bluuebunny/crossref_metadata_2025_split huggingface dataset:
A genome-wide screening for RNAi pathway proteins in Acari
Authors: Nganso Beatrice T. , Sela Noa , Soroker Victoria 
Published: November 2020

Abstract
Background
RNA interference (RNAi) is a highly conserved, sequence-specific gene silencing mechanism present in Eukaryotes. Three RNAi pathways are known, namely micro-RNA (miRNA), piwi-interacting RNA (piRNA) and short interfering RNA (siRNA). However, little knowledge exists about the proteins involved in these pathways in Acari. Moreover, variable successes has been obtained in gene knockdown via siRNA pathway in their functional genomics and management. We hypothesized that the clue may be in the variability of the composition and the efficacy of siRNA machinery among Acari.

Results
Both comparative genomic analyses and domain annotation suggest that all the analyzed species have homologs of putative core proteins that mediate cleaving of targeted genes via the three RNAi pathways. We identified putative homologs of Caenorhabditis elegans RNA-dependent RNA polymerase (RdRP) protein in all species though no secondary Argonaute homologs that operate with this protein in siRNA amplification mechanism were found, suggesting that the siRNA amplification mechanism present in Acari may be distinct from that described in C. elegans. Moreover, the genomes of these species do not encode homologs of C. elegans systemic RNAi defective-1 (Sid-1) protein that mediate silencing of the mRNA target throughout the treated organisms suggesting that the phenomena of systemic RNAi that has been reported in some Acari species probably occur through a different mechanism. However, homologs of putative RNAi spreading defective-3 (Rsd-3) protein and scavenger receptors namely Eater and SR-CI that mediate endocytosis cellular update of dsRNA in C. elegans and Drosophila melanogaster were found in Acari genomes. This result suggests that cellular dsRNA uptake in Acari is endocytosis-dependent. Detailed phylogenetic analyses of core RNAi pathway proteins in the studied species revealed that their evolution is compatible with the proposed monophyletic evolution of this group.

Conclusions
Our analyses have revealed the potential activity of all three pathways in Acari. Still, much experimental work remains to be done to confirm the mechanisms behind these pathways in particular those that govern systemic/parental RNAi and siRNA amplification in Acari. Disclosure of these mechanisms will facilitate the development of new and specific management tools for the harmful species and enrichment of the beneficial species.
The stability of the coiled-coil structure near to N-terminus influence the heat resistance of harpin proteins from Xanthomonas
Authors: Liu Yue , Zhou Xiaoyun , Liu Wenbo , Miao Weiguo 
Published: November 2020

Abstract
Background
Heat resistance is a common characteristic of harpins, a class of proteins found in Gram-negative bacteria, which may be related to the stability of coiled-coil (CC) structure. The CC structure is a ubiquitous protein folding and assembly motif made of α-helices wrapping around each other forming a supercoil. Specifically, whether the stability of the CC structure near to N-terminus of four selected harpin proteins from Xanthomonas (hereafter referred to as Hpa1) would influence their characteristics of heat resistance was investigated. We used bioinformatics approach to predict the structure of Hpa1, used the performance of hypersensitive response (HR)-induction activity of Hpa1 and circular dichroism (CD) spectral analyses to detect the relationship between the stability of the CC structure of Hpa1 and heat resistance.

Results
Each of four-selected Hpa1 has two α-helical regions with one in their N-terminus that could form CC structure, and the other in their C-terminus that could not. And the important amino acid residues involved in the CC motifs are located on helices present on the surface of these proteins, indicating they may engage in the formation of oligo mericaggregates, which may be responsible for HR elicitation by harpins and their high thermal stability. Increased or decreased the probability of forming a CC could either induce a stronger HR response or eliminate the ability to induce HR in tobacco after high temperature treatment. In addition, although the four Hpa1 mutants had little effect on the induction of HR by Hpa1, its thermal stability was significantly decreased. The α-helical content increased with increasing temperature, and the secondary structures of Hpa1 became almost entirely α-helices when the temperature reached 200 °C. Moreover, the stability of the CC structure near to N-terminus was found to be positively correlated with the heat resistance of Hpa1.

