bluuebunny/crossref_metadata_2025_split huggingface dataset:
ExplorATE: a new pipeline to explore active transposable elements from RNA-seq data
Authors: Femenias Martin M , Santos Juan C , Sites Jack W , Avila Luciano J , Morando Mariana 
Published: May 2022

Abstract

Motivation
Transposable elements (TEs) are ubiquitous in genomes and many remain active. TEs comprise an important fraction of the transcriptomes with potential effects on the host genome, either by generating deleterious mutations or promoting evolutionary novelties. However, their functional study is limited by the difficulty in their identification and quantification, particularly in non-model organisms.

Results
We developed a new pipeline [explore active transposable elements (ExplorATE)] implemented in R and bash that allows the quantification of active TEs in both model and non-model organisms. ExplorATE creates TE-specific indexes and uses the Selective Alignment (SA) to filter out co-transcribed transposons within genes based on alignment scores. Moreover, our software incorporates a Wicker-like criteria to refine a set of target TEs and avoid spurious mapping. Based on simulated and real data, we show that the SA strategy adopted by ExplorATE achieved better estimates of non-co-transcribed elements than other available alignment-based or mapping-based software. ExplorATE results showed high congruence with alignment-based tools with and without a reference genome, yet ExplorATE required less execution time. Likewise, ExplorATE expands and complements most previous TE analyses by incorporating the co-transcription and multi-mapping effects during quantification, and provides a seamless integration with other downstream tools within the R environment.

Availability and implementation
Source code is available at https://github.com/FemeniasM/ExplorATEproject and https://github.com/FemeniasM/ExplorATE_shell_script. Data available on request.

Supplementary information
Supplementary data are available at Bioinformatics online.
Associations of lung cancer risk with biomarkers of Helicobacter pylori infection
Authors: Yoon Hyung-Suk , Shu Xiao-Ou , Cai Hui , Zheng Wei , Wu Jie , Wen Wanqing , Courtney Regina , Shidal Chris , Waterboer Tim , Blot William J , Cai Qiuyin 
Published: May 2022

Abstract
Helicobacter pylori infection has been suggested to be associated with lung cancer risk. However, information is lacking on whether the association differs by H. pylori antigen. We conducted a nested case-control study within the Southern Community Cohort Study, including 295 incident lung cancer cases and 295 controls. Helicobacter pylori multiplex serology assay was performed to detect antibodies to 15 H. pylori proteins. Conditional logistic regression was used to estimate odds ratios (ORs) and confidence intervals (95% CIs) after adjustment for covariates. Overall H. pylori+ was associated with a non-statistically significant increased risk of lung cancer (OR: 1.29; 95% CI: 0.85–1.95). Significant associations, however, were observed for H. pylori+ VacA+ (OR: 1.64; 95% CI: 1.02–2.62) and H. pylori+ Catalase+ (OR: 1.75; 95% CI: 1.11–2.77). The positive association of H. pylori+ Catalase+ with lung cancer risk was predominantly seen among African Americans (OR: 2.09; 95% CI: 1.11–3.95) but not European Americans (OR: 1.20; 95% CI: 0.56–2.54). Among participants who smoked ≥ 30 pack-years, overall H. pylori+ (OR: 1.85; 95% CI: 1.02–3.35), H. pylori+ CagA+ (OR: 2.77; 95% CI: 1.35–5.70), H. pylori+ VacA+ (OR: 2.53; 95% CI: 1.25–5.13) and H. pylori+ HP1564+ (OR: 2.01; 95% CI: 1.07–3.77) were associated with increased risk of lung cancer. Our study provides novel evidence that associations of H. pylori infection with lung cancer risk differ by H. pylori biomarker, may be more evident among African Americans and may be modified by smoking habits. Furthermore, studies are warranted to confirm our findings.
Paving the Way Towards Precision Vaccinology: The Paradigm of Myocarditis After Coronavirus Disease 2019 (COVID-19) Vaccination
Authors: Lagousi Theano , Papadatou Ioanna , Strempas Petros , Chatzikalil Elena , Spoulou Vana 
Published: May 2022

