bluuebunny/crossref_metadata_2025_split huggingface dataset:
A de novo assembled high-quality chromosome-scale Trifolium pratense genome and fine-scale phylogenetic analysis
Authors: Yan Zhenfei , Sang Lijun , Ma Yue , He Yong , Sun Juan , Ma Lichao , Li Shuo , Miao Fuhong , Zhang Zixin , Huang Jianwei , Wang Zengyu , Yang Guofeng 
Published: July 2022

Abstract
Background
Red clover (Trifolium pratense L.) is a diploid perennial temperate legume with 14 chromosomes (2n = 14) native to Europe and West Asia, with high nutritional and economic value. It is a very important forage grass and is widely grown in marine climates, such as the United States and Sweden. Genetic research and molecular breeding are limited by the lack of high-quality reference genomes. In this study, we used Illumina, PacBio HiFi, and Hi-C to obtain a high-quality chromosome-scale red clover genome and used genome annotation results to analyze evolutionary relationships among related species.

Results
The red clover genome obtained by PacBio HiFi assembly sequencing was 423 M. The assembly quality was the highest among legume genome assemblies published to date. The contig N50 was 13 Mb, scaffold N50 was 55 Mb, and BUSCO completeness was 97.9%, accounting for 92.8% of the predicted genome. Genome annotation revealed 44,588 gene models with high confidence and 52.81% repetitive elements in red clover genome. Based on a comparison of genome annotation results, red clover was closely related to Trifolium medium and distantly related to Glycine max, Vigna radiata, Medicago truncatula, and Cicer arietinum among legumes. Analyses of gene family expansions and contractions and forward gene selection revealed gene families and genes related to environmental stress resistance and energy metabolism.

Conclusions
We report a high-quality de novo genome assembly for the red clover at the chromosome level, with a substantial improvement in assembly quality over those of previously published red clover genomes. These annotated gene models can provide an important resource for molecular genetic breeding and legume evolution studies. Furthermore, we analyzed the evolutionary relationships among red clover and closely related species, providing a basis for evolutionary studies of clover leaf and legumes, genomics analyses of forage grass, the improvement of agronomic traits.
Differential seedling growth and tolerance indices reflect drought tolerance in cotton
Authors: Mahmood Tahir , Iqbal Muhammad Shahid , Li Hongge , Nazir Mian Faisal , Khalid Shiguftah , Sarfraz Zareen , Hu Daowu , Baojun Chen , Geng Xiaoli , Tajo Sani Muhammad , Dev Washu , Iqbal Zubair , Zhao Pan , Hu Guanjing , Du Xiongming 
Published: July 2022

Abstract
Background
Cotton production is adversely effected by drought stress. It is exposed to drought stress at various critical growth stages grown under a water scarcity environment. Roots are the sensors of plants; they detect osmotic stress under drought stress and play an important role in plant drought tolerance mechanisms. The seedling stage is very sensitive to drought stress, and it needed to explore the methods and plant characteristics that contribute to drought tolerance in cotton.

Results
Initially, seedlings of 18 genotypes from three Gossypium species: G. hirsutum, G. barbadense, and G. arboreum, were evaluated for various seedling traits under control (NS) and drought stress (DS). Afterward, six genotypes, including two of each species, one tolerant and one susceptible, were identified based on the cumulative drought sensitivity response index (CDSRI). Finally, growth rates (GR) were examined for shoot and root growth parameters under control and DS in experimental hydroponic conditions. A significant variation of drought stress responses was observed across tested genotypes and species. CDSRI allowed here to identify the drought-sensitive and drought-resistant cultivar of each investigated species. Association among root and shoots growth traits disclosed influential effects of enduring the growth under DS. The traits including root length, volume, and root number were the best indicators with significantly higher differential responses in the tolerant genotypes. These root growth traits, coupled with the accumulation of photosynthates and proline, were also the key indicators of the resistance to drought stress.

