bluuebunny/crossref_metadata_2025_split huggingface dataset:
Associations between echocardiographic manifestations and bacterial species in patients with infective endocarditis: a cohort study
Authors: Damlin A. , Westling K. , Maret E. , Stålsby Lundborg C. , Caidahl K. , Eriksson M. J. 
Published: December 2019

Abstract
Background
The diagnosis of infective endocarditis (IE) is based on microbiological analyses and diagnostic imaging of cardiac manifestations. Echocardiography (ECHO) is preferred for visualization of IE-induced cardiac manifestations. We investigated associations between bacterial infections and IE manifestations diagnosed by ECHO.

Methods
In this cohort study, data from patients aged 18 years or above, with definite IE admitted at the Karolinska University Hospital between 2008 and 2017 were obtained from Swedish National Registry of Endocarditis. Bacteria registered as pathogen were primarily selected from positive blood culture and for patients with negative blood culture, bacteria found in culture or PCR from postoperative material was registered as pathogen. Patients with negative results from culture or PCR, and patients who did not undergo ECHO during hospital stay, were excluded. IE manifestations diagnosed by ECHO were obtained from the registry. Chi-squared test and two-sided Fisher’s exact test was used for comparisons between categorical variables, and student’s t test was used for continuous numerical variables. Multivariable analyses were performed using logistic regression. Secular trend analyses were performed using linear regression. Associations and the strength between the variables were estimated using odds ratios (ORs) with 95% confidence intervals (CIs). P < 0.05 was considered significant.

Results
The most common bacteria were Staphylococcus aureus (n = 239, 49%) and viridans group streptococci (n = 102, 21%). The most common manifestations were vegetation in the mitral (n = 195, 40%), aortic (n = 190, 39%), and tricuspid valves (n = 108, 22%). Associations were seen between aortic valve vegetations and Enterococcus faecalis among patients with native aortic valves, between mitral valve vegetations and streptococci of group B or viridans group, between tricuspid valve vegetations and S. aureus among patients with intravenous drug abuse, and between perivalvular abscesses as well as cardiovascular implantable electronic device (CIED)-associated IE and coagulase negative staphylococci (all P < 0.05).

Conclusions
Associations were found between certain bacterial species and specific ECHO manifestations. Our study contributes to a better understanding of IE manifestations and their underlying bacterial etiology, which pathogens can cause severe infections and might require close follow-up and surgical treatment.
Perceived barriers and enablers for preventing the spread of carbapenem producing gram-negative bacteria during patient transfers: a mixed methods study among healthcare providers
Authors: van Dulm Eline , van der Veldt Wendy , der Meiden Katja Jansen-van , van Renselaar Gerry , Bovée Lian , Ros Jeanette , Davidovich Udi , van Duijnhoven Yvonne 
Published: December 2019

AbstractBackgroundAntimicrobial resistance (AMR) increasingly threatens public health. Carbapenem-producing gram-negative bacteria (CPB) pose the biggest threat. The risk for CPB spread is heightened during the transfer of a CPB-positive patient between different healthcare institutions or healthcare providers. We aimed to gain insight into the frequency of CPB-positive patients in the Dutch provinces of Noord-Holland (NH) and Flevoland (FL). Secondly, we aimed to obtain a deeper understanding of the communication between healthcare providers during transfers of CPB-positive patients and explore possible communication-related risk situations for CPB spread.MethodsThis mixed-methods study consisted of a quantitative and qualitative section. For the quantitative section, 14 laboratories that provide diagnostics in NH and FL voluntarily reported carbapenem-producingEnterobacteriaceae(CPE) positive patients between February 2018 and February 2019. Additionally, two laboratories reported carbapenem-resistantAcinetobacter spp.(CRA) and carbapenem-resistantPseudomonas aeruginosa(CRP) positive patients. For the qualitative section, healthcare providers of reported patients were interviewed about information exchange during patient transfers, precautionary measures and knowledge and beliefs concerning CPB.ResultsIn total, 50 CPE-positive, 10 CRA-positive and 4 CRP-positive patients were reported during the inclusion period. Eighteen index-specific and 2 general interviews were conducted with 20 different care providers of 9 patients. The interviews revealed that, in most cases, information concerning the patient was transferred timely, but often a standardized method for sharing the information within and between institutions was lacking. Factors that enhanced care providers’ motivation to adhere to precautionary measures were taking responsibility for the health of other patients, (pregnant) colleagues and for ones own health. Factors that reduced motivation were not acknowledging the relevance of the precautionary measures, a perceived negative impact of the measures on patients’ recovery, differences in precautionary measures between healthcare settings and incomprehension for changes in precautionary measures.ConclusionsCPB-positivity occurred more frequently than expected in the Dutch provinces of NH and FL. Standardizing the transference of information concerning CPB-positive patients, implementing transmural agreements, training personnel on CPB knowledge and procedures, launching a national website on CPB and assigning one or several designated employees for CPB within healthcare institutions could improve communication between healthcare providers and thereby decrease the risk of CPB transmission.
Tuberculosis treatment outcomes among people living with HIV diagnosed using Xpert MTB/RIF versus sputum-smear microscopy in Botswana: a stepped-wedge cluster randomised trial
Authors: Agizew Tefera , Chihota Violet , Nyirenda Sambayawo , Tedla Zegabriel , Auld Andrew F. , Mathebula Unami , Mathoma Anikie , Boyd Rosanna , Date Anand , Pals Sherri L. , Lekone Phenyo , Finlay Alyssa 
Published: December 2019