Abstract
Systems vaccinology approaches have introduced novel tools for the evaluation of the safety profile of novel vaccine antigens by developing biomarkers of vaccine reactogenicity associated with potential adverse events. The use of such approaches may prove extremely advantageous in the context of a global pandemic where accelerated approval of new vaccine formulations for all ages is essential for the containment of the epidemic. The spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has had devastating effects on global health, but the emergency authorization of mRNA vaccines significantly reduced SARS-CoV-2–associated morbidity and mortality. Despite their favorable safety profile in adult populations, recent reports have raised concerns about an association of the mRNA-based vaccines with acute myocarditis, predominantly among male adolescents and young adults following the second vaccine dose. Here, we review data on myocarditis epidemiology following SARS-CoV-2 mRNA vaccination and describe potential mechanisms involved that may explain the sex- and age-related differences, focusing on mRNA immune reactivity. The case of vaccine-associated myocarditis highlights the need to incorporate precision vaccinology approaches for the development of safe and effective vaccines for everyone.
How Drivers of Seasonality in Respiratory Infections May Impact Vaccine Strategy: A Case Study in How Coronavirus Disease 2019 (COVID-19) May Help Us Solve One of Influenza’s Biggest Challenges
Authors: Lofgren Eric T , Naumova Elena N , Gorski Jack , Naumov Yuri , Fefferman Nina H 
Published: May 2022

Abstract
Vaccines against seasonal infections like influenza offer a recurring testbed, encompassing challenges in design, implementation, and uptake to combat a both familiar and ever-shifting threat. One of the pervading mysteries of influenza epidemiology is what causes the distinctive seasonal outbreak pattern. Proposed theories each suggest different paths forward in being able to tailor precision vaccines and/or deploy them most effectively. One of the greatest challenges in contrasting and supporting these theories is, of course, that there is no means by which to actually test them. In this communication we revisit theories and explore how the ongoing coronavirus disease 2019 (COVID-19) pandemic might provide a unique opportunity to better understand the global circulation of respiratory infections. We discuss how vaccine strategies may be targeted and improved by both isolating drivers and understanding the immunological consequences of seasonality, and how these insights about influenza vaccines may generalize to vaccines for other seasonal respiratory infections.
Constitutive expression of the global regulator AbrB restores the growth defect of a genome-reduced Bacillus subtilis strain and improves its metabolite production
Authors: Yamamoto Junya , Chumsakul Onuma , Toya Yoshihiro , Morimoto Takuya , Liu Shenghao , Masuda Kenta , Kageyama Yasushi , Hirasawa Takashi , Matsuda Fumio , Ogasawara Naotake , Shimizu Hiroshi , Yoshida Ken-ichi , Oshima Taku , Ishikawa Shu 
Published: May 2022

Abstract
Partial bacterial genome reduction by genome engineering can improve the productivity of various metabolites, possibly via deletion of non-essential genome regions involved in undesirable metabolic pathways competing with pathways for the desired end products. However, such reduction may cause growth defects. Genome reduction of Bacillus subtilis MGB874 increases the productivity of cellulases and proteases but reduces their growth rate. Here, we show that this growth defect could be restored by silencing redundant or less important genes affecting exponential growth by manipulating the global transcription factor AbrB. Comparative transcriptome analysis revealed that AbrB-regulated genes were upregulated and those involved in central metabolic pathway and synthetic pathways of amino acids and purine/pyrimidine nucleotides were downregulated in MGB874 compared with the wild-type strain, which we speculated were the cause of the growth defects. By constitutively expressing high levels of AbrB, AbrB regulon genes were repressed, while glycolytic flux increased, thereby restoring the growth rate to wild-type levels. This manipulation also enhanced the productivity of metabolites including γ-polyglutamic acid. This study provides the first evidence that undesired features induced by genome reduction can be relieved, at least partly, by manipulating a global transcription regulation system. A similar strategy could be applied to other genome engineering-based challenges aiming toward efficient material production in bacteria.
Syncope in a pregnant woman with repaired Tetralogy of Fallot: a case report
Authors: Ghazaryan Nare , Adamyan Miqayel , Khachatryan Lianna , Hovakimyan Tatevik 
Published: May 2022

Abstract

Background
Tetralogy of Fallot (TOF) is one of the most widespread cyanotic congenital heart disease (CHD), which can be successfully repaired in the neonatal period. However, residual problems and the surgical technique itself can create a favourable basis for arrhythmias and conduction abnormalities in these patients. Sometimes, these arrhythmias may worsen during pregnancy and require urgent intervention.

