bluuebunny/crossref_metadata_2025_split huggingface dataset:
A systematic analysis of nucleosome core particle and nucleosome-nucleosome stacking structure
Authors: Korolev Nikolay , Lyubartsev Alexander P. , Nordenskiöld Lars 
Published: January 2018

AbstractChromatin condensation is driven by the energetically favourable interaction between nucleosome core particles (NCPs). The close NCP-NCP contact, stacking, is a primary structural element of all condensed states of chromatin in vitro and in vivo. However, the molecular structure of stacked nucleosomes as well as the nature of the interactions involved in its formation have not yet been systematically studied. Here we undertake an investigation of both the structural and physico-chemical features of NCP structure and the NCP-NCP stacking. We introduce an “NCP-centred” set of parameters (NCP-NCP distance, shift, rise, tilt, and others) that allows numerical characterisation of the mutual positions of the NCPs in the stacking and in any other structures formed by the NCP. NCP stacking in more than 140 published NCP crystal structures were analysed. In addition, coarse grained (CG) MD simulations modelling NCP condensation was carried out. The CG model takes into account details of the nucleosome structure and adequately describes the long range electrostatic forces as well as excluded volume effects acting in chromatin. The CG simulations showed good agreement with experimental data and revealed the importance of the H2A and H4 N-terminal tail bridging and screening as well as tail-tail correlations in the stacked nucleosomes.
Optimization reconstruction method of object profile using flexible laser plane and bi-planar references
Authors: Xu Guan , Yuan Jing , Li Xiaotao , Su Jian 
Published: January 2018

AbstractAn optimization method to reconstruct the object profile is performed by using a flexible laser plane and bi-planar references. The bi-planar references are considered as flexible benchmarks to realize the transforms among two world coordinate systems on the bi-planar references, the camera coordinate system and the image coordinate system. The laser plane is confirmed by the intersection points between the bi-planar references and laser plane. The 3D camera coordinates of the intersection points between the laser plane and a measured object are initially reconstructed by the image coordinates of the intersection points, the intrinsic parameter matrix and the laser plane. Meanwhile, an optimization function is designed by the parameterized differences of the reconstruction distances with the help of a target with eight markers, and the parameterized reprojection errors of feature points on the bi-planar references. The reconstruction method with the bi-planar references is evaluated by the difference comparisons between true distances and standard distances. The mean of the reconstruction errors of the initial method is 1.01 mm. Moreover, the mean of the reconstruction errors of the optimization method is 0.93 mm. Therefore, the optimization method with the bi-planar references has great application prospects in the profile reconstruction.
Proteomic Analysis of Nucleus Pulposus Cell-derived Extracellular Matrix Niche and Its Effect on Phenotypic Alteration of Dermal Fibroblasts
Authors: Yuan Minting , Pai Pei-Jing , Liu Xiaofen , Lam Henry , Chan Barbara P. 
Published: January 2018

AbstractReconstituting biomimetic matrix niche in vitro and culturing cells at the cell niche interface is necessary to understand the effect and function of the specific matrix niche. Here we attempted to reconstitute a biomimetic extracellular matrix (ECM) niche by culturing nucleus pulposus cells (NPCs) in a collagen microsphere system previously established and allowing them to remodel the template matrix. The reconstituted NPC-derived complex ECM was obtained after decellularization and the composition of such niche was evaluated by proteomic analysis. Results showed that a complex acellular matrix niche consisting of ECM proteins and cytoskeletal proteins by comparing with the template collagen matrix starting material. In order to study the significance of the NPC-derived matrix niche, dermal fibroblasts were repopulated in such niche and the phenotypes of these cells were changed, gene expression of collagen type II and CA12 increased significantly. A biomimetic NPC-derived cell niche consisting of complex ECM can be reconstituted in vitro, and repopulating such matrix niche with fibroblasts resulted in changes in phenotypic markers. This work reports a 3D in vitro model to study cell niche factors, contributing to future understanding of cellular interactions at the cell-niche interface and rationalized scaffold design for tissue engineering.
Variants of the 5′-terminal region of p53 mRNA influence the ribosomal scanning and translation efficiency
Authors: Zydowicz-Machtel Paulina , Swiatkowska Agata , Popenda Łukasz , Gorska Agnieszka , Ciesiołka Jerzy 
Published: January 2018

