bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparison of the efficacy of a bougie and stylet in patients with endotracheal intubation: A meta-analysis of randomized controlled trials
Authors: Sheu Yu-Jia , Yu Sung-Wei , Huang Tsai-Wei , Liu Feng-Lin , Lin Yen-Kuang , Tam Ka-Wai 
Published: February 2019

BACKGROUND
Endotracheal intubation (ETI) is a procedure widely performed for several clinical indications. In typical ETI, an endotracheal tube is placed into a patient's trachea with the help of a malleable metal rod covered with a clear plastic sheath (called a stylet). However, another intubation aid, a bougie (also named a gum elastic bougie or endotracheal tube introducer), was also introduced in the clinical setting to improve the efficacy of conventional ETI.

METHODS
This study performed a systematic review and meta-analysis of randomized controlled trials to compare the efficacy of bougie and stylet approaches in ETI. PubMed, Embase, and Cochrane Library databases were searched for studies published before November 2018. Randomized controlled trials comparing the clinical outcomes of bougie and stylet approaches in patients who underwent orotracheal intubation were included. Meta-analyses were conducted by using a random effects model, and treatment efficacy was measured by evaluating the first-attempt success rate and intubation duration.

RESULTS
A total of 5 randomized controlled trials and 1,038 patients were included. Although a bougie resulted in a better first-attempt success rate, no significant difference was observed between the approaches (risk ratios, 1.03; 95% confidence interval, 0.85–1.24). Moreover, no significant differences were observed in the intubation duration and esophageal intubation rate between the bougie and stylet approaches.

CONCLUSION
Endotracheal intubation performed with a bougie was not superior over ETI performed with a stylet. Therefore, intubation approaches should be selected by considering personal preference and clinician expertise.

LEVEL OF EVIDENCE
Systematic review and meta-analysis, level II.
Structure and function of a trauma intensive care unit: A report from the Trauma Intensive Care Unit Prevalence Project
Authors: Michetti Christopher P. , Fakhry Samir M. , Brasel Karen , Martin Niels D. , Teicher Erik J. , Liu Chang , Newcomb Anna 
Published: February 2019

BACKGROUND
Specialized trauma intensive care unit (TICU) care impacts patient outcomes. Few studies describe where and how TICU care is delivered. We performed an assessment of TICU structure and function at a sample of US trauma center TICUs.

METHODS
This was a multicenter study in which participants supplied information about their trauma centers, staff, clinical protocols, processes of care, and study TICU (the ICU admitting the majority of trauma patients).

RESULTS
Forty-five Level I trauma centers trauma centers enrolled through the American Association for the Surgery of Trauma multi-institutional trials platform; 71.1% had less than 750 beds and 55.5% treated 1,000 to 2,999 trauma activations/year. The median number of hospital ICU beds was 109 [66–185]. 46.7% were “closed” ICUs, 20% were “open,” and 82.2% had mandatory intensivist consultation. 42.2% ICUs were classified as trauma (≥80% of patients were trauma), 46.7% surgical/trauma, and 11.1% medical-surgical. Trauma ICUs had a median 10 [7–12] intensivists. Intensivists were present 24 hours/day in 80% of TICUs. Centers reported a median of 8 (interquartile range [IQR], 6–10) full-time trauma surgeons, whose ICU duties comprised 25% (IQR, 20%–40%) of their clinical time and 20% (IQR, 20–33) of total work time. A median 16 (IQR, 12–23) ICU beds in use were staffed by 10 (IQR, 7–14) nurses. There was considerable variation in the number and type of protocols used and in diagnostic methods for ventilator-associated pneumonia. Daily patient care checklists were used by 80% of ICUs. While inclusion of families on rounds was performed in 91.1% of ICUs, patient- and family-centered support programs were less common.

CONCLUSION
A study of structure and function of TICUs at a sample of Level I trauma centers revealed that presence of nontrauma patients was common, critical care is a significant component of trauma surgeons' professional practice, and significant variation exists in care delivery models and protocol use. Opportunities may exist to improve care through sharing of best practices.