Conclusions
The stability of the CC structure might sever as an inner drive for mediating the heat resistance of harpin proteins. Our results offer a new insight into the interpretation of the mechanism involved in the heat resistance of harpin protein and provide a theoretical basis for further harpin function investigations and structure modifications.
Variance constraints strongly influenced model performance in growth mixture modeling: a simulation and empirical study
Authors: Sijbrandij Jitske J. , Hoekstra Tialda , Almansa Josué , Peeters Margot , Bültmann Ute , Reijneveld Sijmen A. 
Published: November 2020

Abstract
Background
Growth Mixture Modeling (GMM) is commonly used to group individuals on their development over time, but convergence issues and impossible values are common. This can result in unreliable model estimates. Constraining variance parameters across classes or over time can solve these issues, but can also seriously bias estimates if variances differ. We aimed to determine which variance parameters can best be constrained in Growth Mixture Modeling.

Methods
To identify the variance constraints that lead to the best performance for different sample sizes, we conducted a simulation study and next verified our results with the TRacking Adolescent Individuals’ Lives Survey (TRAILS) cohort.

Results
If variance parameters differed across classes and over time, fitting a model without constraints led to the best results. No constrained model consistently performed well. However, the model that constrained the random effect variance and residual variances across classes consistently performed very poorly. For a small sample size (N = 100) all models showed issues. In TRAILS, the same model showed substantially different results from the other models and performed poorly in terms of model fit.

Conclusions
If possible, a Growth Mixture Model should be fit without any constraints on variance parameters. If not, we recommend to try different variance specifications and to not solely rely on the default model, which constrains random effect variances and residual variances across classes. The variance structure must always be reported Researchers should carefully follow the GRoLTS-Checklist when analyzing and reporting trajectory analyses.
Asymptomatic hepatic artery dissection early after living-donor liver transplantation with simultaneous splenectomy: two case reports
Authors: Shimata Keita , Sugawara Yasuhiko , Irie Tomoaki , Sambommatsu Yuzuru , Kadohisa Masashi , Ibuki Sho , Kawabata Seiichi , Isono Kaori , Honda Masaki , Yamamoto Hidekazu , Hibi Taizo 
Published: November 2020

Abstract
Background
Hepatic artery dissection after liver transplantation is an uncommon morbidity. The onset mechanism and management for this disorder remain unclear. The present report describes the cases of two patients with hepatic artery dissection after living-donor liver transplantation (LDLT) with simultaneous splenectomy and provides new insight into the onset mechanism of this disorder.

Case presentation: Case 1
A 51-year-old man with liver cirrhosis caused by hepatitis B virus underwent LDLT with a right lobe graft and splenectomy simultaneously. The recipient’s right hepatic artery had partial dissection at the anastomosis site; therefore, his left hepatic artery was anastomosed. Contrast-enhanced computed tomography (CT) on postoperative day (POD) 27 showed dissection from his celiac artery to his left hepatic artery with bleeding in the false lumen. There was a risk of rupture of the false lumen; therefore, emergency interventional radiology and coil embolization of the false lumen were performed. The patient was doing well at 6 months after LDLT.

Case 2
A 58-year-old woman with liver cirrhosis caused by primary biliary cholangitis underwent LDLT with a left lobe graft and splenectomy simultaneously. Her hepatic artery had a dissection that extended from her left hepatic artery to the proper hepatic artery. The gastroduodenal artery was anastomosed. Contrast-enhanced CT on POD 8 revealed dissection from the celiac artery to the common hepatic artery as well as a pseudoaneurysm at the celiac artery. We managed the patient with conservative treatment and performed daily follow-ups with Doppler ultrasonography examination and serial contrast-enhanced CT. At the time of writing this report, the patient was doing well at 34 months after LDLT.

Conclusions
Patients who have an intimal dissection at the anastomosis site and/or simultaneous splenectomy are at a higher risk of hepatic artery dissection. Most patients with asymptomatic hepatic artery dissections can be treated conservatively. Blood flow in the intrahepatic artery should be checked frequently using Doppler ultrasonography or contrast-enhanced CT soon after diagnosis.
Incidence and risk factors of surgical site infection following colorectal surgery in China: a national cross-sectional study
Authors: Zhang Xufei , Wang Zhiwei , Chen Jun , Wang Peige , Luo Suming , Xu Xinjian , Mai Wei , Li Guangyi , Wang Gefei , Wu Xiuwen , Ren Jianan 
Published: November 2020

Abstract
Purposes
Surgical site infection (SSI) after colorectal surgery is a frequent complication associated with the increase in morbidity, medical expenses, and mortality. To date, there is no nationwide large-scale database of SSI after colorectal surgery in China. The aim of this study was to determine the incidence of SSI after colorectal surgery in China and to further evaluate the related risk factors.

