bluuebunny/crossref_metadata_2025_split huggingface dataset:
Cell trace far-red is a suitable erythrocyte dye for multi-color Plasmodium falciparum invasion phenotyping assays
Authors: Thiam Laty G , Aniweh Yaw , Quansah Evelyn B , Donkor Jacob K , Gwira Theresa M , Kusi Kwadwo A , Niang Makhtar , Awandare Gordon A 
Published: January 2020

Plasmodium falciparum erythrocyte invasion phenotyping assays are a very useful tool for assessing parasite diversity and virulence, and for characterizing the formation of ligand–receptor interactions. However, such assays need to be highly sensitive and reproducible, and the selection of labeling dyes for differentiating donor and acceptor erythrocytes is a critical factor. We investigated the suitability of cell trace far-red (CTFR) as a dye for P. falciparum invasion phenotyping assays. Using the dyes carboxyfluorescein diacetate succinimidyl ester (CFDA-SE) and dichloro dimethyl acridin one succinimidyl ester (DDAO-SE) as comparators, we used a dye-dilution approach to assess the limitations and specific staining procedures for the applicability of CTFR in P. falciparum invasion phenotyping assays. Our data show that CTFR effectively labels acceptor erythrocytes and provides a stable fluorescent intensity at relatively low concentrations. CTFR also yielded a higher fluorescence intensity relative to DDAO-SE and with a more stable fluorescence intensity over time. Furthermore, CTFR did not affect merozoites invasion of erythrocytes and was not toxic to the parasite’s intraerythrocytic development. Additionally, CTFR offers flexibility in the choice of combinations with several other DNA dyes, which broaden its usage for P. falciparum erythrocyte invasion assays, considering a wider range of flow cytometers with various laser settings. Impact statement In recent years, flow cytometry has become a cornerstone in investigating P. falciparum phenotypic diversity using multiple dyes to discriminate between donor and acceptor erythrocytes. To broaden the applicability of such assays, we optimized the staining conditions of a newly developed cytoplasmic dye, cell trace far-red (CTFR), and assessed its suitability for use in P. falciparum invasion phenotyping assays. We showed that CTFR has a very narrow emission peak excited by red lasers. Furthermore, CTFR labeling of target erythrocytes, achieved even at low concentrations, is stable over time and did not impair parasite development. P. falciparum erythrocyte invasion phenotyping assays revealed that CTFR is suitable for use in combination with several DNA dyes in multiplex assays. This will allow for high throughput phenotyping of parasites as well as facilitate the evaluation of preference of erythrocytes by merozoites. Altogether, these make screening for potential invasion-blocking interventions possible.
Low VWF levels in children and lack of association with bleeding in children undergoing tonsillectomy
Authors: Gill Joan Cox , Conley Stephen F. , Johnson Victoria P. , Christopherson Pamela A. , Haberichter Sandra L. , Diaz Christina D. , Strong Tatyana C. , Zhang Jian , Simpson Pippa , Abshire Thomas C. , Montgomery Robert R. , Flood Veronica H. 
Published: January 2020

Key Points
In children undergoing tonsillectomy, low VWF levels did not predict surgical bleeding in the absence of major bleeding history. Children have lower VWF levels than adults and these lower levels do not appear to be associated with bleeding.
Enhanced recovery protocol versus standard protocol for patients undergoing radical cystectomy: results of a prospective randomized study
Authors: Ibrahim Hisham , Kotb Sameh , Abd Allah Ahmed , Kassem Ayman , Salem Ahmed , Abd ElHamid Mahmoud , ElFayoumy Hany , Mosharafa Ashraf , Saad Ismail Rady , Mursi Khaled , Abdel-Razzak Omar 
Published: January 2020

Abstract
Background
To assess patients undergoing radical cystectomy using enhanced recovery protocol and standard protocol in terms of intraoperative and postoperative outcomes and complications.

Results
All operative and postoperative complications were recorded. In group B, time to normal bowel activity ranged from 1 to 4 days, and the mean was 1.8 days (± 1.02), while it ranged from 1 to 5 days, and the mean was 3.17 days (± 1.14) in group A which was statistically significant (p value < 0.001). The length of hospital stay in group B ranged from 6 to 50 days, the mean was 13.16 days (± 7.83), while it ranged from 8 to 35 days, and the mean was 14.71 days (± 5.78) in group A which was statistically significant (p value = 0.033). Postoperative mortality was similar in both groups.

