistic regression to identify predictors for cluster membership.

Results
Among 71 patients admitted to the ICU after OHCA during the study period, 50 were included in the study. The overall circulatory development after OHCA was two-phased. Low cardiac output (CO) and high systemic vascular resistance (SVR) characterized the initial phase, whereas high CO and low SVR characterized the later phase. Most patients were stabilized with respect to circulatory state within 72 h after cardiac arrest. We identified four clusters of circulatory trajectories. Initial shockable cardiac rhythm was associated with a favorable circulatory trajectory, whereas low base excess at admission was associated with an unfavorable circulatory trajectory.

Conclusion
Circulatory failure after OHCA exhibits time-dependent characteristics. We identified four distinct circulatory trajectories and their characteristics. These findings may guide clinical support for circulatory failure after OHCA.

Trial registration

ClinicalTrials.gov: NCT02648061
Rapid diagnosis of SARS-CoV-2 pneumonia on lower respiratory tract specimens
Authors: De Pace Vanessa , Caligiuri Patrizia , Ricucci Valentina , Nigro Nicola , Galano Barbara , Visconti Valeria , Da Rin Giorgio , Bruzzone Bianca 
Published: September 2021

Abstract
Background
The ongoing SARS-CoV-2 pandemic requires the availability of accurate and rapid diagnostic tests, especially in such clinical settings as emergency and intensive care units. The objective of this study was to evaluate the diagnostic performance of the Vivalytic SARS-CoV-2 rapid PCR kit in lower respiratory tract (LRT) specimens.

Methods
Consecutive LRT specimens (bronchoalveolar lavage and bronchoaspirates) were collected from Intensive Care Units of San Martino Hospital (Genoa, Italy) between November 2020 and January 2021. All samples underwent RT-PCR testing by means of the Allplex™ SARS-CoV-2 assay (Seegene Inc., South Korea). On the basis of RT-PCR results, specimens were categorized as negative, positive with high viral load [cycle threshold (Ct) ≤ 30] and positive with low viral load (Ct of 31–35). A 1:1:1 ratio was used to achieve a sample size of 75. All specimens were subsequently tested by means of the Vivalytic SARS-CoV-2 rapid PCR assay (Bosch Healthcare Solutions GmbH, Germany). The diagnostic performance of this assay was assessed against RT-PCR through the calculation of accuracy, Cohen’s κ, sensitivity, specificity and expected positive (PPV) and negative (NPV) predictive values.

Results
The overall diagnostic accuracy of the Vivalytic SARS-CoV-2 was 97.3% (95% CI: 90.9–99.3%), with an excellent Cohen’s κ of 0.94 (95% CI: 0.72–1). Sensitivity and specificity were 96% (95% CI: 86.5–98.9%) and 100% (95% CI: 86.7–100%), respectively. In samples with high viral loads, sensitivity was 100% (Table 1). The distributions of E gene Ct values were similar (Wilcoxon’s test: p = 0.070), with medians of 35 (IQR: 25–36) and 35 (IQR: 25–35) on Vivalytic and RT-PCR, respectively (Fig. 1). NPV and PPV was 92.6% and 100%, respectively.

Conclusions
Vivalytic SARS-CoV-2 can be used effectively on LRT specimens following sample liquefaction. It is a feasible and highly accurate molecular procedure, especially in samples with high viral loads. This assay yields results in about 40 min, and may therefore accelerate clinical decision-making in urgent/emergency situations.
Informing antimicrobial management in the context of COVID-19: understanding the longitudinal dynamics of C-reactive protein and procalcitonin
Authors: Ming Damien K. , Myall Ashleigh C. , Hernandez Bernard , Weiße Andrea Y. , Peach Robert L. , Barahona Mauricio , Rawson Timothy M. , Holmes Alison H. 
Published: September 2021

Abstract
Background
To characterise the longitudinal dynamics of C-reactive protein (CRP) and Procalcitonin (PCT) in a cohort of hospitalised patients with COVID-19 and support antimicrobial decision-making.

