bluuebunny/crossref_metadata_2025 huggingface dataset:
Diphtheria Antitoxin Administration, Outcomes, and Safety: Response to a Diphtheria Outbreak in Cox’s Bazar, Bangladesh
Authors: Eisenberg Nell , Panunzi Isabella , Wolz Anja , Burzio Chiara , Cilliers Anna , Islam Md Ariful , Noor Waqar Mohammad , Jalon Oren , Jannat-Khah Deanna , Gil Cuesta Julita
Published: November 2020

Background

Diphtheria has re-emerged over the past several years. There is a paucity of data on the administration and safety of diphtheria antitoxin (DAT), the standard treatment for diphtheria. The 2017–2018 outbreak among Rohingya refugees in Bangladesh was the largest in decades. We determined the outcomes of DAT-treated patients and describe the occurrence and risk factors associated with adverse reactions to DAT.

Methods

We conducted a retrospective study at the Médecins Sans Frontières Rubber Garden Diphtheria Treatment Center from December 2017–September 2018. Diphtheria was diagnosed based on the World Health Organization clinical case criteria. High-acuity patients were eligible for DAT. Safety precautions were meticulously maintained. We calculated the presence of adverse events by age, duration of illness, and DAT dosage using bivariate comparisons.

Results

We treated 709 patients with DAT; 98% (n = 696) recovered and were discharged. One-fourth (n = 170) had at least 1 adverse reaction. Common reactions included cough (n = 115, 16%), rash (n = 66, 9%), and itching (n = 37, 5%). Three percent (n = 18) had severe hypersensitivity reactions. Five patients died during their DAT infusion or soon afterwards, but no deaths were attributed to DAT.

Conclusions

Outcomes for DAT-treated patients were excellent; mortality was <1%. Adverse reactions occurred in one-quarter of all patients, but most reactions were mild and resolved quickly. DAT can be safely administered in a setting with basic critical care, provided there is continuous patient monitoring during the infusion, staff training on management of adverse effects, and attention to safety precautions.
A Verifier-Based Password-Authenticated Key Exchange Using Tamper-Proof Hardware
Authors: Shin Ji Sun , Jo Minjae , Hwang Jung Yeon , Lee Jaehwan
Published: November 2020

Password-based authenticated key exchange (PAKE) allows two parties to compute a common secret key. PAKE offers the advantage of allowing two parties to pre-share only a password. However, when it is executed in a client–server environment, server corruption can expose the clients’ passwords. To be resilient against server compromises, verifier-based authenticated key exchange (VPAKE) is proposed, as an augmented version of PAKE. Thus far, there are two known major VPAKE constructions formally proven secure. However, both involve strong assumptions, such as random oracles. In this paper, we propose a simple and efficient VPAKE using tamper-proof hardware without random oracles to support resilient infrastructures. In particular, we transform Katz–Vaikuntanathan one-round PAKE into two-round VPAKE so as to instill resilience to server compromises. We provide a formal definition of VPAKE using tamper-proof hardware and security proof without random oracles. Finally, we provide a performance analysis and comparisons to previous VPAKE and PAKE protocols. Our transformation supports an efficient VPAKE protocol with six group element communications when the underlying Katz–Vaikuntanathan PAKE is instantiated by Cramer–Shoup ciphertext following the proposal by Benhamouda et al.
Satellite Cell Depletion Disrupts Transcriptional Coordination and Muscle Adaptation to Exercise
Authors: Englund Davis A , Figueiredo Vandré C , Dungan Cory M , Murach Kevin A , Peck Bailey D , Petrosino Jennifer M , Brightwell Camille R , Dupont Alec M , Neal Ally C , Fry Christopher S , Accornero Federica , McCarthy John J , Peterson Charlotte A
Published: November 2020

Satellite cells are required for postnatal development, skeletal muscle regeneration across the lifespan, and skeletal muscle hypertrophy prior to maturity. Our group has aimed to address whether satellite cells are required for hypertrophic growth in mature skeletal muscle. Here, we generated a comprehensive characterization and transcriptome-wide profiling of skeletal muscle during adaptation to exercise in the presence or absence of satellite cells in order to identify distinct phenotypes and gene networks influenced by satellite cell content. We administered vehicle or tamoxifen to adult Pax7-DTA mice and subjected them to progressive weighted wheel running (PoWeR). We then performed immunohistochemical analysis and whole-muscle RNA-seq of vehicle (SC+) and tamoxifen-treated (SC−) mice. Further, we performed single myonuclear RNA-seq to provide detailed information on how satellite cell fusion affects myonuclear transcription. We show that while skeletal muscle can mount a robust hypertrophic response to PoWeR in the absence of satellite cells, growth, and adaptation are ultimately blunted. Transcriptional profiling reveals several gene networks key to muscle adaptation are altered in the absence of satellite cells.
The Order of Trait Emergence in the Evolution of Cyanobacterial Multicellularity
Authors: Hammerschmidt Katrin , Landan Giddy , Domingues Kümmel Tria Fernando , Alcorta Jaime , Dagan Tal
Published: November 2020

