bluuebunny/crossref_metadata_2025 huggingface dataset:
Radiological findings in low-dose CT for COVID-19 pneumonia in 182 patients
Authors: BiebaÛ Charlotte M. , Desmet Jeroen N. , Dubbeldam Adriana , Cockmartin Lesley , Coudyzer Walter M. , Coolen Johan , Verschakelen Johny A. , De Wever Walter
Published: March 2022

To characterize computed tomography (CT) findings of coronavirus disease 2019 (COVID-19) pneumonia and their value in outcome prediction.

Chest CTs of 182 patients with a confirmed diagnosis of COVID-19 infection by real-time reverse transcription polymerase chain reaction were evaluated for the presence of CT-abnormalities and their frequency. Regarding the patient outcome each patient was categorized in 5 progressive stages and the duration of hospitalization was determined. Regression analysis was performed to find which CT findings are predictive for patient outcome and to assess prognostic factors for the hospitalization duration.

Multivariate statistical analysis confirmed a higher age (OR = 1.023, P 
= 
.025), a higher total visual severity score (OR = 1.038, P 
= 
.002) and the presence of crazy paving (OR = 2.160, P 
= 
.034) as predictive parameters for patient outcome. A higher total visual severity score (+0.134 days; P 
= 
.012) and the presence of pleural effusion (+13.985 days, P 
= 
0.005) were predictive parameters for a longer hospitalization duration. Moreover, a higher sensitivity of chest CT (false negatives 10.4%; true positives 78.6%) in comparison to real-time reverse transcription polymerase chain reaction was obtained.

An increasing percentage of lung opacity as well as the presence of crazy paving and a higher age are associated with a worse patient outcome. The presence of a higher total visual severity score and pleural effusion are significant predictors for a longer hospitalization duration. These results are underscoring the value of chest CT as a diagnostic and prognostic tool in the pandemic outbreak of COVID-19, to facilitate fast detection and to preserve the limited (intensive) care capacity only for the most vulnerable patients.
Traditional Chinese medicine intervention for autism spectrum disorders: Retraction
Authors: Feng Xiang , Li Keshang , Jiang Quanrui , Zhang Yuxing , Gong Zhichao , Zhi Hui , Yu Jun , Li Wu , Li Jiangshan
Published: March 2022

Background:

Autism spectrum disorder (ASD) is a neurodevelopmental disorder characterized by impairments in social communication, social interaction, and restrictive or repetitive behaviors. Traditional Chinese medicine (TCM) has been used in the clinical management of ASD, especially in mainland China, where studies have shown promising efficacy. However, this remains to be further explored and clarified. Therefore, the purpose of this study was to evaluate the effectiveness and safety of conventional treatment-based TCM interventions for ASD.

Method:

The study will be conducted from January 2022, and the following electronic databases will be searched: China Biological Medicine Database, Chinese Scientific Journals Database, Wan Fang database, and China National Knowledge Infrastructure, the Cochrane Library, Web of Science, PubMed, and EMBASE Database. Only randomized controlled trials of TCM interventions for ASD will be included. The Autism Diagnostic Observation Scale, Autism Diagnostic Interview-Revised, and Childhood Autism Rating Scale will be the primary outcome indicators. The methodological quality of this Bayesian-based network meta-analysis will be performed using the “Risk of Bias” tool. Stata 14.0 and WinBUGS 1.4.3 will be used to analyze the data. In addition, assessment of heterogeneity, inconsistency, subgroups, sensitivity, and publication bias will be conducted using the Cochrane Collaboration's tools.

Results:

The results of this study will be submitted to a peer-reviewed journal for publication.

Conclusion:

This study will help patients recover better, provide clinical evidence for practitioners, and promote the use of TCM in ASD interventions.
Acupuncture in the emergency department for pain management
Authors: Dusek Jeffery A. , Kallenberg Gene A. , Hughes Robert M. , Storrow Alan B. , Coyne Christopher J. , Vago David R. , Nielsen Arya , Karasz Alison , Kim Ryung S. , Surdam Jessica , Segall Tracy , McKee M. Diane
Published: March 2022

Purpose:

Pain accounts for up to 78% of emergency department (ED) patient visits and opioids remain a primary method of treatment despite risks of addiction and adverse effects. While prior acupuncture studies are promising as an alternative opioid-sparing approach to pain reduction, successful conduct of a multi-center pilot study is needed to prepare for a future definitive randomized control trial (RCT).

Methods:

Acupuncture in the Emergency Department for Pain Management (ACUITY) is funded by the National Center for Complementary and Integrative Health. The objectives are to: conduct a multi-center feasibility RCT, examine feasibility of data collection, develop/deploy a manualized acupuncture intervention and assess feasibility/implementation (barrier/facilitators) in 3 EDs affiliated with the BraveNet Practice Based Research Network.

Adults presenting to a recruiting ED with acute non-emergent pain (e.g., musculoskeletal, back, pelvic, noncardiac chest, abdominal, flank or head) of ≥4 on a 0-10-point Numeric Rating Scale will be eligible. ED participants (n = 165) will be equally randomized to Acupuncture or Usual Care.

At pre-, post-, and discharge time-points, patients will self-assess pain and anxiety using the Numeric Rating Scale. Pain, anxiety, post-ED opioid use and adverse events will be assessed at 1 and 4 weeks. Opioid utilization in the ED and discharge prescriptions will be extracted from patients’ electronic medical records.

