bluuebunny/crossref_metadata_2025_split huggingface dataset:
A statistical approach for detecting genomic aberrations in heterogeneous tumor samples from single nucleotide polymorphism genotyping data
Authors: Yau Christopher , Mouradov Dmitri , Jorissen Robert N , Colella Stefano , Mirza Ghazala , Steers Graham , Harris Adrian , Ragoussis Jiannis , Sieber Oliver , Holmes Christopher C 
Published: October 2019

AbstractWe describe a statistical method for the characterization of genomic aberrations in single nucleotide polymorphism microarray data acquired from cancer genomes. Our approach allows us to model the joint effect of polyploidy, normal DNA contamination and intra-tumour heterogeneity within a single unified Bayesian framework. We demonstrate the efficacy of our method on numerous datasets including laboratory generated mixtures of normal-cancer cell lines and real primary tumours.
Preparation and Pharmacokinetic Study of Daidzein Long-Circulating Liposomes
Authors: Wang Qiao , Liu Wenjin , Wang Junjun , Liu Hong , Chen Yong 
Published: October 2019

Abstract
In this study, daidzein long-circulating liposomes (DLCL) were prepared using the ultrasonication and lipid film-hydration method. The optimized preparation conditions by the orthogonal design was as follows: 55 to 40 for the molar ratio of soybean phosphatidylcholine (SPC) to cholesterol, 1 to 10 for the mass ratio of daidzein to total lipid (SPC and cholesterol) (w:w), the indicated concentration of 5% DSPE-mPEG2000 (w:w), 50 °C for the hydration temperature, and 24 min for the ultrasonic time. Under these conditions, the encapsulation efficiency and drug loading of DLCL were 85.3 ± 3.6% and 8.2 ± 1.4%, respectively. The complete release times of DLCL in the medium of pH 1.2 and pH 6.9 increased by four- and twofold of that of free drugs, respectively. After rats were orally administered, a single dose of daidzein (30 mg/kg) and DLCL (containing equal dose of daidzein), respectively, and the MRT0−t (mean residence time, which is the time required for the elimination of 63.2% of drug in the body), t1/2 (the elimination half-life, which is the time required to halve the plasma drug concentration of the terminal phase), and AUC0−t (the area under the plasma drug concentration-time curve, which represents the total absorption after a single dose and reflects the drug absorption degree) of daidzein in DLCL group, increased by 1.6-, 1.8- and 2.5-fold as compared with those in the free group daidzein. Our results indicated that DLCL could not only reduce the first-pass effect of daidzein to promote its oral absorption, but also prolong its mean resident time to achieve the slow-release effect.
Unravelling the hybrid vigor in domestic equids: the effect of hybridization on bone shape variation and covariation
Authors: Hanot Pauline , Herrel Anthony , Guintard Claude , Cornette Raphaël 
Published: October 2019

AbstractBackgroundHybridization has been widely practiced in plant and animal breeding as a means to enhance the quality and fitness of the organisms. In domestic equids, this hybrid vigor takes the form of improved physical and physiological characteristics, notably for strength or endurance. Because the offspring of horse and donkey is generally sterile, this widely recognized vigor is expressed in the first generation (F1). However, in the absence of recombination between the two parental genomes, F1 hybrids can be expected to be phenotypically intermediate between their parents which could potentially restrict the possibilities of an increase in overall fitness. In this study, we examine the morphology of the main limb bones of domestic horses, donkeys and their hybrids to investigate the phenotypic impact of hybridization on the locomotor system. We explore bone shape variation and covariation to gain insights into the morphological and functional expressions of the hybrid vigor commonly described in domestic equids.ResultsOur data reveal the occurrence of transgressive effects on several bones in the F1 generation. The patterns of morphological integration further demonstrate that the developmental processes producing covariation are not disrupted by hybridization, contrary to functional ones.ConclusionsThese results suggest that an increase in overall fitness could be related to more flexibility in shape change in hybrids, except for the main forelimb long bones of which the morphology is strongly driven by muscle interactions. More broadly, this study illustrates the interest of investigating not only bone shape variation but also underlying processes, in order to contribute to better understanding how developmental and functional mechanisms are affected by hybridization.
RADseq population genomics confirms divergence across closely related species in blue coral (Heliopora coerulea)
Authors: Iguchi Akira , Yoshioka Yuki , Forsman Zac H. , Knapp Ingrid S.S. , Toonen Robert J. , Hongo Yuki , Nagai Satoshi , Yasuda Nina 
Published: October 2019

