bluuebunny/crossref_metadata_2025_split huggingface dataset:
Prognostic value of chest computed tomography in community-acquired pneumonia patients
Authors: Nemoto Masahiro , Nakashima Kei , Noma Satoshi , Matsue Yuya , Yoshida Kazuki , Matsui Hiroki , Shiraishi Atsushi , Ishifuji Tomoko , Morimoto Konosuke , Ariyoshi Koya , Aoshima Masahiro 
Published: November 2020

BackgroundChest computed tomography (CT) is commonly used to diagnose pneumonia in Japan, but its usability in terms of prognostic predictability is not obvious. We modified CURB-65 (confusion, urea >7 mmol·L−1, respiratory rate ≥30 breaths·min−1, blood pressure <90 mmHg (systolic) ≤60 mmHg (diastolic), age ≥65 years) and A-DROP scores with CT information and evaluated their ability to predict mortality in community-acquired pneumonia patients.MethodsThis study was conducted using a prospective registry of the Adult Pneumonia Study Group – Japan. Of the 791 registry patients, 265 hospitalised patients with chest CT were evaluated. Chest CT-modified CURB-65 scores were developed with the first 30 study patients. The 30-day mortality predictability of CT-modified, chest radiography-modified and original CURB-65 scores were validated.ResultsIn score development, infiltrates over four lobes and pleural effusion on CT added extra points to CURB-65 scores. The area under the curve for CT-modified CURB-65 scores was significantly higher than that of chest radiography-modified or original CURB-65 scores (both p<0.001). The optimal cut-off CT-modified CURB-65 score was ≥4 (positive-predictive value 80.8%; negative-predictive value 78.6%, for 30-day mortality). For sensitivity analyses, chest CT-modified A-DROP scores also demonstrated better prognostic value than did chest radiography-modified and original A-DROP scores. Poor physical status, chronic heart failure and multiple infiltration hampered chest radiography evaluation.ConclusionChest CT modification of CURB-65 or A-DROP scores improved the prognostic predictability relative to the unmodified scores. In particular, in patients with poor physical status or chronic heart failure, CT findings have a significant advantage. Therefore, CT can be used to enhance prognosis prediction.
Amending Research on the Expression of the Contact Force of the Spindle Barrel Finishing Based on EDEM Simulation
Authors: Wang Na , Yang Shengqiang , Zhao Tingting , Cao Bo , Wang Chengwei 
Published: November 2020

AbstractThe spindle barrel finishing is commonly used to improve the surface integrity of the important parts of the high-end equipment while it is difficult to provide enough test artifacts for the traditional trial and error experiment to obtain the desirable processing technology. The EDEM simulation of the spindle barrel finishing can provide effective help for the process design, however, the difference between the simulation and experiment is closely related to the selection of the contact model during simulation. In this paper, simulations and experiments are conducted based on the identical apparatus and conditions to facilitate the comparison and validation between each other. Based on the Hertz contact theory, the effect of the material properties of contact objects and the relative position of the workpiece on the contact force is qualified. The expression of the correlation coefficient of the contact model is deduced. Then the formula for calculating the contact force between the barrel finishing abrasive and the workpiece that includes influence coefficient of the material properties and the relative positions is established. Finally, the contact force calculation formula is verified by changing the rotating speed. The result shows that the material correction coefficient ranges from 1.41 to 2.38, which is inversely related to the equivalent modulus E. The position correction coefficient ranges from 2.0 to 2.3. The relative error value between the calculation result and the experimental test result is from 0.58% to 14.07%. This research lay a theoretical foundation for the correction theory of the core elements of the spindle barrel finishing process.
Ancestral morphology of Ecdysozoa constrained by an early Cambrian stem group ecdysozoan
Authors: Howard Richard J. , Edgecombe Gregory D. , Shi Xiaomei , Hou Xianguang , Ma Xiaoya 
Published: November 2020

Abstract
Background
Ecdysozoa are the moulting protostomes, including arthropods, tardigrades, and nematodes. Both the molecular and fossil records indicate that Ecdysozoa is an ancient group originating in the terminal Proterozoic, and exceptional fossil biotas show their dominance and diversity at the beginning of the Phanerozoic. However, the nature of the ecdysozoan common ancestor has been difficult to ascertain due to the extreme morphological diversity of extant Ecdysozoa, and the lack of early diverging taxa in ancient fossil biotas.