Methods
Longitudinal CRP and PCT concentrations and trajectories of 237 hospitalised patients with COVID-19 were modelled. The dataset comprised of 2,021 data points for CRP and 284 points for PCT. Pairwise comparisons were performed between: (i) those with or without significant bacterial growth from cultures, and (ii) those who survived or died in hospital.

Results
CRP concentrations were higher over time in COVID-19 patients with positive microbiology (day 9: 236 vs 123 mg/L, p < 0.0001) and in those who died (day 8: 226 vs 152 mg/L, p < 0.0001) but only after day 7 of COVID-related symptom onset. Failure for CRP to reduce in the first week of hospital admission was associated with significantly higher odds of death. PCT concentrations were higher in patients with COVID-19 and positive microbiology or in those who died, although these differences were not statistically significant.

Conclusions
Both the absolute CRP concentration and the trajectory during the first week of hospital admission are important factors predicting microbiology culture positivity and outcome in patients hospitalised with COVID-19. Further work is needed to describe the role of PCT for co-infection. Understanding relationships of these biomarkers can support development of risk models and inform optimal antimicrobial strategies.
Reduced serum albumin as a risk factor for poor prognosis in critically ill patients receiving renal replacement therapy
Authors: Zheng Lang Jing , Jiang Weiming , Pan Lingling , Pan Jingye 
Published: September 2021

Abstract
Background
Albumin is the primary body protein, which can predict the poor prognosis of several critical diseases. However, there are a few scientific studies on the relationship between albumin and the prognosis of dialysis patients. This study aims to explore the impact of hypoalbuminemia on the prognosis of critically ill patients with acute kidney injury (AKI) receiving continuous renal replacement therapy (CRRT).

Methods
This was a secondary study. Clinical, biochemical, and 28-day and 90-day mortality rates for critical patients with AKI who received CRRT between 2009 and 2016 were searched from the database to determine the effect of hypoalbuminemia on poor outcomes by univariate, multivariate, smooth curve fitting, and subgroup analysis.

Results
A total of 837 participants were enrolled in this study. Multivariate Cox proportional hazard regression analysis showed that hypoalbuminemia was associated with both 28-day and 90-day mortality risks after full adjustment for confounding variables, with an adjusted hazard ratio (95% confidence interval) of 0.63 (0.50–0.80) and 0.63 (0.51–0.78), respectively for each 1 g/dL increase of albumin. Stratified analysis showed that hypoalbuminemia was not associated with poor prognosis in oliguria.

Conclusion
Hypoalbuminemia is associated with poor prognosis in critically ill AKI patients with CRRT; therefore, measuring albumin may be helpful for predicting the prognosis. However, in those with oliguria, this conclusion is not valid.
Exosomal ERp44 derived from ER-stressed cells strengthens cisplatin resistance of nasopharyngeal carcinoma
Authors: Xia Tian , Tian Hui , Zhang Kaiwen , Zhang Siyu , Chen Wenhui , Shi Si , You Yiwen 
Published: September 2021

