bluuebunny/crossref_metadata_2025_split huggingface dataset:
Predicting antifreeze proteins with weighted generalized dipeptide composition and multi-regression feature selection ensemble
Authors: Wang Shunfang , Deng Lin , Xia Xinnan , Cao Zicheng , Fei Yu 
Published: June 2021

Abstract
Background
Antifreeze proteins (AFPs) are a group of proteins that inhibit body fluids from growing to ice crystals and thus improve biological antifreeze ability. It is vital to the survival of living organisms in extremely cold environments. However, little research is performed on sequences feature extraction and selection for antifreeze proteins classification in the structure and function prediction, which is of great significance.

Results
In this paper, to predict the antifreeze proteins, a feature representation of weighted generalized dipeptide composition (W-GDipC) and an ensemble feature selection based on two-stage and multi-regression method (LRMR-Ri) are proposed. Specifically, four feature selection algorithms: Lasso regression, Ridge regression, Maximal information coefficient and Relief are used to select the feature sets, respectively, which is the first stage of LRMR-Ri method. If there exists a common feature subset among the above four sets, it is the optimal subset; otherwise we use Ridge regression to select the optimal subset from the public set pooled by the four sets, which is the second stage of LRMR-Ri. The LRMR-Ri method combined with W-GDipC was performed both on the antifreeze proteins dataset (binary classification), and on the membrane protein dataset (multiple classification). Experimental results show that this method has good performance in support vector machine (SVM), decision tree (DT) and stochastic gradient descent (SGD). The values of ACC, RE and MCC of LRMR-Ri and W-GDipC with antifreeze proteins dataset and SVM classifier have reached as high as 95.56%, 97.06% and 0.9105, respectively, much higher than those of each single method: Lasso, Ridge, Mic and Relief, nearly 13% higher than single Lasso for ACC.

Conclusion
The experimental results show that the proposed LRMR-Ri and W-GDipC method can significantly improve the accuracy of antifreeze proteins prediction compared with other similar single feature methods. In addition, our method has also achieved good results in the classification and prediction of membrane proteins, which verifies its widely reliability to a certain extent.
RNA sequencing reveals transcriptomic changes in tobacco (Nicotiana tabacum) following NtCPS2 knockdown
Authors: He Lingxiao , Liu Huabing , Cheng Changhe , Xu Min , He Lei , Li Lihua , Yao Jian , Zhang Wenjun , Zhai Zhengguang , Luo Qinzhan , Sun Jutao , Yang Tiezhao , Xu Shixiao 
Published: June 2021

Abstract
Background
Amber-like compounds form in tobacco (Nicotiana tabacum) during leaf curing and impact aromatic quality. In particular, cis-abienol, a polycyclic labdane-related diterpenoid, is of research interest as a precursor of these compounds. Glandular trichome cells specifically express copalyl diphosphate synthase (NtCPS2) at high levels in tobacco, which, together with NtABS, are major regulators of cis-abienol biosynthesis in tobacco.

Results
To identify the genes involved in the biosynthesis of cis-abienol in tobacco, we constructed transgenic tobacco lines based on an NtCPS2 gene-knockdown model using CRISPR/Cas9 genome-editing technology to inhibit NtCPS2 function in vitro. In mutant plants, cis-abienol and labdene diol contents decreased, whereas the gibberellin and abscisic acid (ABA) contents increased compared with those in wild-type tobacco plants. RNA sequencing analysis revealed the presence of 9514 differentially expressed genes (DEGs; 4279 upregulated, 5235 downregulated) when the leaves of wild-type and NtCPS2-knockdown tobacco plants were screened. Among these DEGs, the genes encoding cis-abienol synthase, ent-kaurene oxidase, auxin/ABA-related proteins, and transcription factors were found to be involved in various biological and physiochemical processes, including diterpenoid biosynthesis, plant hormone signal transduction, and plant-pathogen interactions.

