bluuebunny/crossref_metadata_2025_split huggingface dataset:
Trans-Esophageal Doppler Assessment of Acute Hemodynamic Changes Due to Prone Positioning in Acute Respiratory Distress Syndrome Patients
Authors: Saran Sai , Gurjar Mohan , Azim Afzal , Mishra Prabhaker , Ghosh Pralay S. , Baronia Arvind K. , Poddar Banani , Singh Ratender K. 
Published: November 2018

ABSTRACT

Background:
Effect of prone positioning on acute hemodynamic changes (within 10 min) in acute respiratory distress syndrome (ARDS) has not been studied.

Methods:
In this prospective observational study, hemodynamic assessment by trans-esophageal Doppler (TED) was done with the primary aim of measuring early changes in cardiac index (CI), if any, after prone positioning in moderate to severe ARDS patients. A subgroup analysis was also done based on the response to passive leg raise (PLR).

Results:
The baseline hemodynamic variables of 26 included patients were: CI 3.5 (3.1–4.3) L/min/m2, peak velocity (PV) 83.2 (60.9–99.3) cm/s, flow time corrected (FTc) 341 (283–377) ms, mean acceleration (MA) 9.0 (7.04–11.7) m/s2. After prone position, there were no statistically significant changes in CI, 3.5 (P=0.83), 3.75 (P = 0.96), 3.7 (P = 0.34), and 3.9 (P = 0.95) at 5, 10, 20, and 30 min respectively. FTc, mainly indicator of preload, showed decreasing trend to 315 (275–367) ms at 30 min post prone (P = 0.06). On the basis of PLR test also, CI did not change significantly in both PLR+ and PLR− groups. In PLR+ group, PV increased from 72.4 to 83 (P = 0.01), 74.9 (P = 0.03), 82 (P = 0.02), and 82 (P = 0.03) cm/s; while in PLR− group, MA increased from 8.8 to 9.7 (P = 0.03), 10.1 (P = 0.03), 9.3 (P = 0.04), and 10.6 (P = 0.01) m/s2 at 5, 10, 20, and 30 min respectively.

Conclusions:
In moderate to severe ARDS patients, there were no significant changes in CI during first 30 min after prone positioning, even in the subgroups on the basis of PLR response.
Transgender Surgery and Outcomes: Focused for the FPMRS Provider
Authors: Hughes Michael , Nikolavsky Dmitriy , Ginzburg Natasha 
Published: November 2018

Overview
As visibility of the transgender population increases, understanding of the social, psychological, medical, and surgical aspects of these patients care is vital for the practicing female pelvic medicine and reconstructive surgery urologist. The aim of this review is to describe proper terminology, psychosocial considerations specific to transgender patients, in addition to outlining contemporary surgical techniques and complications.
Correlates and Outcomes of Low Physical Activity Posttransplant: A Systematic Review and Meta-Analysis
Authors: Berben Lut , Engberg Sandra J. , Rossmeissl Anja , Gordon Elisa J. , Kugler Christiane , Schmidt-Trucksäss Arno , Klem Mary Lou , Sereika Susan M. , De Simone Paolo , Dobbels Fabienne , De Geest Sabina M. 
Published: November 2018

Background.
Little is known about associations between low physical activity (PA) and its correlates and outcomes in solid organ transplant recipients. This systematic review with meta-analysis examined correlates and outcomes associated with low PA (ie, not meeting individual study’s definition of being physically active) following solid organ transplantation.

Methods.
We searched PubMed, CINAHL, PsycINFO, and EMBASE from inception to February 2016 to identify peer-reviewed data-based articles. Articles published in English, German, Spanish, French, Italian, Portuguese, or Dutch that examined correlates or outcomes associated with low PA in adult single, solid organ transplant recipients were included. Studies’ quality was assessed using a 14-item checklist. Pooled odds ratios and 95% confidence intervals were computed for correlates and outcomes examined in ≥5 studies.

Results.
Of 7401 publications screened, 34 studies met inclusion criteria and were included in the overall synthesis with 15 included in the meta-analysis. Most focused on renal transplantation (n = 18, 53%) and used cross-sectional designs (n = 26, 77%). Of 30 correlates examined, [condition-related (n = 11), social/economic-related (n = 9), patient-related (n = 4), healthcare system-related (n = 3), and treatment-related (n = 3)], only 4 were examined ≥5 times and included in meta-analyses. None were significantly related to low PA. Of 19 outcomes assessed, only physical health-related quality of life was examined ≥5 times. Low PA was significantly associated with low physical health-related quality of life (odds ratio = 0.172, 95% confidence interval = 0.08–0.37).

