bluuebunny/crossref_metadata_2025_split huggingface dataset:
Extracting postmarketing adverse events from safety reports in the vaccine adverse event reporting system (VAERS) using deep learning
Authors: Du Jingcheng , Xiang Yang , Sankaranarayanapillai Madhuri , Zhang Meng , Wang Jingqi , Si Yuqi , Pham Huy Anh , Xu Hua , Chen Yong , Tao Cui 
Published: January 2021

AbstractObjectiveAutomated analysis of vaccine postmarketing surveillance narrative reports is important to understand the progression of rare but severe vaccine adverse events (AEs). This study implemented and evaluated state-of-the-art deep learning algorithms for named entity recognition to extract nervous system disorder-related events from vaccine safety reports.Materials and MethodsWe collected Guillain-Barré syndrome (GBS) related influenza vaccine safety reports from the Vaccine Adverse Event Reporting System (VAERS) from 1990 to 2016. VAERS reports were selected and manually annotated with major entities related to nervous system disorders, including, investigation, nervous_AE, other_AE, procedure, social_circumstance, and temporal_expression. A variety of conventional machine learning and deep learning algorithms were then evaluated for the extraction of the above entities. We further pretrained domain-specific BERT (Bidirectional Encoder Representations from Transformers) using VAERS reports (VAERS BERT) and compared its performance with existing models.Results and ConclusionsNinety-one VAERS reports were annotated, resulting in 2512 entities. The corpus was made publicly available to promote community efforts on vaccine AEs identification. Deep learning-based methods (eg, bi-long short-term memory and BERT models) outperformed conventional machine learning-based methods (ie, conditional random fields with extensive features). The BioBERT large model achieved the highest exact match F-1 scores on nervous_AE, procedure, social_circumstance, and temporal_expression; while VAERS BERT large models achieved the highest exact match F-1 scores on investigation and other_AE. An ensemble of these 2 models achieved the highest exact match microaveraged F-1 score at 0.6802 and the second highest lenient match microaveraged F-1 score at 0.8078 among peer models.
Response Rate and Survival at Key Timepoints With PD-1 Blockade vs Chemotherapy in PD-L1 Subgroups: Meta-Analysis of Metastatic NSCLC Trials
Authors: Man Johnathan , Millican Jared , Mulvey Arthur , Gebski Val , Hui Rina 
Published: January 2021

Abstract

Background
Expression of programmed cell death ligand 1 (PD-L1) on tumor cells with or without immune cells is widely reported in clinical trials of programmed cell death receptor 1 (PD-1) blockade in metastatic non-small cell lung cancer. Various cutpoints have been studied.

Methods
We performed a systematic search of MEDLINE, EMBASE, and conference proceedings up to December 2019 for randomized and nonrandomized clinical trials of anti-PD-1 or anti-PD-L1 monotherapy in metastatic non-small cell lung cancer. We retrieved data on objective response rate (ORR), 1-year and 2-year progression-free survival (PFS), and 2-year and 3-year overall survival (OS) in various PD-L1 subgroups. Results were pooled and analyzed based on different cutpoints, with nonrandomized comparisons made with pooled chemotherapy outcomes.

Results
A total of 9810 patients in 27 studies were included. In treatment-naïve patients, benefits with PD-1 blockade over chemotherapy were seen in ORR in patients having PD-L1 50% or greater, in 2-year OS for PD-L1 1% or greater, and in 1-year PFS, 2-year PFS, and 3-year OS for unselected patients. First-line PD-1 blockade compared with chemotherapy demonstrated higher ORR, 2-year PFS, and 3-year OS if PD-L1 was 50% or greater; lower ORR, higher 2-year PFS, and similar 3-year OS if PD-L1 was 1%-49%; and lower ORR, similar 1-year PFS, and lower 2-year OS if PD-L1 was less than 1%. In previously treated patients, PD-1 blockade demonstrated similar or superior outcomes to chemotherapy in all PD-L1 subgroups.