AbstractBackgroundNasopharyngeal carcinoma (NPC) is one of the most common malignancies in head and neck. Platinum-based chemotherapy is an important treatment for NPC. However, the molecular mechanism of resistance to platinum drug remains unknown. Endoplasmic reticulum resident protein 44(ERp44), an unfolded protein response (UPR)-induced endoplasmic reticulum(ER) protein, is induced during ER stress. This research explored the mechanism of ERp44 in strengthening cisplatin resistance in NPC.MethodsWestern blot and immunohistochemistry were used to investigate the expression of ERp44 and Glucose-Regulated Protein 78(GRP78) in NPC. We took CCK8 to detect the role of ERp44 on cell chemosensitivity. Flow cytometric analysis and western blot were taken to analyze cell apoptosis. We performed differential centrifugation to isolate exosomes from serum or conditioned media of cells and analyzed the impact of exosomal ERp44 on cells cisplatin sensitivity. Finally, the results were confirmed in vivo.ResultsWe found the increased expression of ERp44 and GRP78 in NPC and ERp44 was highly expressed in ER-stressed tissues. Cell proliferation was inhibited after cisplatin treatment when ERp44 was knocked down and ERp44 strengthened cisplatin resistance by influencing cell apoptosis and pyroptosis. Then we also collected exosomes and cell viability was increased after the addition of NPC-derived-exosomes with cisplatin treatment. More importantly, our results showed under ERS, NPC cells secreted exosomes containing ERp44 and could transfer them to adjacent cells to strengthen chemoresistance.ConclusionOur data suggested that exosomal ERp44 derived from ER-stressed NPC cells took an inevitable role in NPC chemoresistance and might act as a treatment target.
Vision screening in newborns and early childhood
Authors: Jullien Sophie 
Published: September 2021

AbstractWe looked at existing recommendations and supporting evidence on the effectiveness of screening for visual disorders in newborns and small infants, and in children between six months and five years of age.We conducted a literature search up to the 5th of August 2019 by using key terms and manual search in selected sources. We summarized the recommendations and the strength of the recommendations when and as reported by the authors. We summarized the main findings of systematic reviews with the certainty of the evidence as reported on the accuracy of screening tests for detecting visual alterations; the efficacy of treatment for improving visual acuity, school performance, and quality of life; and potential harms derived from vision screening and treating visual alterations.Although there is little evidence supporting its validity and effectiveness, examining all newborns for congenital cataract and retinoblastoma through the red reflex examination is widely accepted due to the severity of both diseases and the good outcomes reached by early detection and treatment.Overall, there is a moderate certainty of evidence that visual screening in children between three and five years provides a moderate net benefit, as assessed by the US Preventive Services Task Force: vision screening tests are accurate for detecting amblyopia and its risk factors, and their treatment is associated with visual improvement. There is uncertain evidence on whether vision screening in children under three years of age provides net benefits. Among populations with a low prevalence of vision abnormalities, screening the youngest is associated with an increased rate of false positives, leading to unnecessary additional assessment.
Screening of iron deficiency anaemia in early childhood
Authors: Jullien Sophie 
Published: September 2021

AbstractWe looked at existing recommendations and supporting evidence on the effectiveness of universal screening of iron deficiency anaemia (IDA) in children under five years of age for improving growth, cognitive function, and psychomotor development. We assessed the accuracy of the screening tests for detecting IDA, the efficacy of existing treatment for children with IDA, and the potential harms associated with screening and treatment.We conducted a literature search up to the 18th of August 2019 by using key terms and manual search in selected sources. We summarized the recommendations and the strength of the recommendation when and as reported by the authors. We summarized the main findings of systematic reviews with the certainty of the evidence as reported.There is no suitable test for IDA screening that is non-invasive with high accuracy for detecting IDA and there is uncertainty whether IDA in children causes cognitive and psychomotor delays. There is a lack of evidence on the effects of routine screening for IDA in asymptomatic children under five years of age on growth, cognitive and psychomotor development outcomes.Universal screening of IDA in children under five years of age is not recommended by most organisations such as the Spanish Association of Primary Care Paediatrics, the United Kingdom National Screening Committee, and the United States Preventive Services Task Force, but is recommended by the American Academy of Paediatrics. However, selective screening of IDA is recommended in infants and children with risk factors including prematurity, low birth weight, and dietary risk factors.
Impact of experienced HIV stigma on health is mediated by internalized stigma and depression: results from the people living with HIV stigma index in Ontario
Authors: Lo Hog Tian Jason M. , Watson James R. , Ibáñez-Carrasco Francisco , Tran Billy , Parsons Janet A. , Maunder Robert G. , Card Kiffer G. , Baral Stefan , Hui Christian , Boni Anthony R. , Ajiboye Monisola , Lindsay Joanne D. , Rourke Sean B. ,   The Ontario HIV Stigma Index Team
Published: September 2021