Case summary
This is a case of a 25-year-old woman, who underwent a surgical repair of TOF at the age of 2 years. She suffered an ischaemic stroke postoperatively, which was complicated with secondary seizures and syncope. These episodes were evaluated as epilepsy. The patient was admitted to our hospital with the above-mentioned complaints in the 10th week of pregnancy. A comprehensive cardiac examination was performed. Her presyncopal event was captured during Holter monitoring, which documented a severe dysfunction of the sinus node. She was diagnosed with postoperative sick sinus syndrome and implanted with a permanent dual-chamber pacemaker (PM). After the operation, the patient did not have any episodes of syncope or seizures and the PM check-up showed almost 30% of atrial pacing.

Conclusion
No matter how obvious the neurological or other nature of syncope may seem, it is advised to exclude the cardiac origin of syncope, especially in patients with repaired CHD. One of the most common complications after surgery of CHD is rhythm and conduction disturbances. In some of these cases, permanent PM implantation can be unavoidable, even during pregnancy. The implantation of the PM device during pregnancy can be performed safely.
A case report of distal radial puncture in a patient with acute upper limb ischaemia: the last hope of the cardiologist?
Authors: Giusca Sorin , Schmidt Andrej , Korosoglou Grigorios 
Published: May 2022

Abstract

Background
Patients with acute limb ischaemia (ALI) present with acute symptoms, requiring prompt diagnosis and expedited treatment to preserve the viability of the affected ischaemic tissue.

Case summary
We present an 83-year-old female patient with upper ALI due to thrombotic occlusion of the left brachial artery. Concomitantly, the patient had a first diagnosis of atrial fibrillation and was not on treatment with oral anticoagulation. Transfemoral thrombectomy using a 6F Rotarex® catheter resulted in removal of the thrombus from the brachial artery. However, significant amounts of debris embolized distally, causing occlusion of both the radial and ulnar arteries. The debris was successfully removed after puncture of the distal radial artery and retrograde thrombus aspiration using a 5F Envoy catheter. This manoeuver led to flow restoration in both the radial and ulnar arteries and to complete resolution of ischaemic symptoms of the patient.

Discussion
Interventionists may consider distal radial puncture not only as an access site for coronary angiography but also as an option for the endovascular management of ALI in cases of cardiac embolism, as described herein or in cases of thrombotic complications during routine catheterization and percutaneous coronary intervention. Herein, we describe the case of an 83-year-old patient, who presented with acute upper limb ischaemia. Due to embolization of thrombotic debris during Rotarex® catheter thrombectomy, flow further diminished in the ulnar and radial arteries. The last hope for successful interventional treatment was thrombectomy from distally after retrograde puncture of the distal radial artery. This unique manoeuver led to flow restoration and complete recovery of the patient without the need for open surgery.
Bet-hedging in innate and adaptive immune systems
Authors: Tate Ann T , Van Cleve Jeremy 
Published: May 2022

Abstract
Immune system evolution is shaped by the fitness costs and trade-offs associated with mounting an immune response. Costs that arise mainly as a function of the magnitude of investment, including energetic and immunopathological costs, are well-represented in studies of immune system evolution. Less well considered, however, are the costs of immune cell plasticity and specialization. Hosts in nature encounter a large diversity of microbes and parasites that require different and sometimes conflicting immune mechanisms for defense, but it takes precious time to recognize and correctly integrate signals for an effective polarized response. In this perspective, we propose that bet-hedging can be a viable alternative to plasticity in immune cell effector function, discuss conditions under which bet-hedging is likely to be an advantageous strategy for different arms of the immune system, and present cases from both innate and adaptive immune systems that suggest bet-hedging at play.
Chronic unrelenting cough secondary to pericardial cyst impingement of right phrenic nerve
Authors: Mikhail John , Kennedy Gregory , Singhal Sunil , Resta Isabella Tondi , Nadeem Bilal , Azari Feredun 
Published: May 2022

