bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genome-wide methylation and transcriptome of blood neutrophils reveal the roles of DNA methylation in affecting transcription of protein-coding genes and miRNAs in E. coli-infected mastitis cows
Authors: Ju Zhihua , Jiang Qiang , Wang Jinpeng , Wang Xiuge , Yang Chunhong , Sun Yan , Zhang Yaran , Wang Changfa , Gao Yaping , Wei Xiaochao , Hou Minghai , Huang Jinming 
Published: January 2020

Abstract
Background
Neutrophils are the first effectors of inflammatory response triggered by mastitis infection, and are important defense cells against pathogenic Escherichia coli (E. coli). DNA methylation, as a critical epigenetic mechanism for regulating gene function, is involved in bovine mastitis.

Results
In this study, we sequenced the blood neutrophils of healthy and E. coli-infected mastitic half-sib cows for the overall DNA methylation levels using transcriptome sequencing and reduced representation bisulfite sequencing. The methylation levels in the mastitis cows (MCs) were decreased compared with healthy cows (HCs). A total of 494 differentially methylated regions were identified, among which 61 were up-methylated and 433 were down-methylated (MCs vs. HCs). The expression levels of 1094 differentially expressed genes were up-regulated, and 245 genes were down-regulated. Twenty-nine genes were found in methylation and transcription data, among which seven genes’ promoter methylation levels were negatively correlated with expression levels, and 11 genes were differentially methylated in the exon regions. The bisulfite sequencing PCR and quantitative real-time PCR validation results demonstrated that the promoter methylation of CITED2 and SLC40A1 genes affected differential expression. The methylation of LGR4 exon 5 regulated its own alternative splicing. The promoter methylation of bta-miR-15a has an indirect effect on the expression of its target gene CD163. The CITED2, SLC40A1, and LGR4 genes can be used as candidates for E. coli-induced mastitis resistance.

Conclusions
This study explored the roles of DNA methylation in affecting transcription of protein-coding genes and miRNAs in E. coli-induced mastitis, thereby helping explain the function of DNA methylation in the pathogenesis of mastitis and provided new target genes and epigenetic markers for mastitis resistance breeding in dairy cattle.
Comparative genomic analysis of the secondary flagellar (flag-2) system in the order Enterobacterales
Authors: De Maayer Pieter , Pillay Talia , Coutinho Teresa A. 
Published: January 2020

Abstract
Background
The order Enterobacterales encompasses a broad range of metabolically and ecologically versatile bacterial taxa, most of which are motile by means of peritrichous flagella. Flagellar biosynthesis has been linked to a primary flagella locus, flag-1, encompassing ~ 50 genes. A discrete locus, flag-2, encoding a distinct flagellar system, has been observed in a limited number of enterobacterial taxa, but its function remains largely uncharacterized.

Results
Comparative genomic analyses showed that orthologous flag-2 loci are present in 592/4028 taxa belonging to 5/8 and 31/76 families and genera, respectively, in the order Enterobacterales. Furthermore, the presence of only the outermost flag-2 genes in many taxa suggests that this locus was far more prevalent and has subsequently been lost through gene deletion events. The flag-2 loci range in size from ~ 3.4 to 81.1 kilobases and code for between five and 102 distinct proteins. The discrepancy in size and protein number can be attributed to the presence of cargo gene islands within the loci. Evolutionary analyses revealed a complex evolutionary history for the flag-2 loci, representing ancestral elements in some taxa, while showing evidence of recent horizontal acquisition in other enterobacteria.

Conclusions
The flag-2 flagellar system is a fairly common, but highly variable feature among members of the Enterobacterales. Given the energetic burden of flagellar biosynthesis and functioning, the prevalence of a second flagellar system suggests it plays important biological roles in the enterobacteria and we postulate on its potential role as locomotory organ or as secretion system.
A randomized double-blind comparison of the double-space technique versus the single-space technique in combined spinal-epidural anesthesia for cesarean section
Authors: Chun Eun Hee , Cho Sooyoung , Woo Jae Hee , Kim Youn Jin 
Published: January 2020

Abstract
Background
Combined spinal-epidural anesthesia (CSEA) can be performed with either a single-space technique or a double-space technique for cesarean section. We performed a double-blind randomized controlled study to compare the effect of the double-space technique with that of the single-space technique on sensory block level and side effects.