Conclusion
In patients undergoing radical cystectomy, enhanced recovery protocol is considered as a safe procedure and not associated with any increase in intraoperative and postoperative complications compared to standard protocol. The length of hospital stay and time to return to full diet are reduced.
Identification and characterization of genes frequently responsive to Xanthomonas oryzae pv. oryzae and Magnaporthe oryzae infections in rice
Authors: Kong Weiwen , Ding Li , Xia Xue 
Published: January 2020

AbstractBackgroundDisease resistance is an important factor that impacts rice production. However, the mechanisms underlying rice disease resistance remain to be elucidated.ResultsHere, we show that a robust set of genes has been defined in rice response to the infections ofXanthomonas oryzaepv.oryzae(Xoo) andMagnaporthe oryzae(Mor). We conducted a comprehensive analysis of the available microarray data from a variety of rice samples with inoculation ofXooandMor. A set of 12,932 genes was identified to be regulated byXooand another set of 2709Mor-regulated genes was determined. GO enrichment analysis of the regulated genes byXooorMorsuggested mitochondrion may be an arena for the up-regulated genes and chloroplast be another for the down-regulated genes byXooorMor. Cytokinin-related processes were most frequently repressed byXoo, while processes relevant to jasmonic acid and abscisic acid were most frequently activated byXooandMor. Among genes responsive toXooandMor, defense responses and diverse signaling pathways were the most frequently enriched resistance mechanisms. InterPro annotation showed the zinc finger domain family, WRKY proteins, and Myb domain proteins were the most significant transcription factors regulated byXooandMor. KEGG analysis demonstrated pathways including ‘phenylpropanoid biosynthesis’, ‘biosynthesis of antibiotics’, ‘phenylalanine metabolism’, and ‘biosynthesis of secondary metabolites’ were most frequently triggered byXooandMor, whereas ‘circadian rhythm-plant’ was the most frequent pathway repressed byXooandMor.ConclusionsThe genes identified here represent a robust set of genes responsive to the infections ofXooandMor, which provides an overview of transcriptional reprogramming during rice defense againstXooandMorinfections. Our study would be helpful in understanding the mechanisms of rice disease resistance.
A highly efficient organogenesis protocol based on zeatin riboside for in vitro regeneration of eggplant
Authors: García-Fortea Edgar , Lluch-Ruiz Agustín , Pineda-Chaza Benito José , García-Pérez Ana , Bracho-Gil Juan Pablo , Plazas Mariola , Gramazio Pietro , Vilanova Santiago , Moreno Vicente , Prohens Jaime 
Published: January 2020

AbstractBackgroundEfficient organogenesis induction in eggplant (Solanum melongenaL.) is required for multiple in vitro culture applications. In this work, we aimed at developing a universal protocol for efficient in vitro regeneration of eggplant mainly based on the use of zeatin riboside (ZR). We evaluated the effect of seven combinations of ZR with indoleacetic acid (IAA) for organogenic regeneration in five genetically diverseS. melongenaand oneS. insanumL. accessions using two photoperiod conditions. In addition, the effect of six different concentrations of indolebutyric acid (IBA) in order to promote rooting was assessed to facilitate subsequent acclimatization of plants. The ploidy level of regenerated plants was studied.ResultsIn a first experiment with accessions MEL1 and MEL3, significant (p < 0.05) differences were observed for the four factors evaluated for organogenesis from cotyledon, hypocotyl and leaf explants, with the best results obtained (9 and 11 shoots for MEL1 and MEL3, respectively) using cotyledon tissue, 16 h light / 8 h dark photoperiod conditions, and medium E6 (2 mg/L of ZR and 0 mg/L of IAA). The best combination of conditions was tested in the other four accessions and confirmed its high regeneration efficiency per explant when using both cotyledon and hypocotyl tissues. The best rooting media was R2 (1 mg/L IBA). The analysis of ploidy level revealed that between 25 and 50% of the regenerated plantlets were tetraploid.ConclusionsAn efficient protocol for organogenesis of both cultivated and wild accessions of eggplant, based on the use of ZR, is proposed. The universal protocol developed may be useful for fostering in vitro culture applications in eggplant requiring regeneration of plants and, in addition, allows developing tetraploid plants without the need of antimitotic chemicals.
Transcriptomic and metabolomic analyses provide insight into the volatile compounds of citrus leaves and flowers
Authors: Zhang Haipeng , Chen Mengjun , Wen Huan , Wang Zhenhua , Chen Jiajing , Fang Liu , Zhang Hongyan , Xie Zongzhou , Jiang Dong , Cheng Yunjiang , Xu Juan 
Published: January 2020