LEVEL OF EVIDENCE
Therapeutic/Care management, level IV.
Nondisjunction and unequal spindle organization accompany the drive ofAegilops speltoidesB chromosomes
Authors: Wu DanDan , Ruban Alevtina , Fuchs Jörg , Macas Jiri , Novák Petr , Vaio Magdalena , Zhou YongHong , Houben Andreas 
Published: February 2019

AbstractSupernumerary B chromosomes (Bs), which are often preferentially inherited, deviating from usual Mendelian segregation. This chromosome drive is one of the most important features of Bs. Here we analyzed the drive mechanism ofAegilops speltoidesBs and provide direct insight into its cellular mechanism. Comparative genomics resulted in the identification of the tandem repeat AesTR-183 ofAe. speltoidesBs, which also can be found on the Bs ofAe. muticaand rye, was used to track Bs during microgametogenesis. Nondisjunction of CENH3-positive, tubulin interacting B sister chromatids and an asymmetric spindle during first pollen grain mitosis are likely components of the accumulation process. A quantitative flow cytometric approach revealed, that independent on the number of Bs present in the mother plant Bs accumulate in the generative nuclei with more than 93%. Nine of eleven tested (peri)centromeric repeats were shared by A and B chromosomes. A common origin of the drive process inPoaceaeis likely.
Sox17expression in endocardium precursor cells regulates heart development in mice
Authors: Saba Rie , Kitajima Keiko , Rainbow Lucille , Engert Sylvia , Uemura Mami , Ishida Hidekazu , Kokkinopoulos Ioannis , Shintani Yasunori , Miyagawa Shigeru , Kanai Yoshiakira , Azuma-Kanai Masami , Koopman Peter , Meno Chikara , Kenny John , Lickert Heiko , Saga Yumiko , Suzuki Ken , Sawa Yoshiki , Yashiro Kenta 
Published: February 2019

AbstractThe endocardium is the endothelial component of the vertebrate heart and plays a key role in heart development. Cardiac progenitor cells (CPCs) that express the homeobox geneNkx2-5give rise to the endocardium. Where, when, and how the endocardium segregates during embryogenesis have remained largely unknown, however. We now show thatNkx2-5+CPCs that express the Sry-type HMG box geneSox17specifically differentiate into the endocardium in mouse embryos. Approximately 20% to 30% ofNkx2-5+CPCs transiently expressSox17from embryonic day (E) 7.5 to E8.5.AlthoughSox17is not essential or sufficient for endocardium fate, it can bias the fate of CPCs toward the endocardium. On the other hand,Sox17expression in the endocardium is required for heart development. Deletion ofSox17specifically in the mesoderm markedly impaired endocardium development with regard to cell proliferation and behavior. The proliferation of cardiomyocytes, ventricular trabeculation, and myocardium thickening were also impaired in a non–cell-autonomous manner in theSox17mutant, resulting in anomalous morphology of the heart, likely as a consequence of down-regulation of NOTCH signaling. Changes in gene expression profile in both the endocardium and myocardium preceded the reduction in NOTCH-related gene expression in the mutant embryos, suggesting thatSox17expression in the endocardium regulates an unknown signal required for nurturing of the myocardium. Our results thus provide insight into differentiation of the endocardium and its role in heart development.SignificanceThe endocardium is vital for vertebrate heart development; however, the molecular mechanisms regulating fate determination and differentiation remain largely unknown. Here, we show that a part of the earliest cardiac progenitor cells (CPCs) transiently and exclusively expressSry-type HMG box geneSox17in the mouse embryo.Sox17-expressing CPCs specifically differentiate to the endocardium.Sox17biases the fate of CPCs toward the endocardium, and regulates proliferation and cellular behavior cell autonomously. Conversely,Sox17in the endocardium regulates the myocardium non-cell autonomously. Notably,Sox17is required for the ventricular trabeculation via the NOTCH signal that is not directly induced but maintained bySox17. This study, thus, sheds light on endocardium development.
The Genetic Basis of Transcriptional and Spatial Heterogeneity of Squamous Features in Pancreatic Ductal Adenocarcinoma
Authors: Hayashi Akimasa , Fan Jun , Chen Ruoyao , Ho Yu-jui , Makohon-Moore Alvin P. , Zhong Yi , Hong Jungeui , Sakamoto Hitomi , Attiyeh Marc A. , Kohutek Zachary A. , Zhang Lance , Huang Jinlong , Boumiza Aida , Kappagantula Rajya , Baez Priscilla , Wood Laura D. , Hruban Ralph H. , Marta Lisi , Chadalavada Kalyani , Nanjangud Gouri J. , Basturk Olca , Klimstra David S. , Overholtzer Michael , Iacobuzio-Donahue Christine A. 
Published: February 2019

