bluuebunny/crossref_metadata_2025_split huggingface dataset:
EgJUB1 and EgERF113 transcription factors as potential master regulators of defense response in Elaeis guineensis against the hemibiotrophic Ganoderma boninense
Authors: Sakeh Nurshafika Mohd , Abdullah Siti Nor Akmar , Bahari Mohammad Nazri Abdul , Azzeme Azzreena Mohamad , Shaharuddin Noor Azmi , Idris Abu Seman 
Published: January 2021

AbstractBackgroundHemibiotrophic pathogen such as the fungal pathogenGanoderma boninensethat is destructive to oil palm, manipulates host defense mechanism by strategically switching from biotrophic to necrotrophic phase. Our previous study revealed two distinguishable expression profiles of oil palm genes that formed the basis in deducing biotrophic phase at early interaction which switched to necrotrophic phase at a later stage of infection.ResultsThe present report is a continuing study from our previous published transcriptomic profiling of oil palm seedlings againstG. boninense. We focused on identifying differentially expressed genes (DEGs) encoding transcription factors (TFs) from the same RNA-seq data; resulting in 106 upregulated and 108 downregulated TFs being identified. The DEGs are involved in four established defense-related pathways responsible for cell wall modification, reactive oxygen species (ROS)-mediated signaling, programmed cell death (PCD) and plant innate immunity. We discovered upregulation ofJUNGBRUNNEN 1(EgJUB1) during the fungal biotrophic phase whileEthylene Responsive Factor 113(EgERF113) demonstrated prominent upregulation when the palm switches to defense against necrotrophic phase. EgJUB1 was shown to have a binding activity to a 19 bp palindromic SNBE1 element, WNNYBTNNNNNNNAMGNHW found in the promoter region of co-expressing EgHSFC-2b. Further in silico analysis of promoter regions revealed co-expression of EgJUB1 with TFs containing SNBE1 element with single nucleotide change at either the 5th or 18th position. Meanwhile, EgERF113 binds to both GCC and DRE/CRT elements promoting plasticity in upregulating the downstream defense-related genes. Both TFs were proven to be nuclear-localized based on subcellular localization experiment using onion epidermal cells.ConclusionOur findings demonstrated unprecedented transcriptional reprogramming of specific TFs potentially to enable regulation of a specific set of genes during different infection phases of this hemibiotrophic fungal pathogen. The results propose the intricacy of oil palm defense response in orchestrating EgJUB1 during biotrophic and EgERF113 during the subsequent transition to the necrotrophic phase. Binding of EgJUB1 to SNBE motif instead of NACBS while EgERF113 to GCC-box and DRE/CRT motifs is unconventional and not normally associated with pathogen infection. Identification of these phase-specific oil palm TFs is important in designing strategies to tackle or attenuate the progress of infection.
The genetics and physiology of seed dormancy, a crucial trait in common bean domestication
Authors: Soltani Ali , Walter Katelynn A. , Wiersma Andrew T. , Santiago James P. , Quiqley Michelle , Chitwood Daniel , Porch Timothy G. , Miklas Phillip , McClean Phillip E. , Osorno Juan M. , Lowry David B. 
Published: January 2021

Abstract
Background
Physical seed dormancy is an important trait in legume domestication. Although seed dormancy is beneficial in wild ecosystems, it is generally considered to be an undesirable trait in crops due to reduction in yield and / or quality. The physiological mechanism and underlying genetic factor(s) of seed dormancy is largely unknown in several legume species. Here we employed an integrative approach to understand the mechanisms controlling physical seed dormancy in common bean (Phaseolus vulgaris L.).

Results
Using an innovative CT scan imaging system, we were able to track water movements inside the seed coat. We found that water uptake initiates from the bean seed lens. Using a scanning electron microscopy (SEM) we further identified several micro-cracks on the lens surface of non-dormant bean genotypes. Bulked segregant analysis (BSA) was conducted on a bi-parental RIL (recombinant inbred line) population, segregating for seed dormancy. This analysis revealed that the seed water uptake is associated with a single major QTL on Pv03. The QTL region was fine-mapped to a 118 Kb interval possessing 11 genes. Coding sequence analysis of candidate genes revealed a 5-bp insertion in an ortholog of pectin acetylesterase 8 that causes a frame shift, loss-of-function mutation in non-dormant genotype. Gene expression analysis of the candidate genes in the seed coat of contrasting genotypes indicated 21-fold lower expression of pectin acetylesterase 8 in non-dormant genotype. An analysis of mutational polymorphism was conducted among wild and domesticated beans. Although all the wild beans possessed the functional allele of pectin acetylesterase 8, the majority (77%) of domesticated beans had the non-functional allele suggesting that this variant was under strong selection pressure through domestication.