Abstract
Background
Experiences of HIV stigma remain prevalent across Canada, causing significant stress and negatively affecting the health and wellbeing of people living with HIV. While studies have consistently demonstrated that stigma negatively impacts health, there has been limited research on the mechanisms behind these effects. This study aims to identify which dimensions of stigma have significant relationships with self-rated health and examine the mechanisms by which those types of stigma impact self-rated health.

Methods
We recruited 724 participants to complete the People Living with HIV Stigma Index in Ontario, designed by people living with HIV to measure nuanced changes in stigma and discrimination. The present study utilizes data from externally validated measures of stigma and health risks that were included in the survey. First, we conducted multiple regression analyses to examine which variables had a significant impact on self-rated health. Results from the multiple regression guided the mediation analysis. A parallel mediation model was created with enacted stigma as the antecedent, internalized stigma and depression as the mediators, and self-rated health as the outcome.

Results
In the multiple regression analysis, internalized stigma (coefficient = −0.20, p < 0.01) and depression (coefficient = −0.07, p < 0.01) were both significant and independent predictors of health. Mediation analyses demonstrated that the relationship between enacted stigma and self-rated health is mediated in parallel by both internalized stigma [coefficient = −0.08, se = 0.03, 95% CI (−0.14, −0.02)] and depression [coefficient = −0.16, se = 0.03, 95% CI (−0.22, −0.11)].

Conclusions
We developed a mediation model to explain how HIV-related stigma negatively impacts health. We found that that enacted stigma, or experiences of prejudice or discrimination, can lead to internalized stigma, or internalization of negative thoughts regarding one’s HIV status and/or increased depressive symptoms which then may lead to worse overall health. Highlighting the importance of internalized stigma and depression has the potential to shape the development of targeted intervention strategies aimed at reducing the burden of stigma and improving the health and wellbeing of people living with HIV.
The relationship of supportive roles with mental health and satisfaction with life in female household heads in Karaj, Iran: a structural equations model
Authors: Shadabi Nooshin , Saeieh Sara Esmaelzadeh , Qorbani Mostafa , Babaheidari Touran Bahrami , Mahmoodi Zohreh 
Published: September 2021

Abstract
Background
Female household heads are faced with more problems than men due to their multiple concurrent roles. The present study was conducted to determine the relationship of supportive roles with mental health and satisfaction with life in female household heads in Karaj, Iran using a structural equations model.

Methods
The present descriptive-analytical study was conducted on 286 eligible female household heads in Karaj, Iran, in 2020, who were selected by convenience sampling. Data were collected using Vaux’s Social Support, the perceived social support scale, the general health questionnaire (GHQ), and the satisfaction with life questionnaire plus a socio-demographic checklist, and were analyzed in SPSS-16 and Lisrel-8.8.

Results
The participants’ mean age was 43.1 ± 1.7 years. According to the path analysis results, satisfaction with life had the highest direct positive relationship with perceived social support (B = 0.33) and the highest indirect positive relationship with age (B = 0.13) and the highest direct and indirect positive relationship with education and social support (B = 0.13). Also, mental health had a direct negative relationship with satisfaction with life (B = -0.29), an indirect negative relationship with social support, and both a direct and indirect negative relationship with perceived support (B = -0.26).

Conclusion
Based on the results, supportive roles had a negative relationship with mental health; in other words, mental health problems increase as supportive roles decrease. They also had a positive relationship with satisfaction with life in female household heads.
Accordingly, given the status and role of women in the health of family members and the community and their greater vulnerability, further attention and support should be directed toward these women by the government and relevant organizations like establishment of counseling-support centers.