Conclusions.
We found few studies examining most correlates and outcomes related to low PA despite growing evidence that improving PA might be an effective intervention in improving posttransplant outcomes.
Human Atrial Natriuretic Peptide in Cold Storage of Donation After Circulatory Death Rat Livers: An Old but New Agent for Protecting Vascular Endothelia?
Authors: Nigmet Yermek , Hata Koichiro , Tamaki Ichiro , Okamura Yusuke , Tsuruyama Tatsuaki , Miyauchi Hidetaka , Kusakabe Jiro , Tajima Tetsuya , Hirao Hirofumi , Kubota Toyonari , Inamoto Osamu , Yoshikawa Junichi , Goto Toru , Tanaka Hirokazu , Uemoto Shinji 
Published: November 2018

Background.
Current critical shortage of donor organs has increased the use of donation after circulatory death (DCD) livers for transplantation, despite higher risk for primary nonfunction or ischemic cholangiopathy. Human atrial natriuretic peptide (hANP) is a cardiovascular hormone that possesses protective action to vascular endothelia. We aimed to clarify the therapeutic potential of hANP in cold storage of DCD livers.

Methods.
Male Wistar rats were exposed to 30-minute warm ischemia in situ. Livers were then retrieved and cold-preserved for 6 hours with or without hANP supplementation. Functional and morphological integrity of the livers was evaluated by oxygenated ex vivo reperfusion at 37°C.

Results.
hANP supplementation resulted in significant reduction of portal venous pressure (12.2 ± 0.5 versus 22.5 ± 3.5 mm Hg, P < 0.001). As underlying mechanisms, hANP supplementation significantly increased tissue adenosine concentration (P = 0.008), resulting in significant upregulation of endothelial nitric oxide synthase and significant downregulation of endothelin-1 (P = 0.01 and P = 0.004 vs. the controls, respectively). Consequently, hANP significantly decreased transaminase release (P < 0.001) and increased bile production (96.2 ± 18.2 versus 36.2 ± 15.2 μL/g-liver/h, P < 0.001). Morphologically, hepatocytes and sinusoidal endothelia were both better maintained by hANP (P = 0.021). Electron microscopy also revealed that sinusoidal ultrastructures and microvilli formation in bile canaliculi were both better preserved by hANP supplementation. Silver staining also demonstrated that hANP significantly preserved reticulin fibers in Disse space (P = 0.017), representing significant protection of sinusoidal frameworks/architectures.

Conclusions.
Supplementation of hANP during cold storage significantly attenuated cold ischemia/warm reperfusion injury of DCD livers.
A degenerate polar lattice for cloaking in full two-dimensional elastodynamics and statics
Authors: Nassar H. , Chen Y. Y. , Huang G. L. 
Published: November 2018

A lattice design of a cloak for full two-dimensional elasticity is suggested when the background continuum is isotropic with Lamé parameters (λ,
μ
) satisfying
μ
≤ λ. The lattice is
polar
in the sense that it elastically resists rotations; and is
degenerate
meaning it admits a stressless collapse mechanism. These characteristics are attained through the use of appropriately distributed restoring torques in conjunction with hinge-like spring-mass contacts. Thus, the lattice is proven to exhibit a rank-3 elasticity tensor lacking the minor symmetries. Accordingly, it rigorously adheres to the form-invariance requirements of the transformation method under the Brun–Guenneau–Movchan gauge. The cloak is numerically tested in statics and in dynamics under pressure and shear incident waves and shows satisfactory performance. Finally, a theoretical generalization extends the design to three dimensions and to arbitrarily anisotropic backgrounds so as to enable cloaking as well as other transformation-based static and dynamic field manipulation techniques in these cases.
Effects of Fermented Idesia Polycarpa Residues supplementation on laying performance of Laying Quails
Authors: Liu Xinanbei , Li Na , Shu Yueyue , Sun Yiran , Li Yu , Hua Wang , Ye Yang , Chen Fang , Tang Lin 
Published: November 2018