Results
Here we re-describe Acosmia maotiania from the early Cambrian Chengjiang Biota of Yunnan Province, China and assign it to stem group Ecdysozoa. Acosmia features a two-part body, with an anterior proboscis bearing a terminal mouth and muscular pharynx, and a posterior annulated trunk with a through gut. Morphological phylogenetic analyses of the protostomes using parsimony, maximum likelihood and Bayesian inference, with coding informed by published experimental decay studies, each placed Acosmia as sister taxon to Cycloneuralia + Panarthropoda—i.e. stem group Ecdysozoa. Ancestral state probabilities were calculated for key ecdysozoan nodes, in order to test characters inferred from fossils to be ancestral for Ecdysozoa. Results support an ancestor of crown group ecdysozoans sharing an annulated vermiform body with a terminal mouth like Acosmia, but also possessing the pharyngeal armature and circumoral structures characteristic of Cambrian cycloneuralians and lobopodians.

Conclusions
Acosmia is the first taxon placed in the ecdysozoan stem group and provides a constraint to test hypotheses on the early evolution of Ecdysozoa. Our study suggests acquisition of pharyngeal armature, and therefore a change in feeding strategy (e.g. predation), may have characterised the origin and radiation of crown group ecdysozoans from Acosmia-like ancestors.
Mal-Prec: computational prediction of protein Malonylation sites via machine learning based feature integration
Authors: Liu Xin , Wang Liang , Li Jian , Hu Junfeng , Zhang Xiao 
Published: November 2020

Abstract
Background
Malonylation is a recently discovered post-translational modification that is associated with a variety of diseases such as Type 2 Diabetes Mellitus and different types of cancers. Compared with experimental identification of malonylation sites, computational method is a time-effective process with comparatively low costs.

Results
In this study, we proposed a novel computational model called Mal-Prec (Malonylation Prediction) for malonylation site prediction through the combination of Principal Component Analysis and Support Vector Machine. One-hot encoding, physio-chemical properties, and composition of k-spaced acid pairs were initially performed to extract sequence features. PCA was then applied to select optimal feature subsets while SVM was adopted to predict malonylation sites. Five-fold cross-validation results showed that Mal-Prec can achieve better prediction performance compared with other approaches. AUC (area under the receiver operating characteristic curves) analysis achieved 96.47 and 90.72% on 5-fold cross-validation of independent data sets, respectively.

Conclusion
Mal-Prec is a computationally reliable method for identifying malonylation sites in protein sequences. It outperforms existing prediction tools and can serve as a useful tool for identifying and discovering novel malonylation sites in human proteins. Mal-Prec is coded in MATLAB and is publicly available at https://github.com/flyinsky6/Mal-Prec, together with the data sets used in this study.
gCAnno: a graph-based single cell type annotation method
Authors: Yang Xiaofei , Gao Shenghan , Wang Tingjie , Yang Boyu , Dang Ningxin , Ye Kai 
Published: November 2020

Abstract
Background
Current single cell analysis methods annotate cell types at cluster-level rather than ideally at single cell level. Multiple exchangeable clustering methods and many tunable parameters have a substantial impact on the clustering outcome, often leading to incorrect cluster-level annotation or multiple runs of subsequent clustering steps. To address these limitations, methods based on well-annotated reference atlas has been proposed. However, these methods are currently not robust enough to handle datasets with different noise levels or from different platforms.

Results
Here, we present gCAnno, a graph-based Cell type Annotation method. First, gCAnno constructs cell type-gene bipartite graph and adopts graph embedding to obtain cell type specific genes. Then, naïve Bayes (gCAnno-Bayes) and SVM (gCAnno-SVM) classifiers are built for annotation. We compared the performance of gCAnno to other state-of-art methods on multiple single cell datasets, either with various noise levels or from different platforms. The results showed that gCAnno outperforms other state-of-art methods with higher accuracy and robustness.