Conclusion
Tolerant genotypes have advanced growth rates and the capacity to cop with drought stress by encouraging characteristics, including root differential growth traits coupled with physiological traits such as chlorophyll and proline contents. Tolerant and elite genotypes of G. hirsutum were more tolerant of drought stress than obsolete genotypes of G. barbadense and G. arboreum. Identified genotypes have a strong genetic basis of drought tolerance, which can be used in cotton breeding programs.
High genetic diversity and low population differentiation of a medical plant Ficus hirta Vahl., uncovered by microsatellite loci: implications for conservation and breeding
Authors: Lu Yi , Chen Jianling , Chen Bing , Liu Qianqian , Zhang Hanlin , Yang Liyuan , Chao Zhi , Tian Enwei 
Published: July 2022

AbstractBackgroundWuzhimaotao (Radix Fici Hirtae) originates from the dry root ofFicushirta(Moraceae), which is widely known as a medical and edible plant distributed in South China. As the increasing demand for Wuzhimaotao, the wildF.hirtahas been extremely reduced during the past years. It is urgent to protect and rationally develop the wild resources ofF.hirtafor its sustainable utilization. However, a lack of genetic background ofF.hirtamakes it difficult to plan conservation and breeding strategies for this medical plant. In the present study, a total of 414 accessions ofF.hirtafrom 7 provinces in southern China were evaluated for the population genetics using 9 polymorphic SSR markers.ResultsA mean of 17.1 alleles per locus was observed. The expected heterozygosity (He) varied from 0.142 to 0.861 (mean = 0.706) in nine SSR loci. High genetic diversity (He = 0.706, ranged from 0.613 to 0.755) and low genetic differentiation among populations (G’ST = 0.147) were revealed at population level. In addition, analysis of molecular variance (AMOVA) indicated that the principal molecular variance existed within populations (96.2%) was significantly higher than that among populations (3.8%). Meanwhile, the three kinds of clustering methods analysis (STRUCTURE, PCoA and UPGMA) suggested that the sampled populations were clustered into two main genetic groups (K = 2). Mantel test showed a significant correlation between geographic and genetic distance among populations (R2 = 0.281,P < 0.001). Pollen flow, seed flow and/or geographical barriers might be the main factors that formed the current genetic patterns ofF.hirtapopulations.ConclusionsThis is a comprehensive study of genetic diversity and population structure ofF.hirtain southern China. We revealed the high genetic diversity and low population differentiation in this medicinal plant and clarified the causes of its current genetic patterns. Our study will provide novel insights into the exploitation and conservation strategies forF.hirta.
Anesthetic management of a giant paraganglioma resection: a case report
Authors: Wang WeiBing , Zhou Hui , Sun AiJiao , Xiao JingBo , Wang DongShu , Huang DaXiang 
Published: July 2022

Abstract
Background
Patients with pheochromocytomas are often diagnosed with acute myocardial infarction (AMI) due to initial symptoms of palpitations and chest tightness. We describe a case of AMI syndrome where a giant paraganglioma was unexpectedly identified. The anesthetic management of the paraganglioma resection was challenging and complex.

Case presentation
A 66-year-old woman was admitted to the emergency department for complaints of palpitations, chest tightness and vomiting. A laboratory test revealed that troponin I and N-terminal pro-brain natriuretic peptide levels were dramatically increased. Emergency percutaneous coronary angiography (CAG) showed normal coronary arteries. In addition, the serum levels of free catecholamines were increased, and computed tomography and magnetic resonance imaging revealed a heterogenous mass lesion in the right retroperitoneal. All of this ultimately confirmed the diagnosis of pheochromocytoma. After three weeks of careful preoperative preparation by a multidisciplinary team, and an anesthesiologist team develops detailed perianesthesia management strategies to maintain hemodynamics and blood glucose stability and regulate acid–base balance, pheochromocytoma resection was performed successfully. About 2 weeks later, the patient was discharged healthy. A postoperative pathology test confirmed paraganglioma.

Conclusions
To our knowledge, giant pheochromocytoma resection is a complex challenge for the anesthesiologists, this clinical case may supply a thoughtful experience for anesthetic management in the resection of giant pheochromocytomas. Adequate preoperative evaluation and prudent perianesthesia management by anesthesiologists are important guarantees for patients to obtain a good prognosis and discharge healthily.
Predictors and outcome of cardiac arrest in paediatric patients presenting to emergency medicine department of tertiary hospitals in Tanzania
Authors: Yussuf Amne O. , Kilindimo Said S. , Sawe Hendry R. , Premji Elishah N. , Manji Hussein K. , Simbila Alphonce N. , Mfinanga Juma A. , Weber Ellen J. 
Published: July 2022

Abstract
Background
The survival of children who suffer cardiac arrest is poor. This study aimed to determine the predictors and outcome of cardiac arrest in paediatric patients presenting to an emergency department of a tertiary hospital in Tanzania.