Acupuncture recipients will asked to participate in a brief qualitative interview about 3 weeks after their discharge. ED providers and staff will also be interviewed about their general perspectives/experiences related to acupuncture in the ED and implementation of acupuncture in ACUITY.

Results:

Recruitment began on 5/3/21. As of 12/7/21: 84 patients have enrolled, the responsive acupuncture intervention has been developed and deployed, and 26 qualitative interviews have been conducted.

Conclusion:

Successful conduct of ACUITY will provide the necessary framework for conducting a future, multi-center, definitive RCT of acupuncture in the ED.

Clinical Trials.gov:

NCT04880733 https://clinicaltrials.gov/ct2/show/NCT04880733
Investigation and influencing factors about well-being level of elderly chronic patients during COVID-19 postpandemic period in Beijing
Authors: Wu Chen , Liu Yu-Xuan , Liu Tie-Jun , Yan Xu-Ling , Zhao Yu-Xi , Zeng Hong , Zhou Tian , Rao Ping , Sun Lan-Ying , Jiao Yang , Xi Jia-Ning
Published: March 2022

The Corona Virus Disease 2019 (COVID-19) pandemic has huge impacts on the world, including human health and economic decline. The COVID-19 has severe infectivity, especially the elderly with chronic diseases will cause various complications after infection and accelerate the disease process. In addition, COVID-19 will also affect their mental health. Therefore, the mental health of elderly patients with chronic diseases cannot be ignored. The aim of this study was to investigate the well-being level of elderly people with chronic disease during COVID-19 postpandemic period in Beijing and analysis related influencing factors, so as to provide a basis for improving the well-being level of elderly chronic patients during the postpandemic period.

Elderly patients with chronic diseases who met the inclusion criteria in 5 different administrative regions in Beijing were selected to carry out a questionnaire survey. The contents of the questionnaire included general data, the Memorial University of Newfoundland Happiness scale and the awareness situation of the COVID-19 pandemic. A total of 500 questionnaires were distributed by WeChat and 486 valid questionnaires were collected. The t test and one-way analysis of variance were used to compare Memorial University of Newfoundland Happiness scores between 2 or more groups, multiple linear regression analysis was used to conduct multiple factor analysis to explore the related factors about well-being level of elderly chronic patients.

A total of 109 cases (22.43%) were evaluated high well-being level, 319 cases (65.64%) were evaluated moderate well-being level and 58 cases (11.93%) were evaluated low well-being according to the Memorial University of Newfoundland Happiness (MUNSH) scores rating. The multiple linear regression indicated that the education level, number of chronic diseases, medical expenses, frequency of children's visits, taking care of grandchildren or not, and group activity frequency significantly affected the well-being of patients with chronic diseases during COVID-19 postpandemic period in Beijing (P < .05).

Most elderly patients with chronic diseases had moderate or above sense of well-being during postpandemic period, but we should still pay attention to the mental health of those elderly chronic patients with low education level, much comorbidity, more medical expenses, less visits by children, not take care of grandchildren and never participate in group activities.
Upregulated miR-328-3p and its high risk in atrial fibrillation
Authors: Huang Haitao , Chen Hao , Liang Xiao , Chen Xiuting , Chen Xiaoxin , Chen Can
Published: March 2022

Background:

Several studies have shown miR-328-3p increased in atrial fibrillation (AF), but some researches indicated no difference or even decreased. This inconsistent result confuses researchers, and it is urgent to know the truth. This study is to assess the association between miR-328-3p levels in plasma/atrial tissue and patients with AF.

Methods:

PubMed, EMBASE, Scopus, Web of Science, and ProQuest were searched from inception to February 1, 2021. The standardized mean differences (SMD) with their 95% confidence interval (CI) were calculated to evaluate the association between miR-328-3p levels and AF.

Results:

Twelve studies met the inclusion criteria and were used for our meta-analysis. Overall, the levels of miR-328-3p were higher in patients with AF than in the control group (SMD = 0.69, 95% CI [0.10, 1.28], P = .022). After adjustment, the overall SMD was 0.82 (95% CI [0.22, 1.42], P = .007). Sensitivity analysis indicated that the results were stable, and the trim-fill analysis showed that the results were credible. Subgroup analyses showed that AF patients, n ≥ 30, various of comorbidity, articles published earlier, and Asia groups had higher levels of expression of miR-328-3p.

Conclusions:

High levels of miR-328-3p are significantly associated with an increased risk of AF. It implies that miR-328-3p played an important role in diagnosis and may serve as a potential momentous, and useful biomarker to identify AF.
Managers’ awareness of mental health measures for their employees in small and medium-sized enterprises in a depopulated mountainous area in Japan
Authors: Fukita Susumu , Kawasaki Hiromi , Yamasaki Satoko
Published: March 2022

The local economy is often supported by small and medium-sized enterprises. There is a need to consider effective promotion methods for mental health measures in these enterprises in depopulated mountainous areas. It is important to understand managers’ awareness when considering effective mental health measures in these enterprises. The study's aim is to explore managers’ awareness of mental health measures for employees in small and medium-sized enterprises in depopulated mountainous areas in Japan.

