bluuebunny/crossref_metadata_2025_split huggingface dataset:
The association of CASC16 variants with breast Cancer risk in a northwest Chinese female population
Authors: Zuo Xiaoxiao , Wang Huanhuan , Mi Yin , Zhang Yue , Wang Xiaofei , Yang Ya , Zhai Suna 
Published: January 2020

Abstract
Purpose
Genetic variants play a critical role in the development of breast cancer. This investigation aimed to explore the association between CASC16 polymorphisms and breast cancer susceptibility.

Methods
We conducted a case-control study of 681 patients and 680 healthy individuals to investigate the correlation of five SNPs with breast cancer in a Northwest Chinese female population. Odds ratios (OR) and 95% confidence intervals (CIs) were used to assess the association.

Results
Our study found that rs4784227 and rs12922061 were significantly related to an increased susceptibility to breast cancer (OR 1.22, p = 0.022; OR 1.21, p = 0.026). While rs3803662 was a protective role in breast cancer risk (OR 0.69, p = 0.042). Stratified analyses indicated that rs4784227 and rs12922061 would increase breast cancer susceptibility at age >  50 years. Rs3803662 was a reduced factor of breast cancer risk by age ≤ 50 years. Rs4784227 was significantly increased risk of breast cancer in stage III/IV. The rs45544231 and rs3112612 had a protective effect on breast cancer with tumor size > 2 cm. Rs4784227 and rs12922061 could enhance breast cancer risk in lymph node metastasis positive individuals. CASC16 rs12922061 and rs4784227 polymorphisms correlated with an increased risk of breast cancer in BMI >  24 kg/m2. Haplotype analyses revealed that Grs45544231 Trs12922061 Ars3112612 and Grs45544231 Crs12922061 Ars3112612 haplotypes decreased breast cancer risk.

Conclusion
Our study revealed that CASC16 genetic variants were significantly related to breast cancer susceptibility, which might give scientific evidence for exploring the molecular mechanism of breast cancer.
Characterization of cyclitic membranes by ultrabiomicroscopy in patients with pars planitis
Authors: Concha del Río Luz Elena , Duarte González Gonzalo Alejandro , Mayorquín Ruiz Mariana , Arellanes-García Lourdes 
Published: January 2020

Abstract
Background
In previous studies, authors use ultrasound biomicroscopy (UBM) to analyze the characteristics of cyclitic membranes and the associated complications in patients with pars planitis. However, there are no reports regarding the prevalence of cyclitic membranes or complications at diagnosis and during follow-up.

Purpose
To describe the characteristics and complications of cyclitic membranes, as determined by UBM in patients with pars planitis using AVISO-S™ (Quantel Medical) equipment with a 50-MHz linear probe with a focus at the pars plana.

Design
This retrospective study reviewed UBM images of patients diagnosed with pars planitis, from the Inflammatory Eye Disease Clinic in Mexico City from January 2010 to June 2016.

Results
Cyclitic membranes were observed in the first UBM image in 67 eyes (56.7%) and during follow-up in 81 eyes (68.62%). In 67 eyes (82.71%), the cyclitic membranes extended through one or two quadrants. Extension toward the posterior lens capsule was recognized in 15 eyes (18.52%) and extension toward the peripheral retina in 12 eyes (14.81%). Complications included ciliary body detachments in 10 eyes (12.35%) and peripheral retinal traction in 8 eyes (9.88%).

Conclusions
UBM is a valuable tool for the diagnosis of cyclitic membranes at admittance and during follow-up of patients with pars planitis; it helps the clinician to detect this complication early.
Unlocking the transcriptomic potential of formalin-fixed paraffin embedded clinical tissues: comparison of gene expression profiling approaches
Authors: Turnbull Arran K. , Selli Cigdem , Martinez-Perez Carlos , Fernando Anu , Renshaw Lorna , Keys Jane , Figueroa Jonine D. , He Xiaping , Tanioka Maki , Munro Alison F. , Murphy Lee , Fawkes Angie , Clark Richard , Coutts Audrey , Perou Charles M. , Carey Lisa A. , Dixon J. Michael , Sims Andrew H. 
Published: January 2020

Abstract
Background
High-throughput transcriptomics has matured into a very well established and widely utilised research tool over the last two decades. Clinical datasets generated on a range of different platforms continue to be deposited in public repositories provide an ever-growing, valuable resource for reanalysis. Cost and tissue availability normally preclude processing samples across multiple technologies, making it challenging to directly evaluate performance and whether data from different platforms can be reliably compared or integrated.