Conclusions
PD-L1 should guide the choice of PD-1 blockade vs chemotherapy in treatment-naïve patients. In previously treated patients, PD-1 blockade provides a favorable outcome profile to chemotherapy in all PD-L1 subgroups.
Refugees’ Transnational Livelihoods and Remittances: Syrian Mobilities in the Middle East Before and After 2011
Authors: Zuntz Ann-Christin 
Published: January 2021

Abstract
Pursuing an ethnographic approach, this article explores how Syrians’ pre-war kinship-based networks have oriented livelihoods strategies for refugees in Jordan after 2011. Drawing on long-term fieldwork (2015–2017) in northern Jordan, I argue that seasonal migration was a livelihoods strategy for Syria’s rural poor long before 2011, serving as their old-age provision and contributing to rural development. Since 2011, conflict-induced displacement and border closures have reshaped Syrians’ transnational kinship-based networks: geographically, but also with regard to the diversification of sources of income and gendered responsibilities. In Jordan, Syrian refugees mobilize pre-war transnational ties to access jobs in agriculture and the humanitarian sector, and distribute their income through kinship-based cross-border networks. These ethnographic findings challenge a localized understanding of refugee livelihoods, demonstrating that the household economies of refugees, migrants, and those left behind, in Syria, Jordan, the Gulf countries, and now Europe, are intertwined. In closing, I provide recommendations about how a networked understanding of refugee livelihoods can inform the COVID-19 emergency response, and help create decent jobs for displaced people in the Global South.
A logic of knowledge based on abstract arguments
Authors: Wáng Yì N , Li Xu 
Published: January 2021

AbstractWe introduce a logic of knowledge in a framework in which knowledge is treated as a kind of belief. The framework is based on a standard KD45 characterization of belief, and the characterization of knowledge undergoes the classical tripartite analysis that knowledge is justified true belief, which has a natural link to the studies of logics of evidence and justification. The interpretation of knowledge avoids the unwanted properties of logical omniscience, independent of the choice of the base logic of belief. We axiomatize the logic, prove its soundness and completeness and study the computational complexity results of the model checking and satisfiability problems. We extend the logic to a multi-agent setting and introduce a variant in which belief is characterized in a weaker system to avoid the problem of logical omniscience.
Heterogeneity of Psychological Profiles in French Army Units and Psychological Changes Between Pre- and Post-deployment: Two Pilot Studies
Authors: Verdonk Charles , Duffaud Anaïs M , Claverie Damien , Fromage Dominique , Vieira Céline , Canini Frédéric , Trousselard Marion 
Published: January 2021

ABSTRACT

Introduction
Over the past two decades, overseas deployments of the French Army have been characterized by the exposure of its service personnel to sustained, high levels of combat stress. There is a need to assess their mental health throughout the deployment cycle, identify risk factors associated with stress-related disorders, and characterize the factors that promote long-term well-being.

Methods
We conducted two pilot studies within four units of the French Army: a conventional combat unit, a counterterrorist unit, a combat service support unit, and a medical support unit. Study 1 (n = 65) analyzed the psychological functioning of service personnel with respect to their personality and stress management characteristics. Study 2 (n = 40) analyzed the impact of overseas deployment on stress-related psychological outcomes.

Results
Overall, results from study 1 showed that service personnel have a protective psychological functioning, which is particularly developed in the counterterrorist unit. In study 2, although no stress-related disorder symptoms were observed with the psychometric tools used, a certain degree of psychological dysfunction (social dysfunction and lower positive affect) was detected post-deployment.

Conclusions
These two complementary studies are key elements in developing a better understanding of unmet, medico-military needs that lie on the pathway that links exposure to stressors to impaired health. Certain personnel enrolled in the French Army (notably, the counterterrorist unit) were found to have a high level of protective psychological functioning, largely due to the training they receive. Nevertheless, overall, overseas deployment was associated with poorer psychological functioning and the emergence of social dysfunction, especially in units responsible for the care of service personnel (medical support and combat service support units).
Propensity-Adjusted Comparative Analysis of Radial Versus Femoral Access for Neurointerventional Treatments
Authors: Catapano Joshua S , Ducruet Andrew F , Nguyen Candice L , Majmundar Neil , Wilkinson D Andrew , Cole Tyler S , Baranoski Jacob F , Cavalcanti Daniel D , Fredrickson Vance L , Srinivasan Visish M , Rutledge Caleb , Lawton Michael T , Albuquerque Felipe C 
Published: January 2021

Abstract

BACKGROUND
Transradial artery (TRA) catheterization for neuroendovascular procedures is associated with a lower risk of complications than transfemoral artery (TFA) procedures. However, the majority of literature on TRA access pertains to diagnostic procedures rather than interventional treatments.

