bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identification of Transmission Chains and Clusters Associated with COVID-19 in Tunisia
Authors: Safer Mouna , Letaief Hejer , Hechaichi Aicha Hechaichi , Harizi Chahida , Dhaouadi Sonia , Bouabid Leila , Darouiche Sondes , Gharbi Donia , Elmili Nawel , Salah Hamida Ben , Hammami Mongi , Talmoudi Khouloud , Moussa Rim , Chraa Nejib , Termiz Hasna , Ltaief Fethi , Tounekti Habib , Makhlouf Mohamed , Belgu Asma Sriha , Fredj Manel Ben , Khalfallah Sonia , Jabrane Houcine , Mchirgui Selma , Amich Chedli , Dabghi Radhia , Anez Zid , Abdelkader Latifa , Mhamdi Moncef , Ouerfeli Nabil , Zoghlami Salah , Bougatef Souha , Chahed Mohamed Kouni , Alaya Nissaf Bouafif Ben 
Published: December 2020

Abstract
Background: The aim of this study was to characterize the transmission chains and clusters of COVID-19 infection in TunisiaMethods: All cases were confirmed by RT-PCR of a nasopharyngeal specimen. Contact tracing is undertaken for all confirmed cases in order to identify close contacts that will be systematically screened and quarantined. Transmission chains were identified based on field investigation, contact tracing, results of screening tests and by assessing all probable mode of transmission and interactions.Results: As of May 18, 2020, 656 cases out of a total of 1043 confirmed cases of COVID-19 belong to 127 transmission chains identified during the epidemic (mean age 42.36 years, Standard deviation 19.56 and sex ratio 0.86). The virus transmission is the most concentrated in the governorate of Tunis (31.5%), Ariana (10.2%) and Ben Arous (10.2%). Virus transmission occurred 50 times (9.72% of secondary transmission events) between two different governorates. A maximum of seven generations of secondary infection was identified, whereas 62% of these secondary infections belong the first generation. A total of 11 “superspreader” cases were identified in this investigation. Four large clusters have been identified. The evolution of secondary cases highlighted two peaks: one in 2nd April and a second in 16 th April whereas imported cases caused local transmission of virus during the early phase of the epidemic.Conclusion: Correct contact tracing and early active case finding is useful to identify transmission chains and source of infection in order to contain the widespread transmission in the community.
SlGT11 Controls Floral Organ Patterning and Floral Determinacy in Tomato
Authors: Yang Liling , Qi Shilian , touqeer Arfa , Li Haiyang , Zhang Xiaolan , Liu XiaoFeng , wu shuang 
Published: December 2020

Abstract
Background: Flower development directly affects fruit production in tomato. Despite the framework mediated by ABC genes have been established in Arabidopsis, the spatiotemporal precision of floral development in tomato has not been well examined.Results: Here, we analyzed a novel tomato stamenless like flower (slf) mutant in which the development of stamens and carpels is disturbed, with carpelloid structure formed in the third whorl and ectopic formation of floral and shoot apical meristem in the fourth whorl. Using bulked segregant analysis (BSA), we assigned the causal mutation to the gene Solanum lycopersicum GT11 (SlGT11) that encodes a transcription factor belonging to Trihelix gene family. SlGT11 is expressed in the early stages of the flower and the expression becomes more specific to the primordium position corresponding to stamens and carpels in later stages of the floral development. Further RNAi silencing of SlGT11 verifies the defective phenotypes of the slf mutant. The carpelloid stamen in slf mutant indicates that SlGT11 is required for B-function activity in the third whorl. The failed termination of floral meristem and the occurrence of floral reversion in slf indicate that part of the C-function requires SlGT11 activity in the fourth whorl. Furthermore, we find that at higher temperature, the defects of slf mutant are substantially enhanced, with petals transformed into sepals, all stamens disappeared, and the frequency of ectopic shoot/floral meristem in fourth whorl increased, indicating that SlGT11 functions in the development of the three inner floral whorls. Consistent with the observed phenotypes, it was found that B, C and an E-type MADS-box genes were in part down regulated in slf mutants.Conclusions: Together with the spatiotemporal expression pattern, we suggest that SlGT11 functions in floral organ patterning and maintenance of floral determinacy in tomato.
Heart rate and swimming activity as indicators of post-surgical recovery time of Atlantic salmon (Salmo salar)
Authors: Føre Martin , Svendsen Eirik , Økland Finn , Gräns Albin , Alfredsen Jo Arve , Finstad Bengt , Hedger Richard , Uglem Ingebrigt 
Published: December 2020