Abstract
Background
Previous reports have mainly focused on the volatiles in citrus fruits, and there have been few reports about the volatiles in citrus leaves and flowers. However, citrus leaves and flowers are also rich in volatile compounds with unique aromas. Here, to investigate the volatiles in citrus leaves and flowers, volatile profiling was performed on leaves from 62 germplasms and flowers from 25 germplasms.

Results
In total, 196 and 82 volatile compounds were identified from leaves of 62 citrus germplasms and flowers of 25 citrus germplasms, respectively. The dominant volatile terpenoids were more diverse in citrus leaves than in peels. A total of 34 volatile terpenoids were commonly detected in the leaves of at least 20 germplasms, among which 31 were overaccumulated in the leaves of wild or semiwild germplasms. This result was consistent with the high expression levels of five genes and one key gene of the mevalonate and 2-C-methyl-D-erythritol-4-phosphate (MEP) biosynthetic pathways, respectively, as well as the low expression levels of geranylgeranyl diphosphate synthase of the MEP pathway, relative to the levels in cultivars. Fully open flowers showed increased levels of four terpene alcohols and a decrease in sabinene content compared with balloon-stage flowers, especially in sweet orange. A monoterpene synthase gene was identified and functionally characterized as a sabinene synthase in vitro.

Conclusions
Collectively, our results suggest that 31 important terpenoids are abundant in wild or semiwild citrus germplasms, possibly because of a negative effect of domestication on the volatiles in citrus leaves. The sweet smell of fully open flowers may be attributed to increased levels of four terpene alcohols. In addition, a sabinene synthase gene was identified by combined transcriptomic and metabolomic analyses.
Treatment of chronic active antibody-mediated rejection in renal transplant recipients – a single center retrospective study
Authors: Chiu Hsien-Fu , Wen Mei-Chin , Wu Ming-Ju , Chen Cheng-Hsu , Yu Tung-Min , Chuang Ya-Wen , Huang Shih-Ting , Tsai Shang-Feng , Lo Ying-Chih , Ho Hao-Chung , Shu Kuo-Hsiung 
Published: January 2020

Abstract
Background
Chronic active antibody-mediated rejection is a major etiology of graft loss in renal transplant recipients. However, there is no consensus on the optimal treatment strategies.

Methods
Computerized records from Taichung Veterans General Hospital were collected to identify renal transplant biopsies performed in the past 7 years with a diagnosis of chronic active antibody-mediated rejection. The patients were divided into two groups according to treatment strategy: Group 1 received aggressive treatment (double filtration plasmapheresis and one of the followings: rituximab, intravenous immunoglobulin, antithymogycte globulin, bortezomib, or methylprednisolone pulse therapy); and group 2 received supportive treatment.

Results
From February 2009 to December 2017, a total of 82 patients with biopsy-proven chronic antibody mediated rejection were identified. Kaplan-Meier analysis of death-censored graft survival showed a worse survival in group 2 (P = 0.015 by log-rank test). Adverse event-free survival was lower in group 1, whereas patient survival was not significantly different. Proteinuria and supportive treatment were independent risk factors for graft loss in multivariate analysis.

