bluuebunny/crossref_metadata_2025_split huggingface dataset:
The loss of photosynthesis pathway and genomic locations of the lost plastid genes in a holoparasitic plant Aeginetia indica
Authors: Chen Jingfang , Yu Runxian , Dai Jinhong , Liu Ying , Zhou Renchao 
Published: May 2020

Abstract
Background
With three origins of holoparasitism, Orobanchaceae provides an ideal system to study the evolution of holoparasitic lifestyle in plants. The evolution of holoparasitism can be revealed by plastid genome degradation and coordinated changes in the nuclear genome, since holoparasitic plants lost the capability of photosynthesis. Among the three clades with holoparasitic plants in Orobanchaceae, only Clade VI has no available plastid genome sequences for holoparasitic plants. In this study, we sequenced the plastome and transcriptome of Aeginetia indica, a holoparasitic plant in Clade VI of Orobanchaceae, to study its plastome evolution and the corresponding changes in the nuclear genome as a response of the loss of photosynthetic function.

Results
The plastome of A. indica is reduced to 86,212 bp in size, and almost all photosynthesis-related genes were lost. Massive fragments of the lost plastid genes were transferred into the mitochondrial and/or nuclear genomes. These fragments could not be detected in its transcriptomes, suggesting that they were non-functional. Most protein coding genes in the plastome showed the signal of relaxation of purifying selection. Plastome and transcriptome analyses indicated that the photosynthesis pathway is completely lost, and that the porphyrin and chlorophyll metabolism pathway is partially retained, although chlorophyll synthesis is not possible.

Conclusions
Our study suggests the loss of photosynthesis-related functions in A. indica in both the nuclear and plastid genomes. The lost plastid genes are transferred into its nuclear and/or mitochondrial genomes, and exist in very small fragments with no expression and are thus non-functional. The Aeginetia indica plastome also provides a resource for comparative studies on the repeated evolution of holoparasitism in Orobanchaceae.
Coordination between GROWTH-REGULATING FACTOR1 and GRF-INTERACTING FACTOR1 plays a key role in regulating leaf growth in rice
Authors: Lu Yuzhu , Meng Yunlong , Zeng Jia , Luo Ying , Feng Zhen , Bian Liying , Gao Suyun 
Published: May 2020

Abstract
Background
The interactions between Growth-regulating factors (GRFs) and GRF-Interacting Factors (GIFs) have been well demonstrated but it remains unclear whether different combinations of GRF and GIF play distinctive roles in the pathway downstream of the complex.

Results
Here we showed that OsGRF1 and OsGIF1 synergistically regulate leaf growth in rice. The expression of OsGIF1 emerged in all tissues with much higher level while that of OsGRF1 appeared preferentially only in the stem tips containing shoot apical meristem (SAM) and younger leaves containing leaf primordium. Overexpression of an OsmiR396-resistant version of mOsGRF1 resulted in expanded leaves due to increased cell proliferation while knockdown of OsGRF1 displayed an opposite phenotype. Overexpression of OsGIF1 did not exhibit new phenotype while knockdown lines displayed pleiotropic growth defects including shrunken leaves. The crossed lines of mOsGRF1 overexpression and OsGIF1 knockdown still exhibited shrunk leaves, indicating that OsGIF1 is indispensable in leaf growth regulated by OsGRF1. The expression of OsGRF1 could be upregulated by gibberellins (GAs) and downregulated by various stresses while that of OsGIF1 could not.

Conclusion
Our results suggest that OsGIF1 is in an excessive expression in various tissues and play roles in various aspects of growth while OsGRF1 may specifically involve in leaf growth through titrating OsGIF1. Both internal and external conditions impacting leaf growth are likely via way of regulating the expression of OsGRF1.
A case of an unexpected posterior mediastinal functional paraganglioma: case report and literature review
Authors: Yang Zhuqing , Shi Qinye , Bao Fangping 
Published: May 2020