Methods
Parturients undergoing elective cesarean section under regional anesthesia were randomized to receive CSEA with either the double-space technique (double group, n = 20) or the single-space technique (single group, n = 20). In the double group, an epidural catheter was inserted at the L1–2 interspace, and dural puncture was performed at the L3–4 interspace. In the single group, the procedure was performed at the L3–4 interspace using the needle-through-needle technique.

Results
There were no differences in time to readiness or intraoperative level of sensory block between the two groups. The postoperative sensory level was maintained at a higher level in the double group than in the single group (1 h postoperatively, P = 0.029; 6 h postoperatively, P = 0.016). There was no difference between the two groups in terms of side effects. The parturient satisfaction scores 48 h postoperatively were significantly different between groups (9.5 in the double group vs. 8 in the single group, P = 0.004).

Conclusions
We conclude that there were no differences in intraoperative variables between the double-space technique and the single-space technique for CSEA. However, double-space CSEA for cesarean section may be beneficial for controlling postoperative pain and improving parturient satisfaction.

Trial registration
The study was retrospectively registered at https://cris.nih.go.kr under the trial ID KCT0002514. Date of registration: October 27, 2017.
A case report of sinoatrial arrest caused by temporal lobe epilepsy in subclinical glioblastoma
Authors: Reifart Jörg , Tschernatsch Marlene , Hamm Christian W. , Sperzel Johannes , Hain Andreas 
Published: January 2020

Abstract
Background
Atrial fibrillation with symptomatic bradycardia, higher grade atrioventricular block, and sinus node disease are all common indications for permanent pacemaker implantation. The most frequent causes of sinus node disease treated with pacemaker implantation involve degenerative structural changes of the sinus node; less often, extrinsic causes (such as damage due to myocardial infarction or heightened parasympathetic nervous system activity) lead to pacemaker implantation.

Case presentation
A 50-year-old patient with syncope and documented sinoatrial arrest was referred. Neurologic exams (including CT and EEG) revealed no pathologies, so a pacemaker was implanted. Postoperatively, syncope occurred again due to a focal seizure during which sinus rhythm transitioned to atrial pacing by the device. Further neurologic testing revealed focal epilepsy. Six months later, stage IV glioblastoma was diagnosed and the patient was treated surgically.

Conclusion
Intracerebral tumors should be considered in the differential diagnosis for patients with unexplained sinoatrial block, as well as in patients with repeat syncope after pacemaker implantation. Cranial MRI could aid the diagnostic workup of such cases.
Influencing factors of vascular endothelial function in patients with non-obstructive coronary atherosclerosis: a 1-year observational study
Authors: Li Yin-Ping , Fan Zhen-Xing , Gao Jing , Sun Xi-Peng , Zhu Guo-Hua , Zhang Ying-Hua , Si Jin , Zuo Xue-Bing , Liu Zhi , Hua Qi , Li Jing 
Published: January 2020

Abstract
Background
Endothelial dysfunction may play a key role in non-obstructive coronary artery atherosclerosis. Our study aimed to evaluate the vascular endothelial function and its influencing factors in patients with non-obstructive coronary artery atherosclerosis.

Methods
A total of 131 consecutive patients with non-obstructive coronary artery atherosclerosis were enrolled. Flow-mediated dilatation (FMD) was measured at baseline and 1-year follow-up. Endothelial progenitor cells (EPCs) were counted by staining the fasting venous blood with antibodies against CD34 and vascular endothelial growth factor receptor 2.

Results
Systolic blood pressure, pulse pressure and the levels of HbA1c in participants with baseline FMD < 6% (n = 65) were significantly higher than those with baseline FMD ≥ 6% (n = 66). Baseline FMD was negatively associated with EPC counts (r = − 0.199, P < 0.05) and systolic blood pressure (r = − 0.315, P < 0.01). The 1-year FMD was significantly increased compared to the baseline FMD [(9.31 ± 5.62) % vs (7.31 ± 5.26) %, P < 0.001]. Independent predictors of FMD improvement included elevated EPC counts (OR = 1.104, 95% CI: 1.047–1.165, P < 0.001) and decreased levels of serum creatinine (OR = 0.915, 95% CI: 0.843–0.993, P = 0.034).