Methods
This study describes our experiences of nine new and established mRNA profiling techniques including Lexogen QuantSeq, Qiagen QiaSeq, BioSpyder TempO-Seq, Ion AmpliSeq, Nanostring, Affymetrix Clariom S or U133A, Illumina BeadChip and RNA-seq of formalin-fixed paraffin embedded (FFPE) and fresh frozen (FF) sequential patient-matched breast tumour samples.

Results
The number of genes represented and reliability varied between the platforms, but overall all methods provided data which were largely comparable. Crucially we found that it is possible to integrate data for combined analyses across FFPE/FF and platforms using established batch correction methods as required to increase cohort sizes. However, some platforms appear to be better suited to FFPE samples, particularly archival material.

Conclusions
Overall, we illustrate that technology selection is a balance between required resolution, sample quality, availability and cost.
m6Acorr: an online tool for the correction and comparison of m6A methylation profiles
Authors: Li Jianwei , Huang Yan , Cui Qinghua , Zhou Yuan 
Published: January 2020

Abstract
Background
The analysis and comparison of RNA m6A methylation profiles have become increasingly important for understanding the post-transcriptional regulations of gene expression. However, current m6A profiles in public databases are not readily intercomparable, where heterogeneous profiles from the same experimental report but different cell types showed unwanted high correlations.

Results
Several normalizing or correcting methods were tested to remove such laboratory bias. And m6Acorr, an effective pipeline for correcting m6A profiles, was presented on the basis of quantile normalization and empirical Bayes batch regression method. m6Acorr could efficiently correct laboratory bias in the simulated dataset and real m6A profiles in public databases. The preservation of biological signals was examined after correction, and m6Acorr was found to better preserve differential methylation signals, m6A regulated targets, and m6A-related biological features than alternative methods. Finally, the m6Acorr server was established. This server could eliminate the potential laboratory bias in m6A methylation profiles and perform profile–profile comparisons and functional analysis of hyper- (hypo-) methylated genes based on corrected methylation profiles.

Conclusion
m6Acorr was established to correct the existing laboratory bias in RNA m6A methylation profiles and perform profile comparisons on the corrected datasets. The m6Acorr server is available at http://www.rnanut.net/m6Acorr. A stand-alone version with the correction function is also available in GitHub at https://github.com/emersON106/m6Acorr.
A mouse ear skin model to study the dynamics of innate immune responses against Staphylococcus aureus biofilms
Authors: Abdul Hamid Aizat Iman , Nakusi Laurence , Givskov Mickael , Chang Young-Tae , Marquès Claire , Gueirard Pascale 
Published: January 2020

Abstract
Background
Staphylococcus aureus is a human pathogen that is a common cause of nosocomial infections and infections on indwelling medical devices, mainly due to its ability to shift between the planktonic and the biofilm/sessile lifestyle. Biofilm infections present a serious problem in human medicine as they often lead to bacterial persistence and thus to chronic infections. The immune responses elicited by biofilms have been described as specific and ineffective. In the few experiments performed in vivo, the importance of neutrophils and macrophages as a first line of defence against biofilm infections was clearly established. However, the bilateral interactions between biofilms and myeloid cells remain poorly studied and analysis of the dynamic processes at the cellular level in tissues inoculated with biofilm bacteria is still an unexplored field. It is urgent, therefore, to develop biologically sound experimental approaches in vivo designed to extract specific immune signatures from the planktonic and biofilm forms of bacteria.