Conclusions
In this study, we identified the physiological mechanism of physical seed dormancy and have identified a candidate allele causing variation in this trait. Our findings suggest that a 5-bp insertion in an ortholog of pectin acetylesterase 8 is likely a major causative mutation underlying the loss of seed dormancy during domestication. Although the results of current study provide strong evidences for the role of pectin acetylesterase 8 in seed dormancy, further confirmations seem necessary by employing transgenic approaches.
Oxygenation laryngoscope vs. nasal standard and nasal high flow oxygenation in a technical simulation of apnoeic oxygenation
Authors: Herff H. , Wetsch W. A. , Finke S. , Dusse F. , Mitterlechner T. , Paal P. , Wenzel V. , Schroeder D. C. 
Published: January 2021

Abstract
Background
Failed airway management is the major contributor for anaesthesia-related morbidity and mortality. Cannot-intubate-cannot-ventilate scenarios are the most critical emergency in airway management, and belong to the worst imaginable scenarios in an anaesthetist’s life. In such situations, apnoeic oxygenation might be useful to avoid hypoxaemia. Anaesthesia guidelines recommend careful preoxygenation and application of high flow oxygen in difficult intubation scenarios to prevent episodes of deoxygenation. In this study, we evaluated the decrease in oxygen concentration in a model when using different strategies of oxygenation: using a special oxygenation laryngoscope, nasal oxygen, nasal high flow oxygen, and control.

Methods
In this experimental study we compared no oxygen application as a control, standard pure oxygen application of 10 l·min− 1 via nasal cannula, high flow 90% oxygen application at 20 l·min− 1 using a special nasal high flow device, and pure oxygen application via our oxygenation laryngoscope at 10 l·min− 1. We preoxygenated a simulation lung to 97% oxygen concentration and connected this to the trachea of a manikin model simulating apnoeic oxygenation. Decrease in oxygen concentration in the simulation lung was measured continuously for 20 min.

Results
Oxygen concentration in the simulation lung dropped from 97 ± 1% at baseline to 40 ± 1% in the no oxygen group, to 80 ± 1% in the standard nasal oxygen group, and to 73 ± 2% in the high flow nasal oxygenation group. However, it remained at 96 ± 0% in the oxygenation laryngoscope group (p < 0.001 between all groups).

Conclusions
In this technical simulation, oxygenation via oxygenation laryngoscope was more effective than standard oxygen insufflation via nasal cannula, which was more effective than nasal high flow insufflation of 90% oxygen.
Prognosis tools for short-term adverse events in older emergency department users: result of a Québec observational prospective cohort
Authors: Launay Cyrille P. , Lubov Joshua , Galery Kevin , Vilcocq Christine , Maubert Éric , Afilalo Marc , Beauchet Olivier 
Published: January 2021

Abstract
Background
The “Program of Research on the Integration of Services for the Maintenance of Autonomy” (PRISMA-7) and “Emergency room evaluation and recommendations” (ER2) are both clinical tools used in Québec Emergency Departments (EDs) for screening of older ED users at higher risk of poor outcomes, such as prolonged length of stay (LOS) in EDs and in hospital. The study aimed to: 1) examine whether the PRISMA-7 and ER2 risk levels were associated with length of stays in ED and hospital, as well as hospital admission; and 2) compare the criteria performance (i.e., sensitivity, specificity, positive predictive value, negative predictive value, likelihood ratios and area under receiver operating characteristic curve) of the PRISMA-7 and ER2 high-risk levels for these three ED adverse events in Québec older patients visiting ED on a stretcher.

Methods
A total of 1905 older patients who visited the ED of the Jewish General Hospital (Montreal, Québec, Canada) on stretchers were recruited in this prospective observational cohort. Upon their ED arrival, PRISMA-7 and ER2 were performed. The outcomes were LOS in ED and in hospital, and hospital admission.

Results
The PRISMA-7 and ER2 risk levels were associated with length of stay in ED and hospital as well as with hospital admission. Prolonged stays and higher hospitalization rates were associated with high-risk levels, whereas those in low-risk level groups had significantly shorter LOS and a lower rate of hospital admission (P < 0.006). While performance measures were poor for both assessment tools, ER2 had a greater prognostic testing accuracy compared with PRISMA-7.