Conclusions
The present study provides insight into the unique transcriptome profile of NtCPS2 knockdown tobacco, allowing for a better understanding of the biosynthesis of cis-abienol in tobacco.
Effects of head positions on awake fiberoptic bronchoscope oral intubation: a randomized controlled trial
Authors: Liu Zhuo , Zhao Li , Ma Zhongfeng , Liu Meiqi , Qi Xiaohang , Jia Qianqian , Liang Shujuan , Yang Xiaochun 
Published: June 2021

Abstract
Background
There are many factors affecting the success rate of awake orotracheal intubation via fiberoptic bronchoscope. We performed this study was to investigate the effects of head positions on awake Fiberoptic bronchoscope oral intubation.

Methods
Seventy-five adult patients, received general anaesthesia were included in this study. After written informed consent, these patients were undergoing awake orotracheal intubation via fiberoptic-bronchoscope and according to the head position, the patients were randomized allocated to neutral position group (NP group), sniffing position group (SP group) or extension position group (EP group). After sedation the patients were intubated by an experienced anesthesiologist. The time to view the vocal cords, the percentage of glottic opening scores (POGO), the time to insert the tracheal tube into trachea and the visual analog scale (VAS) scores for ease experienced of passing the tracheal tube through glottis, the hemodynamic changes and the adverse events after surgery were recorded.

Results
The time to view the vocal cords was significantly shorter and the POGO scores was significantly higher in the EP group compared with the other two groups (P < 0.05); The SpO2 in the EP group was higher than NP group at before intubation and higher than SP group and NP group at immediate after intubation (P < 0.05); The time to insert the tracheal tube into trachea, the VAS scores for passing the tracheal tube through glottis, the coughing scores had no significant differences among groups (P > 0.05). There were also no significant differences regard to the incidence of postoperative complications, mean arterial pressure and heart rate among the groups (P > 0.05).

Conclusions
The head at extension position had a best view of glottic opening than neutral position or sniffing position during awake Fiberoptic bronchoscope oral intubation, so extension position was recommended as the starting head position for awake Fiberoptic bronchoscope oral intubation.

Trial registration
Clinical Trials.gov. no. NCT02792855. Registered at https://register.clinicaltrials.gov on 23 september 2017.
Evaluation of different DNA extraction methods and loop-mediated isothermal amplification primers for the detection of Mycobacterium ulcerans in clinical specimens
Authors: Ablordey Anthony , Ahotor Evans , Narh Charles A. , King Sandra A. , Cruz Isra , Ndung’u Joseph M. , de Souza Dziedzom K. 
Published: June 2021

Abstract
Background
Early diagnosis and treatment of Buruli ulcer is critical in order to avoid the debilitating effects of the disease. In this regard, the development of new diagnostic and point of care tools is encouraged. The loop-mediated isothermal amplification for the detection of Mycobacterium ulcerans represents one of the new tools with a good potential of being developed into a point of care test. There is however the need to standardize the assays, reduce sample preparation times, improve the detection/visualization system and optimize them for high-throughput screening, adaptable to low resourced laboratories.

Methods
In this study, we assessed two DNA extraction protocols (modified Boom and EasyNAT methods), three previously published LAMP primer sets (BURULI, MU 2404 and BU-LAMP), and compared the sensitivity and specificity of LAMP assays on three DNA amplification platforms.

Results
Our results show that Buruli ulcer diagnosis using primers targeting IS2404 for the LAMP method is sensitive (73.75–91.49%), depending on the DNA extraction method used. Even though the modified Boom DNA extraction method provided the best results, its instrumentation requirement prevent it from being field applicable. The EasyNAT method on the other hand is simpler and may represent the best method for DNA extraction in less resourced settings.

Conclusions
For further work on the development and use of LAMP tests for Buruli diagnosis, it is recommended that the BURULI sets of primers be used, as these yielded the best results in terms of sensitivity (87.50–91.49%) and specificity (89.23–100%), depending on the DNA extraction methods used.
Clinical features and development of Sepsis in Klebsiella pneumoniae infected liver abscess patients: a retrospective analysis of 135 cases
Authors: Li Shixiao , Yu Sufei , Peng Minfei , Qin Jiajia , Xu Chunyan , Qian Jiao , He Minmin , Zhou Peng 
Published: June 2021

Abstract
Background
Klebsiella pneumoniae is a primary pathogen of pyogenic liver abscess (PLA). However, little data are available on combination with sepsis. In this study, we aimed to evaluate the clinical characteristics and prognostic differences of PLA patients with sepsis.