Abstract
Background
Xpert® MTB/RIF (Xpert) has high sensitivity for diagnosing tuberculosis (TB) compared to sputum-smear microscopy (smear) and can reduce time-to-diagnosis, time-to-treatment and potentially unfavorable patient-level treatment outcome.

Methods
People living with HIV (PLHIV) initiating antiretroviral therapy at 22 HIV clinics were enrolled and underwent systematic screening for TB (August 2012–November 2014). GeneXpert instruments were deployed following a stepped-wedge design at 13 centers from October 2012–June 2013. Treatment outcomes classified as an unfavorable outcome (died, treatment failure or loss-to-follow-up) or favorable outcome (cured and treatment completed). To determine outcome, smear was performed at month 5 or 6. Empiric treatment was defined as initiating treatment without/before receiving TB-positive results. Adjusting for intra-facility correlation, we compared patient-level treatment outcomes between patients screened using smear (smear arm)- and Xpert-based algorithms (Xpert arm).

Results
Among 6041 patients enrolled (smear arm, 1816; Xpert arm, 4225), 256 (199 per 2985 and 57 per 1582 person-years of follow-up in Xpert and smear arms, respectively; adjusted incidence rate ratio, 9.07; 95% confidence interval [CI]: 4.70–17.48; p < 0.001) received TB diagnosis and were treated. TB treatment outcomes were available for 203 patients (79.3%; Xpert, 157; smear, 46). Unfavorable outcomes were reported for 21.7% (10/46) in the smear and 13.4% (21/157) in Xpert arm (adjusted hazard ratio, 1.40; 95% CI: 0.75–2.26; p = 0.268). Compared to smear, in Xpert arm median days from sputum collection to TB treatment was 6 days (interquartile range [IQR] 2–17 versus 22 days [IQR] 3–51), p = 0.005; patients with available sputum test result had microbiologically confirmed TB in 59.0% (102/173) versus 41.9% (18/43), adjusted Odds Ratio [aOR], 2.00, 95% CI: 1.01–3.96, p = 0.048). In smear arm empiric treatment was 68.4% (39/57) versus 48.7% (97/199), aOR, 2.28, 95% CI: 1.24–4.20, p = 0.011), compared to Xpert arm.

Conclusions
TB treatment outcomes were similar between the smear and Xpert arms. However, compared to the smear arm, more patients in the Xpert arm received a TB diagnosis, had a microbiologically confirmed TB, and had a shorter time-to-treatment, and had a lower empiric treatment. Further research is recommended to identify potential gaps in the Botswana health system and similar settings.

Trial registration
ClinicalTrials.gov Identifier: NCT02538952. Retrospectively registered on 2 September 2015.
LRCH1 polymorphisms linked to delayed encephalopathy after acute carbon monoxide poisoning identified by GWAS analysis followed by Sequenom MassARRAY® validation
Authors: Gu Jiapeng , Zeng Jiao , Wang Xi , Gu Xin , Zhang Xiaoli , Zhang Ping , Zhang Fan , Han Yongkai , Han Yazhou , Zhang Hongxing , Li Wenqiang , Gu Renjun 
Published: December 2019

Abstract
Background
We explored the association of leucine-rich repeats and calponin homology domain containing 1 (LRCH1) gene polymorphisms with genetic susceptibility to delayed encephalopathy after acute carbon monoxide poisoning (DEACMP), which might provide a theoretical basis for the pathogenesis, diagnosis, and prognosis research of DEACMP.