AbstractBackgroundParaganglioma can be found in a wide range of locations. However, paraganglioma in the posterior mediastinum is rare. An unexpected paraganglioma located in the posterior mediastinum was found during surgery. The anesthesia management of this patient was challenging.Case presentationA 65-year-old male with a posterior mediastinal tumor was scheduled for thoracoscopic mediastinal tumor resection. Severe hemodynamic changes during the operation and postoperative pathological diagnosis showed that the patient had a rare case of posterior mediastinal functional paraganglioma, which was not found before the operation. Although the patient did not experience side effects after surgery, he did experience a dangerous surgical process.ConclusionsThe correct diagnosis of paraganglioma, intensive preoperative screening, adequate preoperative preparation, and accurate intraoperative anesthesia management could provide better anesthesia for paraganglioma patients.
Clinical and molecular characterization of a patient with mitochondrial Neurogastrointestinal Encephalomyopathy
Authors: Habibzadeh Parham , Silawi Mohammad , Dastsooz Hassan , Bahramjahan Shima , Ezzatzadegan Jahromi Shahrokh , Ostovan Vahid Reza , Yavarian Majid , Mofatteh Mohammad , Faghihi Mohammad Ali 
Published: May 2020

AbstractBackgroundMitochondrial neurogastrointestinal encephalomyopathy (MNGIE) is a rare autosomal recessive disorder caused by mutations inTYMPgene, encoding nuclear thymidine phosphorylase (TP). MNGIE mainly presents with gastrointestinal symptoms and is mostly misdiagnosed in many patients as malabsorption syndrome, inflammatory bowel disease, anorexia nervosa, and intestinal pseudo-obstruction. Up to date, more than 80 pathogenic and likely pathogenic mutations associated with the disease have been reported in patients from a wide range of ethnicities. The objective of this study was to investigate the underlying genetic abnormalities in a 25-year-old woman affected with MNGIE.Case presentationThe patient was a 25-year-old female referred to our center with the chief complaint of severe abdominal pain and diarrhea for 2 years that had worsened from 2 months prior to admission. The clinical and para-clinical findings were in favor of mitochondrial neurogastrointestinal encephalomyopathy syndrome. Subsequent genetic studies revealed a novel, private, homozygous nonsense mutation inTYMPgene (c. 1013 C > A, p.S338X). Sanger sequencing confirmed the new mutation in the proband. Multiple sequence alignment showed high conservation of amino acids of this protein across different species.ConclusionThe detected new nonsense mutation in theTYMPgene would be very important for genetic counseling and subsequent early diagnosis and initiation of proper therapy. This novel pathogenic variant would help us establish future genotype-phenotype correlations and identify different pathways related to this disorder.
Cholestasis and disseminated histoplasmosis in a psoriatic patient on infliximab: case report and review of literature
Authors: Park Steven , Cheong Janice , Kyi Kaitlin , Aranez Jose , Abu-Farsakh Sohaib , Whitney-Miller Christa , Al-Judaibi Bandar , Laryea Marie 
Published: May 2020

AbstractBackgroundHistoplasma capsulatumis the most common endemic mycosis in the United States and frequently presents as an opportunistic infection in immunocompromised hosts. Though liver involvement is common in disseminated histoplasmosis, primary gastrointestinal histoplasmosis of the liver in absence of lung involvement is rare. Similarly, cholestatic granulomatous hepatitis in liver histoplasmosis is rarely seen.Case presentationWe present a rare case of primary gastrointestinal histoplasmosis manifesting with acute granulomatous hepatitis and cholestasis in a 48-year-old female with psoriatic arthritis, receiving methotrexate and infliximab. The epidemiology, risk factors, clinical presentation, diagnosis, and treatment of histoplasmosis is discussed. Furthermore, we review the published cases of biopsy-proven disseminated histoplasmosis with cholestatic jaundice to highlight histoplasmosis involvement in the liver.ConclusionHistoplasmosis should be considered in immunosuppressed patients with fever, chills, abdominal pain and cholestasis with progressive jaundice, particularly in subjects without evidence of biliary obstruction. Future studies are needed to accurately assess the risk of this fungal infection, specifically in patients on immunomodulatory therapy for autoimmune disease.
No evidence for amyloid pathology as a key mediator of neurodegeneration post-stroke - a seven-year follow-up study
Authors: Hagberg Guri , Ihle-Hansen Hege , Fure Brynjar , Thommessen Bente , Ihle-Hansen Håkon , Øksengård Anne Rita , Beyer Mona K. , Wyller Torgeir B. , Müller Ebba Gløersen , Pendlebury Sarah T. , Selnes Per 
Published: May 2020

Abstract
Background
Cognitive impairment (CI) with mixed vascular and neurodegenerative pathologies after stroke is common. The role of amyloid pathology in post-stroke CI is unclear. We hypothesize that amyloid deposition, measured with Flutemetamol (18F-Flut) positron emission tomography (PET), is common in seven-year stroke survivors diagnosed with CI and, further, that quantitatively assessed 18F-Flut-PET uptake after 7 years correlates with amyloid-β peptide (Aβ42) levels in cerebrospinal fluid (CSF) at 1 year, and with measures of neurodegeneration and cognition at 7 years post-stroke.

