bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparative genomic analysis of a Shiga toxin-producing Escherichia coli (STEC) O145:H25 associated with a severe pediatric case of hemolytic uremic syndrome in Davidson County, Tennessee, US
Authors: Guerra Julio A. , Zhang Chengxian , Bard Jonathan E. , Yergeau Donald , Halasa Natasha , Gómez-Duarte Oscar G. 
Published: August 2020

Abstract
Background
Shiga toxin-producing E. coli (STECs) are foodborne pathogens associated with bloody diarrhea and hemolytic uremic syndrome (HUS). Although the STEC O157 serogroup accounts for the highest number of infections, HUS-related complications and deaths, the STEC non-O157, as a group, accounts for a larger proportion of STEC infections and lower HUS cases. There is limited information available on how to recognize non-O157 serotypes associated with severe disease. The objectives of this study were to describe a patient with STEC non-O157 infection complicated with HUS and to conduct a comparative whole genome sequence (WGS) analysis among the patient’s STEC clinical isolate and STEC O157 and non-O157 strains.

Results
The STEC O145:H25 strain EN1I-0044-2 was isolated from a pediatric patient with diarrhea, HUS and severe neurologic and cardiorespiratory complications, who was enrolled in a previously reported case-control study of acute gastroenteritis conducted in Davidson County, Tennessee in 2013. The strain EN1I-0044-2 genome sequence contained a chromosome and three plasmids. Two of the plasmids were similar to those present in O145:H25 strains whereas the third unique plasmid EN1I-0044-2_03 shared no similarity with other STEC plasmids, and it carried 23 genes of unknown function. Strain EN1I-0044-2, compared with O145:H25 and O157 serogroup strains shared chromosome- and plasmid-encoded virulence factors, including Shiga toxin, LEE type III secretion system, LEE effectors, SFP fimbriae, and additional toxins and colonization factors.

Conclusions
A STEC O145:H25 strain EN1I-0044-2 was isolated from a pediatric patient with severe disease, including HUS, in Davidson County, TN. Phylogenetic and comparison WGS analysis provided evidence that strain EN1I-0044-2 closely resembles O145:H25, and confirmed an independent evolutionary path of STEC O145:H25 and O145:H28 serotypes. The strain EN1I-0044-2 virulence make up was similar to other O145:H25 and O157 serogroups. It carried stx2 and the LEE pathogenicity island, and additional colonization factors and enterotoxin genes. A unique feature of strain EN1I-0044-2 was the presence of plasmid pEN1I-0044-2_03 carrying genes with functions to be determined. Further studies will be necessary to elucidate the role that newly acquired genes by O145:H25 strains play in pathogenesis, and to determine if they may serve as genetic markers of severe disease.
Dynamic transcriptome and metabolome analyses of two types of rice during the seed germination and young seedling growth stages
Authors: Yang Jing , Su Ling , Li Dandan , Luo Lixin , Sun Kai , Yang Meng , Gu Fengwei , Xia Aoyun , Liu Yongzhu , Wang Hui , Chen Zhiqiang , Guo Tao 
Published: August 2020

Abstract
Background
Seed germination and young seedling growth are important agricultural traits for developing populations of both irrigated and directly seeded rice. Previous studies have focused on the identification of QTLs. However, there are few studies on the metabolome or transcriptome of germination and young seedling growth in rice.

Results
Here, an indica rice and a japonica rice were used as materials, and the transcripts and metabolites were detected during the germination and young seedling growth periods on a large scale by using RNA sequencing and a widely targeted metabolomics method, respectively. Fourteen shared transcripts and 15 shared metabolites that were continuously differentially expressed in the two materials were identified and may be essential for seed germination and young seedling growth. Enrichment analysis of differentially expressed genes in transcriptome expression profiles at different stages indicated that cell wall metabolism, lipid metabolism, nucleotide degradation, amino acid, etc., were enriched at 0–2 days, and most of the results are consistent with those of previous reports. Specifically, phenylpropanoid biosynthesis and glutathione metabolism were continuously enriched during the seed germination and young seedling growth stages. Next, KO enrichment analysis was conducted by using the differentially expressed genes of the two materials at 2, 3 and 4 days. Fourteen pathways were enriched. Additionally, 44 differentially expressed metabolites at 2, 3 and 4 days were identified. These metabolites may be responsible for the differences in germination and young seedling growth between the two materials. Further attention was focused on the ascorbate–glutathione pathway, and it was found that differences in ROS-scavenging abilities mediated by some APX, GPX and GST genes may be directly involved in mediating differences in the germination and young seedling growth speed of the two materials.