SummaryRecent studies indicate that pancreatic cancer expression profiles are variable and largely reflect a classical or basal-type phenotype. We performed genetic sequencing, RNA-seq, and histologic review of multiregion sampled pancreatic cancers and found that squamous and squamoid features, indicators of poor prognosis, correlate with a “basal-like” expressional type. Cancers with squamous features were more likely to have truncal mutations in chromatin modifier genes and intercellular heterogeneity for MYC amplification that was associated with entosis. In most patients the basal phenotype coexisted with a glandular component, and phylogenetic studies indicated that it arose from a subclonal population in the tumor. These data provide a unifying paradigm for understanding the interrelationship of basal-type features, squamous histology, and somatic mutations in chromatin modifier genes in the context of the clonal evolution of pancreatic cancer.
Thermal cycling-hyperthermia in combination with polyphenols, epigallocatechin gallate and chlorogenic acid, exerts synergistic anticancer effect against human pancreatic cancer PANC-1 cells
Authors: Lu Chueh-Hsuan , Chen Wei-Ting , Hsieh Chih-Hsiung , Kuo Yu-Yi , Chao Chih-Yu 
Published: February 2019

AbstractHyperthermia (HT) has shown feasibility and potency as an anticancer therapy. Administration of HT in the chemotherapy has previously enhanced the cytotoxicity of drugs against pancreatic cancer. However, the drugs used when conducting these studies are substantially conventional chemotherapeutic agents that may cause unwanted side effects. Additionally, the thermal dosage in the treatment of cancer cells could also probably harm the healthy cells. The purpose of this work was to investigate the potential of the two natural polyphenolic compounds, epigallocatechin gallate (EGCG) and chlorogenic acid (CGA), as heat synergizers in the thermal treatment of the PANC-1 cells. Furthermore, we have introduced a novel strategy entitled the thermal cycling-hyperthermia (TC-HT) that is capable of providing a maximum synergy and minimal side effect with the anticancer compounds. Our results demonstrate that the combination of the TC-HT and the CGA or EGCG markedly exerts the anticancer effect against the PANC-1 cells, while none of the single treatment induced such changes. The synergistic activity was attributed to the cell cycle arrest at the G2/M phase and the induction of the ROS-dependent mitochondria-mediated apoptosis. These findings not only represent the first thermal synergistic study of natural compounds in the treatment of pancreatic cancer, but also highlight the potential application of the TC-HT as an alternative strategy in anticancer treatment.
Microbiotyping the sinonasal microbiome
Authors: Bassiouni Ahmed , Paramasivan Sathish , Shiffer Arron , Dillon Matthew R , Cope Emily K , Cooksley Clare , Ali Mohammad Javed , Bleier Benjamin , Callejas Claudio , Cornet Marjolein E , Douglas Richard G , Dutra Daniel , Georgalas Christos , Harvey Richard J , Hwang Peter H , Luong Amber U , Schlosser Rodney J , Tantilipikorn Pongsakorn , Tewfik Marc A , Vreugde Sarah , Wormald Peter-John , Caporaso J Gregory , Psaltis Alkis J 
Published: February 2019

AbstractThis study offers a novel description of the sinonasal microbiome, through an unsupervised machine learning approach combining dimensionality reduction and clustering. We apply our method to the International Sinonasal Microbiome Study (ISMS) dataset of 410 sinus swab samples. We propose three main sinonasal ‘microbiotypes’ or ‘states’: the first is Corynebacterium-dominated, the second is Staphylococcus-dominated, and the third dominated by the other core genera of the sinonasal microbiome (Streptococcus, Haemophilus, Moraxella, and Pseudomonas). The prevalence of the three microbiotypes studied did not differ between healthy and diseased sinuses, but differences in their distribution were evident based on geography. We also describe a potential reciprocal relationship between Corynebacterium species and Staphylococcus aureus, suggesting that a certain microbial equilibrium between various players is reached in the sinuses. We validate our approach by applying it to a separate 16S rRNA gene sequence dataset of 97 sinus swabs from a different patient cohort. Sinonasal microbiotyping may prove useful in reducing the complexity of describing sinonasal microbiota. It may drive future studies aimed at modeling microbial interactions in the sinuses and in doing so may facilitate the development of a tailored patient-specific approach to the treatment of sinus disease in the future.
Investigating on-road lane maintenance and speed regulation in post-stroke driving: a pilot case-control study
Authors: Zhou Heng , Sun Qian (Chayn) , Blane Alison , Hughes Brett , Falkmer Torbjörn , Xia Jianhong (Cecilia) 
Published: February 2019