The transition from unicellular to multicellular organisms is one of the most significant events in the history of life. Key to this process is the emergence of Darwinian individuality at the higher level: Groups must become single entities capable of reproduction for selection to shape their evolution. Evolutionary transitions in individuality are characterized by cooperation between the lower level entities and by division of labor. Theory suggests that division of labor may drive the transition to multicellularity by eliminating the trade off between two incompatible processes that cannot be performed simultaneously in one cell. Here, we examine the evolution of the most ancient multicellular transition known today, that of cyanobacteria, where we reconstruct the sequence of ecological and phenotypic trait evolution. Our results show that the prime driver of multicellularity in cyanobacteria was the expansion in metabolic capacity offered by nitrogen fixation, which was accompanied by the emergence of the filamentous morphology and succeeded by a reproductive life cycle. This was followed by the progression of multicellularity into higher complexity in the form of differentiated cells and patterned multicellularity.
Does Antihypertensive Use Moderate the Effect of Blood Pressure on Cognitive Decline in Older People?
Authors: Lennon Matthew J , Lam Ben Chun Pan , Crawford John , Brodaty Henry , Kochan Nicole A , Trollor Julian N , Numbers Katya , Draper Brian , Thalamuthu Anbupalam , Sachdev Perminder S
Published: November 2020

Background

While midlife hypertension is deleterious, late-life hypertension has been associated with better cognitive outcomes in several studies. Many questions remain, including the relative benefit or harm of a blood pressure (BP) target and antihypertensive therapy of <120 in very old individuals.

Methods

The Sydney Memory and Aging Study (n = 1015) comprises a cohort of 70- to 90-year-olds, who were followed biennially for 8 years. Global cognition was assessed with a battery of 10 neuropsychological tests. Blood pressure was measured at Waves 1 and 2 and classified into 3 systolic groupings: group 1 (≤120 mmHg), group 2 (121–140 mmHg), and group 3 (>140 mmHg). Multiple regression, linear mixed modeling, and Cox regression examined the effect of BP and antihypertensives.

Results

There were no overall significant differences in global cognition or dementia between the disparate BP groups. However, in those not taking antihypertensives, the systolic BP (SBP) > 140 mmHg group had a significantly worse global cognitive trajectory compared to SBP ≤ 120 mmHg (b = −0.067, 95% CI [−0.129, −0.006], p = .030). Within the SBP ≤ 120 mmHg group those taking antihypertensives had significantly worse global cognition trajectories compared to those not taking antihypertensives even when controlling for past history of hypertension (b = −0.077, 95% CI [−0.147, −0.007], p = .030).

Conclusions

Untreated hypertension in old age is related to worse global cognitive decline. However, ongoing treatment at new recommendations of lower SBP targets may be related to poorer cognitive decline and should be considered carefully in older populations.
Clusty, the waveform-based network similarity clustering toolbox: concept and application to image complex faulting offshore Zakynthos (Greece)
Authors: Petersen G M , Niemz P , Cesca S , Mouslopoulou V , Bocchini G M
Published: November 2020

Clusty is a new open source toolbox dedicated to earthquake clustering based on waveforms recorded across a network of seismic stations. Its main application is the study of active faults and the detection and characterization of faults and fault networks. By using a density-based clustering approach, earthquakes pertaining to a common fault can be recognized even over long fault segments, and the first-order geometry and extent of active faults can be inferred. Clusty implements multiple techniques to compute a waveform based network similarity from maximum cross-correlation coefficients at multiple stations. The clustering procedure is designed to be transparent and parameters can be easily tuned. It is supported by a number of analysis visualization tools which help to assess the homogeneity within each cluster and the differences among distinct clusters. The toolbox returns graphical representations of the results. A list of representative events and stacked waveforms facilitate further analyses like moment tensor inversion. Results obtained in various frequency bands can be combined to account for large magnitude ranges. Thanks to the simple configuration, the toolbox is easily adaptable to new data sets and to large magnitude ranges. To show the potential of our new toolbox, we apply Clusty to the aftershock sequence of the Mw 6.9 25 October 2018 Zakynthos (Greece) Earthquake. Thanks to the complex tectonic setting at the western termination of the Hellenic Subduction System where multiple faults and faulting styles operate simultaneously, the Zakynthos data set provides an ideal case-study for our clustering analysis toolbox. Our results support the activation of several faults and provide insight into the geometry of faults or fault segments. We identify two large thrust faulting clusters in the vicinity of the main shock and multiple strike-slip clusters to the east, west and south of these clusters. Despite its location within the largest thrust cluster, the main shock does not show a high waveform similarity to any of the clusters. This is consistent with the results of other studies suggesting a complex failure mechanism for the main shock. We propose the existence of conjugated strike-slip faults in the south of the study area. Our waveform similarity based clustering toolbox is able to reveal distinct event clusters which cannot be discriminated based on locations and/or timing only. Additionally, the clustering results allows distinction between fault and auxiliary planes of focal mechanisms and to associate them to known active faults.
Spontaneous rupture of a coronary artery fistula presenting with post-exertional syncope and haemopericardium
Authors: Desai Manan H , Olivieri Laura J , Ramakrishnan Karthik V , Downing Tacy E
Published: November 2020

An 8-year-old with a known diagnosis of an asymptomatic coronary artery fistula (CAF) presented with exertional syncope and haemopericardium due to contained rupture of CAF. A transcatheter closure was attempted, but the fistula ruptured again prompting emergency surgical repair. Spontaneous rupture is a catastrophic complication of CAF and warrants a high index of suspicion, timely diagnosis and team management.
An unusual complication following stenting in a patient with chronic mesenteric ischaemia due to radiation therapy
Authors: Charfeddine Salma , Gueldiche Majdi , Feki Wiem , Bahloul Amine
Published: November 2020