Conclusions
Aggressive treatment was associated with better graft outcome. However, higher incidence of adverse events merit personalized treatment, especially for those with higher risk of infection. Appropriate prophylactic antibiotics are recommended for patients undergoing aggressive treatment.
Social determinants of health associated with hemodialysis non-adherence and emergency department utilization: a pilot observational study
Authors: Balhara Kamna S. , Fisher Lori , El Hage Naya , Ramos Rosemarie G. , Jaar Bernard G. 
Published: January 2020

Abstract
Background
Dialysis patients who miss treatments are twice as likely to visit emergency departments (EDs) compared to adherent patients; however, prospective studies assessing ED use after missed treatments are limited. This interdisciplinary pilot study aimed to identify social determinants of health (SDOH) associated with missing hemodialysis (HD) and presenting to the ED, and describe resource utilization associated with such visits.

Methods
We conducted a prospective observational study with a convenience sample of patients presenting to the ED after missing HD (cases); patients at local dialysis centers identified as HD-compliant by their nephrologists served as matched controls. Patients were interviewed with validated instruments capturing associated risk factors, including SDOH. ED resource utilization by cases was determined by chart review. Chi-square tests and ANOVA were used to detect statistically significant group differences.

Results
All cases visiting the ED had laboratory and radiographic studies; 40% needed physician-performed procedures. Mean ED length of stay (LOS) for cases was 17 h; 76% of patients were admitted with average LOS of 6 days. Comparing 25 cases and 24 controls, we found no difference in economic stability, educational attainment, health literacy, family support, or satisfaction with nephrology care. However, cases were more dependent on public transport for dialysis (p = 0.03). Despite comparable comorbidity burdens, cases were more likely to have impaired mobility, physical limitations, and higher severity of pain and depression. (p < 0.05).

Conclusions
ED visits after missed HD resulted in elevated LOS and admission rates. Frequently-cited SDOH such as health literacy did not confer significant risk for missing HD. However, pain, physical limitations, and depression were higher among cases. Community-specific collaborations between EDs and dialysis centers would be valuable in identifying risk factors specific to missed HD and ED use, to develop strategies to improve treatment adherence and reduce unnecessary ED utilization.
Fast growing angiosarcoma of the right atrium after radiofrequency catheter ablation: a missed diagnosis or misdiagnosis case report
Authors: Yu Yi , Wang Qunshan , Sun Jian , Zhao Jing , Chen Suyun , Li Yigang 
Published: January 2020

Abstract
Background
Primary angiosarcomas of the right atrium are extremely rare, often resulted in missed diagnosis or misdiagnosis with routine examination tools. These malignant cardiac tumors are highly aggressive with generally poor prognosis. Surgical excision is the mainstay of treatment as it is essentially not responsive to current regimens of chemoradiotherapy.

Case presentation
Herein, we describe a patient who initially presented with paroxysmal atrial fibrillation and was subsequently treated with radiofrequency catheter ablation (RFCA). Prior to RFCA, an initial transesophageal echocardiography revealed a local thickening of the intratrial septum. Three months later, she was hospitalized with progressive dyspnea and massive pericardial effusion. A large immobile, non-pedunculated mass, occupying almost half of the right atrium was detected by transthoracic and transesophageal echocardiogram. Multimodality cardiac imaging was useful in further characterizing this mass, which was ultimately diagnosed as an angiosarcoma based upon biopsy results. The growth rate was extremely rapid following RFCA, and patient underwent surgical excision. After discharge, the angiosarcoma recurred and patient survived for 7 months from the first episode of tamponade.

Conclusions
Primary cardiac angiosarcoma of the right atrium can easily be mistaken for structural anomalies in its early stages, losing the opportunity for initiating earlier treatments to improve potential patient outcomes. The correct diagnosis of this rare case relied on the comprehensive utilization of multimodal imaging techniques including biopsy.
Nomogram for predicting the survival of gastric adenocarcinoma patients who receive surgery and chemotherapy
Authors: Wang Chao-Yang , Yang Jin , Zi Hao , Zheng Zhong-Li , Li Bing-Hui , Wang Yang , Ge Zheng , Jian Guang-Xu , Lyu Jun , Li Xiao-Dong , Ren Xue-Qun 
Published: January 2020

Abstract
Background
Surgery is the only way to cure gastric adenocarcinoma (GAC), and chemotherapy is the basic adjuvant management for GAC. A significant prognostic nomogram for predicting the respective disease-specific survival (DSS) rates of GAC patients who receive surgery and chemotherapy has not been established.