Conclusions
Family history of premature cardiovascular diseases, hypertension, elevated systolic pressure, and HbA1c > 6.5% are independent risk factors for endothelial dysfunction in non-obstructive atherosclerotic patients. Elevated peripheral blood EPC counts and decreased levels of serum creatinine are independent predictors of endothelial function improvement.
Waterpipe smoking cessation: knowledge, barriers, and practices of primary care physicians- a questionnaire-based cross-sectional study
Authors: Romani Maya , Jawhar Sarah , Shalak Manar , Antoun Jumana 
Published: January 2020

Abstract
Background
While cigarette smoking has been considered the most relevant tobacco product worldwide, waterpipe tobacco smoking (WTS) has increased in prevalence globally and calls for more considerable attention now. However, little is known about WTS cessation knowledge and clinical practices among physicians, particularly in Lebanon. This study aims to examine the knowledge, barriers, and cessation practices of primary care practitioners towards WTS.

Methods
A cross-sectional study where an anonymous self-reported questionnaire was completed by physicians attending the Annual Conference of the Lebanese Society of Family Medicine for family medicine physicians, general practitioners, and internists in Lebanon.

Results
Out of 180 attendees, 105 primary care practitioners (PCPs) responded to the questionnaire. Only 38.1% of the physicians think similar techniques are used for the cessation of smoking of both cigarette and waterpipe. Similarly, 30.5% of the physicians believe that nicotine replacement therapy works in the cessation of waterpipe smoking. There was a statistically significant difference between the percentage of physicians who counsel for cigarette smoking and those who counsel for waterpipe smoking cessation (p = 0.005) where 30% of the physicians tend to counsel against cigarette smoking more than waterpipe smoking.

Conclusions
This study shows a difference in the attitude and behavior of PCPs towards cigarette and waterpipe smoking cessation. Moreover, there is a lack of knowledge about water pipe smoking cessation techniques. There is a great room for continued medical education to PCPs in their private practice to improve their knowledge.
High rates of cirrhosis and severe clinical events in patients with HBV/HDV co-infection: longitudinal analysis of a German cohort
Authors: Bockmann Jan-Hendrik , Grube Marcel , Hamed Vanessa , von Felden Johann , Landahl Johanna , Wehmeyer Malte , Giersch Katja , Hall Michaela T. , Murray John M. , Dandri Maura , Lüth Stefan , Lohse Ansgar W. , Lütgehetmann Marc , Schulze Zur Wiesch Julian 
Published: January 2020

Abstract
Background
Chronic hepatitis delta virus (HDV) infection causes severe liver disease which often leads to cirrhosis and hepatocellular carcinoma (HCC). Aim of this study was to establish the disease severity and prognostic factors for disease outcome by analysing frequencies of clinical events and their correlation with baseline virological and biochemical parameters as well as interferon and nucleos(t)ide analogue treatment choice.

Methods
We studied a single-centre cohort of 49 anti-HDAg-positive patients with HBsAg persistence for at least 6 months. Virological and biochemical parameters, interferon and nucleos(t)ide analogue treatment choice as well as clinical events during follow-up were analysed by retrospective chart review (mean follow-up time 3 years, range 0.25–7.67 years).

Results
Severe clinical events occurred in 11/49 hepatitis D patients, including HCC (8/49), death (8/49) or liver transplantation (2/49). HCCs only occurred secondary to liver cirrhosis and their event rates in this cohort of hepatitis D patients did not differ from a matched HBV mono-infected cohort with comparable frequency of liver cirrhosis. A stepwise multivariate logistic regression revealed low platelet count (p = 0. 0290) and older age (p = 0.0337) correlating most strongly with overall clinical events, while serum HDV RNA positivity at baseline did not correlate with any clinical outcome. Interferon-free but not nucleos(t)ide analogue-free patient care correlated with the occurrence of HCC at logistic regression, although only 3/18 interferon-treated patients demonstrated repeatedly negative HDV PCR results post therapy.