Methodology
This was a prospective cohort study of paediatric patients > 1 month to ≤ 14 years presenting to Emergency Medicine Department of Muhimbili National Hospital (EMD) in Tanzania from September 2019 to January 2020 and triaged as Emergency and Priority. We enrolled consecutive patients during study periods where patients’ demographic and clinical presentation, emergency interventions and outcome were recorded. Logistic regression analysis was performed to identify the predictors of cardiac arrest.

Results
We enrolled 481 patients, 294 (61.1%) were males, and the median age was 2 years [IQR 1–5 years]. Among studied patients, 38 (7.9%) developed cardiac arrest in the EMD, of whom 84.2% were ≤ 5 years. Referred patients were over-represented among those who had an arrest (84.2%). The majority 33 (86.8%) of those who developed cardiac arrest died. Compromised circulation on primary survey (OR 5.9 (95% CI 2.1–16.6)), bradycardia for age on arrival (OR 20.0 (CI 1.6–249.3)), hyperkalemia (OR 8.2 (95% CI 1.4–47.7)), elevated lactate levels > 2 mmol/L (OR 5.2 (95% CI 1.4–19.7)), oxygen therapy requirement (OR 5.9 (95% CI 1.3–26.1)) and intubation within the EMD (OR 4.8 (95% CI 1.3–17.6)) were independent predictors of cardiac arrest.

Conclusion
Thirty-eight children developed cardiac arrest in the EMD, with a very high mortality. Those who arrested were more likely to present with signs of hypoxia, shock and acidosis, which suggest they were at later stage in their illness. Outcomes can be improved by strengthening the pre-referral care and providing timely critical management to prevent cardiac arrest.
Meta-analysis using Python: a hands-on tutorial
Authors: Masoumi Safoora , Shahraz Saeid 
Published: July 2022

Abstract
Background
Meta-analysis is a central method for quality evidence generation. In particular, meta-analysis is gaining speedy momentum in the growing world of quantitative information. There are several software applications to process and output expected results. Open-source software applications generating such results are receiving more attention. This paper uses Python’s capabilities to provide applicable instruction to perform a meta-analysis.

Methods
We used the PythonMeta package with several modifications to perform the meta-analysis on an open-access dataset from Cochrane. The analyses were complemented by employing Python’s zEpid package capable of creating forest plots. Also, we developed Python scripts for contour-enhanced funnel plots to assess funnel plots asymmetry. Finally, we ran the analyses in R and STATA to check the cross-validity of the results.

Results
A stepwise instruction on installing the software and packages and performing meta-analysis was provided. We shared the Python codes for meta-analysts to follow and generate the standard outputs. Our results were similar to those yielded by R and STATA.

Conclusion
We successfully produced standard meta-analytic outputs using Python. This programming language has several flexibilities to improve the meta-analysis results even further.
Absence of lenadogene nolparvovec DNA in a brain tumor biopsy from a patient in the REVERSE clinical study, a case report
Authors: Newman Nancy J. , Schniederjan Matthew , Mendoza Pia R. , Calkins David J. , Yu-Wai-Man Patrick , Biousse Valérie , Carelli Valerio , Taiel Magali , Rugiero Francois , Singh Pramila , Rogue Alexandra , Sahel José-Alain , Ancian Philippe 
Published: July 2022

Abstract
Background
Leber Hereditary Optic Neuropathy (LHON) is a rare, maternally-inherited mitochondrial disease that primarily affects retinal ganglion cells (RGCs) and their axons in the optic nerve, leading to irreversible, bilateral severe vision loss. Lenadogene nolparvovec gene therapy was developed as a treatment for patients with vision loss from LHON caused by the most prevalent m.11778G > A mitochondrial DNA point mutation in the MT-ND4 gene. Lenadogene nolparvovec is a replication-defective recombinant adeno-associated virus vector 2 serotype 2 (AAV2/2), encoding the human wild-type MT-ND4 protein. Lenadogene nolparvovec was administered by intravitreal injection (IVT) in LHON patients harboring the m.11778G > A ND4 mutation in a clinical development program including one phase 1/2 study (REVEAL), three phase 3 pivotal studies (REVERSE, RESCUE, REFLECT), and one long-term follow-up study (RESTORE, the follow-up of REVERSE and RESCUE patients).