The endovascular treatment is the first-line revascularization technique in chronic mesenteric ischaemia. We report a case of reperfusion haemorrhage complicating endovascular repair of severe stenosis of the superior mesenteric and coeliac arteries’ anatomic variant following abdominal radiation therapy. The haemorrhage resolved spontaneously after medical management, with successful outcome.
Identity, Land and Revolt in Egyptian Earth: An Ecofeminist Reading
Authors: Zakarriya Jihan
Published: November 2020

This article rethinks the representation of Egyptian rural culture and peasant participation in the nationalist struggle against British colonialism in Abdel Rahman al-Sharqaawi’s well-known novel Egyptian Earth, Al-Ard (1954). It specifically examines the concepts of identity, land, and revolt in Egyptian Earth from an ecofeminist perspective, relating peasants’ resistance against corrupt feudal-imperialist injustices in early twentieth-century Egypt to the dominant patriarchal cultural attitudes towards women’s and nature’s positions in the pre- and post-1952 revolutionary Egypt. It argues that although al-Sharqaawi’s Egyptian Earth gives marginalized Egyptian peasants the opportunity to participate in an important transitional period in the history of modern Egypt, it discusses the invisible psycho-cultural, environmental and social reasons and circumstances that hinder democratic transition in post-1952 revolution, with a particular focus on Egyptian countryside. Within this context, Egyptian villagers in Egyptian Earth are not just colonized people fighting colonial violence and discriminations through reconnecting to their land. They also stand for a patriarchal place and land suffering complicated, deep-seated problems of cultural isolation, sexism, and tribalism. In this way, Egyptian Earth develops ecofeminist ethics that condemn the colonial rule and the nationalist discourse, as both maintain hierarchical relationships between the urban and the rural, the male and the female, culture and nature, and authority and common people.
UMLS-based data augmentation for natural language processing of clinical research literature
Authors: Kang Tian , Perotte Adler , Tang Youlan , Ta Casey , Weng Chunhua
Published: November 2020

Objective

The study sought to develop and evaluate a knowledge-based data augmentation method to improve the performance of deep learning models for biomedical natural language processing by overcoming training data scarcity.

Materials and Methods

We extended the easy data augmentation (EDA) method for biomedical named entity recognition (NER) by incorporating the Unified Medical Language System (UMLS) knowledge and called this method UMLS-EDA. We designed experiments to systematically evaluate the effect of UMLS-EDA on popular deep learning architectures for both NER and classification. We also compared UMLS-EDA to BERT.

Results

UMLS-EDA enables substantial improvement for NER tasks from the original long short-term memory conditional random fields (LSTM-CRF) model (micro-F1 score: +5%, + 17%, and +15%), helps the LSTM-CRF model (micro-F1 score: 0.66) outperform LSTM-CRF with transfer learning by BERT (0.63), and improves the performance of the state-of-the-art sentence classification model. The largest gain on micro-F1 score is 9%, from 0.75 to 0.84, better than classifiers with BERT pretraining (0.82).

Conclusions

This study presents a UMLS-based data augmentation method, UMLS-EDA. It is effective at improving deep learning models for both NER and sentence classification, and contributes original insights for designing new, superior deep learning approaches for low-resource biomedical domains.
Establishment ofAedes(Ochlerotatus)scapularis(Diptera: Culicidae) in Mainland Florida, With Notes on the Ochlerotatus Group in the United States
Authors: Reeves Lawrence E , Medina Johana , Miqueli Evaristo , Sloyer Kristin E , Petrie William , Vasquez Chalmers , Burkett-Cadena Nathan D
Published: November 2020

Aedes scapularis (Rondani), a widespread neotropical vector mosquito species, has been included in the mosquito fauna of Florida on the basis of just three larval specimens that were collected in the middle Florida Keys in 1945. Here, we report numerous recent collections of immature and adult Ae. scapularis from multiple locations in two counties of southern Florida. These specimens represent the first records of Ae. scapularis from mainland Florida and the first records of the species in the state since the initial detection of the species 75 yr ago. Collections of both larvae and adults across several years indicate that Ae. scapularis is now established in Broward and Miami-Dade Counties. These contemporary records of this species in Florida may represent novel dispersal and subsequent establishment events from populations outside the United States or a recent reemergence of undetected endemic populations. To confirm morphological identification of Ae. scapularis specimens from Florida, the DNA barcoding region of the cytochrome c oxidase subunit I gene (COI) was sequenced and compared to all other Ochlerotatus Group species from the United States, specifically Aedes condolescens Dyar and Knab (Diptera: Culicidae), Aedes infirmatus Dyar and Knab (Diptera: Culicidae), Aedes thelcter Dyar (Diptera: Culicidae), Aedes tortilis (Theobald) (Diptera: Culicidae), and Aedes trivittatus (Coquillett) (Diptera: Culicidae). Molecular assays and sequencing confirm morphological identification of Ae. scapularis specimens. Maximum likelihood phylogenetic analysis of COI and ITS2 sequences place Florida Ae. scapularis in a distinct clade, but was unable to produce distinct clades for Florida specimens of Ae. condolescens and Ae. tortilis.
Downregulation of Long Noncoding RNA TUG1 Attenuates MTDH-Mediated Inflammatory Damage via Targeting miR-29b-1-5p After Spinal Cord Ischemia Reperfusion
Authors: Jia Hui , Li Zhe , Chang Yi , Fang Bo , Zhou Yongjian , Ma Hong
Published: November 2020