AbstractAlthough Idesia polycarpa oil has been wildly explored as a raw material for biodiesel, the reports studying the by-product Idesia polycarpa fruit residues (IPR) are few. This study aimed to evaluate the effect of the Idesia polycarpa fruit residues fermented feed additive (IPFF) on the egg production of laying quails. The egg production and related performances include egg quality, yolk cholesterol, yolk fatty acid, quails’ jejunum morphology, and relative gene expression were determined in this study. Compared to the standard diet group, birds fed the 1% IPFF showed a higher egg production (87.7% on average, 11.5% above the control; P<0.01). The yolk fatty acid composition and n6/n3 ratio were affected by IPFF or IPR. Compared to the standard diet group, the egg cholesterol content was lower in both IPFF and IPR groups, and the yolk n6/n3 ratio in the 5% IPFF group (10.3; P<0.01) was more reasonable. Meanwhile, birds under IPFF dietary supplement showed a thicker jejunum wall, higher villus, and deeper crypt than the standard diet group. In addition, the altered mRNA expression of four genes involved in cholesterol and fatty acids metabolism (SREBP-1, SREBP-2, ADGL, APOVLDL-II) in the 1% IPFF group and 5% IPR group indicated that the lipids metabolism and transportation were enhanced in the interclavicular fat pad and liver, relative to the standard diet group.HIGHLIGHTSEgg production was higher in IPFF groupsEgg cholesterol was lower in IPFF groupsLipid metabolism and transportation was enhanced in IPFF groupsIntestine wall was thicker in IPFF groups
‘Fishing’ for Mitochondrial DNA in The Egyptian Sacred Ibis Mummies
Authors: Wasef Sally , Huynen Leon , Millar Craig Donald , Subramanian Sankar , Ikram Salima , Holland Barbra , Willerslev Eske , Lambert David Martin 
Published: November 2018

AbstractThe long-term preservation of DNA requires a number of optimal conditions, including consistent exposure to cool, dry, and dark environments. As a result, the successful recovery of ancient DNA from material from warmer climates such as those in Egypt has often been met with scepticism. Egypt has an abundance of ancient mummified animals and humans, whose genetic analyses would offer important insights into ancient cultural practices. To date, the retrieval of complete genomes from ancient Egyptian remains of humans or other animals has been largely unsuccessful. To test for the presence of even short DNA sequences in Egyptian material, we performed second-generation shotgun sequencing of DNA libraries constructed from ancient Sacred Ibis mummies. Since most of the resulting Illumina libraries were shown to contain extremely low levels (less than 0.06%) of endogenous mitochondrial DNA, we aimed to enrich these samples using targeted in-solution hybridisation methods. Using biotinylated RNA baits designed to Sacred Ibis complete mitochondrial sequences, we trialled a number of conditions and parameters and achieved up to 4705-fold enrichment. We also found that a combination of hybridisation temperature and the use of the polymerase KAPA HiFi significantly increased both the efficiency of targeted hybridisation and post-hybridisation amplification respectively. Furthermore, improved enrichment was accompanied with only minor increases in clonality. Our method enabled us to reconstruct the first complete mitochondrial genomes from ancient Egyptian sub-fossil material.
Structural and biochemical studies define Nudt12 as a new class of RNA deNADding enzyme in mammalian cells
Authors: Grudzien-Nogalska Ewa , Wu Yixuan , Jiao Xinfu , Cui Huijuan , Hart Ronald P. , Tong Liang , Kiledjian Megerditch 
Published: November 2018

ABSTRACTWe recently demonstrated mammalian cells harbor NAD-capped mRNAs that are hydrolyzed by the DXO deNADding enzyme. Here we report the Nudix protein Nudt12 is a second mammalian deNADding enzyme structurally and mechanistically distinct from DXO and targets different RNAs. Crystal structure of mouse Nudt12 in complex with the deNADding product AMP and three Mg2+ ions at 1.6 Å resolution provides exquisite insights into the molecular basis of the deNADding activity within the NAD pyrophosphate. Disruption of the Nudt12 gene stabilizes transfected NAD-capped RNA in cells and its endogenous NAD-capped mRNA targets are enriched in those encoding proteins involved in cellular energetics. Furthermore, exposure of cells to metabolic stress manifests changes in NAD-capped RNA levels indicating an association between NAD-capped RNAs and cellular metabolism. Lastly, we show that the bacterial RppH protein also possesses deNADding activity toward NAD-capped RNA but not free NAD, revealing a third class of deNADding enzymes.
aFARP-ChIP-seq, a convenient and reliable method for genome profiling in as few as 100 cells with a capability for multiplexing ChIP-seq
Authors: Liu Wenbin , Yue Sibiao , Zheng Xiaobin , Cao Jia , Zheng Yixian 
Published: November 2018

