bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genomics-assisted prediction of salt and alkali tolerances and functional marker development in apple rootstocks
Authors: Liu Jing , Shen Fei , Xiao Yao , Fang Hongcheng , Qiu Changpeng , Li Wei , Wu Ting , Xu Xuefeng , Wang Yi , Zhang Xinzhong , Han Zhenhai 
Published: March 2020

Abstract
Background: Saline, alkaline, and saline-alkaline stress severely affect plant growth and development. The tolerance of plants to these stressors has long been important breeding objectives, especially for woody perennials like apple. The aims of this study were to identify quantitative trait loci (QTLs) and to develop genomics-assisted prediction models for salt, alkali, and salt-alkali tolerance in apple rootstock. Results: A total of 3,258 hybrids derived from the apple rootstock cultivars ‘Baleng Crab’ ( Malus robusta Rehd., tolerant) × ‘M9’ ( M. pumila Mill., sensitive) were used to identify 17, 13, and two QTLs for injury indices of salt, alkali, and salt–alkali stress via bulked segregant analysis. The genotype effects of single nucleotide polymorphism (SNP) markers designed on candidate genes in each QTL interval were estimated. The genomic predicted value of an individual hybrid was calculated by adding the sum of all marker genotype effects to the mean phenotype value of the population. The prediction accuracy was 0.6569, 0.6695, and 0.5834 for injury indices of salt, alkali, and salt–alkali stress, respectively. SNP182G on MdRGLG3 , which changes a leucine to an arginine at the vWFA-domain, conferred tolerance to salt, alkali, and salt-alkali stress. SNP761A on MdKCAB , affecting the Kv_beta domain that cooperated with the linked allelic variation SNP11, contributed to salt, alkali, and salt–alkali tolerance in apple rootstock. Conclusions: The genomics-assisted prediction models can potentially be used in breeding saline, alkaline, and saline-alkaline tolerant apple rootstocks. The QTLs and the functional markers may provide insight for future studies into the genetic variation of plant abiotic stress tolerance.
Brain metastases from differentiated thyroid cancer occurring during and after radioactive iodine therapy: a report of four cases and literature review
Authors: Takata Noriko , Hamamoto Yasushi , Miyagawa Masao , Makita Kenji , Ishikawa Hirofumi , Tsuruoka Shintaro , Nagasaki Kei , Mochizuki Teruhito 
Published: March 2020

Abstract
Background Brain metastases from differentiated thyroid cancer are uncommon, and the prognosis of patients with them is poor. To explore the optimal treatment for this entity, we retrospectively investigated incidence and features of brain metastases from differentiated thyroid cancer that appeared during and after radioactive iodine therapy. Methods Between 2002 and 2012, 89 patients of differentiated thyroid cancer were included (median age, 63-years; male/female = 29/60). The median follow-up time from first ablation was 63 months (range: 1–175 months). The median cumulative radioactive iodine dose was 8.51 GBq (range: 1.11–42.55 GBq). Results During the follow-up, brain metastases occurred in four (4.5 %) patients. The median follow-up time after first ablation of four patients was 69 months (22, 63, 76 and 105 months). They had already had extracranial metastases at first ablation (lung metastases: 3, lung and bone metastases: 1), and had one or more lesions resistant to radioactive iodine therapy at diagnosis of brain metastasis. Three of them had experienced major hemorrhage from brain metastasis. Survival time intervals from the diagnosis to brain metastasis were 2.5, 3.6, 13 and 13.1 months. Conclusion Brain metastases of differentiated thyroid cancer were relatively uncommon. Prognosis of patients with brain metastasis was unfavorable because of frequent major brain hemorrhage and frequent existence of concomitant extracranial lesions resistant to radioactive iodine therapy. To prevent intracranial hemorrhage, early treatment seemed to be necessary for brain metastases from differentiated thyroid cancer.
Amyloid-beta peptide and phosphorylated tau in the frontopolar cerebral cortex and in the cerebellum of toothed whales: aging vs hypoxia
Authors: Sacchini Simona , Díaz Josué , Monteros Antonio Espinosa de los , Paz Yania , de Quirós Yara Bernaldo , Sierra Eva , Arbelo Manuel , Herráez Pedro , Fernández Antonio 
Published: March 2020