Methods
208 patients with first-ever stroke or transient Ischemic Attack (TIA) without pre-existing CI were included during 2007 and 2008. At one- and seven-years post-stroke, cognitive status was assessed, and categorized into dementia, mild cognitive impairment or normal. Etiologic sub-classification was based on magnetic resonance imaging (MRI) findings, CSF biomarkers and clinical cognitive profile. At 7 years, patients were offered 18F-Flut-PET, and amyloid-positivity was assessed visually and semi-quantitatively. The associations between 18F-Flut-PET standardized uptake value ratios (SUVr) and measures of neurodegeneration (medial temporal lobe atrophy (MTLA), global cortical atrophy (GCA)) and cognition (Mini-Mental State Exam (MMSE), Trail-making test A (TMT-A)) and CSF Aβ42 levels were assessed using linear regression.

Results
In total, 111 patients completed 7-year follow-up, and 26 patients agreed to PET imaging, of whom 13 had CSF biomarkers from 1 year. Thirteen out of 26 patients were diagnosed with CI 7 years post-stroke, but only one had visually assessed amyloid positivity. CSF Aβ42 levels at 1 year, MTA grade, GCA scale, MMSE score or TMT-A at 7 years did not correlate with 18F-Flut-PET SUVr in this cohort.

Conclusions
Amyloid binding was not common in 7-year stroke survivors diagnosed with CI. Quantitatively assessed, cortical amyloid deposition did not correlate with other measures related to neurodegeneration or cognition. Therefore, amyloid pathology may not be a key mediator of neurodegeneration 7 years post-stroke.

Trial registration
Clinicaltrials.gov (NCT00506818). July 23, 2007. Inclusion from February 2007, randomization and intervention from May 2007 and trial registration in July 2007.
Stereotactic robotic body radiotherapy for patients with oligorecurrent pulmonary metastases
Authors: Berkovic Patrick , Gulyban Akos , Defraene Gilles , Swenen Laurie , Dechambre David , Nguyen Paul Viet , Jansen Nicolas , Mievis Carole , Lovinfosse Pierre , Janvary Levente , Lambrecht Maarten , De Meerleer Gert 
Published: May 2020

Abstract
Background
Our aim is to report treatment efficacy and toxicity of patients treated by robotic (Cyberknife®) stereotactic body radiotherapy (SBRT) for oligorecurrent lung metastases (ORLM). Additionally we wanted to evaluate influence of tumor, patient and treatment related parameters on local control (LC), lung and distant progression free- (lung PFS/Di-PFS) and overall survival (OS).

Methods
Consecutive patients with up to 5 ORLM (confirmed by FDG PET/CT) were included in this study. Intended dose was 60Gy in 3 fractions (prescribed to the 80% isodose volume). Patients were followed at regular intervals and tumor control and toxicity was prospectively scored. Tumor, patient and treatment data were analysed using competing risk- and Cox regression.

Results
Between May 2010 and March 2016, 104 patients with 132 lesions were irradiated from primary lung carcinoma (47%), gastro-intestinal (34%) and mixed primary histologies (19%). The mean tumor volume was 7.9 cc. After a median follow up of 22 months, the 1, 2 and 3 year LC rate (per lesion) was 89.3, 80.0 and 77.8% respectively. The corresponding (per patient) 1, 2 and 3 years lung PFS were 66.3, 50.0, 42.6%, Di-PFS were 80.5, 64.4, 60.6% and OS rates were 92.2, 80.9 and 72.0% respectively. On univariable analysis, gastro-intestinal (GI) as primary tumor site showed a significant superior local control versus the other primary tumor sites. For OS, significant variables were primary histology and primary tumor site with a superior OS for patients with metastases of primary GI origin. LC was significantly affected by the tumor volume, physical and biologically effective dose coverage. Significant variables in multivariable analysis were BED prescription dose for LC and GI as primary site for OS. The vast majority of patients developed no toxicity or grade 1 acute and late toxicity. Acute and late grade 3 radiation pneumonitis (RP) was observed in 1 and 2 patients respectively. One patient with a centrally located lesion developed grade 4 RP and died due to possible RT-induced pulmonary hemorrhage.