Methods
Four single nucleotide polymorphisms, rs1539177 (G/A), rs17068697 (G/A), rs9534475 (A/C), and rs2236592 (T/C), of LRCH1, selected as candidate genes through genome-wide association analysis, were genotyped in 661 patients (DEACMP group: 235 cases; ACMP group: 426 cases) using Sequenom Massarray®. The association analysis of four SNPs and LRCH1 was performed under different genetic models.

Results
LRCH1 polymorphisms (rs1539177, rs17068697, rs9534475) under additive and dominant genetic models were significantly associated with an increased risk of DEACMP, but no significant association under allele and recessive models was found. The LRCH1 rs2236592 polymorphism was susceptible to DEACMP only under the dominant model (TT/TC + CC, OR = 1.616, 95% CI: 1.092–2.390, P = 0.015784). In addition, the A allele gene of rs9534475 polymorphism in LRCH1 might increase the risk for DEACMP (OR = 1.273, 95% CI: 1.013–1.601, P = 0.038445).

Conclusions
We found a significant association between the four LRCH1 polymorphisms and DEACMP. The allelic A of rs9534475 polymorphism in LRCH1 might be a risk factor for DEACMP.
Epidemiology of acute kidney injury in intensive care units in Beijing: the multi-center BAKIT study
Authors:   The Beijing Acute Kidney Injury Trial (BAKIT) workgroup, Jiang Li , Zhu Yibing , Luo Xuying , Wen Ying , Du Bin , Wang Meiping , Zhao Zhen , Yin Yanyan , Zhu Bo , Xi Xiuming 
Published: December 2019

AbstractBackgroundAcute kidney injury (AKI) commonly occurs in intensive care units (ICUs), leading to adverse clinical outcomes and increasing costs. However, there are limited epidemiological data of AKI in the critically ill in Beijing, China.MethodsIn this prospective cohort study in 30 ICUs, we screened the patients up to 10 days after ICU admission. Characteristics and outcomes were compared between AKI and non-AKI, renal replacement therapy (RRT) and non-RRT patients. Nomograms of logistic regression and Cox regression were performed to examine potential risk factors for AKI and mortality.ResultsA total of 3107 patients were included in the final analysis. The incidence of AKI was 51.0%; stages 1 to 3 accounted for 23.1, 11.8, and 15.7%, respectively. The majority (87.6%) of patients with AKI developed AKI on the first 4 days after admission to the ICU. A total of 281 patients were treated with RRT. Continuous RRT with predilution, citrate for anticoagulation and femoral vein for vascular access was the most common RRT pattern (29.9%, 84 of 281). Patients with AKI were associated with longer ICU-LOS and higher mortality and costs (P<0.001). In patients treated with RRT, 78.6 and 28.5% of RRTs were dependent on the 7th and 28th days, respectively. The 28 day mortalities of non-AKI, AKI stages 1–3, and septic shock patients were 6.83, 15.04, 27.99, 45.18 and 36.5%, respectively.ConclusionsApproximately half of our ICU patients experienced AKI. The majority of patients with AKI developed AKI during the first 4 days after admission to the ICU. Continuous RRT with predilution, citrate for anticoagulation and femoral vein for vascular access was the most common RRT pattern in our ICUs. AKI was associated with a higher mortality and costs, incomplete kidney recovery and s series of adverse outcomes.
Delayed diagnosis of X-linked agammaglobulinaemia in a boy with recurrent meningitis
Authors: Zhang Ya-Ni , Gao Yuan-Yuan , Yang Si-Da , Cao Bin-Bin , Zheng Ke-Lu , Wei Ping , Chen Lian-Feng , Chen Wen-Xiong 
Published: December 2019

Abstract
Background
X-linked agammaglobulinaemia (XLA) is a rare inherited primary immunodeficiency disease characterized by the B cell developmental defect, caused by mutations in the gene coding for Bruton’s tyrosine kinase (BTK), which may cause serious recurrent infections. The diagnosis of XLA is sometimes challenging because a few number of patients have higher levels of serum immunoglobulins than expected. In this study, we reported an atypical case with recurrent meningitis, delayed diagnosis with XLA by genetic analysis at the second episode of meningitis at the age of 8 years.

