bluuebunny/crossref_metadata_2025_split huggingface dataset:
Fatty acid photodecarboxylase is an ancient photoenzyme that forms hydrocarbons in the thylakoids of algae
Authors: Moulin Solène L Y , Beyly-Adriano Audrey , Cuiné Stéphan , Blangy Stéphanie , Légeret Bertrand , Floriani Magali , Burlacot Adrien , Sorigué Damien , Samire Poutoum-Palakiyem , Li-Beisson Yonghua , Peltier Gilles , Beisson Fred 
Published: April 2021

Abstract
Fatty acid photodecarboxylase (FAP) is one of the few enzymes that require light for their catalytic cycle (photoenzymes). FAP was first identified in the microalga Chlorella variabilis NC64A, and belongs to an algae-specific subgroup of the glucose–methanol–choline oxidoreductase family. While the FAP from C. variabilis and its Chlamydomonas reinhardtii homolog CrFAP have demonstrated in vitro activities, their activities and physiological functions have not been studied in vivo. Furthermore, the conservation of FAP activity beyond green microalgae remains hypothetical. Here, using a C. reinhardtii FAP knockout line (fap), we showed that CrFAP is responsible for the formation of 7-heptadecene, the only hydrocarbon of this alga. We further showed that CrFAP was predominantly membrane-associated and that &gt;90% of 7-heptadecene was recovered in the thylakoid fraction. In the fap mutant, photosynthetic activity was not affected under standard growth conditions, but was reduced after cold acclimation when light intensity varied. A phylogenetic analysis that included sequences from Tara Ocean identified almost 200 putative FAPs and indicated that FAP was acquired early after primary endosymbiosis. Within Bikonta, FAP was retained in secondary photosynthetic endosymbiosis lineages but absent from those that lost the plastid. Characterization of recombinant FAPs from various algal genera (Nannochloropsis, Ectocarpus, Galdieria, Chondrus) provided experimental evidence that FAP photochemical activity was present in red and brown algae, and was not limited to unicellular species. These results thus indicate that FAP was conserved during the evolution of most algal lineages where photosynthesis was retained, and suggest that its function is linked to photosynthetic membranes.
SeedQuant: a deep learning-based tool for assessing stimulant and inhibitor activity on root parasitic seeds
Authors: Braguy Justine , Ramazanova Merey , Giancola Silvio , Jamil Muhammad , Kountche Boubacar A , Zarban Randa , Felemban Abrar , Wang Jian You , Lin Pei-Yu , Haider Imran , Zurbriggen Matias , Ghanem Bernard , Al-Babili Salim 
Published: April 2021

Abstract
Witchweeds (Striga spp.) and broomrapes (Orobanchaceae and Phelipanche spp.) are root parasitic plants that infest many crops in warm and temperate zones, causing enormous yield losses and endangering global food security. Seeds of these obligate parasites require rhizospheric, host-released stimulants to germinate, which opens up possibilities for controlling them by applying specific germination inhibitors or synthetic stimulants that induce lethal germination in the host’s absence. To determine their effect on germination, root exudates or synthetic stimulants/inhibitors are usually applied to parasitic seeds in in vitro bioassays, followed by assessment of germination ratios. Although these protocols are very sensitive, the germination recording process is laborious, representing a challenge for researchers and impeding high-throughput screens. Here, we developed an automatic seed census tool to count and discriminate germinated seeds (GS) from non-GS. We combined deep learning, a powerful data-driven framework that can accelerate the procedure and increase its accuracy, for object detection with computer vision latest development based on the Faster Region-based Convolutional Neural Network algorithm. Our method showed an accuracy of 94% in counting seeds of Striga hermonthica and reduced the required time from approximately 5 min to 5 s per image. Our proposed software, SeedQuant, will be of great help for seed germination bioassays and enable high-throughput screening for germination stimulants/inhibitors. SeedQuant is an open-source software that can be further trained to count different types of seeds for research purposes.
Risk of coronavirus disease 2019 hospitalization and mortality in rheumatic patients treated with hydroxychloroquine or other conventional disease-modifying anti-rheumatic drugs in Italy
Authors: Spila Alegiani Stefania , Crisafulli Salvatore , Giorgi Rossi Paolo , Mancuso Pamela , Salvarani Carlo , Atzeni Fabiola , Gini Rosa , Kirchmayer Ursula , Belleudi Valeria , Kurotschka Peter Konstantin , Leoni Olivia , Ludergnani Monica , Ferroni Eliana , Baracco Susanna , Massari Marco , Trifirò Gianluca ,   the ITA-COVID-19 Network
Published: April 2021

Abstract

Objectives
To ascertain if the use of hydroxychloroquine(HCQ)/cloroquine(CLQ) and other conventional DMARDs (cDMARDs) and rheumatic diseases per se may be associated with COVID-19-related risk of hospitalization and mortality.