Conclusions
In summary, these results may enhance the understanding of the overall mechanism of seed germination and young seedling growth, and the outcome of this study is expected to facilitate rice breeding for direct seeding.
Functional training added to intradialytic cycling lowers low-density lipoprotein cholesterol and improves dialysis adequacy: a randomized controlled trial
Authors: Bogataj Špela , Pajek Jernej , Buturović Ponikvar Jadranka , Pajek Maja 
Published: August 2020

Abstract
Background
Exercise has various positive effects on hemodialysis patients. However, there is no clear evidence which type of exercise yields better results. This study aimed to determine the effects of guided functional training added to the intradialytic cycling on dialysis adequacy and biochemical parameters in hemodialysis patients. Additionally, we aimed to investigate if patients could transfer functional exercise to an unsupervised home environment and retain gained improvements.

Methods
Randomization was done to a functional training intervention group (INT) (n = 20) or intradialytic cycling control group (CON) (n = 20). The INT attended a pre-dialysis functional training in the first 8 weeks. In the second 8 weeks, they performed functional exercises at unsupervised home environment on non-dialysis days. During the whole study, both groups participated in the intradialytic cycling program.

Results
Both groups demonstrated a significant increase in dialysis adequacy (Kt/V) in the eight (0.15, 95% CI 0.06 to 0.24; p = 0.003 for INT and 0.21, 95% CI 0.11 to 0.3; p < 0.001 for CON) and the 16th study week (0.13, 95% CI 0.03 to 0.24; p = 0.017 for INT and 0.13, 95% CI 0.03 to 0.22; p = 0.013 for CON) compared to their baseline values with no significant between-group differences. At week eight, the total cholesterol was significantly lowered in the INT (− 0.34 mmol/L, 95% CI − 0.6 to − 0.07; p = 0.016) and remained lower at week 16 (− 0.32 mmol/L, 95% CI − 0.64 to − 0.01; p = 0.049) with no significant changes in the CON. Low-density lipoprotein levels in the INT were significantly reduced after 8 weeks (− 0.35 mmol/L, 95% CI − 0.64 to − 0.06; p = 0.022) and remained reduced after 16 weeks (− 0.28 mmol/L, 95% CI − 0.52 to − 0.03; p = 0.030). There were no significant differences found for albumin, high-density lipoprotein cholesterol, triglycerides, C-reactive protein, and hemoglobin in both groups.

Conclusions
We demonstrated that functional training added to intradialytic cycling improved lipid profile and dialysis adequacy. Additionally, the effects of the unsupervised, home-based program were preserved during the second study phase. This study supports the assumption that combined training is more effective compared to solely intradialytic exercise.

Trial registration
ClinicalTrials.Gov, NCT03334123. Registered 07 November 2017.
Urine concentration ability is reduced to the same degree in adult dominant polycystic kidney disease compared with other chronic kidney diseases in the same CKD-stage and lower THAN in healthy control subjects - a CASE control study
Authors: Malmberg M. H. , Mose F. H. , Pedersen E. B. , Bech J. N. 
Published: August 2020

Abstract
Background
Concentration of the urine is primarily regulated via vasopressin dependent aquaporin-2 water channels in the apical membrane of kidney principal cells. It is unclear whether urine concentration ability in ADPKD differs from other patients with similar degree of impaired renal function (non-ADPKD patients). The purpose of this case control study was to measure urine concentration ability in ADPKD patients compared to non-ADPKD patients and healthy controls.

