bluuebunny/crossref_metadata_2025_split huggingface dataset:
Combination of TNM staging and pathway based risk score models in patients with gastric cancer
Authors: Zhou Yang‐Yang , Kang Yan‐Ting , Chen Chao , Xu Fan‐Fan , Wang Hao‐Nan , Jin Rong 
Published: December 2017

AbstractDue to the complexity and heterogeneity of gastric cancer (GC) in individual patient, current staging system is inadequate for predicting outcome of GC. Comprehensive computational and bioinformatics approach may triumph for the prediction. In this study, GC patients were devided according to stage and treatment: curative surgery plus chemoradiotherapy in stage II, curative surgery plus chemoradiotherapy in stages III, and IV, unresectable metastatic gastric cancer. The training sets were downloaded from GEO datasets (GSE26253 and GSE14208). Gene set enrichment analysis (GSEA) was performed to explore enriched difference between recurrence and nonrecurrence. The core enrichment genes of enriched pathways significantly associated with recurrence or progression were identified using Cox proportional hazards analysis. Thereafter, the risk score models were externally validated in independent datasets‐GSE15081 and The Cancer Genome Atlas (TCGA). We generated respective risk score models of patients in different stages and treatment. A five‐gene signature comprising FARP1, SGCE, SGCA, LAMA4, and COL9A2 was strongly associated with recurrence of patients with curative surgery plus chemoradiotherapy in stage II. A six‐gene signature consisting of SHH, NF1, AP4B1, COMP, MATN3, and CCL8 was correlated with recurrence of patients with curative surgery plus chemoradiotherapy in stages III and IV. And a four‐gene signature composing of ABCC2, AHNAK2, RNF43, and GSPT2 was highly related to progression of patients with unresectable metastatic GC. Taking into consideration TNM stage and gene signature reflecting recurrence or progression, the risk score models significantly improved the accuracy in predicting outcome of GC.
Tendon explant cultures to study the communication between adipose stem cells and native tendon niche
Authors: Costa‐Almeida Raquel , Berdecka Dominika , Rodrigues Márcia T. , Reis Rui L. , Gomes Manuela E. 
Published: December 2017

AbstractPoor clinical outcomes of tendon repair, together with limited regenerative capacity of the tissue, have triggered the search for alternative regenerative medicine strategies. Human adipose‐derived stem cells (hASCs) are being investigated as a promising cell source in contributing for tendon repopulation and reconstruction. However, the mechanisms involved in a potential beneficial effect in tendon regeneration are still to be uncovered. To gain further insights on the bi‐directional crosstalk occurring between stem cells and the native tendon niche, it was used an indirect (trans‐well) system for co‐culturing human tendon explants and hASCs. The maintenance of tissue architecture was studied up to 14 days by histological techniques. The secretion of MMPs was evaluated at day 3. The behavior of hASCs was assessed regarding cell elongation and extracellular matrix (ECM) production. The paracrine communication enhanced collagenolytic activity of MMPs in co‐cultures at day 3, in comparison to hASCs alone or tendon explants alone, suggesting that ECM remodeling is triggered early in culture. Moreover, hASCs were spontaneously more elongated in co‐cultures and the deposition of collagen type III and tenascin‐C by hASCs in co‐culture was observed at a lower extent after 7 days, in comparison to hASCs alone, being lately recovered at day 14. Overall, explant co‐cultures established herein may constitute a tool for replicating the first steps in tendon healing and help uncovering the bi‐directional communication occurring between hASCs and the native tendon niche.
Protective effect of HSP27 in atherosclerosis and coronary heart disease by inhibiting reactive oxygen species
Authors: Zhang Hong‐Li , Jia Kai‐Ying , Sun Da , Yang Min 
Published: December 2017