Case presentation
A 67-year-old woman with MT-ND4 LHON, included in the REVERSE clinical study, received a unilateral IVT of lenadogene nolparvovec in the right eye and a sham injection in the left eye in May 2016, 11.4 months and 8.8 months after vision loss in her right and left eyes, respectively. The patient had a normal brain magnetic resonance imaging with contrast at the time of diagnosis of LHON. Two years after treatment administration, BCVA had improved in both eyes. The product was well tolerated with mild and resolutive anterior chamber inflammation in the treated eye. In May 2019, the patient was diagnosed with a right temporal lobe glioblastoma, IDH-wildtype, World Health Organization grade 4, based on histological analysis of a tumor excision. The brain tumor was assessed for the presence of vector DNA by using a sensitive validated qPCR assay targeting the ND4 sequence of the vector.

Conclusion
ND4 DNA was not detected (below 15.625 copies/μg of genomic DNA) in DNA extracted from the brain tumor, while a housekeeping gene DNA was detected at high levels. Taken together, this data shows the absence of detection of lenadogene nolparvovec in a brain tumor (glioblastoma) of a treated patient in the REVERSE clinical trial 3 years after gene therapy administration, supporting the long-term favorable safety of lenadogene nolparvovec.
Circulating tumor cells from melanoma patients show phenotypic plasticity and metastatic potential in xenograft NOD.CB17 mice
Authors: Felici Claudia , Mannavola Francesco , Stucci Luigia Stefania , Duda Loren , Cafforio Paola , Porta Camillo , Tucci Marco 
Published: July 2022

Abstract
Background
Innovative therapies have improved the overall survival in melanoma, although a high number of patients still experience disease progression or recurrence. Ex-vivo culture of circulating tumour cells (CTCs) represents a valuable laboratory resource for in-depth characterization of rare cell populations responsible for disease progression.

Methods
CTCs from patients with metastatic melanoma were in-vitro established. Their stemness was demonstrated by both phenotypic and genotypic assays, as well as by functional studies. Xenograft experiments in NOD.CB17 mice injected with CTCs from a single patient were completed. Data were analysed by Student’s test and results expressed as mean ± SEM.

Results
CTCs share the mutational profile with primary cells, an intermediate epithelial-mesenchymal transition (EMT) phenotype and high expression of the immunosuppressive factors. A subclonal CTC population exhibited stem cell properties as high aldehyde dehydrogenase 1 activity, melanosphere-forming ability, and expression of major stemness transcription factors. Xenograft experiments confirmed the CTC ability to generate melanoma in-vivo and revealed enhanced metastatic propensity.

Conclusions
CTCs play a relevant role in melanoma and may actively contribute to drive the disease progression and metastasis. Thus, they are a unique potential tool for pharmacogenomic studies to guide treatment strategies in advanced disease.
Characteristics of macular morphology and microcirculation in diabetic macular edema patients with serous retinal detachment
Authors: Xu Min , Xu Huirong , Li Xiao , Chen Fang 
Published: July 2022

Abstract
Background
To analyze and compare the characteristics of macular morphology and microcirculation in diabetic macular edema (DME) patients with and without macular serous retinal detachment (SRD).

Methods
One hundred eyes in 81 patients diagnosed with the DME (the central macular thickness (CMT) of ≥ 300 μm) from March 2020 to November 2020 were selected. According to whether complicated with SRD, patients were divided into DME with SRD (60 eyes) and without SRD (40 eyes) groups. We analyzed the following parameters: CMT, central retinal thickness (CRT), subfoveal choroidal thickness (SFCT), number of hyperreflective foci (HF) in the complete retina, inner retina, outer retina, and subretinal space, the integrity of the ellipsoid zone (EZ) and external limiting membrane (ELM), the presence of disorganization of inner retinal layers (DRIL), foveal avascular zone (FAZ) area, and the vascular flow density of superficial capillary plexus (SCP), deep capillary plexus (DCP), and choriocapillaris.