Conclusion
PRISMA-7 and ER2 were both associated with incidental short-term ED adverse events but their overall prognostic testing accuracy was low, suggesting that they cannot be used as prognostic tools for this purpose.
Comparing tuberculosis gene signatures in malnourished individuals using the TBSignatureProfiler
Authors: Johnson W. Evan , Odom Aubrey , Cintron Chelsie , Muthaiah Mutharaj , Knudsen Selby , Joseph Noyal , Babu Senbagavalli , Lakshminarayanan Subitha , Jenkins David F. , Zhao Yue , Nankya Ethel , Horsburgh C. Robert , Roy Gautam , Ellner Jerrold , Sarkar Sonali , Salgame Padmini , Hochberg Natasha S. 
Published: January 2021

Abstract
Background
Gene expression signatures have been used as biomarkers of tuberculosis (TB) risk and outcomes. Platforms are needed to simplify access to these signatures and determine their validity in the setting of comorbidities. We developed a computational profiling platform of TB signature gene sets and characterized the diagnostic ability of existing signature gene sets to differentiate active TB from LTBI in the setting of malnutrition.

Methods
We curated 45 existing TB-related signature gene sets and developed our TBSignatureProfiler software toolkit that estimates gene set activity using multiple enrichment methods and allows visualization of single- and multi-pathway results. The TBSignatureProfiler software is available through Bioconductor and on GitHub. For evaluation in malnutrition, we used whole blood gene expression profiling from 23 severely malnourished Indian individuals with TB and 15 severely malnourished household contacts with latent TB infection (LTBI). Severe malnutrition was defined as body mass index (BMI) < 16 kg/m2 in adults and based on weight-for-height Z scores in children < 18 years. Gene expression was measured using RNA-sequencing.

Results
The comparison and visualization functions from the TBSignatureProfiler showed that TB gene sets performed well in malnourished individuals; 40 gene sets had statistically significant discriminative power for differentiating TB from LTBI, with area under the curve ranging from 0.662–0.989. Three gene sets were not significantly predictive.

Conclusion
Our TBSignatureProfiler is a highly effective and user-friendly platform for applying and comparing published TB signature gene sets. Using this platform, we found that existing gene sets for TB function effectively in the setting of malnutrition, although differences in gene set applicability exist. RNA-sequencing gene sets should consider comorbidities and potential effects on diagnostic performance.
Malignancy in giant cell tumor of bone: analysis of an open-label phase 2 study of denosumab
Authors: Palmerini Emanuela , Seeger Leanne L. , Gambarotti Marco , Righi Alberto , Reichardt Peter , Bukata Susan , Blay Jean-Yves , Dai Tian , Jandial Danielle , Picci Piero 
Published: January 2021

Abstract
Background
Giant cell tumor of bone (GCTB) is a rare osteoclastogenic stromal tumor. GCTB can rarely undergo malignant transformation. This post hoc analysis evaluated and classified malignancies in patients with GCTB who received denosumab.

Methods
This analysis was conducted on patients with pathologically confirmed GCTB and measurable active disease treated with denosumab 120 mg subcutaneously once every 4 weeks, with loading doses on study days 8 and 15, as part of a phase 2, open-label, multicenter study. We identified potential cases of malignancy related to GCTB through an independent multidisciplinary review or medical history, associated imaging or histopathologic reports, and disease course. The findings were summarized and no statistical analysis was performed.

Results
Twenty of five hundred twenty-six patients (3.8%) who received at least one dose of denosumab were misdiagnosed with GCTB that was later discovered to be malignancies: five primary malignant GCTB, five secondary malignant GCTB, four sarcomatous transformations, and six patients with other malignancies (giant cell-rich osteosarcoma, undifferentiated pleomorphic sarcoma, spindle cell sarcoma, osteogenic sarcoma, phosphaturic mesenchymal tumor of mixed connective tissue type, and fibrosarcoma/malignant fibrous histiocytoma). Many malignancies were present before denosumab was initiated (8 definitive cases, 7 likely cases), excluding potential involvement of denosumab in these cases. Signs associated with potential misdiagnoses of GCTB included poor mineralization with denosumab treatment, rapid relapse in pain, or a failure of the typical dramatic improvement in pain normally observed with denosumab.

Conclusions
Although rare, GCTB can undergo malignant transformation, and rates in this study were consistent with previous reports. Signs of poor mineralization or lack of response to denosumab treatment may warrant close monitoring.