Conclusions
gCAnno is a robust and accurate cell type annotation tool for single cell RNA analysis. The source code of gCAnno is publicly available at https://github.com/xjtu-omics/gCAnno.
Virulent secondary metabolites of entomopathogenic bacteria genera, Xenorhabdus and Photorhabdus, inhibit phospholipase A2 to suppress host insect immunity
Authors: Mollah Md. Mahi Imam , Kim Yonggyun 
Published: November 2020

Abstract
Background
Xenorhabdus and Photorhabdus are entomopathogenic bacteria that cause septicemia and toxemia in insects. They produce secondary metabolites to induce host immunosuppression. Their metabolite compositions vary among bacterial species. Little is known about the relationship between metabolite compositions and the bacterial pathogenicity. The objective of this study was to compare pathogenicity and production of secondary metabolites of 14 bacterial isolates (species or strains) of Xenorhabdus and Photorhabdus.

Results
All bacterial isolates exhibited insecticidal activities after hemocoelic injection to Spodoptera exigua (a lepidopteran insect) larvae, with median lethal doses ranging from 168.8 to 641.3 CFU per larva. Bacterial infection also led to immunosuppression by inhibiting eicosanoid biosynthesis. Bacterial culture broth was fractionated into four different organic extracts. All four organic extracts of each bacterial species exhibited insecticidal activities and resulted in immunosuppression. These organic extracts were subjected to GC-MS analysis which predicted 182 compounds, showing differential compositions for 14 bacteria isolates. There were positive correlations between total number of secondary metabolites produced by each bacterial culture broth and its bacterial pathogenicity based on immunosuppression and insecticidal activity. From these correlation results, 70 virulent compounds were selected from secondary metabolites of high virulent bacterial isolates by deducting those of low virulent bacterial isolates. These selected virulent compounds exhibited significant immunosuppressive activities by inhibiting eicosanoid biosynthesis. They also exhibited relatively high insecticidal activities.

Conclusion
Virulence variation between Xenorhabdus and Photorhabdus is determined by their different compositions of secondary metabolites, of which PLA2 inhibitors play a crucial role.
Gene expression profiling of reactive oxygen species (ROS) and antioxidant defense system following Sugarcane mosaic virus (SCMV) infection
Authors: Akbar Sehrish , Wei Yao , Yuan Yuan , Khan Muhammad Tahir , Qin Lifang , Powell Charles A. , Chen Baoshan , Zhang Muqing 
Published: November 2020

AbstractBackgroundViruses are infectious pathogens, and plant virus epidemics can have devastating consequences to crop yield and quality.Sugarcane mosaic virus(SCMV, belonging to familyPotyviridae)is one of the leading pathogens that affect the sugarcane crop every year. To combat the pathogens’ attack, plants generate reactive oxygen species (ROS) as the first line of defense whose sophisticated balance is achieved through well-organized antioxidant scavenging pathways.ResultsIn this study, we investigated the changes occurring at the transcriptomic level of ROS associated and ROS detoxification pathways of SCMV resistant (B-48) and susceptible (Badila) sugarcane genotypes, usingSaccharum spontaneumL. genome assembly as a reference genome. Transcriptomic data highlighted the significant upregulation of ROS producing genes such as NADH oxidase, malate dehydrogenase and flavin-binding monooxygenase, in Badila genotype after SCMV pathogenicity. To scavenge the ROS, the Badila genotype illustrated a substantial enhancement of antioxidants i.e. glutathione s-transferase (GST), as compared to its resistant counterpart. GST is supposed to be a key indicator of pathogen attacks on the plant. A remarkably lower GST expression in B-48, as compared to Badila, indicated the development of resistance in this genotype. Additionally, we characterized the critical transcription factors (TFs) involved in endowing resistance to B-48. Among these, WRKY, AP2, NAC, bZIP, and bHLH showed enhanced expression in the B-48 genotype. Our results also confirmed the linkage of transcriptomic data with the enzymatic and qPCR data. The estimation of enzymatic activities for superoxide dismutase, catalase, ascorbate peroxidase, and phenylalanine ammonia-lyase supported the transcriptomic data and evinced higher resistance in B-48 genotype.ConclusionThe current study supported the efficiency of the B-48 genotype under SCMV infection. Moreover, comparative transcriptomic data has been presented to highlight the role of significant transcription factors conferring resistance to this genotype. This study provides an in-depth knowledge of the expression profiling of defense mechanisms in sugarcane.
Global analysis of the AP2/ERF gene family in rose (Rosa chinensis) genome unveils the role of RcERF099 in Botrytis resistance
Authors: Li Dandan , Liu Xintong , Shu Lizhe , Zhang Hua , Zhang Shiya , Song Yin , Zhang Zhao 
Published: November 2020

Abstract
Background
The AP2/ERFs belong to a large family of transcription factors in plants. The AP2/ERF gene family has been identified as a key player involved in both biotic and abiotic stress responses in plants, however, no comprehensive study has yet been carried out on the AP2/ERF gene family in rose (Rosa sp.), the most important ornamental crop worldwide.