Conclusions
SBRT is a highly effective local therapy for oligorecurrent lung metastases and could achieve long term survival in patients with favourable prognostic features.
Colorectal carcinomas with mucinous differentiation are associated with high frequent mutation of KRAS or BRAF mutations, irrespective of quantity of mucinous component
Authors: Li Xiaodong , Sun Katherine , Liao Xiaoyan , Gao Haijuan , Zhu Hongfa , Xu Ruliang 
Published: May 2020

Abstract
Background
Mucinous adenocarcinoma (MAC) is a distinct type of colorectal cancer (CRC) associated with poor response to treatment and poorer prognosis. MAC is diagnosed by WHO definition when the extracellular mucin is more than 50% of the lesion. We aimed at assessing the gene expression profiles of the CRCs with any mucinous features (> 5%) in a retrospective study.

Methods
The data of a 50-gene next generation sequencing (NGS) panel of 166 CRCs was analyzed and the gene mutational profile with morphologic features was correlated.

Results
We identified the different genetic mutation profiles between CRCs with and without mucinous component, but noticed a similar genetic profile between MACs and CRCs with mucinous component, irrespective of the percentage (if mucinous component more than 5%). The different genetic mutation profile related to MSI status was also identified between two groups of tumors. The most frequent mutations in CRCs with mucinous component are KRAS (28/49, 57.1%) and BRAF (19/49, 38.7%), PIK3CA (16/49, 32.6%), followed by APC (12/49, 24.5%) and TP53 (11/49, 22.5%). The combined mutation frequency of the two key factors in the EGFR signaling pathway, KRAS and BRAF, in the CRCs with and without mucinous component is 95.9 and 52.1%, respectively.

Conclusions
The dysregulation of EGFR pathway plays a critical role in the development of CRCs with mucinous component, irrespective of the percentage. The result suggested that the current cut off of 50% mucin component to define mucinous adenocarcinoma might be challengeable.
Association of Myopia with cognitive function among one million adolescents
Authors: Megreli Jacob , Barak Adiel , Bez Maxim , Bez Dana , Levine Hagai 
Published: May 2020

AbstractBackgroundMyopia is a leading cause of visual impairment worldwide, and its increasing incidence is of public health concern. Cognitive function was associated with myopia among children, but evidence for adolescents is scarce. The purpose of this study was to determine whether myopia is associated with cognitive function, and which cognitive ability, verbal or non-verbal, is involved.MethodsWe conducted a population-based cross-sectional study of 1,022,425 Israeli candidates for military service aged 16.5–18 years. Participants underwent a comprehensive battery of tests assessing verbal and non-verbal intelligence, which yields a summarized cognitive function score (CFS). In addition, subjective visual acuity examination followed by objective non-cycloplegic refraction was carried out for each participant. Association between myopia and cognitive function was evaluated by multivariable logistic regression models adjusted for gender, age, country of origin, socioeconomic status, years of education, body mass index, height and year of examination.ResultsCompared to the intermediate CFS of the entire cohort, participants who had the highest CFS had 1.85-fold (95% CI, 1.81 to 1.89;P < .001) higher odds of having myopia and 2.73-fold (95% CI, 2.58 to 2.88;P < .001) higher odds of high myopia, while participants with the lowest CFS had 0.59-fold (95% CI, 0.57 to 0.61,P < .001) lower odds of having myopia. The verbal components of the cognitive function assessment had stronger associations with myopia than the non-verbal components (P < .001, for all).ConclusionsCognitive function, especially verbal intelligence, is strongly and consistently associated with myopia among adolescents.
Earthquake preparedness of households and its predictors based on health belief model
Authors: Rostami-Moez Masoumeh , Rabiee-Yeganeh Mohammad , Shokouhi Mohammadreza , Dosti-Irani Amin , Rezapur-Shahkolai Forouzan 
Published: May 2020