Qualitative semi-structured interviews were conducted with 6 managers in 2019. The primary issues addressed by the interview were regarding the awareness among managers about mental health promotion measures for employees. These are the primary prevention measures. The interview also addressed issues related to the awareness of measures for mental health problems that are fundamental to the secondary and tertiary prevention measures. A qualitative descriptive analysis was conducted.

Three categories and 8 subcategories emerged regarding the managers’ awareness of mental health promotion measures for employees. The 3 categories were: “Individual support, including their life's aspect, while taking advantage of formal and informal relationships,” “The difficulty of drawing out an employees’ motivation to work, due to the changes over time in the work size or in their working relationships,” and “Creating a comfortable working environment for employees, by complying with the labor standards and adjusting relationships.” Regarding managers’ awareness of the measures for mental health problems, four categories and 8 subcategories emerged. The 4 categories were: “Prevention and awareness of the incidence of mental health problems,” “Individual support based on the enterprise's or employee's characteristics,” “A lack of support for the manager to address employees’ mental health problems,” and “Employees quitting the job, due to the lack of appropriate support.”

Though managers in depopulated mountainous areas were well aware of the mental health activities offered, the categories showed the need to foster social capital. It also showed the need to collaborate with external support organizations, and the difficulties faced by small and medium-sized enterprises.
Health literacy among cancer survivors
Authors: Coughlin Steven S. , Datta Biplab , Vernon Marlo , Hatzigeorgiou Christos , George Varghese
Published: March 2022

Health literacy is a set of knowledge and skills that enables individuals to obtain, communicate, process and understand information, and services to make appropriate health decisions and to successfully navigate the health care system. Health literacy is important to quality of cancer survivorship care and patient self-management of their disease.

We examined health literacy among cancer survivors, using data from the 2016 Behavioral Risk Factor Surveillance System. We compared health literacy across various demographic and socioeconomic groups and estimated the adjusted odds in favor of low health literacy for these characteristics.

We found that about 16% of the cancer survivors had low health literacy. The prevalence was higher among Hispanic and Black individuals, and among those with poor health status, low income and educational attainment.

A sizeable percentage of cancer survivors have low health literacy which is likely to complicate their ability to self-manage their disease and navigate the health care system for optimal care. In order to ensure the quality and appropriateness of cancer survivorship care, effective interventions are needed to address low health literacy in these populations.
The Association Between Sleep Disturbance and Proinflammatory Markers in Patients With Cancer
Authors: Tong Huan-huan , Li Jing-ru , Feng Yuan , Li Shu-wen , Qiu Huan , Hong Jing-fang
Published: March 2022

Background

Sleep disturbance is one of the symptoms with high incidence and negative influence in patients with cancer. A better understanding of the biological factors associated with sleep disturbance is critical to predict, treat, and manage this condition.

Objective

The aim of this study was to determine the correlation between sleep disturbance and proinflammatory markers in adult patients with cancer.

Methods

A systematic search was conducted in 7 databases from inception to March 1, 2020, for this meta-analysis. Two reviewers independently screened the studies, extracted data, and appraised the quality of the studies. Meta-analyses were conducted using Stata 12.0 software.

Results

Sixteen studies were included. Results indicated that sleep disturbance was associated with higher levels of the overall proinflammatory markers and that the effect size was small yet significant. Further subgroup analyses suggested that sleep disturbance was significantly associated with interleukin-6 and C-reactive protein, but not with interleukin-1β or tumor necrosis factor-α. Meta-regression results indicated that only the sample source affected the association between sleep disturbance and proinflammatory markers.

Conclusion

There was a positive relationship between sleep disturbance and selected proinflammatory markers in adult patients with cancer.

Implication for Practice

This review provides empirical support for the association between sleep disturbance and certain proinflammatory markers. Healthcare providers can further explore specific biomarkers to precisely identify the individuals at risk of sleep disturbance and develop targeted strategies for therapeutic and clinical interventions.
Nonopioid drug combinations for cancer pain: a systematic review
Authors: Sohi Gursharan , Lao Nicholas , Caraceni Augusto , Moulin Dwight E. , Zimmermann Camilla , Herx Leonie , Gilron Ian
Published: March 2022

Pain is highly prevalent in patients with cancer—nearly 40% report moderate-severe pain, which is commonly treated with opioids. Increasing cancer survivorship, opioid epidemics in some regions of the world, and limited opioid access in other regions have focused attention on nonopioid treatments. Given the limitations of monotherapy, combining nonopioids—such as antiepileptics and antidepressants—have shown promise in noncancer pain. This review seeks to evaluate efficacy of nonopioid combinations for cancer-related pain. Systematic searches of PubMed, EMBASE, and Cochrane CENTRAL were conducted for double-blind, randomized, controlled trials comparing a nonopioid combination with at least one of its components and/or placebo. This search yielded 4 randomized controlled trials, published between 1998 and 2019 involving studies of (1) imipramine + diclofenac; (2) mitoxantrone + prednisone + clodronate; (3) pentoxifylline + tocopherol + clodronate; and (4) duloxetine + pregabalin + opioid. In the first 3 of these trials, trends favouring combination efficacy failed to reach statistical significance. However, in the fourth trial, duloxetine + pregabalin + opioid was superior to pregabalin + opioid. This review illustrates recognition for the need to evaluate nonopioid drug combinations in cancer pain, although few trials have been published to date. Given the growing practice of prescribing more than 1 nonopioid for cancer pain and the need to expand the evidence base for rational combination therapy, more high-quality trials in this area are needed.
NOVEL RT-qPCR ASSAYS ENABLE RAPID DETECTION AND DIFFERENTIATION BETWEEN SARS-COV-2 OMICRON (BA.1) AND BA.2 VARIANTS
Authors: Erster Oran , Kabat Areej , Asraf Hadar , Levy Virginia , Mannasse Batya , Azar Roberto , Nemet Ital , Kliker Limor , Fleishon Shay , Mandelboim Michal , Mendelson Ella , Zuckerman Neta S
Published: March 2022