Methods
This case–control study nested within a cohort of cDMARD users was conducted in the Lombardy, Veneto, Tuscany and Lazio regions and Reggio Emilia province. Claims databases were linked to COVID-19 surveillance registries. The risk of COVID-19-related outcomes was estimated using a multivariate conditional logistic regression analysis comparing HCQ/CLQ vs MTX, vs other cDMARDs and vs non-use of these drugs. The presence of rheumatic diseases vs their absence in a non-nested population was investigated.

Results
A total of 1275 patients hospitalized due to COVID-19 were matched to 12 734 controls. Compared with recent use of MTX, no association between HCQ/CLQ monotherapy and COVID-19 hospitalization [odds ratio (OR) 0.83 (95% CI 0.69, 1.00)] or mortality [OR 1.19 (95% CI 0.85, 1.67)] was observed. A lower risk was found when comparing HCQ/CLQ use with the concomitant use of other cDMARDs and glucocorticoids. HCQ/CLQ was not associated with COVID-19 hospitalization as compared with non-use. An increased risk for recent use of either MTX monotherapy [OR 1.19 (95% CI 1.05, 1.34)] or other cDMARDs [OR 1.21 (95% CI 1.08, 1.36)] vs non-use was found. Rheumatic diseases were not associated with COVID-19-related outcomes.

Conclusion
HCQ/CLQ use in rheumatic patients was not associated with a protective effect against COVID-19-related outcomes. The use of other cDMARDs was associated with an increased risk when compared with non-use and, if concomitantly used with glucocorticoids, also vs HCQ/CLQ, probably due to immunosuppressive action.
EVALUATION OF VGC ANALYZER BY COMPARISON WITH GOLD STANDARD ROC SOFTWARE AND ANALYSIS OF SIMULATED VISUAL GRADING DATA
Authors: Hansson Jonny , Månsson Lars Gunnar , Båth Magnus 
Published: April 2021

Abstract
The purpose of the present work was to evaluate the use of resampling statistical methods for analysis of visual grading data—implemented in the software VGC Analyzer—by comparing the reanalyzed results from previously performed visual grading studies with the results calculated by gold standard receiver operating characteristic (ROC) methodology, Obuchowski-Rockette (OR)-Dorfman–Berbaum–Metz (DBM) multiple-readers and multiple-case (MRMC) and by analysis of simulated visual grading data where the true distribution was presumed to be known. The reanalysis was performed on two multiple-reader studies with non-paired data and paired data, respectively. The simulation study was performed by simulating a large number of visual grading characteristics (VGC) studies and by analyzing the statistical distribution of null hypothesis (H0) rejection rate. The comparison with OR-DBM MRMC showed good agreement when analyzing non-paired data for both fixed-reader and random-reader settings for the calculated area under the curve values and the confidence intervals (CIs). For paired data analysis, VGC Analyzer showed significantly lower CIs compared with the ROC software. This effect was also illustrated by the simulation study, where the VGC Analyzer, in general, showed good accuracy for simulated studies with stable statistical basis. For simulated studies with unstable statistics, the accuracy in the H0 rejection rate decreased. The present study has shown that resampling methodology can be used to accurately perform the statistical analysis of a VGC study, although the resampling technique used makes the method sensitive to small data sets.
A Systematic Review of Cognition-Brain Morphology Relationships on the Schizophrenia-Bipolar Disorder Spectrum
Authors: Karantonis James A , Carruthers Sean P , Rossell Susan L , Pantelis Christos , Hughes Matthew , Wannan Cassandra , Cropley Vanessa , Van Rheenen Tamsyn E 
Published: April 2021