AbstractObjectiveTo clarify the mechanism of heat shock protein 27 (HSP27) as a diagnostic biomarker in coronary heart disease (CHD) and atherosclerosis (AS).MethodExpressions of HSP27 in patients with CHD and healthy controls were determined by enzyme‐linked immunosorbent assay and the expressions of HSP27 in aortas of patients with CHD and healthy controls were measured by immunohistochemistry. Receiver operating characteristic curve was applied to assess the diagnostic performance of HSP27 in CHD. ApoE−/− mice were included and accordingly grouped. The expressions of HSP27 in AS plaque were measured by quantitative real‐time polymerase chain reaction, immunohistochemistry, and Western blot analysis. AS plaque was observed using hematoxylin and eosin staining. DHE was used to detect reactive oxygen species (ROS) levels in aortas. The expressions of mitochondrial apoptosis‐related proteins were measured by Western blot analysis. Cell apoptosis was determined by TUNEL staining.ResultsHSP27 was highly expressed in patients with CHD than in healthy controls (
P < 0.01). In comparison to the normal group, the model group had increased the relative positive area of HSP27 and higher expressions of HSP27, Bax, caspase‐3, and apoptosis index (AI) but decreased Bcl‐2 expression in AS plaque, as well as larger plaque areas and elevated ROS levels in the aorta (all P < 0.05). The HSP27‐small interfering RNA group had increased expressions of Bax, caspase‐3, and AI but decreased Bcl‐2 and HSP27 expressions in AS plaque, as well as larger plaque areas, the relative positive area of HSP27 and higher ROS levels in aorta when compared with those in the model group (all P < 0.05).ConclusionHSP27 exerts its protective role by suppressing ROS and AS progression by inhibiting mitochondria apoptosis pathway in CHD.
Blocking structures in finite projective planes
Authors: Aguglia Angela , Cossidente Antonio , Pavese Francesco 
Published: December 2017

AbstractExploring the classical Ceva configuration in a Desarguesian projective plane, we construct two families of minimal blocking sets as well as a new family of blocking semiovals in PG(2, 32h). Also, we show that these blocking sets of PG(2, q2), regarded as pointsets of the derived André plane , are still minimal blocking sets in . Furthermore, we prove that the new family of blocking semiovals in PG(2, 32h) gives rise to a family of blocking semiovals in the André plane as well.
Dissecting and analyzing key residues in protein‐DNA complexes
Authors: Kulandaisamy A. , Srivastava Ambuj , Nagarajan R. , Gromiha M. Michael 
Published: December 2017

AbstractProtein‐DNA interactions are involved in various fundamental biological processes such as replication, transcription, DNA repair, and gene regulation. To understand the interaction in protein‐DNA complexes, the integrative study of binding and stabilizing residues is important. In the present study, we have identified key residues that play a dual role in both binding and stability from a nonredundant dataset of 319 protein‐DNA complexes. We observed that key residues are identified in very less number of complexes (29%) and only about 4% of stabilizing/binding residues are identified as key residues. Specifically, stabilizing residues have higher preference to be key residues than binding residues. These key residues include polar, nonpolar, aliphatic, aromatic, and charged amino acids. Moreover, we have analyzed and discussed the key residues in different protein‐DNA complexes, which are classified based on protein structural class, function, DNA strand, and their conformations. Especially, Ser, Thr, Tyr, Arg, and Lys residues are commonly found in most of the subclasses of protein‐DNA complexes. Further, we analyzed atomic contacts, which show that polar‐nonpolar is more enriched than other types of contacts. In addition, the charged contacts are highly preferred in protein‐DNA complexes compared with protein‐protein and protein‐RNA complexes. Finally, we have discussed the sequence and structural features of key residues such as conservation score, surrounding hydrophobicity, solvent accessibility, secondary structure, and long‐range order. This study will be helpful to understand the recognition mechanism and structural and functional aspects of protein‐DNA complexes.
Reproducibility of relaxometry of human lumbar vertebrae at 3 Tesla using 1H MR spectroscopy
Authors: Neumayer Bernhard , Widek Thomas , Stollberger Rudolf , Scheurer Eva 
Published: December 2017