Results
(1) Compared to the group without SRD, the group with SRD had a greater CMT (P < 0.05) and a smaller CRT (P < 0.001); (2) The number of the HF in the complete retina, outer retina, and the subretinal space was larger in the group with SRD (P < 0.001); 3.The proportion of the EZ disruption (P < 0.05) and ELM disruption (P < 0.001) were higher in the group with SRD; 4. The SFCT (P < 0.05) and the vascular flow density of choriocapillaris (P < 0.05) were greater in the group with SRD; 5. There were no significant differences in the FAZ area and the vascular flow density of the DCP and SCP (P > 0.05); 6. The presence of the SRD was correlated with the integrity of the ELM, the number of HF in the complete retina, outer retina, and subretinal space (χ2 = 26.930, OR = 0.707, 0.263, 0.995, P < 0.001), as well as the SFCT (OR = 0.992, P < 0.05).

Conclusions
The results support the hypothesis that the presence of the ELM disruption, the larger number of the HF, and the thickening and hyperperfusion of the choroid may be involved in the pathogenesis of SRD in DME.
An unusual presentation of fucosidosis in a Chinese boy: a case report and literature review (childhood fucosidosis)
Authors: Mao Shao-Jia , Zhao Jia , Shen Zheng , Zou Chao-Chun 
Published: July 2022

AbstractBackgroundFucosidosis is one of the rare autosomal recessive lysosomal storage diseases (LSDs) attributed to FUCA1 variants causing the deficiency of α-L-fucosidase in vivo. Α-L-fucosidase deficiency will cause excessive accumulation of fucosylated glycoproteins and glycolipids, which eventually leads to dysfunction in all tissue systems and presents with multiple symptoms. Fucosidosis is a rare disease which is approximately 120 cases have been reported worldwide (Wang, L. et al., J Int Med Res 48, 1-6, 2020). The number of reported cases in China is no more than 10 (Zhang, X. et al., J Int Med Res 49:3000605211005975, 2021).Case presentationThe patient was an 8-year-old Chinese boy who presented with postnatal motor retardation, intellectual disability, short stature, language development retardation, coarse facial features, hepatomegaly, and diffuse angiokeratoma of both palms. His genetic testing showed the presence of a homozygous pathogenic variant (c.671delC) in the FUCA1 gene. In addition, the enzymatic activity of α-L-fucosidase was low. Ultimately, the patient was diagnosed with fucosidosis.ConclusionsFucosidosis is a rare lysosomal storage disease because of FUCA1 variants that cause the deficiency of α-L-fucosidase in vivo. An explicit diagnosis requires a combination of clinical manifestations, imaging examination, genetic testing and enzyme activity analysis. Early diagnosis plays an important role in fucosidosis.
Investigation of obesity, eating behaviors and physical activity levels living in rural and urban areas during the covid-19 pandemic era: a study of Turkish adolescent
Authors: Gülü Mehmet , Yapici Hakan , Mainer-Pardos Elena , Alves Ana Ruivo , Nobari Hadi 
Published: July 2022

Abstract
Background
The purpose of this study was to determine the eating behaviors, obesity and physical activity status of children of similar ages living in rural and urban areas and to examine these relationships during the coronavirus disease (COVID-19) pandemic process.

Method
The research was conducted using the scanning model. The research group consists of children living in rural and urban areas in Turkey. The sample of the study consists of a total of 733 adolescent participants, 351 females (47.9%) and 382 males (52.1%). After anthropometric measurements were made, the Physical Activity Questionnaire for older children and the Yale Food Addiction Scale for children 2.0 were used to determine the food addiction and physical activity status of children during the COVID19 pandemic process. Since the groups were homogeneously distributed, independent samples t-test and Pearson correlation test were used.

Result
In terms of food addiction and physical activity levels, children living in the urban have higher scores than children living in rural areas. In addition, children living in the urban were taller and have higher body mass values than those in rural areas. In terms of physical activity level and food addiction levels, while girls living in the urban had higher activity levels than those living in rural areas, no statistically significant difference was found between the physical activity levels of boys. When evaluated in terms of general and gender, it was determined that children living in rural areas were overweight and obese at a higher rate. Obese children had higher levels of food addiction and lower physical activity levels than non-obese children.

Conclusion
In order to prevent childhood obesity, the level of food addiction should be reduced as well as increasing the level of physical activity. This study is limited in terms of cross-sectional evaluation. Future research can experimentally reveal how much obesity is reduced by methods such as exercise and diet interventions.