Results
The present study comprises a genome-wide analysis of the AP2/ERF family genes (RcERFs) in the rose, involving their identification, gene structure, phylogenetic relationship, chromosome localization, collinearity analysis, as well as their expression patterns. Throughout the phylogenetic analysis, a total of 131 AP2/ERF genes in the rose genome were divided into 5 subgroups. The RcERFs are distributed over all the seven chromosomes of the rose, and genome duplication may have played a key role in their duplication. Furthermore, Ka/Ks analysis indicated that the duplicated RcERF genes often undergo purification selection with limited functional differentiation. Gene expression analysis revealed that 23 RcERFs were induced by infection of the necrotrophic fungal pathogen Botrytis cinerea. Presumably, these RcERFs are candidate genes which can react to the rose’s resistance against Botrytis cinerea infection. By using virus-induced gene silencing, we confirmed that RcERF099 is an important regulator involved in the B.cinerea resistance in the rose petal.

Conclusion
Overall, our results conclude the necessity for further study of the AP2/ERF gene family in rose, and promote their potential application in improving the rose when subjected to biological stress.
Tuberous Sclerosis Complex with rare associated findings in the gastrointestinal system: a case report and review of the literature
Authors: Reis Larissa Brussa , Konzen Daniele , Netto Cristina Brinckmann Oliveira , Braghini Pedro Moacir Braghirolli , Prolla Gabriel , Ashton-Prolla Patricia 
Published: November 2020

Abstract
Background
Tuberous Sclerosis Complex (TSC) is a complex and heterogeneous genetic disease that has well-established clinical diagnostic criteria. These criteria do not include gastrointestinal tumors.

Case presentation
We report a 45-year-old patient with a clinical and molecular diagnosis of TSC and a family history of cancer, presenting two rare associated findings: gastrointestinal polyposis and pancreatic neuroendocrine tumor. This patient was subjected to a genetic test with 80 cancer predisposing genes. The genetic panel revealed the presence of a large pathogenic deletion in the TSC2 gene, covering exons 2 to 16 and including the initiation codon. No changes were identified in the colorectal cancer and colorectal polyposis genes.

Discussion and conclusions
We describe a case of TSC that presented tumors of the gastro intestinal tract that are commonly unrelated to the disease. The patient described here emphasizes the importance of considering polyposis of the gastrointestinal tract and low grade neuroendocrine tumor as part of the TSC syndromic phenotype.
Factors associated with success in transition care services among older people in Australia
Authors: Cations Monica , Lang Catherine , Crotty Maria , Wesselingh Steven , Whitehead Craig , Inacio Maria C. 
Published: November 2020

Abstract
Background
The Australian Transition Care Program (TCP) is a national intermediate care service aiming to optimise functional independence and delay entry to permanent care for older people leaving hospital. The aim of this study was to describe the outcomes of TCP and identify demographic and clinical factors associated with TCP ‘success’, to assist with clinical judgements about suitable candidates for the program.

Method
We conducted a descriptive cohort study of all older Australians accessing TCP for the first time between 2007 and 2015. Logistic regression models assessed demographic and clinical factors associated with change in performance on a modified Barthel Index from TCP entry to discharge and on discharge to community. Fine-Gray regression models estimated factors associated with transition to permanent care within 6 months of TCP discharge, with death as a competing event.

Results
Functional independence improved from entry to discharge for 46,712 (38.4%) of 124,301 TCP users. Improvement was more common with younger age, less frailty, shorter hospital stay prior to TCP, and among women, those without a carer, living outside a major city, and without dementia. People who received TCP in a residential setting were far less likely to record improved functional impairment and more likely to be discharged to permanent care than those in a community setting. Discharge to community was more common with younger age and among women and those without dementia. Nearly 12% of community TCP and 63% of residential TCP users had transitioned to permanent care 6 months after discharge. Entry to permanent care was more common with older age, higher levels of frailty, and among those with dementia.

