bluuebunny/crossref_metadata_2025_split huggingface dataset:
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

AbstractDarwin, 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

Abstract
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

AbstractBread 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

ABSTRACT

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

Abstract

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

AbstractIn 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 &lt; 0.05) survival rate and extended (P &lt; 0.05) D. melanogaster life span compared with control. L. camara significantly increased (P &lt; 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

Abstract

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 .
Coronavirus 2019: clinical and neuropathological aspects
Authors: Younger David S. 
Published: November 2020

Purpose of review
To understand the role of postinfectious autoimmune vascular inflammation in the pathogenesis of coronavirus disease 2019-related neurological illness caused by the novel severe acute respiratory syndrome coronavirus 2 virus and its effects on the brain in children and adults.

Recent findings
There are a very small number of postmortem neuropathological series of coronavirus disease 2019-related cerebrovascular and parenchymal disease. However, they fall into at least three major categories, with the majority manifesting those of terminal hypoxia, and others demonstrating inflammatory vascular leptomeningeal, cerebral and brainstem interstitial changes suspicious for encephalitis in a minority of cases. It remains uncertain whether these histopathological features have a relationship to post-infectious inflammatory immune mechanisms and microscopic vasculitis in adults as it appears to be in affected children with multisystem inflammatory syndrome.

Summary
The reasons for this dichotomy are unclear but may related to inherent and epigenetic factors that remain poorly understood. Treatment addressing postinfectious mechanisms of pulmonary, systemic, and nervous system injury may avert early mortality.
Widespread Metastasis to the Stomach 10 Years After Primary Breast Cancer
Authors: Fu Ji-Xin , Zou Ya-Nan , Long-Li  , Wang Xin-Jian 
Published: November 2020

Abstract

Rationale:
Breast cancer is a common malignant tumor. The most common metastatic sites of breast cancer are the bone, brain, liver and lung, and gastrointestinal metastases are rare. Considering that the median time interval from the initial breast cancer diagnosis to stomach metastasis is 77.5 months, gastrointestinal metastases are rarely observed 10 years after primary breast cancer.

Patient concerns:
Here, we present a 63-year-old female with unusual endoscopy results that revealed scattered polyps and mucosal infiltration throughout the stomach, which were later confirmed to be metastatic lobular carcinoma of the breast that had been surgically removed 10 years earlier.

Diagnosis:
The patient was diagnosed with gastric metastases of breast cancer by immunohistochemistry.

Interventions:
The patient underwent endocrine therapy with palbociclib and tamoxifen.

Outcomes:
After 1 year of endocrine therapy, the symptoms of upper abdominal discomfort and fatigue were relieved and a new gastroscopy revealed there had been no significant progression of the gastric metastasis. According to the Response Evaluation Criteria in Solid Tumors (RECIST), the patient reached a state of stable disease.

Lessons:
Gastric metastases of breast cancer are rare in the clinical setting. However, considering the possibility of gastric metastases from breast cancer and performing an upper endoscopy are crucial for patients who present with any subtle gastric symptoms and have a past medical history of breast cancer, even if the breast cancer occurred more than 10 years ago.
Cross-sectional evaluation of the interaction between activity relative-time expenditure and comorbidity concerning physical quality of life
Authors: Suarez-Villar Rafael , Martinez-Urbistondo Diego , Fernandez Maria Agud , Lopez-Cano Maria , Fernandez Eva , Dominguez Andrea , Prosper Laura , Rodriguez-Cobo Ana , Tinoco Maria Elena Caro , Nadal Paula , Risco Carlos Risco , Fernández Paula Villares , Martínez Jose Alfredo 
Published: November 2020