BACKGROUNDMR spectroscopy is widely used for fat fraction quantification of human lumbar vertebrae. However, the measurements need to be corrected for relaxation effects.PURPOSEThe aim of this study was to determine the reproducibility of relaxometry in human lumbar vertebrae required for the correction of fat fraction measurements using magnetic resonance spectroscopy at 3 Tesla. Such information provides error estimates and guidance regarding reliability for future studies.STUDY TYPEProspective.SUBJECTSForty‐six healthy volunteers (22 female [f], 24 male [m]) participated in this study.FIELD STRENGTHAll subjects underwent three consecutive multi‐TE/multi‐TR MR spectroscopy measurements at 3 Tesla.ASSESSMENTA total of 2580 spectra of lumbar vertebrae L2 and L3 of 43 subjects (21f, 22m) were quantified using jMRUI software. Data were exported and mono‐exponential fits were applied to the signals of water and fat compartments to derive relaxation times and calculate the fat fraction corrected for relaxation effects. Finally, relaxation times and fat fraction results of repeated measurements were analyzed for reproducibility.STATISTICAL TESTSReproducibility was evaluated by calculating the coefficient of variation (CV). Influences of volunteer age and sex were tested by analysis of covariance.RESULTSThe CV for all calculated parameters ranged between 1.22% (T2 of the fat compartment) and 3.02% (T1 of the fat compartment). Relaxation times and fat fraction were statistically different for female and male volunteers (P < 0.01) and relaxation times of the water compartment showed significant (P < 0.01) correlation with the fat fraction.DATA CONCLUSIONBased on repeated acquisitions using the measurement parameters applied in this study, magnetic resonance spectroscopy allowed a reproducible calculation of the fat fraction corrected for relaxation effects. T1 of the water compartment showed high reproducibility and correlation with the fat fraction. It, therefore, might be considered as a parameter linked to the composition of the water compartment and patient health.Level of Evidence: 1Technical Efficacy Stage 1J. Magn. Reson. Imaging 2017.
The precise subcellular localization of Dlg in the Drosophila larva body wall using improved pre‐embedding immuno‐EM
Authors: Gan Guangming , Zhang Chenchen 
Published: December 2017

AbstractDiscs‐large (Dlg) plays important roles in nerve tissue and epithelial tissue in Drosophila. However, the precise positioning of Dlg in the neuromuscular junction remains to be confirmed using an optimized labeling method. In this study, we improved the method of pre‐embedding immunogold electron microscopy without the osmic tetroxide procedure, and we found that Lowicryl K4M resin and low temperature helped to preserve the authenticity of the labeling signal with relatively good contrast. Dlg was strongly expressed in the entire subsynaptic reticulum (SSR) membrane of type Ib boutons, expressed in parts of the SSR membrane of type Is boutons, weakly expressed in axon terminals and axons, and not expressed in pre‐ or postsynaptic membranes of type Is boutons. In muscle cells and stratum corneum cells, Dlg was expressed both in the cytoplasm and in organelles with biomembranes. The precise location of Dlg in SSR membranes, rather than in postsynaptic membranes, shows that Dlg, with its multiple domains, acts as a remote or indirect regulator in postsynaptic signal transduction.
Time of observation adjustments to daily station precipitation may introduce undesired statistical issues
Authors: Oyler Jared W. , Nicholas Robert E. 
Published: December 2017

ABSTRACTInterstation observations of daily precipitation are often temporally misaligned due to differences in station time of observation. Several time of observation adjustment methods have historically been applied to improve interstation temporal alignment, but the efficacy of such adjustments has not been fully tested. Here, we examine the ability of several time of observation adjustments to improve observation compatibility under three different adjustment scenarios: adjusting morning observations to midnight, adjusting afternoon observations to midnight, and adjusting afternoon observations to morning. We find that all adjustment methods provide necessary improvements to the temporal alignment of daily precipitation observations, especially with respect to morning versus midnight time of observation totals. However, for a majority of the adjustments, improved temporal alignment comes at the cost of significantly altering observed precipitation intensity, frequency, and extremes. We also find adjustments have the potential to overcorrect and increase both general and extreme event spatio‐temporal coherence.
Dynamic evaluation of a trilobal capillary‐channeled polymer fiber shape for reversed phase protein separations and comparison to the eight‐channeled form
Authors: Wang Lei , Stevens Kathryn A. , Haupt‐Renaud Paul , Marcus R. Kenneth 
Published: December 2017

AbstractA new, trilobal‐shaped capillary‐channeled polymer fiber is under development to address the issues of poor A‐term performance of the previous eight‐channeled form. The trilobal geometry should provide better packing homogeneity due to the fewer potential orientations of the symmetric fiber geometry. Comparisons of separation efficiency and peak shape were made between the two fiber shapes through several dynamic parameters. Column hydrodynamics were investigated with two marker compounds, uracil and bovine serum albumin, with van Deemter plots of those two compounds revealing differences in the packing qualities between the different fiber shapes. Parametric fitting to the van Deemter, Knox, and Giddings equations provides insights into the column physical structures. Separation quality for both shapes was evaluated across differences in fiber packing density, gradient rate, and mobile phase linear velocity for the reversed phase separation of a four protein mixture, containing ribonuclease A, cytochrome c, lysozyme, and myoglobin. The results of this study lay the ground work for future efforts in the use of trilobal fibers for the separation of biomacromolecules.
Affinity extraction of emerging contaminants from water based on bovine serum albumin as a binding agent
Authors: Papastavros Efthimia , Remmers Rachael A. , Snow Daniel D. , Cassada David A. , Hage David S. 
Published: December 2017