Trial registration
clinicaltrials.gov, (NCT00680992). Registered May 20, 2008.
Clinico-pathologic determinants of non-e-curative outcome following en-bloc endoscopic submucosal dissection in patients with early gastric neoplasia
Authors: Embaye Kidane Siele , Zhang Chao , Ghebrehiwet Matiwos Araya , Wang Zhihao , Zhang Fengdi , Liu Liwei , Qin Shenghui , Qin Lingzhi , Wang Jun , Wang Xi 
Published: January 2021

Abstract
Background
Endoscopic submucosal dissection (ESD) is gaining enormous popularity in the treatment of early gastric cancers (EGCs) in many institutions across the world. However, appropriate selection of candidates for endoscopic resection is crucial to sufficiently mitigate non-e-curative (NEC) resection. This study aims at identifying the various clinico-pathologic factors that independently predict the NEC outcome and depth of submucosal invasion following ESD procedure in patients with EGC.

Methods
Multiple logistic regression analysis was applied to investigate factors that independently predict both non-curability phenomenon and the level of submucosal invasion in patients with early gastric neoplasia. Statistical Packages for the Social Sciences version 23 was used for analysis.

Results
A total of 153 patients (162 EGC lesions) underwent en-bloc ESD after which the rate of complete resection and non-e-curative outcome were 95% and 22.2%, correspondingly. Multivariate analysis depicted that tumor location in the upper two third of stomach (odds ratio [OR], 5.46; 95% confidence interval [95% CI], 1.65–18.12; p = 0.006), tumor size > 2 cm (OR, 7.63; 95% CI, 2.29–25.42; p = 0.001), histologically undifferentiated tumor (OR, 15.54; 95% CI, 1.65–146.22; p = 0.001), and tumors with 0-IIa/0-IIc or their mixed variants with predominant 0-IIa/0-IIc (OR, 9.77; 95% CI, 1.23–77.65; p = 0.031) were all independent predictors of NEC resection for early gastric tumors. Additionally, location in the upper two third of the stomach (OR, 8.88; 95% CI, 2.90–27.17; p < 0.001), ulcerated lesions (OR, 3.70; 95% CI, 1.15–11.90; p = 0.028), lesions with > 2 cm (OR, 2.94; 95% CI, 1.08–8.02; p = 0.036) and those with poor differentiation (OR, 6.51; 95% CI, 2.23–18.98; p = 0.001) were found to have significant association with submucosal invasion.

Conclusions
Tumors located in the upper two third of the stomach having a larger size (> 2 cm), poor histo-differentiation and a gross type of 0-IIa/0-IIc or their mixed variants with predominant 0-IIa/0-IIc were significantly associated with a risk of NEC after ESD procedure. Thus, early gastric tumors displaying these features need to be handled carefully during endoscopic resection. Our findings may shed light on the pre-procedural detection of clinicopathologic factors that determine non-e-curability in patients with EGC.
Depression, anxiety, fatigue, and quality of life in a large sample of patients suffering from head and neck cancer in comparison with the general population
Authors: Hammermüller C. , Hinz A. , Dietz A. , Wichmann G. , Pirlich M. , Berger T. , Zimmermann K. , Neumuth T. , Mehnert-Theuerkauf A. , Wiegand S. , Zebralla V. 
Published: January 2021

Abstract
Background
Treatment of head and neck cancer (HNC) often leads to visible and severe functional impairments. In addition, patients often suffer from a variety of psychosocial problems, significantly associated with a decreased quality of life. We aimed to compare depression, anxiety, fatigue and quality of life (QoL) between HNC patients and a large sample of the general population in Germany and to examine the impact of sociodemographic, behavioral and clinical factors on these symptoms.

Methods
We assessed data of HNC patients during the aftercare consultation at the Leipzig University Medical Center with a patient reported outcome (PRO) tool named “OncoFunction”. Depression, anxiety, fatigue and QoL were assessed using validated outcome measures including the PHQ-9, the GAD-2, and the EORTC QLQ-C30 questionnaire.

Results
A total of 817 HNC patients were included in our study and compared to a sample of 5018 individuals of the general German population. HNC patients showed significantly higher levels of impairment in all dimensions assessed. Examination of association between depression, anxiety, fatigue and QoL and clinical as well as sociodemographic variables showed significant relationships between occupational status, ECOG-state, body mass index and time since diagnosis.