Abstract
Background: Alzheimer’s disease results from the interplay of multiple risk factors and their effects. Diving mammals may be routinely exposed to severe hypoxia when submerged. Among toothed whales, the beaked whales are particularly cryptic and routinely dive deeper than 1,000 m for about one hour in order to hunt deep-water squid and fish. We hypothesized that hypoxia could be a possible risk factor for neurodegenerative alterations in the central nervous system of beaked whales in particular, and toothed whales in general. Results: Samples of frontal cerebral cortex and cerebellum were collected from nine animals, representing six different species of the suborder Odontoceti. Immunohistochemical analysis employed a monoclonal anti-β-amyloid (Aβ) and a polyclonal anti-neurofibrillary tangle (NFT) antibodies. Six of nine (67%) animals showed positive immunolabeling for Aβ and/or NFT. The most striking findings were intranuclear Aβ immunopositivity in cerebral cortical neurons and NFT immunopositivity in cerebellar Purkinje neurons with granulovacuolar degeneration. Herein, we present immunohistopathological findings classic of Alzheimer’s and other neurodegenerative diseases in humans, in different brain locales of odontocete cetaceans. This study represents the first description of Aβ and NFT in the brain of beaked whales, adding also to the non-existent descriptions of GVD in the brain of non-experimental animals, being specifically the first report of granulovacuolar degeneration in the cerebellum. Our results further confirm the rarely reported intranuclear expression of Aβ. Conclusions: These findings could be linked to hypoxic phenomena, as they were more extensive in the brains of beaked whales, and not only in aged individuals. Therefore, a novel hypothesis linking hypoxia and neurodegeneration microscopic hallmarks in cetaceans is proposed. Despite their adaptations, diving mammals could be vulnerable to sustained and repetitive brain hypoxia. Future comparative pathological and neuroprotective investigations may prove of great value to Alzheimer’s disease and other neurodegenerative diseases in humans.
Obesity and Places Where People Living in Sao Paulo City, Brazil
Authors: Barbosa João Paulo dos Anjos Souza Barbosa , Aguiar Breno Souza , Failla Marcelo Antunes , Barrozo Ligia Vizeu , Fisberg Regina Mara , Florindo Alex Antonio 
Published: March 2020

Abstract
Background The built environment characteristics and urban form can influence health outcomes like obesity in people living in high-income countries. However, there are few studies in megacities from middle-high income countries like Brazil in which the built environment has been modified and obesity has been growing slightly. Therefore, the objectives of this study were: 1) to describe the body mass index (BMI) and obesity in different health administrative areas in Sao Paulo; 2) to investigate the association between BMI and obesity with the places where people lived according to social and demographics variables, health variables, built environment, and family per capita income. Methods This was a cross-sectional study that used the Sao Paulo Health Survey dataset (2015) with 3,145 individuals (18 years or older). The weight and height were self-reported and was calculated the BMI. Residential locations were geocoded, types and the mix of destinations were calculated in 500m buffers. We used multilevel models to examine the association between BMI and obesity with the places where the people lived. Results The Midwest region showed the highest mean of the mix of destinations than other areas and the lowest prevalence of overweight and obesity. The BMI was higher for people that lived in North, Southeast, South, and East than Midwest after adjusted. Individuals that lived in North (OR=1.69 CI95% 1.18-2.43) and Southeast (OR=1.66 CI 95%1.17-2.37) had increased the likelihood for obesity compared with Midwest after adjusted by social and demographic variables, physical activity level, mix of destinations, and family per capita income. Conclusion This study found that individuals that lived in the North, Southeast, South, and East had higher BMI than people who lived in Midwest, and people that lived in the North and Southeast had increased the likelihood of obesity compared with the Midwest area. The place where people living can influence BMI and obesity in megacities like Sao Paulo, Brazil. Key words: Body Mass Index, Obesity, Built Environment, Multilevel analysis.
Diagnosis and Prognosis of Retroperitoneum Liposarcoma: a single Asian center cohort of 57 cases
Authors: Liu Jianghao , Xiao Jianchun , He Xiaodong 
Published: March 2020