OBJECTIVE
To compare TRA and TFA approaches for cerebrovascular interventions.

METHODS
All patients with an endovascular intervention performed at a single center from October 1, 2018 to December 31, 2019 were retrospectively analyzed. Patients were grouped into 2 cohorts on the basis of whether TRA or TFA access was used. Outcomes included complications, fluoroscopy times, and total contrast administered.

RESULTS
A total 579 interventional treatments were performed during the 15-mo study period. TFA procedures (n = 417) were associated with a significantly higher complication rate than TRA (n = 162) procedures (43 cases [10%] vs 5 cases [3%]; P = .008). After excluding patients who underwent thrombectomy and performing a propensity adjustment (including age, sex, pathology, procedure, sheath size, and catheter size), TRA catheterization was associated with decreased odds of a complication (odds ratio, 0.25; 95% CI 0.085-0.72; P = .01), but no significant difference in the amount of contrast administered (6.7-mL increase; 95% CI, −7.2 to 20.6; P = .34) or duration of fluoroscopy (2.1-min increase; 95% CI, −2.5 to 6.7; P = .37) compared with TFA catheterization.

CONCLUSION
Neurointerventional procedures and treatments for a variety of pathologies can be performed successfully using the TRA approach, which is associated with a lower risk of complications and no difference in fluoroscopy duration compared with the TFA approach.
The COVID-19 Symptom to Isolation Cascade in a Latinx Community: A Call to Action
Authors: Rubio Luis A , Peng James , Rojas Susy , Rojas Susana , Crawford Emily , Black Douglas , Jacobo Jon , Tulier-Laiwa Valerie , Hoover Christopher M , Martinez Jackie , Jones Diane , Sachdev Darpun , Cox Chesa , Herrera Eduardo , Valencia Rebecca , Zurita Karla G , Chamie Gabriel ,   The CLIAHUB Consortium, DeRisi Joe , Petersen Maya , Havlir Diane V , Marquez Carina 
Published: January 2021

Abstract

Background
Rapid coronavirus disease 2019 (COVID-19) diagnosis and isolation of infectious persons are critical to stopping forward transmission, and the care cascade framework can identify gaps in the COVID-19 response.

Methods
We described a COVID-19 symptom to isolation cascade and barriers among symptomatic persons who tested polymerase chain reaction positive for severe acute respiratory disease coronavirus 2 (SARS-CoV-2) at a low-barrier testing site serving a low-income Latinx community in San Francisco. Steps in the cascade are defined as days from symptom onset to test, test to result, and result to counseling on self-isolation. We examined SARS-CoV-2 cycle threshold (Ct) values to assess the likelihood of infectiousness on the day of testing and during missed isolation days.

Results
Among 145 persons, 97% were Latinx and 81% had an income of &lt;$50 000. The median time from symptom onset to isolation (interquartile range [IQR]) was 7 (5–10) days, leaving a median (IQR) of 3 (0–6) days of isolation. Eighty-three percent had moderate to high levels of virus (Ct &lt;33), but by disclosure 23% were out of their isolation period. The longest intervals were symptom onset to test (median [IQR], 4 [2–9] days) and test to results notification (median [IQR], 3 [2–4] days). Access to a test site was the most common barrier to testing, and food and income loss was the most common barrier to isolation.

Conclusions
Over half of the 10-day isolation period passed by the time of disclosure, and over a fifth of people were likely outside the window of infectiousness by the time they received results. Improvements in test access and turnaround time, plus support for isolation, are needed for epidemic control of SARS-CoV-2 in highly impacted communities.
Natural variation in plant telomere length is associated with flowering time
Authors: Choi Jae Young , Abdulkina Liliia R , Yin Jun , Chastukhina Inna B , Lovell John T , Agabekian Inna A , Young Pierce G , Razzaque Samsad , Shippen Dorothy E , Juenger Thomas E , Shakirov Eugene V , Purugganan Michael D 
Published: January 2021