AbstractThe p53 protein is one of the major cell cycle regulators. The protein is expressed as at least twelve protein isoforms resulting from the use of alternative promoters, alternative splicing or downstream initiation codons. Importantly, there is growing evidence that translation initiation of p53 mRNA may be regulated by the structure and length of the naturally occurring variants of the 5′-terminal region of p53 mRNA transcripts. Here, several mRNA constructs were synthesized with variable length of the p53 5′-terminal regions and encoding luciferase reporter protein, and their translation was monitored continuously in situ in a rabbit reticulocyte lysate system. Moreover, four additional mRNA constructs were prepared. In two constructs, the structural context of AUG1 initiation codon was altered while in the other two constructs, characteristic hairpin motifs present in the p53 5′-terminal region were changed. Translation of the last two constructs was also performed in the presence of the cap analogue to test the function of the 5′-terminal region in cap-independent translation initiation. Superposition of several structural factors connected with the length of the 5′-terminal region, stable elements of the secondary structure, structural environment of the initiation codon and IRES elements greatly influenced the ribosomal scanning and translation efficiency.
Transport of Photonic Bloch Wave in Arrayed Two-Level Atoms
Authors: Chang Chih-Chun , Lin Lee , Chen Guang-Yin 
Published: January 2018

AbstractIn a quantum system of arrayed two-level atoms interacting with light, the interacted (dressed) photon is propagating in a periodic medium and its eigenstate ought to be of Bloch type with lattice symmetry. As the energy of photon is around the spacing between the two atomic energy levels, the photon will be absorbed and is not in the propagating mode but the attenuated mode. Therefore an energy gap exists in the dispersion relation of the photonic Bloch wave of dressed photon in addition to the nonlinear behaviors due to atom-light interactions. There follows several interesting results which are distinct from those obtained through a linear dispersion relation of free photon. For example, slow light can exist, the density of state of dressed photon is non-Lorentzian and is very large around the energy gap; the Rabi oscillations become monotonically decreasing in some cases; and besides the superradiance occurs at long wavelengths, the spontaneous emission is also very strong near the energy gap because of the high density of state.
Intravenous Immunoglobulin for Congenital Parvovirus Myocarditis
Authors: Kurland Yonatan , Kylat Ranjit I. , Johnson Drew C. , Barber Brent J. , Bedrick Alan D. , Bader Mohammad Y. 
Published: January 2018

AbstractCongenital parvovirus infection has a diverse presentation ranging from asymptomatic infants to intrauterine demise secondary to red cell aplasia or myocarditis. Treatment is aimed at correcting anemia with intrauterine and postnatal transfusions. We report a case of fetal hydrops with severe atrioventricular regurgitation and myocardial dysfunction secondary to parvovirus infection in a preterm infant. Myocarditis and myocardial dysfunction responded to immunoglobulin administration.
Microsurgical Resection of Lateral Tuberculum Sellae Meningioma: Operative Video
Authors: Cândido Duarte , Nakashima Paulo , de Oliveira Jean , Borba Luis 
Published: January 2018

AbstractTuberculum Sellae Meningiomas (TSMs) are lesions dramatically related to the optic apparatus once the principal clinical complain remains on visual alterations. This is the main picture on decision making to evaluate the best time, risk-benefit, and surgical approaches to the patient treatment. In this video, we present a 65 years old female with 30 days complaint of unilateral (right) complete blindness and complete impaired right eye field test. On physical examination, there were normal pupillary function to light tests. The scans demonstrated the presence of a TSM mostly related to the right optic nerve and encasing it altogether with the right internal carotid artery. Promptly, surgery was addressed using a modified one piece cranio-orbital-zygomatic approach with extra-dural anterior clinoidectomy, as this is the procedure of choice of the senior author (LB), with easy access to decompression of the optic canal and nerve. As demonstrated on the video, the optic nerve was encased by the tumor and pushed upwards against the falciform ligament. Complete resection and decompression was established with step by step dissection, starting unroofing the optic canal, opening the ligament and finally with carefully tumor debulking. Pathology demonstrated a grade one meningioma. The patient improved remarkably her visual acuity and visual field tests on the postoperative period, emphasizing the importance of early treatment for nerve function outcome.The link to the video can be found at: https://youtu.be/pALZqDUkltQ.
Extended Endoscopic Endonasal Approach for Suprasellar Craniopharyngioma
Authors: Locatelli D. , Pozzi F. , Agresta G. , Padovan S. , Karligkiotis A. , Castelnuovo P. 
Published: January 2018