Methods
A seventeen hour long water deprivation test was carried out in 17 ADPKD patients (CKD I-IV), 16 non-ADPKD patients (CKD I-IV), and 18 healthy controls. Urine was collected in 4 consecutive periods during water deprivation (12 h, 1 h, 2 h and 2 h, respectively) and analyzed for osmolality (u-Osm), output (UO), fractional excretion of sodium (FENa), aquaporin2 (u-AQP2) and ENaC (u-ENaC). Blood samples were drawn trice (after 13-, 15-, and 17 h after water deprivation) for analyses of osmolality (p-Osm), vasopressin (p-AVP), and aldosterone (p-Aldo).

Results
U-Osm was significantly lower and FENa significantly higher in both ADPKD patients and non-ADPKD patients compared to healthy controls during the last three periods of water deprivation. During the same periods, UO was higher and secretion rates of u-AQP2 and u-ENaC were lower and at the same level in the two groups of patients compared to controls. P-AVP and p-Osm did not differ significantly between the three groups. P-Aldo was higher in both groups of patients than in controls.

Conclusions
Urine concentration ability was reduced to the same extent in patients with ADPKD and other chronic kidney diseases with the same level of renal function compared to healthy controls. The lower urine excretion of AQP2 and ENaC suggests that the underlying mechanism may be a reduced tubular response to vasopressin and aldosterone.

Trial registration
Current Controlled Trial NCT04363554, date of registration: 20.08.2017.
Characteristics of cognitive impairment in adult asymptomatic moyamoya disease
Authors: He Shihao , Duan Ran , Liu Ziqi , Ye Xun , Yuan Li , Li Tian , Tan Cunxin , Shao Junshi , Qin Shusen , Wang Rong 
Published: August 2020

Abstract
Background
Cognitive impairment in adult moyamoya disease (MMD) is thought to be the result of ischemic stroke; however, the presence and extent of cognitive decline in asymptomatic patients is unclear.

Methods
After classification using T2-weighted fluid attenuated inversion recovery (FLAIR) magnetic resonance imaging (MRI), a total of 19 MMD patients with a history of cerebral infarction, 21 asymptomatic MMD patients, and 20 healthy controls matched for age, sex, and years of education were prospectively included in this study. A detailed neuropsychological evaluation of two moyamoya subgroups and normal controls was conducted.

Results
Asymptomatic patients showed varying degrees of decline in intelligence (Raven’s Standard Progressive Matrices, P = 0.001), spatial imagination (mental rotation, P = 0.014), working memory (verbal working memory-backward digit span, P = 0.011), and computational ability (simple subtraction, P = 0.014; complex subtraction, P < 0.001) compared with normal controls. MMD patients with cerebral infarction had more severe impairment in complex arithmetic (P = 0.027) and word short-term memory (P = 0.01) than those without symptoms.

Conclusion
In asymptomatic MMD patients, a variety of cognitive impairment precedes the onset of clinical symptoms such as cerebral infarction, which may be a long-term complication of conservative treatment.
Multi-measure assessment of adherence to antiretroviral therapy among children under five years living with HIV in Jinja, Uganda
Authors: Ssanyu Jacquellyn Nambi , Nakafeero Mary , Nuwaha Fred 
Published: August 2020

AbstractBackgroundAdherence to Antiretroviral Therapy (ART) is required to achieve HIV viral load suppression. However, children under 5 years in Jinja, Uganda, had been shown to have low HIV suppression rates. This study aimed to determine the level of ART non-adherence among these children and the associated factors.MethodsData for the cross-sectional study was collected from April to July 2019, from caregivers of 206 children under 5 years living with HIV who were attending health facilities in Jinja and had been on ART for at least 3 months. Non-adherence was measured using a Visual Analog Scale that assessed both dosing and timing non-adherence, and by determining the Proportion of Days Covered by the medication. A questionnaire administered to the caregivers was used to collect the data, together with medical record review. A child was only considered adherent if they had adherence greater than 95% on all the measures. The data was analysed using Modified Poisson Regression, taking ap-value less than 0.05 as statistically significant.ResultsOf the 206 children, 73.8% were older than 2 years, and 52.9% were female. Likewise, the majority of caregivers were female (93.7%). Using the combined adherence measure, 57.3% of the children were categorised as non-adherent. School/day-care attendance, Prevalence Ratio (PR) = 1.25 (p = 0.042), the caregiver having higher than a primary school education, PR = 0.72 (p = 0.044) and satisfaction with the quality of service at the health facility, PR = 0.97 (p < 0.001) were associated with non-adherence. Household food insecurity was also associated with non-adherence: PR = 1.55 (p = 0.011) for mild food insecurity, PR = 1.75 (p = 0.001) for moderate insecurity and PR = 1.48 (p = 0.015) for severe food insecurity.ConclusionsChildren under 5 years in Jinja had a high level of ART non-adherence. It is important to engage schools to support adherence among children living with HIV. Addressing household food insecurity and improving the quality of paediatric ART services would also reduce the barriers to optimal adherence.
Pathogenic characteristics of sputum and bronchoalveolar lavage fluid samples from patients with lower respiratory tract infection in a large teaching hospital in China: a retrospective study
Authors: Peng Zheng , Zhou Jin’an , Tian Lei 
Published: August 2020