Abstract
Background Liposarcoma is a form of malignancy found in soft tissues, mostly observed in the extremities. However, retroperitoneum liposarcoma has been seldom reported, and such diagnosis is also neglected. This study aims to present the clinical characteristics, diagnosis and prognosis of 5 different subtypes of liposarcoma and report our experience of treatment of the patients. Methods We conducted a single-center non-intervention retrospective study of 57 retroperitoneal liposarcoma patients who were admitted to Peking Union Medical College Hospital (PUMCH, Beijing, China) from December 2007 to May 2018. We collected and analyzed the demographic, clinical, imaging, histologic, therapeutic and prognostic data for these patients over a mean 4.5-year follow up period. Results Twenty-five (44%) patients were asymptomatic prior to diagnosis, with abdominal distension as the chief complaint for 18 (32%) patients and abdominal pain observed in 16 (28%) patients. Masses were evaluated by CT (n=48, 84%) or ultrasound (n=25, 44%). Laparotomy (n=52, 91%) was the preferred dominant therapeutic modality rather than laparoscopy (n=5, 9%). All patients were treated with R0 resection except 2 patients who underwent R2 resection. We conducted regular follow-up every 6 months after surgery for a mean duration of 4.5 years. Recurrence was experienced by 15 (26%) patients and a further 11 (19%) died during follow up. Conclusions Abdominal distension and pain are main chief complaints of liposarcoma. As extremity is the main location for liposarcoma occurrence, diagnosis of retroperitoneum liposarcoma is usually neglected. Since half of the patients are asymptomatic, timely diagnosis and treatment are highly dependent on regular ultrasound and CT imaging. R0 resection is the key to retroperitoneal liposarcoma treatment. Comparingly, patients underwent R2 resection, which is considered as a palliative treatment, have bad prognosis. Dedifferentiated liposarcoma, especially those with organ invasion, tend to have bad prognosis, and prognosis for well-differentiated or myxoid liposarcoma is relatively good.
The prognostic values and clinical implications of m6A methylation regulators in epithelial ovarian cancer
Authors: shen huimin , Cao Tiefeng , Li Jinhui 
Published: March 2020

Abstract
Background: N6-methyladenosine (m6A) exists in both DNA and RNA modification. RNA m6A modification drives tumor initiation and metastasis through regulating cancer stem cells. However, the detailed mechanisms and the distinct m6A regulatory gene type underlying ovarian cancer mRNA modification remain unclear. Results: We analyzed copy number variation (CNVs) and mRNA expression of ovarian cancer cases in TCGA dataset to determine the copy number variation patterns of m6A regulatory genes, and the associations between m6A dysregulation or certain regulatory gene and overall survival. We showed the KIAA1429, as the writer gene, had highest amplification percentage and were associated with overall survival, or disease-free survival, whereas the associations with prognostic survival were independent of other prognostic factors including stage, grade, and debulking status of the tumour. Besides, METTL14 and YTHDC2, one as the writer gene and the other as reader gene, was also related with clinical outcome. Furthermore, subgroups analysis addressed that m6A upregulation especially writer gain contributed to prognosis in epithelial ovarian cancer. Conclusions: Collectively, our data addressed that m6A upregulation is likely to be critical to the clinical outcome, and KIAA1429 showed the highest correlation with clinical outcome in ovarian cancer among m6A regulatory genes.
Microbial diversity characterization of seawater in a pilot study using Oxford Nanopore Technologies long-read sequencing
Authors: Liem Michael , Regensburg-Tuïnk A.J.G. , Henkel C.V. , Spaink H.P. 
Published: March 2020

Abstract
Objective Currently the majority of non-culturable microbes in sea water are yet to be discovered, Nanopore offers a solution to overcome the challenging tasks to identify the genomes and complex composition of oceanic microbiomes. In this study we evaluate the utility of Oxford Nanopore Technologies (ONT) sequencing to characterize microbial diversity in seawater from multiple locations. We compared the microbial species diversity of retrieved environmental samples from two different locations and time points. Results With only three ONT flow cells we were able to identify thousands of organisms, including bacteriophages, from which a large part at species level. It was possible to assemble genomes from environmental samples with Flye. In several cases this resulted in >1 Mbp contigs and in the particular case of a Thioglobus singularis species it even produced a near complete genome. k-mer analysis reveals that a large part of the data represents species of which close relatives have not yet been deposited to the database. These results show that our approach is suitable for scalable genomic investigations such as monitoring oceanic biodiversity and provides a new platform for education in biodiversity.
The role of routine flexible sigmoidoscopy in patients presenting with fistula-in-ano: an observational study
Authors: Waidyasekera Ruvindu H , Jayarajah Umesh , Samarasekera Dharmabandhu Nandadeva 
Published: March 2020