Conclusions
Our data indicate that progressive liver disease at baseline plays a major role as predictive factor for overall clinical outcome of hepatitis D patients. In particular, HCC risk may not be underestimated in hepatitis D virus RNA negative hepatitis D patients with advanced liver fibrosis.
Patient characteristics, clinical manifestations, prognosis, and factors associated with gastrointestinal cytomegalovirus infection in immunocompetent patients
Authors: Chaemsupaphan Thanaboon , Limsrivilai Julajak , Thongdee Chenchira , Sudcharoen Asawin , Pongpaibul Ananya , Pausawasdi Nonthalee , Charatcharoenwitthaya Phunchai 
Published: January 2020

AbstractBackgroundGastrointestinal (GI) cytomegaloviral (CMV) infection is common among patients with immunocompromised status; however, data specific to GI-CMV infection in immunocompetent patients are comparatively limited.MethodsThis retrospective study included patients diagnosed with GI-CMV infection at Siriraj Hospital (Bangkok, Thailand) during 2008–2017. Baseline characteristics, presentations, comorbid conditions, endoscopic findings, treatments, and outcomes were compared between immunocompetent and immunocompromised.ResultsOne hundred and seventy-three patients (56 immunocompetent, 117 immunocompromised) were included. Immunocompetent patients were significantly older than immunocompromised patients (73 vs. 48.6 years,p < 0.0001). Significantly more immunocompetent patients were in the ICU at the time of diagnosis (21.0% vs. 8.6%,p = 0.024). GI bleeding was the leading presentation in immunocompetent, while diarrhea and abdominal pain were more common in immunocompromised. Blood CMV viral load was negative in significantly more immunocompetent than immunocompromised (40.7% vs. 12.9%,p = 0.002). Ganciclovir was the main treatment in both groups. Significantly more immunocompetent than immunocompromised did not receive any specific therapy (25.5% vs. 4.4%,p ≤ 0.01). Six-month mortality was significantly higher among immunocompetent patients (39.0% vs. 22.0%,p = 0.047). Independent predictors of death were old age and inpatient or ICU clinical setting. Treatment with antiviral agents was the only independent protective factor.ConclusionGI-CMV infection was frequently observed among immunocompetent elderly patients with comorbidities or severe concomitant illnesses. GI bleeding was the most common presentation. Blood CMV viral load was not diagnostically helpful. Significantly higher mortality was observed in immunocompetent than in immunocompromised patients, but this could be due to more severe concomitant illnesses in the immunocompetent group.
Does Xpert® MTB/RIF assay give rifampicin resistance results without identified mutation? Review of cases from Addis Ababa, Ethiopia
Authors: Alemu Ayinalem , Tadesse Mengistu , Seid Getachew , Mollalign Helina , Eshetu Kirubel , Sinshaw Waganeh , Abebaw Yeshiwork , Amare Misikir , Dagne Biniyam , Diriba Getu , Yenew Bazezew , Getu Melak , Zerihun Betselot 
Published: January 2020

Abstract
Background
Xpert® MTB/RIF assay is currently used in Ethiopia for the rapid diagnosis of Mycobacterium tuberculosis (MTB) and mutations that confer Rifampicin resistance. Rifampicin resistance is determined based on any mutation in the 81 bp of rpoB gene using five overlapping probes represented as Probe A (codons 507–511), Probe B (codons 512–518), Probe C (codons 518–523), Probe D (codons 523–529) and Probe E (codons 529–533). In this review, we assessed the frequency of missed probe types for Rifampicin Resistance results.

Methods
Data were reviewed from specimens received and tested using Xpert® MTB/RIF assay at Ethiopian National Tuberculosis Reference Laboratory, in Addis Ababa from 15 July 2016 to 31 December 2018 retrospectively. All archived data were reviewed carefully to describe missed probe types and the quantity of DNA in the sample.

Results
A total of 100 specimens were reported as MTB Detected Rifampicin Resistance Detected by Xpert® MTB/RIF assay. More than half (55%) of these results were reported from male patients. The median age was 28.0 years (5 months to 88 years). Majorities (62%) of the cases were detected from sputum. Among the total of 38 extrapulmonary samples, lymph node aspirates were accounted for 50% (19/38). The most common mutations (81.0%) were found in the Probe E region followed by Probe D (10.0%), and Probe B (3.0%). Mutations in Probe A and Probe C regions were not observed. However, six (6.0%) Rifampicin resistance cases were found without any missed probe type. The delta Ct max is ≥4.3. No specimen yielded Rifampicin resistance associated with more than one probe failure or mutation combinations.