AbstractMuch effort has been devoted to understand how chromatin modification regulates development and disease. Despite recent progress, however, it remains difficult to achieve high sensitivity and reliability of chromatin-immunoprecipitation-coupled deep sequencing (ChIP-seq) to map the epigenome and global transcription factor binding sites in cell populations of low cell abundance. We present a new Atlantis dsDNase-based technology, aFARP-ChIP-seq, that provides accurate profiling of genome-wide histone modifications in as few as 100 cells. By mapping histone lysine trimethylation (H3K4me3) and H3K27Ac in group I innate lymphoid cells from different tissues, aFARP-ChIP-seq uncovers potentially distinct active promoter and enhancer landscapes of several tissue-specific NK and ILC1. aFARP-ChIP-seq is also highly effective in mapping transcription factor binding sites in small number of cells. Since aFARP-ChIP-seq offers reproducible DNA fragmentation, it should allow multiplexing ChIP-seq of both histone modifications and transcription factor binding sites for low cell samples.
Reorganization of 3D Genome Structure May Contribute to Gene Regulatory Evolution in Primates
Authors: Eres Ittai E. , Luo Kaixuan , Hsiao Chiaowen Joyce , Blake Lauren E. , Gilad Yoav 
Published: November 2018

AbstractA growing body of evidence supports the notion that variation in gene regulation plays a crucial role in both speciation and adaptation. However, a comprehensive functional understanding of the mechanisms underlying regulatory evolution remains elusive. In primates, one of the crucial missing pieces of information towards a better understanding of regulatory evolution is a comparative annotation of interactions between distal regulatory elements and promoters. Chromatin conformation capture technologies have enabled genome-wide quantifications of such distal 3D interactions. However, relatively little comparative research in primates has been done using such technologies. To address this gap, we used Hi-C to characterize 3D chromatin interactions in induced pluripotent stem cells (iPSCs) from humans and chimpanzees. We also used RNA-sequencing to collect gene expression data from the same lines. We generally observed that lower-order, pairwise 3D genomic interactions are conserved in humans and chimpanzees, but higher order genomic structures, such as TADs, are not as conserved. Inter-species differences in 3D genomic interactions are often associated with gene expression differences between the species. To provide additional functional context to our observations, we considered previously published chromatin data from human iPSCs. We found that inter-species differences in 3D genomic interactions, which are also associated with gene expression differences between the species, are enriched for both active and repressive marks. Overall, our data demonstrates that, as expected, an understanding of 3D genome reorganization is key to explaining regulatory evolution.
Mathematical Modeling Reveals the Factors Involved in the Phenomena of Cancer Stem Cells Stabilization
Authors: Bessonov N. , Pinna G. , Minarsky A. , Harel-Bellan A. , Morozova N. 
Published: November 2018

AbstractCancer Stem Cells (CSC), a subset of cancer cells resembling normal stem cells with self-renewal and asymmetric division capabilities, are present at various but low proportions in many tumors and are thought to be responsible for tumor relapses following conventional cancer therapies. In vitro, most intriguingly, when isolated, CSCs return to their original proportion level as shown by various investigators. This phenomenon still remains to be explained.We suggest a mathematical model of cancer cell population dynamics, based on the main parameters of cell population dynamics, including the proliferation rates, the rates of cell death and the frequency of symmetric and asymmetric cell divisions both in CSCs and in non-CSCs. This model should help elucidating some important factors underlying the dynamics of the two populations, first of all, the phenomena of cancer stem cell population stabilization.Author SummaryCancer Stem Cells (CSC) present a subset of cancer cells which is thought to be responsible for tumor growth. That is why CSC are also named “tumor initiation cells”. Additionally, it was shown that CSC are resistant to chemo- and radio-therapies which suggests that these cells can be responsible for tumor relapses after these treatments. Experimental data in cancer cell lines have shown the intriguing phenomena of CSC population stability, which means that isolated CSC population rapidly stabilizes at its characteristic level (the relative proportion of CSC in a whole cancer population). We suggest a mathematical model of cancer cell population dynamics, based on experimentally measured dynamics of CSC population stabilization and including main parameters of cell population growth.We have computationally predicted probability of different scenarios of cancer cell behavior for each experimental case with measurable growth parameters. Moreover, we provide an analytical tool for elucidating important biochemical factors responsible for a particular dynamics of CSC population.The results may have important implications in therapeutic, because the destroying of a set of factors underlying CSC stability may help to avoid tumor relapses.
RUPEE: A fast and accurate purely geometric protein structure search
Authors: Ayoub Ronald , Lee Yugyung 
Published: November 2018