Abstract
Objective: Flexible sigmoidoscopy is useful to look for an underlying aetiology in fistula-in-ano. This study was aimed to assess the yield of routine flexible sigmoidoscopy in patients presenting with fistula-in-ano. A retrospective analysis of 159 consecutive patients with fistula-in-ano who underwent routine flexible sigmoidoscopy was performed. Sigmoidoscopy findings were recorded on a standard uniform format using a computer database. Those with a known aetiology were excluded. Results: The median age was 39(range:14-74) years and the majority were males(n=128,80.5%). Forty-nine patients(30.8%) presented with a recurrent fistula-in-ano. On flexible sigmoidoscopy, internal opening was seen in only 23 patients (14.4%). Furthermore, incidental findings of haemorrhoids (n=5, 3.1%) and polyps (n=7, 4.4%) were found. One patient(0.6%) had a healed anal fissure, 5 patients(3.1%) had inflamed mucosa and 2 patients(1.3%) had ulcers. Only two patients with inflamed mucosa were diagnosed to have Crohn’s disease on histology. Therefore, flexible sigmoidoscopy was not helpful in the majority to locate the internal opening. Only two patients had evidence of an underlying aetiology, which was Crohn’s disease. However, they had recurrent complex fistulae and other associated symptoms. Therefore, flexible sigmoidoscopy may be reserved for selected group of patients with symptoms of an underlying aetiology.
Pituitary metastasis in breast cancer: case report and literature review
Authors: Sha Xiaosong , Zhang Xiejun , Chen Lei , Yang Jihu , Huang Guodong 
Published: March 2020

Abstract
Background: Breast cancer commonly metastasizes to the lung, vertebrae or liver but rarely to the pituitary gland. The majority of cases have been reported during autopsy; however, with the improvements in diagnostic methods, there has been an increasing number of cases reported in the clinical setting. The main symptoms of pituitary metastasis are reported to be headache, diabetes insipidus and visual field defects, which may cause confusion regarding the clinical diagnosis.Case presentation: The present study describes a case of pituitary metastasis symptoms of diabetes insipidus and loss of vision in a patient with breast cancer. After the patient completed the evaluation, a neuroendoscopy-assisted endonasal transsphenoidal tumor resection was performed. The postoperative biopsy revealed metastatic breast cancer.Conclusions: The present study analyzed this patient and 16 other cases of pituitary metastases collected from the PubMed database. Lung cancer, breast cancer and lymphoma could metastasize to the sellar region, while certain other tumors from the liver, parotid, colon, prostate, stomach, kidney, thyroid or skin were also observed. The clinical manifestation was often dominated by pituitary dysfunction, intracranial hypertension and visual field defects. Certain patients may suffer from oculomotor nerve paralysis, electrolyte imbalance, diabetes insipidus or a loss of vision. Imaging findings revealed that sellar metastases often invaded the suprasellar region. In a few cases, the lesion enclosed intracranial vessels, and invaded the cavernous sinus or Meckel's cave. These characteristics resulted in difficulties during surgery.
Development and Validation of Liver Depression Type Infertility Quality of Life Scale Based on Traditional Chinese Medicine
Authors: Wang Ying , Liu Chang , Wang Xuan , Zhang Mengpei , Wang Zhiheng , Zhang Haoxiang , Wang Xiaomei , Pan Jie , Zuo Kaini , Zhu Wentao 
Published: March 2020

Abstract
Background Traditional Chinese medicine (TCM) liver depression infertility quality of life scale is developed to provide a scientific and reliable tool for TCM treatment and intervention in the treatment of liver depression patients with infertility, as well as basis and assistance for clinical decision-making.Methods Literature research method: Through the retrieval of Chinese knowledge network (CNKI), Wanfang (WANFANG), Vip (VIP), Springer, PubMed database of existing Chinese life quality scale and infertility dedicated quality of life scale, an entry pool is built with symptoms, emotional state, social function state and satisfaction as dimensions. Using the Delphi method to screen the entries. Screening entries according to the results of expert review, and evaluating the positive degree coefficient, authority degree and coordination coefficient by the experts. Using the clinical questionnaire method to screen the entries further. To form the Chinese medicine liver depression infertility life of quality scale. Scale evaluation: the reliability and validity of the scale were evaluated based on the results of the clinical questionnaire. Results After two rounds of Delphi method, there are 33 entries remained. The clinical questionnaire rescreened entries, formed the traditional Chinese medicine liver depression infertility quality of life scale containing 4 dimensions of symptoms, emotional states, social function states and satisfaction, with total of 29 entries and VAS score scale. Evaluation results: the Kronbach alpha coefficients performed well in total and each aspect. The validity of the scale: the structural efficiency evaluation results are in good agreement with the scale structure envisioned at the time of design. The relationship between the quality of life scale and the standard scale (FertiQoL International2008) showed a high absolute value.Conclusion In this study, the quality of life scale of Chinese medicine liver depression type infertility was developed by literature research, Delphi method and clinical questionnaire, with good reliability and validity of the scale evaluated. It could be used as a tool for efficacy judgment tool or quality of life evaluation in Chinese medicine treatment or intervention for patients with liver depression infertility.
Transcriptome-wide identification and validation of reference genes of Black rockfish (Sebastes schlegelii) for quantitative RT-PCR
Authors: Jin Chaofan , Song Weihao , Wang Mengya , Qi Jie , Zhang Quanqi , He Yan 
Published: March 2020