AbstractAffinity sorbents using bovine serum albumin as a binding agent were developed and tested for the extraction of environmental contaminants from water. Computer simulations based on a countercurrent distribution model were also used to study the behavior of these sorbents. Several model drugs, pesticides, and hormones of interest as emerging contaminants were considered in this work, with carbamazepine being used as a representative analyte when coupling the albumin column on‐line with liquid chromatography and tandem mass spectrometry. The albumin column was found to be capable of extracting carbamazepine from aqueous solutions that contained trace levels of this analyte. Further studies of the bovine serum albumin sorbent indicated that it had higher retention under aqueous conditions than a traditional C18 support for most of the tested emerging contaminants. Potential advantages of using these protein‐based sorbents included the low cost of bovine serum albumin and its ability to bind to a relatively wide range of drugs and related compounds. It was also shown how simulations could be used to describe the elution behavior of the model compounds on the bovine serum albumin sorbents as an aid in optimizing the retention and selectivity of these supports for use with liquid chromatography or methods such as liquid chromatography with tandem mass spectrometry.
The effect of emulsifier type on the formation and stability of nanoemulsion gels
Authors: Patel Aakash , Kadiya Kunal , Ghosh Supratim 
Published: December 2017

SummaryLiquid nanoemulsions are shown to transform into viscoelastic gels by reducing droplet size, increasing interfacial repulsive barrier between the nanodroplets and therefore increasing the effective oil volume fraction. The repulsive gelation in nanoemulsions can be achieved at a significantly lower oil volume fraction compared to conventional emulsion gels, making the nanoemulsion gel an attractive material for various low‐fat food applications. Gelation in nanoemulsions stabilized by anionic small molecule emulsifier and polymeric protein are compared in terms of gel strength, average droplet size, effective oil volume fraction, and long‐term gel stability. It is expected that higher stability and large surface area of nanoscale droplet size can further extend the application of nanoemulsion gels in the field of functional foods, cosmetics and pharmaceuticals.
Novel 3D Neuron Regeneration Scaffolds Based on Synthetic Polypeptide Containing Neuron Cue
Authors: Wang Zhen‐Hua , Chang Yen‐Yu , Wu Jhih‐Guang , Lin Chia‐Yu , An Hsiao‐Lung , Luo Shyh‐Chyang , Tang Tang K. , Su Wei‐Fang 
Published: December 2017

AbstractNeural tissue engineering has become a potential technology to restore the functionality of damaged neural tissue with the hope to cure the patients with neural disorder and to improve their quality of life. This paper reports the design and synthesis of polypeptides containing neuron stimulate, glutamic acid, for the fabrication of biomimetic 3D scaffold in neural tissue engineering application. The polypeptides are synthesized by efficient chemical reactions. Monomer γ‐benzyl glutamate‐N‐carboxyanhydride undergoes ring‐opening polymerization to form poly(γ‐benzyl‐l‐glutamate), then hydrolyzes into poly(γ‐benzyl‐l‐glutamate)‐r‐poly(glutamic acid) random copolymer. The glutamic acid amount is controlled by hydrolysis time. The obtained polymer molecular weight is in the range of 200 kDa for good quality of fibers. The fibrous 3D scaffolds of polypeptides are fabricated using electrospinning techniques. The scaffolds are biodegradable and biocompatible. The biocompatibility and length of neurite growth are improved with increasing amount of glutamic acid in scaffold. The 3D scaffold fabricated from aligned fibers can guide anisotropic growth of neurite along the fiber and into 3D domain. Furthermore, the length of neurite outgrowth is longer for scaffold made from aligned fibers as compared with that of isotropic fibers. This new polypeptide has potential for the application in the tissue engineering for neural regeneration.
A “Cell‐Friendly” Window for the Interaction of Cells with Hyaluronic Acid/Poly‐l‐Lysine Multilayers
Authors: Madaboosi Narayanan , Uhlig Katja , Schmidt Stephan , Vikulina Anna S. , Möhwald Helmuth , Duschl Claus , Volodkin Dmitry 
Published: December 2017