Abstract
Located in the mediastinum, pericardial cysts are rare and benign congenital abnormalities commonly identified as incidental findings on imaging. However, some patients with abnormally enlarged cysts present with compressive symptoms, which include recurrent infections, tamponade from cardiac compression and respiratory complications. Our report highlights a challenging case of a patient with recurrent respiratory symptoms secondary to phrenic nerve compression. Misdiagnosis over the past decade resulted in ineffective interventions. After clear identification of the cyst compression of the ipsilateral phrenic nerve, the patient underwent a minimally invasive robotically assisted cyst resection with phrenic nerve preservation that alleviated respiratory symptoms.
Optimum Urine Cotinine and NNAL Levels to Distinguish Smokers from Non-Smokers by the Changes in Tobacco Control Policy in Korea from 2008 to 2018
Authors: Park Eun Young , Lim Min Kyung , Park Eunjung , Kim Yoonjung , Lee Dohoon , Oh Kyungwon 
Published: May 2022

Abstract

Introduction
We examined the age- and sex-specific distributions of biomarkers of tobacco smoke exposure to determine the optimal cutoffs to distinguish smokers from non-smokers over the last 10 years in Korea, during which smoking prevalence and secondhand smoke (SHS) exposure declined due to changes in tobacco control policy.

Methods
We analyzed data from the Korea National Health and Nutrition Examination Survey on creatinine-adjusted urinary cotinine (2008–2018; 33 429 adults: 15 653 males and 17 776 females) and 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanol (NNAL; 2016–2018; 6337 adults: 3091 males and 3246 females). We determined the optimal cutoffs and confidence intervals (CIs) to distinguish smokers from non-smokers using receiver operator characteristic curve analysis and bootstrapping (1000 resamples).

Results
The optimal cutoff values of creatinine-adjusted urine cotinine and NNAL concentration were 20.9 ng/mg (95% CI: 20.8–21.0, sensitivity: 96.6%, specificity: 93.8%) and 8.9 pg/mg (95% CI: 8.8–8.9, sensitivity: 94.0%, specificity: 94.7%), respectively, in 2016–2018. The optimal cutoffs of both biomarkers increased with age and were higher in females than in males for NNAL concentration. In both sexes, the optimal cutoff of urine cotinine continuously declined over the study period.

Conclusions
The optimal cotinine cutoff declined along with smoking prevalence and levels of SHS exposure due to enforcement of tobacco control policies, including smoke-free ordinances and tax increases. Monitoring of biomarkers of tobacco exposure appears necessary for verification of smoking status and regulatory use.

Implications
Our results based on nationally representative data suggest that a large decrease in the optimal cutoff value of urine cotinine to distinguish smokers from non-smokers was caused by decreases in smoking prevalence and SHS exposure following enforcement of tobacco control policies over the last 10 years. We determined the optimal cutoff values of urine 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanol (NNAL), which were not previously reported in representative population in Asia, to enable more accurate estimation of exposure to tobacco smoke and proper assessment of disease risks. Gender- and age-specific differences in the optimal cutoffs require further study. Monitoring of biomarkers of tobacco smoke exposure seems necessary for verification of smoking status and regulatory use.
KIL1 terminates fertility in maize by controlling silk senescence
Authors: Šim�škov� M�ria , Daneva Anna , Doll Nicolas , Schilling Neeltje , Cubr�a-Rad�o Marta , Zhou Liangzi , De Winter Freya , Aesaert Stijn , De Rycke Riet , Pauwels Laurens , Dresselhaus Thomas , Brugi�re Norbert , Simmons Carl R , Habben Jeffrey E , Nowack Moritz K 
Published: May 2022

Abstract
Plant flowers have a functional life span during which pollination and fertilization occur to ensure seed and fruit development. Once flower senescence is initiated, the potential to set seed or fruit is irrevocably lost. In maize, silk strands are the elongated floral stigmas that emerge from the husk-enveloped inflorescence to intercept airborne pollen. Here we show that KIRA1-LIKE1 (KIL1), an ortholog of the Arabidopsis NAC (NAM (NO APICAL MERISTEM), ATAF1/2 (Arabidopsis thaliana Activation Factor1 and 2) and CUC (CUP-SHAPED COTYLEDON 2)) transcription factor KIRA1, promotes senescence and programmed cell death (PCD) in the silk strand base, ending the window of accessibility for fertilization of the ovary. Loss of KIL1 function extends silk receptivity and thus strongly increases kernel yield following late pollination. This phenotype offers new opportunities for possibly improving yield stability in cereal crops. Moreover, despite diverging flower morphologies and the substantial evolutionary distance between Arabidopsis and maize, our data indicate remarkably similar principles in terminating floral receptivity by PCD, whose modulation offers the potential to be widely used in agriculture.
Benchmarking in Academic Physical Therapy Using the PT-GQ Survey: Wave 2 Update With Application to Accreditation Reporting
Authors: Dudley-Javoroski Shauna , Shields Richard K 
Published: May 2022

