bluuebunny/crossref_metadata_2025_split huggingface dataset:
Prevalence of fluoroquinolone resistance and mutations in the gyrA, parC and parE genes of Riemerella anatipestifer isolated from ducks in China
Authors: Zhu Dekang , Zheng Mingyu , Xu Jinge , Wang Mingshu , Jia Renyong , Chen Shun , Liu Mafeng , Zhao Xinxin , Yang Qiao , Wu Ying , Zhang Shaqiu , Huang Juan , Liu Yunya , Zhang Ling , Yu Yanling , Pan Leichang , Chen Xiaoyue , Cheng Anchun 
Published: December 2019

Abstract
Background
Riemerella anatipestifer is one of the most serious infectious disease-causing pathogens in the duck industry. Drug administration is an important method for prevention and treatment of infection in duck production, leading to widespread drug resistance in R. anatipestifer.

Methods
For a total of 162 isolates of R. anatipestifer, the MICs were determined for a quinolone antimicrobial agent, namely, nalidixic acid, and three fluoroquinolones, namely, ciprofloxacin, enrofloxacin and ofloxacin. The gyrA, parC, and parE gene fragments were amplified by PCR to identify the mutation sites in these strains. Site-directed mutants with mutations that were detected at a high frequency in vivo were constructed (hereafter referred to as site-directed in vivo mutants), and the MICs of these four drugs for these strains were determined.

Results
In total, 100, 97.8, 99.3 and 97.8% of the 137 R. anatipestifer strains isolated between 2013 and 2018 showed resistance to nalidixic acid, ciprofloxacin, enrofloxacin, and ofloxacin, respectively. The high-frequency mutation sites were detected in a total of 162 R. anatipestifer strains, such as Ser83Ile and Ser83Arg, which are two types of substitution mutations of amino acid 83 in GyrA; Val799Ala and Ile811Val in ParC; and Val357Ile, His358Tyr, and Arg541Lys in ParE. MIC analysis results for the site-directed in vivo mutants showed that the strains with only the Ser83Ile mutation in GyrA exhibited an 8–16-fold increase in MIC values, and all mutants showed resistance to ampicillin and ceftiofur.

Conclusions
The resistance of R. anatipestifer to quinolone agents is a serious problem. Amino acid 83 in GyrA is the major target mutation site for the fluoroquinolone resistance mechanism of R. anatipestifer.
QTL identification for seed weight and size based on a high-density SLAF-seq genetic map in peanut (Arachis hypogaea L.)
Authors: Zhang Shengzhong , Hu Xiaohui , Miao Huarong , Chu Ye , Cui Fenggao , Yang Weiqiang , Wang Chunming , Shen Yi , Xu Tingting , Zhao Libo , Zhang Jiancheng , Chen Jing 
Published: December 2019

Abstract
Background
The cultivated peanut is an important oil and cash crop grown worldwide. To meet the growing demand for peanut production each year, genetic studies and enhanced selection efficiency are essential, including linkage mapping, genome-wide association study, bulked-segregant analysis and marker-assisted selection. Specific locus amplified fragment sequencing (SLAF-seq) is a powerful tool for high density genetic map (HDGM) construction and quantitative trait loci (QTLs) mapping. In this study, a HDGM was constructed using SLAF-seq leading to identification of QTL for seed weight and size in peanut.

Results
A recombinant inbred line (RIL) population was advanced from a cross between a cultivar ‘Huayu36’ and a germplasm line ‘6–13’ with contrasting seed weight, size and shape. Based on the cultivated peanut genome, a HDGM was constructed with 3866 loci consisting of SLAF-seq and simple sequence repeat (SSR) markers distributed on 20 linkage groups (LGs) covering a total map distance of 1266.87 cM. Phenotypic data of four seed related traits were obtained in four environments, which mostly displayed normal distribution with varied levels of correlation. A total of 27 QTLs for 100 seed weight (100SW), seed length (SL), seed width (SW) and length to width ratio (L/W) were identified on 8 chromosomes, with LOD values of 3.16–31.55 and explaining phenotypic variance (PVE) from 0.74 to 83.23%. Two stable QTL regions were identified on chromosomes 2 and 16, and gene content within these regions provided valuable information for further functional analysis of yield component traits.