Abstract
Telomeres are highly repetitive DNA sequences found at the ends of chromosomes that protect the chromosomes from deterioration duringcell division. Here, using whole-genome re-sequencing and terminal restriction fragment assays, we found substantial natural intraspecific variation in telomere length in Arabidopsis thaliana, rice (Oryza sativa), and maize (Zea mays). Genome-wide association study (GWAS) mapping in A. thaliana identified 13 regions with GWAS-significant associations underlying telomere length variation, including a region that harbors the telomerase reverse transcriptase (TERT) gene. Population genomic analysis provided evidence for a selective sweep at the TERT region associated with longer telomeres. We found that telomere length is negatively correlated with flowering time variation not only in A. thaliana, but also in maize and rice, indicating a link between life-history traits and chromosome integrity. Our results point to several possible reasons for this correlation, including the possibility that longer telomeres may be more adaptive in plants that have faster developmental rates (and therefore flower earlier). Our work suggests that chromosomal structure itself might be an adaptive trait associated with plant life-history strategies.
Impact of COVID-19 on corticosteroids and antibiotics prescribing in England: an interrupted time series analysis
Authors: Chalitsios Christos V , McKeever Tricia M , Langley Tessa E , Shaw Dominick E 
Published: January 2021

Abstract
Inhaled corticosteroids (ICS), prednisolone and antibiotics all play a crucial role in the management of respiratory diseases. The aim of this study was to analyse whether the declaration of the COVID-19 pandemic affected prescribing rates, as public health measures were implemented to reduce transmission of SARS-CoV-2. Monthly practise-level prescribing data published by NHS Digital were analysed. At the point, the COVID-19 outbreak was declared a pandemic, ICS prescriptions rose significantly. This was followed by a decrease in ICS and prednisolone prescribing in the following months. There was no difference in the antibiotic prescribing trend.
The State Price Density Implied by Crude Oil Futures and Option Prices
Authors: Christoffersen Peter , Jacobs Kris , Pan Xuhui (Nick) 
Published: January 2021

Abstract
Both large oil price increases and decreases are associated with deteriorating economic conditions. The projection of the state price density (SPD) onto oil returns estimated from oil futures and option prices displays a U-shaped pattern. Because investors assign high state prices to large negative and large positive oil returns, the U-shaped SPD may steepen in either tail when economic conditions deteriorate. The positive return region of the SPD is more closely related to economic conditions. The oil SPD contains information about economic conditions and future security returns that is distinct from the information in the stock index SPD.
Association between Toxoplasma gondii infection and coronary atherosclerosis
Authors: Alhusseiny Samar M , Saleh Nora E , El-Zayady Wafaa M , Hussein Mohammed S , El-Beshbishi Samar N 
Published: January 2021

Abstract

Background
Toxoplasma gondii is a worldwide protozoon that can infect all nucleated vertebrate cells. Little information is available about the association between T. gondii infection and coronary atherosclerosis.

Methods
A total of 320 cases were enrolled (160 patients with coronary atherosclerosis and 160 non-atherosclerotic individuals). Blood samples were collected to measure anti–T. gondii immunoglobulin G (IgG) antibodies using enzyme-linked immunosorbent assay (ELISA) and serum lipid profile. Coronary angiogram was also performed.

Results
The seroprevalence of anti-Toxoplasma antibodies in atherosclerotic and non-atherosclerotic individuals was 63.1% and 46.2%, respectively, with higher levels of anti–T. gondii IgG in atherosclerotic patients. Consumption of contaminated water, unwashed fruits and vegetables and raw meat and contact with soil were significant risk factors for Toxoplasma infection. Significant differences were detected in serum levels of low-density lipoproteins, triglycerides and cholesterol between both groups. Positive correlations were detected between ELISA titres and serum levels of low-density lipoproteins, triglycerides and cholesterol, disease severity and the number of affected vessels. Male gender and contact with soil had a significant association with positive T. gondii serology in atherosclerotic patients.

Conclusions
Patients with coronary atherosclerosis have a high prevalence of T. gondii infection. More studies are crucial to elucidate the mechanisms underlying the effects of chronic toxoplasmosis on coronary atherosclerosis.
Predicting the impact of COVID-19 interruptions on transmission of gambiense human African trypanosomiasis in two health zones of the Democratic Republic of Congo
Authors: Aliee Maryam , Castaño Soledad , Davis Christopher N , Patel Swati , Miaka Erick Mwamba , Spencer Simon E F , Keeling Matt J , Chitnis Nakul , Rock Kat S 
Published: January 2021