ABSTRACTThe post-stroke population is expected to rise and the cohort of post-stroke individuals who wish to return to driving is likely to rapidly increase too. Stroke can adversely affect coordination and judgement of drivers due to the executive dysfunction, which is relatively common in the post-stroke population but often undetected. Quantitatively examining vehicle control performance in post-stroke driving becomes essential to inspect whether and where post-stroke drivers are risky. To date, it is unclear as to which indicators, such as lane keeping or speed control, can differentiate driving performance of post-stroke drivers from that of normal (neurotypical) older drivers. By employing a case-control design using advanced vehicle movement tracking and analysis technology, this pilot study aimed to compare the variations in driving trajectory, lane keeping and speed control between the two groups using spatial and statistical techniques. The results showed that the mean Standard Deviation of Lane Deviation (SDLD) in post-stroke participants was higher than those of normal participants in complex driving tasks (U-turn and left turn) but almost the same in simple driving tasks (straight-line sections). No statistically significant differences were found in the speed maintenance between the post-stroke drivers and the normal adults. The findings indicate that, although older drivers can still drive as they need to after a stroke, the decline in cognitive abilities still imposes higher cognitive workload and more effort for post-stroke older drivers. Future studies can investigate post-stroke adults’ driving behaviour at more challenging driving scenarios, or design driving intervention program to improve their executive function in driving.
Identification of genetic markers for cortical areas using a Random Forest classification routine and the Allen Mouse Brain Atlas
Authors: Weed Natalie , Bakken Trygve , Graddis Nile , Gouwens Nathan , Millman Daniel , Hawrylycz Michael , Waters Jack 
Published: February 2019

AbstractThe mammalian neocortex is subdivided into a series of ‘cortical areas’ that are functionally and anatomically distinct, and are often distinguished in brain sections using histochemical stains and other markers of protein expression. We searched the Allen Mouse Brain Atlas, a database of gene expression, for novel markers of cortical areas. We employed a random forest algorithm to screen for genes that change expression at area borders. We found novel genetic markers for 19 of 39 areas and provide code that quickly and efficiently searches the Allen Mouse Brain Atlas.
Isolation and characterization of live yeast cells from ancient vessels as a tool in bio-archeology
Authors: Aouizerat Tzemach , Gutman Itai , Paz Yitzhak , Maeir Aren M. , Gadot Yuval , Gelman Daniel , Szitenberg Amir , Drori Elyashiv , Pinkus Ania , Schoemann Miriam , Kaplan Rachel , Ben-Gedalya Tziona , Coppenhagen-Glazer Shunit , Reich Eli , Saragovi Amijai , Lipschits Oded , Klutstein Michael , Hazan Ronen 
Published: February 2019

AbstractAncient fermented food has been studied based on recipes, residue analysis and ancient-DNA techniques and reconstructed using modern domesticated yeast. Here, we present a novel approach. We hypothesize that enriched yeast populations in fermented beverages could have become the dominant species in storage vessels and the descendants of these yeast could be isolated and studied long after. To this end, using a pipeline of yeast isolation from clay vessels developed here, we screened for yeast cells in beverage-related and non-related ancient vessels and sediments, from several archeological sites. We found that yeast cells could be successfully isolated specifically from clay containers of fermented beverages. Genomic analysis revealed that these yeast are similar to those found in traditional African beverages. Phenotypically, they grow similar to modern-beer producing yeast. Both strongly suggesting that they are descendants of the original fermenting yeast. These findings provide modern microorganisms as a new tool in bio-archeology.ImportanceSo far, most of the study of ancient organisms was based mainly on the analysis of ancient DNA. Here we show that it is possible to isolate and study microorganisms, yeast in this case, from thousands of years old clay vessels, used for fermentation. We demonstrate that it is highly likely that these cells are descendants of the original yeast strains which participated in the fermentation process and were absorbed into the pottery vessels. Moreover, we characterize the isolated yeast their genome and the beer they produce. These results open new and exciting avenues in the study of domesticated microorganisms and contribute significantly to the fields of bio and experimental –archeology that aims to reconstruct ancient artifacts and products.
The successful invasion of the European earwig across North America reflects adaptations to thermal regimes but not mean temperatures
Authors: Tourneur Jean-Claude , Meunier Joël 
Published: February 2019