Long noncoding RNAs and microRNAs (miRNAs) play a vital role in spinal cord ischemia reperfusion (IR) injury. The aim of this study was to identify the potential interactions between taurine upregulated gene 1 (TUG1) and miRNA-29b-1-5p in a rat model of spinal cord IR. The IR injury was established by 14-minute occlusion of aortic arch. TUG1 and metadherin (MTDH) knockdown were induced by respective siRNAs, and miR-29b-1-5p expression was modulated using specific inhibitor or mimics. The interactions between TUG1, miR-29b-1-5p, and the target genes were determined using the dual-luciferase reporter assay. We found that IR respectively downregulated and upregulated miR-29b-1-5p and TUG1, and significantly increased MTDH expression. MTDH was predicted as a target of miR-29b-1-5p and its knockdown downregulated NF-κB and IL-1β levels. A direct interaction was observed between TUG1 and miR-29b-1-5p, and knocking down TUG1 upregulated the latter. Furthermore, overexpression of miR-29b-1-5p or knockdown of TUG1 alleviated blood-spinal cord barrier leakage and improved hind-limb motor function by suppressing MTDH and its downstream pro-inflammatory cytokines. Knocking down TUG1 also alleviated MTDH/NF-κB/IL-1β pathway-mediated inflammatory damage after IR by targeting miR-29b-1-5p, whereas blocking the latter reversed the neuroprotective effect of TUG1 knockdown and restored MTDH/NF-κB/IL-1β levels.
The Cyclical Relation Between Chronic Pain, Executive Functioning, Emotional Regulation, and Self-Management
Authors: Caes Line , Dick Bruce , Duncan Christina , Allan Julia
Published: November 2020

Objective 

To propose a new model outlining a hypothesized cyclical relation between executive functioning, emotional regulation, and chronic pain in adolescence and to highlight the likely importance of such a relation for self-management behavior and pain-related disability.

Methods 

A review of the existing literature that critically explores the role of executive functioning in understanding chronic pain experiences and self-management in adolescence in order to develop the Cyclical model Of Pain, Executive function, emotion regulation, and Self-management (COPES).

Results 

Growing evidence points towards a potential cyclical relation between chronic pain and impaired executive functioning, which forms the basis of COPES. The COPES model proposes that the relative immaturity of executive functioning in adolescence negatively influences their ability to engage with self-management, which in turn increases adolescents’ disability due to pain and contributes to the maintenance of chronic pain, which perpetuates the reduced capacity of executive functioning. The moderating influence of flexible parental support is hypothesized to offset some of these influences. However, the available evidence is limited due to methodological shortcomings such as large variety in executive functioning operationalization, reliance on self-report and cross-sectional designs.

Conclusions 

It is anticipated that the COPES model will stimulate more systematic, theory-driven research to further our understanding of the links between executive functioning, chronic pain, self-management, and wellbeing. Such enhanced understanding has the potential to drive forward intervention development and refinement aimed at improving self-management uptake and adherence amongst adolescents with chronic pain.
Temperament and Health-Related Quality of Life in Newly Diagnosed Pediatric Inflammatory Bowel Disease
Authors: Shih Sharon , Cushman Grace , Reed Bonney
Published: November 2020

Objective

Health-related quality of life (HRQOL) is typically examined from a deficit standpoint, meaning that little is known about factors associated with higher HRQOL in pediatric illness samples. The aim of the current study was to investigate demographic, disease, and temperamental factors associated with child and parent-report of HRQOL in youth newly diagnosed with inflammatory bowel disease (IBD).

Methods

Participants included 52 youth ages 8–17 diagnosed with IBD and their caregivers who each completed ratings of the child’s HRQOL. Parents rated their child’s emotional reactivity, conceptualized as a temperamental risk factor, and adaptability, conceptualized as a temperamental protective factor. Disease symptoms were rated by youth, and physician global assessment of disease activity was obtained.

Results

HRQOL was rated lower by children and their parents as self-reported disease symptoms and parent-rated emotional reactivity increased. Conversely, total HRQOL was higher for children with higher parent-ratings of adaptability. In multiple regression analyses, higher levels of adaptability along with male sex and lower child-reported disease symptoms were associated with higher child and parent-reported HRQOL.

Conclusions

Higher HRQOL at time of diagnosis in pediatric IBD is associated with greater adaptability when accounting for variability due to child sex and disease symptoms. Consideration of temperament, including emotional reactivity and adaptability, may offer insight into patients’ typical ways of responding when stressed and provide preliminary information about factors related to post-diagnosis HRQOL. Attention should be given to both protective and risk factors to inform future intervention development, including strengths-based approaches.
Anxiety and Depression Correlates at Age 10 in Children Born Extremely Preterm
Authors: Moore Phoebe S , Mokrova Irina , Frazier Jean A , Joseph Robert M , Santos Hudson P , Dvir Yael , Hooper Stephen R , O’Shea T Michael , Douglass Laurie M , Kuban Karl C K
Published: November 2020