Results
We propose an in vivo transgenic mouse model, used in conjunction with intravital confocal microscopy to study the dynamics of host inflammatory responses to bacteria. Culture conditions were created to prepare calibrated inocula of fluorescent planktonic and biofilm forms of bacteria. A confocal imaging acquisition and analysis protocol was then drawn up to study the recruitment of innate immune cells in the skin of LysM-EGFP transgenic mice. Using the mouse ear pinna model, we showed that inflammatory responses to S. aureus can be quantified over time and that the dynamics of innate immune cells after injection of either the planktonic or biofilm form can be characterized. First results showed that the ability of phagocytic cells to infiltrate the injection site and their motility is not the same in planktonic and biofilm forms of bacteria despite the cells being considerably recruited in both cases.

Conclusion
We developed a mouse model of infection to compare the dynamics of the inflammatory responses to planktonic and biofilm bacteria at the tissue and cellular levels. The mouse ear pinna model is a powerful imaging system to analyse the mechanisms of biofilm tolerance to immune attacks.
Sexual dimorphism following in vitro ischemia in the response to neurosteroids and mechanisms of injury
Authors: Altaee Raeed , Gibson Claire L. 
Published: January 2020

Abstract
Background
Cerebral ischemic stroke is a significant cause of morbidity and mortality. Sex differences exist following stroke in terms of incidence, symptoms, outcomes and response to some treatments. Importantly, molecular mechanisms of injury, activated following ischemia may differ between the sexes and if so may account, at least in part, for sex differences seen in treatment response. Here we aimed to determine, using single-sex organotypic hippocampal slice cultures, whether the effectiveness of a potential treatment option, i.e. sex steroids, exhibited any sexual dimorphism and whether sex affected the mechanisms of apoptosis activated following ischemia.

Results
Following exposure to ischemia, male-derived tissue exhibited higher levels of cell death than female-derived tissue. Various sex steroid hormones, i.e. progesterone, allopregnanolone, and estradiol, were protective in terms of reducing the amount of cell death in male- and female-derived tissue whereas medoxyprogesterone acetate (MPA) was only protective in female-derived tissue. The protective effect of progesterone was abolished in the presence of finasteride, a 5α-reductase inhibitor, suggesting it was largely mediated via its conversion to allopregnanolone. To test the hypothesis that sex differences exist in the activation of specific elements of the apoptotic pathway activated following ischemia we administered Q-VD-OPH, a caspase inhibitor, or PJ34, an inhibitor of poly (ADP ribose) polymerase (PARP). Caspase inhibition was only effective, in terms of reducing cell death, in female-derived tissue, whereas PARP inhibition was only protective in male-derived tissue. However, in both sexes, the protective effects of progesterone and estradiol were not observed in the presence of either caspase or PARP inhibition.

Conclusions
Sex differences exist in both the amount of cell death produced and those elements of the cell death pathway activated following an ischemic insult. There are also some sex differences in the effectiveness of steroid hormones to provide neuroprotection following an ischemic insult—namely MPA was only protective in female-derived tissue. This adds further support to the notion sex is an important factor to consider when investigating future drug targets for CNS disorders, such as ischemic stroke.
Comparative proteomic analysis reveals that exogenous 6-benzyladenine (6-BA) improves the defense system activity of waterlogged summer maize
Authors: Hu Juan , Ren Baizhao , Dong Shuting , Liu Peng , Zhao Bin , Zhang Jiwang 
Published: January 2020

Abstract
Background
Exogenous 6-benzyladenine (6-BA) could improve leaf defense system activity. In order to better understand the regulation mechanism of exogenous 6-benzyladenine (6-BA) on waterlogged summer maize, three treatments including control (CK), waterlogging at the third leaf stage for 6 days (V3–6), and application of 100 mg dm− 3 6-BA after waterlogging for 6 days (V3–6-B), were employed using summer maize hybrid DengHai 605 (DH605) as the experimental material. We used a labeling liquid chromatography-based quantitative proteomics approach with tandem mass tags to determine the changes in leaf protein abundance level at the tasseling stage.