AbstractGiven the close relationship between protein structure and function, protein structure searches have long played an established role in bioinformatics. Despite their maturity, existing protein structure searches either use simplifying assumptions or compromise between fast response times and quality of results. These limitations can prevent the easy and efficient exploration of relationships between protein structures, which is the norm in other areas of inquiry. We have developed RUPEE, a fast, scalable, and purely geometric structure search combining techniques from information retrieval and big data with a novel approach to encoding sequences of torsion angles.Comparing our results to the output of mTM, SSM, and the CATHEDRAL structural scan, it is clear that RUPEE has set a new bar for purely geometric big data approaches to protein structure searches. RUPEE in top-aligned mode produces equal or better results than the best available protein structure searches, and RUPEE in fast mode demonstrates the fastest response times coupled with high quality results.The RUPEE protein structure search is available athttp://www.ayoubresearch.com. Code and data are available athttps://github.com/rayoub/rupee.
Genetic mechanisms of primary chemotherapy resistance in pediatric acute myeloid leukemia: A report from the TARGET initiative
Authors: McNeer Nicole A. , Philip John , Geiger Heather , Ries Rhonda E. , Lavallée Vincent-Philippe , Walsh Michael , Shah Minita , Arora Kanika , Emde Anne-Katrin , Robine Nicolas , Alonzo Todd A , Kolb E. Anders , Gamis Alan S , Smith Malcolm , Gerhard Daniela Se , Guidry-Auvil Jaime , Meshinchi Soheil , Kentsis Alex 
Published: November 2018

AbstractAcute myeloid leukemias (AML) are characterized by mutations of tumor suppressor and oncogenes, involving distinct genes in adults and children. While certain mutations have been associated with the increased risk of AML relapse, the genomic landscape of primary chemotherapy resistant AML is not well defined. As part of the TARGET initiative, we performed whole-genome DNA and transcriptome (RNA and miRNA) sequencing analysis of pediatric AML with failure of induction chemotherapy. We identified at least three genetic groups of patients with induction failure, including those withNUP98rearrangements, somatic mutations ofWT1in the absence ofNUP98mutations, and additional recurrent variants including those inKMT2CandMLLT10.Comparison of specimens before and after chemotherapy revealed distinct and invariant gene expression programs. While exhibiting overt therapy resistance, these leukemias nonetheless showed diverse forms of clonal evolution upon chemotherapy exposure. This included selection for mutant alleles ofFRMD8,DHX32,PIK3R1,SHANK3,MKLN1, as well as persistence ofWT1andTP53mutant clones, and elimination or contraction ofFLT3,PTPN11, andNRASmutant clones. These findings delineate genetic mechanisms of primary chemotherapy resistance in pediatric AML, which should inform improved approaches for its diagnosis and therapy.
Population genomics and demographic sampling of the ant-plantVachellia drepanolobiumand its symbiotic ants from sites across its range in East Africa
Authors: Boyle John H. , Martins Dino , Musili Paul M. , Pierce Naomi E. 
Published: November 2018

AbstractThe association between the African ant plant,Vachellia drepanolobium, and the ants that inhabit it has provided insight into the boundaries between mutualism and parasitism, the response of symbioses to environmental perturbations, and the ecology of species coexistence. We use a landscape genomics approach at sites sampled throughout the range of this system in Kenya to investigate the demographics and genetic structure of the different partners in the association. We find that different species of ant associates ofV. drepanolobiumshow striking differences in their spatial distribution throughout Kenya, and these differences are only partly correlated with abiotic factors. A comparison of the population structure of the host plant and its three obligately arboreal ant symbionts,Crematogaster mimosae,Crematogaster nigriceps, andTetraponera penzigi, shows that the ants exhibit somewhat similar patterns of structure throughout each of their respective ranges, but that this does not correlate in any clear way with the respective genetic structure of the populations of their host plants. A lack of evidence for local coadaptation in this system suggests that all partners have evolved to cope with a wide variety of biotic and abiotic conditions.