Abstract
The nature of the relationship between cognition and brain morphology in schizophrenia-spectrum disorders (SSD) and bipolar disorder (BD) is uncertain. This review aimed to address this, by providing a comprehensive systematic investigation of links between several cognitive domains and brain volume, cortical thickness, and cortical surface area in SSD and BD patients across early and established illness stages. An initial search of PubMed and Scopus databases resulted in 1486 articles, of which 124 met inclusion criteria and were reviewed in detail. The majority of studies focused on SSD, while those of BD were scarce. Replicated evidence for specific regions associated with indices of cognition was minimal, however for several cognitive domains, the frontal and temporal regions were broadly implicated across both recent-onset and established SSD, and to a lesser extent BD. Collectively, the findings of this review emphasize the significance of both frontal and temporal regions for some domains of cognition in SSD, while highlighting the need for future BD-related studies on this topic.
Contribution and Acceptability of Bacteriological Collection Tools in the Diagnosis of Tuberculosis in Children Infected with HIV
Authors: Sanogo Bintou , Kiema Pegdewende Eliane , Barro Makoura , Nacro Sahoura Fatimata , Ouermi Saga Alain , Msellati Philippe , Nacro Boubacar 
Published: April 2021

Abstract

Objective
The objective of this study is to evaluate the feasibility and tolerability of new bacteriological samples to diagnose tuberculosis (TB) in HIV-infected children.

Method and patients
HIV1-infected children with suspicion of TB in Universitary Hospital Sourô Sanon (Burkina Faso) were included in a prospective cohort study. Children underwent three gastric aspirates (GA) if aged &lt;4 years; two GA, one string test (ST) if aged 4–9 years and three sputum, one ST if aged 10–13 years. All children underwent one nasopharyngeal aspirate (NPA) and one stool sample. To assess feasibility and tolerability of procedures, adverse events were identified and pain was rated on different scales. Samples were tested by microscopy, culture, GeneXpert® (Xpert®).

Results
Sixty-three patients were included. Mean age was 8.92 years, 52.38% were females. Ninety-five GA, 67 sputum, 62 NPA, 60 stool and 55 ST had been performed. During sampling, the main adverse events were cough at 68/95 GA and 48/62 NPA; sneeze at 50/95 GA and 38/62 NPA and vomiting at 4/55 ST. On the behavioral scale, the average pain score during collection was 6.38/10 for GA; 7.70/10 for NPA and 1.03/10 for ST. Of the 31 cases of TB, bacteriological confirmation was made in 12 patients.

Conclusion
ST, stool is well-tolerated alternatives specimens for diagnosing TB in children. NPA has a poor feasibility and tolerability in children.
Long-Term Outcomes in Children Surviving Tropical Arboviral Encephalitis: A Systematic Review
Authors: Chow Christal , Dehority Walter 
Published: April 2021

Abstract

Background
Survivors of childhood encephalitis often suffer from physical and neurocognitive sequelae, particularly in tropical, resource-limited areas with a large burden of arboviral, neurotropic pathogens and limited resources with which to address chronic morbidities. Research into overall and pathogen-specific outcomes following childhood encephalitis may help identify risk factors for poor outcomes, quantify the burden of sequelae, assist with resource allocation and help focus rehabilitative efforts. However, such research is limited. To this end, we systematically reviewed the literature on this topic to identify gaps in knowledge worthy of future investigation.

Methods
A search of PubMed, Web of Knowledge and the Cochrane databases was performed 10 January through 20 February 2020, using 17 search terms for sequelae and 14 for tropical, arboviral pathogens. Eligible reports demonstrated post-discharge follow-up of ≥3 months and assessment of clinical outcome in a child with an arboviral encephalitis ≤18 years of age at diagnosis.

Results
Of 1513 articles, 35 were eligible, comprising 693 children. Japanese encephalitis accounted for 18 articles and 93.2% of all subjects (646 total). Sequelae were documented in ∼60% of subjects overall and in those with Japanese encephalitis. For non-Japanese encephalitis virus encephalitides (47 children), sequelae were found in 78.1%. No studies utilized comprehensive neurocognitive testing or assessed the efficacy of rehabilitative efforts. Only nine studies reported data from ≥1 follow-up visit.

Conclusion
Investigation into long-term outcomes following tropical childhood encephalitis is limited, particularly for neurocognitive sequelae, serial assessments over time and the effect of rehabilitative measures.