Abstract
Many control programmes against neglected tropical diseases have been interrupted due to the coronavirus disease 2019 (COVID-19) pandemic, including those that rely on active case finding. In this study we focus on gambiense human African trypanosomiasis (gHAT), where active screening was suspended in the Democratic Republic of Congo (DRC) due to the pandemic. We use two independent mathematical models to predict the impact of COVID-19 interruptions on transmission and reporting and achievement of the 2030 elimination of transmission (EOT) goal for gHAT in two moderate-risk regions of the DRC. We consider different interruption scenarios, including reduced passive surveillance in fixed health facilities, and whether this suspension lasts until the end of 2020 or 2021. Our models predict an increase in the number of new infections in the interruption period only if both active screening and passive surveillance were suspended, and with a slowed reduction—but no increase—if passive surveillance remains fully functional. In all scenarios, the EOT may be slightly pushed back if no mitigation, such as increased screening coverage, is put in place. However, we emphasise that the biggest challenge will remain in the higher-prevalence regions where EOT is already predicted to be behind schedule without interruptions unless interventions are bolstered.
Prediction of Delivery Complications by First-Trimester Ultrasound Measurement of the Gestational Sac's Distance From a Previous Cesarean Section Scar
Authors: Li Cong , Yang Pan , Luo Hong 
Published: January 2021

(Abstracted from J Ultrasound Med 2020;39:1563–1571)
Cesarean delivery has been increasing globally. The cesarean section (CS) scar has been thought to be involved in the etiology of several specific conditions, such as cesarean scar pregnancy (CSP), placental abnormalities, and scar dehiscence.
HPV Vaccination and the Risk of Invasive Cervical Cancer
Authors: Lei Jiayao , Ploner Alexander , Elfström K. Miriam , Wang Jiangrong , Roth Adam , Fang Fang , Sundström Karin , Dillner Joakim , Sparén Pär 
Published: January 2021

(Abstracted from N Engl J Med 2020;383:1340–1348)
Because of the well-established association between oncogenic types of human papillomavirus (HPV) and cervical cancer, as of December 2019 a total of 124 countries and territories had implemented HPV vaccination programs. Studies have demonstrated that HPV vaccination protects against HPV infection, genital warts, and high-grade precancerous cervical lesions.
Risk Factors for Bowel Injury in Hysterectomy for Benign Indications
Authors: Zhu Cici R. , Mallick Ranjeeta , Singh Sukhbir S. , Auer Rebecca , Solnik Jonathon , Choudhry Abdul Jamil , Chen Innie 
Published: January 2021

(Abstracted from Obstet Gynecol 2020;136:803–810)
The vast majority of hysterectomies are performed for benign indications. Visceral injuries are major intraoperative complications of hysterectomy.
Cost and Reimbursement of Providing Routine Vaccines in Outpatient Obstetrician/Gynecologist Settings
Authors: Dempsey Amanda F. , Pyrzanowski Jennifer , Campbell Jonathan , Brewer Sarah , Sevick Carter , O'Leary Sean T. 
Published: January 2021

(Abstracted from Am J Obstet Gynecol 2020;223:562.e1–562.e8)
Both nationally and globally, immunization rates among adults are poor. Greater efforts are needed to improve vaccination rates.
Hemadsorption
Authors: Cutuli Salvatore Lucio , Grieco Domenico Luca , De Pascale Gennaro , Antonelli Massimo 
Published: January 2021

Purpose of review
To review pathophysiological pathways of immune system response to infections, which may justify mediators removal by extracorporeal blood purification therapies (EBPTs) in critically ill septic patients. Moreover, we presented an overview of the EBPTs mostly used in clinical practice with the aim to modulate immune system dysfunction in sepsis.

Recent findings
Sepsis is a life-threatening disease and recent findings showed that its pathophysiology relies on dysregulated immune system response to pathogen invasion of the body. In the light of this view, EBPTs have been demonstrated effective to remove specific mediators and foster balance between pro- and anti-inflammatory pathways.

Summary
EBPTs have been widely used in clinical practice, with the aim to modulate immune system dysfunction by the removal of pathogens and inflammatory mediators in critically ill patients with sepsis. Such therapies are characterised by specific structural features, which allow selective and nonselective removal of mediators by adsorption. However, few evidences support their role in the management of critically ill patients with sepsis. Accordingly, an evidence-based and personalized approach to EBPTs in sepsis is strongly advocated, in order to solve controversies in this field and optimise the management of critically ill septic patients.