AbstractPolyelectrolyte multilayers assembled from hyaluronic acid (HA) and poly‐l‐lysine (PLL) are most widely studied showing excellent reservoir characteristics to host molecules of diverse nature; however, thick (HA/PLL)n films are often found cell repellent. By a systematic study of the adhesion and proliferation of various cells as a function of bilayer number “n” a correlation with the mechanical and chemical properties of films is developed. The following cell lines have been studied: mouse 3T3 and L929 fibroblasts, human foreskin primary fibroblasts VH‐Fib, human embryonic kidney HEK‐293, human bone cell line U‐2‐OS, Chinese hamster ovary CHO‐K and mouse embryonic stem cells. All cells adhere and spread well in a narrow “cell‐friendly” window identify in the range of n = 12–15. At n < 12, the film is inhomogeneous and at n > 15, the film is cell repellent for all cell lines. Cellular adhesion correlates with the mechanical properties of the films showing that softer films at higher “n” number exhibiting a significant decrease of the Young's modulus below 100 kPa are weakly adherent to cells. This trend cannot be reversed even by coating a strong cell‐adhesive protein fibronectin onto the film. This indicates that mechanical cues plays a major role for cell behavior, also in respect to biochemical ones.
Microvascular replantation of a composite facial avulsion in a 24‐month‐old child after dog bite
Authors: Macias David , Kwon Daniel I. , Walker Paul C. , Peterson Nathaniel R. 
Published: December 2017

Dog bite injuries are common sources of morbidity with an estimated incidence of 4.5 million bites per year with over 350,000 requiring treatment in the emergency room. Children under the age of 14 are most likely to be affected with a peak age of 5–9 years old. We report a case of a 24‐month‐old female who sustained a large composite facial avulsion injury from a pit bull dog bite. The avulsed tissue involved a substantial portion of the patient's mid‐face, including the entire soft tissue of the nose, upper lip, part of the left cheek, and left oral commissure. Artery‐only microvascular replantation was performed because no recipient vein could be identified from the facial defect. Medicinal leech therapy was used for eight days postoperatively to prevent venous congestion. The patient experienced significant blood loss due to leech therapy and required nearly 29 L of blood product replacement. At the last follow up of 8 months postoperatively, the patient was recovering well with significant improvement in function and cosmesis of the mid‐face. This case describes a successful artery‐only replantation of an avulsive bite injury to the face of a young child. Despite the technical difficulty of cases such as this one, microvascular replantation should be attempted because when successful it provides a superior cosmetic and functional result to other reconstructive techniques.
Impact of a shift in nuchal translucency measurements on the detection rate of first‐trimester Down syndrome screening: A population‐based study
Authors: Fries Nicolas , Salomon Laurent J. , Muller Françoise , Dreux Sophie , Houfflin‐Debarge Véronique , Coquel Philippe , Kleinfinger Pascale , Dommergues Marc ,   for the BioNuQual User Club, Paris
Published: December 2017

AbstractObjectiveTo assess the distribution of nuchal translucency (NT) measurements following a national policy without credentialing and its impact on first‐trimester Down syndrome screening (DSS) detection rate.MethodAll first‐trimester DSS data recorded in France (2010‐2014) were collected by the laboratories in charge via an Internet database (https://www.bionuqual.org/echo.php). There was no minimal requirement for image quality to allow sonographers to enter the screening process. A subgroup of DSS with complete DS follow‐up corresponded to 1614 sonographers. Based on the distribution of maternal age, DS detection rate was calculated and split as a function of the distribution of NT multiple of the median (MoM).ResultsFour thousand nine hundred forty‐three sonographers performed 2,337,372 NT measurements. Median NT expressed in MoM was 0.83. Screenings with complete follow‐up consisted of 197,417 screenings, in which DSS detection rates were respectively 70.4%, 70.9%, 79.4%, 87.7%, and 79.5% for the following median NT MoM ranges: <0.7, 0.70 to 0.79, 0.80 to 0.89, 0.90 to 0.99, and >0.99 (trend χ = 12.21; P = .0158).ConclusionIn France, following a policy of quality assessment without standardized credentialing, the distribution of NT measurements did not fit the expected distribution. Down syndrome detection rate was 10% lower in screenings by sonographers with a median NT < 0.80 MoM.