Conclusions
This study represents a new HDGM based on the cultivated peanut genome using SLAF-seq and SSRs. QTL mapping of four seed related traits revealed two stable QTL regions on chromosomes 2 and 16, which not only facilitate fine mapping and cloning these genes, but also provide opportunity for molecular breeding of new peanut cultivars with improved seed weight and size.
Emergent airway management outside of the operating room – a retrospective review of patient characteristics, complications and ICU stay
Authors: Yoon Uzung , Mojica Jeffrey , Wiltshire Matthew , Segna Kara , Block Michael , Pantoja Anthony , Torjman Marc , Wolo Elizabeth 
Published: December 2019

Abstract
Background
Emergent airway management outside of the operating room is a high-risk procedure. Limited data exists about the indication and physiologic state of the patient at the time of intubation, the location in which it occurs, or patient outcomes afterward.

Methods
We retrospectively collected data on all emergent airway management interventions performed outside of the operating room over a 6-month period. Documentation included intubation performance, and intubation related complications and mortality. Additional information including demographics, ASA-classification, comorbidities, hospital-stay, ICU-stay, and 30-day in-hospital mortality was obtained.

Results
336 intubations were performed in 275 patients during the six-month period. The majority of intubations (n = 196, 58%) occurred in an ICU setting, and the rest 140 (42%) occurred on a normal floor or in a remote location. The mean admission ASA status was 3.6 ± 0.5, age 60 ± 16 years, and BMI 30 ± 9 kg/m2. Chest X-rays performed immediately after intubation showed main stem intubation in 3.3% (n = 9). Two immediate (within 20 min after intubation) intubation related cardiac arrest/mortality events were identified. The 30-day in-hospital mortality was 31.6% (n = 87), the overall in-hospital mortality was 37.1% (n = 102), the mean hospital stay was 22 ± 20 days, and the mean ICU-stay was 14 days (13.9 ± 0.9, CI 12.1–15.8) with a 7.3% ICU-readmission rate.

Conclusion
Patients requiring emergent airway management are a high-risk patient population with multiple comorbidities and high ASA scores on admission. Only a small number of intubation-related complications were reported but ICU length of stay was high.
A comparison of methods to estimate the survivor average causal effect in the presence of missing data: a simulation study
Authors: McGuinness Myra B. , Kasza Jessica , Karahalios Amalia , Guymer Robyn H. , Finger Robert P. , Simpson Julie A. 
Published: December 2019

Abstract
Background
Attrition due to death and non-attendance are common sources of bias in studies of age-related diseases. A simulation study is presented to compare two methods for estimating the survivor average causal effect (SACE) of a binary exposure (sex-specific dietary iron intake) on a binary outcome (age-related macular degeneration, AMD) in this setting.

Methods
A dataset of 10,000 participants was simulated 1200 times under each scenario with outcome data missing dependent on measured and unmeasured covariates and survival. Scenarios differed by the magnitude and direction of effect of an unmeasured confounder on both survival and the outcome, and whether participants who died following a protective exposure would also die if they had not received the exposure (validity of the monotonicity assumption). The performance of a marginal structural model (MSM, weighting for exposure, survival and missing data) was compared to a sensitivity approach for estimating the SACE. As an illustrative example, the SACE of iron intake on AMD was estimated using data from 39,918 participants of the Melbourne Collaborative Cohort Study.

Results
The MSM approach tended to underestimate the true magnitude of effect when the unmeasured confounder had opposing directions of effect on survival and the outcome. Overestimation was observed when the unmeasured confounder had the same direction of effect on survival and the outcome. Violation of the monotonicity assumption did not increase bias. The estimates were similar between the MSM approach and the sensitivity approach assessed at the sensitivity parameter of 1 (assuming no survival bias). In the illustrative example, high iron intake was found to be protective of AMD (adjusted OR 0.57, 95% CI 0.40–0.82) using complete case analysis via traditional logistic regression. The adjusted SACE odds ratio did not differ substantially from the complete case estimate, ranging from 0.54 to 0.58 for each of the SACE methods.