Methods
Two multicenter, prospective, cross-sectional studies covering 55 hospitals in China and enrolling adult patients undergoing colorectal surgery were conducted from May 1 to June 30 of 2018 and the same time of 2019. The demographic and perioperative characteristics were collected, and the main outcome was SSI within postoperative 30 days. Multivariable logistic regressions were conducted to predict risk factors of SSI after colorectal surgery.

Results
In total, 1046 patients were enrolled and SSI occurred in 74 patients (7.1%). In the multivariate analysis with adjustments, significant factors associated with SSI were the prior diagnosis of hypertension (OR, 1.903; 95% confidence interval [CI], 1.088–3.327, P = 0.025), national nosocomial infection surveillance risk index score of 2 or 3 (OR, 3.840; 95% CI, 1.926–7.658, P < 0.001), laparoscopic or robotic surgery (OR, 0.363; 95% CI, 0.200–0.659, P < 0.001), and adhesive incise drapes (OR, 0.400; 95% CI, 0.187–0.855, P = 0.018). In addition, SSI group had remarkably increased length of postoperative stays (median, 15.0 d versus 9.0d, P < 0.001), medical expenses (median, 74,620 yuan versus 57,827 yuan, P < 0.001), and the mortality (4.1% versus 0.3%, P = 0.006), compared with those of non-SSI group.

Conclusion
This study provides the newest data of SSI after colorectal surgery in China and finds some predictors of SSI. The data presented in our study can be a tool to develop optimal preventive measures and improve surgical quality in China.
Performance of Xpert® MTB/RIF in diagnosing tuberculous pleuritis using thoracoscopic pleural biopsy
Authors: Li Chengjun , Liu Chang , Sun Bingqi , Zhang Wei , Wang Yang , Sun Jiao , Ma Fang , Chen Yu 
Published: November 2020

Abstract
Background
Etiological diagnosis of tuberculous pleuritis is challenging, owing to a paucity of Mycobacterium tuberculosis (MTB) in the affected region. Moreover, currently available methods, such as the detection of acid-fast bacilli and microbiological culture, are not always conducive to timely diagnosis and treatment. In this study, we evaluated the performance of Xpert® MTB/RIF assay (hereinafter referred to as “Xpert”) in detecting MTB in difficult-to-diagnose patients using suspensions of pleural biopsy tissue specimens obtained under direct thoracoscopic guidance.

Methods
One hundred and sixty patients with an unexplained pleural effusion were included from the Shenyang Tenth People’s Hospital and Shenyang Chest Hospital, China, between 2017 and 2018. The included patients underwent thoracoscopy under local anesthesia, with an intercostal incision of approximately 1.0 cm for biopsy. The biopsy specimens were used for pathological and etiological examinations. The Xpert test was evaluated for its sensitivity and specificity, as well as positive and negative predictive values (PPV and NPV, respectively), against data obtained using standards: the BACTEC™ MGIT™ 960 liquid culture system and a composite reference standard (CRS).

Results
The sensitivity and specificity of Xpert were 68.8 and 64.6%, respectively, against the MGIT 960 culture data. The PPV and NPV of Xpert were 56.4 and 75.6%, respectively. The sensitivity of Xpert was 69.0% against the CRS data, which was significantly higher than that of MGIT 960 culture (56.6%). The PPV and NPV of Xpert against the CRS data were 100.0 and 57.3%, respectively.

Conclusions
Xpert is a good rule-in test but has limited value as a rule-out test for the diagnosis of tuberculosis pleuritis.
Preoperative AminoIndex Cancer Screening (AICS) abnormalities predict postoperative recurrence in patients undergoing curative resection for non-small cell lung cancer
Authors: Higashiyama Masahiko , Miyazaki Ryohei , Yamamoto Hiroshi , Anayama Takashi , Kikuchi Shinya , Hirohashi Kentaro , Okami Jiro , Maniwa Tomohiro , Kimura Toru , Orihashi Kazumasa , Imamura Fumio 
Published: November 2020

Abstract
Background
AminoIndex™ Cancer Screening (AICS (lung)) was developed as a screening test for lung cancer using a multivariate analysis of plasma-free amino acid (PFAA) profiles. According to the developed index composed of PFAA, the probability of lung cancer was categorized into AICS (lung) ranks A, B, and C in order of increasing risk. The aim of the present study was to investigate the relationship between the preoperative AICS (lung) rank and surgical outcomes in patients who underwent curative resection for non-small cell lung cancer (NSCLC).