Objectives We illustrate a suprasellar craniopharyngiomas treated with an extended endoscopic endonasal approach (EEEA).
Design Case report of a 43-year-old male affected by cerebral lesion located in suprasellar region involving the third ventricle and compressing the neurovascular structures, causing an anterosuperior dislocation of the chiasma. There is a complete disruption of the pituitary stalk that can explain the clinical finding of partial anterior hypopituitarism and hyperprolactinemia. The lesion is characterized by a solid and cystic component. Considering the absence of lateral extension and the suprasellar location of the lesion, an EEEA is preferred.
Setting University Hospital “Ospedale di Circolo,” Department of Neurosurgery, Varese, Italy.
Participants Neurosurgical and ENT Skull Base Team.
Main Outcome Measures A bilateral parasagittal approach is performed using a four-hand technique. The first step of the surgery is the preparation of the Hadad's flap. The approach is extended to the planum sphenoidalis to expose the suprasellar region. The lesion is completely removed employing also an ultrasound aspirator. Skull base reconstruction is performed with three-layer technique: graft of fat tissue, fascia lata, and nasoseptal flap.
Results No postoperative complications occurred. In the post-op, the patient presents a panhypopituitarism and an improvement in neurological status. The visual deficit remains stable. Post-op magnetic resonance imaging at 1 year documents the complete absence of pathological contrast enhancement.
Conclusions EEEA is a feasible approach in treating craniopharyngioma with suprasellar extension. The advantages include optimal visualization, good resection rate, and absence of brain retraction.The link to the video can be found at: https://youtu.be/IYm-8P1jbBo.
Mesenteric Vessel Patency Following HIFU Therapy in Patients with Locally Invasive Pancreatic Cancer
Authors: Strunk Holger , Lützow Caroline , Henseler Jana , Mücke Martin , Rauch Maximilian , Marx Christian , Schild Hans , Marinova Milka 
Published: January 2018

Abstract
Purpose To evaluate the effects of HIFU therapy on visceral vessel patency in patients with inoperable locally invasive pancreatic cancer.
Materials and Methods 50 pancreatic cancer patients (26 men, 24 women) aged 41 – 82 years (65.0 ± 10.2) underwent ultrasonography (US) and computed tomography (CT) examinations before and within one day after HIFU treatment, as well as at follow-up at six weeks, three months and six months. Evaluation and grading were performed by two experienced independent radiologists according to a classification scheme based on vessel involvement, vessel diameter, patency, and defects in flow.
Results Before HIFU treatment, arterial vessel involvement was noted in 42 patients, venous involvement in 47, and 47 patients presented with both. Superior mesenteric artery occlusion was found in three carcinomas while nearly half of the cases (n = 24) displayed signs of superior mesenteric vein, portal vein, or splenic vein occlusion. High-grade tumor-associated arterial narrowing was seen in ten patients. Despite vessel encasement and partially extensive propagation of collateral vessels, it was possible to safely perform HIFU treatment in all patients without complications. US and CT studies performed within one day after therapy did not show any change in vessel patency in 47 patients (94 %). Follow-up controls at the six-week mark revealed increased vessel narrowing and finally occlusion after six months in 11 patients due to tumor progression.
Conclusion This study demonstrates that HIFU treatment can be safely applied to pancreatic cancers enveloping large mesenteric vessels despite vessel narrowing or extensive collateral propagation. Most patients (94 %) did not experience adverse effects regarding vessel patency.
Technique selection in young female gymnasts: Elbow and wrist joint loading during the cartwheel and round‐off
Authors: Farana Roman , Exell Timothy , Strutzenberger Gerda , Irwin Gareth 
Published: January 2018

AbstractBiophysical loading of the elbow and wrist is a potential reason for chronic lesions in gymnastics and present a real concern for coaches, scientist and clinicians. Previous research has identified injury risk factors during round‐off (RO) skills in elite female gymnasts. The aim of this study was to investigate key elbow and wrist joint injury risk factors during different techniques of fundamental cartwheel (CW) and RO skills performed by young female artistic gymnasts. Seventeen active young female gymnasts performed 30 successful trials of both CW and RO from a hurdle step with three different hand positions (parallel (10), T‐shape (10) and reverse (10)). Synchronised kinematic (240 Hz) and kinetic (1200 Hz) data were collected for each trial. One‐way repeated measures ANOVA and effect size (ES) were used for statistical analysis. The results showed statistically significant differences (P < .05) and large ES (>0.8) among hand positions for peak vertical ground reaction force (VGRF), peak elbow compression force, peak wrist compression force, elbow internal adduction moment and wrist dorsiflexion angle. In conclusion, the parallel and reverse techniques increase peak VGRF, elbow and wrist compression forces, and elbow internal adduction moment. These differences indicate that the parallel and reverse techniques may increase the potential of elbow and wrist injuries in young gymnasts compared with the T‐shape technique; this is of particular importance with the high frequency of the performance of these fundamental skills.
ADEPTUS: a discovery tool for disease prediction, enrichment and network analysis based on profiles from many diseases
Authors: Amar David , Vizel Amir , Levy Carmit , Shamir Ron 
Published: January 2018

Abstract

Motivation
Large-scale publicly available genomic data on many disease phenotypes could improve our understanding of the molecular basis of disease. Tools that undertake this challenge by jointly analyzing multiple phenotypes are needed.