AbstractBackgroundHeliopora coerulea, the blue coral, is the octocoral characterized by its blue skeleton. Recently, twoHelioporaspecies were delimited by DNA markers: HC-A and HC-B. To clarify the genomic divergence of theseHelioporaspecies (HC-A and HC-B) from sympatric and allopatric populations in Okinawa, Japan, we used a high throughput reduced representation genomic DNA sequencing approach (ezRAD).ResultsWe found 6742 biallelic SNPs shared among all target populations, which successfully distinguished the HC-A and HC-B species in both the sympatric and allopatric populations, with no evidence of hybridization between the two. In addition, we detected 410 fixed SNPs linking functional gene differences, including heat resilience and reproductive timing, between HC-A and HC-B.ConclusionsWe confirmed clear genomic divergence betweenHelioporaspecies and found possible genes related to stress-responses and reproduction, which may shed light on the speciation process and ecological divergence of coral species.
DNA methylomes and transcriptomes analysis reveal implication of host DNA methylation machinery in BmNPV proliferation in Bombyx mori
Authors: Huang Haoling , Wu Ping , Zhang Shaolun , Shang Qi , Yin Haotong , Hou Qirui , Zhong Jinbo , Guo Xijie 
Published: October 2019

Abstract

Background
Bombyx mori nucleopolyhedrosis virus (BmNPV) is a major pathogen that threatens the sustainability of the sericultural industry. DNA methylation is a widespread gene regulation mode in epigenetics, which plays an important role in host immune response. Until now, little has been known about epigenetic regulation on virus diseases in insects. This study aims to explore the role of DNA methylation in BmNPV proliferation.

Results
Inhibiting DNA methyltransferase (DNMT) activity of silkworm can suppress BmNPV replication. The integrated analysis of transcriptomes and DNA methylomes in silkworm midguts infected with or without BmNPV showed that both the expression pattern of transcriptome and DNA methylation pattern are changed significantly upon BmNPV infection. A total of 241 differentially methylated regions (DMRs) were observed in BmNPV infected midguts, among which, 126 DMRs were hyper-methylated and 115 DMRs were hypo-methylated. Significant differences in both mRNA transcript level and DNA methylated levels were found in 26 genes. BS-PCR validated the hypermethylation of BGIBMGA014008, a structural maintenance of chromosomes protein gene in the BmNPV-infected midgut. In addition, DNMT inhibition reduced the expression of inhibitor of apoptosis family genes, iap1 from BmNPV, Bmiap2, BmSurvivin1 and BmSurvivin2.

Conclusion
Our results indicate that DNA methylation plays positive roles in BmNPV proliferation and loss of DNMT activity could induce the apoptosis of infected cells to suppress BmNPV proliferation. Our results may provide a new idea and research direction for the molecular mechanism on insect-virus interaction.
Comparative transcriptomic analysis and endocuticular protein gene expression of alate adults, workers and soldiers of the termite Reticulitermes aculabialis
Authors: Rasheed Humaira , Ye Chenxu , Meng Yufeng , Ran Yuehua , Li Jing , Su Xiaohong 
Published: October 2019

Abstract

Background
The insect cuticle is mainly composed of exocuticle and endocuticle layers that consist of a large number of structural proteins. The thickness and synthesis of the exocuticle depend on different castes that perform various functions in alates, workers and soldiers. However, it is not clear whether the soft endocuticle is involved in the division of labour in termite colonies. To reveal the structural characteristics of the endocuticle in different castes, we investigated the thickness of endocuticle layers in alates, workers and soldiers of the termite Reticulitermes aculabialis, and then we sequenced their transcriptome and detected the endocuticle protein genes. The differential expression levels of the endocuticular protein genes were confirmed in the three castes.