Abstract
Background: Fish telemetry using electronic transmitter or data storage tags has become a common method for studying free-swimming fish both in the wild and in aquaculture. However, fish used in telemetry studies must be handled, anaesthetised and often subjected to surgical procedures to be equipped with tags, processes that will shift the fish from their normal physiological and behavioural states. In many projects, information is needed on when the fish has recovered after handling and tagging so that only the data recorded after the fish has fully recovered are used in analyses. We aimed to establish recovery times of adult Atlantic salmon (Salmo salar) after an intraperitoneal tagging procedure featuring handling, anaesthesia and surgery. Results: Based on ECG and accelerometer data collected with telemetry from nine individual Atlantic salmon during the first period after tagging, we found that heart rate was initially elevated in all fish, and that it took an average of ≈4 days and a maximum of 6 days for heart rate to return to an assumed baseline level. One activity tag showed no consistent decline in activity, and two others did not show strong evidence of complete recovery by the end of the experiment: baseline levels of the remaining tags were on average reached after ≈ 3.3 days. Conclusion: Our findings showed that the Atlantic salmon used in this study required an average of ≈ 4 days, with a maximum interval of 6 days, of recovery after tagging before tag data could be considered valid. Moreover, the differences between recovery times for heart rate and activity imply that recovery time recommendations should be developed based on a combination of indicators and not just on e.g. behavioural observations.
Pulmonary rehabilitation to improve physical capacity, dyspnea and quality of life following pulmonary embolism (the PeRehab study): Study protocol for a two-centre randomized controlled trial
Authors: Haukeland-Parker Stacey , Jervan Øyvind , Johannessen Hege Hølmo , Gleditsch Jostein , Stavem Knut , Steine Kjetil , Spruit Martijn A , Holst Rene , Tavoly Mazdak , Klok Erik , Ghanima Waleed 
Published: December 2020

Abstract
Background: Recently, a large group of patients with persistent dyspnea, poor physical capacity and reduced health-related quality of life (HRQoL) following pulmonary embolism (PE) has been identified and clustered under the name “post pulmonary embolism syndrome” (PPS). These patients seem good candidates for pulmonary rehabilitation. The aim of the study is to explore whether a pulmonary rehabilitation program can improve physical capacity, dyspnea and HRQoL in PPS patients.Methods: A two-centre randomized controlled trial (RCT) is being performed at Østfold Hospital and Akershus University Hospital in Norway. Patients with PPS are 1:1 randomized into an intervention or a control group. The intervention consists of a supervised, outpatient rehabilitation program twice weekly (1 hour) for 8 weeks provided by experienced physiotherapists. The intervention involves individually adapted exercises based on existing pulmonary rehabilitation programs (relaxation, interval and resistance training), and an educational session including topics such as normal anatomy and physiology of the respiratory and circulatory system, information on PE/PPS, breathing strategies, and benefits of exercise/physical activity. Patients randomized to the control group receive usual care without specific instructions to exercise.Participants in the intervention and control groups will be compared based on assessments conducted at baseline, 12 weeks and 36 weeks after inclusion using the incremental shuttle walk test (primary outcome) and endurance shuttle walk test (exercise capacity), Sensewear activity monitor (daily physical activity), the Modified Medical Research Council scale, the Shortness of Breath questionnaire (dyspnea), and EQ-5D-5L and the Pulmonary Embolism Quality of Life Questionnaire (HRQoL).Recruitment of 190 patients is currently ongoing.Discussion: Results from this study may provide a currently untreated group of PPS patients with an effective treatment resulting in reduced symptoms of dyspnea, improved exercise capacity and better HRQoL following PE.Trial registration: NCT03405480, Clinical Trials (registered prospectively.Protocol version 1 (from original protocol September 2017).The study protocol has been reported in accordance with the Standard Protocol Items: Recommendations for Clinical Interventional Trials (SPIRIT) guidelines (Additional file 1).
Perception of childbirth experiences of Japanese women in Bali, Indonesia: A qualitative study
Authors: Tanaka Kazuko , Kurniasari Ni Made Dian , Widyanthini Desak Nyoman , Suariyani Ni Luh Putu , Listyowati Rina , Urayama Akimi , Wirawan I Made Ady , Yoshimura Koichi 
Published: December 2020