Case report
An 8-year-old Chinese boy presented with fever, dizziness and recurrent vomiting for 3 days. The cerebrospinal fluid (CSF) and magnetic resonance imaging (MRI) results were suggestive of bacterial meningoencephalitis, despite the negative gram staining and cultures of the CSF. The patient was treated with broad-spectrum antibiotics and responded well to the treatment. He had history of another episode of acute pneumococci meningitis 4 years before. The respective level of Immunoglobulin G (IgG), Immunoglobulin A (IgA) and Immunoglobulin M (IgM) was 4.85 g/L, 0.93 g/L and 0.1 g/L at 1st episode, whereas 1.9 g/L, 0.27 g/L and 0 g/L at second episode. The B lymphocytes were 0.21 and 0.06% of peripheral blood lymphocytes at first and second episode respectively. Sequencing of the BTK coding regions showed that the patient had a point mutation in the intron 14, hemizyous c.1349 + 5G > A, while his mother had a heterozygous mutation. It was a splice site mutation predicted to lead to exon skipping and cause a truncated BTK protein.

Conclusion
Immunity function should be routinely checked in patients with severe intracranial bacterial infection. Absence of B cells even with normal level of serum immunoglobulin suggests the possibility of XLA, although this happens only in rare instances. Mutational analysis of BTK gene is crucial for accurate diagnosis to atypical patients with XLA.
Trends in maternal use of snus and smoking tobacco in pregnancy. A register study in southern Norway
Authors: Rygh Ellen , Gallefoss Frode , Grøtvedt Liv 
Published: December 2019

Abstract
Background
The use of tobacco products including Swedish snus (moist snuff) in pregnancy may cause adverse health outcomes. While smoking prevalence has decreased among fertile women in Norway, snus use has increased during the last years. We investigated whether these trends were reflected also during pregnancy in a population of women in Southern Norway.

Methods
Data on smoking tobacco and snus use at three time points before and during pregnancy for 20,844 women were retrieved from the electronic birth record for the years 2012–2017. The results for the three-year period 2015–2017 were compared with a previously studied period 2012–2014. Prevalence and quit rates of tobacco use within groups of age, parity and education were reported. Within the same groups adjusted quit rates were analyzed using logistic regression. Mean birthweight and Apgar score of offspring were calculated for tobacco-users and non-users.

Results
There was an increase of snus use before pregnancy from the period 2012–2014 to the period 2015–2017 from 5.1% (CI; 4.6 to 5.5) to 8.4% (CI; 7.8 to 8.9). Despite this, the use of snus during pregnancy did not increase from the first to the second period, but stabilized at 2.8% (CI; 2.5 to 3.2) in first trimester and 2.0% (CI; 1.7 to 2.2) in third trimester. Cigarette smoking decreased significantly both before and during pregnancy. Snus use and smoking during pregnancy were associated with a reduction in average birthweight, but no significant effects on Apgar scores. Odds ratios for quitting both snus and smoking tobacco during pregnancy were higher for women aged 25–34 years, for the primiparas and for those with a high level of education. Pregnant women were more likely to have quit tobacco use in the last time period compared to the first.

Conclusions
While smoking during pregnancy was decreasing, the use of snus remained constant, levelling off to around 3% in first trimester and 2% in third trimester. Approximately 25% of those that used snus, and 40% that smoked before pregnancy, continued use to the third trimester. This calls for a continuous watch on the use of snus and other nicotine products during pregnancy.
Clonal relationship of synchronous head and neck cancer and esophageal cancer assessed by single nucleotide polymorphism-based loss of heterozygosity analysis
Authors: Sunpaweravong Somkiat , Bunbanjerdsuk Sacarin , Pongrujikorn Tanjitti , Naktang Chaiwat , Sunpaweravong Patrapim , Nitiruangjaras Anupong , Dechaphankul Tanadech , Jinawath Natini 
Published: December 2019

Abstract
Background
The prognoses of head and neck squamous cell carcinoma (HNSCC) and esophageal squamous cell carcinoma (ESCC) are poor, especially when both tumors occur at the same time. We examined the clonal relatedness of HNSCCs with synchronous ESCCs to confirm whether the second tumors were metastasis or separate second primary malignancies (SPMs) using loss of heterozygosity (LOH) analysis.

Methods
Twenty-one pairs of formalin-fixed paraffin-embedded tissue from HNSCC patients with synchronous esophageal cancer were analyzed by single nucleotide polymorphism (SNP) array using the Illumina HumanCytoSNP FFPE-12 BeadChip (San Diego, CA), which contains approximately 300,000 probes. LOH was identified using Nexus Copy Number software (El Segundo, CA).