ABSTRACTUnderstanding the mechanisms by which an introduced species adapt to newly encountered habitats is a major question in ecology. A key method to address this question is to collect data on introduced species that have successfully invaded a broad diversity of novel environments, and analyze how their life-history traits changed with these new constraints. Here, we present and analyze such a unique data set in the European earwigForficula auriculariaL, an insect that invaded North America during the last century. We conducted a common garden experiment, in which we measured 13 life-history traits in 4158 individuals from 19 populations across North America. Our results demonstrate that the successful invasion of this species came with changes in 10 of their life-history traits in response to thermal regimes (winter-summer and autumn-spring temperatures), but with no change in response to the overall mean temperatures of the invaded locations. Importantly, we show that some of these changes are by-products of novel thermal regimes, whereas others reflect adaptive strategies of females to these constraints. Overall, our findings reveal the importance of thermal regimes over mean temperatures in climate adaptation, and emphasize that studying adaptive capabilities is crucial to predict the limits of biological invasions.
The pharmacodynamic inoculum effect from the perspective of bacterial population modeling
Authors: Baeder Desiree Y. , Regoes Roland R. 
Published: February 2019

SynopsisBackgroundThe quantitative determination of the effects of antimicrobials is essential for our understanding of pharmacodynamics and for their rational clinical application. However, common pharmacodynamic measures of antimicrobial efficacy, such as the MIC and the pharmacodynamic function, fail to capture the observed dependence of efficacy on the bacterial population size — a phenomenon called inoculum effect.ObjectivesWe aimed to assess the relationship between bacterial inoculum size and pharmacodynamic parameters, and to determine the consequences of the inoculum effect on bacterial population dynamics under treatment with antimicrobials.MethodsWe used the mathematical multi-hit model to quantify the effect of the inoculum on the pharmacodynamic parameters. The model describes antimicrobial action mechanistically, which allowed us to test various hypotheses concerning the mechanistic basis of the inoculum effect.ResultsOur model showed that the inoculum effect can arise from the binding dynamics of antimicrobial molecules to bacterial targets alone and does not require enzymatic degradation of antimicrobials. With enzymatic degradation, however, the inoculum effect is more pronounced. We propose to include the inoculum effect when measuring antimicrobial efficacy, i. e. to extend the pharmacodynamic function with the inoculum effect. This extended pharmacodynamic function mimiced simple long-term population dynamics well. More complex scenarios were only captured with the mechanism-based multi-hit model. In simulations with competing antimicrobial-sensitive and -resistant bacteria, neglecting the inoculum effect lead to an overestimation of the competitive ability of the resistant strain.ConclusionsOur work emphasizes that the pharmacodynamic function — and in general any efficacy measure, e.g. the MIC — should include information about the inoculum size on which it is based, and ideally account for the inoculum effect.
CompScore: boosting structure-based virtual screening performance by incorporating docking scoring functions components into consensus scoring
Authors: Perez-Castillo Yunierkis , Sotomayor-Burneo Stellamaris , Jimenes-Vargas Karina , Gonzalez-Rodriguez Mario , Cruz-Monteagudo Maykel , Armijos-Jaramillo Vinicio , Cordeiro M. Natália D. S. , Borges Fernanda , Sánchez-Rodríguez Aminael , Tejera Eduardo 
Published: February 2019

AbstractConsensus scoring has become a commonly used strategy within structure-based virtual screening (VS) workflows with improved performance compared to those based in a single scoring function. However, no research has been devoted to analyze the worth of docking scoring functions components in consensus scoring. We implemented and tested a method that incorporates docking scoring functions components into the setting of high performance VS workflows. This method uses genetic algorithms for finding the combination of scoring components that maximizes the VS enrichment for any target. Our methodology was validated using a dataset that contains ligands and decoys for 102 targets that has been widely used in VS validation studies. Results show that our approach outperforms other methods for all targets. It also boosts the initial enrichment performance of the traditional use of whole scoring functions in consensus scoring by an average of 45%. CompScore is freely available at: http://bioquimio.udla.edu.ec/compscore/