Results
We found that there was a great difference in the thickness of the endocuticle among the alates, soldiers and workers. The thickest endocuticle layers were found in the heads of the workers 7.88 ± 1.67 μm. The endocuticle layer in the head of the workers was approximately three-fold and nine-fold thicker than that in the heads of soldiers and alates, respectively. The thinnest endocuticle layers occurred in the head, thorax and abdomen of alates, which were 0.86 ± 0.15, 0.76 ± 0.24 and 0.52 ± 0.17 μm thick, respectively, and had no significant differences. A total of 43,531,650 clean sequencing reads was obtained, and 89,475 unigenes were assembled. Of the 70 identified cuticular protein genes, 10 endocuticular genes that belong to the RR-1 family were selected. qRT-PCR analysis of the five endocuticular genes (SgAbd-2, SgAbd-9, Abd-5, SgAbd-2-like and Abd-4-like) revealed that the endocuticle genes were more highly expressed in workers than in soldiers and alates.

Conclusion
These results suggest that SgAbd and Abd are the key components of the endocuticle. We infer that the thicker endocuticle in workers is helpful for them to perform their functions against environmental stress.
Effect of root exudates of Eucalyptus urophylla and Acacia mearnsii on soil microbes under simulated warming climate conditions
Authors: Wu Jiahui , Yu Shixiao 
Published: October 2019

AbstractBackgroundRecent studies demonstrated that warming and elevated carbon dioxide (CO2) indirectly affect the soil microbial community structure via plant root exudates. However, there is no direct evidence for how the root exudates affect soil microbes and how the compositions of root exudates respond to climate change.ResultsThe results showed that warming directly decreased biomass of soil-borne bacteria and fungi forAcacia mearnsiiDe Willd but it did not impact soil microbial community forEucalyptus urophylla S.T. Blake. In contrast, elevated CO2had strong direct effect on increasing soil microbial biomass for both plant species. However, plant roots could significantly increase the secretion of antibacterial chemicals (most probable organic acids), which inhibited the growth of bacteria and fungi in elevated CO2environment. This inhibitory effect neutralized the facilitation from increasing CO2concentration on microbial growth.ConclusionsWe concluded that climate change can directly affect microorganisms, and indirectly affect the soil microbial community structure by changes in composition and content of plant root exudates.
Lack of association between intraoperative handoff of care and postoperative complications: a retrospective observational study
Authors: O’Reilly-Shah Vikas N. , Melanson Victoria G. , Sullivan Cinnamon L. , Jabaley Craig S. , Lynde Grant C. 
Published: October 2019

Abstract

Background
The significance of intraoperative anesthesia handoffs on patient outcomes are unclear. One aspect differentiating the disparate results is the treatment of confounding factors, such as patient comorbidities and surgery time of day. We performed this study to quantify the significance of confounding variables on composite adverse events during intraoperative anesthesia handoffs.

Methods
In this retrospective study, we analyzed data from the American College of Surgeons National Surgical Quality Improvement Project (ACS NSQIP). We examined the effects of intraoperative handoffs between anesthesia personnel. A total of 12,111 cases performed examined at two hospitals operated by a single healthcare system that were that included in the ACS NSQIP database performed. The presence of attending and anesthetist or resident handoffs, patient age, sex, body mass index, American Society of Anesthesiologists Physical Status (ASA-PS) classification, case length, surgical case complexity, and evening/weekend start time were measured.

Results
A total of 2586 of all cases in the NSQIP dataset experienced a handoff during the case. When analyzed as a single variable, attending handoffs were associated with higher rates of adverse outcomes. However, once confounding variables were added into the analysis, attending handoffs and complete care transitions were no longer statistically significant.