Results
Waterlogging significantly hindered plant growth and decreased the activities of SOD, POD and CAT. In addition, the activity of LOX was significantly increased after waterlogging. As a result, the content of MDA and H2O2 was significantly increased which incurred serious damages on cell membrane and cellular metabolism of summer maize. And, the leaf emergence rate, plant height and grain yield were significantly decreased by waterlogging. However, application of 6-BA effectively mitigated these adverse effects induced by waterlogging. Compared with V3–6, SOD, POD and CAT activity of V3–6-B were increased by 6.9, 12.4, and 18.5%, LOX were decreased by 13.6%. As a consequence, the contents of MDA and H2O2 in V3–6-B were decreased by 22.1 and 17.2%, respectively, compared to that of V3–6. In addition, the leaf emergence rate, plant height and grain yield were significantly increased by application of 6-BA. Based on proteomics profiling, the proteins involved in protein metabolism, ROS scavenging and fatty acid metabolism were significantly regulated by 6-BA, which suggested that application of 6-BA exaggerated the defensive response of summer maize at proteomic level.

Conclusions
These results demonstrated that 6-BA had contrastive effects on waterlogged summer maize. By regulating key proteins related to ROS scavenging and fatty acid metabolism, 6-BA effectively increased the defense system activity of waterlogged summer maize, then balanced the protein metabolism and improved the plant physiological traits and grain yield.
Knockout of VvCCD8 gene in grapevine affects shoot branching
Authors: Ren Chong , Guo Yuchen , Kong Junhua , Lecourieux Fatma , Dai Zhanwu , Li Shaohua , Liang Zhenchang 
Published: January 2020

Abstract
Background
Shoot branching is an important trait of plants that allows them to adapt to environment changes. Strigolactones (SLs) are newly identified plant hormones that inhibit shoot branching in plants. The SL biosynthesis genes CCD7 (carotenoid cleavage dioxygenase 7) and CCD8 have been found to regulate branching in several herbaceous plants by taking advantage of their loss-of-function mutants. However, the role for CCD7 and CCD8 in shoot branching control in grapevine is still unknown due to the lack of corresponding mutants.

Results
Here we employed the CRISPR/Cas9 system to edit the VvCCD7 and VvCCD8 genes in the grape hybrid 41B. The 41B embryogenic cells can easily be transformed and used for regeneration of the corresponding transformed plants. Sequencing analysis revealed that gene editing has been used successfully to target both VvCCD genes in 41B embryogenic cells. After regeneration, six 41B plantlets were identified as transgenic plants carrying the CCD8-sgRNA expression cassette. Among these, four plants showed mutation in the target region and were selected as ccd8 mutants. These ccd8 mutants showed increased shoot branching compared to the corresponding wild-type plants. In addition, no off-target mutation was detected in the tested mutants at predicted off-target sites.

Conclusions
Our results underline the key role of VvCCD8 in the control of grapevine shoot branching.
Hospital-acquired influenza infections detected by a surveillance system over six seasons, from 2010/2011 to 2015/2016
Authors:   the Working Group on the Surveillance of Severe Influenza Hospitalized Cases in Catalonia, Godoy P. , Torner N. , Soldevila N. , Rius C. , Jane M. , Martínez A. , Caylà JA. , Domínguez A. 
Published: January 2020

Abstract
Background
In addition to outbreaks of nosocomial influenza, sporadic nosocomial influenza infections also occur but are generally not reported in the literature.
This study aimed to determine the epidemiologic characteristics of cases of nosocomial influenza compared with the remaining severe cases of severe influenza in acute hospitals in Catalonia (Spain) which were identified by surveillance.

Methods
An observational case-case epidemiological study was carried out in patients aged ≥18 years from Catalan 12 hospitals between 2010 and 2016. For each laboratory-confirmed influenza case (nosocomial or not) we collected demographic, virological and clinical characteristics. We defined patients with nosocomial influenza as those admitted to a hospital for a reason other than acute respiratory infection in whom ILI symptoms developed ≥48 h after admission and influenza virus infection was confirmed using RT-PCR. Mixed-effects regression was used to estimate the crude and adjusted OR.