Conclusions
More than half of TCP users are discharged to home and remain at home after 6 months. However, residential-based TCP may have limited efficacy. Age, frailty, carer status, and dementia are key factors to consider when assessing program suitability. Future studies comparing users to a suitably matched control group will be very helpful for confirming whether the TCP program is meeting its aims.
Malnutrition and its determinants among older adults people in Addis Ababa, Ethiopia
Authors: Abate Tadele , Mengistu Berhanu , Atnafu Asmamaw , Derso Terefe 
Published: November 2020

Abstract
Background
In Ethiopia, malnutrition among older adults is under detected and, neglected area because the entire problem related with aging considered as fate of aging. Also, older adults are often omitted from public health research. Literatures are scarce in Ethiopia; there is limited information in the current study area among older adults using Min Nutritional Assessment (MNA). Therefore, this paper investigated the prevalence of malnutrition and its predictors among older adults people aged 65 years or above in Addis Ababa, Ethiopia.

Methods
A community-based cross-sectional study was employed from January 1 to march 30, 2020 in Addis Ababa. Nutritional status of the older adults was measured by using Min nutritional assessment (MNA). Data from 662 older adults were collected through face to face interviews using a structured questionnaire. Bivariable and multivariable logistic regression analysis was done to identify factors associated with malnutrition.

Result
The prevalence of malnutrition among older adults was found to be 26.6%[95% Confidence interval (CI):22.8, 30.1]. Depression [Adjusted Odds Ratio (AOR) = 7.57 95%CI: 5.01, 11.45], being poor [AOR = 1.95 95% CI: 1.166, 3.25], occupation; daily laborer and guard [AOR = 2.78 95% CI: 1.12, 7.17] and being old old [AOR = 2.62 95% CI: 1.62, 4.25] were significantly associated with the higher odds of malnutrition.

Conclusion
This study illustrated that considerably high proportion of older adults were malnourished in Addis Ababa. Socio-economic characteristics and depression were significantly associated with malnutrition. Therefore, nutritional and social support activities are essential for older adults, particularly of those who are socio-economically disadvantaged and advanced age. In addition, regular nutritional screening and management as well as behavioral interventions should be strengthened as a pillar component of therapeutic interventions. Specific nutritional requirements, at later stages of life is changing, and with the population aged over 65 years increasing in low-income countries like Ethiopia, the research in this field is likely to increase further.
Atypical presentation of COVID-19; an observational retrospective study
Authors: Haghighi-Morad Maryam , Alavi Darazam Ilad , Bahrami-Moltagh Hooman , Amerifar Maryam , Zamani Nasim , Hassanian-Moghaddam Hossein 
Published: November 2020

AbstractBackgroundCOVID-19 infection may present with atypical signs and symptoms and false negative polymerase chain reaction (PCR) tests predisposing healthy people and health care workers to infection. The aim of the current study is to evaluate the features of atypical presentations in COVID-19 infection in a referral center in Tehran, Iran.MethodsHospital database of inpatients admitted to Loghman Hakim hospital between February 20th and May 11th, 2020 was reviewed and all patients with final diagnosis of COVID-19 infection were evaluated for their presenting symptoms. Patients with chief complaints of “fever”, “dyspnea”, and/or “cough” as typical presentations of COVID-19 were excluded and those with other clinical presentations were included.ResultsNineteen patients were included with a mean age of 51 ± 19 years, of whom, 17 were males (89%). Median [IQR] Glasgow coma scale (GCS) was 14 [13, 15]. Almost 10 had referred with chief complaint of methanol poisoning and overdose on substances of abuse. Only 8 cases (42%) had positive COVID-19 test. Nine (47%) needed invasive mechanical ventilation, of whom, two had positive COVID-19 test results (p = ns). Eight patients (42%) died with three of them having positive PCRs.ConclusionsIn patients referring to emergency departments with chief complaint of poisoning (especially poisonings that can result in dyspnea including substances of abuse and toxic alcohols), gastrointestinal, and constitutional respiratory symptoms, attention should be given not to miss possible cases of COVID-19.