Conclusion
Mutations associated with Probe E (codons 529–533) region were identified as the commonest rpoB gene mutations. The Rifampicin resistance results found without any identified missing probe needs further study. The lower DNA amount was observed in extrapulmonary specimens compared with sputum.
Preliminary application of 3.0 T magnetic resonance chemical exchange saturation transfer imaging in brain metastasis of lung cancer
Authors: Yang Yonggui , Qu Xiaobo , Huang Yihui , Afsar Khan , Yan Gen , Guo Gang , Duan Shaoyin 
Published: February 2020

Abstract
Background
Lung cancer brain metastases are very common and one of the common causes of treatment failure. We aimed to examine the clinical use of chemical exchange saturation transfer (CEST) technology in the evaluation of brain metastases for lung cancer diagnosis and prognosis.

Methods
We included26 cases of lung cancer brain metastases, 15 cases of gliomas, and 20 cases with normal tests. The magnetization transfer ratio (MTR;3.5 ppm) image from the GRE-EPI-CEST sequence was analyzed using the ASSET technique and APT technology. The MTR values were measured in the lesion-parenchymal, edema, and non-focus regions, and the MTR image was compared with the conventional MRI. ANOVA and t-test were used for statistical analysis.

Results
The lesion-parenchymal, edema, and non-focus areas in the metastatic-tumor-group were red-yellow, yellow-green, and green-blue, and the MTR values were 3.29 ± 1.14%,1.28 ± 0.36%,and 1.26 ± 0.31%, respectively. However, in the glioma-group, the corresponding areas were red, red-yellow, and green-blue, and the MTR values were 6.29 ± 1.58%, 2.87 ± 0.65%, and 1.03 ± 0.30%, respectively. The MTR values of the corresponding areas in the normal-group were 1.07 ± 0.22%,1.04 ± 0.23%, and 1.06 ± 0.24%, respectively. Traditional MR images are in black-white contrast and no metabolic information is displayed.
The MTRvalues of the three regions were significantly different among the three groups. The values were also significantly different between the parenchymal and edema areas in the metastatic-tumor-group. There were significant differences in the MTR values between the non-lesion and edema regions, but there was no significant difference between the edema and non-focus areas. In the glioma-group, there were significant differences in the MTR values between the parenchymal and edema areas, between the parenchymal and non-focus areas, and between the edema and non-focus areas.

Conclusions
CEST reflects the protein metabolism; therefore, early diagnosis of brain metastases and assessment of the prognosis can be achieved using molecular imaging.
Incidence, predictors and prognosis of acute kidney injury in nonagenarians: an in-hospital cohort study
Authors: Sousa Andre Luis Bastos , de Souza Leticia Mascarenhas , Santana Filho Osvaldino Vieira , e Léda Victor Hugo Ferreira , Rocha Paulo Novis 
Published: January 2020

AbstractBackgroundGiven the aging of the population, nephrologists are ever more frequently assisting nonagenarians with acute kidney injury (AKI). The management of these patients presents unique characteristics, including bioethical dilemmas, such as the utilization of renal replacement therapy (RRT) at this extreme age.MethodsWe conducted a retrospective cohort study at a tertiary hospital. Over a 10-year period, 832 nonagenarians were hospitalized for two or more days. A random sample of 461 patients was obtained; 25 subjects were excluded due to lack of essential data. AKI was defined and staged according to the Kidney Disease Improving Global Outcomes (KDIGO) criteria.ResultsWe analyzed data from 436 patients, mean age 93.5 ± 3.3 years, 74.3% female; 76.4% required intensive care unit (ICU). The incidence of AKI was 45%. Length of hospital stay, ICU admission, vasopressors, and mechanical ventilation (MV) were independent predictors of AKI. Overall in-hospital mortality was 43.1%. Mortality was higher in the AKI compared to the no AKI group (66.8% vs. 23.8%,p < 0.001). Only 13 patients underwent RRT; all were critically ill, requiring vasopressors and 76.9% in MV. Mortality for this RRT group was 100% but not significantly higher than that observed in 26 non-RRT controls (96.1%,p = 1.0) obtained by proportional random sampling, matched by variables related to illness severity. In multivariable analysis, age, Charlson’s score, vasopressors, MV, and AKI – but not RRT – were independent predictors of mortality.ConclusionsAKI is common in hospitalized nonagenarians and carries a grave prognosis, especially in those who are critically iil. The use of RRT was not able to change the fatal prognosis of this subgroup of patients. Our data may help guide informed decisions about the utility of RRT in this scenario.