AbstractBackgroundEarthquakes are one of the most destructive natural disasters in which many people are injured, disabled, or died. Iran has only 1 % of the world’s population, but the percentage of its earthquake-related deaths is absolutely higher. Therefore, this study aimed to determine the level of earthquake preparedness of households and its predictors using the Health Belief Model (HBM).MethodsThis observational descriptive and analytical study was conducted on 933 households in Hamadan province, located in the west of Iran, in 2019. Multi-stage cluster random sampling was used for selecting the participants. The inclusion criteria were being at least 18 years old and being able to answer the questions. A questionnaire was used for data collection including earthquake preparedness, awareness of earthquake response, predictors of earthquake preparedness based on the HBM, and demographic information. Analysis of variance, independent t-test, and a linear regression model was used.ResultsThe mean age of participants was 38.24 ± 12.85 years. The average score of earthquake preparedness was low (approximately 30%). There was a significant relationship between earthquake preparedness and gender (P < 0.001), homeownership (P < 0.001), marriage status (P < 0.001), education (P < 0.001), and previous earthquake experience (P < 0.001). Regarding the HBM constructs, perceived benefits (P < 0.001), cues to action (P < 0.001), and self-efficacy (P < 0.001) were significant predictors of earthquake preparedness.ConclusionsEarthquake preparedness was insufficient. Besides, perceived benefits, cues to action, and self-efficacy were predictors of earthquake preparedness. These predictors can be taken into account, for designing and implementing related future interventions.
Cone-beam computed tomography investigation of middle mesial canals and isthmuses in mandibular first molars in a Chinese population
Authors: Xu Shuaimei , Dao Junfeng , Liu Zhongjun , Zhang Zhiyong , Lu Yu , Zeng Xiongqun 
Published: May 2020

AbstractBackgroundWhile there is ample research into the anatomy of mandibular molars, little is known regarding isthmuses and middle mesial (MM) canals in Chinese populations. The goal of this study was to determine the prevalence of MM canals and isthmuses in the mesial root of mandibular first molars using Cone-beam Computed Tomography.MethodsCone-beam Computed Tomography images of 357 mature mandibular first molars were retrospectively analyzed. Presence of isthmuses and MM canals, and the length of isthmuses in the mesial root were recorded. Meanwhile, we also recorded possible correlated factors such as demographics, side of mandible, presence of separated distal-lingual roots.ResultsOf these 357 teeth, 209 showed evidence of either complete or partial communication in the mesial root. Of these, 11(3.1%) exhibited true MM canals while 198(55.5%) exhibited isthmuses. Sex or side of mandible was not correlated with the prevalence of isthmuses (P > 0.05). However, there was a significant association between the presence of a distal-lingual root and the prevalence of such communication (P < 0.001). The average length of isthmuses was 4.3 ± 3.1 mm.ConclusionsWe detected high rate of isthmuses and low rate of MM canals in mesial roots of mandibular first molars, which is important as such areas should be identified and cleaned during root canal treatment.
How students and specialists appreciate the mini-clinical evaluation exercise (mini-CEX) in Indonesian clerkships
Authors: Suhoyo Yoyo , Schönrock-Adema Johanna , Emilia Ova , Kuks Jan B. M. , Cohen-Schotanus Janke 
Published: May 2020

Abstract
Background
Cultural differences might challenge the acceptance of the implementation of assessment formats that are developed in other countries. Acceptance of assessment formats is essential for its effectiveness; therefore, we explored the views of students and specialists on the practicality and impact on learning of these formats. This study was conducted to explore Indonesian students’ and specialists’ appreciation of the implementation of the Mini-Clinical Evaluation Exercise (Mini-CEX) in Indonesian clerkships.

Methods
This study was conducted at the Universitas Gadjah Mada, Indonesia. Participants were 52 students and 21 specialists in neurology and 78 students and 50 specialists in internal medicine. They were asked to complete a 19-item questionnaire that covered the characteristics of the mini-CEX such as its practicality, and the impact on learning and professional development. We used a Mann-Whitney U test to analyse the data.

Results
In total, 124 students (46 from neurology and 78 from internal medicine) and 38 specialists (13 from neurology and 25 from internal medicine) participated in this study.
Students and specialists were positive about the practicality of the mini-CEX and the impact of this assessment format on learning and on professional development. The Mann-Whitney U test showed that there were no significant differences between students’ and specialists’ opinions on the mini-CEX, except for 2 items: specialists’ appreciation of direct observation (mean rank = 93.16) was statistically significantly higher than students’ appreciation of it (mean rank = 77.93; z = 2.065; p < 0.05), but students’ appreciation of the item that students’ past mini-CEX results affected their recent mini-CEX outcomes (mean rank = 85.29) was significantly higher than specialists’ appreciation of it (mean rank = 69.12; z = 2140; p < 0.05).

Conclusion
Students and specialists were positive about the mini-CEX in Indonesian clerkships, although it was developed and validated in another culture. We found only small differences between their appreciations, which could be explained by the patterns of specialist-student interaction in Indonesian culture as large power distance and low individualism country.