AbstractObjectiveThe Benchmarking in Academic Physical Therapy study uses the Physical Therapist-Graduation Questionnaire (PT-GQ) survey to develop comprehensive performance benchmarks for physical therapist education. These benchmarks facilitate interprofessional comparisons and have application to accreditation self-study reporting. The purpose of this study is to report updated benchmarks from enrollment Wave 2 of the study, with an emphasis on curricular areas that align with accreditation standards.MethodsSeventy doctor of physical therapy (DPT) programs (26.5% national sample) administered the survey to graduates during 2020–2021. Where possible, respondent data were contextualized by statistical comparison with published medical student data (Welch t test, Hedges g).ResultsThere were 1894 respondents who participated in the study (response rate: 63.9%). The average survey duration was 32.9 minutes. White-only, non-Hispanic/Latino/a/x individuals (78.8%) exceeded the 2020 US Census prevalence (60.1%), and only one-half of respondents perceived a benefit to their training from the diversity present in their programs. Over 94% of respondents indicated that their curricula were characterized by “problem solving/critical thinking” and “clinical reasoning,” but nearly one-half indicated “busywork” was prevalent. High curricular satisfaction ratings clustered in content areas relating to profession-specific technical skills and low ratings clustered in foundational sciences. DPT respondents reported significantly lower tolerance for ambiguity, significantly more exhaustion, and significantly less disengagement than medical students. Respondents endorsed higher levels of “adaptive” perfectionism (striving for high performance) than “maladaptive” perfectionism (concern over negative evaluations). Respondents with loans (27.7%) had debt exceeding $150,000, the benchmark above which the DPT degree loses economic power.ConclusionPT-GQ benchmarks revealed strengths (eg, curricula emphasizing problem solving/critical thinking and clinical reasoning) and challenges (eg, low diversity, problematic student debt) in physical therapist education.ImpactPrograms can use benchmarking for quality-improvement efforts and as a data source for accreditation self-study reports. The ongoing study will refine national benchmarks and pilot items to address new research questions.
The Occurrence Birth–Death Process for Combined-Evidence Analysis in Macroevolution and Epidemiology
Authors: Andréoletti Jérémy , Zwaans Antoine , Warnock Rachel C M , Aguirre-Fernández Gabriel , Barido-Sottani Joëlle , Gupta Ankit , Stadler Tanja , Manceau Marc 
Published: May 2022

Abstract
Phylodynamic models generally aim at jointly inferring phylogenetic relationships, model parameters, and more recently, the number of lineages through time, based on molecular sequence data. In the fields of epidemiology and macroevolution, these models can be used to estimate, respectively, the past number of infected individuals (prevalence) or the past number of species (paleodiversity) through time. Recent years have seen the development of “total-evidence” analyses, which combine molecular and morphological data from extant and past sampled individuals in a unified Bayesian inference framework. Even sampled individuals characterized only by their sampling time, that is, lacking morphological and molecular data, which we call occurrences, provide invaluable information to estimate the past number of lineages. Here, we present new methodological developments around the fossilized birth–death process enabling us to (i) incorporate occurrence data in the likelihood function; (ii) consider piecewise-constant birth, death, and sampling rates; and (iii) estimate the past number of lineages, with or without knowledge of the underlying tree. We implement our method in the RevBayes software environment, enabling its use along with a large set of models of molecular and morphological evolution, and validate the inference workflow using simulations under a wide range of conditions. We finally illustrate our new implementation using two empirical data sets stemming from the fields of epidemiology and macroevolution. In epidemiology, we infer the prevalence of the coronavirus disease 2019 outbreak on the Diamond Princess ship, by taking into account jointly the case count record (occurrences) along with viral sequences for a fraction of infected individuals. In macroevolution, we infer the diversity trajectory of cetaceans using molecular and morphological data from extant taxa, morphological data from fossils, as well as numerous fossil occurrences. The joint modeling of occurrences and trees holds the promise to further bridge the gap between traditional epidemiology and pathogen genomics, as well as paleontology and molecular phylogenetics. [Birth–death model; epidemiology; fossils; macroevolution; occurrences; phylogenetics; skyline.]