Results
Comparing the LOH pattern between HNSCC and paired ESCC, we found that 20 out of 21 paired tissues had a high number of discordant LOHs (LOH identified solely in the primary HNSCC but not in synchronous ESCC at the same genomic location) and a low number of concordant LOHs (LOH at the same genomic location in both HNSCC and ESCC). Only one case fell into the undetermined category. Therefore, these 20 ESCCs were classified as SPMs or second field tumors (SFTs). Moreover, the HNSCC patients with molecularly confirmed esophageal SPM had significantly poorer survival than the other patients.

Conclusions
We propose the use of a genome-wide SNP array as a tool to differentiate metastatic tumors from SPM/SFT. The SNP array offers genome-wide LOH information that earlier microsatellite analysis studies lack. The ability to accurately identify SPM should contribute to a better treatment plan and follow-up care of these patients.
Dickkopf-related protein 1, a new biomarker for local immune status and poor prognosis among patients with colorectal liver Oligometastases: a retrospective study
Authors: Sui Qiaoqi , Zheng Jian , Liu Dingxin , Peng Jianhong , Ou Qingjian , Tang Jinghua , Li Yuan , Kong Lingheng , Jiang Wu , Xiao Binyi , Chao Xue , Pan Zhizhong , Zhang Huizhong , Ding Pei-Rong 
Published: December 2019

Abstract
Background
It was reported that tumor-expressed dickkopf-related (DKK) proteins affect micro-environment. However, the influence of DKK1 on colorectal cancer (CRC) liver oligometastases (CRCLOM) remains unclear.

Methods
CRC cases after resection of liver oligometastases were enrolled in Sun Yat-Sen University Cancer Center with intact clinical data. Serum DKK1 was detected by ELISA assay. Immunofluorescent staining examination for CD3 and CD8 in slices were also conducted.

Results
Among 65 patients included, the recurrence-free survival (RFS) and overall survival (OS) were significantly better in the low serum DKK1 group (RFS: P = 0.021; OS: P = 0.043). DKK1 was overexpressed in stage IV CRC patients in TCGA data. The number of CD8+ tumor-infiltrating lymphocytes (TILs) in invasive margin of CRC liver oligometastases was significantly higher in low serum DKK1 group (P = 0.042).

Conclusion
Elevated serum DKK1 level was associated with poorer RFS and OS, and less CD8+ TILs in invasive margin in CRC liver oligometastases. DKK1 might serve as a supplementalprognostic factor for clinical risk score and a potential target for immunotherapy.
ROS as a novel indicator to predict anticancer drug efficacy
Authors: Zaidieh Tarek , Smith James R. , Ball Karen E. , An Qian 
Published: December 2019

Abstract
Background
Mitochondria are considered a primary intracellular site of reactive oxygen species (ROS) generation. Generally, cancer cells with mitochondrial genetic abnormalities (copy number change and mutations) have escalated ROS levels compared to normal cells. Since high levels of ROS can trigger apoptosis, treating cancer cells with low doses of mitochondria-targeting / ROS-stimulating agents may offer cancer-specific therapy. This study aimed to investigate how baseline ROS levels might influence cancer cells’ response to ROS-stimulating therapy.

Methods
Four cancer and one normal cell lines were treated with a conventional drug (cisplatin) and a mitochondria-targeting agent (dequalinium chloride hydrate) separately and jointly. Cell viability was assessed and drug combination synergisms were indicated by the combination index (CI). Mitochondrial DNA copy number (mtDNAcn), ROS and mitochondrial membrane potential (MMP) were measured, and the relative expression levels of the genes and proteins involved in ROS-mediated apoptosis pathways were also investigated.

Results
Our data showed a correlation between the baseline ROS level, mtDNAcn and drug sensitivity in the tested cells. Synergistic effect of both drugs was also observed with ROS being the key contributor in cell death.

Conclusions
Our findings suggest that mitochondria-targeting therapy could be more effective compared to conventional treatments. In addition, cancer cells with low levels of ROS may be more sensitive to the treatment, while cells with high levels of ROS may be more resistant. Doubtlessly, further studies employing a wider range of cell lines and in vivo experiments are needed to validate our results. However, this study provides an insight into understanding the influence of intracellular ROS on drug sensitivity, and may lead to the development of new therapeutic strategies to improve efficacy of anticancer therapy.