Methods
This retrospective cohort study was conducted to investigate 135 patients with confirmed Klebsiella pneumoniae-caused liver abscesses (KPLA) from a tertiary teaching hospital, from 2013 to 2019. The patients were divided into two groups, KPLA with sepsis and KPLA without sepsis. The demographic characteristics, clinical features as well as laboratory and microbiologic findings were analyzed.

Results
A total of 135 patients with KPLA were analyzed. The mean age of patients was 60.9 ± 12.7 years, and the percentage of men was 59.3%. Among them, 37/135 (27.4%) of patients had sepsis and the mortality rate was 1.5%. The most common symptom was fever (91.1%). KPLA patients with sepsis had a significantly higher proportion of frailty, diarrhea, fatty liver, chronic renal insufficiency, and hepatic dysfunction compared to KPLA patients without sepsis (p < 0.05). Antibiotic therapy and percutaneous drainage were most frequently therapeutic strategy. Furthermore, the incidences of sepsis shock and acute respiratory distress syndrome were higher in the sepsis group compared to the non-sepsis group. As for metastatic infections, the lung was the most common site. In addition, KPLA patients with sepsis showed respiratory symptoms in 11 patients, endophthalmitis in 4 patients, and meningitis in 1 patient.

Conclusion
Our findings emphasize that KPLA patients combined with or without sepsis have different clinical features, but KPLA patients with sepsis have higher rates of complications and metastatic infections. Taken together, further surveillance and control of septic spread is essential for KPLA patients.
Development of a preliminary conceptual model of the patient experience of chronic kidney disease: a targeted literature review and analysis
Authors: Flythe Jennifer E. , Karlsson Niklas , Sundgren Anna , Cordero Paul , Grandinetti Amanda , Cremisi Henry , Rydén Anna 
Published: June 2021

AbstractBackgroundPatient-reported outcome (PRO) instruments should capture the experiences of disease and treatment that patients consider most important in order to inform patient-centred care and product development. The aim of this study was to develop a preliminary conceptual model of patient experience in chronic kidney disease (CKD) based on a targeted literature review and to characterize existing PRO instruments used in CKD.MethodsPubMed, EMBASE and Cochrane databases and recent society meetings were searched for publications reporting signs/symptoms and life impacts of CKD. Concepts identified in the literature review were used to develop a preliminary conceptual model of patient experience of CKD, overall, and within patient subpopulations of differing CKD causes, severities and complications. PRO instruments, identified from PRO databases, CKD literature and CKD clinical trials, were assessed for content validity, psychometric strength and coverage of concepts in the literature review.ResultsIn total, 100 publications met criteria for analysis; 56 signs/symptoms and 37 life impacts of CKD were identified from these sources. The most frequently mentioned signs/symptoms were pain/discomfort (57% of publications) and tiredness/low energy/lethargy/fatigue (42%); the most commonly reported life impacts were anxiety/depression (49%) and decrements in physical functioning (43%). Signs/symptoms and life impacts varied across the subpopulations and were more frequent at advanced CKD stages. The preliminary conceptual model grouped signs/symptoms into seven domains (pain/discomfort; energy/fatigue; sleep-related; gastrointestinal-related; urinary-related; skin−/hair−/nails-related; and other) and life impacts into six domains (psychological/emotional strain; cognitive impairment; dietary habit disruption; physical function decrements; interference with social relationships; and other). Eleven PRO instruments were considered to be promising for use in CKD; all had limitations.ConclusionsAlthough preliminary, the proposed conceptual model highlights key PROs for people with CKD and is intended to spur development of more tailored PRO instruments to assess these concepts.
The impact of COVID-19 pandemic on the health-seeking behaviour of an Asian population with acute respiratory infections in a densely populated community
Authors: Tan Hwee Mian Jane , Tan Mui Suan , Chang Zi Ying , Tan Kee Tung , Ee Guan Liang Adrian , Ng Chee Chin David , Hwang Ying Khee William , Koh Yi Ling Eileen , Low Yan Ping Sarah , Tan Ngiap Chuan 
Published: June 2021