Conclusions
HNC patients suffer significantly from psychological distress. The used questionnaires are suitable for the use in daily routine practice and can be helpful to increase the detection of depression, anxiety and fatigue and therefore can improve HNC aftercare.
Raptor and rictor expression in patients with human papillomavirus-related oropharyngeal squamous cell carcinoma
Authors: Kondo Shunsuke , Hirakawa Hitoshi , Ikegami Taro , Uehara Takayuki , Agena Shinya , Uezato Jin , Kinjyo Hidetoshi , Kise Noritomo , Yamashita Yukashi , Tanaka Katsunori , Hasegawa Narumi , Kiyuna Asanori , Maeda Hiroyuki , Suzuki Mikio , Gahana Akira 
Published: January 2021

Abstract
Background
Despite reports of a link between human papillomavirus (HPV) infection and mechanistic target of rapamycin (mTOR) signaling activation, the role of the mTOR pathway, especially raptor and rictor, in HPV-related head and neck cancer is still unclear. The aim of the present study was to elucidate the role of the mTOR pathway in HPV-related oropharyngeal squamous cell carcinoma (OPSCC).

Methods
The present study involved two strategies. The first was to investigate the activity of mTOR and mTOR-related complexes in high-risk HPV-positive (UM-SCC47 and CaSki) and HPV-negative (SCC-4 and SAS) cancer cell lines. The second was to elucidate mTOR complex expression in 80 oropharyngeal cancer tissues and to examine the relationship between mTOR complex expression and survival in patients with OPSCC.

Results
The UM-SCC47 and CaSki cell lines showed high gene and protein expression of raptor. They also exhibited G1/S and G2/M phase cell cycle arrest following 24 h incubation with 6 μM temsirolimus, a rapamycin analog, and temsirolimus administration inhibited their growth. HPV-related OPSCC samples showed high gene and protein expression of raptor and rictor compared with HPV-unrelated OPSCC. In addition, HPV-related OPSCC patients with high raptor and rictor expression tended to have a worse prognosis than those with low or medium expression.

Conclusions
These results suggest that raptor and rictor have important roles in HPV-related OPSCC and that temsirolimus is a potential therapeutic agent for patients with HPV-related OPSCC. This is the first report to reveal the overexpression of raptor and rictor in HPV-related OPSCC.
Prioritisation for future surveillance, prevention and control of 98 communicable diseases in Belgium: a 2018 multi-criteria decision analysis study
Authors:   Working group Disease and Criteria selection, Klamer Sofieke ,   Working group Epidemiologists, Van Goethem Nina , Thomas Daniel , Duysburgh Els , Braeye Toon , Quoilin Sophie 
Published: January 2021

Abstract
Background
National public health agencies are required to prioritise infectious diseases for prevention and control. We applied the prioritisation method recommended by the European Centre for Disease Prevention and Control to rank infectious diseases, according to their relative importance for surveillance and public health, to inform future public health action in Belgium.

Methods
We applied the multi-criteria-decision-analysis approach. A working group of epidemiologists and statisticians from Belgium (n = 6) designed a balanced set of prioritisation criteria. A panel of Belgian experts (n = 80) allocated in an online survey each criteria a weight, according to perceived relative importance. Next, experts (n = 37) scored each disease against each criteria in an online survey, guided by disease-specific factsheets referring the period 2010–2016 in Belgium. The weighted sum of the criteria’s scores composed the final weighted score per disease, on which the ranking was based. Sensitivity analyses quantified the impact of eight alternative analysis scenarios on the top-20 ranked diseases. We identified criteria and diseases associated with data-gaps as those with the highest number of blank answers in the scoring survey. Principle components of the final weighted score were identified.

Results
Working groups selected 98 diseases and 18 criteria, structured in five criteria groups. The diseases ranked highest were (in order) pertussis, human immunodeficiency virus infection, hepatitis C and hepatitis B. Among the five criteria groups, overall the highest weights were assigned to ‘impact on the patient’, followed by ‘impact on public health’, while different perceptions were identified between clinicians, microbiologists and epidemiologists. Among the 18 individual criteria, ‘spreading potential’ and ‘events requiring public health action’ were assigned the highest weights. Principle components clustered with thematic disease groups. Notable data gaps were found among hospital-related diseases.

Conclusions
We ranked infectious diseases using a standardised reproducible approach. The diseases ranked highest are included in current public health programs, but additional reflection for example about needs among risk groups is recommended. Cross-reference of the obtained ranking with current programs is needed to verify whether resources and activities map priority areas. We recommend to implement this method in a recurrent evaluation cycle of national public health priorities.