In this report, we describe the development and initial validation of novel SARS-COV-2 Omicron-specific reactions that enable the identification of Omicron (BA.1) and BA.2 variants. Mutations that are either shared by both BA.1 and BA.2, or are exclusive for BA.1 or for BA.2 were identified by bioinformatic analysis, and corresponding probe-based quantitative PCR reactions were developed to identify them. We show that multiplex combinations of these reactions provide a single-reaction identification of the sample as BA.1, BA.2, or as non-Omicron SARS-COV-2. All four reactions described herein have a sensitivity of less than ten copies per reaction, and are amendable for multiplexing. The results of this study suggest that the new assays may be useful for testing both clinical and environmental samples to differentiate between these two variants.
Identifying risk factors associated with death among patients with MDR-TB in KwaZulu-Natal, South Africa: an illustration using Weibull parametric model
Authors: Mbona Sizwe Vincent , Mwambi Henry , Chifurira Retius
Published: March 2022

Background

This study aim was to identify the risk factors associated with multidrug-resistant tuberculosis (MDR-TB) disease. The Weibull model has shown to perform better than the Cox proportional models with respect to the accuracy and efficient of the estimates. Therefore, a Weibull parametric model was employed to identify predictors of death in patients with MDR-TB and the efficiency of the models using current dataset.

Methods

Patients diagnosed with MDR-TB were studied in four decentralised sites located in rural areas and one centralised hospital in KwaZulu-Natal, South Africa from July 2008 to July 2012. Patients were followed from the date of MDR-TB diagnosis until death or the last follow-up date.

Results

A total of 1 542 patients were included in the analyses: 812 and 730 from the centralised hospital and decentralised sites, respectively. Of the 1 542 enrolled, 15.9% patients died. We found that the hazard of death was significantly higher among patients treated in decentralised sites (aHR) = 1.84, 95% CI = 1.38 – 2.75; SE = 0.81 than that of those who were treated in the centralised hospital. However, the results from the Cox PH model showed an insignificant hazard of death between the decentralised sites and the centralised hospital (aHR = 1.46, 95% CI = 0.69 – 2.36; SE = 0.92). Patients who are between 31 – 40 years of age had increased hazard of death compared to those between 18 – 30 years (aHR = 1.52, 95% CI = 1.04 - 2.23). The hazard of death in female patients was 24% higher compared to male patients (aHR = 1.24, 95% CI = 0.93 - 1.63). Furthermore, patients with previous MDR-TB episodes had an increased hazard of death (aHR = 1.79, 95% CI = 0.23 – 0.62) compared to those with no previous MDR-TB episodes. The hazard of death in HIV negative patients was low compared to those who were HIV positive (aHR = 0.95, 95% CI = 0.57 – 0.77).

Conclusion

More health facilities are needed especially in decentralised places and that can help the 2030 World Health Organisation strategy to reduce or end TB infection.
A gene expression map of host immune response in human brucellosis
Authors: Mitroulis Ioannis , Chrysanthopoulou Akrivi , Divolis Georgios , Ioannidis Charalampos , Ntinopoulou Maria , Tasis Athanasios , Konstantinidis Theocharis , Soteriou Natalia , Lallas George , Mitka Stella , Lesche Mathias , Dahl Andreas , Gembardt Stephanie , Panopoulou Maria , Sideras Paschalis , Wielockx Ben , Coskun Ünal , Ritis Konstantinos , Skendros Panagiotis
Published: March 2022