Abstract
Quality of life (QoL) is a matter of concern in both healthy and diseased individuals. Lifestyle factors such as physical activity and sleep have a direct impact on QoL. In this context, interactions between activity time expenditure and QoL might be different in comorbid and non comorbid patients. Besides, the quantification and evaluation of time expenditure is ordinarily measured as the absolute time devoted to each activity. The objective of this study is the evaluation of the influence and interactions of activity-relative time expenditure and co-morbidity in Physical QoL.
The study involved 302 consecutive patients, from an Internal Medicine ambulatory evaluation. Validated questionnaires were used to collect demographic variables and time expenditure variables. QoL was gathered with de survey short form-36questionnaire. Comorbidity was compiled with de Charlson Comorbidity Index. SPSS v20.0 was used for statistical analysis.
As hypothesized, healthy subjects had higher Physical QoL score than comorbid subjects (P < .05). Physical activity and sleep relative time expenditure were statistically significant and associated to a better QoL in comorbid patients (P < .05). Interestingly, sleep was found to have statistically significant interaction with a score of ≥2 in the Charlson Comorbidity Index. Age, gender, comorbidity, physical activity relative time expenditure, and the interaction between relative time dedicated to sleep and comorbidity were found statistically significant in a multivariate model on Physical QoL prediction.
Activity-relative time expenditure could be an adequate measure of daily activity pattern in the evaluation of QoL. Relative time spent in physical activity and sleep might be positively associated to Physical QoL. Sleep and comorbidity could have a statistically significant interaction in the prediction of Physical QoL.
Evaluation of circulating microRNA expression in patients with trigeminal neuralgia
Authors: Li Xihan , Wang Dongxu , Zhou Jianbin , Yan Yanfeng , Chen Leiyao 
Published: November 2020

Abstract
Trigeminal neuralgia (TN) is a chronic neuropathic pain that seriously affects the daily life of patients. There is increasing evidence that microRNAs (miRNAs) play an important role in the development of neuropathic pain.
In this study, the TaqMan Low Density Array (TLDA) was used to analyze the serum miRNA levels of 28 TN patients, and 31 healthy people without any neuropathic pain were used as controls.
The results showed that the expression profile of serum miRNA in TN patients was different from that in healthy controls. Compared with the control group, 13 miRNAs in the serum of TN patients were up-regulated and 115 miRNAs were down-regulated by >2 times. Quantitative reverse transcription PCR (RT-qPCR) analysis and receiver operating characteristic (ROC) curve were performed. The analysis further confirmed that the expression levels of 4 miRNAs, including miR-132-3p, miR-146b-5p, miR-155-5p, and miR-384, were significantly higher than those of healthy controls, and the difference was statistically significant.
This study preliminarily confirmed the changes of serum miRNA expression profile in TN patients. Among them, 4 kinds of serum miRNA are likely to be related to the occurrence and development of TN.
Hypertension in adolescents and young adults referred to a tertiary hypertension clinic in Cape Town, South Africa
Authors: Jones Erika S. W. , Esack Ilhaam , Mangena Phetho , Rayner Brian L. 
Published: November 2020

Abstract
To audit the young patients referred to the Hypertension Clinic at Groote Schuur Hospital that predominately serves the underprivileged communities of Cape Town.
Folders of patients between the ages of 15 and 30 years over a 2 year period were reviewed. The data collected included demographic, clinical and laboratory data, investigations, causes of hypertension, and presence of hypertensive organ damage.
Of the 110 patients reviewed, 61 (55.5%) were females, 22 (20%) Black African, and 88 (80%) of Mixed Ancestry. Eight (7.3%) were found to be normotensive, 16 (14.5%) had a secondary cause and 86 (78.2%) had essential hypertension. Thirty five (31.8%) were current or previous smokers, and 11 (10%) admitted to current or prior use of metamphetamines. A family history of hypertension in a first degree relative was present in 80 (72.7%) patients. Comorbidities present were diabetes in 7 (6.4%) patients, metabolic syndrome in 13 (11.8%), and obesity in 26 (23.6%), but 42.6% had a body mass index (BMI) <25 kg/m2. Chronic kidney disease (CKD) was present in 29 (26.4%) patients and ECG left ventricular hypertrophy in 56 (50.9%). Overall organ damage was present in 72 (65.5%) patients.
In this cohort of young hypertensives most patients had essential hypertension with a strong family history. Significant organ damage was identified. High risk behavior, including smoking and illicit drug use, and obesity were identified as contributing factors. Secondary causes were identified in 14.2%. These results suggest a targeted approach to the investigation of young hypertensives for secondary causes, and significant opportunities for lifestyle intervention.