Objective  Anxiety and depression rates are known to be elevated in prematurely-born children and adolescents. This prospective study examines demographic, academic, and physical health correlates of anxiety and depression symptoms in a sample of 10-year-old children who were born extremely preterm. Methods  Participants were 889 (51.2% male; 62.3% White) children who were born <28 weeks gestation. Child and family demographic data were collected at birth. When the children were 10, parents (n = 871) and teachers (n = 640) rated the level of anxiety and depression in children through the Child Symptom Inventory-4. Child academic functioning was assessed via the Wechsler Individual Achievement Test-III. Parents completed questionnaires about child academic functioning and physical health issues. Data analyses were conducted with multivariate linear modeling. Results  Level of prematurity was significantly related to both parent and teacher reports of anxiety. Public health insurance and individualized education program (IEP) status were associated with both parent and teacher reports of depression. Hispanic ethnicity, public insurance, IEP status, and asthma were significantly associated with both parent-reported anxiety and depression. Gross motor impairment was associated with parent-reported anxiety and teacher-reported depression. Child obesity was associated with teacher reports of anxiety, while male sex was significantly related to teacher reports of depression. Conclusion  This pattern of findings may suggest hypotheses for future research on models of the development and persistence of anxiety and depression within this particularly vulnerable group of children.
Squamous cell carcinoma mimics small cell carcinoma of the lung: a case report
Authors: Kmeid Michael , Gillie Breanne , Asarian Armand , Xiao Philip
Published: November 2020

Squamous cell carcinomas (SCC) accounts for roughly 20% of lung cancers in the USA. The 2015 World Health Organization classification of lung tumors further categorizes SCC as three subtypes: keratinizing, non-keratinizing and basaloid variant. The non-keratinizing subtype is a poorly differentiated tumor that can present histologically in different ways, and one of which is a rare variant that strongly resembles small cell carcinoma. As a result, histological diagnosis alone is not sufficient to properly diagnose lung carcinomas. Immunohistochemistry has been increasingly used over the past few years to differentiate between lung tumors. The combination of morphological and immunohistochemical staining should be the mainstay for diagnosis of all lung carcinomas as more targeted therapies become more available.
GeoSentinel: past, present and future
Authors: Hamer Davidson H , Rizwan Aisha , Freedman David O , Kozarsky Phyllis , Libman Michael
Published: November 2020

Rationale for review

In response to increased concerns about emerging infectious diseases, GeoSentinel, the Global Surveillance Network of the International Society of Travel Medicine in partnership with the US Centers for Disease Control and Prevention (CDC), was established in 1995 in order to serve as a global provider-based emerging infections sentinel network, conduct surveillance for travel-related infections and communicate and assist global public health responses. This review summarizes the history, past achievements and future directions of the GeoSentinel Network.

Key findings

Funded by the US CDC in 1996, GeoSentinel has grown from a group of eight US-based travel and tropical medicine centers to a global network, which currently consists of 68 sites in 28 countries. GeoSentinel has provided important contributions that have enhanced the ability to use destination-specific differences to guide diagnosis and treatment of returning travelers, migrants and refugees. During the last two decades, GeoSentinel has identified a number of sentinel infectious disease events including previously unrecognized outbreaks and occurrence of diseases in locations thought not to harbor certain infectious agents. GeoSentinel has also provided useful insight into illnesses affecting different traveling populations such as migrants, business travelers and students, while characterizing in greater detail the epidemiology of infectious diseases such as typhoid fever, leishmaniasis and Zika virus disease.

Conclusions

Surveillance of travel- and migration-related infectious diseases has been the main focus of GeoSentinel for the last 25 years. However, GeoSentinel is now evolving into a network that will conduct both research and surveillance. The large number of participating sites and excellent geographic coverage for identification of both common and illnesses in individuals who have traversed international borders uniquely position GeoSentinel to make important contributions of travel-related infectious diseases in the years to come.
SAW homeodomain transcription factors regulate initiation of leaf margin serrations
Authors: Jeon Hyung-Woo , Byrne Mary E
Published: November 2020

Plant leaves are the main photosynthetic organ of plants and they occur in an array of different shapes. Leaf shape is determined by morphogenesis whereby patterning of the leaf margin can result in interspaced leaf serrations, lobes, or leaflets, depending on the species, developmental stage, and in some instances the environment. In Arabidopsis, mutations in the homeodomain transcription factors SAW1 and SAW2 result in more prominent leaf margin serrations. Here we show that serrations appear precociously in the saw1 saw2 mutant. The pattern of auxin maxima, and of PIN1 and CUC2 expression, which form a feedback loop that drives serration outgrowth, is altered in saw1 saw2 and correlates with precocious serration initiation. SAW1 is not expressed in the outer epidermal cell layer where PIN1 convergence points generate auxin maxima. Instead, SAW1 is expressed on the adaxial side of the leaf and expression in this domain is sufficient for function. We suggest that SAW1 and SAW2 repress serration initiation and outgrowth by promoting the transition to a determinate fate in the leaf margin.
Influence of iron on growth and on susceptibility to itraconazole in Sporothrix spp
Authors: da Silva Hellwig Alessandra Helena , Pagani Danielle Machado , Rios Iasmin da Silva , Ribeiro Amanda Carvalho , Zanette Régis A , Scroferneker Maria Lúcia
Published: November 2020

We evaluated the growth and the susceptibility to oxidative stress of Sporothrix spp., exposed to different iron concentrations in culture medium, and the susceptibility of Sporothrix spp. to itraconazole, alone and in combination with to the iron chelator deferasirox. The results showed that the growth of S. brasiliensis isolates was more affected by iron availability in comparison to S. schenckii, but both fungal species conidia became more prone to oxidative stress when iron was added to culture medium. Conversely, the combination of itraconazole and deferasirox only resulted in synergism against a minority of S. schenckii isolates.
Mode angular degree identification in subgiant stars with convolutional neural networks based on power spectrum
Authors: Du Minghao , Bi Shaolan , Zhang Xianfei , Li Yaguang , Li Tanda , Shi Ruijie
Published: November 2020