Abstract
Background: Maternal healthcare services in Indonesia have seen dramatic improvements over the past 25 years and yet there is still room for improvement. The perception, by the women, of the perinatal care provided, is a vital input to further improving these services. This study examines how the perinatal care provided is experienced by Japanese women in Bali, using an interview survey.Methods: We conducted semi-structured interviews, from August to October 2017, with 14 Japanese women living in Badung Regency and Denpasar City in Bali Province, Indonesia to report their perception of the perinatal care they experienced during their pregnancies. The interview guide included among others, the reasons for choosing specific (perinatal care) health facilities and their satisfaction with their experience of using the antenatal, delivery, and postnatal care services. The data were analysed using the qualitative content analysis method.Results: From the interview data, 12 categories across five themes were extracted. Participants reported experiencing various concerns during their pregnancies such as difficulty in obtaining perinatal care related information. From the beginning of their pregnancies, participants gradually established trusting relationships with midwives, but in many situations, they were disappointed with their childbirth experiences, as they felt that the care provided was not woman-centred. Through their own efforts and with the support of family members and other Japanese residents, many women were able to eventually regard their childbirth experiences as positive. Nevertheless, some women could not overcome their negative impressions even years after childbirth.Conclusions: Participants desired close attention and encouragement from nurses and midwives. Our results suggest that Japanese women in Bali expected a woman-centred perinatal care and active support from nursing/midwifery staff during their pregnancies and postnatal care.
Genome-wide identification, phylogenetic&nbsp;and expression&nbsp;pattern analysis&nbsp;of GATA&nbsp;family genes in Brassica napus
Authors: Zhu Weizhuo , Guo Yiyi , Chen Yeke , Wu Dezhi , Jiang Lixi 
Published: December 2020

Abstract
Background: Transcription factors GATAs are involved in plant developmental processes and respond to environmental stresses through binding DNA regulatory regions to regulate their downstream genes. However, little information on the GATA genes in Brassica napus is available. The release of the reference genome of B. napus provides a good opportunity to perform a genome-wide characterization of GATA family genes in rapeseed.Results: In this study, 96 GATA genes randomly distributing on 19 chromosomes were identified in B. napus, which were classified into four subfamilies based on phylogenetic analysis and their domain structures. The amino acids of BnGATAs were obvious divergence among four subfamilies in terms of their GATA domains, structures and motif compositions. Gene duplication and synteny between the genomes of B. napus and A. thaliana were also analyzed to provide insights into evolutionary characteristics. Moreover, BnGATAs showed different expression patterns in various tissues and under diverse abiotic stresses. Single nucleotide polymorphisms (SNPs) distributions of BnGATAs in a core collection germplasm are probably associated with functional disparity under environmental stress condition in different genotypes of B. napus.Conclusion: The present study was investigated genomic structures, evolution features, expression patterns and SNP distributions of 96 BnGATAs. The results enrich our understanding of the GATA genes in rapeseed.
Preoperative platelet count predicts posttransplant portal vein complications in orthotopic liver transplantation: a propensity score analysis
Authors: Li Qingshan , Wang Yue , Ma Tao , Ren Fenggang , Mu Fan , Wu Rongqian , Lv Yi , Wang Bo 
Published: December 2020

Abstract
Background: The role of platelets on the prognosis of patients with liver transplantation remains unclear. Thus, we aimed to evaluate the influence of preoperative platelet count on postoperative morbidity after liver transplantation. Methods: Clinical data of the patients who received liver transplantation from January 2015 to September 2018 were evaluated. Results: Of the 329 patients included, the average age was 46.71±0.55 years, and 243 were men (75.2%). The incidence of posttransplant portal vein complication was significantly higher in the high platelet count group (> 49.5×109/L; n=167) than in the low platelet count group (≤ 49.5×109/L, n=162, 12.6% vs. 1.9%). After multivariable regression analysis, high platelet count was independently associated with postoperative portal vein complication (odds ratio [OR]: 8.821, 95% confidence interval [CI]: 2.260 to 34.437). After the inverse probability of treatment weighting analysis, patients in the high platelet count group had significantly higher risk of portal vein complication (OR: 9.210, 95%CI: 1.907 to 44.498, p=0.006) and early allograft dysfunction (OR: 2.087, 95%CI: 1.131 to 3.853, p=0.019). Conclusions: Preoperative platelet count > 49.5×109/L was an independent risk factor for posttransplant portal vein complication and early allograft dysfunction. High preoperative platelet count could be an adverse prognostic predictor for liver transplantation recipients.
Clinicopathological features and recurrence patterns of combined hepatocellular-cholangiocarcinoma
Authors: Ishii Takamichi , Ito Takashi , Sumiyoshi Shinji , Ogiso Satoshi , Fukumitsu Ken , Seo Satoru , Taura Kojiro , Uemoto Shinji 
Published: December 2020