Results
One thousand seven hundred twenty-two hospitalized patients with severe laboratory-confirmed influenza virus infection were included: 96 (5.6%) were classified as nosocomial influenza and more frequently had > 14 days of hospital stay (42.7% vs. 27.7%, P < .001) and higher mortality (18.8% vs. 12.6%, P < .02). The variables associated with nosocomial influenza cases in acute-care hospital settings were chronic renal disease (aOR 2.44 95% CI 1.44–4.15) and immunodeficiency (aOR 1.79 95% CI 1.04–3.06).

Conclusions
Nosocomial infections are a recurring problem associated with high rates of chronic diseases and death. These findings underline the need for adherence to infection control guidelines.
Investigating associated factors with glomerular filtration rate: structural equation modeling
Authors: Jamshidi Parastoo , Najafi Farid , Mostafaei Shayan , Shakiba Ebrahem , Pasdar Yahya , Hamzeh Behrooz , Moradinazar Mehdi 
Published: January 2020

AbstractBackgroundGlomerular filtration rate (GFR) is a valid indicator of kidney function. Different factors can affect GFR. The purpose of this study is to assess the direct and indirect effects of GFR-related factors using structural equation modeling.Patients and methodsWe analyzed data from the baseline phase of the Ravansar Non-Communicable Disease cohort study. Data on socio-behavioral, nutritional, cardiovascular, and metabolic risk factors were analyzed using a conceptual model in order to test direct and indirect effects of factors related to GFR, separately in male and female, using the structural equation modeling.ResultsOf 8927 individuals who participated in this study, 4212 subjects were male (47.20%). The mean and standard deviation of GFR was 76.05 (±14.31) per 1.73m2. GFR for 0.2, 11.3, 73.0 and 15.5% of people were < 30, 30 − 59, 60 − 90 and >90, respectively. Hypertension and aging in both sexes and atherogenic factor in males directly, and in females, directly and indirectly, had decreasing effects on GFR. Blood urea nitrogen and smoking in male and female, directly or indirectly through other variables, were associated with a lower GFR. In females, diabetes had a direct and indirect decreasing effect on GFR. Obesity in females was directly associated with upper and indirectly associated with lower GFR.ConclusionAccording to our results, aging, hypertension, diabetes, obesity, high lipid profile, and BUN had a decreasing direct and indirect effect on GFR. Although low GFR might have different reasons, our findings, are in line with other reports and provide more detailed information about important risk factors of low GFR. Public awareness of such factors can improve practice of positive health behaviors.
SMART coils for intracranial aneurysm repair – a single center experience
Authors: Daniel Behme , Henrik Sack , Ioannis Tsogkas , Veit Rohde , Marios-Nikos Psychogios 
Published: January 2020

Abstract
Background
Due to uniform stiffness of standard platinum coils, dense packing of intracranial aneurysms can be difficult to achieve, since stiffer coils can cause microcatheter prolapse or coil migration. SMART coils have a varying softness along the length of the coils to improve deliverability. We report our initial 2 year experience with the SMART coil system, including direct and follow-up results.

Methods
We performed a retrospective study of all patients who underwent coil embolization of an intracranial aneurysm with SMART coils between July 2016 and August 2018 at our institution. We analyzed clinical and angiographic data before and directly after treatment as well as at 6 months follow-up.

Results
A total of 49 patients harboring 49 aneurysms were treated; 23 (47%) were ruptured aneurysms. Most aneurysms (57%) were located in the anterior circulation. Median patient age was 55 (31–88), 63% were female. Mean aneurysm size was: neck 3.4 (±1.5), height 6.3 (±2.9) and width 5.2 (±2.3) mm. SMART coils were solely used in 96% of cases. Initial favorable angiographic results were achieved in 45 (92%) of 49 cases, which were stable at 6 months in 26/29 (90%). Thromboembolic complications occurred in 4 (8%) cases without clinical sequelae; microcatheter prolapse occurred in 1 case. No aneurysm rupture or device malfunction was observed.

Conclusion
The treatment of ruptured and unruptured intracranial aneurysms with SMART Coils was safe and efficacious in our cohort.