The identification of the angular degrees l of oscillation modes is essential for asteroseismology and it depends on visual tagging before fitting power spectra in a so-called peakbagging analysis. In oscillating subgiants, radial (l = 0) mode frequencies are distributed linearly in frequency, while non-radial (l ≥ 1) modes are p–g mixed modes that have a complex distribution in frequency that increases the difficulty of identifying l. In this study, we trained a one-dimensional convolutional neural network to perform this task using smoothed oscillation spectra. By training simulation data and fine-tuning the pre-trained network, we achieved 95 per cent accuracy for Kepler data.
Epididymosomes: the black box of Darwin’s pangenesis?
Authors: Nejabati Hamid Reza , Shahnazi Vahideh , Faridvand Yousef , Fathi-Maroufi Nazila , Bahrami-Asl Zahra , Nikanfar Saba , Nouri Mohammad
Published: November 2020

Darwin, in the pangenesis theory, imagined particles, named as ‘gemmules’, which are released from all (‘pan’) cells of the body. By cell–cell communication and also circulation through the body, they finally reach the germ cells to participate in the generation (‘genesis’) of the new individual. It has been shown that circulatory exosomes are affected by environmental stressors and they can reach the parental germ cells. Therefore, in the mirror of his theory, circulatory exosomes could interact with epididymosomes: epididymis-derived exosomes which have a wide spectrum of variation in content and size, are very sensitive to environmental stressors, and may be involved in translating external information to the germ cells. The protein and RNA cargo would be transferred by epididymosomes to sperm during sperm maturation, which would be then delivered to the embryo at fertilization and inherited by offspring. Therefore, in this study, we will briefly discuss Darwin’s pangenesis theory and its possible relation with epididymosomes. We believed that epididymosomes could be considered as an attractive candidate for the storage of RNA contents, changing the epigenome of the next generations, and allowing the reappearance acquired characteristics of ancestors. Therefore, epididymosomes, as a black box of Darwin’s pangenesis, may unravel parental life history and also disclose the historical events that affect the life of offspring.
A new decade and new data at SoyBase, the USDA-ARS soybean genetics and genomics database
Authors: Brown Anne V , Conners Shawn I , Huang Wei , Wilkey Andrew P , Grant David , Weeks Nathan T , Cannon Steven B , Graham Michelle A , Nelson Rex T
Published: November 2020

SoyBase, a USDA genetic and genomics database, holds professionally curated soybean genetic and genomic data, which is integrated and made accessible to researchers and breeders. The site holds several reference genome assemblies, as well as genetic maps, thousands of mapped traits, expression and epigenetic data, pedigree information, and extensive variant and genotyping data sets. SoyBase displays include genetic, genomic, and epigenetic maps of the soybean genome. Gene expression data is presented in the genome viewer as heat maps and pictorial and tabular displays in gene report pages. Millions of sequence variants have been added, representing variations across various collections of cultivars. This variant data is explorable using new interactive tools to visualize the distribution of those variants across the genome, between selected accessions. SoyBase holds several reference-quality soybean genome assemblies, accessible via various query tools and browsers, including a new visualization system for exploring the soybean pan-genome. SoyBase also serves as a nexus of announcements pertinent to the greater soybean research community. The database also includes a soybean-specific anatomic and biochemical trait ontology. The database can be accessed at https://soybase.org.
De Novo Genome Assembly of the Japanese Wheat Cultivar Norin 61 Highlights Functional Variation in Flowering Time andFusarium-Resistant Genes in East Asian Genotypes
Authors: Shimizu Kentaro K , Copetti Dario , Okada Moeko , Wicker Thomas , Tameshige Toshiaki , Hatakeyama Masaomi , Shimizu-Inatsugi Rie , Aquino Catharine , Nishimura Kazusa , Kobayashi Fuminori , Murata Kazuki , Kuo Tony , Delorean Emily , Poland Jesse , Haberer Georg , Spannagl Manuel , Mayer Klaus F X , Gutierrez-Gonzalez Juan , Muehlbauer Gary J , Monat Cecile , Himmelbach Axel , Padmarasu Sudharsan , Mascher Martin , Walkowiak Sean , Nakazaki Tetsuya , Ban Tomohiro , Kawaura Kanako , Tsuji Hiroyuki , Pozniak Curtis , Stein Nils , Sese Jun , Nasuda Shuhei , Handa Hirokazu
Published: November 2020

Bread wheat is a major crop that has long been the focus of basic and breeding research. Assembly of its genome has been difficult because of its large size and allohexaploid nature (AABBDD genome). Following the first reported assembly of the genome of the experimental strain Chinese Spring (CS), the 10+ Wheat Genomes Project was launched to produce multiple assemblies of worldwide modern cultivars. The only Asian cultivar in the project is Norin 61, a representative Japanese cultivar adapted to grow across a broad latitudinal range, mostly characterized by a wet climate and a short growing season. Here, we characterize the key aspects of its chromosome-scale genome assembly spanning 15 Gb with a raw scaffold N50 of 22 Mb. Analysis of the repetitive elements identified chromosomal regions unique to Norin 61 that encompass a tandem array of the pathogenesis-related 13 family. We report novel copy-number variations in the B homeolog of the florigen gene FT1/VRN3, pseudogenization of its D homeolog and the association of its A homeologous alleles with the spring/winter growth habit. Furthermore, the Norin 61 genome carries typical East Asian functional variants different from CS, ranging from a single nucleotide to multi-Mb scale. Examples of such variation are the Fhb1 locus, which confers Fusarium head-blight resistance, Ppd-D1a, which confers early flowering, Glu-D1f for Asian noodle quality and Rht-D1b, which introduced semi-dwarfism during the green revolution. The adoption of Norin 61 as a reference assembly for functional and evolutionary studies will enable comprehensive characterization of the underexploited Asian bread wheat diversity.
No cases of asymptomatic SARS-CoV-2 infection among healthcare staff in a city under lockdown restrictions: lessons to inform ‘Operation Moonshot’
Authors: Martin Christopher A , Jenkins David R , Patel Prashanth , Goss Charles , Price Arthur , Barton Linda , Gupta Pankaj , Zaccardi Francesco , Brunskill Nigel J , Haldar Pranab , Khunti Kamlesh , Pareek Manish
Published: November 2020