LAY SUMMARY
Encephalitis, an infection of the brain, is frequently caused by arboviruses (viruses spread via the bite of infected arthropods, such as mosquitoes) in tropical locales. Following infection, surviving children may be plagued with severe physical and cognitive deficits. Unfortunately, research into the type of deficits, their frequency and their responsiveness to rehabilitative efforts is lacking. We identified and reviewed 35 studies describing outcomes in children recovering from tropical, arboviral encephalitis at least 3 months following hospital discharge. Poor outcomes were common and found in up to 60% of children. Long-term and serial follow-up visits were rare, as was the use of comprehensive neurocognitive testing. No studies assessed the efficacy of rehabilitative measures. Further study into these areas is recommended.
New specimens from Mid-Cretaceous Myanmar amber illuminate the phylogenetic placement of Lagonomegopidae (Arachnida: Araneae)
Authors: Guo Xiangbo , Selden Paul A , Ren Dong 
Published: April 2021

Abstract
New lagonomegopid spiders are described from Mid-Cretaceous Myanmar (Burmese) amber. Two new genera and species based on single specimens, Scopomegops fax gen. & sp. nov. and Hiatomegops spinalis gen. & sp. nov. are described. Two specimens belonging to Lineaburmops beigeli are further described. Additionally, after re-examining the holotype of Odontomegops titan, a detailed description of its basal ventral abdomen is added here. A phylogenetic analysis was performed to investigate the phylogenetic placement of Lagonomegopidae. A matrix of 79 morphological characters, scored for six lagonomegopid taxa and 26 non-lagonomegopid taxa, was analysed through parsimony and Bayesian phylogenetic inference. Our results recover extant Palpimanoidea as a monophyletic group and partly suggest that Lagonomegopidae is the sister-group to extant Palpimanoidea. The external sexual organs, retrolateral tibial apophysis on the male palp and tracheal spiracle in lagonomegopids are discussed.
Mechanisms and primary prevention of atherosclerotic cardiovascular disease among people living with HIV
Authors: Durstenfeld Matthew S. , Hsue Priscilla Y. 
Published: April 2021

Purpose of review
To highlight mechanisms of elevated risk of atherosclerotic cardiovascular disease (ASCVD) among people living with HIV (PLWH), discuss therapeutic strategies, and opportunities for primary prevention.

Recent findings
HIV-associated ASCVD risk is likely multifactorial and due to HIV-specific factors and traditional risk factors even in the setting of treated and suppressed HIV disease. Although a growing body of evidence suggests that inflammation and immune activation are key drivers of atherogenesis, therapies designed to lower inflammation including colchicine and low-dose methotrexate have not improved secondary cardiovascular endpoints among PLWH. Statins continue to be the mainstay of management of hyperlipidemia in HIV, but the impact of newer lipid therapies including proprotein convertase subtilisin/kexin type 9 inhibitors on ASCVD risk among PLWH is under investigation. Aside from the factors mentioned above, healthcare disparities are particularly prominent among PLWH and thus likely contribute to increased ASCVD risk.

Summary
Our understanding of mechanisms of elevated ASCVD risk in HIV continues to evolve, and the optimal treatment for CVD in HIV aside from targeting traditional risk factors remains unknown. Future studies including novel therapies to lower inflammation, control of risk factors, and implementation science are needed to ascertain optimal ways to treat and prevent ASCVD among PLWH.
Prednisone reduction for metastatic castration-resistant prostate cancer with recurrent pulmonary tuberculosis
Authors: Zhu Xiaojuan , Shi Zhenguo , Gao Shegan , Wang Xiaohong , Wang Pei , Kang Chongzhao , Zhao Fangzong , Hou Peng 
Published: April 2021

Abstract

Introduction:
Prednisone (10 mg/d) is often used in combination with docetaxel or abiraterone in the treatment of advanced prostate cancer. LATITUDE studies have confirmed that the combination of abiraterone and prednisone (5 mg/d) can be used for the treatment of newly diagnosed high-risk metastatic castration-sensitive prostate cancer, and have achieved satisfactory results. However, it has not been reported that abiraterone combined with prednisone (5 mg/d) in the treatment of metastatic castration-resistant prostate cancer (mCRPC).

Patient concerns:
Here, we present a case of high-risk advanced prostate cancer with old pulmonary tuberculosis (PTB). The patient developed a relapse of old tuberculosis in both lungs that were discovered following 14 months of continuous application of prednisone (10 mg/d).

Diagnosis:
The histopathological findings showed prostate adenocarcinoma carcinoma with a Gleason score of 10 (5+5). Further laboratory investigations were suggestive of positive mycobacterium tuberculosis complex DNA in pleural effusion and sputum.

Interventions:
The patient underwent endocrine therapy, chemotherapy of docetaxel plus prednisone, radiotherapy, and abiraterone combined with prednisone treatment, but he eventually developed into the mCRPC stage. Then, prednisone was reduced to 5 mg/d plus abiraterone, and combined with anti-tuberculosis treatment according to multi-disciplinary diagnosis and treatment.