Brucellosis is a common zoonotic disease caused by intracellular pathogens of the genus Brucella. Brucella infects macrophages and evades clearance mechanisms, which results in chronic parasitism. Herein, we studied the molecular changes that take place in human brucellosis bothin vitroandin vivo. RNA sequencing was performed in primary human macrophages (Μφ) and polymorphonuclear neutrophils (PMNs) infected with clinical strains ofB. melitensis. We observed a downregulation in the expression of genes involved in host response, such as TNF signaling, IL-1β production and phagosome formation in Μφ, and phosphatidylinositol signaling and TNF signaling in PMNs, being in line with the ability of the pathogen to survive within phagocytes. Further transcriptomic analysis of isolated peripheral blood mononuclear cells (PBMCs) and PMNs from patients with acute brucellosis before treatment initiation and after successful treatment revealed a positive correlation of the molecular signature of active disease with pathways associated with response to interferons (IFN). We identified 24 common genes that were significantly altered in both PMNs and PBMCs, including genes involved in IFN signaling that were downregulated after treatment in both cell populations, andIL1R1that was upregulated. The levels of several inflammatory mediators were evaluated in the serum of these patients, and we observed increased levels of IFN-γ, IL-1β and IL-6 before the treatment of acute brucellosis. An independent cohort of patients with chronic brucellosis also revealed the increased levels of IFN-γ during relapse compared to remissions. Taken together, this study provides for the first time an in-depth analysis of the molecular alterations that take place in human phagocytes upon infection, and in peripheral blood immune populations during active disease.
Proteogenomics refines the molecular classification of chronic lymphocytic leukemia
Authors: Herbst Sophie A. , Vesterlund Mattias , Helmboldt Alexander J. , Jafari Rozbeh , Siavelis Ioannis , Stahl Matthias , Schitter Eva C. , Liebers Nora , Brinkmann Berit J. , Czernilofsky Felix , Roider Tobias , Bruch Peter-Martin , Iskar Murat , Kittai Adam , Huang Ying , Lu Junyan , Richter Sarah , Mermelekas Georgios , Umer Husen Muhammad , Knoll Mareike , Kolb Carolin , Lenze Angela , Cao Xiaofang , Österholm Cecilia , Wahnschaffe Linus , Herling Carmen , Scheinost Sebastian , Ganzinger Matthias , Mansouri Larry , Kriegsmann Katharina , Kriegsmann Mark , Anders Simon , Zapatka Marc , Poeta Giovanni Del , Zucchetto Antonella , Bomben Riccardo , Gattei Valter , Dreger Peter , Woyach Jennifer , Herling Marco , Müller-Tidow Carsten , Rosenquist Richard , Stilgenbauer Stephan , Zenz Thorsten , Huber Wolfgang , Tausch Eugen , Lehtiö Janne , Dietrich Sascha
Published: March 2022

Cancer heterogeneity at the proteome level may explain differences in therapy response and prognosis beyond the currently established genomic and transcriptomic based diagnostics. The relevance of proteomics for disease classifications remains to be established in clinically heterogeneous cancer entities such as chronic lymphocytic leukemia (CLL). Here, we characterized the proteome and transcriptome in-depth alongside genetic and ex-vivo drug response profiling in a clinically well annotated CLL discovery cohort (n= 68). Unsupervised clustering of the proteome data revealed six subgroups. Five of these proteomic groups were associated with genetic features, while one group was only detectable at the proteome level. This new group was characterized by accelerated disease progression, high spliceosomal protein abundances associated with aberrant splicing, and low B cell receptor signaling protein abundances (ASB-CLL). We developed classifiers to identify ASB-CLL based on its characteristic proteome or splicing signature in two independent cohorts (n= 165, n= 169) and confirmed that ASB-CLL comprises about 20 % of CLL patients. The inferior overall survival observed in ASB-CLL was independent of both TP53- and IGHV mutation status. Our multi-omics analysis refines the classification of CLL and highlights the potential of proteomics to improve cancer patient stratification beyond genetic and transcriptomic profiling.

Single sentence summary

We performed the largest proteogenomic analysis of CLL, linked proteomic profiles to clinical outcomes, and discovered a new poor outcome subgroup (ASB-CLL).
VIsoQLR: an interactive tool for the detection, quantification and fine-tuning of isoforms using long-read sequencing
Authors: Núñez-Moreno Gonzalo , Tamayo Alejandra , Ruiz-Sánchez Carolina , Cortón Marta , Mínguez Pablo
Published: March 2022

DNA variants altering the pre-mRNA splicing process represent an underestimated cause of human genetic diseases. Their association with disease traits should be confirmed using functional assays from patient cell lines or other alternative models to detect the formation of aberrant mRNAs. Long-read sequencing is a suitable technique to identify and quantify mRNA isoforms. Available isoform clusterization and/or quantification tools are generally designed for the whole transcriptome analysis. Experiments focusing on a single locus analysis need more precise data fine-tuning and visualization tools.

Here we describe VIsoQLR, an interactive analyzer, viewer and editor for the semi-automated identification and quantification of known and novel isoforms using long-read sequencing data. VIsoQLR is tailored to thoroughly analyze mRNA expression and maturation in low-throughput splicing assays. This tool takes sequences aligned to a reference, defines consensus splice sites, and quantifies isoforms. Users can edit splice sites through dynamic and interactive graphics and tables as part of their manual curation. Known transcripts, or isoforms detected by other methods, can also be imported as references for comparison. Here, we explain VIsoQLR principles and features, and show its applicability in a case study example using Nanopore sequencing. VIsoQLR is available at https://github.com/TBLabFJD/VIsoQLR.
Manipulating prior beliefs causally induces under- and overconfidence
Authors: Van Marcke Hélène , Le Denmat Pierre , Verguts Tom , Desender Kobe
Published: March 2022

Making a decision is invariably accompanied by a sense of confidence in that decision. Across subjects and tasks, there is widespread variability in the exact level of confidence, even for tasks that do not differ in objective difficulty. Such expressions of under- and overconfidence are of vital importance, as they relate to fundamental life outcomes. Yet, a computational account specifying the mechanisms underlying under- and overconfidence is currently missing. Here, we propose that prior beliefs in the ability to perform a task, based on prior experience with this or a similar task, explain why confidence can differ dramatically across subjects and tasks, despite similar performance. In two perceptual decision-making experiments, we provide evidence for this hypothesis by showing that manipulating prior beliefs about task performance in a training phase causally influences reported levels of confidence in a test phase, while leaving objective performance in the test phase unaffected. This is true both when prior beliefs are induced via manipulated comparative feedback and via manipulating task difficulty during the training phase. We account for these results within an accumulation-to-bound model by explicitly modeling prior beliefs based on earlier exposure to the task. Decision confidence is then quantified as the probability of being correct conditional on these prior beliefs, leading to under- or overconfidence depending on the task context. Our results provide a fundamental mechanistic insight into the computations underlying under- and overconfidence in perceptual decision-making.
Molecular and cognitive signatures of ageing partially restored through synthetic delivery of IL2 to the brain
Authors: Lemaitre Pierre , Tareen Samar , Pasciuto Emanuela , Mascali Loriana , Martirosyan Araks , Callaerts-Vegh Zsuzsanna , Dooley James , Holt Matthew G. , Yshii Lidia , Liston Adrian
Published: March 2022