Objective
We were planning to establish a survival nomogram model for GAC patients who receive surgery and chemotherapy.

Methods
We identified 5764 GAC patients who had received surgery and chemotherapy from the record of Surveillance, Epidemiology, and End Results (SEER) database. About 70% (n = 4034) of the chosen GAC patients were randomly assigned to the training set, and the rest of the included ones (n = 1729) were assigned to the external validation set. A prognostic nomogram was constructed by the training set and the predictive accuracy of it was validated by the validation set.

Results
Based on the outcome of a multivariate analysis of candidate factors, a nomogram was developed that encompassed age at diagnosis, number of regional lymph nodes examined after surgery, number of positive regional lymph nodes, sex, race, grade, derived AJCC stage, summary stage, and radiotherapy status. The C-index (Harrell’s concordance index) of the nomogram model was some larger than that of the traditional seventh AJCC staging system (0.707 vs 0.661). Calibration plots of the constructed nomogram displayed that the probability of DSS commendably accord with the survival rate. Integrated discrimination improvement (IDI) revealed obvious increase and categorical net reclassification improvement (NRI) showed visible enhancement. IDI for 3-, 5- and 10- year DSS were 0.058, 0.059 and 0.058, respectively (P > 0.05), and NRI for 3-, 5- and 10- year DSS were 0.380 (95% CI = 0.316–0.470), 0.407 (95% CI = 0.350–0.505), and 0.413 (95% CI = 0.336–0.519), respectively. Decision curve analysis (DCA) proved that the constructed nomogram was preferable to the AJCC staging system.

Conclusion
The constructed nomogram supplies more credible DSS predictions for GAC patients who receive surgery and chemotherapy in the general population. According to validation, the new nomogram will be beneficial in facilitating individualized survival predictions and useful when performing clinical decision-making for GAC patients who receive surgery and chemotherapy.
Longitudinal observation of OCT imaging is a valuable tool to monitor primary vitreoretinal lymphoma treated with intravitreal injections of methotrexate
Authors: Zhao Huiying , Wang Xiaona , Mao Yu , Peng Xiaoyan 
Published: January 2020

Abstract
Background
Developing objective and repeatable indicators to evaluate the efficacy of PVRL treatment is important. The quantification of vitreous cells is a traditional criterion; however slight changes are difficult to ascertain. Spectral domain optical coherence tomography (SD-OCT) is objective, repeatable, and easily explained. The purpose of this study is to provide a longitudinal observation of OCT in PVRL treated with intravitreal injections of methotrexate (MTX) and to evaluate the utility of OCT in monitoring responsiveness of PVRL to treatment.

Methods
The medical records of patients with biopsy-positive PVRL attending our hospital between January 2016 and September 2017 who received intravitreal injections of MTX were included in this study. Pre- and post-treatment OCT images were reviewed independently by two researchers.

Results
Of the 24 cases reviewed, 10 patients (18 eyes) were included. SD-OCT abnormalities at the initial visit included vitreous cells (18/18), OR (outer retina) fuzzy borders (12/18), PED (pigment epithelium detachments) (9/18), subretinal hyperreflective infiltration (3/18), intraretinal infiltration (8/18), and SRF (subretinal fluid) (4/18). Post induction treatment, SRF in cases with RD (retinal detachment) was absorbed, and subretinal fibrosis appeared. Other lesions were significantly reduced. Post consolidation treatment, OR fuzzy borders, PED and SRF disappeared in 2 eyes, intraretinal infiltration disappeared in 1 eye, and other abnormalities further improved. Additionally, retinal fibrosis was observed in 3 eyes. One month post maintenance treatment, all abnormalities observed at the first visit vanished. At the last visit, OCT showed subretinal fibrosis and in 3 eyes (16.7%), the disruption of outer retina in 9 eyes (50%) and thinning of the whole layer in 4 eyes (22.2%).

Conclusions
Our observations reveal that characteristic OCT features in PVRL patients can reduce gradually and finally vanish with therapy. We propose that SD-OCT may be employed to monitor the responsiveness of PVRL to treatment, which may influence decision making in the management of this disease.