Conclusions
Inclusion of significant covariates is essential to fully understanding the impact provider handoffs have on patient outcomes. Case timing and lengthy case duration are more likely to result in both a handoff and an adverse event. The impact of handoffs on patient outcomes seen in the literature are likely due, in part, to how covariates were addressed.
Impact of multi-disciplinary treatment strategy on systolic heart failure outcome
Authors: Chen Shyh-Ming , Fang Yen-Nan , Wang Lin-Yi , Wu Ming-Kung , Wu Po-Jui , Yang Tsung-Hsun , Chen Yung-Lung , Hang Chi-Ling 
Published: October 2019

Abstract

Background
Patients with reduced ejection fraction have high rates of mortality and readmission after hospitalization for heart failure. In Taiwan, heart failure disease management programs (HFDMPs) have proven effective for reducing readmissions for decompensated heart failure or other cardiovascular causes by up to 30%. However, the benefits of HFDMP in different populations of heart failure patients is unknown.

Method
This observational cohort study compared mortality and readmission in heart failure patients who participated in an HFDMP (HFDMP group) and heart failure patients who received standard care (non-HFDMP group) over a 1-year follow-up period after discharge (December 2014 retrospectively registered). The components of the intervention program included a patient education program delivered by the lead nurse of the HFDMP; a cardiac rehabilitation program provided by a physical therapist; consultation with a dietician, and consultation and assessment by a psychologist. The patients were followed up for at least 1 year after discharge or until death. Patient characteristics and clinical demographic data were compared between the two groups. Cox proportional hazards regression analysis was performed to calculate hazard ratios (HRs) for death or recurrent events of hospitalization in the HFDMP group in comparison with the non-HFDMP group while controlling for covariates.

Results
The two groups did not significantly differ in demographic characteristics. The risk of readmission was lower in the HFDMP group, but the difference was not statistically significant (HR = 0.36, p = 0.09). In patients with ischemic cardiomyopathy, the risk of readmission was significantly lower in the HFDMP group compared to the non-HFDMP group (HR = 0.13, p = 0.026). The total mortality rate did not have significant difference between this two groups.

Conclusion
The HFDMP may be beneficial for reducing recurrent events of heart failure hospitalization, especially in patients with ischemic cardiomyopathy.

Trial registration
Longitudinal case-control study ISRCTN98483065, 24/09/2019, retrospectively registered.
The reliability and accuracy of operational system data in a nationwide helicopter emergency medical services mission database
Authors: Heino A. , Iirola T. , Raatiniemi L. , Nurmi J. , Olkinuora A. , Laukkanen-Nevala P. , Virkkunen I. , Tommila M. 
Published: October 2019

Abstract

Aim
The aim of this study was to evaluate the reliability and accuracy of documentation in FinnHEMS database, which is a nationwide helicopter emergency service (HEMS) clinical quality registry.

Methods
This is a nationwide study based on written fictional clinical scenarios. Study subjects were HEMS physicians and paramedics, who filled in the clinical quality registry based on the clinical scenarios. The inter-rater -reliability of the collected data was analyzed with percent agreement and free-marginal multi-rater kappa.

Results
Dispatch coding had a percent agreement of 91% and free-marginal multi-rater kappa value of 0.83. Coding for transportation or mission cancellation resulted in an agreement of 84% and free-marginal kappa value of 0.68. An agreement of 82% and a kappa value of 0.73 for dispatcher coding was found. Mission end, arrival at hospital and HEMS unit dispatch -times had agreements from 80 to 85% and kappa values from 0.61 to 0.73. The emergency call to dispatch centre time had an agreement of 71% and kappa value of 0.56. The documentation of pain had an agreement of 73% on both the first and second measurements. All other vital parameters had less than 70% agreement and 0.40 kappa value in the first measurement. The documentation of secondary vital parameter measurements resulted in agreements from 72 to 91% and kappa values from 0.43 to 0.64.

Conclusion
Data from HEMS operations can be gathered reliably in a national clinical quality registry. This study revealed some inaccuracies in data registration and data quality, which are important to detect to improve the overall reliability and validity of the HEMS clinical quality register.
Acute poisoning related to the recreational use of prescription drugs: an observational study from Oslo, Norway
Authors: Grimsrud Marit Mæhle , Brekke Mette , Syse Victoria Lykke , Vallersnes Odd Martin 
Published: October 2019

Abstract

Background
Recreational use of prescription drugs is widespread. We describe acute poisonings related to the recreational use of prescription drugs.