Methods
Preoperative blood samples were collected from 297 patients who underwent curative resection for NSCLC between 2006 and 2015. PFAA concentrations were measured. The relationship between the preoperative AICS (lung) rank and clinicopathological factors was examined. The effects of the preoperative AICS (lung) rank on postoperative outcomes were also analyzed.

Results
The AICS (lung) rank was A in 93 patients (31.3%), B in 82 (27.6%), and C in 122 (41.1%). The AICS (lung) rank did not correlate with any clinicopathological factors, except for age. Based on follow-up data (median follow-up period of 6 years), postoperative recurrence was observed in 22 rank A patients (23.7%), 15 rank B (18.3%) and 49 rank C (40.2%). In the univariate analysis, preoperative AICS (lung) rank C was a worse factor of recurrence-free survival (p = 0.0002). The multivariate analysis identified preoperative AICS (lung) rank C (HR: 2.17, p = 0.0005) as a significant predictor of postoperative recurrence, particularly in patients with early-stage disease or adenocarcinoma.

Conclusion
Preoperative AICS (lung) rank C is a high-risk predictor of postoperative recurrence in patients undergoing curative resection for NSCLC.
Adherence to post-surgery follow-up assessment and its association with sociodemographic and disease characteristics in patients with breast cancer in Central China
Authors: Feng Ran , Jing Jingfeng , Zhang Xiaojun , Li Ming , Gao Jinnan 
Published: November 2020

Abstract

Background
Follow-up after curative surgery is increasingly recognized as an important component of breast cancer care. Although current guideline regulates the follow-ups, there are no relevant studies on the adherence to it in China. This study investigated the post-surgery follow-up and explored its association with patients, tumor and treatment characteristics.

Methods
A total of 711 patients underwent surgical treatment in Shanxi Bethune Hospital from March 2012 to May 2018 were included in this study. Baseline sociodemographic, tumor, and treatment characteristics were obtained from the hospital electronic medical records. The post-surgery follow-up was reviewed and assessed from the patient’s follow-up examination record. Factors associated with the first three-year follow up was evaluated using logistic regression analysis.

Results
The annual follow-up rate after surgery decreased gradually from 67.1% at the 1st year, 60.2% at the 3rd year to 51.9% at the 4th year, and 43.5% at the 5th year. Loss of follow-up during the first 3 years after surgery was significantly associated with older age (> 65 years), lower medical insurance coverage, axillary lymph node dissection, and less intensity of systemic treatment.

Conclusion
A significant downtrend of annual follow-up rate for breast cancer survivors was confirmed in this study. Loss of follow-up within the first 3 years after surgery was associated with both patient’s characteristics and treatment. These results will provide evidence to help clinicians to develop tailored patient management after curative surgery.
Gardner syndrome with giant abdominal desmoid tumor during pregnancy: a case report
Authors: Jin Liquan , Tan Yunbo , Su Ziting , Huang Shan , Pokhrel Sita , Shi Hongbo , Chen Yiming 
Published: November 2020

Abstract
Background
Gardner syndrome is a subtype of familial adenomatous polyposis (FAP), characterized by a combination of adenomatous intestinal polyps and extracolonic lesions such as multiple osteomas, dental abnormalities, and soft tissue tumors. Although 12% of patients with intestinal polyposis of FAP may occur intra-abdominal desmoid tumors, pregnancy complicating with giant abdominal desmoid tumors is a relatively rare case.

Case presentation
A 28-year-old pregnant woman was diagnosed with Gardner syndrome in whom an intra-abdominal tumor was found a year after undergoing a laparoscopic total colectomy due to family adenomatous polyposis. At 32 weeks’ gestation, she presented to our department for the third time complaining upper abdominal pain caused by the giant abdominal mass about 21 × 12 cm2 in size. After multidisciplinary consultation and discussion, the decision of fetal preservation treatment was made. After the delivery of a baby girl, abdominal mass resection was performed, and pathological examination revealed a fibrous adenoma. The patient was discharged after a week and was uneventful in the follow-up for half a year.