Conclusions
On average, MSMs with weighting for exposure, missing data and survival produced biased estimates of the SACE in the presence of an unmeasured survival-outcome confounder. The direction and magnitude of effect of unmeasured survival-outcome confounders should be considered when assessing exposure-outcome associations in the presence of attrition due to death.
Patient involvement in assessing consultation quality: validation of patient enablement instrument (PEI) in Lithuanian general practice
Authors: Skarbalienė Aelita , Jurgutis Arnoldas , Strandberg Eva Lena , Pawlikowska Teresa 
Published: December 2019

Abstract
Background
The Patient Enablement Instrument (PEI) was designed to encapsulate consultation outcome from the perspective that increasing their understanding and coping ability would underpin a positive consultation outcome for patients. The objective of the study was the validation of the PEI in Lithuanian general practice and comparison of Lithuanian patients’ enablement with previous studies in Europe to see if factors associated with patient enablement in Lithuania were reflective of those in the previous studies.

Methods
The Patient Enablement Instrument was translated into Lithuanian and included in the questionnaire along with the questions about a person’s health, reasons for visiting the doctor and feeling about the consultation. Practices from 4 different municipalities that are situated in different geographical regions which have both town and rural areas were sampled randomly. Patients scheduled consecutively aged 18 years or more were the subjects of the study. The data analyses focused on internal reliability and concept validity.

Results
The overall mean patient enablement score was 6.43. Enablement scores declined with increasing patient age, and female patients were more enabled. Patients with biomedical problems had the highest enablement results, while patients with complex problems had the lower results. Enablement was positively related to receiving a prescription and knowing a doctor, and negatively related to wish having consultation with another doctor.

Conclusions
This study substantiates the rationality of using PEI in assessing primary care consultations in Lithuania. The correlations of enablement largely reflect the situation in Western and Central Europe: longer consultation and access to the same physician increases patient enablement.
Different imaging patterns of PCNSL and IVL: a case report
Authors: Jeon Seung-Ho , Kang Mi-Kyoung , Lee Seung Jae , Shin Byoung-Soo , Kang Hyun Goo 
Published: December 2019

Abstract
Background
Primary central nervous system lymphoma (PCNSL) is a rare, malignant, non-Hodgkin’s lymphoma of the brain, leptomeninges, and rarely the spinal cord. PCNSL has characteristic magnetic resonance imaging (MRI) findings, and effective treatment strategies are available. It is characterized predominately by neurological symptoms, which are caused by tumor infiltration into the nervous system as well as ischemia. Chemotherapy is an effective treatment, if started prior to the ischemic damage.

Case presentation
A 62-year-old male patient with PCNSL presented with altered mental status. The initial brain MRI revealed high signal intensity on the T2-weighted images (T2WIs) of the putamen area of the right basal ganglia, and the clinical symptoms improved after steroid administration. However, the symptoms were later deteriorated, we considered the possibility of autoimmune encephalitis and, consequently, conducted an immunomodulatory therapy. In a follow-up brain MRI, enlargement lesions of T2WI in basal ganglia and pons were simultaneously enhanced. Subsequently, the patient’s mental status deteriorated to a semi-coma and PCNSL was diagnosed after a surgical biopsy. Chemotherapy was started immediately; however, the patient died.

Conclusions
Effective treatments are available for PCNSL and intravascular lymphoma; thus, their prognosis is generally good if they are diagnosed early. Herein, we report the case of a patient suspected with autoimmune encephalitis after brain MRI and treated with immunomodulation therapy. However, PCNSL was confirmed by a surgical biopsy. It is, therefore recommended to consider lymphoma in patients with neurological symptoms that are difficult to localize and rapidly progressive enhancing lesions showing a mass effect on brain MRI.
Tumor suppressor HIC1 is synergistically compromised by cancer-associated fibroblasts and tumor cells through the IL-6/pSTAT3 axis in breast cancer
Authors: Sun Xueqing , Qu Qing , Lao Yimin , Zhang Mi , Yin Xiaoling , Zhu Huiqin , Wang Ying , Yang Jie , Yi Jing , Hao Mingang 
Published: December 2019

Abstracts
Background
Interleukin-6 (IL-6) is commonly highly secreted in the breast cancer (BrCA) microenvironment and implicated in disease development. In this study, we aimed to determine the role of the IL-6/pSTAT3/HIC1 axis in the breast cancer microenvironment, including in cancer-associated fibroblasts (CAFs) and breast cancer cells.