Outcome:
Two months later, pleural effusion and atelectasis were relieved, and PSA was remained stable at a low level. The patient achieved complete remission.

Conclusion:
We cannot, with complete certainty, say that this patient, or any patient, developed old PTB recurrence due to the use of prednisone. Based on the current evidence, endocrine therapy is the foundation, radiotherapy can reduce the tumor load, and early application of abiraterone is beneficial to survival for the high-risk mCRPC. The long-term use of prednisone can be appropriately reduced in mCRPC with old PTB, and a satisfactory curative effect can be achieved. More prospective trials are warranted before a definite recommendation could be drawn.
Effectiveness of different types of skin grafting for treating venous leg ulcers
Authors: Pan Junqing , Hu Xiangjun , Yin Hongwei , Zhang Congzhong , Yan Zhangren 
Published: April 2021

Abstract

Background:
Venous leg ulcers (VLUs) are the most common ulcer on the lower extremity, with 4% of patients over the age of 65 suffering from VLUs worldwide. As a recurrent, chronic, disabling disease, VLUs are associated with prolonged disability, substantial socioeconomic impact, and significant psychosocial morbidity. At present, Skin grating is one of the most effective treatments for non-healing ulcers. However, there are still no new studies based on the latest research and new research methods to evaluate and compare the effect of different types of skin grafts for treating venous leg ulcers. Therefore, a Bayesian network meta-analysis (NMA) will be conducted to systematically assess skin grafting efficacy for VLUs.

Methods:
We will include randomized controlled trials (RCTs) involving patients with VLUs treated by skin grafts. Electronic databases and clinical trials registries will be searched from their inception until June 2021, without language or publication restrictions on status. The search strategy mainly includes Medical Subject Headings (MeSH) and free-text terms. Two review authors will independently perform data extraction and assessment of study quality. And We will use Bayesian NMA to evaluate all available evidence in STATA 14.0 and WinBUGS software.

Results:
This protocol will use Bayesian NMA to assess the effectiveness of different types of skin grafting for treating venous leg ulcers.

Conclusion:
This study aims to synthesize the available evidence from RCTs in a network meta-analysis to summarize the best research available and provide consistency among treatment protocols given to patients, resulting in improved efficacy and the quality of care and reduced cost.
Does Iron Deficiency Affect the Heart in Children?
Authors: Demir Fadime , Kayali Seyma , Gokcebay Dilek G. 
Published: April 2021

Introduction:
It is well known that serum iron parameters are closely related to cardiovascular health. Iron deficiency may lead to significant cardiac problems, such as atrioventricular conduction abnormalities, and systolic and/or diastolic dysfunction. Studies related to the effect of iron deficiency on cardiac functions are limited in children. Therefore, the aim of this study was to evaluate the effect of low iron stores on cardiac repolarization parameters which are used to predict arrhythmia and cardiac functions.

Materials and Methods:
Onehundred thirty-five children 2 to 18 years of age without structural heart disease who were referred to the Pediatric Cardiology Department for various reasons such as chest pain, heart murmur, or evaluation before sports participation were evaluated prospectively. The cases were separated into 3 groups according to ferritin levels (group 1: ferritin <15 ng/mL [n=48], group 2: ferritin 15 to 25 ng/mL [n=51], and group 3: ferritin >25 ng/mL [n=36]). Evaluations were made with detailed 12-lead surface electrocardiography (ECG) and transthoracic echocardiogram. Cardiac repolarization parameters were measured from surface ECG and systolic functions, left ventricular wall diameters were evaluated from transthoracic echocardiogram.

Results:
Eighty-four (62.2%) girls and 51 (37.8%) boys are included in the study. The average age of the groups was similar. In children with low ferritin levels (group 1); Pw, Pw max, and Pw dis; QT, QTc, and QTc dis; Tp-Te, Tp-Te dis, Tp-Te/QT, and Tp-Te/QTc were significantly longer compared with the group 3 (P<0.05). There was a negative correlation between ferritin level and Pw, P max, and Pw dis; QT, QT dis, QTc, and QTc dis; Tp-Te, Tp-Te dis, Tp-Te/QT, and Tp-Te/QTc (P<0.05). No correlation was found between ferritin level and Pw min. There was no difference between the groups in respect of ejection phase indices, heart wall measurements, and end-diastolic diameter measurements.

Conclusion:
Iron deficiency may be related to the tendency of arrhythmias in children without structural heart disease. Therefore, careful evaluation of ECG parameters of healthy children with low iron stores, and follow up with intermittent monitoring is highly important.