Abstract
Background
Lower respiratory tract infection (LRIs) is very common both in terms of community-acquired infection and hospital-acquired infection. Sputum and bronchoalveolar lavage fluid (BALF) are the most important specimens obtained from patients with LRI. The choice of antibiotic with which to treat LRI usually depends on the antimicrobial sensitivity of bacteria isolated from sputum and BALF. However, differences in the antimicrobial sensitivity of pathogens isolated from sputum and BALF have not been evaluated.

Methods
A retrospective study was conducted to analyze the differences between sputum and BALF samples in terms of pathogen isolation and antimicrobial sensitivity in hospitalized patients with LRI.

Results
Between 2013 and 2015, quality evaluation of sputum samples was not conducted before performing sputum culture; however, between 2016 and 2018, quality evaluation of sputum samples was conducted first, and only quality-assured samples were cultured. The numbers of sputum and BALF in 2013–2015 were 15,549 and 1671, while those in 2016–2018 were 12,055 and 3735, respectively. The results of pathogen culture showed that Pseudomonas aeruginosa, Acinetobacter baumannii, Klebsiella pneumoniae, Staphylococcus aureus, Hemophilus influenzae, Escherichia coli, Stenotrophomonas maltophilia, and Streptococcus pneumoniae were in the top ten pathogens isolated from sputum and BALF. An antimicrobial susceptibility test showed that the susceptibility of BALF isolates to most antibiotics was higher compared with the susceptibility of sputum isolates, especially after quality control of sputum samples (2016–2018).

Conclusions
Our findings suggest that caution is needed in making therapeutic choices for patients with LRI when using antimicrobial sensitivity results from sputum isolates as opposed to BALF isolates.
Lateral Unicompartmental knee arthroplasty for a secondary osteonecrosis of the lateral femoral condyle. A case report
Authors: Yang Tao , Xue Huaming , Ma Tong , Wen Tao , Xue Long , Guan Mengyin , Tu Yihui 
Published: August 2020

Abstract
Background
Secondary osteonecrosis of the knee is a rare event. There are few reports regarding management of this condition. The aim of the present study is to report treatment outcomes for secondary osteonecrosis of the lateral condyle treated with unicompartmental knee arthroplasty (UKA).

Case presentation
A 54-year-old woman with idiopathic thrombocytopenic purpura, who received low-dosage corticosteroids, complained of knee pain for 5 years and difficulty walking in the last 5 months. Fixed-bearing lateral UKA was performed under general anesthesia combined with midthigh saphenous nerve block. The patient could walk without ambulation aid shortly after the operation and achieved satisfactory knee joint function at the 6-week follow-up. The knee society score (KSS) increased from 68 to 91. The follow-up period was up to 1 year. There was no pain, loosening, or fracture of the prosthesis at the latest follow-up.