Methods
Retrospective observational study. We retrospectively registered all patients presenting from October 2013 through March 2015 at a primary care emergency outpatient clinic in Oslo, Norway, with an acute poisoning related to recreational drug use. We registered demographic data, toxic agents taken, clinical course and treatment. From this data set we extracted the 819/2218 (36.9%) cases involving one or more prescription drugs.

Results
Among the 819 included cases, 190 (23.2%) were female. Median age was 37 years. The drugs most commonly involved were benzodiazepines in 696 (85.0%) cases, methadone in 60 (7.3%), buprenorphine in 53 (6.5%), other opioids in 56 (6.8%), zopiclone/zolpidem in 26 (3.2%), and methylphenidate in 11 (1.3%). Prescription drugs were combined with other toxic agents in 659 (80.5%) cases; heroin in 351 (42.9%), ethanol in 232 (28.3%), amphetamine in 141 (17.2%), cannabis in 70 (8.5%), gamma-hydroxybutyrate (GHB) in 34 (4.2%), cocaine in 29 (3.5%), and other illegal drugs in 46 (5.6%). The patient was given naloxone in 133 (16.2%) cases, sedation in 15 (1.8%), and flumazenil in 3 (0.4%). In 157 (19.2%) cases, the patient was sent on to hospital.

Conclusions
One in three acute poisonings related to recreational drug use involved prescription drugs. Benzodiazepines were by far the most common class of drugs. Prescription drugs had mostly been taken in combination with illegal drugs or ethanol.
Prevalence of mild hyponatremia and its association with falls in older adults admitted to an emergency geriatric medicine unit (the MUPA unit)
Authors: Boyer Sophie , Gayot Caroline , Bimou Charlotte , Mergans Thomas , Kajeu Patrick , Castelli Muriel , Dantoine Thierry , Tchalla Achille 
Published: October 2019

Abstract

Background
Hyponatremia is the most common electrolyte disorder in older adults and it can increase morbidity and mortality. Approximately one in three older adults fall each year; mild chronic hyponatremia can predispose this group to injurious falls and fractures and serum levels of sodium can also influence bone health. Little is known regarding the association between mild chronic hyponatremia and injurious fall prevalence in elderly patients admitted to the Emergency Department (ED). Therefore, the present study investigated the link between mild hyponatremia and the risk of injurious falls in elderly patients admitted to the Emergency Geriatric Medicine Unit (The MUPA Unit).

Methods
This cross-sectional study was conducted over 4 months and included patients ≥75 years of age who were admitted to the MUPA Unit of University Hospital Center of Limoges (France). Sociodemographic factors, fall events, comorbidities, medications, and sodium levels were assessed (hyponatremia was considered as sodium level < 136 mEq/L). Additionally, the short Comprehensive Geriatric Assessment (short-CGA), the Frailty score on the Short Emergency Geriatric Assessment (SEGA), and the Katz Activity of Daily Living (ADL) scale were administered.

Results
Of the 696 cases included in the final analysis, the mean age was 86.1 ± 5.6 years and 63.1% were female. The prevalence of falls was 27.9% (95% confidence interval [CI]: 24.6–31.2%) and that of mild hyponatremia was 15.9% (95% CI: 13.2–18.6%). The prevalence rate of mild hyponatremia was 13.2% (95% CI: 10.1–16.3%) in patients without falls and 26.1% (95% CI: 19.8–32.4%) in patients admitted for falls. Mild hyponatremia was significantly associated with falls (P < 0.001) and the adjusted odds ratio (OR) was 3.02 (95% CI: 1.84–4.96).

Conclusions
Because mild hyponatremia might be a risk factor for injurious falls and ED admission, determination of sodium levels during basic biomarker assessment on ED admission could be an important component of fall prevention strategies for the elderly.