Cognitive decline is a common pathological outcome during aging, with an ill-defined cellular or molecular basis. Among the cellular changes observed with age are alterations to neuronal plasticity, changes in the glial compartment and the decline of the neurogenic niche. In the recent years, the concept of inflammaging, defined as a low-grade inflammation increasing with age, has emerged as a nexus for age-related diseases. This increase of basal inflammation is also observed in the central nervous system. While not classically considered a neurological cell type, infiltrating T cells increase in the brain with age, and may be responsible for amplification of inflammatory cascades and disruptions to the neurogenic niche. Recently, a small resident population of regulatory T cells has been identified in the brain, and the capacity of IL2-mediated expansion of this population to counter neuroinflammatory disease has been demonstrated. Here we test a brain-specific IL2 delivery system for the prevention of neurological decline in aging mice. We identify the molecular hallmarks of aging in the brain glial compartments, and identify partial restoration of this signature through IL2 treatment. At a behavioral level, brain IL2 delivery prevented the age-induced defect in spatial learning, without improving the general decline in motor skill or arousal. These results identify immune modulation as a potential path to preserving cognitive function for healthy ageing.
Ascorbic acid derived carbon dots promote circadian rhythm and contribute to attention deficit hyperactivity disorder
Authors: Huang Jian , Wang Yun , Zhong Zhaomin , Ma Yurong , Liu Changhong , Deng Keru , Huang Hui , Liu Yang , Ding Xin , Kang Zhenhui
Published: March 2022

Attention deficit hyperactivity disorder (ADHD) is one of the most prevalent psychiatric disorders in children, and ADHD patients always display circadian abnormalities. While, the ADHD drugs currently used in clinic have strong side effects, such as psychosis, allergic reactions and heart problems. Here, we demonstrated carbon dots derived from the ascorbic acid (VCDs) could strongly rescue the hyperactive and impulsive behaviour of a zebrafish ADHD disease model caused byper1bmutation. VCDs prolonged the circadian period of zebrafish for more than half an hour. In addition, the amplitude and circadian phase were also changed. The dopamine level was specifically increased, which may be caused by stimulation of the dopaminergic neuron development in the midbrain. Notably, it was found that the serotonin level was not altered by VCDs treatments. Also, the gene transcriptome effects of VCDs were discussed in present work. Our results provided the dynamic interactions of carbon dots with circadian system and dopamine signaling pathway, which illustrates a potential application of degradable and bio-safe VCDs for the treatment of the attention deficient and hyperactive disorder through circadian intervention.

Brief summary
Optimal vaccination with time-varying based on immunity barrier in Hunan Province, China
Authors: Guo Xiaohao , Liu Ziyan , Yang Shiting , Zhao Zeyu , Guo Yichao , Abudurusuli Guzainuer , Rui Jia , Wang Yao , Zhao Shanlu , Zeng Ge , Hu Shixiong , Luo Kaiwei , Chen Tianmu
Published: March 2022

The current outbreak of novel coronavirus disease 2019 (COVID-19) is already causing a serious disease burden worldwide, this paper analyzed data of a delta variant Covid-19 outbreak in Hunan, China, and proposed an optimal dose-wise dynamical vaccinating process based on local contact pattern and vaccine coverage that minimize the accumulative cases in a certain future time interval. The optimized result requires an immediate vaccination to that none vaccinated at age group 30 to 39, which is coherent to the prevailing strategies. The dose-wise optimal vaccinating process can be directive for countries or regions where vaccines are not abundant. We recommend that vaccination should be further intensified to increase the coverage of booster shots, thus effectively reducing the spread of COVID-19.
Predictive Model of Risk Factors of High Flow Nasal Cannula Using Machine Learning in COVID-19
Authors: Matsunaga Nobuaki , Kamata Keisuke , Asai Yusuke , Tsuzuki Shinya , Sakamoto Yasuaki , Ijichi Shinpei , Akiyama Takayuki , Yu Jiefu , Yamada Gen , Terada Mari , Suzuki Setsuko , Suzuki Kumiko , Saito Sho , Hayakawa Kayoko , Ohmagari Norio
Published: March 2022

Background

With the rapid increase in the number of COVID-19 patients in Japan, the number of patients receiving oxygen at home has also increased rapidly, and some of these patients have died. An efficient approach to identify high-risk patients with slowly progressing and rapidly worsening COVID-19, and to avoid missing the timing of therapeutic intervention will improve patient prognosis and prevent medical complications.

Methods

Patients admitted to medical institutions in Japan from November 14, 2020 to April 11, 2021 and registered in the COVID-19 Registry Japan were included. Risk factors for patients with High Flow Nasal Cannula invasive respiratory management or higher were comprehensively explored using machine learning. Age-specific cohorts were created, and severity prediction was performed for the patient surge period and normal times, respectively.