Abstract
Background: Combined hepatocellular-cholangiocarcinoma (cHCC-CCA) is a primary liver carcinoma with both hepatocellular carcinoma (HCC) and cholangiocarcinoma (CCA) components. We examined the clinicopathological characteristics and recurrence patterns of cHCC-CCA. Because of the rarity of cHCC-CCA, its etiology, clinicopathological features, and prognosis in comparison with other primary liver carcinoma remain unknown. Its recurrence pattern and sites in particular also need to be elucidated.Methods: All patients who underwent hepatectomy for primary liver malignancies between 2005 and 2015 were retrospectively included in this study. Results: Eight hundred and ninety-four hepatectomies were performed. Nineteen cases of cHCC-CCA (2.1%) in 16 patients were enrolled. Three patients underwent re-hepatectomy. The background of hepatitis viruses and tumor marker patterns of cHCC-CCA were similar to those of HCC and dissimilar to those of intrahepatic CCA (iCCA). Biliary invasion was common in cHCC-CCA and iCCA. The 5-year overall survival values of the cHCC-CCA, HCC, and iCCA patients were 44.7%, 56.6%, and 38.5%, respectively. The 5-year recurrence-free survival values of the cHCC-CCA, HCC, and iCCA patients were 12.2%, 28.7%, and 32.9%, respectively. The liver was the most common recurrence site. Unlike HCC, however, the lymph node was the second-most common recurrence site in both cHCC-CCA and iCCA. Pathological samples of the recurrent lesions were obtained in six patients, and four had cHCC-CCA recurrence pathologically.Conclusion: cHCC-CCA had a mixture of characteristics of HCC and iCCA. Many cases of cHCC-CCA remained cHCC-CCA pathologically even after recurrence.
Required concentration index quantifies effective drug combinations against hepatitis C virus infection
Authors: Kakizoe Yusuke , Koizumi Yoshiki , Ikoma Yukino , Ohashi Hirofumi , Wakita Takaji , Iwami Shingo , Watashi Koichi 
Published: December 2020

Abstract
Successful clinical drug development requires rational design of combination treatments based on preclinical data. Anti-HCV drugs exhibit significant diversity in antiviral effect. Dose-response assessments can be used to determine parameters profiling the diverse antiviral effect during combination treatment. In the current study, a combined experimental and mathematical approaches were used to compare and score different combinations of anti-hepatitis C virus (HCV) treatments. A “required concentration index” was generated and used to rank the antiviral profile of possible double- and triple-drug combinations against HCV genotype 1b and 2a. Rankings varied based on target HCV genotype. Interestingly, multidrug (double and triple) treatment not only augmented antiviral activity, but also reduced genotype-specific efficacy, suggesting another advantage of multidrug treatment. The current study provides a quantitative method for profiling drug combinations against viral genotypes, to better inform clinical drug development.
Systemic inflammation-based predictors of pathological response to neoadjuvant chemoradiotherapy in locally advanced rectal cancer patients: A propensity score matching analysis
Authors: Xu Ning , Li Wenliang , Huang Fengchang , Yang Jun , Wen Zhengqi , Yin Liang , Zhang Yunfei , Zhao Jingjiao , Zhou Ruize , Yang Jingyu 
Published: December 2020