Conclusions
This case study demonstrates successful management of secondary osteonecrosis of the lateral femoral condyle is possible with a fixed bearing lateral UKA. Early diagnosis, rigorous indication, and appropriate surgical techniques were critical to maximizing prosthesis stability in lateral UKA.
A new method for assessment of nickel-titanium endodontic instrument surface roughness using field emission scanning electronic microscope
Authors: Van Pham Khoa , Vo Canh Quang 
Published: August 2020

AbstractBackgroundTo introduce a new method for measurement of surface roughness of the endodontic instrument, before and after instrumentation, using the Field Emission Scanning Electronic Microscope (FE-SEM) combined with the ImageJ software.MethodsTwenty J-shape resin blocks were divided into two groups, ten blocks of each group. Simulated root canal inside the resin block was 16 mm length, 600angle of curvature, and radius of 4.5 mm. Ten WaveOne Gold Primary and 10 Reciproc Blue R25 instruments were used for root canal instrumentation. The instruments were scanned before and after instrumentation with special molds made to ensure the same areas at the point located 3 mm from the tips of the instruments using the FE-SEM. These scanned images were analyzed using the ImageJ. The arithmetical mean roughness (Ra), root mean square roughness (Rq), and the average distance between the highest peak and lowest valley in each sampling length (Rz) were calculated by ImageJ for quantitative analyses. The paired-t test was performed to analyze the data using the SPSS 22.0 at the significance of .05.ResultsAlmost all surface roughness values were decreased. However, these decreases were not statistically significant (P > .05).ConclusionsThe FE-SEM combined with the ImageJ was the reliable and appropriate modality for measurement surface roughness of instruments.
Prevalence of high-risk behaviors in reproductive age women in Alborz province in 2019 using unmatched count technique
Authors: Bahadivand Samira , Doosti-Irani Amin , Karami Manoochehr , Qorbani Mostafa , Mohammadi Younes 
Published: August 2020

Abstract
Background
Our knowledge on the prevalence of high-risk behaviors among women of Alborz is not reliable due to the sensitivity of the issue. This study aimed to estimate the prevalence of seven risk behaviors among the reproductive age women in Alborz Province, Iran.

Method
In this cross-sectional study, 2000 women were randomly selected from a registered healthcare system in 2019. A researcher-made questionnaire was used to collect the required data. The prevalence of the risk behaviors including drug abuse, hookah, alcohol drinking, tobacco smoking, extramarital intercourse, and gambling was estimated using the unmatched count technique, and the prevalence rate was reported at a 95% confidence interval.

Results
The response rate for this study was 95%. The estimated prevalence for drug abuse, hookah, alcohol drinking, tobacco smoking, extramarital intercourse, and gambling were 3% (95%CI: 2.78 to 3.22), 10.5% (95%CI: 10.29 to 10.71), 7% (95%CI: 6.78 to 7.22), 10% (95%CI: 9.78 to 10.22), 8.7% (95%CI, 8.29 to 8.71), and 7.5% (95%CI, 4.71 to 7.28), respectively.

Conclusion
High risk behaviors are highly prevalent among Iranian women. Enforcing laws, prohibition, marketing restrictions, increasing taxation, expanding treatment, promoting condom distribution and providing community-based service are recommended to reduce the effects of high risk behaviors among women.
Continuing nursing education: use of observational pain assessment tool for diagnosis and management of pain in critically ill patients following training through a social networking app versus lectures
Authors: Deldar Kolsoum , Froutan Razieh , Sedaghat Alireza , Mazlom Seyed Reza 
Published: August 2020

AbstractBackgroundNursing staff training in using observational pain assessment tools is highly important to improve the assessment of pain. The present study was conducted to examine the effect of two different training methods (lectures vs. a social networking app) on the diagnosis and management of pain in mechanically-ventilated patients.MethodsThis quasi-experimental study was conducted on 70 nurses working in two Intensive Care Units (ICU) in Mashhad, Iran. The nurses were trained in the application of observational pain assessment tools by lectures or through a social networking app. Before and after the intervention, the nurses’ performance was evaluated in both groups using a checklist based on Critical-Care Pain Observation Tool (CPOT).ResultsIn the pre-intervention phase, the nurses’ performance scores in the domains of pain diagnosis and pain management were not significantly different between the two groups (P > 0.05). Following the intervention, the mean score of pain diagnosis was 82 ± 19 in the lecture group and 97 ± 8 in the social networking app group (P < 0.01), and the mean pain management scores were 30 ± 17 and 90 ± 18 (P < 0.01), respectively.ConclusionThis study showed that learning through a social networking app led to improved diagnosis and management of pain in mechanically-ventilated patients when compared with lectures. Training through social networking applications can therefore be considered as a feasible instructional method for developing nurses’ pain management skills.