Methods
Stromal fibroblasts from the breast cancer tissue were isolated, and the supernatants of the fibroblasts were analyzed. Recombinant human IL-6 (rhIL-6) was applied to simulate the effect of CAF-derived IL-6 to study the mechanism of HIC1 (tumor suppressor hypermethylated in cancer 1) downregulation. IL-6 was knocked down in the high IL-6-expressing BrCA cell line MDA-MB-231, which enabled the investigation of the IL-6/pSTAT3/HIC1 axis in the autocrine pathway.

Results
Increased IL-6 was found in the supernatant of isolated CAFs, which suppressed HIC1 expression in cancer cells and promoted BrCA cell proliferation. After stimulating the BrCA cell line SK-BR-3 (where IL-6R is highly expressed) with rhIL-6, signal transducers and activators of transcription 3 (STAT3) was found to be phosphorylated and HIC1 decreased, and a STAT3 inhibitor completely rescued HIC1 expression. Moreover, HIC1 was restored upon knocking down IL-6 expression in MDA-MB-231 cells, accompanied by a decrease in STAT3 activity.

Conclusions
These findings indicate that IL-6 downregulates the tumor suppressor HIC1 and promotes BrCA development in the tumor microenvironment through paracrine or autocrine signaling.
Comparing biological information contained in mRNA and non-coding RNAs for classification of lung cancer patients
Authors: Smolander Johannes , Stupnikov Alexey , Glazko Galina , Dehmer Matthias , Emmert-Streib Frank 
Published: December 2019

Abstract
Background
Deciphering the meaning of the human DNA is an outstanding goal which would revolutionize medicine and our way for treating diseases. In recent years, non-coding RNAs have attracted much attention and shown to be functional in part. Yet the importance of these RNAs especially for higher biological functions remains under investigation.

Methods
In this paper, we analyze RNA-seq data, including non-coding and protein coding RNAs, from lung adenocarcinoma patients, a histologic subtype of non-small-cell lung cancer, with deep learning neural networks and other state-of-the-art classification methods. The purpose of our paper is three-fold. First, we compare the classification performance of different versions of deep belief networks with SVMs, decision trees and random forests. Second, we compare the classification capabilities of protein coding and non-coding RNAs. Third, we study the influence of feature selection on the classification performance.

Results
As a result, we find that deep belief networks perform at least competitively to other state-of-the-art classifiers. Second, data from non-coding RNAs perform better than coding RNAs across a number of different classification methods. This demonstrates the equivalence of predictive information as captured by non-coding RNAs compared to protein coding RNAs, conventionally used in computational diagnostics tasks. Third, we find that feature selection has in general a negative effect on the classification performance which means that unfiltered data with all features give the best classification results.

Conclusions
Our study is the first to use ncRNAs beyond miRNAs for the computational classification of cancer and for performing a direct comparison of the classification capabilities of protein coding RNAs and non-coding RNAs.
The treatment of a hypertrophic bleb after XEN gel implantation with the “Drainage Channel with sutures” method: a case report
Authors: Yavuzer Kamil , Meşen Ali 
Published: December 2019

Abstract
Background
The placement of a XEN gel stent is an ab-interno, minimally invasive glaucoma surgery which provides a subconjunctival drainage pathway and decreases intraocular pressure (IOP).

Case presentation
A 75-year-old male patient who had undergone XEN45 gel implantation after phacoemulsification and intraocular lens implantation appealed to the clinic. A filtration bleb was seen that extended through the nasal 180 degrees of the eye which caused ectropion of the lower eyelid. The value of the IOP was 12 mm Hg (mmHg). By the “Drainage Channel with Sutures” method this complication was effectively treated. As with every new method, there is a lack of knowledge about long-term outcomes in terms of effectiveness, technique and complications.

Conclusion
The “Drainage Channel with Sutures” method has not been described in the literature yet. By this minimal invasive method, hypertrophic bleb complication of XEN gel implant has been successfully treated.
Integrating HIV, syphilis, malaria and anaemia point-of-care testing (POCT) for antenatal care at dispensaries in western Kenya: discrete-event simulation modelling of operational impact
Authors: Young N. , Taetgmeyer M. , Zulaika G. , Aol G. , Desai M. , Ter Kuile F. , Langley I. 
Published: December 2019