Abstract
Background: In the management of locally advanced rectal cancer (LARC) treated with neoadjuvant chemoradiotherapy (CRT), the relationship between systemic inflammation-based predictors and tumor response remains unclear. This study aimed to determine whether these inflammatory factors can predict tumor response.Methods: Totally 205 LARC patients underwent neoadjuvant CRT and curative surgery between 2008 and 2017 were analyzed. After propensity score matching, 146 patients (73 matched pairs) were included in this study. The hematological parameters were collected and their relationship with tumor response was investigated.Results: After propensity score matching, the neutrophil-lymphocyte-ratio (NLR) and platelet-lymphocyte-ratio (PLR) before CRT in good response group were significantly lower than those in poor response group, while there was no significant difference in all hematological characteristics between two groups after CRT. The cutoff values​​ of pre-CRT NLR and pre-CRT PLR were 3.10 and 198.7 after receiver operating characteristic analysis. Multivariate analysis model indicated that pre-CRT PLR was not related with tumor response, while pre-CRT NLR≥3.1 was the predictor of poor tumor response (OR=2.047, 95%CI =1.241-3.377, p=0.005). Besides, patients with NLR≥3.1 had a significantly poor tumor regression grade rates compared with patients with NLR<3.1 (p=0.036).Conclusion: The increased NLR before CRT can be regarded as a hematological factor for poor tumor response in LARC, and higher NLR also represents worse tumor regression grade.
Automatic Segmentation of Coronary Lumen and External Elastic Membrane in Intravascular Ultrasound Images Using 8-layer U-Net
Authors: Dong Liang , Lu Wei , Jiang Jun , Zhao Ya , Song Xiangfen , Leng Xiaochang , Zhao Hang , Wang Jian’an , Li Changling , Xiang Jianping 
Published: December 2020

Abstract
Background: Intravascular ultrasound (IVUS) is the golden standard in accessing the coronary lesions, stenosis, and atherosclerosis plaques. In this paper, a fully-automatic approach by an 8-layer U-Net is developed to segment the coronary artery lumen and the area bounded by external elastic membrane (EEM), i.e. cross section area (EEM-CSA). The database comprises of single-vendor and single-frequency IVUS data. Particularly, the proposed data augmentation of MeshGrid combined with flip and rotation operations is implemented, improving the model performance without pre- or post-processing of the raw IVUS images.Results: The mean intersection of union (mIoU) of 0.937 and 0.804 for the lumen and EEM-CSA respectively were achieved, which exceeded the manual labeling accuracy of the clinician.Conclusion: The accuracy shown by the proposed method is sufficient for subsequent reconstruction of 3D IVUS images, which is essential for doctors’ diagnosis in the tissue characterization of coronary artery walls and plaque compositions, qualitatively and quantitatively.
Erythropoietin supports the growth and function of Sca-1+ stem cells and promotes myocardial infarction repair in mice
Authors: Zuo Lin , Li Duan-duan , Ma Xiu-Xia , Shi Shan-Hui , Lü Ding-Chao , Shen Jing , Zhang Wei-Fang , Gao Er-he , Cao Ji-min 
Published: December 2020

Abstract
Background：Myocardial infarction (MI) is the leading cause of death in the world-wide population. With the improvement of clinical therapy, the mortality in acute MI cases has been significantly reduced. This study was to demonstrate that erythropoietin (EPO) is an effective supporter for Sca-1+ stem cells (SCs) and can promote the repair of myocardial infarction (MI) partially via the way of enhancing Sca-1+ SCs activities. Methods: Darbepoetin alpha (a long-acting EPO analog, EPOanlg) (30 mg/kg) was injected into the border zone of MI in adult mice. Infarct size, cardiac remodeling and performance, cardiomyocytes apoptosis and regenerations and microvessels density were measured. Lin− Sca-1+ SCs were isolated from neonatal and adult mice hearts and were respectively used to identify the colony forming ability and the supporting effect of EPO on these Sca-1+ SCs. Results: Compared to MI alone, EPOanlg reduced the infarct percentage and cardiomyocyte apoptosis ratio and LV chamber dilatation, improved cardiac performance, increased the regenerated cardiomyocyte ratio in the border zone and the numbers of coronary microvessels, while without obvious adverse effects in vivo. In vitro, EPO increased the proliferation, migration and clone formation of Lin- Sca-1+ SCs likely via the EPO receptor and Stat5-p38MAPK signaling. Conclusions: EPO promotes Sca-1+ SCs activities and MI repair. The study enlightens the prospects of Sca-1+ SC supporters in the treatment of MI.