Results

We were able to obtain a model that was able to predict severe disease with a sensitivity of 57% when the specificity was set at 90% for those aged 40-59 years, and with a specificity of 50% and 43% when the sensitivity was set at 90% for those aged 60-79 years and 80 years and older, respectively. We were able to identify lactate dehydrogenase level (LDH) as an important factor in predicting the severity of illness in all age groups.

Discussion

Using machine learning, we were able to identify risk factors with high accuracy, and predict the severity of the disease. Using machine learning, we were able to identify risk factors with high accuracy, and predict the severity of the disease. We plan to develop a tool that will be useful in determining the indications for hospitalisation for patients undergoing home care and early hospitalisation.
Effects of BA.1/BA.2 subvariant, vaccination, and prior infection on infectiousness of SARS-CoV-2 Omicron infections
Authors: Qassim Suelen H. , Chemaitelly Hiam , Ayoub Houssein H. , AlMukdad Sawsan , Tang Patrick , Hasan Mohammad R. , Yassine Hadi M. , Al-Khatib Hebah A. , Smatti Maria K. , Abdul-Rahim Hanan F. , Nasrallah Gheyath K. , Al-Kuwari Mohamed Ghaith , Al-Khal Abdullatif , Coyle Peter , Kaleeckal Anvar Hassan , Shaik Riyazuddin Mohammad , Latif Ali Nizar , Al-Kuwari Einas , Jeremijenko Andrew , Butt Adeel A. , Bertollini Roberto , Al-Romaihi Hamad Eid , Al-Thani Mohamed H. , Abu-Raddad Laith J.
Published: March 2022

BACKGROUND

Qatar experienced a large SARS-CoV-2 Omicron (B.1.1.529) wave that started on December 19, 2021 and peaked in mid-January, 2022. We investigated effects of Omicron subvariant (BA.1 and BA.2), previous vaccination, and prior infection on infectiousness of Omicron infections, between December 23, 2021 and February 20, 2022.

METHODS

Univariable and multivariable regression analyses were conducted to estimate the association between the RT-qPCR cycle threshold (Ct) value of PCR tests (a proxy for SARS-CoV-2 infectiousness) and each of the Omicron subvariants, mRNA vaccination, prior infection, reason for RT-qPCR testing, calendar week of RT-qPCR testing (to account for phases of the rapidly evolving Omicron wave), and demographic factors.

RESULTS

Compared to BA.1, BA.2 was associated with 3.53 fewer cycles (95% CI: 3.46-3.60), signifying higher infectiousness. Ct value decreased with time since second and third vaccinations. Ct values were highest for those who received their boosters in the month preceding the RT-qPCR test—0.86 cycles (95% CI: 0.72-1.00) higher than for unvaccinated persons. Ct value was 1.30 (95% CI: 1.20-1.39) cycles higher for those with a prior infection compared to those without prior infection, signifying lower infectiousness. Ct value declined gradually with age. Ct value was lowest for those who were tested because of symptoms and was highest for those who were tested for travel-related purposes. Ct value was lowest during the exponential-growth phase of the Omicron wave and was highest after the wave peaked and was declining.

CONCLUSIONS

The BA.2 subvariant appears substantially more infectious than the BA.1 subvariant. This may reflect higher viral load and/or longer duration of infection, thereby explaining the rapid expansion of this subvariant in Qatar.
Prevalence of Bacterial Coinfection and Patterns of Antibiotics Prescribing in Patients with COVID-19: A Systematic review and Meta-Analysis
Authors: Alshaikh Faisal Salman , Sindi Oula Nawaf , Godman Brian , Seaton R Andrew , Kurdi Amanj
Published: March 2022

Background

Evidence around prevalence of bacterial coinfection and pattern of antibiotic use in COVID-19 is controversial although high prevalence rates of bacterial coinfection have been reported in previous similar global viral respiratory pandemics. Early data on the prevalence of antibiotic prescribing in COVID-19 indicates conflicting low and high prevalence of antibiotic prescribing which challenges antimicrobial stewardship programmes and increases risk of antimicrobial resistance (AMR).

Aim

To determine current prevalence of bacterial coinfection and antibiotic prescribing in COVID-19 patients

Data Source

OVID MEDLINE, OVID EMBASE, Cochrane and MedRxiv between January 2020 and June 2021.

Study Eligibility

English language studies of laboratory-confirmed COVID-19 patients which reported (a) prevalence of bacterial coinfection and/or (b) prevalence of antibiotic prescribing with no restrictions to study designs or healthcare setting

Participants

Adults (aged ≥ 18 years) with RT-PCR confirmed diagnosis of COVID-19, regardless of study setting.

Methods

Systematic review and meta-analysis. Proportion (prevalence) data was pooled using random effects meta-analysis approach; and stratified based on region and study design.

Results

A total of 1058 studies were screened, of which 22, hospital-based studies were eligible, compromising 76,176 of COVID-19 patients. Pooled estimates for the prevalence of bacterial co-infection and antibiotic use were 5.62% (95% CI 2.26 – 10.31) and 61.77% (CI 50.95 – 70.90), respectively. Sub-group analysis by region demonstrated that bacterial co-infection was more prevalent in North American studies (7.89%, 95% CI 3.30-14.18).