Background

Leicester was the first city in the UK to have ‘local lockdown’ measures imposed in response to high community rates of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) transmission. As part of this response, a directive was issued by NHS England to offer testing of asymptomatic healthcare workers (HCWs) at University Hospitals of Leicester NHS Trust (UHL) for SARS-CoV-2 infection.

Methods

Between 20 July and 14 August 2020, we invited all HCWs at UHL to attend for SARS-CoV-2 testing by nucleic acid amplification (NAAT). We combined the result of this assay with demographic information from the electronic staff record.

Results

A total of 1150 staff (~8% of the workforce) volunteered. The median age was 46 years (IQR 34–55), 972 (84.5%) were female; 234 (20.4%) were of South Asian and 58 (5.0%) of Black ethnicity; 564 (49.0%) were nurses/healthcare assistants. We found no cases of asymptomatic infection. In comparison, average community test positivity rate in Leicester city was 2.6%.

Conclusions

Within the context of local lockdowns due to high community transmission rates, voluntary testing of asymptomatic staff has low uptake and low yield and thus its premise and cost-effectiveness should be re-considered.
Real-world experience of effectiveness of non-medical switch from originator to biosimilar rituximab in rheumatoid arthritis
Authors: Melville Andrew R , Md Yusof Md Yuzaiful , Fitton John , Garcia-Montoya Leticia , Bailey Lynda , Dass Shouvik , Emery Paul , Buch Maya H , Saleem Benazir
Published: November 2020

Objective

To evaluate the impact of non-medical switch from rituximab originator (RTX-O) to biosimilar (RTX-B) in patients with RA.

Methods

Between October 2017 and October 2019, all patients on RTX-O in our centre requiring re-treatment were switched to RTX-B unless declined by the patient or specified by the treating clinician. Switch strategy effectiveness was assessed retrospectively using DAS28-CRP(3) and RTX retention, with patients remaining on RTX-O as a comparator group.

Results

The number of patients switching to RTX-B was 255/337 (75.7%) while 82 (24.3%) remained on RTX-O. There was no difference in DAS28-CRP(3) 4 months post-RTX-B switch vs the same time point post-RTX-O previous cycle (paired data available in 60%). Eighteen-month retention estimates were 75.6% (95% CI: 69.4, 80.7%) for RTX-B group and 82.3% (95% CI: 70.4, 89.8%) for RTX-O [adjusted hazard ratio 1.52 (95% CI: 0.85, 2.73)]. The number of patients who discontinued RTX-B for loss of effectiveness (LOE) was 42/255 (16.5%), five (2.0%) for adverse effects (AEs). Risk of RTX-B discontinuation was associated with comorbidities and ≥2 previous biologic DMARDs. Risk of adverse outcome RTX cessation was associated with comorbidities, and reduced risk with number of previous RTX-O cycles and pre-switch cycle B cell depletion. The number of patients who switched back to RTX-O was 34/255 (13.3%) (LOE: 30, AEs: 4), while 13/255 (5.1%) started other biologic/targeted synthetic DMARDs. Of patients who switched back for LOE, 28/30 remained on RTX-O at a mean 7.7 months follow-up.

Conclusion

Non-medical switch to RTX-B was largely effective. Factors associated with RTX-B discontinuation, including comorbidities, previous biologic DMARDs, and RTX-O treatment history, may inform switch decisions. Most patients who switched back to RTX-O for LOE remained on treatment at short-term follow-up.
Lantana camaraethanolic leaves extracts exhibit anti-aging properties inDrosophila melanogaster: survival-rate and life span studies
Authors: Etuh M A , Ohemu L T , Pam D D
Published: November 2020

In this article, we aimed to investigate the anti-aging activity of Lantana camara ethanolic leaves-extract in Drosophila melanogaster: survival and longevity (life span). L. camara leaves were collected and washed thoroughly of sand particles, air-dried, ground, and extracted by the maceration method using ethanol as a solvent. Phytochemical screening was carried out. 168-hour LC50 was determined by exposing fruit flies to concentrations ranging from 5 to 5000 mg/10 g diet for 7-days. Twenty-eight-day survival and longevity studies were carried out by administering L. camara ethanolic leaves extract at 5, 10, and 20 mg/10 g diet to 1–3 days old fruit flies. Each concentration was replicated four times with 50 fruit flies each. The emergence rate of young fruit flies from eggs laid by fruit flies administered L. camara leaves-extracts were also carried out. The total yield of the extraction was determined to be 18%. Phytochemical analysis revealed the presence of alkaloids, Flavonoids, Phenol, steroids, cardiac glycosides, and carbohydrates. 168-hour LC50 of L. camara was also determined to be 1135 mg/10 g diet. L. camara significantly prolonged (P < 0.05) survival rate and extended (P < 0.05) D. melanogaster life span compared with control. L. camara significantly increased (P < 0.05) emergence rate of young fruit flies from eggs laid by fruit flies administered L. camara ethanolic leaves extracts. From the experimental results, it can be concluded that the ethanol extract of L. camara leaves extended the life span of D. melanogaster at these concentrations. Due to similarities of conserved genes between humans and fruit flies, the use of L. camara ethanolic leaves extract at these concentrations is safe and may be recommended as herbal medicine in humans.
Modelling the impact of COVID-19-related control programme interruptions on progress towards the WHO 2030 target for soil-transmitted helminths
Authors: Malizia Veronica , Giardina Federica , Vegvari Carolin , Bajaj Sumali , McRae-McKee Kevin , Anderson Roy M , de Vlas Sake J , Coffeng Luc E
Published: November 2020