Abstract
Background
The COVID-19 pandemic led to the implementation of various non-pharmaceutical interventions (NPI) as the Singapore government escalated containment efforts from DORSCON Orange to Circuit Breaker. NPI include mandatory mask wearing, hand hygiene, social distancing, and closure of schools and workplaces. Considering the similar mode of transmission of COVID-19 and other pathogens related to acute respiratory infections (ARI), the effects of NPI could possibly lead to decreased ARI attendances in the community. This study aims to determine the year-on-year and weekly changes of ARI attendances across a cluster of polyclinics following the implementation of NPI.

Methods
The effect of the nation-wide measures on the health-seeking behaviour of the study population was examined over three periods: (1) 9 weeks prior to the start of Circuit Breaker (DORSCON Orange period), (2) 8 weeks during the Circuit Breaker, and (3) 9 weeks after easing of Circuit Breaker. Data on ARI attendances for the corresponding periods in 2019 were also extracted for comparison and to assess the seasonal variations of ARI. The average weekly workday ARI attendances were compared with those of the preceding week using Wilcoxon signed rank test.

Results
ARI attendances dropped steadily throughout the study period and were 50–80% lower than in 2019 since Circuit Breaker. They remained low even after Circuit Breaker ended. Positivity rate for influenza-like illnesses samples in the community was 0.0% from the last week of Circuit Breaker to end of study period.

Conclusions
NPI and public education measures during DORSCON Orange and Circuit Breaker periods appear to be associated with the health-seeking behaviour of the public. Changing levels of perceived susceptibility, severity, benefits and barriers, and widespread visual cues based on the Health Belief Model may account for this change. Understanding the impact of NPI and shifts in the public’s health-seeking behaviour will be relevant and helpful in the planning of future pandemic responses.
Association between socio-environmental factors, coverage by family health teams, and rainfall in the spatial distribution of Zika virus infection in the city of Rio de Janeiro, Brazil, in 2015 and 2016
Authors: Raymundo Carlos Eduardo , de Andrade Medronho Roberto 
Published: June 2021

Abstract
Background
Zika virus (ZIKV) infection caused outbreak in Brazil, in 2015 and 2016. Disorganized urban growth, facilitates the concentration of numerous susceptible and infected individuals. It is useful to understand the mechanisms that can favor the increase in ZIKV incidence, such as areas with wide socioeconomic and environmental diversity. Therefore, the study analyzed the spatial distribution of ZIKV in the city of Rio de Janeiro, Brazil, in 2015 and 2016, and associations between the incidence per 1000 inhabitants and socio-environmental factors.

Methods
The census tracts were used as the analytical units reported ZIKV cases among the city’s inhabitants. Local Empirical Bayesian method was used to control the incidence rates’ instability effect. The spatial autocorrelation was verified with Moran’s Index and local indicators of spatial association (LISA). Spearman correlation matrix was used to indicate possible collinearity. The Ordinary Least Squares (OLS), Spatial Lag Model (SAR), and Spatial Error Model (CAR) were used to analyze the relationship between ZIKV and socio-environmental factors.

Results
The SAR model exhibited the best parameters: R2 = 0.44, Log-likelihood = − 7482, Akaike Information Criterion (AIC) = 14,980. In this model, mean income between 1 and 2 minimum wages was possible risk factors for Zika occurrence in the localities. Household conditions related to adequate water supply and the existence of public sewage disposal were associated with lower ZIKV cumulative incidence, suggesting possible protective factors against the occurrence of ZIKV in the localities. The presence of the Family Health Strategy in the census tracts was positively associated with the ZIKV cumulative incidence. However, the results show that mean income less than 1 minimum wage were negatively associated with higher ZIKV cumulative incidence.