Results
ADEPTUS is a web-tool that enables various functional genomics analyses based on a high-quality curated database spanning &gt;38, 000 gene expression profiles and &gt;100 diseases. It offers four types of analysis. (i) For a gene list provided by the user it computes disease ontology (DO), pathway, and gene ontology (GO) enrichment and displays the genes as a network. (ii) For a given disease, it enables exploration of drug repurposing by creating a gene network summarizing the genomic events in it. (iii) For a gene of interest, it generates a report summarizing its behavior across several studies. (iv) It can predict the tissue of origin and the disease of a sample based on its gene expression or its somatic mutation profile. Such analyses open novel ways to understand new datasets and to predict primary site of cancer.

Availability and implementation
Data and tool: http://adeptus.cs.tau.ac.il/home Analyses: Supplementary Material.

Supplementary information
Supplementary data are available at Bioinformatics online.
Estimating Time to the Common Ancestor for a Beneficial Allele
Authors: Smith Joel , Coop Graham , Stephens Matthew , Novembre John 
Published: January 2018

AbstractThe haplotypes of a beneficial allele carry information about its history that can shed light on its age and the putative cause for its increase in frequency. Specifically, the signature of an allele’s age is contained in the pattern of variation that mutation and recombination impose on its haplotypic background. We provide a method to exploit this pattern and infer the time to the common ancestor of a positively selected allele following a rapid increase in frequency. We do so using a hidden Markov model which leverages the length distribution of the shared ancestral haplotype, the accumulation of derived mutations on the ancestral background, and the surrounding background haplotype diversity. Using simulations, we demonstrate how the inclusion of information from both mutation and recombination events increases accuracy relative to approaches that only consider a single type of event. We also show the behavior of the estimator in cases where data do not conform to model assumptions, and provide some diagnostics for assessing and improving inference. Using the method, we analyze population-specific patterns in the 1000 Genomes Project data to estimate the timing of adaptation for several variants which show evidence of recent selection and functional relevance to diet, skin pigmentation, and morphology in humans.
Flow through axial-flow-turbomachinery blading
Authors: Escudier Marcel 
Published: January 2018

Abstract
This chapter is concerned primarily with the flow of a compressible fluid through stationary and moving blading, for the most part using the analysis introduced in Chapter 11. The principles of dimensional analysis are applied to determine the appropriate non-dimensional parameters to characterise the performance of a turbomachine. The analysis of incompressible flow through a linear cascade of aerofoil-like blades is followed by the analysis of compressible flow. Velocity triangles for flow relative to blades, and Euler’s turbomachinery equation, are introduced to analyse flow through a rotor. The concepts introduced are applied to the analysis of an axial-turbomachine stage comprising a stator and a rotor, which applies to either a compressor or a turbine.
Does the bonobo have a (chimpanzee-like) theory of mind?
Authors: Krupenye Christopher , MacLean Evan L. , Hare Brian 
Published: January 2018

Abstract
Theory of mind—the ability to reason about the thoughts and emotions of others—is central to what makes us human. Chimpanzees too appear to understand some psychological states. While less is known about bonobos, several lines of evidence suggest that the social-cognitive abilities of the two sister taxa may differ in key respects. This chapter outlines a framework to guide future research on bonobo social cognition based on the predictions of two potentially complementary hypotheses. The self-domestication hypothesis suggests that selection against aggression and for prosociality in bonobos may have impacted the ontogeny of their social-cognitive skills relative to chimpanzees. The empathizing–systemizing hypothesis links degree of prenatal brain masculinization, a potential result of self-domestication, to adult cognition. Specifically, relative feminization may yield more flexible theory of mind skills in bonobos than chimpanzees. Finally, directions for future study, including development of new paradigms that maximize ecological validity for bonobos, are discussed. La théorie de l’esprit—le pouvoir de raisonner les pensées et émotions des autres—est centrale à notre nature humaine. Il parait que les chimpanzés peuvent comprendre quelques états psychologiques. Tandis que nous savons moins des bonobos, plusieurs témoignages suggèrent que les capacités socio-cognitives des deux taxons soeur peuvent différer dans des aspects clefs. Nous traçons un cadre pour guider les prochaines recherches sur la cognition sociale des bonobos, basé sur les prédictions de deux hypothèses potentiellement complémentaires. L’hypothèse d’auto-domestication suggère que l’anti-agression et la prosocialité des bonobos a influé leur ontogenèse et leur capacités socio-cognitives relativement aux chimpanzés. L’hypothèse d’empathie systématique (Empathizing–Systemizing) forme un lien entre le degré de masculinisation prénatale du cerveau, le résultat potentiel d’auto-domestication, et la cognition adulte. Spécifiquement, la féminisation relative génère des théories de l’esprit plus flexibles chez les bonobos que chez les chimpanzés. Enfin, nous discutons le directions pour les prochaines études, inclut le développement de nouveaux paradigmes qui maximisent la validité écologique des bonobos.