Background

On 1 April 2020, the WHO recommended an interruption of all activities for the control of neglected tropical diseases, including soil-transmitted helminths (STH), in response to the COVID-19 pandemic. This paper investigates the impact of this disruption on the progress towards the WHO 2030 target for STH.

Methods

We used two stochastic individual-based models to simulate the impact of missing one or more preventive chemotherapy (PC) rounds in different endemicity settings. We also investigated the extent to which this impact can be lessened by mitigation strategies, such as semiannual or community-wide PC.

Results

Both models show that without a mitigation strategy, control programmes will catch up by 2030, assuming that coverage is maintained. The catch-up time can be up to 4.5 y after the start of the interruption. Mitigation strategies may reduce this time by up to 2 y and increase the probability of achieving the 2030 target.

Conclusions

Although a PC interruption will only temporarily impact the progress towards the WHO 2030 target, programmes are encouraged to restart as soon as possible to minimise the impact on morbidity. The implementation of suitable mitigation strategies can turn the interruption into an opportunity to accelerate progress towards reaching the target.
A Network of Phosphate Starvation and Immune-Related Signaling and Metabolic Pathways Controls the Interaction between Arabidopsis thaliana and the Beneficial Fungus Colletotrichum tofieldiae
Authors: Frerigmann Henning , Piotrowski Markus , Lemke René , Bednarek Paweł , Schulze-Lefert Paul
Published: November 2020

The beneficial root-colonizing fungus Colletotrichum tofieldiae mediates plant growth promotion (PGP) upon phosphate (Pi) starvation in Arabidopsis thaliana. This activity is dependent on the Trp metabolism of the host, including indole glucosinolate (IG) hydrolysis. Here, we show that C. tofieldiae resolves several Pi starvation-induced molecular processes in the host, one of which is the downregulation of auxin signaling in germ-free plants, which is restored in the presence of the fungus. Using CRISPR/Cas9 genome editing, we generated an Arabidopsis triple mutant lacking three homologous nitrilases (NIT1 to NIT3) that are thought to link IG-hydrolysis products with auxin biosynthesis. Retained C. tofieldiae-induced PGP in nit1/2/3 mutant plants demonstrated that this metabolic connection is dispensable for the beneficial activity of the fungus. This suggests that either there is an alternative metabolic link between IG-hydrolysis products and auxin biosynthesis, or C. tofieldiae restores auxin signaling independently of IG metabolism. We show that C. tofieldiae, similar to pathogenic microorganisms, triggers Arabidopsis immune pathways that rely on IG metabolism as well as salicylic acid and ethylene signaling. Analysis of IG-deficient myb mutants revealed that these metabolites are, indeed, important for control of in planta C. tofieldiae growth: however, enhanced C. tofieldiae biomass does not necessarily negatively correlate with PGP. We show that Pi deficiency enables more efficient colonization of Arabidopsis by C. tofieldiae, possibly due to the MYC2-mediated repression of ethylene signaling and changes in the constitutive IG composition in roots.

[Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .
Xanthomonas translucens pv. undulosa Identified on Common Weedy Grasses in Naturally Infected Wheat Fields in Minnesota
Authors: Ledman Kristi E. , Curland Rebecca D. , Ishimaru Carol A. , Dill-Macky Ruth
Published: November 2020

Bacterial leaf streak (BLS) of wheat, caused by Xanthomonas translucens pv. undulosa, has been a notable disease in Minnesota wheat fields over the past decade. Potential sources of the pathogen include infested seed and crop debris. Perennial weeds are also considered a possible inoculum source, but no surveys have been conducted to evaluate which X. translucens pathovars are present on weedy grasses that are common in Minnesota wheat fields. Multilocus sequence analysis (MLSA) of four housekeeping genes (rpoD, dnaK, fyuA, and gyrB) was used to identify 77 strains isolated from six weedy grass species, wheat, and barley in and around naturally infected wheat fields in Minnesota. The MLSA phylogeny identified all strains originating from weedy grass species, except smooth brome, as X. translucens pv. undulosa, whereas strains isolated from smooth brome were determined to be X. translucens pv. cerealis. In planta character states corroborated these identifications on a subset of 41 strains, as all strains from weedy grasses caused water-soaking on wheat and barley in greenhouse assays. Multilocus sequence typing was used to evaluate genetic diversity and revealed that sequence types of X. translucens pv. undulosa originating from weedy grass hosts are similar to those found on wheat. This study identifies both annual and perennial poaceous weeds common in Minnesota that harbor X. translucens pv. undulosa and expands our understanding of the diversity of the pathogen population.