Conclusion
The results demonstrate the importance of socio-environmental variables in the dynamics of ZIKV transmission and the relevance for the development of control strategies.
Safety and efficacy of single CHAP Hyaluronan injection versus three injections of linear Hyaluronan in pain relief for knee osteoarthritis: a prospective, 52-week follow-up, randomized, evaluator-blinded study
Authors: Huang Teng-Le , Tsai Chun-Hao 
Published: June 2021

Abstract
Background
The hyaluronic acid (HA) injections are widely used in knee osteoarthritis (OA) patients. We conducted the study comparing the efficacy and safety of single injection of Crosslinked Hyaluronic Acid Platform Hyaluronan (CHAP-HA) with 3-injection of linear hyaluronan in knee OA patients.

Methods
This was a randomized two-arms, evaluator-blinded, controlled, single-center study. Participants with knee OA received single CHAP-HA or three-injection of linear-HA. The 140 patients aged 35–85 years with radiographically confirmed knee OA were enrolled. At week 4, 12, 26, 39, and 52, visual analog scale (VAS) pain score, Western Ontario and McMaster Universities Osteoarthritis (WOMAC) index, timed up and go (TUG) and subject’s adverse events (AE) of these 2 groups were recorded. Primary outcome of the differences of VAS pain score at week 26 between groups was analyzed with analysis of covariance (ANCOVA). At week 52, those who met the inclusion criteria could receive a CHAP-HA injection and being followed-up for the adverse events for 4 weeks.

Results
The trial was conducted from September 2015 to April 2017. A total 140 subjects were available for analysis (71 in the CHAP-HA group and 69 in the linear-HA group). At 26th week, there were significant more improvements in VAS pain scores in CHAP-HA compared with linear-HA. Both CHAP-HA and linear-HA showed significant improvements in the VAS pain score at week 26 compared with the baseline, and the occurrence of adverse events during the study period showed no between-group difference. In subjects with KL = 2, both groups showed significant improvements in VAS pain scores within 26 weeks. In patients with KL = 3, only CHAP-HA group showed significant improvement in VAS pain from 4 to 39 weeks. No unexpected or severe AEs were reported.

Conclusions
A single injection of CHAP-HA may be safe and more effective for 26 weeks in patients with knee OA by comparing to linear-HA; moreover, the pain relief effect of CHAP-HA may remain until 52 weeks. For patients with more severe OA, CHAP-HA was demonstrated to be more preferable to relieve OA pain. Furthermore, repeat treatment of CHAP-HA or using CHAP-HA after a three-injection HA was proved to be safe.

Trial registration
ClinicalTrials.gov: NCT03643588. Date: August 23, 2018 (retrospectively registered).
Level of Evidence: Therapeutic Level I.
Type 2 diabetes and its characteristics are associated with poor oral health: findings from 60,590 senior women from the E3N study
Authors: Laouali Nasser , El Fatouhi Douae , Aguayo Gloria , Balkau Beverley , Boutron-Ruault Marie-Christine , Bonnet Fabrice , Fagherazzi Guy 
Published: June 2021

AbstractBackgroundType 2 diabetes (T2D) has been identified as a risk factor for poor oral health, however, a limited number of oral health and T2D characteristics have been studied so far. We sought to assess T2D status, age at diagnosis, duration since diagnosis and treatment in relation to a variety of oral diseases.MethodsCross-sectional data were analyzed from the E3N (Etude Epidémiologique auprès de femmes de l'Education Nationale) cohort study which enrolled 60,590 women. Participants self-reported oral health status, and T2D cases were identified using diabetes-specific questionnaires and drug reimbursement insurance databases. Multivariable-adjusted ORs and 95% CIs were estimated using logistic regression models.ResultsThe mean age (SD) of the women was 70 years (7.2), and 4.7% (n = 2857) had T2D. Compared to women without T2D, women with T2D were more likely to report a poor perceived oral health (OR 1.37 [95% CI 1.18, 1.60]), wearing dental prostheses (1.26 [1.14, 1.39]) and having problems of biting and chewing food (1.19 [1.07, 1.33]). In addition, for women with T2D the age at diagnosis (inversely) and the duration (positively) were associated with the likelihood to report poor oral health.ConclusionsFor women with T2D, duration and age at diagnosis are associated with wearing prostheses, problems of biting and chewing, periodontitis and gingivitis.