Abstract
Background: The quantitative real-time reverse transcription PCR (qRT-PCR) is a widely used technique that relies on the reference gene for gene expression normalization. Selecting a suitable reference gene is a crucial step to obtain an accurate result in qRT-PCR. However, most previous studies of fishes adopted reference genes that were commonly used in mammals without validation. Results: In this study, we utilized 89 transcriptome datasets covering early developmental stages and adult tissues, and carried out transcriptome-wide identification and validation of reference genes in Sebastes schlegelii. Finally, 121 candidate reference genes were identified based on four criteria. Eight candidates (METAP2, BTF3L4, EIF5A1, TCTP, UBC, PAIRB, RAB10, and DLD) and four commonly used reference genes (TUBA, ACTB, GAPDH, RPL17) in mammals were selected for validation via qRT- PCR and four statistical methods (delta-Ct, BestKeeper, geNorm, and NormFinder). The results revealed that the candidate reference genes we recommended are more stable than traditionally used ones. Conclusions: This is the first study to conduct transcriptome-wide identification and validation of reference genes for quantitative RT-PCR in the black rockfish, and lay an important foundation for gene expression analysis in teleost.
Determining the different mechanisms used by Pseudomonas strains to cope with minimal inhibitory concentrations of zinc via comparative transcriptomic and metabolic analyses
Authors: Liu Pulin , Chen Jiahui , Liao Weifang , Miao Lihong 
Published: March 2020

Abstract
Background Pseudomonas is one of the most diverse bacterial genera identified in soil, water, plants and clinical samples. Genome sequence analysis has indicated that this genus can be clustered into three lineages and ten groups. Each group can adopt different mechanisms to thrive under zinc-depleted or high-zinc conditions, two environments that are frequently encountered during their environmental propagation. Results The response mechanisms of three prominent Pseudomonas strains (Pseudomonas aeruginosa PAO1, Pseudomonas putida KT2440, and Pseudomonas fluorescence ATCC13525T) under high-zinc condition were compared using RNA-seq and ultra-performance liquid chromatography–tandem mass spectrometry analysis. Results demonstrated that the three strains shared only minimal similarity at the transcriptional level. Only four genes responsible for zinc efflux were commonly upregulated. P. aeruginosa PAO1 specifically downregulated the operons involved in siderophore synthesis and the genes that encode ribosomal protein, while upregulated the genes associated with antibiotic efflux and cell envelope biosynthesis. The membrane transporters in P. putida KT2440 were globally downregulated, indicating changes in cell permeability. Compared with P. aeruginosa PAO1 and P. putida KT2440, the most remarkable transcriptional variation in P. fluorescence ATCC13525 is the significant downregulation of the type VI secretion system. Metabolite quantitative analysis showed that low concentrations of the metabolites involved in central carbon metabolism and amino acid synthesis were detected in the three strains. Dipeptides containing branched-chain amino acids seems played an important role in alleviating stress caused by zinc ions. Conclusion The exclusion of cytoplasmic ions and reducing the intrusion of excess zinc are equally important for P. aeruginosa, P. putida, and P. fluorescence to withstand external zinc stress. Although similar metal efflux systems were commonly upregulated, these three strains apparently used different pathways to reduce zinc entry. In addition, zinc treatment can increase the difficulties of scavenging P. aeruginosa from its colonisation area, and reduce the effectiveness of P. fluorescence as a biocontrol agent.