AbstractBackgroundDespite WHO advocating for an integrated approach to antenatal care (ANC), testing coverage for conditions other than HIV remains low and women are referred to distant laboratories for testing. Using point-of-care tests (POCTs) at peripheral dispensaries could improve access to testing and timely treatment. However, the effect of providing additional services on nurse workload and client wait times are unknown. We use discrete-event simulation (DES) modelling to understand the effect of providing four point-of-care tests for ANC on nurse utilization and wait times for women seeking maternal and child health (MCH) services.MethodsWe collected detailed time-motion data over 20 days from one high volume dispensary in western Kenya during the 8-month implementation period (2014–2015) of the intervention. We constructed a simulation model using empirical arrival distributions, activity durations and client pathways of women seeking MCH services. We removed the intervention from the model to obtain wait times, length-of-stay and nurse utilization rates for the baseline scenario where only HIV testing was offered for ANC. Additionally, we modelled a scenario where nurse consultations were set to have minimum durations for sufficient delivery of all WHO-recommended services.ResultsA total of 183 women visited the dispensary for MCH services and 14 of these women received point-of-care testing (POCT). The mean difference in total waiting time was 2 min (95%CI: < 1–4 min,p = 0.026) for MCH women when integrated POCT was given, and 9 min (95%CI: 4–14 min,p < 0.001) when integrated POCT with adequate ANC consult times was given compared to the baseline scenario. Mean length-of-stay increased by 2 min (95%CI: < 1–4 min,p = 0.015) with integrated POCT and by 16 min (95%CI: 10–21 min,p < 0.001) with integrated POCT and adequate consult times compared to the baseline scenario. The two nurses’ overall daily utilization in the scenario with sufficient minimum consult durations were 72 and 75%.ConclusionThe intervention had a modest overall impact on wait times and length-of-stay for women seeking MCH services while ensuring pregnant women received essential diagnostic testing. Nurse utilization rates fluctuated among days: nurses experienced spikes in workload on some days but were under-utilized on the majority of days. Overall, our model suggests there was sufficient time to deliver all WHO’s required ANC activities and offer integrated testing for ANC first and re-visits with the current number of healthcare staff. Further investigations on improving healthcare worker, availability, performance and quality of care are needed. Delivering four point-of-care tests together for ANC at dispensary level would be a low burden strategy to improve ANC.
A community-based pragmatic, controlled trial for preventing and reducing oral diseases among 1–6-year-old children visiting Anganwadi centers, under the Integrated Child Development Scheme, India
Authors: Goyal Ashima , Grover Ashoo , Gauba Krishan , Gupta Arpit , Mehta Nishant , Dutta Sourabh , Pandey R. M. , Joshi Ashish , Thakur J. S. , Mohanty Utkal , Dhaliwal R. S. 
Published: December 2019

Abstract
Background
Early childhood caries (ECC) has reached epidemic proportions affecting millions of children worldwide. Its prevention becomes imperative owing to the significant morbidity and financial implications involved with its treatment. The Integrated Child Development Scheme (ICDS), launched in India to provide mid-day meals, pre-school education and primary healthcare to children, can be utilised to counsel and deliver oral health education to mothers. The purpose of the study is to compare the effect of an oral health care package (OHCP) with usual care on the change in dental disease status among 1 to 3-year-old children at Anganwadi centres (AWC) in periurban areas of Chandigarh and rural areas of Cuttack, Orissa over a follow-up period of three years.

Methods
Two geographically distant ICDS blocks would be selected at each of the two study sites and would be randomly allocated to intervention and control group. Closely located AWCs under each of the selected blocks shall constitute the study setting. OHCP would be delivered to the mothers of the 1–6-year-old children enrolled in the AWCs of the experimental group whereas mothers under control group would receive usual care advice available at the AWCs.

Discussion
ECC prevention had conventionally focused upon testing effectiveness of programs targeting behaviour change among the caregivers and children, but surprisingly minimal efforts have been made to seek translation of these efforts into reduction of ECC at the community level. The present study has two components; testing effect of altering maternal and child behavioral aspects on ECC incidence through cohort follow up of 1–3-year-old children for three consecutive years and cross-sectional follow up of all available 1–6-year old children at the selected AWCs at regular intervals to look for change in prevalence of ECC at community level. In other regions of the world surveys of ECC prevalence before and after the intensive educational programs have shown a significant reduction in ECC prevalence. A similar decline can be anticipated through this program.

Trial registration
This trial has been prospectively registered at Clinical Trials Registry, India (CTRI/2019/02/017556, 08 February 2019).