Conclusions
Gardner syndrome is characterized by typical syndrome including family adenomatous polyposis and extra-intestinal tissue tumor. Were desmoid tumors rarely as large as fetus and local aggressively. In our case, we selected surgery to remove the intra-abdominal desmoid tumor after the natural delivery of the fetus and no abnormalities were observed during the 6 months follow-up. Women during pregnancy have an increased risk for the development of desmoid tumors, likely with the sex hormone to be one of the triggers. Therefore, we suggested that when a patient with Gardner syndrome desire to conceive again, they should go to the hospital for a regular review at least once every 3 months.
Prediction of metabolic syndrome based on sleep and work-related risk factors using an artificial neural network
Authors: Eyvazlou Meysam , Hosseinpouri Mahdi , Mokarami Hamidreza , Gharibi Vahid , Jahangiri Mehdi , Cousins Rosanna , Nikbakht Hossein-Ali , Barkhordari Abdullah 
Published: November 2020

AbstractBackgroundMetabolic syndrome (MetS) is a major public health concern due to its high prevalence and association with heart disease and diabetes. Artificial neural networks (ANN) are emerging as a reliable means of modelling relationships towards understanding complex illness situations such as MetS. Using ANN, this research sought to clarify predictors of metabolic syndrome (MetS) in a working age population.MethodsFour hundred sixty-eight employees of an oil refinery in Iran consented to providing anthropometric and biochemical measurements, and survey data pertaining to lifestyle, work-related stressors and sleep variables. National Cholesterol Education Programme Adult Treatment Panel ІІI criteria was used for determining MetS status. The Management Standards Indicator Tool and STOP-BANG questionnaire were used to measure work-related stress and obstructive sleep apnoea respectively. With 17 input variables, multilayer perceptron was used to develop ANNs in 16 rounds of learning. ANNs were compared to logistic regression models using the mean squared error criterion for validation.ResultsSex, age, exercise habit, smoking, high risk of obstructive sleep apnoea, and work-related stressors, particularlyRole,all significantly affected the odds of MetS, but shiftworking did not. Prediction accuracy for an ANN using two hidden layers and all available input variables was 89%, compared to 72% for the logistic regression model. Sensitivity was 82.5% for ANN compared to 67.5% for the logistic regression, while specificities were 92.2 and 74% respectively.ConclusionsOur analyses indicate that ANN models which include psychosocial stressors and sleep variables as well as biomedical and clinical variables perform well in predicting MetS. The findings can be helpful in designing preventative strategies to reduce the cost of healthcare associated with MetS in the workplace.
Effect of apexification on occlusal resistance of immature teeth
Authors: Lee WooCheol , Yoo Yeon-Jee 
Published: November 2020

Abstract
Background
Strain distribution was investigated to assess the occlusal resistance alterations in immature teeth under different occlusal force.

Methods
In vitro apexification models of teeth with a funnel-shaped immature apex were obturated with mineral trioxide aggregate (MTA; ProRoot MTA) using different combinations of core materials (10/group): group 1, full-length orthograde obturation of MTA; group 2, a 5-mm MTA apical plug with a composite core; group 3, a 5-mm MTA apical plug and back-filling with warm gutta-percha. Teeth with calcium hydroxide (CH)-medicated canals and untreated teeth with normal apices were tested as controls. The teeth were arranged between two adjacent normal-apex teeth, embedded in a resin mold with a simulated periodontal ligament space. Strain data were recorded from the 3-unit teeth assembly under static compressive occlusal forces (50, 100, 200, and 300 N). Measurements were repeated 20 times for each condition, and the data were statistically analyzed.

Results
The immature teeth showed altered occlusal force resistance, placing increased strain on adjacent teeth. Teeth with CH-medicated canals showed significantly inferior occlusal resistance under all tested forces (P < 0.05). Application of an MTA plug with deep composite resin core resulted in significantly better stress-bearing capacity especially under forces of 50 and 300 N (P < 0.05).

Conclusions
The pattern of occlusal force distribution in immature teeth differed according to the canal obturation materials used for apexification. Immature teeth with an MTA apical plug showed more favorable occlusal force resistance than those with CH-medicated canals.