Conclusion

Prevalence of bacterial coinfection in COVID-19 is low, yet prevalence of antibiotic prescribing is high, indicating the need for targeted COVID-19 antimicrobial stewardship initiatives to reduce the global threat of AMR.
Identifying SARS-CoV-2 Variants of Concern through saliva-based RT-qPCR by targeting recurrent mutation sites
Authors: Ham Rachel E. , Smothers Austin R. , Che Rui , Sell Keegan J. , Peng Congyue Annie , Dean Delphine
Published: March 2022

SARS-CoV-2 variants of concern (VOCs) continue to pose a public health threat which necessitates a real-time monitoring strategy to compliment whole genome sequencing. Thus, we investigated the efficacy of competitive probe RT-qPCR assays for six mutation sites identified in SARS-CoV-2 VOCs and, after validating the assays with synthetic RNA, performed these assays on positive saliva samples. When compared with whole genome sequence results, the SΔ69-70 and ORF1aΔ3675-3677 assays demonstrated 93.60% and 68.00% accuracy, respectively. The SNP assays (K417T, E484K, E484Q, L452R) demonstrated 99.20%, 96.40%, 99.60%, and 96.80% accuracies, respectively. Lastly, we screened 345 positive saliva samples from December 7-22, 2021 using Omicron-specific mutation assays and were able to quickly identify rapid spread of Omicron in Upstate South Carolina. Our workflow demonstrates a novel approach for low-cost, real-time population screening of VOCs.

Importance

SARS-CoV-2 variants of concern and their many sublineages can be characterized by mutations present within their genetic sequences. These mutations can provide selective advantages such as increased transmissibility and antibody evasion, which influences public health recommendations such as mask mandates, quarantine requirements, and treatment regimens. Our real-time RT-qPCR workflow allows for strain identification of SARS-CoV-2 positive saliva samples by targeting common mutation sites shared between VOCs and detecting single nucleotides present at the targeted location. This differential diagnostic system can quickly and effectively identify a wide array of SARS-CoV-2 strains, which can provide more informed public health surveillance strategies in the future.
Deep Sequence Modeling for Pressure Controlled Mechanical Ventilation
Authors: Belgaid Abdelghani
Published: March 2022

This paper presents a deep neural network approach to simulate the pressure of a mechanical ventilator. The traditional mechanical ventilator has a control pressure monitored by a medical practitioner, which could behave inaccurately by missing the proper pressure. This paper exploits recent studies and provides a simulator based on a deep sequence model to predict the airway pressure in the respiratory circuit during the inspiratory phase of a breath given a time series of control parameters and lung attributes. This approach demonstrates the effectiveness of neural network-based controllers in tracking pressure waveforms significantly better than the current industry standard and provides insights to build effective and robust pressure-controlled mechanical ventilators.
Deep sequencing of early T stage colorectal cancers reveals disruption of homologous recombination repair in microsatellite stable tumours with high mutational burdens
Authors: Li Jun , Steffen Pascal , Tse Benita C. Y. , Ahadi Mahsa S. , Gill Anthony J , Engel Alexander F. , Molloy Mark P.
Published: March 2022

Early T stage colorectal cancers (CRC) that invade lymph nodes (Stage IIIA) are greatly under-represented in large-scale genomic mapping projects such as TCGA datasets. We retrieved 10 Stage IIIA CRC cases, matched these to 16 Stage 1 CRC cases (T1 depth without lymph node metastasis) and carried out deep sequencing of 409 genes using the IonTorrent system. Tumour mutational burdens (TMB) ranged from 2.4-77.2/Mb sequenced. Using mean TMB as a cut-point to define groups, TMB-low (TMB-L) specimens showed higher frequency of KRAS and TP53 mutations in Stage IIIA compared to Stage I, consistent with TCGA data. TMB-High (TMB-H) specimens consisted of both microsatellite instable high (MSI-H) and microsatellite stable (MSS) genotypes. Comparison of TMB-H with TMB-L groups revealed clear differences in mutations of ATM, KDM5C, PIK3CA and APC. APC was less frequently mutated in the TMB-H group although variant composition was more diverse. Variants in ATM were restricted to the TMB-H group, and in four of five MSS specimens we observed the co-occurrence of mutations in homologous recombination repair (HRR) genes in either two of ATM, CDK12, PTEN or ATR, with at least one of these being a truncating mutation. No MSI-H specimens carried nonsense mutations in these genes. These findings add to our knowledge of early T stage CRC and highlight a potential therapeutic vulnerability in the HRR pathway of TMB-H MSS CRC.
Class-Controlled Copy-Paste Based Cell Segmentation for CoNIC Challenge
Authors: Ahn Heeyoung , Hong Yiyu
Published: March 2022

Muti-class cell segmentation in histopathology images is a challenging task. Here, we propose a copy-paste augmentation-based method for CoNIC challenge. As the challenge train data is severely class imbalanced. To deal with it, we copy all cell objects of train data and paste them to the train image on the fly while training model. The paste strategy is that we paste more cell objects of the insufficient classes and paste less cell objects for the sufficient classes. We experimented the method by stratified splitting train data in 4:1 ratio, the result shows the copy paste method can reach PQ 64.84 and mPQ 53.72, which improved and 0.66 compared to without copy pasted. Moreover, the improvements in those insufficient classes is more obvious.